The gOpenMol Effort for Analyzing Molecular Dynamics Trajectories

The gOpenMol Effort
Leif Laaksonen Center for Scientific Computing, Espoo, FINLAN Version 3.00 (23.09.2005) !"L# http#$$%%%&csc&fi$gopenmol$
Intro'uction
A few words about version 3.00 This version has been prepared by the same people as version 2.3. More of the kernel code has been rewritten with some extensions in the contour facility. Bugs have been corrected and anomalities removed. A few words about version 2.3 This version has been prepared by the same people as version 2.2. There are not so many new features but some parts of the source code has been modified or rewritten for the speed and formability. A few words about version 2.2 This version took a long time to finish and I strongly doubt it would never have been finished without the help from cott !nderson" #evin Boyd" $ero %&kkinen and
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Maintained by Leif Laaksonen (Leif.Laaksonen@csc.fi)
Center for Scientific Computing P.O. Box 405 !"#02101 $spoo !"%&"' P(one) *35+ 9 45,23,+ -x) *35+ 9 45,2302
gOpenMol manual version 0.92 on 23th September 2005
Minna 'aris. (ew features have been added including the possibility to extend g)penMol trough plugins *dll files on +indows and sharable ob,ects on -inux./nix0 and old routines have been improved. Minna has designed the new g)penMol web pages and created a splendid basis for further support extensions. A few words about version 2.1 This version of g)penMol is the product of a fruitful collaboration between the author and cott !nderson" 1im #ress and !rlen 'iste. There are some new features like the cartoon display type of protein secondary structures and the hydrogen bond display engine. The filter programs for 2aussian33 and 4c2amess have been modified to allow the display of density gradient vectors. g)penMol has now also a general display engine to display vectors. The internal usage of Tcl variables has been improved and documented. The author is grateful for all the suggestion" commens and critics over the years. This shows that there are users who care. 4lease continue your active role in this process. A few words about version 2.0 This is a release with some new features and some of the engines 5under the hood6 have been rewritten. cott !nderson at the /niversity of /tah has been kind to extend his tutorial. It can be found at the end of this document and in the help.tutorials directory. The new features include arbitrary cut and clip planes defined from three atoms or coordinates. The atom coordinate input engine has been extended and should work now for molecular systems up to 788"888 atoms. It will of course work even for bigger systems but it takes some time to assign the atom types. A few words about version 1.4 The current version took a long time to finish. ! lot longer in fact than I would have imagined. There are not so many new things you can see on the screen but a lot of the code inside g)penMol has changed. This time I have tried to debug the code a lot more than ever before. I have received invaluable help from cott !nderson at the /niversity of /tah. +ithout the help from cott some of the new features would not have been ready for this release. ome user code has also been included in the current version. igismondo Boschi at 9I($9! *%igh 4erformance ystems0 in Italy provided the code for hardware based stereo *stereo in a window0 on 2I e:uipment. ;obert Best contributed with some byte swap code and finally pushed me to implement an on<the<fly byte swap for the
binary files g)penMol reads. (ow it is possible to read binary tra,ectories and plt files from other hardware platforms without the formatting.unformatting in between. ! list of some of the new features in version 2.8 can be found in appendix =. How it all started The g)penMol program has a long future behind. The history goes back to the late >8?s when I become curious to know if even I was capable of programming graphics for the at the time new ilicon 2raphics workstations. -earning the 9<language and the usage of the 2raphics -ibrary *2-0 was an exciting trip to new areas in computer technology. I can still remember the first exciting time I was able to configure the workstation to send and accept mail messages and take a telnet connection to the computers at the 9enter for cientific 9omputing *9 90. The graphics was not always what I believed to see but with the help from some professionals at 9 9 I was able to converge to something that at least distantly looked like molecules. )riginally I was not very pleased with the commercial software available for the analysis of molecular dynamics tra,ectories and I firmly was in the believe that even I could program something more helpful. That?s about the background to the 9!;$;)+2 program" which was introduced during the beginning of the @8?s. In fact I still believe that there are some 9!;$9;)+ users out there. My colleague !atto -aaksonen pointed out" already at an early stage" that if I would like to get more users I should change the name of the program to something more attractive. !nyway" I think the program has got some keen users over the years. That?s at least the impression I got from all the messages I?ve received over the years. It was all fun and I haven?t regretted the time I?ve spent in front of the workstations over the years. /nfortunately 2I was not fast enough to react to the change that was happening in the workstation market. 2I created the very nice )pen2- graphics engine and other players ported it to their own hardware platforms. !t the same time the Intel processors become powerful enough and the Intel.49 based graphics cards become fast enough for useful rendering. Aor most graphics applications in the molecular modelling field the Intel or !lpha processors with an )pen2- supported graphics card become well enough. !t some stage I decide to give the old 9!;$9;)+ a push and port it to the Intel.!lpha +indows.49 platform. The 9!;$9;)+ program already had a primitive scripting engine but I also wanted something more powerful. In the middle of the @8?s prof. 2eerd Biercksen asked me if I was interested in making a graphical interface for his )penMol3 program. 9ombining my interest to rewrite 9!;$9;)+ with 2eerd?s offer to write a graphical interface for )penMol I
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.(e SC&/$C/O0 progr-m for t(e -n-12sis -n3 3isp1-2 of mo1ecu1-r 32n-mics tr-4ectories. (ttp)55666.csc.fi51u15c(em5sc-recro654mg7sc-re.(tm1 3 Open8o1 set of progr-ms -t (ttp)55666.mp-#g-rc(ing.mpg.3e59opmo1sr:58o1P(2s;roup5in3ex.(tm1.
decided to create g)penMol. I first tried to use the 3<+indows and Motif for the graphical interface and Tcl for the scripting engine but found it far too difficult. !t 9 9 we had already been using Tcl.TkC for a long time so it was a rather smooth translation when I finally did the transition from Motif to Tcl.Tk. !t this stage I had also realiDed that the /nix programming tools we had available was poor compared to the tools available on the +indows platform. I want to thank you 2eerd for all the discussions we have had and your hospitality during my numerous visits to 2arching" over the years. It took me only a couple of days to get the non<graphical part of g)penMol" originally written for /nix.3<+indows.Motif" to run on my +indows (T Intel 49. The entire g)penMol has been rewritten using the Microsoft 'isual Bevelopment environment. The code created run almost as such also on the various /nix platforms. This can be done using the extremely powerful Tcl.Tk scripting and windows engine. I can recommend it for anyone creating software for a variety of platforms. The current version of g)penMol has unfortunately very few )penMol features. In fact there is not too much more in common with the )penMol package than the name. %owever" g)penMol has a lot of features that you can find useful in your work. I have from the beginning wanted to create a program that looks similar and has the same functionality on a variety of hardware platforms and operating systems. I think g)penMol has been :uite a success at lest in that sense. g)penMol looks almost the same now on the +indows and /nix platforms. ome features like the copying of the screen to the paste buffer or making of movies are not supported on the /nix platforms. This must be handled on the /nix boxes with their own tools. I maintain a %TM- based help system for the gOpenMol development effort in Ainland. This help system is under constant development so please check the g)penMol %TM- based help files regularly atE URL httpE..www.csc.fi.gopenmol. I will try to maintain a page with updated information about the program itself and the graphical user interface *2/I0. Fou can also read about bug fixes" updates and new versions. !ll programming efforts should have a motto. I?ve tried to include the feelings I?ve had creating this piece of software over the years using the words by (eil Foung. Motto: One of these days I'm going to sit down and write a long letter To all the good friends I've known
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.c15.< =2 Scriptics -t (ttp)553e:.scriptics.com5
And I'm going to try To thank them all for the good times together Though so apart We've grown Neil Young, One of these days
I owe a lot to very many friends and colleagues over the many development years. It would be impossible to mention you all but I still have to mention some. Thank you very much cott !nderson" 2eerd Biercksen" %enrik #onschin" !atto -aaksonen" 1effry B. Madura and 1uha ;uokolainen. +ithout your support" help and encouragement there would not have been any carecrow or g)penMol. If you use g)penMol in your publications please use the following referenceE -. -aaksonenE ! graphics program for the analysis and display of molecular dynamics tra,ectories. J. Mol. Graphics 10 (1992) 33; B.-. Bergman" -. -aaksonen and !. -aaksonenE 'isualiDation of olvation tructures in -i:uid Mixtures. J. Mol. Graphics & Modelling 15 (1997) 301.
(hat is gOpenMol)
g)penMol is a program or toolbox for the display of molecules and their properties and the analysis of molecular structures and dynamics tra,ectories. g)penMol" as a analysis and display toolbox" can be usedE
for the static display of molecular structures and properties calculated with external programs for the analysis and display of molecular dynamics tra,ectories for the display of molecular orbitals" electron densities and other properties together with electrostatic potentials from programs like the 2aussian33" 2!M$ and 1aguar together with electrostatic potentials from the /%BB */niversity of %ouston Brownian Bynamics0" !utoBock and the 2;IB programs.
g)penMol includes also a set of programs and utility functions.
The soft%are#
g)penMol is entirely written in 9 and the graphics is using )pen2-. The windowing and the scripting are implemented using Tcl.Tk. The Tcl.Tk scripts defining the graphics layout are plain text files and can thus very easily be modified. The gOpenMol manual version 0.92 on 23th September 2005
graphical interface can heavily be changed while using g)penMol. In fact it is possible to write an entirely new molecular graphics package inside g)penMol using the available Tcl.Tk tools and functions. Fou can import" display and analyse several different input coordinate file formats and binary tra,ectory file formats. The program has a graphical user interface *2/I0 and an internal line command interpreter based on the Tcl.Tk. http: !!!.tcl.t" g)penMol can be used for a wide range of analysis and display tasks like the display of isocontour surfaces and cross sections of grid data. g)penMol can be understood as two applications talking to each other through the command line interpreterE 7. the kernel part containing the 9<coding and the graphics *)pen2-0 part 2. and the Tcl.Tk based 2/I. These two parts talk to each other through the command line interpreter located in the kernel part. +hen an option is selected from the 2/I the e:uivalent line command is generated and sent to the interpreter. This is a very handy and simple procedure. %owever" the opposite is not that easy. The kernel can of course talk with the 2/I but it is more complicated and needs a bit more coding and I haven?t been able to create a neat and convenient way to do that. To achieve a flexible way to extend g)penMol without any recompilation of the kernel part I have implemented some of the commands using Tcl.Tk scripting. This means that the kernel 9<coding for a command is in fact calling a Tcl script that does the command and then returns back and gives the control again to the kernel. (ow by ,ust modifying the Tcl code part the command can be extended. Aor example some of the coordinate input routines call Tcl functions that reads in the atom symbols and coordinates and then gives the control back to the kernel modules to detect the atom connectivity matrix" which is computationally very extensive. To learn more please have a look the Tcl scripts in the data directory.
"e*uirements to run gOpenMol

The g)penMol program is currently supported on the following platformsE +indows @=.@>.(T -inux both Intel and !lpha using M$ ! IBM !I3 using )pen2- and M$ ! 9ompa: !lpha ) A.7 using M$ ! 2I using )pen2- or M$ ! gOpenMol manual version 0.92 on 23th September 2005
The main platforms are +indows and Intel -inux. The versions for the other platforms will be available with a small delay. ! rough guess is that you need at least 32 MB of memory and about =8 MB of disk space to run g)penMol. (o special graphics hardware is needed for the +indows and /nix M$ ! versions. Today the )pen2- supported +indows display cards are very powerful and produce very satisfying graphical possibilities. M$ ! is using 3< +indows so g)penMol can be used also over the network. The special )pen2supported graphics cards on the +indows platform gives a very convenient rendering speed. To be able to render acceptable graphics :uality it is recommended that you run your display in either 7G bit graphics mode *GC #colours0 or in the true colour mode *7G Mcolours0. Today most of the 49 graphics cards already support )pen2- and can display by default true colour *7G Mcolours0.
Supporte' file formats#

g)penMol is hopefully a multipurpose analysis program. 9urrently the program has all of the molecular dynamics analysis features of the old 9!;$9;)+ and a lot of new features. 9urrently g)penMol supports a wide range of molecular coordinate input formatsE
!BA" !msterdam Bensity Aunctional output log files. If file contains multiple coordinates the coordinates will be merged to a multi<coordinate set 3M)file to be displayed using the tra,ectory analysis tools. 9%!;Mm.9%!;MM. 9M- file format. 9hem3B binary file *plugin must be enabled0. B-H4oly 9)(AI2 coordinate file format. ! frame from a tra,ectory *please look at the supported tra,ectory formats0. 2aussian formatted checkpoint file. 2romos@G coordinate file format. 2romacs coordinate file format. %yper9hem. Insight *car files0. 1aguar coordinates from a 1aguar output log file. Mol2. Mumod. )penMol *center binary file0. 4BB *Brookhaven 4rotein Bata Bank format0. Tinker coordinate file. partan binary file *plugin must be enabled0. gOpenMol manual version 0.92 on 23th September 2005
/niversity of %ouston Brownian Bynamics */%BB0 close to 4BB format. 3mol single and multi xyD coordinate set file. 3FI general xyD coordinate file. F! 4.
g)penMol supports several binar! tra,ectory formats. Those formats marked with a 5J6 should be readable by g)penMol independent of the hardware platform on which they have been created. This means that these tra,ectory files can be moved from one platform to an other without the need conversion. upported file formats includeE

!mberJ. 4rogram included for the unformatting of formatted !MB$; tra,ectories. 9erius2J 9%!;MmJ.9%!;MMJ. 4rogram included for the formatting.unformatting of 9%!;Mm.9%!;MM tra,ectories. Biscover B-H4oly 2;)M) J * upporting the old 2;)M) format0 2;)M!9 J *trn" trr and xtc formats0 %yper9hem *I havenKt tested with the latest version0 M/M)B J 34-);J F! 4J
and the following as"ii tra,ectory formatsE

!mber formatted tra,ectory format. B-H4oly tra,ectory format. 2;)M) @G tra,ectory format. TI(#$; multi frame coordinate tra,ectory format. 3M)- xyD multi<step data sets. The included 3vibs program enables the display of vibrational modes from the 2!/ I!(33 and 2!M$ programs.
The surfaces are displayed through plt plot files. g)penMol should be able to read the plot files from all hardware platforms. There is now no need to format and unformat the files when moving them from one hardware platform to an other. $xtensive display isocontour surfaces and cut planes forE )rbitals" densities" gradients" -aplacian ... from 2!/ I!(33 set of programs. )rbitals" densities" gradients" -aplacian ... from 4c2amess . )rbitals and densities from 1aguar. )rbitals and densities from TurboMole. 9onnolly type of surfaces using the 4robe urf program. $lectrostatic potentials. gOpenMol manual version 0.92 on 23th September 2005
Bisplay and analysis of iso<contour surfaces from the /%BB program. Bisplay and analysis if iso<contour surfaces from the 2;IB program. Bisplay of !utoBock electrostatic grid data files.
!tilit+ programs
!ll these executable programs are located in the bin. directory and the source code is in the utility. directory. a#bera2b 9onverts a formatted ascii !MB$; tra,ectory into a unformatted one. g)penMol can only handle unformatted !MB$; tra,ectories. autodo"$2plt 9onverts a !utoBock map file to a plt file known by g)penMol. The program creates both formatted and unformatted plt files. "%ar##tr& This program makes the formatted.binary tranformation for a 9%!;MM dynamics tra,ectory file. "ont#an 4erforms a variety of operations on a contour *plt0 file. "onvert 9onverts the output search results *AB!T0 from 9ambridge tructural Batabase into separate 4BB files. ga#ess2plt 9onverts the Lcube? information in the 49 2amess *v. G0 4/(9% file into a binary format known by g)penMol. g"ube2plt and g'4"ub2pl 9onverts a cube file from the 2aussian33 program into a binary format known by g)penMol. 9an also save the gradient and -aplacian data. gridas"2plt 9onverts a /%BB formatted 4%I grid file into the plt format used by the g)penMol progra" gridbin2plt 9onverts a /%BB unformatted 4%I grid file into the plt format used by g)penMol. gOpenMol manual version 0.92 on 23th September 2005
$ont2plt 9onvert 2;IB electrostatic grid files into the plt format used by g)penMol. The program creates both formatted and unformatted plt files. The formatted plt pltfile This program can be used to format a binary plot file or to make a formatted file into binary. This program is helpful if you want to move the plot file from one computer hardware platform to a other platform. This is not needed anymore. g)penMol is able to read plt files from all hardware platforms. s!b!l2a#ber 9onverts a formatted ascii ybyl tra,ectory into an unformatted !MB$; one. t#ole2plt 9onvert T/;B)M)-$ moloch grids into a format recogniDed by g)penMol. tra&#erge Merges two 9%!;MM tra,ectory files into one. (plor2"%ar## 9onverts an 34-); tra,ectory into a 9%!;MM tra,ectory.
gOpenMol as a helper application for +our (e, ,ro%ser

It is possible to use g)penMol as a helper application to your favourite /nix.-inux.+indows (T.@= +eb browser. 4lease look into your favourite +eb browser setup on how to start the rungOpenMol.bat file in the bin. directory. /sing g)penMol you can transport complete 3B molecular models including solid.transparent surfaces and 94#" licorice representations of your molecular models over the network. If you use g)penMol as a helper application you can put up g)penMol *.gom0 files on your +eb server to distribute graphics. I will make an effort to make new network features into g)penMol in the future. This interface will be based on Tcl.Tk.
Intro'uction to gOpenMol
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U)*+ +e assume that g)penMol is properly installed on your system and you know how to run the rung)penMol script that sets various aliases and environment values. In case you are using M$ ! and you are using a ><bit display I recommend you to set the following environment variableE setenv M,-A.R/0.1*-UAL 23seudo4olor 52 This variable tells M$ ! about your display type and assigns a proper visual to it. +rite gopen#ol and g)penMol starts and if your display supports )pen2- or you are using M$ ! you get two new windows on your screen. The first window contains a pull down menu and some buttons to be used as the input window for g)penMol. The other one is the graphics window where the molecular structures and other graphics ob,ects are displayed. Before we look at the 2/I in more detail it is worth describing some of the things you donKt see but yet they are still thereE +hen g)penMol starts it reads a lot of information about atoms" which will be needed for the display or other purposes. This information is taken from the gopenmol.data directory. The user can modify a lot of the default parameters or variables at startup through two startup filesE 7. !t startup g)penMol reads first the system startup file *gopen#olr".t"l0 located in the gopenmol.data directory. This file contains information related rather to all users. 2. The second file is .gopen#olr".t"l from your login directory which can contain information specific for one user. Both startup files can contain internal g)penMol tcl<commands. 6*)32 To start g)penMol on the +I(32 platform run the rungOpenMol.bat file in the bin. directory. This is easily done by making a shortcut from the file to your desktop. Before we look at the 2/I in more detail it is worth describing some of the things you donKt see but still are thereE +hen g)penMol starts it reads a lot of information about atoms" which will be needed for the display or other purposes. This information is taken from the gopenmol.data directory. The user can modify a lot of the default parameters or variables at startup through a startup fileE !t startup g)penMol reads first the system.user startup file *gopen#olr".t"l0 located in the gopenmol.data directory. This file calls further tcl files to set up many features of g)penMol. gOpenMol manual version 0.92 on 23th September 2005
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-o% to ,egin +our gOpenMol session

gOpenMol startup line comman'
Fou donKt always need the graphics when you use g)penMol. In fact in some cases itKs an advantage not to use the graphics if you ,ust want to use g)penMol as a scripting engine. The command line options *you have to edit the rung)penMol.bat or rungopenmol files in the bin. directory0 when you start g)penMol areE gopen#ol 7"*nput4oord.,(t 7% 87t 7s9 7ln 7#Model.go# 7p:ile.)a#e 4oord.:ile <mModel.gom start 2openMol with the model file Model.gom <cInput9oord.$xt start g)penMol with coordinate file <pfile.name start g)penMol with parameter file KAile.(ameK <t start g)penMol without any graphics <ln do not write a log file *2)4$(M)-.-)20 <ly force g)penMol to write the log file *2)4$(M)-.-)20 <s start g)penMol with the hardware stereo *stereo in a window0 option <h print this help any coordinate file with a predefined file extension *pdb" crd" M0 -tart up windows The input window looks like *after reading in a structure0E
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g)penMol starts with two windows *3B graphics window and 2/I window0. +indow ! contains the 3B graphics and the other windows contain the 2/I with the various buttons. The various regions are defined asE A The graphics 3B window. 0 In the 2/I window there are various important regions. In the upper left corner there is a list describing the currently read input files and a checkbutton attached to the file name showing if the structure is active *checked0 or inactive *not checked0. 4 4ressing the g)penMol logo generates a display command for g)penMol. !lways when you want to display a scene press this button. ; 4ressing the left mouse button and moving the mouse rotates the structure*s0 in the 3B window if the rotation radiobutton is checked. If the translation radiobutton is checked the structure will be translated. , It is possible to choose a full structure or fragments of a structure. If the selection radiobutton is checked the rotation or translation is applied to this selection. : g)penMol does not automatically redisplay a scene after a command has been applied. 9hecking the instant update to on will generate an automatic redisplay after all commands. / 4icking mode can be put on and off. H The line command entry widget.
3lease alwa!s re#e#ber to press t%e logo button to <re=displa! t%e view or "li"$ t%e >*nstant update On?@
"otate a structure in gOpenMol

!ll rotations and translations are applied according to a fi(ed coordinate system where the NimaginaryN coordinate system is located so that the positive x<axis points from the left side of the screen to the right side. The positive y<axis points up from the bottom of the screen and the positive D<axis points from the screen to your nose. ;emembet to have the 5;otate6 mode selected in the main widgetO The molecular ob,ect on the screen can be manipulated *rotated0 in the following wayE *70 4ressing the L,:A mouse button and moving the mouse in the x<axis direction rotates the ob,ect around the !7a(is. 4ressing the L,:A mouse button and moving the mouse in the y<axis direction rotates the ob,ect around the (7a(is.
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*20
4ressing the R*/HA mouse button and moving the mouse in the Py<axis direction Dooms the ob,ect upwards and the <y<axis direction Dooms the ob,ect downwards. 4ressing the M*;;L, mouse button and moving the mouse in the x<axis direction rotates the ob,ect around the B7a(is. If you only have a two button mouse you will not have this feature available.
*30
To enable :uick rotation" translation and picking it is possible to enable the translation mode by pressing the hift key before one presses the left mouse. !s long as the hift key is and the left mouse button are pressed the structure will translate when the mouse is moved. Be careful to understand that if the hift key will be released before the left mouse button the 5Translate6 state will be left on. In the other case 5Translate6 mode will return to 5;otate6 mode. By pressing the 9trl key first and keeping it pressed it is possible to pick or mark atoms in the graphics screen by pressing the left mouse button. The selected atom*s0 can then be dragged to an input widget. If one releases the 9trl key before releasing the left mouse button g)penMol will stay in the picking mode. 4ressing the !lt key and the left mouse button and moving the mouse in the x<axis direction rotates the molecule around the D<axis. This is the same as using the middle mouse on a three button mouse.
Translate a structure in gOpenMol

;emember to have the 5Translate6 mode selected in the main widgetO The molecular ob,ect on the screen can be manipulated *rotated0 in the following wayE *70 4ressing the -$AT mouse button and moving the mouse in the x<axis direction or moving the mouse in the y<axis direction translates the ob,ect in that direction.
efine the set on %hich the action %ill appl+

If the selection is in the 5)ff6 position all rotations and translations are applied on the main set *display0. +hen the selection is in the 5)n6 position all rotations and translations are applied on the atoms that have been selected with the 5 elect6 facility. The select facility can be used for docking when one selects the atoms of a ligand and then translate and rotate the ligand to fit into an active site.
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Control of the re'ispla+

This controls the redisplay of the graphics. If the button is in the 5)n6 position the display will automatically be redisplayed" when needed. If the 5)ff6 position is selected the graphics has to be redisplayed either by pressing the g)penMol logo or by executing the 5display6 line command. If one is working with a complicated picture that takes a long time to be redisplayed it is often useful not to have the redisplay on to save time.
Transformation options
g)penMol can operate on two different viewing or transformation modesE In the 2lobal mode g)penMol calculates one coordinate center around which the system*s0 rotate. Aor example if you have a protein in one file and a ligand in an other file and you read both files into g)penMol. +hen you read in both files into g)penMol you would like to rotatet the whole system around a common point. In the local mode all the read structures rotate around their own coordinate center and translate relative to their own coordinate center. In this mode you can read in a protein and a ligan and move.rotate the ligan according to the protein structure.
By clicking on the 52lobal6 and 5-ocal6 radio buttons you can change modes. By default changing the modes returns your structures to their starting positions. %owever" the user can define an option where the structures keep their current postions while changing modes. %owever" while this stage changes the coordinate values any surface displayed will have the structure orientation changed.
The coor'inate s+stem

g)penMol uses a fixed global coordinate system where the centre of the coordinate system is in the middle of the graphics screen. The positive x<axis is running to the right and the negative x<axis to the left. The positive y<axis is running upwards and the negative y<axis downwards. The 4ositive D<axis is running out of the screen and the negative D<axis into the screen. The local coordinate system is rotating and translating with the molecule. The local coordinate system on any atom or an arbitrary position in the x" y" D space can always be displayed with the plot a(is line command or using the 54lot !xis6 widget.
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The rotations and translations are always done in the global coordinate space. The plotting of the local coordinate axis on an atom or set of atoms is helpful for example in docking.
-an'ling of input files

The g)penMol program communicates with the environment in many ways. The simple way is through files. !n input file can be a coordinate" tra,ectory" mesh data or an other file. The file can be located on the local or shared disk or it can be located on an other machines accessible through the +eb or using http. +hen ever an input file name is give like #!"oord.pdb g)penMol expects the file is on a local or shared disk. If the name is given like %ttp CC#!.#a"%ine.netC#!"oord.pdb g)penMol tries to download the file #!"oord.pdb over the network. Input coordinate files are handled in the following wayE 7. 2. 3. C. Aile is read into g)penMol !toms are assigned type and properties according to their type The connectivity *bonds0 are calculated !fter the first 3 steps have been passed g)penMol calls the tcl procedure lul3ostReadAto#4oordinates in the gopen#olr".t"l file in the data directory with two parametersE a. Type of atom coordinate set i. 9%!;MMH9));B 7 ii. A;$$H9));B 2 iii. I( I2%TH9));B 3 iv. !MB$;H9));B C v. F! 4H9));B = vi. M/M)BH9));B G vii. 2;)M) H9));B Q viii. M)4!9H9));B > ix. 4BBH9));B @ x. 2!M$ H9));B 78 xi. )4$(M)-H9));B 77 xii. %F4$;H9));B 72 xiii. 3FIH9));B 73 xiv. )9#$TH9));B 7C xv. BF(!A;!M$H9));B 7= xvi. 2!/ I!(H9));B 7G xvii. M)-2H9));B 7Q xviii. 3M)-H9));B 7> xix. T3FIH9));B 7@ xx. / $;H9));B 28 xxi. 2;)M) @GH9));B 27 gOpenMol manual version 0.92 on 23th September 2005
16
xxii. xxiii. xxiv. xxv. xxvi. xxvii.
/%BBH9));B 4BBRH9));B !BAH9));B 2;)M!9 H9));B B-H4)-FH9));B 1!2/!;H9));B
22 23 2C 2= 2G 2Q
There might also be some new files supported not mentioned here. b. ;eturn state from the coordinate reader i. If the 3 steps have been successful the parameter is 8 ii. If the 3 steps have been unsuccessful the parameter is 7 9urrently the lul3ostReadAto#4oordinates procedure looks the followingE
################################################################# # PROC # e e!ute this s!ript always after having read in the !oordinate # file # # type" defines the type of the input !oordinate file >
17
# there are two input states" # # #" ok return from the !oordinate stage # $#" error return from the !oordinate stage # pro! lulPostReadAtomCoordinates % Type &tate ' % glo(al gomTinkerInputConne!tivity # )RROR if %*&tate' % # O+ ' else % ################################################################### # this is for the TI,+)R !oordinate files that has the !onne!tivity # in!luded # # the array is set during the pro!ess when the !oordinates are read in # the !onne!tivity !an not (e set at that stage (e!ause the !onne!tivity # will later (e reset and re!al!ulated # if %-array e ists gomTinkerInputConne!tivity.' % !at!h % for %set i /' %*i 01 -array si2e gomTinkerInputConne!tivity.' 3 %in!r i' % edit (ond !reate 4 4 -linde *gomTinkerInputConne!tivity5*i6 #. 3 4 4 -linde *gomTinkerInputConne!tivity5*i6 /.7 ' ' array unset gomTinkerInputConne!tivity ' ################################################################### ' '
This enables an automatic procedure to include commands after a file has been read into g)penMol. 9urrently it supports the inclusion of the connectivity information from TI(#$; coordinate files.
Multi%in'o%ing in gOpenMol
g)penMol can in some cases use a display mode where two windows are open. The simple case is when a linear distance plot *-B40 and a structure window can be used simultaneously. ! linear distance plot can be used for example to display and analyse the secondary structure of a protein or to display a distance profile for example in a docking. The multiwindow mode can be put on or of in the 5$dit Bisplay properties6 widget. 4lease select from the 5+indowing type6 either 5 ingle6 or 5Multi6.
18
To see the effect import a protein file" for example the optCpti.crd from the demo directory. )pen the 54lot -B46 widget" turn the -B4 plot on by clicking the 5-B4 plotE )n6.and press the 5!pply6 button to select the 9! atoms. (ow you will see a distance plot showing the distances between the 9! atoms in the structure. )pen the 5$dit Bisplay properties6 and click the Multi. (ow you will see two windows a window with a structure and the -B4 window. If you now click with the -eft mouse button in the -B4 window you will see an arrow in the structure window showing the two atoms connected. The residue and atom numbers of the clicked atoms will also be shown in the startup *text0 window. This helps you identify the atoms involved in the secondary structure. The mode can be changed again by going to the 5$dit Bisplay properties6 widget and clicking 5 ingle6.
The multiwindow mode can also be used while looking at tra,ectories. Import the optCpti.crd from the demo directory. )pen the 5Tra,ectory Main6 widget and import the dynaCpti.dcd file.
19
)pen the 54lot -B46 widget" turn the -B4 plot on by clicking the 5-B4 plotE )n6.and press the 5!pply6 button to select the 9! atoms. (ow you will see a distance plot showing the distances between the 9! atoms in the structure. )pen the 5$dit Bisplay properties6 and click the Multi. Fou can now scan or loop through the structures.conformations by having one window showing the structure and the other window showing the -B4 plot.
The main i'ea of the comman' interface

A%e #enu driven interfa"e is i#ple#ented using t%e line "o##ands. A%e pulldown #enu options generate a A"lCA$CgOpenMol "o##andD w%i"% is sent to t%e gOpenMol parser. The gOpenMol line command interface is extremely powerful and useful. The pulldown menus in the window *so far0 areE
|File|Edit|View|Colour|Calculate|Plot|Trajectory|Run|Tools|Help|
.1/ FILE menu has the options#

,ew8 Open8 Close8 &ave8 &ave as8 &tarts a new gOpen9ol session and destroy all internal data stru!tures and data: Open a previously written model 5stru!ture gom file6: Close the !urrent session and destroy all internal data: &ave the !urrent stru!ture and display in a model gom file: &ave the !urrent stru!ture and display in a new gom file:
Import8 Import various things into gOpen9ol: Cluster data Coordinates in various formats ;i!tionary file defining the mapping (etween atom la(el to atom type <aussian (asis set for Open9ol Atom ve!tor data Read a ve!tor data file = C>AR99 for!e ve!tor file = ?ormatted flat file with ve!tor data Read@edit a T!l s!ript and e e!ute it Import partial atomi! !harges from various program output files
20
<AA&&IA, !harges from 5e tra!ted from a <aussian output file6 - ,atural population analysis - 9er2=+ollmann - Chelpg ICO,B atom !harges 5e tra!ted from an ICO,B output file6 9OPAC atom !harges Aser defined !harges
) port18 ) port various things out from gOpen9ol Cluster data Coordinates into some formats Correlation data Input18 <enerate raw input to <A9)&& program ICO,B program 9OPAC program Pro(esurf program Aser defined program Radial distri(ution fun!tion Root mean sCuare deviation &ave time series to disk Reset18 Reset various things: Atom !olour7 Reset atom !olours to default$ Atom !onne!tivity:::7 Reset@!al!ulate atom !onne!tivity$ gOpen9ol7 Reset gOpen9ol and free all reserved memory$ Diew7 Reset view to the startup view$
>ard!opy7 Produ!e a hard!opy or s!reen dump in some (itmap formats: )EIT7 >alt program e e!ution 5&hut down program6:
.0/ E IT menu has the options#

::Copy18 Copy various things to the !lip(oard: Fitmap7 Copy !urrent graphi!s window into !lip(oard Correlation7 Copy !orrelation data into the !lip(oard 9&;7 Copy the 9ean &Cuare ;ispla!ement data into !lip(oard R;?7 Copy the radial distri(ution fun!tion into !lip(oard Timeseries7 Copy time series into !lip(oard: )dit the !ell dimensions: ;efine new rotation !enter: )dit 5!reate@(reak6 (onds: Identify an atom (y pi!king:
)dit Cell8 )dit Center8 )dit Conne!tivity8 Identify Atom8
21
Gight Properties8 9aterial Properties8 9erge &tru!tures8 9ole!ule8 Rotate@Translate8 &ele!t8 &tere8 &uperimpose8 ;isplay attri(s8 H; to I;8
)dit light properties: )dit surfa!e material properties: 9erge all the !urrent stru!tures into one: )dit mole!ule 5(reak and !reate (onds6: Control widget for rotation and translation: &ele!t atoms into the sel!tion (uffer: &tereo pair display mode: &uperimpose two stru!tures Change display attri(utes: 9ake a H; to I; transformation of your system:
.1/ 2IE( menu has the options#

Atom !olour8 Atom la(el5s68 Atom tree Atom mask8 Atom type8 9easure8 Periodi! ta(le8 &tereo8 Change atom !olour: ;isplay atom la(el5s6: Gist and pi!k atoms from a tree like widget Change atom display mask: Change atom type display: 9easure mole!ular geometry: Diew and !hange atom parameters using the atom periodi! ta(le:
&tereo pair display: >ardware stere 5&<I68 stereo in a window: ;isplay gOpen9ol output te t:
Te t output8
.3/ COLO!" menu has the options#

Fa!kground18 Change (a!kground !olour in graphi!s window: Fa!kground8 Change (a!kground !olour with a T!l@Tk tool: Fa!kground8 Change (a!kground !olour with a R<F tool: Atoms8 Change atom !olour:
.4/ CALC!LATE menu has the options#

Average str!urure8 Cal!ulate the average stru!ture from a traJe!tory:
22
Cluster8 Conne!tivity8 Correlation8 <eometry8 >ydrogen (onds8 9ean sgr displ8 R;?8 &uperimpose8 &urfa!e !entroid8
Cal!ulate and plot !luster matri TraJe!tory file: Cal!ulate atom !onne!tivity:
from a
Cal!ulate !orrelation series from time series: Cal!ulate mole!ular geometry: Cal!ulate and display hydrogen (onds: Cal!ulate mean sCuare displa!ement values from a traJe!tory file: Cal!ulate a single or an average radial ;istri(ution fun!tion from a frame or traJe!tory: &uperimpose two stru!tures: Cal!ulate the !entroid for an isosurfa!e:
.5/ 6LOT menu has the options#

A is Clip plane8 Colour s!ale8 Contour8 Cutplane8 G;P8 Plum(er8 R9&;8 De!tor file8 Plot the lo!al !oordinate system: ;efine a !lip plane for a surfa!e: Plot a !olour s!ale: ;isplay !ontour surfa!es: Plot a !utplane trough a !ontour surfa!e: Plot a linear distan!e plot for sele!ted atoms: Plot a tu(e or ri((on trough sele!ted atoms: Plot root mean sCuare deviation of atom movement: Plot the set of ve!tors read from a file:
.7/ T"A8ECTO"9 menu has the options#

?ill18 4 4 4 4 4 4 ?ill time series ve!tors: ;istan!e array Angle array Torsion array ;elete time series ve!tors: ;istan!e array Angle array Torsion array
;elete18
23
9ain8 9onitor18
9ain traJe!tory !ontrol widget: 9onitor mole!ular geometry: ;istan!e5s6 Angle5s6 Torsion5s6 9anipulate time series widget: Tra!e the movement of sele!ted atoms: 9ake animations:
Time series8 Tra!e8 9ake video8
.:/ "!N menu has the options#

autodo!kIplt8 Run the autodo!kIplt program to !onvert an Auto;o!k map file to the plt format 5formatted and unformatted6: Run the !ontour management program: Run the gamessIplt program to !onvert the The K!u(eL information in the PA,C> file Into a format known (y gOpen9ol:
!ontman8 gamessIplt8
gCu(eIplt@gMN!u(Iplt8 Run the gCu(eIplt@gMNCu(Ipl to !onvert a <aussianEE !u(e file into a format known (y gOpen9ol: JaguarIplt8 Run the JaguarIplt program to !onvert Oaguar or(ital data to a format known (y gOpen9ol:
Ooin <amess IRC files Ooin <amess IRC files into one: kontIplt pltfile8 pro(esurf8 tmoleIplt A>F;Iplt vi(s Run the kontIplt program to !onvert a <rid data file to the plt format: Run the Pltfile program to !onvert the gOpen9ol plot file (etween (inary and formatted: Run the Pro(esurf program to generate a Connolly type of surfa!e: Run the tmoleIplt file to !onvert a Tur(o9ole <rid file to the plt file format: Run the uh(dIplt file to !onvert a A>F; grid ?ile to the plt file format: Run the vi(s program to generate the Coordinate data to display vi(rations:
.;/ TOOLS menu has the options#

;GG@&O plugins8 ) tensions implemented as plugins 4 ChemH; !oordinate reader plugin
24
Auto;o!k8
4 &partan !oordinate reader plugin 4 DR9G e port plugin Auto;o!k display and analysis fa!ility:
.1</ -EL6 menu has the options#

A(out8 ;emo8 >elp8 Peek version8 &how the a(out te t a(out gOpen9ol: ;emo widget: &how this file: Che!k the gOpen9ol version availa(le:
.1/ File menu

)ew
tart a new g)penMol session and destroy all internal data structures and data.
Open a previousl! written #odel <stru"ture go# file=

;ead in a previously saved model *go#0 file. The file is an ascii readable file containing information about the molecular display at the time when the file was saved. 9urrently it will contain information about the atoms" rotation matrix" contour data. 9urrently there are still things which will not be saved but eventually all the information will be saved to continue a session from the previously saved stage. ;ead in the go# file using the following widgetE
-ine command optionE #open "o##and
25
-ave t%e "urrent stru"ture and displa! in a #odel go# file

ave current display information into a go# file. This file can later be read back and the session can continue. ave the session using the widgetE
-ine command optionE see #save "o##and
*#port infor#ation into gOpenMol Read "luster file widget

;ead in precalculated cluster data for display *in future there will also be an analysis part0. The cluster data has been calculated using the "al"ulate "luster menu option.
26
-ine command optionE see i#port "o##and
*#port 4oordinates in various for#ats

This is the main facility to import atom information *including coordinates0 into g)penMol. This is almost always the first step because g)penMol has to know the molecular topology of the system before it can plot properties or analyse tra,ectory information. The supported file types can bee seen on the right side with the radio buttons. There is also a button to indicate that the next structure is added *appended0 to the current display. This new structure goes into e new data structure and it is not possible to make bonds between atoms in different data structures. +ith the file browser it is possible to change the directory and filter the files with special file extensions. If the user has not done any reconfiguration the default file extensions are applied. The file extensions can be changed with the define command.
Supporte' file formats

g)penMol support a variety of coordinate input files. Most are fully readable formatted files. The supported file formats areE !BA !msterdam Bensity Aunctional program output log files. !MB$; !mber coordinate files are a special dialect of 4BB files. More information about the !MB$; file formats can be found at httpE..www.amber.ucsf.edu.amber.formats.html. gOpenMol manual version 0.92 on 23th September 2005
27
9%!;Mm.9%!;MM 9%!;MM coordinate *crd0 file. Aor the format please look into your R/!(T!.9%!;MM documentation or the source code. B-H4oly B-H4oly 9)(AI2 coordinate file. Arame The coordinates are taken from a tra,ectory file. 2!M$ The 2!M$ 4/(9% file *dat0 containing the M)-4-T information produced with the M)-4-TS.T;/$. option. 2aussian The coordinates are imported from a 2!/ 2;)M!9 2;)M!9 gro coordinate file. 2;)M) @G 2;)M) @G coordinate data file. %F4$;9%$M %yper9hem input coordinate *hin0 file. I( I2%T Insight coordinate *car0 file. 1aguar 1aguar output log file. Mol2 Mol2 coordinate file format. M)4!9 9oordinates are imported from a M)4!9 unformatted graphics output file. M/M)B 9oordinate format used by the M/M)B program. gOpenMol manual version 0.92 on 23th September 2005 I!(33 formatted checkpoint file.
28
)4$(M)Aormatted coordinate input file to )penMol. 4BB The standard Brookhaven 4rotein Bata Bank format. /%BB /niversity of %ouston Brownian Bynamics */%BB0 :cd coordinate reader. TI(#$; The Tinker coordinate input format. / $; The user defined coordinate input reader. 3M)3mol coordinate file format. The file can contain multiple entries but g)penMol reads only the first entry. 3FI imple xyD coordinate input format. F! 4 9oordinate input file to the F! 4 program by Br. Alorian MTller<4lathe. ! file is selected to be processed by g)penMol either by a rapid double click on the file name or a single click on the file name and a click at the Open button. It is possible to N4eekN or look into a file before it is imported by pressing the 3ee$ button when a file name is defined. It is also possible to choose or not to choose the calculation of the bonds for the molecular system.
29
The file browser is started by clicking on the 0rowse button.
!ser 'efine' input filter

The U-,R option for the input filters is a user defined Tcl script that reads a user defined input format. The called Tcl procedure isE lulReadU-,R4oordinates FileName Action.
30
+here the #ile$a%e is the name of the file and the variable &ction must be either 0 *Sno append0 or 1 *Sappend0. Bepending on if the structure will be appended to the structure list of if it will be only one.
####################################################################### # PROC # Input file name" ?ile,ame # Read new stru!ture or append to old list" A!tion 51 # new $1 # append6 pro! lulReadA&)RCoordinates %?ile,ame A!tion' % error PAser must supply the !ode$P '
The user has to supply the code. !s a suggestion the Tinker xyD input filter is implemented the same way and it looks likeE
######################## e port TI,+)R !oordinates ##################### # PROC@Geif Gaaksonen # ?ile,ame # Input file name" ?ile,ame # Read new stru!ture or append to old list" A!tion 51 # new $1 # append6 pro! lulReadTinkerEQRCoordinates %?ile,ame A!tion' % # open file ::: set ?ileSp -open *?ile,ame r. if %*?ileSp 11 PP' % !at!h %lul)rror;ialog %)RROR" !an't open TinkerEQR file$'' errRet if %*errRet $1 PP' % puts P)RROR" !an't open TinkerEQR file$P ' error P)RROR" !an't open TinkerEQR file$P return ' # do the Jo( ::: puts PReading Tinker EQR !oordinate file '*?ile,ame':::P gets *?ileSp Input;ata set ,umAtoms -linde *Input;ata #.
if %$*A!tion' % define stru!ture *,umAtoms new ' else % define stru!ture *,umAtoms append ' set &tru!,um -show molstru!tures. for %set i /' %*i 01 *,umAtoms' %in!r i' % gets *?ileSp Input;ata set Atom,ame -linde set E! -linde *Input;ata /. *Input;ata I.
31
set Q! set R!
-linde -linde
*Input;ata H. *Input;ata N. *i *i *i *i *i *i *&tru!,um *&tru!,um *&tru!,um *&tru!,um *&tru!,um *&tru!,um
# put the values into the stru!ture ::: define atom la(el *Atom,ame define residue la(el TI,+ define segment la(el TI,+ define atom !oordinates *E! *Q! *R! define atom !harge #:# define atom resnum(er / ' # !lose file and return ::: puts ;one$ !lose *?ileSp '
The code is in the .data.gopenmolrc.tcl file. -ine commandE i#port "o##and
Import ictionar+ file 'efining the mapping ,et%een atom la,el to atom t+pe#
This facility imports a dictionary file. ! dictionary file defines the mapping between a residue and atom name into the atom type space *and atom partial charge0.
The dictionary file can look like the followingE J!tom dictionary file !-! ( 32 <8.3= !-! %( 7 8.2= !-! 9! 78 8.88 gOpenMol manual version 0.92 on 23th September 2005
32
!-! %! 3 !-! 9B 78
8.78 <8.38
It contains a residue name" an atom name and maps these into an atom type in the used force field *9%!;MM in this case0 and an atom partial charge. This is one of the possibilities to assign an atom type and an atom partial charge to the atoms. -ine commandE see i#port "o##and
Import =aussian ,asis set for OpenMol

This part will most likely not be helpful for anybody! erhaps it could be a starting point for somebody who wants to write a basis set editor for a !uantum chemistry package" This is the )penMol 2aussian Basis set widget browser.editor. !s it is now implemented the file *database0 can only be viewed not edited. /se the file browser to select a data file. There is one sample file *gblHHlineHinput.data0 in the gopenmol data directory. 4ress the NBrowseN button to select an input basis set database. 4ress the N!pplyN button to inport the database. 4ress on any of the basis set tags" in the left widget" to show the basis set for that tag.
33
Aile browser to select the basis set database.
Most likely this will only be useful for a )penMol user. -ine commandE i#port "o##and
34
*#port Ato# ve"tor data

g)penMol can read in two types of vector dataE Import information defining a vector property for the atoms in a molecule. The format is the same as in the 4R; files apart from that the coordinate information defines now the vector direction in the x" y and D directions. Alat formatted text file containing the vector information. -ook at the !ppendix at the end of this document for the file format.
-ine commandE i#port "o##and
*#portD edit and e(e"ute a A"lCA$ s"ript

Import" edit a tcl script and execute it. It is the same as writing sour"e file.na#e.t"l on the line command.
35
The Tcl code in the window can be edited.
36
-ine commandE see import command
*#port partial ato#i" "%arges fro# various progra# output files
2!/ I!( charges from *extracted from a 2aussian output file0 (atural population analysis MerD<#ollmann 9helpg I9)(> atom charges *extracted from an I9)(> output file0 M)4!9
g)penMol will prompt for a file containing the atom charges.
The 5Aile of typeE6 field will be different depending on from where the charge information is coming.
,(port infor#ation out fro# gOpenMol 6rite "luster widget

! previously calculated cluster matrix can be exported from g)penMol to be used by other programs or to be read back to g)penMo at a later time.
37
,(port "oordinates widget
$xport atom coordinate information in some formats. 9hoose first the file format and select then a file name or click at the NBrowseN button to get a file selector. If several molecular systems are read into g)penMol select which structure will be exported. The ';M- file export facility is very crude. 9urrently it only supports line drawing" 94# and the licorice display styles.
+rite a file name or click at one of the files in the window.
38
-ine commandE see e(port "o##and
6rite "orrelation widget

+rite to disk correlation data calculated during the time analysis in tra,ectory analysis for molecular dynamics tra,ectory files.
/enerate raw input to

2!M$ program I9)(> program M)4!9 program 4robesurf program gOpenMol manual version 0.92 on 23th September 2005
39
)wn / $; program
E>port input for e>ternal porgrams

/sing this widget it is possible to export *mostly very raw0 input files for the following programsE

/AM,-- *raw input0 *4O)5 $xtended %uckel program *:uite complete0 MO3A4 *raw input0 3robesurf" a 9onnolly type of program *complete0 User defined. To use this part one needs to program the output rules *Tcl.Tk coding0 into the lulMa$eU-,Rinput procedure in the gopenmolrc.tcl script in the data directory
3robe-urf progra# input 4robe urf program is the program to generate 9onnolly type of surfaces. The probe surface program 4;)B$ /;A generates a mesh with grid values from 8 to 788. The value 788 is at the vd+ value and value 8 is at the vd+ P max. probe diameter value. There are two methods available to calculate the values between 8.8 and 788.8.

Birect distance *r0 where the value is direct proportional to distance r and :uared distance *rJJ20 where the value is proportional to the s:uare rJJ2 of the distance.
It is possible to generate the surface for different probe values. The method is based on the article by ;. 'oorintholt et al. *'oorintholt ;." #oster M.T. " 'egter 2. " 'riend 2. and %ol +.2.1." N! very fast program for visualiDing protein surfaces" channels and cavitiesN" 1. Mol. 2raphics Q *7@>@0 2C3<2C=0 9urrently only the 3robesurf program has some extra options available. It is possible to define the max and min x<" y< and D< values to define the place of the box for which the grid values are calculated. It is also possible to define the number of grid points in the x<" y< and D<directions. The max probe radius defines the largest probe radius that can be displayed using the current grid values. 9hoose the output option and file name *or click the 0rowse button to browse0.
40
!fter pressing the Appl! button the file is written to disk and a widget containg the file input is shown. It is possible to edit the data in the widget and save the new content to disk by clicking the -ave button. The file will always have the same name as the original file had.
-ine command E see e(port "o##and gOpenMol manual version 0.92 on 23th September 2005
41
6rite rdf widget

+rite a pre<calculated radial distribution function *;BA0 to disk. The file can then be read into your favorite plot program to be displayed graphically.
4op! ti#e series to dis$ widget
9opy time series data to a file on the disk. elect the type of time series array and the number of the distance" angle or torsion array to be copied to the disk. 2ive the file a name direct or choose a name using the file browser by clicking the 0rowse button. To write the information on disk press the the Appl! button.
-ine commandE see "op! "o##and gOpenMol manual version 0.92 on 23th September 2005
42
Reset various t%ings.

Atom !olour7 Atom !onne!tivity:::7 gOpen9ol7 Diew7 Reset atom !olours to default$ Reset@!al!ulate atom !onne!tivity$ Reset gOpen9ol and free all reserved memory$ Reset view to the startup view$
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ reset command -eif -aaksonen 9 9 7@@G JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ reset U U reset atom colours U ato#"Eolours U U ;eset g)penMol U gopeEn#ol U U ;eset the view to the original U reseEt view U U ;eset atom connectivity U "onnEe"tivit! -eg#ent Residue Ato#
43
4al"ulate ato# "onne"tion widget

This widget is helpful when one wants to recalculate atom connections *bonds0 in case you you have deleted some or if you donKt get all hydrogen atoms bonded in your structure. g)penMol uses a very simple algorithm to calculate possible bonds. It runs over all the atoms in the structure and uses a window *range0 of atoms inside which it thinks the bonded atoms are located. By default there is a range defined *use s%ow ato# window command to display the current value0 so when g)penMol looks at atom ( it checks range atoms backwards and range atoms forward from atom ( to find the bonded neighbours. ome programs place added hydrogens at the end of the file" which might prevent g)penMol from finding the right bonds. To solve this problem the range can be redefined. 4lease supply a new value" inside which you think all bonded atoms will be. It is also possible to recalculate the connectivity only for a set of atoms.
Ma$e a %ard"op! widget
This is the main facility for producing a hardcopy of the picture in the graphics window. 9urrently g)penMol supports the following output formatsE

Microsoft +indows BM4 format 4ost cript format ilicon 2raphics ;2B format
44
Targa format *this format is used for the mpeg animation part0 3<+indows 3+B format
These formats should be enough to export the pictures to almost any text processing or image editing program for further processing. )n top of the page are the radio buttons for the supported formats. /se the file selection browser to select a file name. Aor the 4ost cript case it is possible to define the picture orientation.
-ine commandE see %ard"op! "o##and
,(it Halt progra# e(e"ution .0/ E IT menu has the options# Cop+ ?arious things to the "lipboard paste buffer <wor$s onl! on 6indows=.
BitmapV 9orrelationV M BV ;BAV TimeseriesV 9opy current graphics window into clipboard 9opy correlation data into the clipboard 9opy the Mean :uare Bisplacement data into clipboard 9opy the radial distribution function into clipboard 9opy time series into clipboard.
;efine "ell widget
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The purpose of this widget is to define the properties of a cell *box0 and control the display of the cell *box0. The cell *box0 can be usefull when one is displaying a molecular dynamics simulation *tra,ectory0" that is using periodic boundary conditions. Befine the cell properties" a" b and c distances *in !ngstrom0. The cell is by default placed in the center of the screen *or around the 8.8" 8.8" 8.80. %owever" the cell can be translated by defining the translation distances. The alpha" beta and gamma angles can *hopefully0 some time be defined. 4urrentl! t%e angles "an onl! be '0 degrees. The cell can be displayed by changing the NBisplay stateN to O). The colour of the cell and the width of the cell *in pixels0 can also be changed. 9lick on the N9olourN button to change the colour.
4ick the colour from the colour palette.
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-ine commandE see define "o##and
4enter s!ste# widget
9enter the system according to the given atom*s0. It is also possible to give an absolute x"y D coordinate. The x coordinate value is placed in the segment field" y coordinate value in the residue field and D coordinate value is placed in the atom field. 4ress then the N!pplyN button.
-ine commandE see "enter "o##and
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,dit #ole"ule widget
$dit molecule geometry. 9urrently the only supported actions areE

9reate bond*s0 Break bond*s0 Aind < bonds in proteins
elect the atom*s0 and click on either the N9reate bondN or NBreak BondN buttons. The < bond algorithm looks for atoms inside a search radius" which can be changed by editing the input widget. It is also possible to delete or create all bonds from a certain atom or atoms by deleting the atom selection input from the atom selection U2 list widgets.
-ine commandE see edit "o##and
*dentif! ato# widget
This widget enables the user to click on an atom and identify the full properties for that atom. (ormally pressing the left mouse button and moving the mouse rotates the molecular system and pressing the rig%t mouse button and moving the mouse Dooms the molecular system. gOpenMol manual version 0.92 on 23th September 2005
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9licking the NIdentify atom*s0N state to on turns the left mouse button to a pointer into the molecular system. Move the arrow over an atom and press the left mouse button and the widget will be filled with atom information about the that particular atom.
-ine commandE see )o line "o##and available
,dit lig%t properties widget
$dit properties of the light *colour components0 and the position of the light. It is possible to the change the red" green and blue colour intensity of the light using the colour sliders. The position of the light is by default along the D<axis but it can be changed according to the nort%" nort% east" east" sout% east" sout%" sout% west" west and nort% west scheme. elect the new light position by clicking the radio button. To update the display while changing the value click the NInstant updateN button.
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,dit #aterial properties widget
$dit surface material properties. It is possible to change the following propertiesE

Material specular red colour. Material specular green colour. Material specular blue colour. Material specular #aterial s%ininess.
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The colour components define the colour of the reflecting light and the material shininess defines the NwidthN of the reflecting light *8 S wide and 72> S very concentrated0. )bserve that the new properties are not shown until the NBisplayN command is executed or before the user presses the gOpenMol logo logi in the right upper corner. If you want the new properties to be shown immediately while you change the slider values click the N9ontinuous displayN on.
-ine commandE see edit "o##and
RotateCtranslate "ontrol widget
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;otate and translation control widget. 9licking on < or P rotates or translates the display with the value *step0 defined in the entry between the signs. The step can be changed by writing a new value into the entry space. The new display will not be showed before the NBisplayN command is executed or the g)penMol logo is pressed. The operations *rotation.translation0 will be applied either on the display or the selection. !ccording to the N!pply onN radiobutton.
Line "o##and see

rotate "o##and translate "o##and
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-ele"t ato#s widget
elect atoms into a selection buffer. If there are several systems available select the one you want by clicking the structure through the radio buttons available. The selection buffer can be used for applying rotations or translations ,ust to a subsection of a molecular system.
-ine commandE see sele"t "o##and
-uperi#pose ato#s widget
uperimpose two structures. elect the atoms from the both sets. The number of atoms have to be the same in both sets.
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-ine commandE see "al"ulate Fuatfit "o##and
,dit displa! attributes widget
Befine the distance to the near clipping plane. 4ressing 7 and G signs decreases or increases the distance to the near clipping plane with the defined step length. The new view will not be displayed before the NBisplayN command is applied or the gOpenMol logo is pressed. To update the display after the changed value click the NInstant updateN button.
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.1/ 2IE( menu has the options#
-ele"t ato# "olour widget
elect atom colour by defining the atoms and click the N9hoose colourN button to show the colour editor. If the atom partial charges have been defined itKs also possible to colour the atoms according to the partial charges. Befine the partial atom charge range and press the N!pplyN button. The colour range is blue for the lower limit and red for the upper and the colour goes through green.
4ick or choose the colour using the colour editor and press the N)kN button. Then press the N!pplyN button to colour the selected atoms with the picked colour. The new colour will not be seen before the scene is redrawn.
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-ine commandE see ato# "o##and
Ato# displa! #as$ widget
elect atom mask to be used for the display ot atoms. elect first the atoms to be displayed or not displayed by giving the atom mask end then defining the action *N)nN or N)ffN0 and press the N!pplyN button. It is also possible to use more complicated schemesE

Bisplay all atoms of a particular type around a predefined set of atoms within a particular radius. Bisplay all atoms of a particular type around a predefined set of atoms within a particular radius in a selected colour.
The atom selection can be based on eitherE

!ll atoms inside whole residues. 1ust the atoms that satisfy the selected radius.
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Measure /eo#etr! 6idget
Measure distance*s0" angle*s0 and.or torsion angle*s0 between selected atoms. To define a distance you have to define two atoms" for an angle three atoms and for a torsion angle four atoms. Two atoms can only define a distance" three atoms will also define two distances and four atoms defines three distances" two angles and one torsion angle. 9lick on the N!pplyN button and the widget will show you the values defined by the atoms.
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-ine commandE see "al"ulate "o##and
3lot stereo pair <2"rossed e!e2= widget
It is possible to generate a stereo pair or Ncrossed eyeN view of a system. The view is built by duplicating the ob,ect" with a defined distance" and rotating the two pictures with a small angle. There are two values that have to be definedE

The distance with which the ob,ects are separated. The angle with which the ob,ects are NtiltedN. The left ob,ect is NtiltedN <angle and the right ob,ect Pangle around the y<axis.
/sually there is no need to change the NtiltN angle but the distance between the two images of the structure needs to be specified. 9lick on the Bisplay stateE N)nN and theon the N!pplyN button to activate the display. If you need to change the distance between the two images write in a new value into the widget and press the N!pplyN button. gOpenMol manual version 0.92 on 23th September 2005
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The display should look like the following when the NcrossedN eye stereo is on.
-ine commandE plot spair
3lot %ardware stereo widget

If your display device supports hardware based stereo *stereo in a window0 it is possible to start g)penMol in the :uadstereo mode and turn the hardware stereo on.
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g)penMol can be started in the :uadstereo mode at startup using the N<sN startup command line option. rungopen#ol 7s There is only one value that have to be definedE
The angle with which the ob,ects are NtiltedN. The left ob,ect is NtiltedN <angle and the right ob,ect Pangle around the y<axis.
The default angle should work for most cases. To enable the display click the Bisplay stateE to N)nN and then the N!pplyN button.
-ine commandE no line "o##and available

@44444444444444444444444444444444444444444444444444444444444444444444444@ @4 Added (y &igismondo Fos!hi = CI,)CA = Italy" &tereo for >igh=end graphi! ma!hines8 e:g: &<I Ony I The high=end &tereo graphi!s is so !alled PCuad (ufferP or Pstereo=in=a=windowP: It allows to have stereo and dou(le=(uffering without the need of splitting verti!ally the viewport = and !onseCuenty you do not need to have full=s!reen resolution: The (asi! steps are" /6 to have a stereo=!apa(le visual 5<GATS&T)R)O6 I6 draw the left eye in the FAC+SG)?T drawing (uffer" gl;rawFuffer5<GSFAC+SG)?T67 H6 draw the right eye in the FAC+SRI<>T drawing (uffer" gl;rawFuffer5<GSFAC+SRI<>T67 H6 put them in the ?RO,TSG)?T T ?RO,TSRI<>T (y swapping on!e the (uffers" glut&wapFuffers567 If you need to plot Pnon=stereoP staff Just plot it to the FAC+ (uffer" gl;rawFuffer5<GSFAC+67 It will (e authomati!ally plotted in (oth the (a!k (uffers: In this way you !an have non=stereo images in a stereo=window: In order to setup the stereo you need to give a setmon8 (ut the argument ;epends on the hardware ar!hite!ture: In our ma!hine the frame(uffer setups are in @usr@gf @u!ode@vf!@vfs@: The ones with an PsP are the stereo
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ones8 e:g:" /IB# /#INSMUs:vfo On our Ony we use ir!om(ine8 sin!e the ma!hine has many graphi! pipelines8 and many !hannels 5displays6: Ir!om(ine manage all of them: A(out left and right (uffers" (eware they e ists only if you have a PCuad (ufferP frame(uffer = also !alled Pstereo=in=a=windowP !apa(le: If stereo is not a!tive only the left (uffer is proJe!ted8 and so it is normal you see only the left eye output: It is also possi(le you !an draw the right (uffer8 (ut if stereo is not a!tivated8 you have no way to see it: Anyway8 if it runs8 it should means the display is Cuad (uffer !apa(le8 (ut not !orre!tly set=up: That is what !omes from my small e perien!e anyway: When you invoke Pswap(uffersP (oth (uffers are swapped in the same moment" (a!kSleft goes frontSleft and (a!kSright goes frontSright and vi!eversa: On other low=end ma!hines8 like &<I OI8 usually you have not Pstereo=in=a=windowP8 (ut Just Pfull=s!reen=stereoP8 that is8 you open a full s!reen window8 and the upper part of the s!reen is proJe!ted to the left eye8 the lower to the right one: I !an give you some pointers8 where I have !olle!ted the information: = Pman stereoP on an &<I = http"@@te!hpu(s:sgi:!om@ = and look here for PstereoP: 4@ @44444444444444444444444444444444444444444444444444444444444444444444444@
4ontour Manager 6idget
This is the main contour display widget. Through this widget you can control the contour files" isosurface values" colours" surface smoothing and many more things. The data is defined as scalar values in a grid box. Before you can display any isosurface contour you have to read in the molecular system for which the grid data has been generated *this is usually a coordinate data file0. The steps to doE 7. ;ead the atom coordinate information *through import coordinates0 for your molecular system. 2. )pen the contour manager widget *if it is not open alredy0. 3. The contour data files are usually J.plt files *you can of course use your own file name extension0. 9lick on the NBrowseN button to open the file browser to see the J.plt files. Bouble click on the file *or a single click and then press the N)penN button0 to select the file. C. 4ress the NImport fileN button to read in the grid data to g)penMol. gOpenMol manual version 0.92 on 23th September 2005
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Aile browser widget used to select a plot *J.plt0 fileE
!fter importing the plot fileE
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7. +rite the isocontour value into the input field *starting upwards0. 2. 9lick on the N9olour*number0N button to choose a colour for the surface
3.
If you want to map *colour0 the surface according to the grid values of an other grid *J.plt0 file press the NMappingN button.
C. The contour surface renderer can be used in three different modesE

o o
dire"t mode where the polygons are drawn directly on the screen" "a"%ed mode where the polygons are saved into memory drawn from memory" displa! lists are used for the display of the polygons. the last displayed contour polygon data information is saved in an array and can be retrieved with the show command in dire"t and "a"%ed modes. gOpenMol manual version 0.92 on 23th September 2005
o o
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=. 4ress the N!pplyN buttonNO !fter defining the individual contour calues it is possible to change the surface detailsE
If you want the surface to be smoothed press the NBetailsN button. If you want to make the surface transparent press the NBetailsN button. If you want to switch between mesh and solid type of surfaces press the NBetailsN button. If you want to turn a particular surface off press the NBetailsN button
Fou can change either the isocontour value" colour" smoothing by pressing the NBetailsN button for the chosen isocontour value. Fou can also manipulate your mesh data files with the NcontmanN program. +ith the NcontmanN program you can add or sustract two contour files *! S B P 90 or you can make a smooth transition from one contour file to an other using ! S w J B P *7 < w0 gOpenMol manual version 0.92 on 23th September 2005
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9" where w is a mixing constant * 8.8 ... 7.80. To have a look at the input to the NcontmanN program write Ncontman <hN. +idget to select the colour for a surfaceE
+idget to change detailed contour parametersE

9lick to set the display state" smoothing state" contour type *mesh.solid0. 9hange the transparency of the surface. Re#e#ber to press t%e 2Appl!2 button to appl! t%e sele"tion.
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-ine commandE see "ontour "o##and
4ontour Mapping 6idget
This is the contour mapping widget. Through this widget you can control the mapping *colouring0 of an isocontour surface according to the grid values of an other grid *J.plt0 file. The colouring can be scaled according to any grid value range.
The steps to doE 7. ;ead the atom coordinate information *through import coordinates0 for your molecular system. 2. )pen the contour manager widget *if it is not open alredy0. 3. The contour data files are usually J.plt files *you can of course use your own file name extension0. 9lick on the NBrowseN button to open the file browser to see the J.plt files. Bouble click on the file *or a single click and then press the N)penN button0 to select the file. C. 4ress the NImport fileN button to read in the grid data to g)penMol. =. ;epeat the previous steps to read at least one more grid *J.plt0 files. G. 9lick on the radio button for the file for which you want to generate the isocontour surface. Q. 9lick on the NMappingN button to open the NMapping control widgetN. This you already did because you got this help text. >. 9lick on the option menu button to select the file from which the colouring *mapping0 will be taken. Ainish by pressing the N!cceptN button. @. +rite the isocontour value into the input field *starting upwards0. If you want to apply an other colour range than the default fill in on the same line the #in. and #a(. values for the range. The colouring will be from min *blue0 to max
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*red0. If the values are filled from #a(. to #in. the colouring will be the opposite. 78. 4ress the N!pplyN buttonNO urface detailsE

4lease observe that the two grid files have to have the same number of grid points in the x" y and D directions and the grid data has to be defined in the same x" y and D space for the both grid files. If you donKt know the grid space you can run the format to unformat J.plt file converter *pltfile0 in the bin. directory. Fou can change either the isocontour value" colour" smoothing by pressing the NBetailsN button for the chosen isocontour value.
Surface mapping e>ample

The idea of the surface mapping can be demonstrated using the density.crd coordinate file" the density.plt and orbital.plt files in the demo. directory. The idea of the example is to plot the electron density at an isocontour value *8.70 and map the orbital grid values upon this surface. Bo the followingE 7. Import the density.crd file into gopenmol. 2. Import the density.plt file through the 5'iew 3. Import the orbital.plt file through the 5'iew 4. 9lick to select the density.plt file 9ontour6 widget. 9ontour6 widget.
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5. 4ress the 5Mapping6 button to define which grid data is to be mapped on the density.plt isocontour surface.
?.
elect from the list and press the 5!ccept6 button. In some cases the 59ontour Mapping 9ontrol6 widget may disappear behind the 59ontour 9ontrol6 widget. This will not work until you have pressed the 5!ccept button6. 4ress then the 5Bismiss6 button to close the widget.
,. +rite then 58.7 W8.7= 8.7=6 into the first line. This means that an isocontour surface with the density value 8.7 is generated. /pon this surface the orbital values are mapped so that the values are scaled between W8.7= and P8.7=. The lower value will be blue and the high value is red while the value in the
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middle is green. 4ress then the 5!pply6 button.
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+. Fou will the see this picture in the graphics screen.
@. The same can be achieved after reading the two plot files with the following line commandE "ontour plot H1 2I 0.1 70.1J 0.1J. 4lease observe that the plot files have to be read in the order density.plt and then orbital.plt. If you read the files in the opposite order the line command isE "ontour plot H2 1I 0.1 70.1J 0.1J.
Surface @glueingA e>ample

The main contour widget has a button with the text 52lue SSX 76 included. This defines the structure number to which the contour file should be glued *attached0. By default any contour file is always glued *attached0 to structure number 7 and the button has no meaning if there is only one structure. The following example demonstrates how two structures are read into g)penMol" how they are translated independently and two contour files are glued *attached0 to the structures. 7. Import the coordinate file oxaD.crd in the demo. directory. 2. Import the coordinate file orbital.crd in the demo. directory with the append option clicked.
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3. 9lick the TransformationE -ocal option on the main window. The two structures have now a local center around which they rotate. C. /nclick first the orbital.crd in the main window. !ll rotations and translations will now only apply on the oxaD.crd structure. =. 4ress the left hift key and then the left mouse button and move the mouse. Fou can now move the oxaD.crd structure to a new position on the screen. ;emember to release first the mouse buttonO G. 9lick the orbital.crd and unclick the oxaD.crd. ,. 4ress the left hift key and then the left mouse button and move the mouse. Fou can now move the orbital.crd structure to a new position on the screen. ;emember to release first the mouse buttonO
+. )pen the 5'iew 9ontour6 widget and import the oxaD.plt *9onnolly type of surface0 and orbital.plt *molecular orbital0 files from the demo. directory. 9. 9lick on the button 52lue SSX oxaD.crd6 orbital.plt file line to get the structure selection widget and select the orbital.crd. 4ress then the 5!pply6 button. Be
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careful because the widget can disappear behind the contour widget.
10. Four 9ontour widget should now look likeE
77. 9lick now the radio button for oxaD.plt and fill in the value C8. on the first input line. elect a colour for that value. 4ress the 5!pply6 button. 72. 9lick now the radio button for orbital.plt and fill in the values 8.7 on the first line and W8.7. on the second input line. elect a colour for the values. 4ress the 5!pply6 button.
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13. The result should look something like *if you have used the same colours0E
Ae(t output widget
+hile running g)penMol the program writes a lot of messages or results from various calculation routines to the output. The text can be seen in the window that started the process. %owever" if you are running +indows you will not be able to scroll the window. ome times some commands generates also a lot of output and one wants to cut and past the result to other applications. By opening the text output widget one gets a better control over the text output.
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.3/ COLO!" menu has the options# 4%ange ba"$ground "olour in grap%i"s window.
Background" 9hange background colour with a Tcl.Tk tool. Background" 9hange background colour with a ;2B tool. 9hange atom colour.
Ato#s"
-ele"t ba"$ground "olour widget

elect the back ground colour from the widget. gOpenMol manual version 0.92 on 23th September 2005
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-ine commandE define "o##and
-ele"t ba"$ground "olour widget <R0/=

/se the red" green and blue sliders to define the background colour.
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-ele"t ato# "olour widget
elect atom colour by defining the atoms and click the N9hoose colourN button to show the colour editor. If the atom partial charges have been defined itKs also possible to colour the atoms according to the partial charges. Befine the partial atom charge range and press the N!pplyN button. The colour range is blue for the lower limit and red for the upper and the colour goes through green.
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4ick or choose the colour using the colour editor and press the N)kN button. Then press the N!pplyN button to colour the selected atoms with the picked colour. The new colour will not be sen before the scene is redrawn.
.4/ CALC!LATE menu has the options#
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4al"ulate "luster widget "o##and

9alculate for display a cluster matrix displaying the root mean s:uare *;M 0 value" after a superimpose of the selected atoms over the frames in a tra,ectory. elect the segment" residue and atoms defining the structure to be superimposed with the e:uivalent part in the other frames. !fter selecting the atoms press the Appl! button to perform the calculation over the frames. !fter the calculation the matrix can be displayed by selecting the N9luster plot onN option. To free the reserved matrix space press the NBelete cluster dataN button.
-ine command optionE "al"ulate "o##and
4al"ulate ato# "onne"tion widget

This widget is helpful when one wants to recalculate atom connections *bonds0 in case you have deleted some or if you donKt get all hydrogen atoms bonded in your structure. g)penMol uses a very simple algorithm to calculate possible bonds. It runs over all the atoms in the structure and uses a window *range0 of atoms inside which it thinks the bonded atoms are located. By default there is a range defined *use s%ow ato# window command to display the current value0 so when g)penMol looks at atom ( it checks range atoms backwards and range atoms forward from atom ( to find the bonded neighbours. ome programs place added hydrogens at the end of the file" which might prevent g)penMol from finding the right bonds. To solve this problem the range can be redefined. 4lease supply a new value" inside which you think all bonded atoms will be.
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It is also possible to recalculate the connectivity only for a set of atoms.
4al"ulate "orrelation widget "o##and

9alculate correlation and autocorrelation functions from two time series. There are three types of time seriesE

Bistance !ngle Torsion angle
The time series fro these three possibilities are stored with a running number. 9hoose first type of time series and then the running number of the time series inside this group. If you choose the same time series for U7 and U2 you calculate the autocorrelation function.
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4al"ulate #ean sFuare displa"e#ent widget "o##and
4al"ulate radial distribution fun"tion widget
It is possible to calculate a distribution function *g*r00 for an atom using g)penMol from one frame or as an average from a se:uence of frames like a molecular dynamics simulation. It is possible to arbitrarily choose the center atom and the atom around that. If you have only one frame available *you have not a tra,ectory file defined0 and you select the N9alculate ;BAN from the N9alculateN pulldown menu you will get the following widgetE
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The NArom atom*s0EN define the center atom*s0 around which the distribution will be calculated. The NTo atom*s0EN define the atom*s0 which distribution will be calculated. The N;cutEN value defines the distance to which the distribution will be calculated and N(binsEN define the number of intermediate values *bins0 for which the distribution will be calulated. If the periodic cell *most likely you have been using period boundaries0" inside which your atoms and molecules are located" has not been defined before it has to be defined here. 4ressing now the N!pplyN button calculates the radial distribution function of the NTo atom*s0N around the NArom atom*s0N for the structure displayed in the graphics window. !fter pressing the N!pplyN buttonN one gets the following widgetE
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There is now one furter entry and button displayed. !n entry titled N(umber of setsN defining for how many structures the ;BA has been calculated and accumulated. It is thus possible to read by hand more frames into g)penMol and successively calculate the ;BA. !fter the number of ;BAs has been calculated *accumulated0 it is possible to calculate the average for these ;BAs by pressing the Ncalc averageN button. %owever" if a tra,ectory file has been defined before the N9alculate ;BAN is selected from the N9alculateN pulldown menu one gets the following widgetE
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It is now possible to automaticly get the average calculated for the entire frame by pressing the N9alculate average ;BAN button. g)penMol goes now through your tra,ectory file frame by frame and calculates and accumulates the ;BA. !fter the last frame an average ;BA is calculated. It is always possible to export the calculated *accumulated0 ;BA through the Nexport rdfN command or the N$xportN pulldown menu. )n the +indows platform it is also possible to copy the ;BA to the 4aste buffer through the N$ditN < N9opyN < N;BAN pulldown menu. -ine commandE see "al"ulate "o##and
-uperi#pose stru"tures widget "o##and

uperimpose two structures by giving the atoms that should match. The number of atoms in the two sets must match but they do not necessarily have to be the same atoms.
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2ive the atoms for the two structures and press the Appl! button. It is possible to display a short or a long display list of the matching structures. elect the one you want.
.5/ 6LOT menu has the options# 3lot a(is widget
/sing this widget it is possible to select atoms and plot the local coordinate system on the atoms. It is also possible to give the x" y and D coordinate where the local coordinate system is placed. 2ive the atom*s0 and press the N!pplyN button. The selection is additive which means that the new set is added to the old set. The whole selection can be deleted by pressing the NBeleteN button.
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-ine commandE see plot "o##and
3lot "olour s"ale widget
It is possible to include into pictures" using colours to to display a range of values" a colour scale. If a molecular dynamics tra,ectory is defined it is possible to plot the ;oot Mean :uare Beviation *;M B0 of a selected set of atoms as ellipsoids. The plot is always in the global x" y" D coordinate system. 4lease supply the min and max values and the number of values *bins0 for the scale. The scale can be toggled between the on *display0 and off *do not display0 states.
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4ontour Manager 6idget
This is the main contour display widget. Through this widget you can control the contour files" isosurface values" colours" surface smoothing and many more things. The data is defined as scalar values in a grid box. Before you can display any isosurface contour you have to read in the molecular system for which the grid data has been generated *this is usually a coordinate data file0. The steps to doE 7. ;ead the atom coordinate information *through import coordinates0 for your molecular system. 2. )pen the contour manager widget *if it is not open alredy0. 3. The contour data files are usually J.plt files *you can of course use your own file name extension0. 9lick on the NBrowseN button to open the file browser to see the J.plt files. Bouble click on the file *or a single click and then press the N)penN button0 to select the file. C. 4ress the NImport fileN button to read in the grid data to g)penMol. =. +rite the isocontour value into the input field *starting upwards0. G. 9lick on the N9olour*number0N button to choose a colour for the surface Q. If you want to map *colour0 the surface according to the grid values of an other grid *J.plt0 file press the NMappingN button. >. The contour surface renderer can be used in two different modesE
o
dire"t *fast0 mode where no contour polygon data information is saved or save *slow0 mode where the last displayed contour polygon data information is save in an array and can be retrieved with the s%ow "o##and.
@. 4ress the N!pplyN buttonNO urface detailsE

If you want the surface to be smoothed press the NBetailsN button. If you want to make the surface transparent press the NBetailsN button. If you want to switch between mesh and solid type of surfaces press the NBetailsN button.
86
If you want to turn a particular surface off press the NBetailsN button
Fou can change either the isocontour value" colour" smoothing by pressing the NBetailsN button for the chosen isocontour value. Fou can also manipulate your mesh data files with the NcontmanN program. +ith the NcontmanN program you can add or sustract two contour files *! S B P 90 or you can make a smooth transition from one contour file to an other using ! S w J B P *7 < w0 9" where w is a mixing constant *8.8 ... 7.80. To have a look at the input to the NcontmanN program write Ncontman <hN.
Aile browser widget used to select a plot *J.plt0 fileE
87
+idget to select the colour for a surfaceE
+idget to change detailed contour parametersE

9lick to set the display state" smoothing state" contour type *mesh.solid0. 9hange the transparency of the surface. Re#e#ber to press t%e 2Appl!2 button to appl! t%e sele"tion.
88
-ine commandE see "ontour "o##and
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ 4ontour Mapping 6idget Leif Laa$sonen 4-4 1''5 JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ This is the contour mapping widget. Through this widget you can control the mapping *colouring0 of an isocontour surface according to the grid values of an other grid *J.plt0 file. The colouring can be scaled according to any grid value range.
The steps to doE 7. ;ead the atom coordinate information *through import coordinates0 for your molecular system. 2. )pen the contour manager widget *if it is not open alredy0. 3. The contour data files are usually J.plt files *you can of course use your own file name extension0. 9lick on the NBrowseN button to open the file browser to see the J.plt files. Bouble click on the file *or a single click and then press the N)penN button0 to select the file. gOpenMol manual version 0.92 on 23th September 2005
89
C. 4ress the NImport fileN button to read in the grid data to g)penMol. =. ;epeat the previous steps to read at least one more grid *J.plt0 files. G. 9lick on the radio button for the file for which you want to generate the isocontour surface. Q. 9lick on the NMappingN button to open the NMapping control widgetN. This you already did because you got this help text. >. 9lick on the option menu button to select the file from which the colouring *mapping0 will be taken. Ainish by pressing the N!cceptN button. @. +rite the isocontour value into the input field *starting upwards0. If you want to apply an other colour range than the default fill in on the same line the #in. and #a(. values for the range. The colouring will be from min *blue0 to max *red0. If the values are filled from #a(. to #in. the colouring will be the opposite. 78. 4ress the N!pplyN buttonNO urface detailsE

4lease observe that the two grid files have to have the same number of grid points in the x" y and D directions and the grid data has to be defined in the same x" y and D space for the both grid files. If you donKt know the grid space you can run the format to unformat J.plt file converter *pltfile0 in the bin. directory. Fou can change either the isocontour value" colour" smoothing by pressing the NBetailsN button for the chosen isocontour value.
4ontour 3lane Manager 6idget
90
Befine a cutplane trough the contour surface grid data. The planes are defined to be perpendicular to the x" y and D axis. It is possible to animate or move the planes NsmoothlyN using the animate facility behind the N3"F and I <<<XPN buttons. 4ress respective button to show the display along the 3"F or I axis.

Befine first the plane *yD" xD or.and xy0 by clicking the selection box. Then define the coordinate of the x" y or.and D axis through which the plane will go. Then define the minimum and maximum value of the range. -ater there will also be a feature to smooth the range.
To delete all data click the NBelete all contoursN button It is not always easy to find the best plane *Splain with most information0. To make this procedure a bit easier a Nprofile graphN can be generated. The graph is generated by dividing the range of observations in bins where the grid data is then placed. ! blue colour shows very few observations in that bin" while a read colour shows a high number of observations in the bin. The current picture applies a bin cut value of 7.8" which means that the region shown is the region where there is 7 or more values in the bin. This bin cut value can be changed by changing the default value 7.8 in the input widget to an other value. /sing the value of 7.8 gives already a good insight into the grid space.
91
The horiDontal<axis *in the graph0 defines the min and max values of the grid data and the vertical<axis *in the graph0 is the range inside which the plane can move along the chosen axis x<" y< or D<axis in the 3B space. The following example shows that an FI<plane can move along the x axis *in 3B0 between the values <2.8 and 7.@ !ngstrom" while the grid values varies between 8.8 and 3.3@Q. Arom the graph one can read that most information is for a plane at x S 8.8 and a grid range of 8.8 to 7.G.
The smooth or animate displayE
92
Linear distan"e plot <L;3= widget
elect the atoms to be include in the linear distance plot *-B40. elect the atoms" set the -B4 plot state to N)(N and press the apply button
4al"ulate and plot a tube or a ribbon t%roug% ato#s widget
elect the atoms through which the ribbon.tube will go through. Then select the type Tube" ;ibbon" olid %elix" Alat %elix and !rrow" 9olour and radius. everal ribbons.tubes can be defined by selecting the N!ppendN mode. The define display can be displayed by setting the Bisplay mode N)nN.
93
The tube.ribbon colour can be selected from the colour menu.
If the 4BB coordinate file contain secondary structure information g)penMol can use that information to define the ob,ects. elect the type from the widget and click N!pplyN button and the information is moved to the main 4lumber widget. The only thing the user has to define is the colour. gOpenMol manual version 0.92 on 23th September 2005
94
-ine commandE see plu#ber "o##and
4al"ulate and plot t%e RM-; widget
+hen a molecular dynamics tra,ector is defined it is possible to plot the ;oot Mean :uare Beviation *;M B0 of a selected set of atoms as ellipsoids. The plot is always in the global x" y" D coordinate system. elect the atoms and press the Appl! button. There are two different approaches to generate the ellipsoidsE
The individual frames are not superimposed on the average structure *S nofit0. gOpenMol manual version 0.92 on 23th September 2005
95
The individual frames are superimposed on the average structure *S fit0.
The plot can be deleted by pressing the ;elete button. If the fluctuation has a small amplitude it is possible to magnify the amplitude by a factor.
%ine comm-n3) p.r#sd -eg#ent Residue Ato#<s= -"ale fitCnofit
3lot ve"tor widget

It is possible to plot vectors from a flat text file using this widget. 2ive first the name of the text file containg the vector data. It can come from a 2aussian33 calculation or from an other program. There are two different display styles availableE

'ectors are shown as a line drawing. This is the fastest display mode. olid vectors with a defined radius. This is a slow display mode and should not be used for a display with many vectors.
It is also possible to give a vector length range that defines the range. Those vectors hanving a vector length inside this range will be displayed. The vector display mode can be N)nN or N)ffN. If you donKt need the display anymore free all the reserved vector space by clicking on the NBelete all vectord and spaceN button.
96
$xample for a water molecule with the electron gradient vectors with a length between 7.8 and 7.e+25 shown both as simple lines and solid vectors.
-ine commandE plot "o##and
.7/ T"A8ECTO"9 menu has the options#
97
Monitor #ole"ular geo#etr!.

;istan"e<s= Angle<s= Aorsion<s=
Monitor ;istan"e 6idget
elect the atom in set U7 and U2 to define a distance" choose a line colour and click the apply button. To display the selected distance put the display state to N)nN 4ress the NBelete allN button to delete all selected line segments
9hoose the line colour from the colour menu.
98
To edit any of the defined sets press the N$ditN button. (ow you can redefine the selected atoms or delete this particular defined distance.
-ine commandE see #onitor "o##and
Monitor Angle 6idget
elect the atom in set U7" U2 and U3 to define an angle" choose an angle colour and click the apply button. To display the selected angle put the display state to N)nN 4ress the NBelete allN button to delete all selected angle segments To edit any of the defined sets press the N$ditN button. (ow you can redefine the selected atoms or delete this particular defined angle.
99
9hoose the angle colour from the colour menu.
100
Monitor Aorsion 6idget
elect the atom in set U7" U2" U3 and UC to define a torsion" choose a torsion colour and click the apply button. To display the selected torsion put the display state to N)nN 4ress the NBelete allN button to delete all selected torsion segments
9hoose the torsion colour from the colour menu. gOpenMol manual version 0.92 on 23th September 2005
101
To edit any of the defined sets press the N$ditN button. (ow you can redefine the selected atoms or delete this particular defined torsion.
Aill time series vectors.

;istan"e arra! Angle arra! Aorsion arra!
:ill distan"e arra! widget "o##and

Aill the time series array according to the definitions given in the monitor distance widget. -ine commandE see fill "o##and
102
:ill angle arra! widget "o##and

Aill the time series array according to the definitions given in the monitor angle widget. -ine commandE see fill "o##and
:ill torsion arra! widget "o##and

Aill the time series array according to the definitions given in the monitor torsion widget. -ine commandE see fill "o##and
Belete time series vectors.

;istan"e arra! Angle arra! Aorsion arra!
;elete distan"e arra! widget "o##and

Belete all stored distance array information and buffers defined in the monitor distance widget.
;elete angle arra! widget "o##and

Belete all stored angle array information and buffers defined in the monitor angle widget.
;elete torsion arra! widget "o##and

Belete all stored torsion array information and buffers defined in the monitor torsion widget.
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Ara&e"tor! Manager 6idget
This is the main tra,ectory control widget. Before you can process a tra,ectory file you have to import a coordinate file to define the molecule topology and the atom labels because some tra,ectories contain only atom coordinate information. teps to doE 7. 9lick of the button for the tra,ectory type you will analyDe or look at. The buttons are on the right. 2. elect a file from using file browser *Browse button0.
3. 4ress the NImport fileN button to read the tra,ectory information. C. +hen the file has properly been processes you can reed the number of frames in the file down on the page. There will also be display information about from which frame the display will start and at which frame it will stop and the frame step. /sually you donKt have to touch this information att all. =. To display the frames as loop starting from the first defined to the last click at the button with a triangle. To stop the display press the button with a s:uare. The supported tra,ectory formats areE !MB$; Unfor#atted !mber tra,ectory file. In the utility directory there is program for the conversion of a formatted tra,ector into a unformatted one. More information can be found from the !MB$; +eb pages httpE..www.amber.ucsf.edu.amber.formats.html. !MB$;*A0 :or#atted !mber tra,ectory file. In the utility directory there is program for the conversion of a formatted tra,ector into a unformatted one. More information can be found from the !MB$; +eb pages httpE..www.amber.ucsf.edu.amber.formats.html. 9$;I/ 2 /nformatted binary 9$;I/ 2 tra,ectory file. 9%!;MM.9%!;Mm /nformatted binary 9%!;MM.9%!;Mm tra,ectory file. BI 9)'$; /nformatted binary BI 9)'$; tra,ectory file. 2;)M!9 /nformatted 2;)M!9 tra,ectory files *trn" trr and xtc0. 2;)M) /nformatted 2;)M) tra,ectory file. 2;)M) @G Aormatted ascii 2;)M) @G tra,ectory file. gOpenMol manual version 0.92 on 23th September 2005
104
%F4$;9%$M /nformatted binary %yper9hem tra,ectory file. M/M)B /nformatted binary M/M)B tra,ectory file. The M/M)B program is developed by Br. )lle Teleman. TI(#$; Aormatted TI(#$; tra,ectory file. 3M)Aormatted ascii 3M)- *multiset0 tra,ectory file. 34-); /nformatted binary 34-); tra,ectory file. F! 4 /nformatted binary F! 4 tra,ectory file. The F! 4 program is developed by Br. Alorian Muller<4lathe *. Tra,ectory display controlE

KL... go to first frame L... back one frame 89... halt display loop KM... play forward one frame at the time in a loop M... forward one frame MK... go to last frame
By default the atom connection table is ()T recalculated in between the different frames. %owever" sometimes itKs preferable to recalculate the connection table. This can be done by clicking the N!tom reconnectionN to N)(N. Aor the formatted tra,ectory files there are two methods availableE

e:uential reading of frames. 'ery robust but :uite inefficient and slow. ;andom access of the frames. $fficient but can cause problems" specially if you donKt know that there is a different between /nix and +indows ascii files.
ItKs possible to display the frame number of the current frame. To display the frame number click NBisplay frame numberE onN or off to turn it off.
105
Aile browser to select a tra,ectory file.
-ine commandE see tra&e"tor! "o##and
106
Manipulate Ai#e -eries 6idget
Manipulate the distance" angle and torsion time series through the following operationsE Types of operations *manipulations0E B!'$rage V R/!re V 9) V 9) 2 V R;T V BI(Itial V 9)4F nr V !BB nr V -)2 V $34 V 4)+er real V M/-T real V BI'Ide real V %IAt real V BMI( V !B V BI'Airst V BI'Maximum V 4 4$ctrum nr V I$;) V R*t0 S R*t0 < R*t0 S R*t0 JJ 2 R*t0 S cos*R*t00 R*t0 S 3Jcos*R*t00JJ2 < 7 R*t0 S s:rt*R*t00 R*t0 S R*t0 < R*80 R*t0 S R2*t0 R*t0 S R*t0 P R2*t0 R*t0 S log*R*t00 R*t0 S exp*R*t00 R*t0 S R*t0 JJ real R*t0 S real J R*t0 R*t0 S R*t0 . real R*t0 S R*t0 P real R*t0 S R*t0 < R*min0 R*t0 S abs*R*t00 R*t0 S R*t0 . R*80 R*t0 S R*t0 .max*R*t00 4ower spectrum R*t0 S 8.8
9lick on the radio button for the desired operation. If the operation re:uires a further value or index" please fill it in the input widget. 9hoose the distance" angle or torsion option. Aill in the number index for the desired time series.
107
-ine commandE see #anipulate "o##and
Ara"e Ato#s widget
108
Trace atom*s0 or follow up the atom movement through your tra,ectory file. Befine first the atom*s0 to trace and pres the N!pplyN button. Fou can put the display state to N)nN by clicking the N)nN radio button. The whole temporary space can be freed by pressing the NBeleteN button.
-ine commandE see tra"e "o##and
Trace exampleE 7. Import the optCpti.crd file form the demo. directory. 2. Import the dynCpti.dcd tra,ectory file using the 5Tra,ectory 3. Bisplay only the back bone atoms with the commandE a. ato# Ndispla! VU turn first all atoms off b. ato# displa! O O 4AD)D4 VU display the back bone Main6 widget.
109
4. )pen the 5Tra,ectory Trace6 widget and write into the 5!tomE6 field 9! and press the 5!pply6 button.
5. To display the trace for all 9! atoms click the 5BisplayE6 to 5)n6 and you should be able to see.
110
Ma$e ani#ation widget
The automatic creation of mpeg files works only on the +indows platform. )n /nix you have to find your own program to create M4$2 files from your separate frames. 4repare animations by first producing discrete files and then make a mpg file from the files. 9urrently g)penMol only supports Targa *tga0 files but it is still possible to make the discrete screen dumps in other formats. )nly small picture siDes can be used up to about C88 J C88 pixels with the program supplied on +indows.

Airst choose the discrete file format. 9hoose then the basis file name. Aor example if a name test.tga is chosen the files will be named test0.tgaD test1.tgaD test2.tga ... By default the the files will be placed in the g)penMol temp. directory. 4ress the apply button and g)penMol runs through the frames in your tra,ectory and makes a screendump for every frame. !fter this test.#pg will be produced.
-ine commandE see t%ere is no line "o##and for #a$ing ani#ations
.:/ "!N menu has the options# Run autodo"$2plt progra# widget
;un the !utoBock2plt program to convert a !utoBock map file into the plt file format used by g)penMol. The !utoBock map file can then be displayed using the g)penMol contour utilities +rite the input and output file names or click the 0rowse buttons to define the file names. The press the Appl! button to do the conversion. gOpenMol manual version 0.92 on 23th September 2005
111
-ine commandE "anPt be run fro# gOpenMol line #ode. Use t%e Uni(C;os "o##and line #ode
Run 4ontMan progra# widget
;un the 9ontMan to subract or add two g)penMol plt grid mesh files and write the result out to a plt file format used by g)penMol. 2ive input7" input2 and output file names. 9hoose either Minus <7= or 3lus <G= action. 9lick the Appl! button to do the operation.
112
-ine commandE no line "o##and available inside gOpenMol. Use Uni(C;os s%ell line "o##and.
Run g4ube2plt progra# widget
;un one of the two available programs to convert the 9ube output from the 2aussian33 program into the plt file format used by g)penMol.
113
The programs available areE

gcube2pltE the old version that converts only one orbital.density at a time. )ne needs to give the orbital number in the input field. g@Ccub2plE a modified version made by Boug Moffatt that converts all the information in the file into separate files in one batch.
-ine commandE t%ere is no line "o##and available inside gOpenMol. Use Uni(C;os s%ell line "o##ands.
114
Run Qont2plt progra# widget
;un the #ont24lt program to convert a grid mesh file produced by the 2rid program into a formatted or unformatted plt file format used by g)penMol. 2ive input and output file names. 9hoose either unfor#atted or for#atted output plt file. 9lick the Appl! button to do the conversion.
115
Run pltfile progra# widget
;un the plotfile to convert a plt file from binary to ! 9II or ! 9II to binary. The operation is mostly used to move a plt file between different hardware platforms.
-ine commandE see run "o##and
116
Run probesurf progra# widget
;un the 4rob urface program to produce a 9onnolly type of surface around a molecule system. Fou have to have an input file ready for the program which you define in the NInput file nameN entry. If you donKt remember the name and location of the input file you can browse by pressing the 0rowse button. The output file is the name of the contour grid file. If no name is given the program uses the default name" which will be placed in the N)utput file nameN entry. The 4rob urf calculation can be done either in foreground or ba"$ground. The foreground calculation locks g)penMol until the calulation has finished. The background mode enables the further usage of g)penMol while the calculation continues. The 4rob urf program uses a direct <r= and s:uared <rOO2= distance method for the calculation of the surfaces. 9hoose the method to be used. !fter the calculation has finished it is possible to read in the contour file and display the surface. !nswer !es or no to the :uestion.
117
-ine commandE see run "o##and
Run turbo#ole2plt progra# widget
;un the TurboMole2plt program to convert a TurboMole grid file into the plt file format used by g)penMol. The TurboMole grid file can then be displayed using the g)penMol contour utilities
118
+rite the input and output file names or click the 0rowse buttons to define the file names. The press the Appl! button to do the conversion.
-ine commandE "anPt be run fro# gOpenMol line #ode. Use t%e Uni(C;os "o##and line #ode
Run UH0;2plt progra# widget
;un the /%BB2plt program to convert a formatted or unformatted /%BB phi grid file to a plt file format used by g)penMol.
119
2ive the input and output file names. 9hoose as the input file type either for#atted or unfor#atted. 9lick the Appl! button to do the operation.
Run +vibs progra# widget
120
2ive the input file name and specify which vibrations you want to convert into 3M)files using the xvibs program. 9lick on the 5!pply6 button to make the conversion.
4lease observer the xvibs program by Bradley !. mith *YyeldarZhome.comX0 included with g)penMol is not the latest version availableO If you want to run xvibs as a separate stand<alone program and use all the power of this program please download the latest version fromE httpE..members.home.net.yeldar.xvibs. The xvibs program page for the xvibs version g)penMol is usingE
121
+1ibs ! utility for animating molecular vibrations. (ormal modes are read from a file automatically determined to be from !ces2" 2amess" 49 2amess" 2aussian @2.@C.@>" or !BA. eparate animation files are written for each vibration. The animation is a simple cosine tra,ectory of the normal mode vectors. The output files are in 3FI format with normal mode vectors attached to each atom. If you would like this program extended to other input or output formats" please send your files to Bradley !. mith and I will gladly extend it for you. end bug reports to Bradley !. mith *YyeldarZhome.comX0. /sage
vi(s -=version. -=(oun!e. -=frames n. file freCuen!ySnum(er
Options
=version =(oun!e =frames n file freCuen!ySnum(er 3isp1-2 t(e :ersion of x:i=s. cre-te =ouncing r-t(er t(-n 1ooping -nim-tions. pro3uce n fr-mes in t(e -nim-tions. t(e fi1e from 6(ic( to re-3 3-t-. t(e num=er of t(e fre@uenc2 to output. Specif2ing AallA 6i11 output -11 fre@uencies.
E>amples
vi(s !hHohSgam:out all
Outputs -11 :i=r-tions into fi1es n-me3 B!hHohSgam:C001# 01+D: y2B

vi(s !hHohSgam:out /V
Outputs on12 :i=r-tion 15 into t(e fi1e n-me3 B!hHohSgam:#/V: y2B B2 3ef-u1tE FGH fi1es cre-te3 -re in 1oop -nim-tion. .(e option =(oun!e 6i11 cre-te =ouncing -nim-tions. Bownload The current release of xvibs is version =.2" and is distributed under 2(/ 2eneral 4ublic -icense. Binaries are available for 1ava" +indows" -inux" and 2I. The source code and sample data are available in a Iip archive.
122
Br-31e2 &. Smit(Bs 0e= site -ine commandE see run "o##and
.;/ TOOLS menu has the options# Auto;o"$ tools

This is the main widget for the Auto;o"$ tra,ectory display and analysis facility. There are first C file readersE

;ead a J.pdb: file *ligans0 ;ead a J.pdb: file *system into which the ligand is docked0 ;ead the !utoBock tra,ectory ;ead an !utoBock log file to extract the included initila and docked coordinate sets. The cruncher creates a set of files with the coordinates
+ith an !utoBock tra,ectory I mean the Nligand.toutN file as in the followingE The tra, command which is used in the tra,ectory output" creates tra,ectories in two formats" one in 4BB format which is written to the log file specified by the <l flag" and one in a raw ! 9II format which is written to the standard output. Aor example" if the command issued wasE autodo"$ 7p ligand.dpf 7l ligand.tr&."onv.log 7" L tr&."onv."o# M ligand.tout the file ligand.tr,.conv.log will contain a 4BB formatted list of all the tra,ectory steps" while the ligand.tout file will contain raw ! 9II data" with one row for each atom in the ligand" and each column containing data. The command file tr,.conv.com contains only the commandsE tra' ligand.tr' stop This was taken from +eb pages and manuals atE httpE..www.scripps.edu.pub.olson<web.doc.autodock. To read and display a tra,ectory from the !utoBock do the followingE
123
7. Airst define the file name of the ligand either by directly writing the file and or by using the file browser. Then press the NImportN button to apply the file. 2. If you also want to include the system *into which the ligand is docked0 do the same as in the previous section but for the system. 3. -ast but not least define the tra,ectory file. /se the same approach as in the previous sections. ;emember to press the NImportN button. !fter this you should be able to see the number of frames displayed. By default the display goes from the first frame to the last with the step 7. This can be changed by supplying new values in the respective fields. It is possible to display the tra,ectory in a loop" one frame at the the backwards and forwards or go to the first and last frames. Arame controlE

KL... go to first frame L... back one frame 89... halt display loop KM... play forward one frame at the time in a loop M... forward one frame MK... go to last frame The fast method uses a pre<calculated index *,ump0 vector into the tra,ectory file for the various frames. This method is capable of retrieving a frame at a speed independent of the frame position in the file. %owever" be careful with this if you move files between /nix and +indows systemsO The slow method is a NstupidN read process that always reads all the frames up to the needed frame. This process becomes very slow for big files but it is not sensitive to the characters at the end of the line.
There are two tra,ectory retrieval methods availableE
!t the bottom of the widget there is also a file writer to write out the ligand and system coordinates as J.pdb: files. This is very handy in case you import the atom partial charges and want to write a J.pdb: file with the new charges.
124
.1</ -EL6 menu has the options#

!bout" how the about text about g)penMol.
About gOpenMol widget

Bisplay the N!bout g)penMolN information.
125
Bemo"
Bemo widget.
;e#o widget
This is the demo widget. 9lick on the button to run a demo. $xamples ofE

simple molecule display molecular dynamics display and analysis orbital and electron density display and analysis the usage of some of the g)penMol ob,ect display manipulation of structures
9lick button to run your demo of choiceO
126
%elp"
how this file.
Help widget
The help system is built upon a Tcl.Tk based +eb browser that has very few features compared to the modern (etscape or Microsoft Internet $xplorer +eb browsers. The %elp system supports the following functionsE

About shows the short list of information about g)penMol. ;e#o gives a list of demos available. Help shows the help pages for running g)penMol. Menu %elp shows the information about the pulldown menu system. 3ee$ version takes a http connection to the g)penMol distribution site and checks for the latest version available. This feature will help you to upgrade and maintain g)penMol in the future. Autorials gives you a list of tutorials about how to run g)penMol. If you have prepared a good tutorial please let me know and I will include it here.
Internal 'ata structure for gOpenMol

To be able to fully use g)penMol it?s useful to understand how the atom assignment is done and how the internal storage is structured.
-o% are the atoms 'efine')

The molecule.atom information is organised as in the 9%!;MM.9%!;Mm program*s0. !ll atoms in a molecule system can be defined.identified through a seg%ent na%e" resid(e na%e and.or resid(e n(%)er and an ato% na%e. This arrangement is very flexible and can be used to define :uite complicated set ups and commands. The line commands" when they want to be applied on a set of atoms" must always be given asE -eg#ent.na#e Residue.na#eCnu#ber Ato#.na#eCnu#ber gOpenMol manual version 0.92 on 23th September 2005
127
The segment" residue and atom name can be 7<C characters long. The names are assigned when one reads a coordinate file. Aor a command the data is supplied as three fields separated by KEK. $xample set atom colour #$ % &A yellow sets all 9! atoms in all residues in segment 7 to the colour yellow. The general identifier looks like seg#ent residue ato# where the segment name is always a character string. The wild character KJK and the K[K characters can be used. The KJK character matches all strings and K[K matches any character at itKs position. In the residue and atom field residue numbers and atom numbers can be used or a combination of characters and integer numbers. $xampleE set atom colour -1 ARRD1D10D3074J 4AD)D4 blue command sets all 9!"( and 9 atoms in all tyrosine residues and residues 7"78 and range 38<C= in segment 7 to the colour blue. 3lease note The interpreter for g)penMol interprets the lower and upper case letters as different. This applies for both commands and segment.residue.atom names. Install g)penMol Begin a g)penMol session Bisplay contour data Import a structure into g)penMol Manipulate a structure in g)penMol
Tcl line comman' interface to gOpenMol

The command line parser is implemented using the Tcl *Tool command language0. The language is rich of commands and I strongly recommend you first to have a look the the Tcl commands *httpE..www.sunlabs.comE>8.research.tcl.0. Aor most commands it is enough ,ust to use the four first characters to uni:uely define the command. ! clear exception is the KcontourK command where the first five characters are needed not to mix the command with the KcontinueK statement. Through the help files I have used a dollar *\0 sign to indicate there characters needed to define a command. Fou can also get a list of all available commands by typing the :uestion *[0 mark at the command prompt. 'ery many of the commands return a parameter *or several0 which can be used as an input to a new command. 4lease observe that when using the commands in s"ripts one needs to fill in the full command nameO The dollar sign *\0 in the commands indicates the length of the command or the characters needed to uni:uely define the command. The dollar sign must not be included in the command. 9ommands availableE
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atom calc\ulate conto\ur defi\ne displ\ay edit expo\rt fill find gom$rror NtextN gom4rint NtextN gscal\e hard\copy help impo\rt mani\pulate moni\tor mope\n msav\e pause Avalue plot plum\ber ptra\ce :uit rese\t rota\te run sele\ct show tra,\ectory tran\slate wind\ow
de*ine +ario(s properties a)o(t ato%s calc(late %olec(lar properties displa, and de*ine isis(r*ace plots de*ine general properties displa, the c(rrent pict(re (sa%e as clic"ing the logo )(tton) edit %olec(le and %olec(le properties e-port %olec(lar str(ct(res or ato% coordinates *ill ti%e series +ectors *ind calc(late +ario(s things print the .te-t. thro(gh the /0010 %od(le print the .te-t. thro(gh the 2rint %od(le scale the c(rrent graphics displa, %a"e a hardcop, print o* the c(rrent displa, help s,ste% i%port %olec(lar coordinates and other things %anip(late ti%e series %onitor %olec(lar properties *ro% a tra'ector, open and i%port an old %odel *ile sa+e %odel *ile pa(se *or #+al(e seconds (there is also a 3cl 3" co%%and) plot +ario(s things plot a ri))on or t()e thro(gh ato%s trace ato%s thro(gh the tra'ector, stop progra% and e-it reset the s,ste% rotate the c(rrent displa, r(n +ario(s e-ternal progra%s %a"e a selection *ro% the c(rrent ato%s sho! +ario(s things tra'ector, displa, and anal,sis control translate the c(rrent displa, !indo! operations
44444444444444444444444444444444444444444444444444444444444444444444444444 atom !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 The 'atom' !ommand !ontrols the display and the display style of the atoms: One !an !hoose (etween the atom@style on or off using the P=P sign in front of the !ommand: # # display the atoms with name segment name &eg # residue name Res # atom name Atm #
129
atom
disp$lay
e!
Res
"tm
# # display all atoms with a radius of ?loat around &eg/ Res Atm/ # disp$lay e!# Res# "tm# around Float
# # display all atoms of name &egI ResI AtmI with a radius ?loat around # &egI ResI AtmI # # this fun!tion returns also the num(er of atoms sele!ted # around Float e!$ Res$ "tm$
# # display all atoms of name &egI ResI AtmI with a radius ?loat around # &egI ResI AtmI with !olour ColourSname # # this fun!tion returns also the num(er of atoms sele!ted # around Float e!$ Res$ "tm$ Color%name
# # display all atoms of name &egI ResI AtmI with a radius ?loat around # &egI ResI AtmI with !olour Int Int Int 5R<F !olour inde es8 #=IVV6 # # this fun!tion returns also the num(er of atoms sele!ted # &'nt 'nt 'nt& # # display all atoms of name &egI ResI AtmI with a radius ?loat around # &egI ResI AtmI with !olour ?loat ?loat ?loat 5R<F !olour8 #:# = /:#6 # # this fun!tion returns also the num(er of atoms sele!ted # &Float Float Float& # # turn the display off for &eg Res Atm # atom (dis$play e! Res "tm
# # turn the display off for atoms within radius ?loat around &eg/ Res Atm/ # (dis$play e!# Res# "tm# around Float
130
# # turn the &egI ResI AtmI atom display off for atoms within a radius ?loat # around &eg/ &egI AtmI # around Float around Float Float& e!$ Res$ "tm$ e!$ Res$ "tm$ Color%name &'nt 'nt 'nt& &Float Float
# # !hange the atom !olour for &eg Res Atm to ColourSname@R<F inde # atom color e! Res "tm Color%name &'nt 'nt 'nt& &Float Float Float&
# # !olour atoms &eg Res Atm a!!ording to the ve!tor array value # from ?min to ?ma # )y*e$ctor e! Res "tm Fmin Fma+
# # !olour atoms &eg Res Atm a!!ording to their atomi! partial !harge value # from ?min to ?ma # )yc,$ar!e e! Res "tm Fmin Fma+
# # display atoms &eg Res Atm as CP+ spheres # atom cpe! Res "tm
# # turn the CP+ display off for atoms &eg Res Atm # atom (cpe! Res "tm
# # display atom la(els 5full or minumum6 # full in!ludes segment8 residue and atom names 5num(ers6 # (y default only the atom la(el 5name6 is shown # atom la)e$l (la)$el e! Res "tm e! Res "tm full
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# # display atoms &eg Res Atm in the li!ori!e display style # atom lico$rice e! Res "tm
# # turn the li!ori!e display style off for atoms &eg Res Atm # atom (lico$rice e! Res "tm
# # s!ale the CP+ sphere5s6 for &eg Res Atm with a value of ?loat # atom scal$e cpFloat e! Res "tm
# # when e e!uting a !ommand to in!lude atoms a!!ording to a radius # the atoms in!luded will (e sele!ted either (y atom or (y whole residue # this !ommand sele!ts either the atom (ased or whole residue (ase sele!tion # default" atom atom sele$ction atom resi$due
44444444444444444444444444444444444444444444444444444444444444444444444444 !al!ulate !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # !al!ulate average stru!ture from a traJe!tory # calc$ulate a*st$ructure
# # !al!ulate (a!k(one dihedral angles for a protein # ))di$,edrals # # !al!ulate the !lustering for atoms &eg Res Atm through the frames # in a traJe!tory # clus$ter # # delete all !luster data # e! Res "tm
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(clu$ster # # 5re6!al!ulate the atom !onne!tivity information for &eg Res Atm # conn$ecti*ity e! Res "tm
# # !al!ulate !orrelation array for distan!e@angle@torsion array5s6 # num(ered Iserie/ and IserieI # corr$elation dist$ance an!l$e tors$ion 'serie# 'serie$ 'serie# 'serie$ 'serie# 'serie$
# # !al!ulate geometri!al !enter for atoms &eg Res Atm # !eomc$enter e! Res "tm
# # !al!ulate mass !enter for atoms &eg Res Atm # massc$enter e! Res "tm
# # !al!ulate distan!e (etween &eg/ Res/ Atm/ &egI ResI AtmI # dist$ance e!# Res# "tm# e!$ Res$ "tm$
# # !al!ulate angle (etween &eg/ Res/ Atm/ &egI ResI AtmI &egH ResH AtmH # an!l$e e!# Res# "tm# e!$ Res$ "tm$ e!. Res. "tm.
# # !al!ulate torsion (etween &eg/ Res/ Atm/ &egI ResI AtmI &egH ResH AtmH &egN ResN # Res/ "tm/ tors$ion e!# Res# "tm# e!$ Res$ "tm$ e!. Res. "tm. e!/
# # !al!ulate mean sCuare displa!ement for atoms &eg Res Atm using # geometri!al !enter # msdi$splacement # atom e! Res "tm
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# !al!ulate mean sCuare displa!ement for atoms &eg Res ATm using # mass !enter # msdi$splacement mass$center e! Res "tm
# # fit the atoms &eg/ Res/ Atm/ in system #/ to # atoms &egI ResI AtmI in system #I # # 1 numeri!al display off8 / 1 numeri!al display on # 0uat$fit truc1# e!# Res# "tm# truc1$ e!$ Res$ "tm$ 23#
# # !al!ulate root mean sCuare flu!tuation for atoms &eg Res Atm # through the frames # rmsf$luctuation # # # # # # # # # # # e! Res "tm
!al!ulate radial distri(ution fun!tion for atoms &egI ResI AtmI !al!ulated from &eg/ Res Atm/: The !al!ulation will only (e done for the !urrent stru!ture 5system6 displayed$ >owever applying the !ommand su!!essively will add the new !al!ulated rdf to the previous one5s6 !al!ulated: This ena(les the !al!ulation of rdf for the full set of frames in a traJe!tory: To reset the !al!ulation apply the P!al! =rdfP !ommand: To !al!ulate the average from a set of applied P!al! rdfP !ommands apply the P!al! rdfmeanP !ommand: rdf (rdf rdfm$mean e!# Res# "tm# e!$ Res$ "tm$ Fcut T)in
44444444444444444444444444444444444444444444444444444444444444444444444444 !enter !ommand Geif Gaaksonen C&C /MMM 44444444444444444444444444444444444444444444444444444444444444444444444444 # # !enter the system a!!ording to the given atoms 5segment8 residue8 atom6 # or !oordinates # # cent$er syst$em e! Res "tm 4coord 5coord 6coord
44444444444444444444444444444444444444444444444444444444444444444444444444 !ontour !ommand Geif Gaaksonen C&C I##/ 44444444444444444444444444444444444444444444444444444444444444444444444444
134
# # Command to handle the various operations for a grid data to (e # displayed as a iso!ontour surfa!e # # # Read a file with the name ?ile:,ame !ontaining grid data and give # the set the name Contour:name # conto$ur file File71ame Contour71ame
# # ;elete all !ontour information for all files # (fil$e dele$te # # Print !ontour information a(out the files # info # # # # # # Plot the isosurfa!e for !ontour with the name Contour:,ame using an isovalue ?value and !olour Colour -?value Colour :::. The !olour !an (e given as a 5/6 name8 5I6 R<F integer value or 5H6 R<F floating values: plot plot plot # # # # # # Contour71ame F*alue Colour F*alue Colour 777 Contour71ame F*alue &F*alue F*alue F*alue& 777 Contour71ame F*alue &'*alue '*alue '*alue& 777
If !ontour mapping is used you have to give 5/6 The !ontour for wi!h one wants to define an iso value 5I6 The !ontour from whi!h the property will (e mapped 5H6 A min and ma value inside whi!h the !olour s!aling will (e done plot 8Contour71ame# Contour71ame$9 F*alue MinVal Ma+Val 777
# # # # # #
Change the transparent value for !ontour with the name Contour:,ame to ?value: If there are several iso!ontour values defined apply on the one with inde Ivalue: ?value is /: for no transparen!y and #:# for full transparen!y: alp,$a)lend Contour71ame F*alue '*alue
# # Ase smoothing for the iso!ontour surfa!e with the name Contour:,ame
135
# and inde #
Ivalue: smoo$t, Contour71ame on '*alue
# # ;o not use smoothing for the iso!ontour surfa!e with the name # Contour:,ame and inde Ivalue: # smoo$t, Contour71ame off '*alue
# # ;isplay iso!ontour surfa!e with name the name Contour:,ame and # inde Ivalue: # disp$lay Contour71ame on '*alue
# # ;o not display iso!ontour surfa!e with name the name Contour:,ame and # inde Ivalue: # disp$lay Contour71ame off '*alue
# # Change the surfa!e display type to solid for iso!ontour surfa!e with # the name name Contour:,ame and inde Ivalue: # type Contour71ame soli$d '*alue
# # Change the surfa!e display type to mesh for iso!ontour surfa!e with # the name name Contour:,ame and inde Ivalue: # type # # # # # # Contour71ame mes, '*alue
It is possi(le to display a !ontour so that the !ontour polygon values are saved in an array: The default is dire!t whi!h do not save the information: To get the polygon data look into the show !ommand: It is impossi(le to differ the !ontour levels from the data array: The array is Just an array of triangular meshes: met,$od dire$ct sa*e
# # Command to !ontrol the !olour mapping of the values from one grid file # on the surfa!e of an other iso!ontour file # Contour,ame#I will now (e mappend on the surfa!e of Contour,ame#/ # mapp$in! Contour1ame:# Contour1ame:$
136
# Command to !om(ine a !ontour file to a parti!ular stru!ture # <lue !ontour with name PContour:,ameP to stru!ture num(er P&tru!ture#P # com)$ine # # # # # # # # # # Contour71ame tructure:
Contour !lip plane !ommands Put a !lip plane at ?value with the !lipping in the W@= dire!tion along the defined a is: Put the defined !lip 5 8 y or 2 a is6 plane on@off or to display@turn off O(serve that the !lip plane is always related to the local !oordinate system$ clip$plane clip$plane clip$plane clip$plane clip$plane clip$plane clip$plane clip$plane clip$plane clip$plane clip$plane clip$plane clip$plane +; +( y; y( <; <( + + y y < < +y<# +y<$ +y<. +y<# +y<$ +y<. F*alue F*alue F*alue F*alue F*alue F*alue on off on off on off +# y# <# +$ y$ <$ +. y. <. +# y# <# +$ y$ <$ +. y. <. +# y# <# +$ y$ <$ +. y. <. on off on off on off
clip$plane
44444444444444444444444444444444444444444444444444444444444444444444444444 define command =eif =aa-sonen C C #>>? 44444444444444444444444444444444444444444444444444444444444444444444444444 # # define (a!kground !olour (y defining a !olour name or # integer or float triplet 5rg(6 values # defi$ne )!co$lour Colour71ame &Fred F!reen F)lue&
137
# # define (ond display style options" # smooth 5atom !olour !hanges smoothly along the (ond6 # half or default 5half of the (ond is in the !olour of the !onne!ted atom6 # )ondst$yle smoo$t, ,alf
defa$ult
# # define !ell dimensions8 line width and !olour # cell dime$nsions an!l$es line$widt, colour Fa F) Fc Falp,a F)eta F!amma '*alue Colour1ame &Fred F!reen F)lue&
# # define !olour mapping for values (etween #:# ::: /:# # the s!ale goes from 5#:#6 (lue to 5/:#6 red through green at 5#:V6 # colorm$appin! te+ture rain)ow
# # define the draw (uffer 5default is (a!k6 # draw)$uffer )acfron$t # # define the near plane distan!e and step values # near$plane step F*alue *alu$e F*alue
# # define the far plane distan!e and step values # farp$lane step F*alue *alu$e F*alue
# # define viewing angle for perspe!tive proJe!tion # *iewa$n!le # F*alue
138
# define material spe!ular 5#:# = X /IB:#6 # mate$rial spec$ular F*alue
# # mole!ule line width in pi els # mlin$ewidt, '*alue # # not in use # node 1ode71ame
# # !ontour line width in pi els # clin$ewidt, '*alue # # define li!ori!e sphere and !ylinder for the mole!ule display # good for the (all and sti!k display # licos$p,ere F*alue licoc$ylinder F*alue # # define the !ylinder and sphere Cuality # cyli$nder0uality '*alue : any num)er @ 2 Adefault #2B sp,e$re0uality '*alue : any num)er @ 2 Adefault #2B # # not in use # ,url we))$rowser CR=7"ddress De)Erowser71ame
# # define default !oordinate file type and e tension # defa$ult coor$dinate type am)e$r c,ar$mm !aus$sian ,ype$rc,em insi$!,t mol$ mumo$d open$mol
139
e+te$nsion
pd) +mol +y< yasp am)e$r trin! c,ar$mm trin! !aus$sian trin! ,ype$rc,em trin! insi$!,t trin! mol$ trin! mumo$d trin! open$mol trin! pd) trin! +mol trin! +y< trin! yasp trin!
# # define default traJe!tory file type and e tension # traj$ectory type am)e$r ceri$us$ c,ar$mm disc$o*er !romo$s ,ype$rc,em mumo$d +mol +plor yasp am)e$r trin! ceri$us$ trin! c,ar$mm trin! disc$o*er trin! !rom$os trin! ,ype$rc,em trin! mumo$d trin! +mol trin! +plo$r trin! yasp trin!
e+te$nsion
# # <romosMU uses a !onstant with whi!h the !oordinates will (e # multiplied 5default 1 /#:#6: # !romos>? coorda$mplifier F*alue
# # toggle rotations state (etween on@off # rota$tion # stat$e on off
140
# toggle translation state (etween on@off # tran$slation stat$e on off # # a!tivate or deavtivate the state for pi!king atoms # iden$ntify on off # # define atom neigh(our sear!h window 5in atoms6 # atom wind$ow 'num)er
# # defines whether the system is translated around origo or not # this is a!tive (oth at reading a new stru!ture or when there # already are stru!tures read # syst$em tran$slation on off
# # define the proJe!tion method orthographi!@perspe!tive # proj$ection # # define window a!tions # single@multi windowing # update is automati!@manual # wind$owin! sin!$le multi upda$te ort,$o!rap,ic pers$pecti*e
auto$matic manu$al
# # put the traJe!tory frame num(er display on@off # traj$ectory fid on off
# # define the !utplane Hd magnitude: Constant with whi!h the magnitude is # multiplied with: The range is (etween #:# and /:#: #
141
cutp$lane damp$in! F*alue # # put the stereo pair display mode on@off # define the distan!e (etween the o(Je!ts in the stereo pair mode # define the PtiltP angle for the o(Je!ts 5W=6 # spai$r on off distance F*alue an!le F*alue
# # put the harware stereo 5stereo in a window mode on@off # define the PtiltP angle for the o(Je!ts 5W=6 # 0uad$stereo on off an!l$e
F*alue
# # # # # # # #
(e !areful with these !ommands ::: do not use them$ re!onne!tivity defines if the atom !onne!tion ta(le is re!al!ulated (etween the frames or ont: ma !onne!tivity is the ma num(er of !onne!tions 5(onds6 an atom !an have atom coor$dinates c,ar$!e la)e$l resn$um)er *dw iden$ntify F+ Fy Fy F*alue 1ame '*alue F*alue on off reco$nnecti*ity on off ma+c$onnecti*ity la)e$l la)e$l truc1ame 1ame 1ame 'atoms '"inde+ '"inde+ '"inde+ '"inde+ '"inde+ ' ' ' ' ' inde+ inde+ inde+ inde+ inde+
resi$due se!m$ent stru$cture
'"inde+ ' inde+ '"inde+ ' inde+ new appe$nd
44444444444444444444444444444444444444444444444444444444444444444444444444 display command =eif =aa-sonen C C $22# 44444444444444444444444444444444444444444444444444444444444444444444444444 # # display the s!ene 5this is usually always need6 #
142
# !he!k opition 5default6 will look into the event Cueue during the display # no!he!k will not look into the event Cueue # sleep Ivalue guarantees that the display takes at least Ivalue # millise!onds # this !an (e used for demos to slow down the display freCuen!y if you have # a very fast ma!hine # disp$lay c,ec$noc,$ecslee$p '*alue disp$lay 44444444444444444444444444444444444444444444444444444444444444444444444444 edit !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # edit atom (onding # edit )ond )rea$crea$te e!# Res# "tm# e!# Res# "tm# e!# Res# "tm# e!$ Res$ "tm$ e!$ Res$ "tm$
44444444444444444444444444444444444444444444444444444444444444444444444444 e port !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # e port dihedral 5(a!k(one6 angles for a protein # e+po$rt # # # # # # # # ))di$,edrals File71ame
e port !oordinates in various format the stru!ture num(er 5Istru!t6 need also to (e defined 5/6 Fall T &ti!k8 5I6 C>AR99@C>AR9m8 5H6 C>AR99 free8 5N6 +arplus 1 C>AR998 5V6 OP),9OG8 5U6 P;F8 5Y6 P;FZ 5Auto;o!k68 5B6 TI,+)R y28 5M6 A>F; 5C!d68 5/#6 Aser defina(le8 5//6 &imple y2 coor$dinates 'struct )ands$tic- File71ame File71ame c,ar$mm File71ame File71ame free File71ame File71ame -arp$lus File71ame File71ame open$mol File71ame File71ame pd) File71ame
disp$laymasdisp$laymasdisp$laymasdisp$laymasdisp$laymas-
143
pd)0 t+y< u,)d user +y<
File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame
disp$laymasdisp$laymasdisp$laymasdisp$laymasdisp$laymasdisp$laymas-
# # e port input 5raw6 input to e ternal programs # <A9)&&8 e tended >u!kel program ICO,B8 9OPAC8 # Open9ol and Pro(esurf # inpu$t !ame$ss icon$F mopa$c open$mol pro)$esurf ' ' ' ' ' tr1um tr1um tr1um tr1um tr1um File7name File7name File7name File7name File7name
# # e port !luster matri # clus$ter # # e port !orrelation array # corr$elation File71ame File71ame &File la)el te+t&
# # e port model file 5default gOpen9ol stru!ture file6 # mode$l File71ame and file name6 '*alue '*alue File71ame File71ame
# # e port distan!e time series 5inde # dist$ance dist$ance list seri$es
# # e port angle time series 5inde # an!l$e an!l$e # list seri$es
and file name6 '*alue '*alue File71ame File71ame
144
# e port torsion time series 5inde # tors$ion tors$ion list seri$es
and file name6 '*alue '*alue File71ame File71ame
# # e port radial distri(ution fun!tion # rdf File7name
# # e port mean sCuare displa!ement data # msdi$splacement File71ame
# # e port root mean sCuare flu!tuation data # rmsf$luctuation File7name
44444444444444444444444444444444444444444444444444444444444444444444444444 fill !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # fill a pre defined distan!e array from a traJe!tory file # fill dist$ance arra$y list
# # delete distan!e list5s6 and all free all tempoary spa!e # (dis$tance # # fill a pre defined angle array from a traJe!tory file # an!l$e arra$y list
# # delete angle list5s6 and all free all tempoary spa!e # (an!$le # # fill a pre defined torsion array from a traJe!tory file
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# tors$ion arra$y list
# # delete torsion list5s6 and all free all tempoary spa!e # (tor$sion # # fill the atom parameter information into atom stru!ture for # the atom with inde Inum(er # stru$cture 'num)er
44444444444444444444444444444444444444444444444444444444444444444444444444 find !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # # # # # ?ind &=& (onds in a stru!ture Appply the sear!h on all stru!tures availa(le or Just to the stru!ture with num(er P&tru!ture,um(erP: It is also possi(le to give a distan!e ?(ond inside whi!h the &=& must (e: ss)o$nds all GF)ondH tructure1um)er GF)ondH
find
44444444444444444444444444444444444444444444444444444444444444444444444444 gs!ale !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # &!ale the graphi!al display 5eCually in the 8y and 2 dire!tions6 # !scal$e disp$lay F*alue
44444444444444444444444444444444444444444444444444444444444444444444444444 hard!opy !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # make a s!reen dump of the s!reen in a sele!ted format # into a file # # Win,r is the window num(er from the left upper !orner or # the running num(er in whi!h the windows have (een !reated #
146
# for the Post&!ript option it is also possi(le to define the # lands!ape orientation through the P=lP and the pi els@in!h # density through the P=ppi elsperin!hP # ,ard$copy Din1R )mp post$script r!) tar!a +wd File71ame File71ame 8(l | (ppi+elsperinc,9 File71ame File71ame File71ame
44444444444444444444444444444444444444444444444444444444444444444444444444 import !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # import !oordinate 5atom6 information from a file # /: "m)er input coordinates IJK 1KT C EI # I" Charmm 4:!rd input !oordinates # H" A frame from a traJe!tory file # N" <aussian formatted !he!kpoint file # V" <roma!s !oordinate file format # U" <romosMU formatted !oordinate file # Y" >yperChem 4:hin input !oordinates # B" Insight 4:!ar input !oordinates # M" 9olI 4:molI input !oordinates #/#" 9opa! output graphi!s file 5,OT WOR+I,<6 #//" Open9ol input file #/I" Frookhaven 4:pd( input !oordinates #/H" E9OG 4: mol input !oordinates #/N" Plain y2 4: y2 input !oordinates #/V" QA&P 4:yasp input !oordinates impo$rt coor$dinates am)e$r c,ar$mm fram$e !aus$sian !roma$cs !room$s>?a ,ype$rc,em insi$!,t ja!u$ar mol$ mopa$c mumo$d open$mol pd) +mol +y< yasp File71ame IJK 1KT C EI File71ame '*alue File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame File71ame
# # import a pre !al!ulated !luster matri #
147
clus$ter
File7name
# # import a di!tionary file 5!ontaining atom information6 # into gOpen9ol # dict$ionary # # # # # # # File71ame
import a ve!tor file defining the si2e and dire!tion of an array property atta!hed to the atoms there are !urrently two options the C>AR99 for!e file and a flat file !ontaing the ve!tor data *ect$or c,ar$mm fatf$ile File71ame File71ame
# # import <aussian (asis set data (ase # !)as$is File71ame
# # import a gOpen9ol model file # mode$l File71ame
# # import atom partial !harges from # /: ICO,B output file # c,ar$!e iconF File71ame
44444444444444444444444444444444444444444444444444444444444444444444444444 manipulate !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 mani$pulate mani$pulate mani$pulate time$serie dist$ance time$serie an!l$e time$serie tors$ion "ction "ction "ction 'serie 'serie 'serie
The A!tion is one of the following" dave*rage sCua*re !os !osI sCrt dini*tial
148
log e p dmin a(s divf*irst divm*a imum pspe*!trum 2ero mani$pulate mani$pulate mani$pulate time$serie dist$ance time$serie an!l$e time$serie tors$ion "ction "ction "ction 'serie# 'serie$ 'serie# 'serie$ 'serie# 'serie$
The A!tion is one of the following" !opy add mani*pulate mani*pulate mani*pulate time*serie dist*an!e time*serie angl*e time*serie tors*ion A!tion A!tion A!tion Iserie ?value Iserie ?value Iserie ?value
The A!tion is one of the following" powe*rreal mult*real divi*dereal shif*treal 44444444444444444444444444444444444444444444444444444444444444444444444444 monitor !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # # # # # 9onitor a distan!e8 angle or torsion The operation with the P=P sign deletes the whole preset stru!ture Change the line type or the line !olour of list num(er Ilist dist$ance (dis$tance an!l$e (an!$le tors$ion e!# Res# "tm# e!$ Res$ "tm$ colo$ur C1ame 'list type 'num 'list e!# Res# "tm# e!$ Res$ "tm$ colo$ur C1ame 'list type 'num 'list e!# Res# "tm# e!$ Res$ "tm$ e!. Res. "tm.
moni$tor
Res/ "tm/
e!. Res. "tm.
e!/
Res/ "tm/
di,e$dral
colo$ur C1ame 'list type 'num 'list e!# Res# "tm# e!$ Res$ "tm$ colo$ur C1ame 'list
e!. Res. "tm.
e!/
149
(tor$sion (di,$edral
type
'num
'list
# # Put the display swit!h on for the defined distan!e8 angle and # torsion # disp$lay dist$ance an!l$e tors$ion di,e$dral on off on off on off on off
44444444444444444444444444444444444444444444444444444444444444444444444444 mopen !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # Open an gOpen9ol model file # mope$n File71ame
44444444444444444444444444444444444444444444444444444444444444444444444444 msave !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # &ave the stru!ture information into a gOpen9ol model file # msa*$e File71ame
44444444444444444444444444444444444444444444444444444444444444444444444444 plot !ommand Geif Gaaksonen C&C /MMB 44444444444444444444444444444444444444444444444444444444444444444444444444 # # Plot various things # # # plot an arrow # plot arro$w 4c# 5c# 6c# 4c$ 5c$ 6c$ Radius Colour appe$nd
150
(arro$w # # # # # # # # # #
4c# 5c# 6c# 4c$ 5c$ 6c$ Radius Colour
Plot a !ut plane through the !ontour data Choose through whi!h a is the plane goes 5 8y or 26 <ive the tag name for the !ontour <ive the !oordinate on the a is8 through whi!h the plane goes <ive ma and min s!ale 5(lue =X red6 ;efine if the !utplane will (e in Id 5flat6 or Hd for the respe!tive plane Ar(itrary !ut planes !an (e defined from three !oordinates: cutp$lane + Contour1ame 4coord + Contour1ame 4coord Fmin Fma+ + Contour1ame 4coord Fmin Fma+ lo!#23lo! y Contour1ame 5coord y Contour1ame 5coord Fmin Fma+ y Contour1ame 5coord Fmin Fma+ lo!#23lo! < Contour1ame 6coord < Contour1ame 6coord Fmin Fma+ < Contour1ame 6coord Fmin Fma+ lo!#23lo! $d+ .d+ $dy .dy $d< .d< +y<# Contour1ame +# y# <# +$ y$ <$ +. y. <. Fmin Fma+ +y<$ Contour1ame +# y# <# +$ y$ <$ +. y. <. Fmin Fma+ +y<. Contour1ame +# y# <# +$ y$ <$ +. y. <. Fmin Fma+ prof$ile Contour1ame + ')ins Fmin Fma+ y ')ins Fmin Fma+ < ')ins Fmin Fma+ + y < +y<# +y<$ +y<. <(direction scalin! Fma+ Fma+ Fma+
(cutp$lane
: : ,ow a profile of t,e !rid data in t,e +(L y( or : T,e data is sampled in ')ins usin! t,e Fmin Fma+ : prof$ile Contour1ame + ')ins Fmin y ')ins Fmin < ')ins Fmin (cutp$lane + y <
# # Plot a sphere at the defined !oordinate #
151
sp,e$re
(sp,$ere
4c 4c 4c 4c
5c 5c 5c 5c
6c 6c 6c 6c
Radius Radius Radius Radius
Colour appe$nd Colour Colour 4scale 5scale 6scale Colour 4scale 5scale 6scale appe$nd
# # Plot a !ylinder from 5 /8y/82/6 to 5 I8yI82I6 with radius Radius and !olour Colour # It is also possi(le to plot a !ylinder with a different radius and !olour at ea!h ends: # cyli$nder Colour$9 (cyl$inder 4c# 5c# 6c# 4c$ 5c$ 6c$ Radius Colour appe$nd 4c# 5c# 6c# 4c$ 5c$ 6c$ Radius Colour 4c# 5c# 6c# 4c$ 5c$ 6c$ 8Radius# Radius$9 8Colour#
# # Plot a line from 5 /8y/82/6 to 5 I8yI82I6 # line (lin$e # # Plot a linear distan!e plot for the sele!ted atoms # Put the display state on@off # ldp atom$s on off e! Res "tm 4c# 5c# 6c# 4c$ 5c$ 6c$ Colour appe$nd 4c# 5c# 6c# 4c$ 5c$ 6c$ Colour
# # Plot a plane through the 8y or 2 a is at the defined !oordinate # ) tend the plane ;[ in the negative and positive dire!tions # plan$e + y < + y < 4coord 5coord 6coord 4coord 5coord 6coord Jy J+ J+ Jy J+ J+ J< J< Jy J< J< Jy Colour Colour Colour Colour append Colour append Colour append
# # Put !luster display toggle on@off # clus$ter (clu$ster on off
152
# # Plot a !olour s!ale with Ilevels from 5min6 ?min to 5ma 6 ?ma # Put the display off # csca$le (csc$ale 'le*els Fmin Fma+
# # Toggle a ve!tor display on@off # The data has (een read (y the Pimport ve!torP !ommand # *ect$or on off atom$s
e!
Res
"tm
Radius
cale
# # Toggle the !ell display (etween on@off # cell # # # # # # # # # on off
A very simple way to plot the t Plot te t 5stati!6 in Colour at Te t&tring Plot te t 5fi ed in the Te t&tring te+t te+t. (te+$t 8y 5#:# = /:#6 with string 8y82 with
8y82 spa!e6 in Colour at
Colour 4coord 5coord Te+t trin! Colour 4coord 5coord 6coord Te+t trin!
# # Plot the lo!al !oordinate system at sele!ted atoms 5&egment Residue Atom6 # # Turn the plot off a+is a+is (a+i$s 44444444444444444444444444444444444444444444444444444444444444444444444444 plum(er !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # ;raw a tu(e or a ri((on through the sele!ted atoms # in Colour,ame and ?rad wide e!ment Residue "tom e!ment Residue "tom 4a+is=en!t, 5a+is=en!t, 6a+is=en!t,
153
# plum$)er atom$s (ato$ms # # Toggle the display state (etween on@off # disp$lay on off e! Res "tm Frad Colour1ame tu)e ri))$on
44444444444444444444444444444444444444444444444444444444444444444444444444 ptra!e !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # Command to tra!e atoms 5parti!le tra!e6 # # &ele!t the atoms to in!lude in the tra!e set # toggle (etween the display on@off states # ptra$ce atom$s (ato$ms disp$lay e!ment Residue "tom Gappe$ndH on off
# # Write a pro(esurfa!e input file using the tra!ed # atoms: This !an (e used to see the volume mova(le # atoms !over during a simulation: # write pro)$esurf File71ame
44444444444444444444444444444444444444444444444444444444444444444444444444 reset !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # reset atom !olours # atomc$olours # # Reset gOpen9ol # !ope$nmol #
154
# Reset the view to the original # rese$t *iew
# # Reset atom !onne!tivity # conn$ecti*ity e!ment Residue "tom
44444444444444444444444444444444444444444444444444444444444444444444444444 rotate !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # Rotate the atom display around the # rota$te disp$lay 8y and 2 a is
F+rot Fyrot F<rot
# # Rotate only the sele!ted atoms # sele$ction F+rot Fyrot F<rot
44444444444444444444444444444444444444444444444444444444444444444444444444 run !ommand Geif Gaaksonen C&C /MMY 44444444444444444444444444444444444444444444444444444444444444444444444444 # # Run various programs # # The Out<rid?ile name is optional if one wants to use # an other name from the default name 5pro(esurf:plt6 # run pro)$esurf +*i)s 'nputFile 'nputFile 'nputFile KutMridFile1ame all #77A.N1(?B palindrome
44444444444444444444444444444444444444444444444444444444444444444444444444 sele!t !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 #
155
# &ele!t atoms from a stru!ture # sele$ct atom$s (ato$ms e! Res "tm
# # &ele!t all atoms in all stru!tures or the defined ones # stru$cture (str$ucture all '*alue# '*alue$ '*alue. all '*alue# '*alue$ '*alue. 7777 7777
44444444444444444444444444444444444444444444444444444444444444444444444444 show !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # &how used !pu time 5not on Windows MV6 # s,ow cput$ime
# # &how pro!ess information 5not on Windows6 # proc$ess # # &how !urrent time # time # # &how save status 5if program needs saving of stru!ture # (efore e it6 # s,ow sa*es$tatus
# These !ommands return values whi!h !an (e used as input to new !ommands: # # Return a value showing the user if the graphi!s is availa(le # Return value 11 # means no graphi!s8 $1 # means E=Windows is on # !rap$,ics #
156
# Return mole!ule sti!k display line width # mlin$ewidt, # # Return dire!tory where the (inary files are # )ind$irectory # # Return dire!tory where the data files are # datad$irectory # # Return login dire!tory # ,omed$irectory # # Return (a!kground !olour as a rg( triplet float float float # )!co$lour # # Return !olor mapping type: The two types are" Pte tureP 5/; te ture6 and # Prain(owP: # colorm$appin! # # Return distan!e to near !lipping plane # near$plane step *alu$e
# # Return distan!e to far !lipping plane # farp$lane step *alu$e
# # return perspe!tive proJe!tion viewing angle # *iewa$n!le #
157
# Return drawing (uffer 5(a!k@front6 # draw)$uffer # # Return !ylinder Cuality fa!tor # cyli$nder0uality # # Return sphere Cuality fa!tor # sp,e$re0uality # # Return a Prain(owP !olour from a s!ale fa!tor 5(lue ::: green ::: red6 # rain$)ow F*alue # # Return num(er of mole!ular stru!tures defined # mols$tructures # # Return num(er of atoms in atom stru!ture Istru!ture # numa$toms 'structureinde+
# # Return atom num(er for &eg Res Atm # atomn$um)er e! Res "tm
# # Return li!ori!e sphere radius # licos$p,ere # # Return li!ori!e !ylinder radius # licoc$ylinder # # Return num(er of frames in the traJe!tory file #
158
numf$rames # # Return num(er of root mean sCuare flu!tuation # atoms in the list # rmsf$luctuation len!$t,
# # Return root mean sCuare flu!tuation 5total8 8y826 for # inde Irmsflu!tuation # 'rmsfluctuation inde+ # # Return real atom inde # from rmsf list for Irmsfatominde atomi$nde+ 'rmsfatominde+
# # Return the system translation state 5translation on or off6 # If on the system will (e translated around origo # syst$em tran$slation
# # Return stru!ture sele!tion status 51 # 8 not sele!ted 8 1 / 8 sele!ted6 # stat$us ' tructure1um)er # # &how if the sele!ted !oordinates are ative or not 5returns on of off6 # sele$ction # # Return # # # # # # # # # # shown6 # shown6 segment8 residue and atom names g(asis set residue num(er !pk s!ale !oordinates y 2 (value wdv value !olour r g ( nu!lear !harge !onne!tivity for atom Iatominde [ atom display state 5# 1 atom will not (e shown8 1 / will (e atom !pk state 5# 1 atom !pk not (e shown8 1 / will (e
159
# atom li!ori!e state 5# 1 atom li!ori!e not (e shown8 1 / will (e shown6 # atom neigh(our sear!h window in atoms # # for Iatominde in # Istru!tureinde # # atom sele!tion mode 5residue@atom6 # atom !onne!tivity is re!al!ulated (etween the frames 5/6 # not re!al!ulated 5#6 # # ma !onne!tivity is the ma num(er of !onne!tions 5(onds6 # an atom !an have # atom se!m$entname 'atominde+ 'structureinde+ resi$duename 'atominde+ 'structureinde+ atom$name 'atominde+ 'structureinde+ !)as$is 'atominde+ 'structureinde+ resn$um)er 'atominde+ 'structureinde+ cp-s$cale 'atominde+ 'structureinde+ coor$dinates 'atominde+ 'structureinde+ )*al$ue 'atominde+ 'structureinde+ *dw 'atominde+ 'structureinde+ colo$ur 'atominde+ 'structureinde+ nucl$earc,ar!e 'atominde+ 'structureinde+ conn$ecti*ity 'atominde+# 'atominde+$ 777 disp$laystate 'atominde+ 'structureinde+ cp-st$ate 'atominde+ 'structureinde+ lico$ricestate 'atominde+ 'structureinde+ wind$ow sele$ction reco$nnecti*ity ma+c$onnecti*ity
# # show (ond style 5smooth@half6 # )ondst$yle # # show atom identify stage on@off 5/@#6 # iden$tify # # &how various !ontour related information # # Contour file name for I!ontourinde # show num(er of !ontours defined # show num(er of levels defined for Ivalueinde # show !ontour type for Ivalueinde # minimum and ma imum values for the !ontour data in I!ontourinde # show display state for I!ontourinde # show tag name for I!ontourinde
160
# show smoothing state 5/ 1 on 8 # 1 off6 # show !ontour !ell dimensions 5 min ma ymin yma 2min 2ma dim ydim 2dim6 # where the dim8 ydim and 2dim are the num(er of points in the 8y 2 # dire!tions: # contou$r file$name defi$ned le*e$ls type tran$sparency alp,$a)lend mini$mum ma+i$mum disp$lay name smoo$t, cu)e cell 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+ 'contourinde+
# # &how !utplane properties # # shows !utplane smoothing for the y28 2 and y planes # damping or the !onstant with whi!h the value (etween #:# and /:# # is multiplied # type returns the !urrent type for the y28 2 and y planes: The # return value !an (e Id or Hd: # cutp$lane smoot$, damp$in! type # # # # # # # # # # # # # # # # # It is possi(le to e tra!t the polygon data from the last displayed surfa!e5s6 using the poly!on !ommand: The first !ommand gives the num(er of polygons 5triangles6 and the se!ond gives" /8y/82/8n /8ny/8n2/8 I8yI82I8n I8nyI8n2I8 H8yH82H8n H8nyH8n2H8 !/8!I8!H where i8yi82i are the !orned points of the triangle8 n i8nyi8n2i are the surfa!e normals at the !orners and !/8 !I and !H are a !olour value (etween #:# and /:#8 whi!h goes from (lue to red through green: The entry num(er )ntryInde is the inde to the data stru!ture: The method option gives either direct or sa*e where direct means that the polygons are are not saved and sa*e means that the polygons are saved to (e retried using the data option y< +< +y
161
poly$!on
entr$ies data met,$od
Entry'nde+
# # Return !ell !olour # dimensions 5a ( ! alpha (eta gamma6 # line width in pi els # cell colo$ur dime$nsions line$widt,
# # Return <aussian (asis sets # tag name for Ivalue inde # entry for Ivalue inde # !)as$is sets ta! entr$y '*alue '*alue
# # Return material spe!ular # mate$rial spec$ular
# # Return monitor distan!e state # !olour for Inde # list of atoms defining the list # num(er of distan!e time series # moni$tor dist$ance stat$e colo$r 'nde+ type 'nde+ list times$eries
# # Return monitor angle state # !olour for Inde # list of atoms defining the list # num(er of distan!e time series # moni$tor an!l$e stat$e colo$r 'nde+ type 'nde+ list times$eries
162
# Return monitor torsion state # !olour for Inde # list of atoms defining the list # num(er of distan!e time series # moni$tor tors$ion stat$e colo$r 'nde+ type 'nde+ list times$eries
# # # # #
Return radial distri(ution fun!tion !al!ulate and return average from !olle!ted entries return num(er of dis!rete o(servations 5(ins6 return status rdf a*er$a!e o)se$r*ations poin$ts stat$us
# # Return num(er of traJe!tory frames # return status value to see if there is a traJe!tory defined # return traJe!tory file name # return traJe!tory display parameters 5first frame8 last frame8 step frame6 # return num(er of !urrent displayed frame # display frame num(er 5on6 or turn frame num(er display off # traj$ectory frames defi$ned file$name disp$lay curr$ent fid
on
off
# # Return the <romosMU !oordinate amplifier with whi!h the !oordinate # values will (e multiplied # !romos>? coorda$mplifier
# # Return num(er of tra!e sets defined # trac$es # # Return rotations state #
163
rota$tion
stat$e 5/ 11 on 8 # 11 off6
# # Return translation array 5 8 y 8 26 and state # tran$slation arra$y stat$e
# # &how the used proJe!tion method # # 1 perspe!tive # / 1 orthographi! # proj$ection # # # # # # # # &how window state returns either single or multi &how window defined returns the !urrently a!tive@defined num(er of windows &how window parameters for window Win,R returns the window lo!ation 5 8 y6 and window width and height wind$ow stat$e defi$ned
para$meters
Din1r
# # &how pairwise 5!rossedeye stereo6 parameters # status returns either PonP or PoffP depending on if the display is on or off # angle returnes the angle in whi!h the pair is PtiltedP # distan!e gives the distan!e with whi!h the pair is translated to ea!h other # spai$r stat$e an!l$e dist$ance
44444444444444444444444444444444444444444444444444444444444444444444444444 traJe!tory !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # ;efine traJe!tory information # # ;efine file type and name # Alloved types are" am(er8 !harmm8 dis!over8 fam(er8 gtoma!s8 # gromos8 gromosMUa 8 hyper!hem8 mumod8 # mol8 plor
164
# traj$ectory file 'type File71ame
# # ;efine traJe!tory display limits 5first 8 last 8 step6 # limi$ts 'first 'last 'step
44444444444444444444444444444444444444444444444444444444444444444444444444 translate !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # Translate the system # tran$slate disp$lay sele$ction 4trans 5trans 6trans 4trans 5trans 6trans
44444444444444444444444444444444444444444444444444444444444444444444444444 window !ommand Geif Gaaksonen C&C /MMU 44444444444444444444444444444444444444444444444444444444444444444444444444 # # # # # # # # # # # Window id is" #" T!l@Tk !ontrol window /" Open<G mole!ule window I" G;P window Resi2e window to Iwidth and Iheight 9ove window to !oordinates I Iy I!onify@dei!onify window 9ake the graphi!s window5s6 full s!reen Din'J Din'J Din'J Din'J resi$<e 'widt, ',ei!,t mo*e '+ 'y icon$ify deic$onify full$screen
window
Tcl$Tk in gOpenMol
g)penMol has the Tcl.Tk command parser included that enables the usage of the Tcl.Tk command sets and a variety of new commands defined for g)penMol. This
165
E>tension
Tcl
Application Init
6arser
Comman' Loop
E>tension Comman's
BuiltCIn Comman's
Application Comman's
feature enables the extension of the application either through 9<coding or Tcl.Tk scripts. !pplication generates scripts. Tcl parses scripts" passes words to command procedures. !pplication extends built<in command setE Befine new ob,ect types in 9. Implement primitive operations as new Tcl commands. Build complex features with Tcl scripts. $xtensions can be developed independentlyE (etwork communication" database access" security" M !pplications can include combinations of extensions.
+hen you learn more you can even send commands to g)penMol from the tclsh programO +hen g)penMol starts it reads first in the gopen#olr".t"l script that defines some essential macros and definitions to be able to run g)penMol. !t the end of this macro it tests to see if a graphics device is attached. If there is a graphics device attached it also reads in the gopen#ol.guir".t"l script that defines the entire 2/I
166
for g)penMol. The gopenmolrc.tcl and gopenmolHguirc.tcl files are the two essential files defining the entire g)penMol environment and 2/I. There is an interaction between these files and the g)penMol engine so be warned if you edit these files. g)penMol will also at start up and at different stages make some working variables into the Tcl.Tk space that are used again by the parser.
gOpenMol !tilit+ Tools

There are a variety of tools available for g)penMol. The tools mentioned here are either A);T;!( or 9 programs. 4lease look into the utility. directory

4rogram to convert a cube output from the 2aussian33 program into a plot format recogniDed by g)penMol. 4rogram to convert T/;B)M)-$ moloch grids into a format recongiDed by g)penMol. 4rogram to convert 5cube6 data in 49 2!M$ 4/(9% files into a format recongiDed by g)penMol. 4rogram to manipulate a contour file in the plt<format. 9onvert a FBF- ascii tra,ectory into an !MB$; binary one. Merge two 9%!;Mm binary tra,ectories into one binary. 9onvert a 9%!;Mm tra,ectory between for#atted LSSM unfor#atted. 9onvert a multistep 3M)- coordinate file into !MB$; binary tra,ectory format. $xtended %uckel program *I9)(>0 in the I9)(> directory 4robesurf program to generate probe surfaces *!ppendix C0 ' program calculates the electrostatic potential from the I9)(> output *!ppendix C0 9onvert 2;IB and !utoBock potential energy grid files into a format recogniDed by g)penMol.
E>ternal li,raries use' ,+ gOpenMol

)pen2- library. Aor more information about the library please look at the web site httpE..www.opengl.org.. Aor those machines that do not have the library available the M$ !3B library *httpE..www.mesa3d.org.0 is used. 2. Tcl.Tk scripting libraries. Aor more information about the libraries please look at the web site httpE..dev.scriptics.com.. 3. The )pen2- /tility Toolkit *2-/T0" originally written by Mark #ilgard and ported to +in32 *+indows0 by (ate ;obins.
1.
167
/nixE httpE..reality.sgi.com.m,kHasd.glut3.glut3.html +indowsE httpE..www.xmission.com.]nate.glut.html C. 14$2 library from the Independent 14$2 2roup *httpE..www.i,g.org.0E I12 is an informal group that writes and distributes a widely used free library for 14$2 image compression. Fou can find our code and some supporting documentation at ftpE..ftp.uu.net.graphics.,peg.. If you canKt cope with tar.gD< format archives" you may prefer the Dip<format release at ftpE..ftp.simtel.net.pub.simtelnet.msdos.graphics.,pegsrGb.Dip. =. 4ython scripting engine can be used inside g)penMol. Aor more information about the libraries please look at the web site httpE..www.python.org.
168
E>ten'ing gOpenMol through o%n co'e

It is possible to extend g)penMol using plugins that are implemented through a dll file *+indows0 or sharable ob,ect */nix.-inux0. Aollowing is a list of plugins available.
Module ';M-" outputs ball<and<stick" 94#" and licorice views. imple stick can be selected" which is a variation of licorice and tra,ectories with start.stop animation. Aut%or #evin Boyd" /niversity of (ew )rleans Lin$ httpE..73Q.38.77Q.23=.chem.vrml.vrml.html -tatus Included with the program. Module Ailters" input coordinate filters for binary 9hem3B and partan data files. Aut%or #evin Boyd" /niversity of (ew )rleans Lin$ not available -tatus Included with the program. Module Ball" is a demo on how to implement a plugin that displays a sphere in the g)penMol graphics window. Aut%or $ero %&kkinen" 9 9 Lin$ The source code is in the src.plugins.ball directory. -tatus Included with the program.
There is also a tutorial for making plugins N$xtending g)penMol in the +indows $nvironmentN by #evin Boyd at the /niversity of (ew )rleans. The link to this resource is httpE..73Q.38.77Q.23=.chem.gopenmol.htm.
169
Appen'i>#
Appen'i> 1
Coor'inate file formats
g)penMol can handle a variety of coordinate and tra,ectory file formats. Most of the file formats are documented elsewhere.

9%!;MM crd coordinate file format 4BB coordinate file format 3M)- coordinate file format 3FI coordinate file format
C-A"MM cr' coor'inate file format

A%is is #odified fro# t%e 4HARMM do"u#entation The 9!;B file format is the standard means in 9%!;MM for providing a human readable and write able coordinate file. The format is as followsE TIT-$ *a line starting with NJN0 (!T)M *I=0 !T)M() ;$ () ;$ TF4$ 3 F I $2IB ;$ IB +eighting I= I= 73 !C 73 !C A78.= A78.= A78.= 73 !C 73 !C A78.= The TIT-$ is a title for the coordinates" (ext comes the number of coordinates. If this number is Dero or too large" the entire file will be read. Ainally" there is one line for each coordinate. !T)M() gives the number of the atom in the file. It is ignored on reading. ;$ () gives the residue number of the atom. It must be specified relative to the first residue in the 4 A. The )AA et option should be specified if one wishes to read coordinates into other positions. It should also be remembered that for card images" residues are identified by ;$ IB/$ (/MB$;. This number can be modified by using the )AA et feature" gOpenMol manual version 0.92 on 23th September 2005
170
which allows coordinates to be read from a different 4 A. Both positive and negative values are allowed. The ;$ Id option will cause the residue number field to be ignored and map atoms from $2IB and ;$ IB labels instead. ;$ gives the residue type of the atom. ;$ is checked against the residue type in the 4 A for consistency. TF4$ gives the I/4!9 name of the atom. The coordinates of an atom within a residue need not be specified in any particular order. ! search is made within each residue in the 4 A for an atom whose I/4!9 name is given in the coordinate file. The ;$ Id option overrides the residue number and fills coordinates based on the $2IB and ;$ IB identifiers in the coordinate file. E>ample# J MI(IMII$B 9));BI(!T$ A); ($+ %!4T *P%FB;)0 +IT% 9%!(2$B (B)(B 4!;!M J B!T$E =. 2.>@ @E3GE 3 9;$!T$B BF / $;E leif J 2Q 7 7 )3!I 97 8.QC=C= 7.32@83 <8.77237 )3!I 7 8.88888 2 7 )3!I 92 <8.GC@2G 7.2>3CG <8.8CQC8 )3!I 7 8.88888 3 7 )3!I 93 <7.38=23 8.8=77Q 8.88>QC )3!I 7 8.88888 C 7 )3!I 9C <8.=G@37 <7.73>2= 8.8887= )3!I 7 8.88888 = 7 )3!I 9= 8.>2G72 <7.8>@77 <8.8GC>Q )3!I 7 8.88888 G 7 )3!I 9G 7.C>3C> 8.7C2>3 <8.7278G )3!I 7 8.88888 Q 7 )3!I 9Q <7.2C8>> <2.C283Q 8.8=>8G )3!I 7 8.88888 > 7 )3!I 9> <7.@3CQ3 <C.=C@CG 8.73C@8 )3!I 7 8.88888 @ 7 )3!I 9@ <3.722Q= <3.GC>7> 8.7Q832 )3!I 7 8.88888 78 7 )3!I )78 <2.=QCC= <2.CC3>> 8.77@Q7 )3!I 7 8.88888 77 7 )3!I (77 <8.Q>C8@ <3.G>7CG 8.8G3Q> )3!I 7 8.88888 72 7 )3!I )72 <C.3288C <3.@2=83 8.2378> )3!I 7 8.88888 73 7 )3!I 973 <2.8C3>3 <=.>>CG> 8.7G>7C )3!I 7 8.88888 7C 7 )3!I 97C <7.2CC=C <>.8GG37 8.7QQGC )3!I 7 8.88888 7= 7 )3!I 97= 8.8=237 <>.>@@8G 8.73=QG )3!I 7 8.88888 7G 7 )3!I )7G <8.@7>QG <G.GG3C3 8.73382 )3!I 7 8.88888 7Q 7 )3!I %7Q 7.2=2@Q 2.2>237 <8.7==QC )3!I 7 8.88888 7> 7 )3!I %7> <7.227QQ 2.28873 <8.8C8=3 )3!I 7 8.88888 7@ 7 )3!I %7@ <2.3>C3G 8.88@@> 8.8=@8@ )3!I 7 8.88888 28 7 )3!I %28 7.3@=27 <2.88>78 <8.8Q7=3 )3!I 7 8.88888 27 7 )3!I %27 2.=G2=C 8.7Q>>= <8.7Q738 )3!I 7 8.88888 22 7 )3!I %22 <3.8332Q <G.3C232 8.22327 )3!I 7 8.88888 23 7 )3!I %23 <7.>GQ=C <>.323QG <8.GQ@23 )3!I 7 8.88888 2C 7 )3!I %2C <7.Q>G88 <>.2>G7= 7.8@>83 )3!I 7 8.88888 2= 7 )3!I %2= <8.7@G2= <@.@=@Q2 8.7GQC8 )3!I 7 8.88888 2G 7 )3!I %2G 8.GQ=8> <>.GCGQ7 8.@@C82 )3!I 7 8.88888 2Q 7 )3!I %2Q 8.=@=G7 <>.G>777 <8.Q>3Q2 )3!I 7 8.88888
171
DMOL coor'inate file format Mo'ifie' from the DMOL help files
3M)-*3FI0 datafiles specify molecular geometries using a 9artesian coordinate system. The 3M)-*3FI0 format supports multi<step datasets. $ach step is represented by a two<line Nheader"N followed by one line for each atom. The first line of a stepKs header is the number of atoms in that step. This integer may be preceded by whitespaceV any< thing on the line after the integer is ignored. The second line of the header leaves room for a descriptive string. This line may be blank" or it may contain some information pertinent to that particular step" but it must exist" and it must be ,ust one line long. $ach line of text describing a single atom must contain at least four fields of information" separated by whitespaceE the atomKs type *a short string of alphanumeric characters0" and its x<" y<" and D<positions. )ptionally" extra fields may be used to specify a charge for the atom" and.or a vector associated with the atom. If an input line contains five or eight fields" the fifth field is interpreted as the atomKs chargeV otherwise" a charge of Dero is assumed. If an input line contains seven or eight fields" the last three fields are interpreted as the components of a vector. These components should be specified in angstroms. The 3M)-*3FI0 format doesnKt contain connectivity informationO
E>ample#
78 Input 2eometry 9 % % % ) 9 % I % %
8.888888 7.8Q8>G8 <8.3=QG=2 <8.3=Q3>G <8.CQG@22 <7.8=8>23 8.87@>8C <7.C=>2@3 <7.3@2GC3 <7.C2>8G>
8.888888 8.888888 7.88Q>G2 <8.=83@8= <8.GQ2=@2 <2.QQGQ=2 <2.Q@3CG3 <C.2Q8Q8= <7.QG3C33 <3.2Q37>2
8.888888 8.888888 8.888888 <8.>QCCC7 7.7GQ8=8 3.22G@C7 3.2727C7 C.G>@CGC 3.233Q>2 2.3=G=QG
8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888
D9E coor'inate file format

This is a very simple coordinate format containingE gOpenMol manual version 0.92 on 23th September 2005
172
The first line contains the number of atom records *lines0 Arom the second record forward comes a record withE !tom symbol x coordinate y coordinate D coordinate
,(a#ple
2Q 97 92 93 9C 9= 9G 9Q 9> 9@ )78 (77 )72 973 97C 97= )7G %7Q %7> %7@ %28 %27 %22 %23 %2C %2= %2G %2Q
8.QC=C= 7.32@83 <8.77237 <8.GC@2G 7.2>3CG <8.8CQC8 <7.38=23 8.8=77Q 8.88>QC <8.=G@37 <7.73>2= 8.8887= 8.>2G72 <7.8>@77 <8.8GC>Q 7.C>3C> 8.7C2>3 <8.7278G <7.2C8>> <2.C283Q 8.8=>8G <7.@3CQ3 <C.=C@CG 8.73C@8 <3.722Q= <3.GC>7> 8.7Q832 <2.=QCC= <2.CC3>> 8.77@Q7 <8.Q>C8@ <3.G>7CG 8.8G3Q> <C.3288C <3.@2=83 8.2378> <2.8C3>3 <=.>>CG> 8.7G>7C <7.2CC=C <>.8GG37 8.7QQGC 8.8=237 <>.>@@8G 8.73=QG <8.@7>QG <G.GG3C3 8.73382 7.2=2@Q 2.2>237 <8.7==QC <7.227QQ 2.28873 <8.8C8=3 <2.3>C3G 8.88@@> 8.8=@8@ 7.3@=27 <2.88>78 <8.8Q7=3 2.=G2=C 8.7Q>>= <8.7Q738 <3.8332Q <G.3C232 8.22327 <7.>GQ=C <>.323QG <8.GQ@23 <7.Q>G88 <>.2>G7= 7.8@>83 <8.7@G2= <@.@=@Q2 8.7GQC8 8.GQ=8> <>.GCGQ7 8.@@C82 8.=@=G7 <>.G>777 <8.Q>3Q2
173
Appen'i> 0
6lot file .plt/ format
The plot files are regular 3B grid files for plotting of molecular orbitals" electron densities or other molecular properties. The plot files are produced by several programs. It is also possible to format.unformat plot files using the pltfile program in the utility directory. It is also possible to produce plot files with external *own0 programs. 4roduce first a formatted text file and use then the pltfile program to unformat the file for g)penMol. The format for the plot files are very simple and a description of the format can be found elsewhere in this manual. g)penMol can read binary plot files from different hardware platforms independent of the system type *little or big endian machines0.
Format of the ,inar+ F&plt file

The J.plt grid data files are the main enginees for ploting isocontour surfaces. The J.plt files can either be generated directly by various programs inside the g)penMol package or be imported from other programs. 4rograms inside g)penMol generating J.plt grid data filesE The probsurf program generates the grid data for plotting 9onnolly type of surfaces. The vss program generates the grid data for plotting electrostatic potentials. To assist in moving the binary J.plt files between different hardware platforms the pltfile program is included. /sing the program it is possible to format a binary grid file and move it to an other platform and unformat the file again. The program can of course also be used interface the grid data from other programs with g)penMol. The J.plt file binary and formatted file formats are very simple but please observe that unformatted files written with a A);T;!( program are not pure binary files because there are file records between the values while pure binary files do not have any records between the values. g)penMol should be able to figure out if the file is pure binary or A);T;!( unformatted but it is not very well tested.
Binar+ F&plt .gri'/ file format

;ecord number and meaningE U7E Integer" rank value must always be S 3 U2E Integer" possible values are 7 ... =8. This value is not used but it can be used to define the type of surfaceO 'alues used *you can use your own value between 7... =80E gOpenMol manual version 0.92 on 23th September 2005
174
7. E '
surface
2. E )rbital.density surface 3. E 4robe surface 288E 2aussian @C.@> 287E 1aguar 282E 2amess 283E !utoBock 28CE Belphi.Insight 28=E 2rid 'alue 788 is reserved for grid data coming from )penMol @ U3E Integer" number of points in D direction UCE Integer" number of points in y direction U=E Integer" number of points in x direction UGE Aloat" Dmin value UQE Aloat" Dmax value U>E Aloat" ymin value U@E Aloat" ymax value U78E Aloat" xmin value U77E Aloat" xmax value U72 ... Aloat" grid data values running *x is inner loop" then y and last D0E 7. -oop in the D direction 2. -oop in the y direction 3. -oop in the x direction The formatted *the first few lines0 file can look likeE 32 G= G= G= <3.388888eP887 3.288888eP887 <3.388888eP887 3.288888eP887 <3.388888eP887 3.288888eP887 <7.G2=G8@eP887 <7.GCCQC7eP887 <7.GG3@23eP887 <7.G>377=eP887 <7.Q822QCeP887 <7.Q273C8eP887 <7.QC82>8eP887 <7.Q=@87>eP887 <7.QQQCQ>eP887 <7.Q@=G3@eP887 <7.>733>QeP887 <7.>38G3=eP887 ...
Formatte' F&plt .gri'/ file format
175
-ine numbers and variables on the lineE U7E Integer" Integer. ;ank and type of surface *rank is always S 30 U2E Integer" Integer" Integer. Idim" Fdim" 3dim *number of points in the D"y"x directions0 U3E Aloat" Aloat" Aloat" Aloat" Aloat" Aloat. Imin" Imax" Fmin" Fmax" 3min"3max *min and max values0 UCE ... Aloat. 2rid data values running *x is inner loop" then y and last D0 with one or several values per lineE 7. -oop in the D direction 2. -oop in the y direction 3. -oop in the x direction A file in t%is for#at "an t%en be "onverted into binar! wit% t%e pltfile progra#. Aor an example of what a formatted J.plt file can look like please look above. If you are a programmer please look at the included utility programs for the code for doing the reading and writing of J.plt files
Appen'i> 1
The format of the colour file
The file is located atE data.colourHtable.data The first line in the colour file is a comment. The following colour table *a small part of it in fact0 contains the rgb code and the name defined for that rgb code. Fou can add your own colour to the table by editing the file. The colour table file is also used by the colour browsers. !s it is now implemented only the first 288 colours are included in the browser. The rgb codes and their namesE J 9olour table to be used by g)penMol *7@@Q<77<270 2== 2== 2== white 8 8 8 black 2== 8 8 red 8 2== 8 green 8 8 2== blue 2== 8 2== magenta 2== 2== 8 yellow 7@2 7@2 7@2 gray 23> 738 23> violet 7G= C2 C2 brown 8 2== 2== cyan gOpenMol manual version 0.92 on 23th September 2005
176
2== 7@2 C> bright mustard 73C 2G 2G dark firebrick 2== 72> 7CC miami pink >8 2== 2== miami tur:uoise >8 C8 38 dark brown 72> 8 8 dark red 2== 2=8 2=8 snow 2C> 2C> 2== ghost white 2C= 2C= 2C= white smoke 2== 23@ 273 papaya whip 2== 27> 7>= peach puff 2== 22> 7>7 moccasin 2== 2C> 228 cornsilk 2== 2== 2C8 ivory 2== 2=8 28= lemon chiffon 2C= 2== 2=8 mint cream 2C8 2== 2== aDure 2C8 2C> 2== alice blue 238 238 2=8 lavender 2== 2C8 2C= lavender blush 78= 78= 78= dim gray 772 72> 7CC slate gray 277 277 277 light grey 2= 2= 772 midnight blue 8 8 72> navy blue 7Q= 23> 23> pale tur:uoise 8 28G 28@ dark tur:uoise 8 788 8 dark green 228 228 228 gainsboro 2=3 2C= 238 old lace 2=8 2C8 238 linen 2== 23= 28= blanched almond 2== 22> 7@G bis:ue 2== 2C= 23> seashell 2C8 2== 2C8 honeydew 78= 78= 78= dim grey .. . The g)penMol 2/I uses sliders for dynamic colour selection but colour names can be used in the line command mode.
177
The format of the 'ata$atomGparam&'ata file

This file contains data for the display of atoms and some other useful parameters as the -ennard<1ones parameters. The following data is taken from !44$(BI3 B of the R/!(T! ;eference Manual 7@@8. The titles of the columns in the atomHparam.data file areE *70E !tom type number *type0. *20E Bonding radius *bndrad0. *30E van der +aals spheres radius *vdwrad0. *C0E phere radius *plurad0 in plots. *(ot used in g)penMol0. *=0E 'alue *global0 is used in global search for bonds. *G"Q0E 'alue *emin and rmin0 used in the calculation of van der +aals and electrostatic energy. *>0E !tom polariDabilities *patom0. *@0E The atom is either a hydrogen bond acceptor *!0" donor *B or $0" or not hydrogen bonded *(0 *780E The 9%!;Mm atom type *atype0. *770E !tom mass *mass0. $xampleE *70 *20 *30 *C0 *=0 *G0 *Q0 *>0 *@0 *780 *770 Type bndrad vdwrad plurad global emin rmin patom hbond atype mass 7 8.C8 8.@= 8.788 A <8.8C@> 8.> 8.8CC B % 7.88> The parameters in R/!(T! 3.8 are similar to those used in 'ersion 27 of 9%!;Mm. The emin rmin values differ for %! and all metalsV bndrad differs for hydrogens. !toms with Mxx are metalsV atoms with 3xx are halogens. If you wish to extend the parameter file to include your own atom types" it is recommended to use atom numbers greater than 388.
The format of the atomDDD&'ic files

The format of the atom.dic file is as following. The first position *70 is the residue name" the next position *20 is the atom name" third position *30 is the atom type according to the 9%!;Mm type and as the last position *C0 comes the atom charge. gOpenMol manual version 0.92 on 23th September 2005
178
The residue and atom names are restricted to C characters" atomic type is an integer and the charge is a floating point number. The user can also use the symbols KJK and K[K for or in the residue and atom names where KJK matches any characters to the end and K[K matches any character at that particular point. Four own molecules can be added to the end of the file before the default atom types. $xample of an atom dictionary fileE J!mino acid dictionary" polar hydrogens only" 9%!;Mm28.3 parameters *Arom R/!(T!0 2-F 9! 72 8.788 4;) ( 33 <8.288 J ( 32 <8.3=8 J (T 3G <8.788 J % 7 8.2=8 J %T[[ 2 8.3=8 J 9! 77 8.788 J 9 7C 8.==8 J ) C8 <8.==8 J )T CC <8.==8 J 9T7 78 J 9T2 78 !-! 9B 73 8.888 !;2 9B 72 8.888 !;2 92 72 8.888 !;2 9B 72 8.788 !;2 ($ 32 <8.C88 !;2 %$ 7 8.388 !;2 9I 7C 8.=88 !;2 (%[ 3Q <8.C=8 !;2 %%[[ 2 8.3=8 ! ( 9B 72 8.888 ! ( 92 7C 8.==8 ! ( )B[ C8 <8.==8 ! ( (B[ 32 <8.G88 ! ( %B[[ 7 8.388 ! 4 9B 72 <8.7G8 ! 4 92 7C 8.3G8 ! 4 )B[ C3 <8.G88 ! 4 %B[ 2 7.888 9F 9B 72 8.87@ 9F 2 Q8 <8.87@ 9F %2 7 8.888 2-( 9B 72 8.888 2-( 92 72 8.888 2-( 9B 7C 8.==8 2-( )$[ C8 <8.==8 2-( ($[ 32 <8.G88 gOpenMol manual version 0.92 on 23th September 2005
179
2-( %$[[ 7 8.388 2-/ 9B 72 8.888 2-/ 92 72 <8.7G8 2-/ 9B 7C 8.3G8 2-/ )$[ C3 <8.G88 2-/ %$[ 2 7.888 %I 9B 72 8.888 %I 92 27 8.788 %I (B[ 3C <8.C88 %I %B[ 7 8.388 %I 9B[ 23 8.788 %I 9$[ 23 8.388 %I ($[ 3C <8.C88 I-$ 9B 77 8.888 I-$ 927 72 8.888 I-$ 922 73 8.888 I-$ 9B[ 73 8.888 -$/ 9B 72 8.888 -$/ 92 77 8.888 -$/ 9B[ 73 8.888 -F 9B 72 8.888 -F 92 72 8.888 -F 9B 72 8.888 -F 9$ 72 8.2=8 -F (I 3G <8.388 -F %I[ 2 8.3=8 M$T 9B 72 8.888 M$T 92 72 8.8G8 M$T B Q8 <8.728 M$T 9$ 73 8.8G8 4%$ 9B 72 8.888 4%$ 92 22 8.888 4%$ 9B[ 2C 8.888 4%$ 9$[ 2C 8.888 4%$ 9I 2C 8.888 4;) 9B 72 8.888 4;) 92 72 8.888 4;) 9B 72 8.788 $; 9B 72 8.2=8 $; )2 C= <8.G=8 $; %2 7 8.C88 T%; 9B 77 8.2=8 T%; )2[ C= <8.G=8 T%; %2[ 7 8.C88 T%; 92[ 73 8.888 T;4 9B 72 8.888 gOpenMol manual version 0.92 on 23th September 2005
180
T;4 92 27 <8.838 T;4 9B7 23 8.8G8 T;4 9B2 2G 8.788 T;4 ($7 3C <8.3G8 T;4 %$7 7 8.388 T;4 9$2 2G <8.8C8 T;4 9$3 2C <8.838 T;4 9I[ 2C 8.888 T;4 9%[ 2C 8.888 TF; 9B 72 8.888 TF; 92 22 8.888 TF; 9B[ 2C 8.888 TF; 9$[ 2C 8.888 TF; 9I 22 8.2=8 TF; )% C= <8.G=8 TF; %% 7 8.C88 '!- 9B 77 8.888 '!- 92[ 73 8.888 +!T )[[[ CQ <8.>3C +!T %[[[ C 8.C7Q %2) )[[[ CQ <8.>3C %2) %[[[ C 8.C7Q )- )[[[ CQ <8.>3C )- %[[[ C 8.C7Q %)% )[[[ CQ <8.>3C %)% %[[[ C 8.C7Q B)B )[[[ CQ <8.>3C B)B B[[[ C 8.C7Q TI4 )[[[ CQ <8.>3C TI4 %[[[ C 8.C7Q TI43 )%2 CQ <8.>3C TI43 %7 C 8.C7Q TI43 %2 C 8.C7Q (!4 (!7 >7 7.888 U U (ew molecule definitions come here U JJ ([[[ 32 JJ 9[[[ 78 JJ [[[ Q8 JJ %T[[ 7 JJ %[[[ 3 JJ )[[[ C= JJ 4[[[ G8 JJ MA$[ >G JJ I([[ >Q gOpenMol manual version 0.92 on 23th September 2005
181
JJ M9![ >C JJ [[[[ C@@ The user can easily add his.her favourite molecules to the end of this file before the default atom types. There are two files supplied atom.dic atom types for amino acids with polar hydrogens and atomh.dic for amino acids with all hydrogen atoms. The files can be found in directory ....data. These files are made from files of the R/!(T! package by M I.
The format of the atomGcon?ersion&'ata file

The purpose if this file is to control the mapping between an atom name in a coordinate file with the real atom type and symbol. Aor example coordinate files can contain the atom symbol 9! that can be mapped to an alpha carbon *90 or calcium *9a0. The mapping works now only against the 9%!;MM force field. Most likely it can also be used for other force fields but then another atomHparam.data file has to be used. AieldE U 7 ;eal atom symbol or atom name as used in the periodic table of elements. U 2 (ame used in the coordinate file. U 3 Index to the atom type in a force field *9%!;MM0 U C 9olour to be used for this atom. U = default basis set for this atom. . $xample *atomHconversion.data0E U U -eif -aaksonen *9 90 7@@C U U This file contains information about atom conversion U U *70 ;eal symbol of an atom and the second U *20 (ame in which the atom can be found in a data file. U *30 Index to the atom type in a force field *9%!;MM0 U *C0 9olour to be used for this atom U *=0 default basis set for this atom U U $xampleE U ) )% CQ red )xygenB U )xygen in )% U Means that an atom label )% is e:uivalent to an oxygen *)0 atom in )% !r !; 7Q8 cyan !rgonB B B Q cyan BoronB 9 9 7C green 9arbonB U default carbon atom % % 7 white %ydrogenB U default hydrogen atom % 7%! 7 white %ydrogenB U default hydrogen atom gOpenMol manual version 0.92 on 23th September 2005
182
% 7%B 7 white %ydrogenB U default hydrogen atom % 7%2 7 white %ydrogenB U default hydrogen atom % 7%B 7 white %ydrogenB U default hydrogen atom % 7%$ 7 white %ydrogenB U default hydrogen atom % 7%I 7 white %ydrogenB U default hydrogen atom % 7%% 7 white %ydrogenB U default hydrogen atom % 2%! 7 white %ydrogenB U default hydrogen atom % 2%B 7 white %ydrogenB U default hydrogen atom % 2%2 7 white %ydrogenB U default hydrogen atom % 2%B 7 white %ydrogenB U default hydrogen atom % 2%$ 7 white %ydrogenB U default hydrogen atom % 2%I 7 white %ydrogenB U default hydrogen atom % 2%% 7 white %ydrogenB U default hydrogen atom %e %e 7G> cyan %eliumB -4 -47 = violet JJ() B JJ U %andle -47" -42" #43 and -4C -4 -42 = violet JJ() B JJ U %andle -47" -42" #43 and -4C -4 -43 = violet JJ() B JJ U %andle -47" -42" #43 and -4C -4 -4C = violet JJ() B JJ U %andle -47" -42" #43 and -4C ( ( 37 blue (itrogenB U default nitrogen atom ) ) C8 red )xygenB U default oxygen atom ) )% CQ red )xygenB 4 4 G8 yellow 4hosphorousB Q8 yellow ulphurB !t 3!T 737 brown !statineB Br 3B; @C brown BromineB 9l 39- @3 brown 9hlorineB 3e 3$ 7Q2 violet 3enonB A 3A @2 brown AluorineB I 3I @= brown IodineB !c M!9 72G magenta !ctiniumB !g M!2 777 magenta ilverB !l M!- @7 magenta !luminumB !m M!M 7=@ magenta !mericiumB !s M! 787 magenta !rsenicB !u M!/ 77@ magenta 2oldB Ba MB! 77= magenta BariumB Be MB$ G magenta BerylliumB Bi MBI 722 magenta BismuthB Bk MB# 7G7 magenta BerkeliumB 9a M9! >C magenta 9alcium B 9d M9B 772 magenta 9admiumB 9e M9$ 72C magenta 9eriumB 9f M9A 7G2 magenta 9aliforniumB 9m M9M 7G8 magenta 9uriumB 9o M9) @@ magenta 9obaltB 9r M9; @> magenta 9hromiumB gOpenMol manual version 0.92 on 23th September 2005
183
9s M9 >@ magenta 9esiumB 9u M9/ @G magenta 9opperB
The ra'ial 'istri,ution function ." F/ format

This is a simple example of what a radial distribution function *;BA0 could look like. Aigure. The radial distribution function for the (a P atom and the oxygen and hydrogen atoms of water.
The format of the ;BA function isE U7E The radial value from the selected atom. U2E The ;BA value. $xampleE 8.888888 8.788888 8.288888 8.388888 8.C88888 8.=88888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 gOpenMol manual version 0.92 on 23th September 2005
184
8.G88888 8.Q88888 8.>88888 8.@88888 7.888888 7.788888 7.288888 7.388888 7.C88888 7.=88888 7.G88888 7.Q88888 7.>88888 7.@88888 2.888888 2.788888 2.288888 2.388888 2.C88888 2.=88888 2.G88888 2.Q88888 2.>88888 2.@88888 3.888888 3.788888 3.288888 3.388888 3.C88888 3.=88888 3.G88888 3.Q88888 3.>88888 3.@88888 C.888888
M
8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.888888 8.3=22QQ 7.388QQ2 3.3722QQ =.833777 C.7G=CG7 2.C2@@7> 2.=88=2G 7.@7>8G8 8.G88G7Q 7.37@82G 7.C273C2 7.88G>88 8.37QCGC 8.Q=7>@> 8.Q733C> 8.>7322G 8.@82C@2
185
Appen'i> 3
The input format to the or,ital an' electron 'ensit+ program ENSIT9&
The program accepts now only wave functions from the I9)(> program. The default name for the wave function file is fort.Q. Input linesE 70 Two Title lines. 20 (ame of the input file to the I9)(> program. This file contains the atom coordinates. The coordinates and the atom names can also be directly included here. 30 This line defines the siDe of the box by defining the x<min" x<max" y<min" y<max" D<min and D<max. C0 This line defines the number of points in the x" y and D directions. =0 The first number defines t he orbital number to be calculated and the second number gives the typeE 8 S orbital plot" 7 S orbital density and 2 S total elctron density. If the total electron density is defined the first number *the orbital number0 has no meaning. $xampleE JJJJJJ test input JJJJJJJ JJJJJJ test input JJJJJJJ Zicon>.inp fort.Q <>.3288 G.=G2= <73.@=@Q G.2>23 <2.Q>3Q 2.8@>8 =8 =8 =8 C7 8 If the input is made by g)penMol the file looks like the followingE Befault title forE B$( ITF Befault title forE B$( ITF G 8.888888 8.GQ8888 8.888888 9 8.888888 <8.GQ8888 8.888888 9 8.@2GG=8 7.28=888 8.888888 % <8.@2GG=8 7.28=888 8.888888 % 8.@2GG=8 <7.28=888 8.888888 % <8.@2GG=8 <7.28=888 8.888888 % fort.Q <3.8 3.8 <3.8 3.8 <3.8 3.8 38 38 38 gOpenMol manual version 0.92 on 23th September 2005
186
G8 The main difference is now that the atom names and coordinates are included in the input file. The program can be run with the command density Y density.inp X density.out. The program has the following optionsE <ofile.name +rite the orbital or density mesh into file file.name instead of the default file orbital.plt.
6ro,e input format to the surface program 6ro,eSurf

The probe surface program 4;)B$ /;A generates a mesh with grid values from 8 to 788. The value 788 is at the vd+ value and value 8 is at the vd+ P max. probe diameter value. It is possible to generate the surface for different probe values. The method is based on the article by ;. 'oorintholt et al. *'oorintholt ;." #oster M.T. " 'egter 2. " 'riend 2. and %ol +.2.1." N! very fast program for visualiDing protein surfaces" channels and cavitiesN" 1. Mol. 2raphics Q *7@>@0 2C3<2C=0. The original article describes a method based on distance s:uared *r 20 but the program can now also calculate a value based on the distance. 4rogram line command optionsE probsurf <iinput.file <ofile.name <llimits <m7^2 <pfile.name Y input.file X output.file <h this text <i defines an input file" name can also be direct using KYK <o defines the name of the contour file *Befault Kprobesurf.pltK0 <l defines the limits asE numx"numy"numD"xmin"xmax"ymin"ymax"Dmin"Dmax where numx"numy"numD are the number of points in the x"y and D directions and the rest are the coordinate limits of the surface <m defines either s:uared *20 or direct *70" given as Wm2 or Wm7 <p defines a log file name A%e input for#at to t%e probe surfa"e progra# 3RO0,-UR:. Input linesE 70 Two Title lines. 20 (umber of atoms. 30 !ll this on one lineE gOpenMol manual version 0.92 on 23th September 2005
187
7E ;unning atom number. 2E egment name. 3E ;esidue name. CE !tom name. =E 3 coordinate. GE F coordinate. QE I coordinate. >E van Ber +aals radius. C0 This line defines the siDe of the box by defining the x<min" x<max" y<min" y<max" D<min and D<max. =0 This line defines the number of points in the x" y and D directions. G0 The maximum probe radius. $xampleE Befault title forE 4;)B$ /;A Befault title forE 4;)B$ /;A 2Q 7 )3!I )3!I 97 8.QC=C=8 7.32@838 <8.772378 7.QQ8888 2 )3!I )3!I 92 <8.GC@2G8 7.2>3CG8 <8.8CQC88 7.QQ8888 3 )3!I )3!I 93 <7.38=238 8.8=77Q8 8.88>QC8 7.QQ8888 C )3!I )3!I 9C <8.=G@378 <7.73>2=8 8.8887=8 7.QQ8888 = )3!I )3!I 9= 8.>2G728 <7.8>@778 <8.8GC>Q8 7.QQ8888 G )3!I )3!I 9G 7.C>3C>8 8.7C2>38 <8.7278G8 7.QQ8888 Q )3!I )3!I 9Q <7.2C8>>8 <2.C283Q8 8.8=>8G8 7.QQ8888 > )3!I )3!I 9> <7.@3CQ38 <C.=C@CG8 8.73C@88 7.QQ8888 @ )3!I )3!I 9@ <3.722Q=8 <3.GC>7>8 8.7Q8328 7.QQ8888 78 )3!I )3!I )78 <2.=QCC=8 <2.CC3>>8 8.77@Q78 7.=28888 77 )3!I )3!I (77 <8.Q>C8@8 <3.G>7CG8 8.8G3Q>8 7.G88888 72 )3!I )3!I )72 <C.3288C8 <3.@2=838 8.2378>8 7.=28888 73 )3!I )3!I 973 <2.8C3>38 <=.>>CG>8 8.7G>7C8 7.QQ8888 7C )3!I )3!I 97C <7.2CC=C8 <>.8GG378 8.7QQGC8 7.QQ8888 7= )3!I )3!I 97= 8.8=2378 <>.>@@8G8 8.73=QG8 7.QQ8888 7G )3!I )3!I )7G <8.@7>QG8 <G.GG3C38 8.733828 7.=28888 7Q )3!I )3!I %7Q 7.2=2@Q8 2.2>2378 <8.7==QC8 8.@88888 7> )3!I )3!I %7> <7.227QQ8 2.288738 <8.8C8=38 8.@88888 7@ )3!I )3!I %7@ <2.3>C3G8 8.88@@>8 8.8=@8@8 8.@88888 28 )3!I )3!I %28 7.3@=278 <2.88>788 <8.8Q7=38 8.@88888 27 )3!I )3!I %27 2.=G2=C8 8.7Q>>=8 <8.7Q7388 8.@88888 22 )3!I )3!I %22 <3.8332Q8 <G.3C2328 8.223278 8.@88888 23 )3!I )3!I %23 <7.>GQ=C8 <>.323QG8 <8.GQ@238 8.@88888 2C )3!I )3!I %2C <7.Q>G888 <>.2>G7=8 7.8@>838 8.@88888 2= )3!I )3!I %2= <8.7@G2=8 <@.@=@Q7@ 8.7GQC88 8.@88888 2G )3!I )3!I %2G 8.GQ=8>8 <>.GCGQ78 8.@@C828 8.@88888 2Q )3!I )3!I %2Q 8.=@=G78 <>.G>7778 <8.Q>3Q28 8.@88888 gOpenMol manual version 0.92 on 23th September 2005
188
<7=.2C282@ 7=.2C282@ <7=.2C282@ 7=.2C282@ <7=.2C282@ 7=.2C282@ G8 G8 G8 7.@88888 The program has the following optionsE <ofile.name +rite the probe surface mesh into file file.name instead of the default file probesurf.plt. The program probsurf is located in the bin. directory. 6%en !ou displa! a probsurf generated O.plt grid file using t%e iso"ontour displa! engine re#e#ber t%at t%e displa! value range is between 100. and 0.0 The atom trace facility in the tra,ectory analysis has a tool to export the atom trace for an atom or atoms into the probsurf program to generate the volume inside which an atom is moving. 7. Import the optCpti.crd file from the demo. directory. 2. Import the dynCpti.dcd tra,ectory file. 3. )pen the 5Tra,ectory Trace6 widget. +rite into the 5;esidueE6 field 7 and into the 5!tomE6 field 9! and press the 5!pply6 button. C. 9lick the 5BisplayE6 to 5)n6. =. +rite into the line commandE ptra"e write probsurf " Cte#pCtest.inp G. ;un the probsurf program with the cE.temp.test.inp to produce a plt file. ,. Import this plt file using the contour facility and display this 9onnolly type of surface to display the volume inside which the 9! has moved during the simulation. /sing a probe of about 7 _ shows the following 9onnolly surfaceE
189
The electrostatic potential program 2SS

The ' program calculates the electrostatic potential created by the electronic distribution and the nuclei of a molecule in the surrounding space. The electronic distribution is supposed to be obtained from the I9)(> program. It correaponds to approximation II of NMolecular electrostatic potentialsE comparison of ab initio and 9(B) resultsN by 9. 2iessner<4rettre and !. 4ullman" Theoret. 9him. !cta *Berl.0 *7@Q20 2=" >3<>>. This program is a direct translation of the fortran version into c. The input is as follows E *70 Title. *20 Title. *30 Title. *C0 (!T S number of atoms (% S number of hydrogens I/ S 8 or 7. I/ S 8 the coordinates are given in atomic units I/ S 7 the coordinates are given in !ngstrom units *=0 the following (!T cards 3" F and I coordinates for atom i II S number of valence electrons *The hydrogen atoms must be entered last0. *G0 the following (!T cards gross atomic population and screening constant for atom i *Q0 Integer always 2 *not used0 *>0 3min" 3max" Fmin" Fmax" Imin and Imax values to define the box. *@0 (umber of points in the 3<" F< and I<directions. $xampleE JJJJJJJ()HI(A)JJJJJJJ JJJJJJJ()HI(A)JJJJJJJ $T%F-$($ GC7 8.8888 8.GQ88 8.8888 C gOpenMol manual version 0.92 on 23th September 2005
190
8.8888 <8.GQ88 8.8888 C 8.@2GQ 7.28=8 8.8888 7 <8.@2GQ 7.28=8 8.8888 7 8.@2GQ <7.28=8 8.8888 7 <8.@2GQ <7.28=8 8.8888 7 C.782Q 7.G2=8 C.782Q 7.G2=8 8.@C>G 7.3888 8.@C>G 7.3888 8.@C>G 7.3888 8.@C>G 7.3888 2 <8.@2GQ 8.@2GQ <7.28=8 7.28=8 8.8888 8.8888 C8 C8 C8 The program has the following optionsE <ofile.name +rite the isoenergy mesh into file file.name instead of the default file vsscont.plt. 9urrently all programs except the I9)(> program are written in c. Bynamic memory allocation has been used in all the c programs. I9)(> currently accepts systems up to 7888 atoms" but can easily be modified to accept more atoms. The problem with the I9)(> code is the memory. To calculate system up to 7888 atoms needs some 7=8 Mbytes of memory. The other programs used dynamic memory allocation and use very little memory.
191
The internal format of a ?ector 'ata file

The file is a simple formatted flat text file with the following structure. -ine U7E 7E the number 3 showing it is a 3 dimensional plot. 2E the next number shows the data type -ine U2E 7E number of points in the x<direction 2E number of points in the y<direction 3E number of points in the D<direction -ine U3E 7E min and max x coordinate 2E min and max y coordinate 3E min and max D coordinate -ine UC W nE 7E x coordinate 2E y coordinate 3E D coordinate CE length of vector in the x direction =E length of vector in the y direction GE length of vector in y,e D direction If the file contains ,ust random vectors the first five lines have no meaning. They are not processed by g)penMol in the current imnplementation. $xample of a flat vector fileE 3 288 C7 C7 C7 <2.GC=>>G 2.GC=>>G <2.GC=>>G 2.GC=>>G <2.GC=>>G 2.GC=>>G <2.GC=>>G <2.GC=>>G <2.GC=>>G 8.888888 8.888888 8.888888 <2.=73=@7 <2.GC=>>G <2.GC=>>G 8.888888 8.888888 8.888888 <2.3>72@Q <2.GC=>>G <2.GC=>>G 8.888888 8.888888 8.888888 <2.2C@883 <2.GC=>>G <2.GC=>>G 8.888888 8.888888 8.888888 <2.77GQ8@ <2.GC=>>G <2.GC=>>G 8.888888 8.888888 8.888888 . . .
192
Appen'i> 4
The tutorial material is available in the help.tutorials.scottanderson7 directory. The material is best viewed through the web. Tutorials
cott !nderson *andersonZchemistry.chem.utah.edu0E 7. 'isualiDing Molecules with g)penMol *version 2.20 from / . httpE..www.chem.utah.edu.chemistry.faculty.anderson.gopen.html 2. 'isualiDing Molecules with g)penMol *version 2.20 from Ainland. httpE..www.csc.fi.gopenmol.tutorials.scott.
The tutorial as a Dip file with the included binary files for +indows @=.@>.Me.(T.2888. httpE..www.csc.fi.gopenmol.tutorials.scott.tutorial.Dip
#evin Boyd at the /niversity of (ew )rleans 7. $xtending g)penMol in the +indows $nvironment using plugins. httpE..73Q.38.77Q.23=.chem.gopenmol.htm
193
Appen'i> 5
The 4BA file reader saves now the secondary structure information in a 4BA file into tcl variables. This information is available for post processing through the following variablesE
1. The array variable go#-e"ondar!-tru"tureRe"ords contains the number of

records of information available for the available structures. $xampleE gom econdary tructure;ecords*70 contains the number of secondary structures available for structure number 7.
2.
The array variable go#-e"ondar!-tru"tureRe"ord contains the actual records. $xampleE gom econdary tructure;ecord*7"30 contains the third secondary structure record for structure number 7.
$xampleE The Cpti.pdb *4;)T$I(! $ I(%IBIT); *T;F4 I(0 2Q< $4<>2 C4TI0 file contains the following secondary structure records.
>)GIE &>))T &>))T / / I >/ &)R &/ I AGA &/ I <GQ NY <GQ /U AGA IB <GQ VU / IV # HU =/ NPTI NPTI NPTI YU YY YB
!fter reading in the Cpti.pdb file g)penMol will have the following information saved. gom econdary tructure;ecords*70E gom econdary tructure;ecord*7"70E 6>)GIE / >/ &)R NY <GQ gom econdary tructure;ecord*7"20E 6&>))T / &/ I AGA /U AGA gom econdary tructure;ecord*7"30E 6&>))T I &/ I <GQ IB <GQ 3
VU IV / # NPTI NPTI NPTI YU\ YY\ YB\
HU =/
This feature is used in the protein secondary structure cartoon display facility.
194
Appen'i> 7
-ist of Tcl variables defined.used by g)penMol 1ariable gom!tom%it-ist Usage !fter commands involving choosing.selecting atoms the atoms selected into the operation are saved in the variable gom!tom%it-ist. Arom this variable it is possible to post<process the command by seeing which atoms have been included in the command. This Tcl variable shows if there are values available in the gom!tom%it-ist. 9ontrols the default text font used when writing atom label *info0 into the graphics window. The default valus is 5BITM!4H%$-'$TI9!H726. The other options are BITM!4H>HBFH73" BITM!4H@HBFH7=" BITM!4HTIM$ H;)M!(H78" BITM!4HTIM$ H;)M!(H2C" BITM!4H%$-'$TI9!H78" BITM!4H%$-'$TI9!H72 and BITM!4H%$-'$TI9!H7>. By default g)penMol has two different display types of atom labels. The simple is ,ust the atom label from the coordinate file. The extended mode shows also the segment name" residue number and running atom index number. To display this information g)penMol either shows the values through a 9< kernel routine or through a link to Tcl. The Tcl mode is :uite slow so it is not usable for a big number of atom labels. By default g)penMol shows the label information through the Tcl interface if the numbers of labels to be shown are less than 5gom!tom-abel(umber-imit6. By changing this value you can manipulate which routine g)penMol is using. Befault value is 288. In the simplest and default display type *,ust plain atom label0 the information is generated through the operation 5`show atom atomname \, \ia6. By changing this further information can be included on the display. The default value is 5b`show atom atomname \, \iac6. )bserve the curly bracketsO
gom!tom%it-ist!ctive gom!tom-abelAont
gom!tom-abel(umber-imit
gom!tom-abel tring
195
gom!tom-abel tring
In the extensive display type. The information is generated through the operation 5`show atom segment \, \iaE`show atom resnumber \, \iaE`show atom atomname \, \ia*\,06. By changing this further information can be included on the display. The default value is 5b`show atom segment \, \iaE`show atom resnumber \, \iaE`show atom atomname \, \ia *\,0c6. )bserve the curly bracketsO 9ontrols the way the cylinder arrow is displayed. The first value gives the hat.cylinder radius ratio and the second defines the arrow length.hat length ratio. $xampleE set gom9ylinder!rrow9ontrol N7.3 8.QN. 9ontrols the d value when calculating atom connections *bonds0. 'alue is float and default value 8.C !ngstrom. This variable defines the coordinates" colour and font of frame number showed on the screen while looping through the frames. Befault value is 5b8.Q= 8.@ red BITM!4H%$-'$TI9!H72c6. It is possible to define a default opa:ue value for solid surfaces. The default value is 57.86. This variable controls if the best isocontour smoothing is used by default or not. Befault value is 586 which means that the best smoothed surface will not be shown by default. This variable controls the display type of isocontour surfaces. The display type can be either 5mesh6 or 5solid6. The default value is 5solid6. 9an be given as a colour name like 5blue6 or as three floating pointvalues *b8.8 8.8 7.8c0. Befault is red. howing tra,ectories with molecules in the stick display mode results in a display where the frames are displayed too fast. To slow down the display fre:uency it is possible to define a 5sleep time6 in milliseconds before the next frame is displayed. This means that the frame will be displayed at least 5gomBisplay-oop leep6 milliseconds. The default value is 586.
gom9ylinder!rrow9ontrol
gom9ovalentBelta
gom9urrentArame4roperty
gomBefault9ontour)pa:ue gomBefault9ontour mooth
gomBefault9ontourType
gomBefault2radien9olor
gomBisplay-oop leep
196
gom%ydrogenBonding4aram s gom14$2:uality gom-ico9ylinder gom-ico phere gomMonitorBistance4recision gomMonitor!ngle4recision gomMonitorTorsion4recision gomTextAont
This is still under developmentO 9ontrols the 14$2 saving :uality. The value is integer and default value is Q=. 9ontrols the licorice cylinder default value. 'alue is float and default value is 8.3 !ngstrom. 9ontrols the licrice sphere default value. 'alue is float and default value is 8.3 !ngstrom. 9ontrols the distance output format *precision0. Bu default the value is Ne.2fN. 9ontrols the angle output format *precision0. Bu default the value is Ne.2fN. 9ontrols the torsion output format *precision0. Bu default the value is Ne.2fN. 9ontrols the default text font used when writing text into the graphics window. The default valus is 5BITM!4H%$-'$TI9!H726. The other options are BITM!4H>HBFH73" BITM!4H@HBFH7=" BITM!4HTIM$ H;)M!(H78" BITM!4HTIM$ H;)M!(H2C" BITM!4H%$-'$TI9!H78" BITM!4H%$-'$TI9!H72 and BITM!4H%$-'$TI9!H7>. 9ontrols the array type when displaying a vector property *density gradient vector0. The default is an array of type line when the value is 8. If one wants to show a solid array there one integer and one float values give. )ne for the array type *70 and a second defing the solid array cylinder radius *float0. 9ontrols the calculation of the connection table. 'alue can be 5yes6 or 5no6. Befault value is 5yes6. This variable controls if the viewing transformation is done when switching between 2lobal.-ocal transformations. Befault value is 586 which means no 'iewing transformation is done. This variable controls the feature to apply the viewing transformation to the atom coordinates when exporting the coordinates. The default value is 586 which means that the original coordinates are written out. This variable controls the switching between a global *80 and a locan *70 trabsformation mode. Befault value is 586 and meaning a global transformation mode.
gom'ectorBefaultType
lul9alculate!tom9onnectivity lulBo'iewTrans2lobal-ocal
lulInput'iew
lulTraceTransformation'alue
197
!ll these variables can be changed in the gopenmolHguirc.tcl file in the data directory. $xamples of using the variables. $xample U7E The font used to controled the atom label font is controlled by the tcl variable 5gom!tom-abelAont6. The default font definition isE set gom!tom-abelAont BITM!4H%$-'$TI9!H72 The other possible values areE BITM!4H>HBFH73" BITM!4H@HBFH7=" BITM!4HTIM$ H;)M!(H78" BITM!4HTIM$ H;)M!(H2C" BITM!4H%$-'$TI9!H78" BITM!4H%$-'$TI9!H72 and BITM!4H%$-'$TI9!H7>. $xample U2E The precision of the monitor values shown in the graphics window are controlled by the tcl variablesE set gomMonitorBistance4recision set gomMonitor!ngle4recision set gomMonitorTorsion4recision Ne.2fN Ne.2fN Ne.2fN
ItKs easy to change the precision by changing the formatting value. set gomMonitorBistance4recision set gomMonitor!ngle4recision set gomMonitorTorsion4recision Ne.CfN Ne.CfN Ne.CfN
This would change the shown precision to C significant digits.
198
Appen'i> : Ne% features in ?ersion 0&0

This version has gone through a :uite comprehensive updating and therefore this list of new features is rather long. %opefully you will find time to read it through. Ato# "onne"tivit!
9iteria to determine atom connectivity can be customised. ! bond between two atoms is created if the distance between the atoms is e:ual to sum of covar radius of the atoms *a small delta is accepted0. The covar radius can be changed temporarily from 4ie! < 2eriodic ta)le and permanently by editing the file data.element.data.
Ato# labels
(ew atom label type has been added. In addition to the previeously available labels atom name and full name it is now possible to display residue name and number. This feature is specially for protein structure analysing. 2o to 4ie! < &to% la)el(s)... to test this.
Ato# pi"$ing
!tom picking has got :uite a few new features. The atom picking mode can be turned on and off by marking the respective radio button. +hen the mode is on" ,ust click on an atom in order to pick it. !tom picking can also be used by pressing down 9trl and clicking with left mouse button *-MB0 on top of the atom one wants to select. This feature can be utilised in the following way when you want to modify an atom or an group of atoms.
o
! single atom can be picked and it can be dragged and dropped to a text widget by picking the atom pressing down -MB and dragging the cursor to the text widget. If several atoms are picked" they can all be dragged and dropped to a text widget by pressing down -MB on an empty space in the 3B window and dragging the cursor to the text widget.
The atoms can be unpicked by holding down 9trl<button and clicking at the same time with -MB over the picked atom" if the N4ick !tomsN radio button is turned off. If N4ick atomsN is turned on" ,ust click with -MB over the picked gOpenMol manual version 0.92 on 23th September 2005
199
atom to unpick it. Fou can also unpick all atoms by clicking the Unpi"$ all< button. Ato# sele"tion
elected atoms are marked using cubes to separate them from picked atoms" which are marked with spheres. !toms can be unselected by clicking Unsele"t all <button in N elect atomsN<window. 2o to /dit < 5elect... to test this
Ato# tree
! new level has added to the !tom tree. This applies only to protein structures" where now the residues will be listed first and atoms in the residues are listed under every residue. tructure and segment names" residue names and numbers and atom names can be modified by clicking once on the item and then clicking it again. )0 3his does not %ean do()le6clic"ing7 3here has to )e a short dela, )et!een the t!o clic"ings. ! box will appear around the selected item and a cursor will start to blink. !fter the editing has been done" press enter and the item is now modified. If the modification had an effect on atom tree hierarchy" the appropriate tree items will not be created automatically. 1ust press the Update<button to update the N!tom treeN.
The element type of the atom" atom coordinates" colour" van der +aals radius and charge can be modified in the same way as the atom names. 9olour can be changed either by giving a ;2B<value for the wanted colour or by typing the name of the colour instead of the numerical values. If you have changed any of the parameters in the N9ontentN<part of the N!tom TreeN<window" the updating is done automatically and you do not have to click the /pdate< button. 2o to 4ie! < &to% tree... to test this.
;ispla! lists
The program supports the use of the )pen2- display lists for all complex ob,ects. The use of display lists reduces the need to repeatedly call the same low level graphics calls and can therefore make graphics display updating faster. This is especially true when running the program over a slow 377 connection and there is an )pen2- extension in 3 server. gOpenMol manual version 0.92 on 23th September 2005
200
2o to /dit < 8ispla, list properties... to turn them on. ,(tension support
upport for extensions *Bynamic -inked -ibraries *B--0 in +indows and hareable )b,ect * )0 in /(I30 in improved.
H!drogen bonds
%ydrogen bonds can be recalculated for tra,ectory frames. 2o to 3ra'ector, < Main... In the NTra,ectory 9ontrolN<window there are NonN and NoffN radio buttons for N%bond recalculationN where this function can be turned on and off. %ydrogen bonds are searched using a search subset. o if one wants to show only some of hydrogen bonds it is possible to define small search subsets around those atoms. In some circumtances this can significantly reduce the search complexity. 2o to 9alc(late < :,drogen )onds...
The criteria how to calculate hydrogen bonds can be changed. 2o to 9alc(late < :,drogen )onds and click 4%ange "riteria
*#port and e(port of t%e "oordinate files
g)penMol can now identify most of the coordinate file types supported by the program based on the file extensions. In the NImport coordinatesN<window this autodetection property is on by default. Aile format can still be selected manually but it should not be necessary unless the file formats" which do not have standard file extension" are being used. In the N$xport coordinatesN< window the autodetection property is off by default but can be turned on if needed. !bility to import from and export to atom coordinates of 9hemical Markup -anguage *9M-0 file is added. The start<up routine uses the same autodetection property when it searches input filter for files given in command line. The coordinate file filter search routine is reimplemented so that support for a new file format can be added without recompailing the program source code.
3lu#bers gOpenMol manual version 0.92 on 23th September 2005
201
In former versions only helices and sheets were listed in plumber secondary structure window. (ow the program also finds loop regions. In addition the whole protein chain is listed as trace. 2o to 2lot < 2l(%)er... and click the 4li"$ for infor#ation <button next to the text N econdary structureEN to view this.
Two new plumber types are addedE strand and trace. Trace will create a line and strand a ribbon through all selected atoms. By using fast draw option in /dit < 8ispla, properties the plumbers are drawn as lines during rotation so they do not disappear completely. 2o to /dit < 8ispla, properties... and mark the ;edispaly type NAastN radio button.
4lumbers can be glued to atoms. The points of glued plumbers are relative atom positions and will therefore move along atoms. This might be useful feature then using tra,ectories. The more important advantage" though" is the extra residue information in plumber list window. 2o to 2lot < 2l(%)er... to test this feature. In the N4lumberN< window there is a box next to text N2lue to atomsN. If this is marked" the gluing is on and if not" the gluing is off.
4lumbers can now be listed" modified and deleted in the N4lumber listN< window. -isting shows the plumber type" the name of the structure containing the plumber" the segment and the residue names and the number of the first and the last residue of the plumber. egment and residue information is available only if the plumber is glued to atoms. The colour of the plumber can be changed and the plumber can be unglued from atoms. 2o to 2lot < 2l(%)er... and click the List plu#ber<s=< button to view and edit the 4lumber list.
)ew "o##and lines
Aour new command lines have been added. To view their properties" type help edit hbsubset" help find" help show plumber or help plumber in the command line interpreter.
202
Ne% features in ?ersion 0&1

7. Tools to display a protein secondary structure using the so called cartoon display type. 2. Tools to calculate and display hydrogen bonds. 3. $xtended filter program to display electron density gradients from 2aussian33 and 4c2amess. C. 2eneral display engine for the display of vector data. =. Improved usage of Tcl variables for the modification of the g)penMol program and the post<processing of g)penMol commands.
Ne% features in ?ersion 0&<

7. !ll the discovered bugs in version 7.C and 7.Cp have been corrected. 2. 9ut planes through the grid data can be defined from 3 coordinates *atoms0 or planes perpendicular to the x" y and D axis. 3. 9lip planes through the grid data can be defined from 3 coordinates *atoms0 or planes perpendicular to the x" y and D axis. C. 9oordinate reader has been improved. =. 9oordinate reader for 1aguar output files. G. Ailter program to convert 1aguar grid data files into g)penMol plt files. Q. Ailter program to convert NcubeN data in 49 2amess 4/(9% files into g)penMol plt files.
Ne% features in ?ersion 1&3

7. !ll the discovered bugs in version 7.3 have been corrected. 2. (ew input coordinate formats have been addedE 7. 9oordinate input can be read from !msterdam Bensity Aunctional *!BA0 output log files. 2. 9oordinates from a 2;)M!9 gro coordinate file. 3. The tra,ectory readers have been changed to enable the reading of binary tra,ectories indipendent of hardware. In principle it should now be able to read gOpenMol manual version 0.92 on 23th September 2005
203
tra,ectories without the need to format.unformat them when moving from one hardware platform to an other. C. (ew tra,ectory file format addedE 7. The 2;)M!9 trn.trr.xtc tra,ectory file types. =. Binary plt plot files can be moved between hardware platforms without the need to reformat them. The g)penMol plt file reader can now do the byte swap on the fly. G. It is now possible to select atoms by clicking on them and dragging them into an input widget. This makes it easier to pick atoms into input widgets. Q. !ll molecular systems read into g)penMol has its own viewing matrix enabling the rotation.translation of individual molecules. The two modes are defined as global and lo"al transformations. In the global mode all the molecular systems rotate.translate to a common center while in the lo"al mode the translation.rotation will be according to an individual coordinate center. >. To enable :uick rotation" translation and picking it is possible to enable the translation mode by pressing the -%ift key before one presses the left mouse. !s long as the -%ift key is and the left mouse button are pressed the structure will translate when the mouse is moved. Be careful to understand that if the -%ift key will be released before the left mouse button the Translate state will be left on. In the other case Translate mode will return to ;otate mode. @. By pressing the 4trl key first and keeping it pressed it is possible to pick or mark atoms in the graphics screen by pressing the left mouse button. The selected atom*s0 can then be dragged to an input widget. If one releases the 4trl key before releasing the left mouse button g)penMol will stay in the picking mode. 78. 4ressing the Alt key and the left mouse button and moving the mouse in the x<axis direction rotates the molecule around the D<axis. This is the same as using the middle mouse on a three button mouse. 77. In the ,dit menu there is now an Ato# 0rowser that opens as a tree. The atoms in the tree can be clicked. The clicked atom will show up in the graphics screen as being selected. It also works the opposite way. 9licking an atom in the graphics window will highlight the clicked atom in the atom tree. The atom tree also shows a lot of atom information. In the future there will be a feature to edit the parameters.
12.
!ll input file names can be given as a http link and thus be read from a +eb server. If you know that there is a file named #!file."rd on a server named
204
#!.server.org the input file name can be given as %ttp CC#!.server.orgC#!file."rd. 73. The currently on the screen seen coordinate orientation can be written out as a coordinate file or input file to an external program.
205
Index
&' ........................................................................., &m=er....................................................2,E 104E 14, &8B$/......................................9E 10E 2,E 104E 1?, &ppen3ix 1..........................................................1,0 &ppen3ix 2..........................................................1,4 &ppen3ix 3..........................................................1,? &ppen3ix 4..........................................................1+? &ppen3ix 5..........................................................193 &ppen3ix ?..........................................................194 &ppen3ix ,..........................................................195 &ppen3ix +..........................................................199 -scii tr-4ector2 form-ts............................................+ &uto'oc<................................................................5 Begin 2our gOpen8o1 session........................11E 12 =in-r2 tr-4ector2 form-ts.........................................+ C-1cu1-te me-n s@u-re 3isp1-cement....................+0 Center for Scientific Computing.............................3 CI&/8m.......................,E 104E 12,E 143E 1?,E 1,+ CI&/88 ,E 9E 10E 2+E 33E 104E 12,E 143E 1,0E 1+2 C(e1pg...................................................................3, Cop2 :-rious t(ings to t(e c1ip=o-r3....................45 '%7Po12.................................................................., $xit I-1t progr-m execution................................45 $xport input...............................................................
TI(#$;..........................................2@ /%BB.............................................2@ / $;.............................................2@ 3mol...............................................2@ 3FI................................................2@ F! 4..............................................2@ !BA...............................................2Q

fr-me from - tr-4ector2..........................................., ;&8$SS......................................+E 21E 2+E 39E 144 ;-ussi-n..................,E 20E 21E 33E 3,E 14,E 14+E 1?2 gomC21in3er&rro6Contro1.................................19? gOpen8o1 st-rtup 1ine comm-n3..........................12 ;r-p(ics....................................................................
Microsoft +indows BM4 format....CC 4ost cript format...........................CC ilicon 2raphics ;2B format.........CC Targa format..................................C= 3<+indows 3+B format................C=
;/!'.....................................................5E 9E 10E 1?, ;rom-cs..........................................................,E 14, ;/O8&CS...................................................2+E 104 ;/O8OS............................................................104 ;romos9?........................................................,E 14, ;/O8OS9?..................................................2+E 104 I-n31ing of input fi1es..........................................1? Io6 -toms -re 3efine3.......................................12, I2perC(em.......................................,E 2+E 105E 14, !CO"+.......21E 3,E 39E 144E 14+E 1?,E 1+?E 190E 191 !nsig(t........................................................,E 2+E 14, !ntern-1 3-t- structure..........................................12, !ntro3uction.............................................................1 J-gu-r......................................................................, 8erK#Lo11m-nn.....................................................3, 8o12..........................................................,E 2+E 14, 8OP&C......................................21E 2+E 3,E 39E 144 8otto.......................................................................4 8u1ti6in3o6ing in gOpen8o1.............................1+ 8umo3...................................................................., 8M8O'.......................................................2+E 105 "-tur-1 popu1-tion -n-12sis...................................3, Open;%...................................................................3 Open8o1.........3E 4E ,E 20E 29E 33E 34E 144E 14,E 1,5 PC ;-mess..............................................................9 P'B.......................................,E 9E 2,E 123E 143E 1,0 P1ot (-r36-re stereo..............................................59 P1ot stereo p-ir (N...................................................5+ Pro=esurf...................................21E 39E 40E 144E 1?, Pro=eSurf............................................................1+,
2!M$ ........................................C8 I9)(>............................................C8 M)4!9..........................................C8 4robesurf.......................................C8 /ser defined...................................C8

$xport input for extern-1 porgr-ms.......................40 i11 torsion -rr-2..................................................103 orm-ts......................................................................
!MB$;..........................................2Q 9%!;Mm.......................................2> Arame.............................................2> 2!M$ ........................................2> 2aussian........................................2> 2;)M!9 ....................................2> 2;)M) @G...................................2> %yper9hem....................................2> Insight............................................2> Mol2...............................................2> M)4!9..........................................2> M/M)B.........................................2> )penM)l........................................2@ 4BB................................................2@
206
/e@uirements to run gOpen8o1..............................? /ot-te - structure in gOpen8o1............................13 SC&/$/O0..........................................................3 Si3gets.......................................................................
9ontour 4lane Manager.................@8

St-rt up 6in3o6s...................................................12 Superimpose structures.........................................+3 Supporte3 coor3in-te fi1e form-ts.........................2, Supporte3 fi1e form-ts............................................., .c1 1ine comm-n3 interf-ce.................................12+ .c1 :-ri-=1es..............................................................
2;)M!9 ......................................> 2;)M) .........................................> 2;)M) @G.....................................> %yper9hem......................................> M/M)B...........................................> TI(#$;............................................> 3M)-...............................................> 34-);.............................................> F! 4................................................>
.r-ns1-te - structure in gOpen8o1........................14 MIB'...........................................5E 9E 29E 119E 143 Mti1it2 progr-ms......................................................9
gom!tom%it-ist............................7@= gom!tom%it-ist!ctive..................7@= gom!tom-abel(umber-imit........7@= gom!tom-abel tringBef..............7@= gom!tom-abel tring$xt..............7@G gom9ovalentBelta.......................7@G gom9urrentArame4roperty..........7@G gomBefault9ontour)pa:ue.........7@G gomBefault9ontour mooth.........7@G gomBefault9ontourType..............7@G gomBefault2radien9olor.............7@G gomBisplay-oop leep.................7@G gom%ydrogenBonding4arams....7@Q gom14$2:uality..........................7@Q gom-ico9ylinder..........................7@Q gom-ico phere............................7@Q gomMonitor!ngle4recision..........7@Q gomMonitorBistance4recision.....7@Q gomMonitorTorsion4recision.......7@Q gomTextAont................................7@Q gom'ectorBefaultType................7@Q lul9alculate!tom9onnectivity......7@Q lulBo'iewTrans2lobal-ocal.........7@Q lulInput'iew..................................7@Q lulTraceTransformation'alue......7@Q
.c15.<......................................................................4 .(e coor3in-te s2stem..........................................15 .in<er..........................................................,E 29E 31 .!"L$/..........................................1+E 31E 105E 143 tr-4ector2...................................................................
ambera2b.........................................@ autodock2plt.....................................@ charmmtr,.........................................@ contman...........................................@ convert.............................................@ g@Ccub2plt.......................................@ gamess2plt.......................................@ gcube2plt.........................................@ gridasc2plt........................................@ gridbin2plt........................................@ kont2plt..........................................78 pltfile...............................................78 sybyl2amber...................................78 tmole2plt........................................78 tra,merge........................................78 xplor2charmm................................78
:i=r-tion-1 mo3es....................................................+ Vip.............................................................................
9%!;MM.........................................>
.r-4ector2..................................................................
!atto -aaksonen..............................3 $ero %&kkinen.................................7 2eerd Biercksen..........................3" = %enrik #onschin...............................= 1effry B. Madura..............................= 1uha ;uokolainen............................= #evin Boyd.......................................7 Minna 'aris......................................2 cott !nderson............................2" = igismondo Boschi..........................2
0(-t is gOpen8o1O................................................5 0i3get.......................................................................
!mber...............................................> !MB$;............................................> 9erius2.............................................> 9%!;Mm.........................................> Biscover...........................................> B-H4oly...........................................>
9alculate atom connection............CC ;eset various things......................C3 )pen a previously written model file 2=
6i3gets......................................................................
Belete angle array.......................783
207
0i3gets.....................................................................
!bout g)penMol..........................72= !tom display mask.........................=G !utoBock tools.............................723 9alculate and plot a tube or a ribbon through atoms.............................@3 9alculate and plot the ;M B. .@=" @G 9alculate atom connection............Q> 9alculate cluster command...........Q> 9alculate correlation .....................Q@ 9alculate radial distribution function >8 9enter system................................CQ 9ontour Manager.....................G7" >G 9ontour Mapping ..........................GG 9opy time series to disk.................C2 Befine cell......................................C= Belete distance array...................783 Belete torsion array.....................783 Bemo...........................................72G $dit display attributes.....................=C $dit light properties........................C@ $dit material properties..................=8 $dit molecule.................................C> $xport coordinates.........................3> Aill angle array.............................783 Aill distance array.........................782 %elp..............................................72Q Identify atom..................................C> Import and execute a Tcl.Tk script 3= Import !tom vector data................3= Import 9oordinates........................2Q Import Bictionary file......................32 -inear distance plot *-B40.............@3 Make a hardcopy...........................CC Make animation...........................777 Manipulate Time eries...............78Q
Measure 2eometry........................=Q Monitor !ngle.................................@@ Monitor Bistance............................@> Monitor molecular geometry..........@> Monitor Torsion............................787 4lot axis.........................................>C 4lot colour scale.............................>= ;ead cluster file.............................2G ;otate.translate control..................=7 ;un autodock2plt program..........777 ;un 9ontMan program................772 ;un g9ube2plt program..............773 ;un #ont2plt program..................77= ;un pltfile program......................77G ;un probesurf program................77Q ;un turbomole2plt program.........77> ;un /%BB2plt program...............77@ ;un 3vibs program......................728 ave the current structure.............2G elect atom colour...................==" QG elect atoms..................................=3 elect background colour *;B20...Q= elect background colour *Tcl.Tk0.QC uperimpose atoms.......................=3 Text output.....................................Q3 Trace !toms.................................78> Tra,ectory Manager......................78C +rite cluster...................................3Q +rite correlation.............................3@ (ew...............................................2=
0rite r3f 6i3get....................................................42 Fmo1..................................................................+E 29 F8O%.............................,E 105E 14,E 1?,E 1,0E 1,2 FP%O/..........................................................10E 105 F:i=s.......................................................................+ FGH..................................................+E 31E 1,0E 1,2 G&SP................................................+E 29E 105E 14, .c1 :-ri-=1es.............................................................
gom!tom-abelAont.....................7@=
208

The gOpenMol Effort for Analyzing Molecular Dynamics Trajectories

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The gOpenMol Effort for Analyzing Molecular Dynamics Trajectories

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The gOpenMol Effort

Maintained by Leif Laaksonen (Leif.Laaksonen@csc.fi)

gOpenMol manual version 0.92 on 23th September 2005

gOpenMol manual version 0.92 on 23th September 2005

gOpenMol manual version 0.92 on 23th September 2005

.c15.< =2 Scriptics -t (ttp)553e:.scriptics.com5

gOpenMol manual version 0.92 on 23th September 2005

g)penMol includes also a set of programs and utility functions.

"e*uirements to run gOpenMol

Supporte' file formats#

and the following as"ii tra,ectory formatsE

gOpenMol as a helper application for +our (e, ,ro%ser

-o% to ,egin +our gOpenMol session

gOpenMol manual version 0.92 on 23th September 2005

"otate a structure in gOpenMol

gOpenMol manual version 0.92 on 23th September 2005

Translate a structure in gOpenMol

efine the set on %hich the action %ill appl+

gOpenMol manual version 0.92 on 23th September 2005

Control of the re'ispla+

The coor'inate s+stem

gOpenMol manual version 0.92 on 23th September 2005

-an'ling of input files

xxii. xxiii. xxiv. xxv. xxvi. xxvii.

/%BBH9));B 4BBRH9));B !BAH9));B 2;)M!9 H9));B B-H4)-FH9));B 1!2/!;H9));B

gOpenMol manual version 0.92 on 23th September 2005

gOpenMol manual version 0.92 on 23th September 2005

gOpenMol manual version 0.92 on 23th September 2005

The main i'ea of the comman' interface

.1/ FILE menu has the options#

gOpenMol manual version 0.92 on 23th September 2005

.0/ E IT menu has the options#

)dit Cell8 )dit Center8 )dit Conne!tivity8 Identify Atom8

gOpenMol manual version 0.92 on 23th September 2005

.1/ 2IE( menu has the options#

.3/ COLO!" menu has the options#

.4/ CALC!LATE menu has the options#

gOpenMol manual version 0.92 on 23th September 2005

.5/ 6LOT menu has the options#

.7/ T"A8ECTO"9 menu has the options#

gOpenMol manual version 0.92 on 23th September 2005

Time series8 Tra!e8 9ake video8

.:/ "!N menu has the options#

.;/ TOOLS menu has the options#

gOpenMol manual version 0.92 on 23th September 2005

.1</ -EL6 menu has the options#

.1/ File menu

Open a previousl! written #odel <stru"ture go# file=

-ine command optionE #open "o##and

gOpenMol manual version 0.92 on 23th September 2005

-ave t%e "urrent stru"ture and displa! in a #odel go# file

-ine command optionE see #save "o##and

*#port infor#ation into gOpenMol Read "luster file widget

gOpenMol manual version 0.92 on 23th September 2005

-ine command optionE see i#port "o##and

*#port 4oordinates in various for#ats

Supporte' file formats

gOpenMol manual version 0.92 on 23th September 2005

The file browser is started by clicking on the 0rowse button.

!ser 'efine' input filter

gOpenMol manual version 0.92 on 23th September 2005

gOpenMol manual version 0.92 on 23th September 2005

Input;ata H. Input;ata N. i i i i i i &tru!,um &tru!,um &tru!,um &tru!,um &tru!,um &tru!,um

9reate bonds0 Break bonds0 Aind < bonds in proteins