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#
# CREATE REPRESENTATIONS
#
# POLAR REP is all atoms in the lipid down to the second carbon in the tail (blu
e)
mol modselect 0 0 (resname DOPC or resname DOPS) and name $polar_carbon $polar_h
ydrogen $polar_other
mol modcolor 0 0 ColorID 0
mol modstyle 0 0 QuickSurf 1.000000 0.500000 1.000000 1.000000
mol showperiodic 0 0 xyXY
mol numperiodic 0 0 1
mol modmaterial 0 0 Goodsell
#
# NONPOLAR REP is all atoms in the lipid below the second carbon in the tail (ye
llow)
mol addrep 0
mol modselect 1 0 (resname DOPC or resname DOPS) and not name $polar_carbon $pol
ar_hydrogen $polar_other
mol modcolor 1 0 ColorID 4
mol modstyle 1 0 QuickSurf 1.000000 0.500000 1.000000 1.000000
mol showperiodic 0 1 xyXY
mol numperiodic 0 1 1
mol modmaterial 1 0 Goodsell
#
# HMMM REP is nonpolar molecules between lipid membranes (yellow) that aren't li
pids - should remove this section if not HMMM simulation
mol addrep 0
mol modselect 2 0 resname DCLE and z < 20 and z > -20
mol modcolor 2 0 ColorID 4
mol showperiodic 0 2 xyXY
mol numperiodic 0 2 1
mol selupdate 2 0 1
mol modstyle 2 0 QuickSurf 1.000000 0.500000 1.000000 1.000000
mol modmaterial 2 0 Goodsell
#
# PROTEIN REP (red) with no PBC so that only in the main cell
mol addrep 0
mol modcolor 3 0 ColorID 1
mol modselect 3 0 protein
mol modstyle 3 0 QuickSurf 1.000000 0.500000 1.000000 1.000000
mol modmaterial 3 0 Goodsell
#
# Delete original rep (lines)
mol delrep 4 0
# SETUP GENERAL IMAGE DISPLAY
# select lights
light 0 on
light 1 on
light 2 off
light 3 off
# turn on orthographic view
display projection Orthographic
# turn off axes in corner
axes location Off
# minimize near clip
display nearclip set 0.010000
# reset view angle and resize according to user-selected dimensions
display resetview
display resize $xsize $ysize
if {$flag == 0} {
render Tachyon $filename "/homes/jbklauda/vmd/vmd-1.9/lib/tachyon/tachyo
n_LINUXAMD64" $filename -lowshade -format BMP -o $filename.bmp
}
}
#
# TOP PROTEIN
# turn on protein rep
mol showrep 0 3 on
cd $top_prot
# loop through the frames
for {set i 0} {$i < $frames} {incr i $int} {
# go to the given frame
animate goto $i
# take the picture
set filename snap.[format "%04d" $i]
set flag [file exists $filename]
if {$flag == 0} {
render Tachyon $filename "/homes/jbklauda/vmd/vmd-1.9/lib/tachyon/tachyo
n_LINUXAMD64" $filename -lowshade -format BMP -o $filename.bmp
}
}
#
# BOTTOM PROTEIN
rotate x by 180
pbc box -center com -centersel protein -shiftcenter {0 0 -60} -color green
cd $bot_prot
# loop through the frames
for {set i 0} {$i < $frames} {incr i $int} {
# go to the given frame
animate goto $i
# take the picture
set filename snap.[format "%04d" $i]
set flag [file exists $filename]
if {$flag == 0} {
render Tachyon $filename "/homes/jbklauda/vmd/vmd-1.9/lib/tachyon/tachyo
n_LINUXAMD64" $filename -lowshade -format BMP -o $filename.bmp
}
}
#
# BOTTOM LIPID
mol showrep 0 3 off
cd $bot_lipid
# loop through the frames
for {set i 0} {$i < $frames} {incr i $int} {
# go to the given frame
animate goto $i
# take the picture
set filename snap.[format "%04d" $i]
set flag [file exists $filename]
if {$flag == 0} {
render Tachyon $filename "/homes/jbklauda/vmd/vmd-1.9/lib/tachyon/tachyo
n_LINUXAMD64" $filename -lowshade -format BMP -o $filename.bmp
}
}
# SIDE VIEW FOR ADDITIONAL QUALITATIVE ANAYSIS (optional)
mol showperiodic top 1 n
mol showperiodic 0 0 xX
mol numperiodic 0 0 1
mol showperiodic 0 1 xX
mol numperiodic 0 1 1
mol showperiodic 0 2 xX
mol numperiodic 0 2 1
mol modmaterial 0 0 Transparent
mol modmaterial 1 0 Transparent
mol modmaterial 2 0 Transparent
mol modmaterial 3 0 Opaque
display resetview
rotate x by 90
scale by 1.5
pbc box -off
mol showrep 0 3 on
cd $side
# loop through the frames
for {set i 0} {$i < $frames} {incr i $int} {
# go to the given frame
animate goto $i
# take the picture
set filename snap.[format "%04d" $i]
set flag [file exists $filename]
if {$flag == 0} {
render Tachyon $filename "/homes/jbklauda/vmd/vmd-1.9/lib/tachyon/tachyo
n_LINUXAMD64" $filename -lowshade -format BMP -o $filename.bmp
}
}