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set beg 0
set skip 24
set end -1
# set end 1400
# mol new PORE.dx
set prefix output/min.trombone-ssb
set prefix output/trombone-ssb2
# set prefix output/trombone-ssb2.1ca96d5c
set IDs [mol new trombone-dna.psf]
set wd [pwd]
set naLength 1
source loadRigidBody.procs.tcl
if [file exists $prefix.0.dcd] {
dcd $prefix.0.dcd skip $skip beg $beg end $end
} else {
dcd $prefix.dcd skip $skip beg $beg end $end
}
if [file exists $prefix.0.rb-traj] {
set rbIDs [loadTrajectory $prefix.0.rb-traj $IDs $skip $beg $end]
} else {
set rbIDs [loadTrajectory $prefix.rb-traj $IDs $skip $beg $end]
}
# loadTrajectoryRbFrame $files [lindex $IDs 0] $skip $beg $endo
cd $wd
foreach ID $IDs {
set sel [atomselect $ID all]
set beta ""
foreach r [$sel get resid] {
lappend beta [expr $r%10 + double($r)/10]
}
$sel set beta $beta
set sel [atomselect $ID "name P"]
$sel set radius 2.5
set sel [atomselect $ID "name B"]
$sel set radius 2
mol color Name
# mol selection all
# mol selection "name P B"
mol selection "name P"
mol material AOChalky
# mol representation Licorice 1.3
mol representation Licorice 2.0
mol modrep 0 $ID
}
# mol color Beta
mol color ColorID 15
# mol color SegName
# mol color Molecule
mol selection "protein"
mol material AOChalky
# mol material GlassBubble
# mol representation VDW 0.8
# mol representation QuickSurf
# mol representation VDW 2.000000 12.000000
# mol representation NewCartoon
mol representation QuickSurf 1.000000 0.500000 1.900000 1.000000
foreach rbID $rbIDs {
# mol color ColorId $rbID
mol modrep 0 $rbID
}
# mol off [lindex $rbIDs 12]
# color Display Background white
color Name P green
color Name B green2
color change rgb green2 0.7 0.9 0.7
color Segname APRO cyan2
color Segname BPRO blue
color Segname CPRO cyan3
color Segname DPRO blue3
# light 0 off
# display depthcue off
# display backgroundgradient off
display shadows on
display ambientocclusion on
display aoambient 0.6
display aodirect 0.6
set sysID [mol new replisome.psf]
mol addfile replisome.pdb
mol material AOChalky
mol representation NewCartoon
# mol color Segname
mol color ColorID 4
mol selection "segname V013 V019 V021 and x > 0"
mol modrep 0 $sysID
mol material GlassBubble
mol representation QuickSurf 1.5
mol addrep $sysID
mol material AOChalky
mol representation NewCartoon
mol color ColorID 10
mol selection "segname V001 V003 V005 V007 V009 V011 and resid > 260 and x > 0"
mol addrep $sysID
mol material GlassBubble
mol representation QuickSurf 1.5
mol addrep $sysID
mol material AOChalky
mol representation NewCartoon
mol color ColorID 11
mol selection "segname V009 V011 V027 V029 V031 V033 and resid <= 260 and x > 0"
mol addrep $sysID
mol material GlassBubble
mol representation QuickSurf 1.5
mol addrep $sysID
mol material AOChalky
mol representation VDW
mol color ColorID 7
mol selection nucleic
mol addrep $sysID
mol top $ID