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set beg 0
set skip 1
# set end -1
set end -1
# mol new PORE.dx
set prefix output/dna-65-70
#set dnaLength 1
set IDs [mol new dna-65-70.psf ]
# set files [sortFileGlob $prefix.dcd]
source loadRigidBody.procs.tcl
dcd $prefix.0.dcd skip $skip beg $beg end $end
set files [sortFileGlob $prefix.rb-traj]
puts "loading $files"
set rbIDs [loadTrajectory $files [lindex $IDs 0] $skip $beg $end]
# loadTrajectoryRbFrame $files [lindex $IDs 0] $skip $beg $endo
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 P0 P1"]
$sel set radius 2.5
set sel [atomselect $ID "name B0 B1"]
$sel set radius 2
# mol color Beta
mol color Name
# mol color Index
mol selection all
mol selection "name P0 B0 P1 B1"
mol material AOChalky
# mol representation VDW 3.000000 12.000000
# mol representation VDW 0.8
mol representation Licorice 1.3
mol modrep 0 $ID
# mol delrep 0 $ID
# mol representation Licorice 0.6
# mol addrep $ID
}
# mol color Beta
# mol color ColorID 0
mol color SegName
# mol color Molecule
mol selection "protein or nucleic"
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
}
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 cyan
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
proc smooth {{s 3}} {
smoothReps $s
smoothRot $s
}
#centerRB ssb
#package require pbctools
#pbc set {200.0 200.0 200.0} -all
#animate goto 0
#pbc join -now
#pbc wrap -now
#pbc unwrap -first now
#pbc unwrap -all -molid 0 -sel "name P0 P1 B1 B0"