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VIS_TEMPLATE.vmd
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VIS_TEMPLATE.vmd
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#!/usr/local/bin/vmd
# VMD script written by save_state $Revision: 1.48 $
# VMD version: 1.9.4a31
set viewplist {}
set fixedlist {}
proc vmdrestoremymaterials {} {
set mlist { Opaque Transparent BrushedMetal Diffuse Ghost Glass1 Glass2 Glass3 Glossy HardPlastic MetallicPastel Steel Translucent Edgy EdgyShiny EdgyGlass Goodsell AOShiny AOChalky AOEdgy BlownGlass GlassBubble RTChrome }
set mymlist [material list]
foreach mat $mlist {
if { [lsearch $mymlist $mat] == -1 } {
material add $mat
}
}
material change ambient Opaque 0.000000
material change diffuse Opaque 0.650000
material change specular Opaque 0.500000
material change shininess Opaque 0.534020
material change mirror Opaque 0.000000
material change opacity Opaque 1.000000
material change outline Opaque 0.000000
material change outlinewidth Opaque 0.000000
material change transmode Opaque 0.000000
material change ambient Transparent 0.000000
material change diffuse Transparent 0.730000
material change specular Transparent 0.540000
material change shininess Transparent 0.480000
material change mirror Transparent 0.000000
material change opacity Transparent 0.600000
material change outline Transparent 0.000000
material change outlinewidth Transparent 0.000000
material change transmode Transparent 0.000000
material change ambient BrushedMetal 0.000000
material change diffuse BrushedMetal 0.750000
material change specular BrushedMetal 0.160000
material change shininess BrushedMetal 0.450000
material change mirror BrushedMetal 0.000000
material change opacity BrushedMetal 1.000000
material change outline BrushedMetal 0.000000
material change outlinewidth BrushedMetal 0.000000
material change transmode BrushedMetal 0.000000
material change ambient Diffuse 0.000000
material change diffuse Diffuse 0.620000
material change specular Diffuse 0.000000
material change shininess Diffuse 0.530000
material change mirror Diffuse 0.000000
material change opacity Diffuse 1.000000
material change outline Diffuse 0.000000
material change outlinewidth Diffuse 0.000000
material change transmode Diffuse 0.000000
material change ambient Ghost 0.000000
material change diffuse Ghost 0.000000
material change specular Ghost 1.000000
material change shininess Ghost 0.230000
material change mirror Ghost 0.000000
material change opacity Ghost 0.100000
material change outline Ghost 0.000000
material change outlinewidth Ghost 0.000000
material change transmode Ghost 0.000000
material change ambient Glass1 0.000000
material change diffuse Glass1 0.570000
material change specular Glass1 0.650000
material change shininess Glass1 0.480000
material change mirror Glass1 0.000000
material change opacity Glass1 0.800000
material change outline Glass1 0.000000
material change outlinewidth Glass1 0.000000
material change transmode Glass1 0.000000
material change ambient Glass2 0.520000
material change diffuse Glass2 0.760000
material change specular Glass2 0.220000
material change shininess Glass2 0.590000
material change mirror Glass2 0.000000
material change opacity Glass2 0.700000
material change outline Glass2 0.000000
material change outlinewidth Glass2 0.000000
material change transmode Glass2 0.000000
material change ambient Glass3 0.150000
material change diffuse Glass3 0.250000
material change specular Glass3 0.750000
material change shininess Glass3 0.800000
material change mirror Glass3 0.000000
material change opacity Glass3 0.500000
material change outline Glass3 0.000000
material change outlinewidth Glass3 0.000000
material change transmode Glass3 0.000000
material change ambient Glossy 0.000000
material change diffuse Glossy 0.650000
material change specular Glossy 1.000000
material change shininess Glossy 0.880000
material change mirror Glossy 0.000000
material change opacity Glossy 1.000000
material change outline Glossy 0.000000
material change outlinewidth Glossy 0.000000
material change transmode Glossy 0.000000
material change ambient HardPlastic 0.000000
material change diffuse HardPlastic 0.720000
material change specular HardPlastic 0.160000
material change shininess HardPlastic 0.200000
material change mirror HardPlastic 0.190000
material change opacity HardPlastic 1.000000
material change outline HardPlastic 0.000000
material change outlinewidth HardPlastic 0.000000
material change transmode HardPlastic 0.000000
material change ambient MetallicPastel 0.000000
material change diffuse MetallicPastel 0.260000
material change specular MetallicPastel 0.300000
material change shininess MetallicPastel 0.200000
material change mirror MetallicPastel 0.000000
material change opacity MetallicPastel 1.000000
material change outline MetallicPastel 0.000000
material change outlinewidth MetallicPastel 0.000000
material change transmode MetallicPastel 0.000000
material change ambient Steel 0.250000
material change diffuse Steel 0.000000
material change specular Steel 0.380000
material change shininess Steel 0.320000
material change mirror Steel 0.000000
material change opacity Steel 1.000000
material change outline Steel 0.000000
material change outlinewidth Steel 0.000000
material change transmode Steel 0.000000
material change ambient Translucent 0.000000
material change diffuse Translucent 0.700000
material change specular Translucent 0.600000
material change shininess Translucent 0.300000
material change mirror Translucent 0.000000
material change opacity Translucent 0.800000
material change outline Translucent 0.000000
material change outlinewidth Translucent 0.000000
material change transmode Translucent 0.000000
material change ambient Edgy 0.000000
material change diffuse Edgy 0.660000
material change specular Edgy 0.000000
material change shininess Edgy 0.750000
material change mirror Edgy 0.000000
material change opacity Edgy 1.000000
material change outline Edgy 0.620000
material change outlinewidth Edgy 0.940000
material change transmode Edgy 0.000000
material change ambient EdgyShiny 0.000000
material change diffuse EdgyShiny 0.660000
material change specular EdgyShiny 0.960000
material change shininess EdgyShiny 0.750000
material change mirror EdgyShiny 0.000000
material change opacity EdgyShiny 1.000000
material change outline EdgyShiny 0.760000
material change outlinewidth EdgyShiny 0.940000
material change transmode EdgyShiny 0.000000
material change ambient EdgyGlass 0.000000
material change diffuse EdgyGlass 0.660000
material change specular EdgyGlass 0.500000
material change shininess EdgyGlass 0.750000
material change mirror EdgyGlass 0.000000
material change opacity EdgyGlass 0.620000
material change outline EdgyGlass 0.620000
material change outlinewidth EdgyGlass 0.940000
material change transmode EdgyGlass 0.000000
material change ambient Goodsell 0.520000
material change diffuse Goodsell 1.000000
material change specular Goodsell 0.000000
material change shininess Goodsell 0.000000
material change mirror Goodsell 0.000000
material change opacity Goodsell 1.000000
material change outline Goodsell 4.000000
material change outlinewidth Goodsell 0.900000
material change transmode Goodsell 0.000000
material change ambient AOShiny 0.000000
material change diffuse AOShiny 0.610000
material change specular AOShiny 0.200000
material change shininess AOShiny 0.200000
material change mirror AOShiny 0.050000
material change opacity AOShiny 1.000000
material change outline AOShiny 0.000000
material change outlinewidth AOShiny 0.000000
material change transmode AOShiny 0.000000
material change ambient AOChalky 0.000000
material change diffuse AOChalky 0.850000
material change specular AOChalky 0.000000
material change shininess AOChalky 0.530000
material change mirror AOChalky 0.000000
material change opacity AOChalky 1.000000
material change outline AOChalky 0.000000
material change outlinewidth AOChalky 0.000000
material change transmode AOChalky 0.000000
material change ambient AOEdgy 0.000000
material change diffuse AOEdgy 0.900000
material change specular AOEdgy 0.200000
material change shininess AOEdgy 0.530000
material change mirror AOEdgy 0.000000
material change opacity AOEdgy 1.000000
material change outline AOEdgy 0.620000
material change outlinewidth AOEdgy 0.930000
material change transmode AOEdgy 0.000000
material change ambient BlownGlass 0.040000
material change diffuse BlownGlass 0.340000
material change specular BlownGlass 1.000000
material change shininess BlownGlass 1.000000
material change mirror BlownGlass 0.000000
material change opacity BlownGlass 0.100000
material change outline BlownGlass 0.000000
material change outlinewidth BlownGlass 0.000000
material change transmode BlownGlass 1.000000
material change ambient GlassBubble 0.250000
material change diffuse GlassBubble 0.340000
material change specular GlassBubble 1.000000
material change shininess GlassBubble 1.000000
material change mirror GlassBubble 0.000000
material change opacity GlassBubble 0.040000
material change outline GlassBubble 0.000000
material change outlinewidth GlassBubble 0.000000
material change transmode GlassBubble 1.000000
material change ambient RTChrome 0.000000
material change diffuse RTChrome 0.650000
material change specular RTChrome 0.500000
material change shininess RTChrome 0.530000
material change mirror RTChrome 0.700000
material change opacity RTChrome 1.000000
material change outline RTChrome 0.000000
material change outlinewidth RTChrome 0.000000
material change transmode RTChrome 0.000000
}
vmdrestoremymaterials
# Atom selection macros
atomselect macro at {resname ADE A THY T
}
atomselect macro acidic {resname ASP GLU
}
atomselect macro cyclic {resname HIS PHE PRO TRP TYR
}
atomselect macro acyclic {protein and not cyclic
}
atomselect macro aliphatic {resname ALA GLY ILE LEU VAL
}
atomselect macro alpha {protein and name CA
}
atomselect macro amino {protein
}
atomselect macro aromatic {resname HIS PHE TRP TYR
}
atomselect macro basic {resname ARG HIS LYS HSP
}
atomselect macro bonded {numbonds > 0
}
atomselect macro buried {resname ALA LEU VAL ILE PHE CYS MET TRP
}
atomselect macro cg {resname CYT C GUA G
}
atomselect macro charged {basic or acidic
}
atomselect macro hetero {not (protein or nucleic)
}
atomselect macro hydrophobic {resname ALA LEU VAL ILE PRO PHE MET TRP
}
atomselect macro small {resname ALA GLY SER
}
atomselect macro medium {resname VAL THR ASP ASN PRO CYS ASX PCA HYP
}
atomselect macro large {protein and not (small or medium)
}
atomselect macro neutral {resname VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HYP
}
atomselect macro polar {protein and not hydrophobic
}
atomselect macro purine {resname ADE A GUA G
}
atomselect macro pyrimidine {resname CYT C THY T URA U
}
atomselect macro surface {protein and not buried
}
atomselect macro lipid {resname DLPE DMPC DPPC GPC LPPC PALM PC PGCL POPC POPE
}
atomselect macro lipids {lipid
}
atomselect macro ion {resname AL BA CA CAL CD CES CLA CL CO CS CU CU1 CUA HG IN IOD K LIT MG MN3 MO3 MO4 MO5 MO6 NA NAW OC7 PB POT PT RB SOD TB TL WO4 YB ZN ZN1 ZN2
}
atomselect macro ions {ion
}
atomselect macro sugar {resname AGLC
}
atomselect macro solvent {not (protein or sugar or nucleic or lipid)
}
atomselect macro glycan {resname NAG BGLN FUC AFUC MAN AMAN BMA BMAN
}
atomselect macro carbon {name "C.*" and not ion
}
atomselect macro hydrogen {name "[0-9]?H.*"
}
atomselect macro nitrogen {name "N.*"
}
atomselect macro oxygen {name "O.*"
}
atomselect macro sulfur {name "S.*" and not ion
}
atomselect macro noh {not hydrogen
}
atomselect macro heme {resname HEM HEME
}
atomselect macro conformationall {altloc ""
}
atomselect macro conformationA {altloc "" or altloc "A"
}
atomselect macro conformationB {altloc "" or altloc "B"
}
atomselect macro conformationC {altloc "" or altloc "C"
}
atomselect macro conformationD {altloc "" or altloc "D"
}
atomselect macro conformationE {altloc "" or altloc "E"
}
atomselect macro conformationF {altloc "" or altloc "F"
}
atomselect macro drude {type DRUD or type LP
}
atomselect macro unparametrized beta<1
atomselect macro addedmolefacture {occupancy 0.8}
atomselect macro qwikmd_protein {(not name QWIKMDDELETE and protein)}
atomselect macro qwikmd_nucleic {(not name QWIKMDDELETE and nucleic)}
atomselect macro qwikmd_glycan {(not name QWIKMDDELETE and glycan)}
atomselect macro qwikmd_lipid {(not name QWIKMDDELETE and lipid)}
atomselect macro qwikmd_hetero {(not name QWIKMDDELETE and hetero and not qwikmd_protein and not qwikmd_lipid and not qwikmd_nucleic and not qwikmd_glycan and not water)}
# Display settings
display eyesep 0.065000
display focallength 2.000000
display height 6.000000
display distance -2.000000
display projection Perspective
display nearclip set 0.010000
display farclip set 20.000000
display depthcue off
display cuestart 0.500000
display cueend 10.000000
display cuestart 0.500000
display cueend 10.000000
display cuedensity 0.100000
display cuemode Exp2
display shadows on
display ambientocclusion on
display aoambient 0.800000
display aodirect 0.300000
display dof off
display dof_fnumber 64.000000
display dof_focaldist 0.700000
mol new ../mytest.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol addfile universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol delrep 0 top
mol representation Licorice 0.100000 11.000000 12.000000
mol color ResName
mol selection {all}
mol material HardPlastic
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol representation VDW 0.200000 9.000000
mol color Type
mol selection {not type A}
mol material AOShiny
mol addrep top
mol selupdate 1 top 0
mol colupdate 1 top 0
mol scaleminmax top 1 0.000000 0.000000
mol smoothrep top 1 0
mol drawframes top 1 {now}
mol clipplane center 0 1 top {0.0 0.0 0.0}
mol clipplane color 0 1 top {0.5 0.5 0.5 }
mol clipplane normal 0 1 top {0.0 0.0 1.0}
mol clipplane status 0 1 top {0}
mol clipplane center 1 1 top {0.0 0.0 0.0}
mol clipplane color 1 1 top {0.5 0.5 0.5 }
mol clipplane normal 1 1 top {0.0 0.0 1.0}
mol clipplane status 1 1 top {0}
mol clipplane center 2 1 top {0.0 0.0 0.0}
mol clipplane color 2 1 top {0.5 0.5 0.5 }
mol clipplane normal 2 1 top {0.0 0.0 1.0}
mol clipplane status 2 1 top {0}
mol clipplane center 3 1 top {0.0 0.0 0.0}
mol clipplane color 3 1 top {0.5 0.5 0.5 }
mol clipplane normal 3 1 top {0.0 0.0 1.0}
mol clipplane status 3 1 top {0}
mol clipplane center 4 1 top {0.0 0.0 0.0}
mol clipplane color 4 1 top {0.5 0.5 0.5 }
mol clipplane normal 4 1 top {0.0 0.0 1.0}
mol clipplane status 4 1 top {0}
mol clipplane center 5 1 top {0.0 0.0 0.0}
mol clipplane color 5 1 top {0.5 0.5 0.5 }
mol clipplane normal 5 1 top {0.0 0.0 1.0}
mol clipplane status 5 1 top {0}
mol rename top DNAorigami
# done with molecule 0
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source surface.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top Surface
# done with molecule 1
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source planeHandle11.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top PlaneHandle11
# done with molecule 2
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source planeHandle00.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top PlaneHandle00
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source planeHandle10.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top PlaneHandle10
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source planeHandle111.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top PlaneHandle111
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source planeHandle01.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top PlaneHandle01
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source vectorsHandle11.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top VectorsHandle11
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source vectorsHandle00.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top VectorsHandle00
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source vectorsHandle10.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top VectorsHandle10
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source vectorsHandle111.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top VectorsHandle111
mol new universe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
source vectorsHandle01.tcl
mol delrep 0 top
mol representation Lines
mol color Name
mol selection {none}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol clipplane center 0 0 top {0.0 0.0 0.0}
mol clipplane color 0 0 top {0.5 0.5 0.5 }
mol clipplane normal 0 0 top {0.0 0.0 1.0}
mol clipplane status 0 0 top {0}
mol clipplane center 1 0 top {0.0 0.0 0.0}
mol clipplane color 1 0 top {0.5 0.5 0.5 }
mol clipplane normal 1 0 top {0.0 0.0 1.0}
mol clipplane status 1 0 top {0}
mol clipplane center 2 0 top {0.0 0.0 0.0}
mol clipplane color 2 0 top {0.5 0.5 0.5 }
mol clipplane normal 2 0 top {0.0 0.0 1.0}
mol clipplane status 2 0 top {0}
mol clipplane center 3 0 top {0.0 0.0 0.0}
mol clipplane color 3 0 top {0.5 0.5 0.5 }
mol clipplane normal 3 0 top {0.0 0.0 1.0}
mol clipplane status 3 0 top {0}
mol clipplane center 4 0 top {0.0 0.0 0.0}
mol clipplane color 4 0 top {0.5 0.5 0.5 }
mol clipplane normal 4 0 top {0.0 0.0 1.0}
mol clipplane status 4 0 top {0}
mol clipplane center 5 0 top {0.0 0.0 0.0}
mol clipplane color 5 0 top {0.5 0.5 0.5 }
mol clipplane normal 5 0 top {0.0 0.0 1.0}
mol clipplane status 5 0 top {0}
mol rename top VectorsHandle01
unset viewplist
unset fixedlist
proc vmdrestoremycolors {} {
color scale colors RWB {1.0 0.0 0.0} {1.0 1.0 1.0} {0.0 0.0 1.0}
color scale colors BWR {0.0 0.0 1.0} {1.0 1.0 1.0} {1.0 0.0 0.0}
color scale colors RGryB {1.0 0.0 0.0} {0.5 0.5 0.5} {0.0 0.0 1.0}
color scale colors BGryR {0.0 0.0 1.0} {0.5 0.5 0.5} {1.0 0.0 0.0}
color scale colors RGB {1.0 0.0 0.0} {0.0 1.0 0.0} {0.0 0.0 1.0}
color scale colors BGR {0.0 0.0 1.0} {0.0 1.0 0.0} {1.0 0.0 0.0}
color scale colors RWG {1.0 0.0 0.0} {1.0 1.0 1.0} {0.0 1.0 0.0}
color scale colors GWR {0.0 1.0 0.0} {1.0 1.0 1.0} {1.0 0.0 0.0}
color scale colors GWB {0.0 1.0 0.0} {1.0 1.0 1.0} {0.0 0.0 1.0}
color scale colors BWG {0.0 0.0 1.0} {1.0 1.0 1.0} {0.0 1.0 0.0}
color scale colors BlkW {0.0 0.0 0.0} {0.5 0.5 0.5} {1.0 1.0 1.0}
color scale colors WBlk {1.0 1.0 1.0} {0.5 0.5 0.5} {0.0 0.0 0.0}
color scale method RWB
set colorcmds {
{color Display {Background} white}
{color Display {BackgroundTop} black}
{color Display {BackgroundBot} blue2}
{color Display {FPS} white}
{color Name {LPA} green}
{color Name {LPB} green}
{color Name {1} pink}
{color Name {3} cyan}
{color Name {5} purple}
{color Name {7} lime}
{color Name {9} mauve}
{color Name {2} ochre}
{color Name {4} iceblue}
{color Name {6} black}
{color Name {8} yellow2}
{color Type {LP} green}
{color Type {DRUD} pink}
{color Type {A} pink}
{color Type {K} cyan}
{color Type {1} purple}
{color Type {3} lime}
{color Type {5} mauve}
{color Type {7} ochre}
{color Type {9} iceblue}
{color Type {2} black}
{color Type {4} yellow2}
{color Type {6} yellow3}
{color Type {8} green2}
{color Element {X} cyan}
{color Element {Ac} ochre}
{color Element {Ag} ochre}
{color Element {Al} ochre}
{color Element {Am} ochre}
{color Element {Ar} ochre}
{color Element {As} ochre}
{color Element {At} ochre}
{color Element {Au} ochre}
{color Element {B} ochre}
{color Element {Ba} ochre}
{color Element {Be} ochre}
{color Element {Bh} ochre}
{color Element {Bi} ochre}
{color Element {Bk} ochre}
{color Element {Br} ochre}
{color Element {Ca} ochre}
{color Element {Cd} ochre}
{color Element {Ce} ochre}
{color Element {Cf} ochre}
{color Element {Cl} ochre}
{color Element {Cm} ochre}
{color Element {Co} ochre}
{color Element {Cr} ochre}
{color Element {Cs} ochre}
{color Element {Cu} ochre}
{color Element {Db} ochre}
{color Element {Ds} ochre}
{color Element {Dy} ochre}
{color Element {Er} ochre}
{color Element {Es} ochre}
{color Element {Eu} ochre}
{color Element {F} ochre}
{color Element {Fe} ochre}
{color Element {Fm} ochre}
{color Element {Fr} ochre}
{color Element {Ga} ochre}
{color Element {Gd} ochre}
{color Element {Ge} ochre}
{color Element {He} ochre}
{color Element {Hf} ochre}
{color Element {Hg} ochre}
{color Element {Ho} ochre}
{color Element {Hs} ochre}
{color Element {I} ochre}
{color Element {In} ochre}
{color Element {Ir} ochre}
{color Element {K} ochre}
{color Element {Kr} ochre}
{color Element {La} ochre}
{color Element {Li} ochre}
{color Element {Lr} ochre}
{color Element {Lu} ochre}
{color Element {Md} ochre}
{color Element {Mg} ochre}
{color Element {Mn} ochre}
{color Element {Mo} ochre}
{color Element {Mt} ochre}
{color Element {Na} ochre}
{color Element {Nb} ochre}
{color Element {Nd} ochre}
{color Element {Ne} ochre}
{color Element {Ni} ochre}
{color Element {No} ochre}
{color Element {Np} ochre}
{color Element {Os} ochre}
{color Element {Pa} ochre}
{color Element {Pb} ochre}
{color Element {Pd} ochre}
{color Element {Pm} ochre}
{color Element {Po} ochre}
{color Element {Pr} ochre}
{color Element {Pt} ochre}
{color Element {Pu} ochre}
{color Element {Ra} ochre}
{color Element {Rb} ochre}
{color Element {Re} ochre}
{color Element {Rf} ochre}
{color Element {Rg} ochre}
{color Element {Rh} ochre}
{color Element {Rn} ochre}
{color Element {Ru} ochre}
{color Element {Sb} ochre}
{color Element {Sc} ochre}
{color Element {Se} ochre}
{color Element {Sg} ochre}
{color Element {Si} ochre}
{color Element {Sm} ochre}
{color Element {Sn} ochre}
{color Element {Sr} ochre}
{color Element {Ta} ochre}
{color Element {Tb} ochre}
{color Element {Tc} ochre}
{color Element {Te} ochre}
{color Element {Th} ochre}
{color Element {Ti} ochre}
{color Element {Tl} ochre}
{color Element {Tm} ochre}
{color Element {U} ochre}
{color Element {V} ochre}
{color Element {W} ochre}
{color Element {Xe} ochre}
{color Element {Y} ochre}
{color Element {Yb} ochre}