Chimie Théorique » OpenPath

#!/usr/local/bin/vmd

# VMD script written by save_state $Revision: 1.1 $

# VMD version: 1.8.5

set viewplist {}

set fixedlist {}

proc vmdrestoremymaterials {} {

  set mlist { Opaque Transparent BrushedMetal Diffuse Ghost Glass1 Glass2 Glossy HardPlastic MetallicPastel Steel }

  set mymlist [material list]

  foreach mat $mlist {

    if { [lsearch $mymlist $mat] == -1 } { 

      material add $mat

    }

  }

  material change ambient Opaque 0.000000

  material change specular Opaque 0.500000

  material change diffuse Opaque 0.650000

  material change shininess Opaque 0.534020

  material change opacity Opaque 1.000000

  material change ambient Transparent 0.000000

  material change specular Transparent 0.500000

  material change diffuse Transparent 0.650000

  material change shininess Transparent 0.534020

  material change opacity Transparent 0.300000

  material change ambient BrushedMetal 0.080000

  material change specular BrushedMetal 0.340000

  material change diffuse BrushedMetal 0.390000

  material change shininess BrushedMetal 0.150000

  material change opacity BrushedMetal 1.000000

  material change ambient Diffuse 0.000000

  material change specular Diffuse 0.000000

  material change diffuse Diffuse 0.700000

  material change shininess Diffuse 0.530000

  material change opacity Diffuse 1.000000

  material change ambient Ghost 0.000000

  material change specular Ghost 1.000000

  material change diffuse Ghost 0.000000

  material change shininess Ghost 0.230000

  material change opacity Ghost 0.100000

  material change ambient Glass1 0.000000

  material change specular Glass1 0.650000

  material change diffuse Glass1 0.500000

  material change shininess Glass1 0.530000

  material change opacity Glass1 0.150000

  material change ambient Glass2 0.520000

  material change specular Glass2 0.220000

  material change diffuse Glass2 0.760000

  material change shininess Glass2 0.590000

  material change opacity Glass2 0.680000

  material change ambient Glossy 0.000000

  material change specular Glossy 1.000000

  material change diffuse Glossy 0.650000

  material change shininess Glossy 0.880000

  material change opacity Glossy 1.000000

  material change ambient HardPlastic 0.000000

  material change specular HardPlastic 0.280000

  material change diffuse HardPlastic 0.560000

  material change shininess HardPlastic 0.690000

  material change opacity HardPlastic 1.000000

  material change ambient MetallicPastel 0.000000

  material change specular MetallicPastel 0.550000

  material change diffuse MetallicPastel 0.260000

  material change shininess MetallicPastel 0.190000

  material change opacity MetallicPastel 1.000000

  material change ambient Steel 0.250000

  material change specular Steel 0.380000

  material change diffuse Steel 0.000000

  material change shininess Steel 0.320000

  material change opacity Steel 1.000000

}

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 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 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 unparametrized beta<1

atomselect macro addedmolefacture {occupancy 0.8}

# Display settings

display eyesep       0.065000

display focallength  2.000000

display height       6.000000

display distance     -2.000000

display projection   Orthographic

display nearclip set 0.500000

display farclip  set 10.000000

display depthcue   off

display cuestart   0.500000

display cueend     10.000000

display cuedensity 0.400000

display cuemode    Exp2

#############################################################

#

# Insert LIST From PATH here

#

#############################################################

mol new Test_frozen_00 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_01 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_02 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_03 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_04 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_05 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_06 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_07 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_08 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol addfile Test_frozen_09 type POSCAR first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all

mol delrep 0 top

mol representation DynamicBonds 1.600000 0.100000 6.000000

mol color Name

mol selection {all}

mol material Opaque

mol addrep top

mol showperiodic top 0 xyXY

mol numperiodic top 0 1

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 CPK 1.000000 0.300000 8.000000 6.000000

mol color Name

mol selection {all}

mol material Opaque

mol addrep top

mol showperiodic top 1 xyXY

mol numperiodic top 1 1

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 Test_frozen_00

set viewpoints([molinfo top]) {{{1.000000 0.000000 0.000000 -1.485553} {0.000000 1.000000 0.000000 -2.166452} {0.000000 0.000000 1.000000 -5.591770} {0.000000 0.000000 0.000000 1.000000}} {{0.882606 0.469283 0.027947 0.000000} {-0.465827 0.864997 0.186501 0.000000} {0.063348 -0.177625 0.982055 0.000000} {0.000000 0.000000 0.000000 1.000000}} {{0.121690 0.000000 0.000000 0.000000} {0.000000 0.121690 0.000000 0.000000} {0.000000 0.000000 0.121690 0.000000} {0.000000 0.000000 0.000000 1.000000}} {{1.000000 0.000000 0.000000 0.000000} {0.000000 1.000000 0.000000 0.000000} {0.000000 0.000000 1.000000 0.000000} {0.000000 0.000000 0.000000 1.000000}}}

lappend viewplist [molinfo top]

set topmol [molinfo top]

# done with molecule 0

foreach v $viewplist {

  molinfo $v set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($v)

}

foreach v $fixedlist {

  molinfo $v set fixed 1

}

unset viewplist

unset fixedlist

mol top $topmol

unset topmol

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 {FPS} white}

    {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}

    {color Element {Zr} ochre}

    {color Resname {} silver}

    {color Chain {X} blue}

    {color Segname {} blue}

    {color Conformation {all} blue}

    {color Molecule {0} blue}

    {color Surface {Grasp} gray}

    {color Labels {Springs} orange}

  }

  foreach colcmd $colorcmds {

    set val [catch {eval $colcmd}]

  }

  color change rgb 0 0.0 0.0 1.0

  color change rgb 2 0.34999999404 0.34999999404 0.34999999404

  color change rgb 3 1.0 0.5 0.0

  color change rgb 4 1.0 1.0 0.0

  color change rgb 5 0.5 0.5 0.20000000298

  color change rgb 6 0.600000023842 0.600000023842 0.600000023842

  color change rgb 7 0.0 1.0 0.0

  color change rgb 9 1.0 0.600000023842 0.600000023842

  color change rgb 11 0.649999976158 0.0 0.649999976158

  color change rgb 12 0.5 0.899999976158 0.40000000596

  color change rgb 13 0.899999976158 0.40000000596 0.699999988079

  color change rgb 14 0.5 0.300000011921 0.0

  color change rgb 15 0.5 0.5 0.75

  color change rgb 17 0.879999995232 0.97000002861 0.019999999553

  color change rgb 18 0.550000011921 0.899999976158 0.019999999553

  color change rgb 19 0.0 0.899999976158 0.0399999991059

  color change rgb 20 0.0 0.899999976158 0.5

  color change rgb 21 0.0 0.879999995232 1.0

  color change rgb 22 0.0 0.759999990463 1.0

  color change rgb 23 0.019999999553 0.379999995232 0.670000016689

  color change rgb 24 0.00999999977648 0.0399999991059 0.930000007153

  color change rgb 25 0.270000010729 0.0 0.980000019073

  color change rgb 26 0.449999988079 0.0 0.899999976158

  color change rgb 27 0.899999976158 0.0 0.899999976158

  color change rgb 28 1.0 0.0 0.660000026226

  color change rgb 29 0.980000019073 0.0 0.230000004172

  color change rgb 30 0.810000002384 0.0 0.0

  color change rgb 31 0.889999985695 0.34999999404 0.0

  color change rgb 32 0.959999978542 0.72000002861 0.0

}

vmdrestoremycolors

label textsize 1.0