VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Aug 02 2007 - 10:20:03 CDT

Dear VMD users,

A colleague of mine is trying to use Save State in VMD and it fails.

I tried to do it myself. I loaded a protein, changed a couple of
representations and then Save State.

However I also get an error "colorinfo: category: couldn't find category
element"

Below is the .vmd file created. I looks as if VMD has a problem in
assigning the color to Element Lu .....

I was almost never using the Save State option in VMD since I am using
tcl scripting for almost every task .. but for beginners is a very good
option ... ...

Does anybody know what could be wrong here ?

Thanks
vlad

#!/usr/local/bin/vmd
# VMD script written by save_state $Revision: 1.41 $
# VMD version: 1.8.6
set viewplist {}
set fixedlist {}
proc vmdrestoremymaterials {} {
  set mlist { Opaque Transparent BrushedMetal Diffuse Ghost Glass1
Glass2 Glossy HardPlastic MetallicPastel Steel Translucent }
  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
  material change ambient Translucent 0.000000
  material change specular Translucent 0.600000
  material change diffuse Translucent 0.700000
  material change shininess Translucent 0.300000
  material change opacity Translucent 0.800000
}
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
mol new /home/cojocavd/P450/Structures/1AKD.pdb type pdb first 0 last -1
step 1 filebonds 1 autobonds 1 waitfor all
mol delrep 0 top
mol representation NewCartoon 0.300000 6.000000 4.100000 0
mol color Structure
mol selection {all}
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 representation Licorice 0.300000 10.000000 10.000000
mol color ResName
mol selection {resname PHE TYR TRP}
mol material Opaque
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 1AKD.pdb
set viewpoints([molinfo top]) {{{1.000000 0.000000 0.000000 -15.857541}
{0.000000 1.000000 0.000000 -24.148613} {0.000000 0.000000 1.000000
-13.321608} {0.000000 0.000000 0.000000 1.000000}} {{-0.236305 0.968102
-0.083224 0.000000} {0.941559 0.249297 0.226507 0.000000} {0.240032
-0.024836 -0.970438 0.000000} {0.000000 0.000000 0.000000 1.000000}}
{{0.054459 0.000000 0.000000 0.000000} {0.000000 0.054459 0.000000
0.000000} {0.000000 0.000000 0.054459 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 {BackgroundTop} black}
    {color Display {BackgroundBot} blue2}
    {color Display {FPS} white}
    {color Name {F} green}
    {color Name {K} white}
    {color Type {F} green}
    {color Type {K} 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} 

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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