VMD 設定
初期画面の各種デフォルトの設定。
Extentions -> Preference
ここでデフォルトの設定を変えて，
[Write Settings to VMDRC]
ユーザーのホームフォルダにvmd.rcができる。
環境変数を編集
Windowsのユーザ環境変数に，
変数： HOME
値： C:\Users\hnishi
を追加。
これで設定完了。
参考
Sample
#
# VMDPrefs Theme File
#
# VMDPrefs was written by:
# Christopher Mayne
# Tajkhorshid Laboratory (http://csbmb.beckman.illinois.edu)
# Beckman Institute for Advanced Science and Technology
# University of Illinois at Urbana-Champaign
#
# VMDPrefs is currently maintained by:
# Christopher Mayne | cmayne2@illinois.edu | http://www.ks.uiuc.edu/~mayne
#
# ------------------------------------------------------------------------------
# WARNING: Do not edit this file by hand!
# VMDPrefs uses a very specific parsing scheme when reading theme files.
# To avoid potentially corrupting the format, please use the GUI to make
# any setting changes and write a new theme file.
# ------------------------------------------------------------------------------
#
after idle {
if { [info exists tk_version] } {
# High-Level Settings
menu main on
# <menus>
# state : active
if { 1 } {
menu main on ; menu main move -478 225
menu graphics off ; menu graphics move 395 500
menu tkcon off
menu files off ; menu files move 125 325
menu apbsrun off
menu autoimd off
menu autoionize off
menu autopsf off
menu bendix off
menu biocorechat off
menu biocorelogin off
menu biocorepubsync off
menu biocoreutil off
menu cggui off
menu chirality_gui off
menu cispeptide_gui off
menu cliptool off
menu clonerep off
menu color off ; menu color move 125 225
menu colorscalebar off
menu contactmap off
menu dataimport off
menu dipwatch off
menu display off ; menu display move 395 30
menu dowser_gui off
menu forcefieldtoolkit off
menu gofrgui off
menu hbonds off
menu heatmapper off
menu ilstools off
menu imd off
menu inorganicbuilder off
menu irspecgui off
menu labels off ; menu labels move 125 525
menu material off
menu mdff_gui off
menu membrane off
menu mergestructs off
menu molefacture off
menu multimolanim off
menu multiseq off
menu multitext off
menu mutator off
menu namdenergy off
menu namdgui off
menu namdplot off
menu nanotube off
menu navfly off
menu navigate off
menu networkview off
menu nmwiz off
menu palettetool off
menu parsefep off
menu pdbtool off
menu plumed off
menu pmepot off
menu propka off
menu qmtool off
menu ramaplot off
menu remote off
menu render off ; menu render move 125 525
menu rmsd off
menu rmsdtt off
menu rmsdvt off
menu ruler off
menu saltbr off
menu save off
menu sequence off
menu solvate off
menu symmetrytool off
menu timeline off
menu tool off
menu vdna off
menu viewchangerender_gui off
menu viewmaster off
menu vmdmovie off
menu vmdprefs off
menu volmap off
}
# </menus>
# <display>
# state : active
if { 1 } {
display reposition 100 1000
display resize 496 474
display projection Orthographic
display depthcue on
display cuemode Exp2
display cuestart 0.50
display cueend 10.00
display cuedensity 0.32
display eyesep 0.07
display focalLength 2.00
display height 6.00
display distance -2.00
display culling off
display fps off
display stereoswap off
display cachemode Off
display rendermode Normal
display shadows off
display ambientocclusion off
display aoambient 0.80
display aodirect 0.30
display stereo "Off"
display nearclip set 0.50
display farclip set 10.00
display backgroundgradient off
axes location LowerLeft
light 0 on
light 1 on
light 2 off
light 3 off
}
# </display>
# <colors>
# state (assign) : active
if { 1 } {
color add item Display Background white
color Display Background white
color add item Display BackgroundTop black
color Display BackgroundTop black
color add item Display BackgroundBot blue2
color Display BackgroundBot blue2
color add item Display Foreground white
color Display Foreground white
color add item Display FPS white
color Display FPS white
color add item Axes X red
color Axes X red
color add item Axes Y green
color Axes Y green
color add item Axes Z blue
color Axes Z blue
color add item Axes Origin cyan
color Axes Origin cyan
color add item Axes Labels white
color Axes Labels white
color add item Name H white
color Name H white
color add item Name O red
color Name O red
color add item Name N blue
color Name N blue
color add item Name C cyan
color Name C cyan
color add item Name S yellow
color Name S yellow
color add item Name P tan
color Name P tan
color add item Name Z silver
color Name Z silver
color add item Name LPA green
color Name LPA green
color add item Name LPB green
color Name LPB green
color add item Type H white
color Type H white
color add item Type O red
color Type O red
color add item Type N blue
color Type N blue
color add item Type C cyan
color Type C cyan
color add item Type S yellow
color Type S yellow
color add item Type P tan
color Type P tan
color add item Type Z silver
color Type Z silver
color add item Type LP green
color Type LP green
color add item Type DRUD pink
color Type DRUD pink
color add item Element X cyan
color Element X cyan
color add item Element Ac ochre
color Element Ac ochre
color add item Element Ag ochre
color Element Ag ochre
color add item Element Al ochre
color Element Al ochre
color add item Element Am ochre
color Element Am ochre
color add item Element Ar ochre
color Element Ar ochre
color add item Element As ochre
color Element As ochre
color add item Element At ochre
color Element At ochre
color add item Element Au ochre
color Element Au ochre
color add item Element B ochre
color Element B ochre
color add item Element Ba ochre
color Element Ba ochre
color add item Element Be ochre
color Element Be ochre
color add item Element Bh ochre
color Element Bh ochre
color add item Element Bi ochre
color Element Bi ochre
color add item Element Bk ochre
color Element Bk ochre
color add item Element Br ochre
color Element Br ochre
color add item Element C cyan
color Element C cyan
color add item Element Ca ochre
color Element Ca ochre
color add item Element Cd ochre
color Element Cd ochre
color add item Element Ce ochre
color Element Ce ochre
color add item Element Cf ochre
color Element Cf ochre
color add item Element Cl ochre
color Element Cl ochre
color add item Element Cm ochre
color Element Cm ochre
color add item Element Co ochre
color Element Co ochre
color add item Element Cr ochre
color Element Cr ochre
color add item Element Cs ochre
color Element Cs ochre
color add item Element Cu ochre
color Element Cu ochre
color add item Element Db ochre
color Element Db ochre
color add item Element Ds ochre
color Element Ds ochre
color add item Element Dy ochre
color Element Dy ochre
color add item Element Er ochre
color Element Er ochre
color add item Element Es ochre
color Element Es ochre
color add item Element Eu ochre
color Element Eu ochre
color add item Element F ochre
color Element F ochre
color add item Element Fe ochre
color Element Fe ochre
color add item Element Fm ochre
color Element Fm ochre
color add item Element Fr ochre
color Element Fr ochre
color add item Element Ga ochre
color Element Ga ochre
color add item Element Gd ochre
color Element Gd ochre
color add item Element Ge ochre
color Element Ge ochre
color add item Element H white
color Element H white
color add item Element He ochre
color Element He ochre
color add item Element Hf ochre
color Element Hf ochre
color add item Element Hg ochre
color Element Hg ochre
color add item Element Ho ochre
color Element Ho ochre
color add item Element Hs ochre
color Element Hs ochre
color add item Element I ochre
color Element I ochre
color add item Element In ochre
color Element In ochre
color add item Element Ir ochre
color Element Ir ochre
color add item Element K ochre
color Element K ochre
color add item Element Kr ochre
color Element Kr ochre
color add item Element La ochre
color Element La ochre
color add item Element Li ochre
color Element Li ochre
color add item Element Lr ochre
color Element Lr ochre
color add item Element Lu ochre
color Element Lu ochre
color add item Element Md ochre
color Element Md ochre
color add item Element Mg ochre
color Element Mg ochre
color add item Element Mn ochre
color Element Mn ochre
color add item Element Mo ochre
color Element Mo ochre
color add item Element Mt ochre
color Element Mt ochre
color add item Element N blue
color Element N blue
color add item Element Na ochre
color Element Na ochre
color add item Element Nb ochre
color Element Nb ochre
color add item Element Nd ochre
color Element Nd ochre
color add item Element Ne ochre
color Element Ne ochre
color add item Element Ni ochre
color Element Ni ochre
color add item Element No ochre
color Element No ochre
color add item Element Np ochre
color Element Np ochre
color add item Element O red
color Element O red
color add item Element Os ochre
color Element Os ochre
color add item Element P tan
color Element P tan
color add item Element Pa ochre
color Element Pa ochre
color add item Element Pb ochre
color Element Pb ochre
color add item Element Pd ochre
color Element Pd ochre
color add item Element Pm ochre
color Element Pm ochre
color add item Element Po ochre
color Element Po ochre
color add item Element Pr ochre
color Element Pr ochre
color add item Element Pt ochre
color Element Pt ochre
color add item Element Pu ochre
color Element Pu ochre
color add item Element Ra ochre
color Element Ra ochre
color add item Element Rb ochre
color Element Rb ochre
color add item Element Re ochre
color Element Re ochre
color add item Element Rf ochre
color Element Rf ochre
color add item Element Rg ochre
color Element Rg ochre
color add item Element Rh ochre
color Element Rh ochre
color add item Element Rn ochre
color Element Rn ochre
color add item Element Ru ochre
color Element Ru ochre
color add item Element S yellow
color Element S yellow
color add item Element Sb ochre
color Element Sb ochre
color add item Element Sc ochre
color Element Sc ochre
color add item Element Se ochre
color Element Se ochre
color add item Element Sg ochre
color Element Sg ochre
color add item Element Si ochre
color Element Si ochre
color add item Element Sm ochre
color Element Sm ochre
color add item Element Sn ochre
color Element Sn ochre
color add item Element Sr ochre
color Element Sr ochre
color add item Element Ta ochre
color Element Ta ochre
color add item Element Tb ochre
color Element Tb ochre
color add item Element Tc ochre
color Element Tc ochre
color add item Element Te ochre
color Element Te ochre
color add item Element Th ochre
color Element Th ochre
color add item Element Ti ochre
color Element Ti ochre
color add item Element Tl ochre
color Element Tl ochre
color add item Element Tm ochre
color Element Tm ochre
color add item Element U ochre
color Element U ochre
color add item Element V ochre
color Element V ochre
color add item Element W ochre
color Element W ochre
color add item Element Xe ochre
color Element Xe ochre
color add item Element Y ochre
color Element Y ochre
color add item Element Yb ochre
color Element Yb ochre
color add item Element Zn silver
color Element Zn silver
color add item Element Zr ochre
color Element Zr ochre
color add item Resname ALA blue
color Resname ALA blue
color add item Resname ARG white
color Resname ARG white
color add item Resname ASN tan
color Resname ASN tan
color add item Resname ASP red
color Resname ASP red
color add item Resname CYS yellow
color Resname CYS yellow
color add item Resname GLY white
color Resname GLY white
color add item Resname GLU pink
color Resname GLU pink
color add item Resname GLN orange
color Resname GLN orange
color add item Resname HIS cyan
color Resname HIS cyan
color add item Resname ILE green
color Resname ILE green
color add item Resname LEU pink
color Resname LEU pink
color add item Resname LYS cyan
color Resname LYS cyan
color add item Resname MET yellow
color Resname MET yellow
color add item Resname PHE purple
color Resname PHE purple
color add item Resname PRO ochre
color Resname PRO ochre
color add item Resname SER yellow
color Resname SER yellow
color add item Resname THR mauve
color Resname THR mauve
color add item Resname TRP silver
color Resname TRP silver
color add item Resname TYR green
color Resname TYR green
color add item Resname VAL tan
color Resname VAL tan
color add item Resname ADE blue
color Resname ADE blue
color add item Resname CYT orange
color Resname CYT orange
color add item Resname GUA yellow
color Resname GUA yellow
color add item Resname THY purple
color Resname THY purple
color add item Resname URA green
color Resname URA green
color add item Resname TIP cyan
color Resname TIP cyan
color add item Resname TIP3 cyan
color Resname TIP3 cyan
color add item Resname WAT cyan
color Resname WAT cyan
color add item Resname SOL cyan
color Resname SOL cyan
color add item Resname H2O cyan
color Resname H2O cyan
color add item Resname LYR purple
color Resname LYR purple
color add item Resname ZN silver
color Resname ZN silver
color add item Resname NA yellow
color Resname NA yellow
color add item Resname CL green
color Resname CL green
color add item Resname HSE cyan
color Resname HSE cyan
color add item Resname HSD cyan
color Resname HSD cyan
color add item Resname HSP cyan
color Resname HSP cyan
color add item Resname CYX yellow
color Resname CYX yellow
color add item Restype Unassigned cyan
color Restype Unassigned cyan
color add item Restype Solvent yellow
color Restype Solvent yellow
color add item Restype Nucleic_Acid purple
color Restype Nucleic_Acid purple
color add item Restype Basic blue
color Restype Basic blue
color add item Restype Acidic red
color Restype Acidic red
color add item Restype Polar green
color Restype Polar green
color add item Restype Nonpolar white
color Restype Nonpolar white
color add item Restype Ion tan
color Restype Ion tan
color add item Chain X blue
color Chain X blue
color add item Segname {} blue
color Segname {} blue
color add item Conformation all blue
color Conformation all blue
color add item Molecule 0 blue
color Molecule 0 blue
color add item Highlight Proback green
color Highlight Proback green
color add item Highlight Nucback yellow
color Highlight Nucback yellow
color add item Highlight Nonback blue
color Highlight Nonback blue
color add item Structure {Alpha Helix} purple
color Structure {Alpha Helix} purple
color add item Structure 3_10_Helix blue
color Structure 3_10_Helix blue
color add item Structure Pi_Helix red
color Structure Pi_Helix red
color add item Structure Extended_Beta yellow
color Structure Extended_Beta yellow
color add item Structure Bridge_Beta tan
color Structure Bridge_Beta tan
color add item Structure Turn cyan
color Structure Turn cyan
color add item Structure Coil white
color Structure Coil white
color add item Surface Grasp gray
color Surface Grasp gray
color add item Labels Atoms green
color Labels Atoms green
color add item Labels Bonds white
color Labels Bonds white
color add item Labels Angles yellow
color Labels Angles yellow
color add item Labels Dihedrals cyan
color Labels Dihedrals cyan
color add item Labels Springs orange
color Labels Springs orange
color add item Stage Even gray
color Stage Even gray
color add item Stage Odd silver
color Stage Odd silver
}
# state (define) : active
if { 1 } {
color change rgb blue 0.000 0.000 1.000
color change rgb red 1.000 0.000 0.000
color change rgb gray 0.350 0.350 0.350
color change rgb orange 1.000 0.500 0.000
color change rgb yellow 1.000 1.000 0.000
color change rgb tan 0.500 0.500 0.200
color change rgb silver 0.600 0.600 0.600
color change rgb green 0.000 1.000 0.000
color change rgb white 1.000 1.000 1.000
color change rgb pink 1.000 0.600 0.600
color change rgb cyan 0.250 0.750 0.750
color change rgb purple 0.650 0.000 0.650
color change rgb lime 0.500 0.900 0.400
color change rgb mauve 0.900 0.400 0.700
color change rgb ochre 0.500 0.300 0.000
color change rgb iceblue 0.500 0.500 0.750
color change rgb black 0.000 0.000 0.000
color change rgb yellow2 0.880 0.970 0.020
color change rgb yellow3 0.550 0.900 0.020
color change rgb green2 0.000 0.900 0.040
color change rgb green3 0.000 0.900 0.500
color change rgb cyan2 0.000 0.880 1.000
color change rgb cyan3 0.000 0.760 1.000
color change rgb blue2 0.020 0.380 0.670
color change rgb blue3 0.010 0.040 0.930
color change rgb violet 0.270 0.000 0.980
color change rgb violet2 0.450 0.000 0.900
color change rgb magenta 0.900 0.000 0.900
color change rgb magenta2 1.000 0.000 0.660
color change rgb red2 0.980 0.000 0.230
color change rgb red3 0.810 0.000 0.000
color change rgb orange2 0.890 0.350 0.000
color change rgb orange3 0.960 0.720 0.000
}
# state (scale) : active
if { 1 } {
color scale method RWB
color scale midpoint 0.50
color scale min 0.10
}
# </colors>
# <representations>
# state : active
if { 1 } {
mol default color Name
mol default material Opaque
mol default style Licorice
mol default selection {all}
}
# </representations>
# <materials>
# state : active
if { 1 } {
set matsVMD [material list]
set matsVMDPREFS {Opaque Transparent BrushedMetal Diffuse Ghost Glass1 Glass2 Glass3 Glossy HardPlastic MetallicPastel Steel Translucent Edgy EdgyShiny EdgyGlass Goodsell AOShiny AOChalky AOEdgy BlownGlass GlassBubble RTChrome}
# deletions
foreach ele $matsVMD { if { [lsearch $matsVMDPREFS $ele] == -1 } { material delete $ele } }
# additions
foreach ele $matsVMDPREFS { if { [lsearch $matsVMD RTChrome] == -1 } { material add $ele } }
# set/change properties
set properties {ambient diffuse specular shininess mirror opacity outline outlinewidth transmode}
foreach ele {
{Opaque 0.000 0.650 0.500 0.534 0.000 1.000 0.000 0.000 0.000}
{Transparent 0.000 0.650 0.500 0.534 0.000 0.300 0.000 0.000 0.000}
{BrushedMetal 0.080 0.390 0.340 0.150 0.000 1.000 0.000 0.000 0.000}
{Diffuse 0.000 0.620 0.000 0.530 0.000 1.000 0.000 0.000 0.000}
{Ghost 0.000 0.000 1.000 0.230 0.000 0.100 0.000 0.000 0.000}
{Glass1 0.000 0.500 0.650 0.530 0.000 0.150 0.000 0.000 0.000}
{Glass2 0.520 0.760 0.220 0.590 0.000 0.680 0.000 0.000 0.000}
{Glass3 0.150 0.250 0.750 0.800 0.000 0.500 0.000 0.000 0.000}
{Glossy 0.000 0.650 1.000 0.880 0.000 1.000 0.000 0.000 0.000}
{HardPlastic 0.000 0.560 0.280 0.690 0.000 1.000 0.000 0.000 0.000}
{MetallicPastel 0.000 0.260 0.550 0.190 0.000 1.000 0.000 0.000 0.000}
{Steel 0.250 0.000 0.380 0.320 0.000 1.000 0.000 0.000 0.000}
{Translucent 0.000 0.700 0.600 0.300 0.000 0.800 0.000 0.000 0.000}
{Edgy 0.000 0.660 0.000 0.750 0.000 1.000 0.620 0.940 0.000}
{EdgyShiny 0.000 0.660 0.960 0.750 0.000 1.000 0.760 0.940 0.000}
{EdgyGlass 0.000 0.660 0.500 0.750 0.000 0.620 0.620 0.940 0.000}
{Goodsell 0.520 1.000 0.000 0.000 0.000 1.000 4.000 0.900 0.000}
{AOShiny 0.000 0.850 0.200 0.530 0.000 1.000 0.000 0.000 0.000}
{AOChalky 0.000 0.850 0.000 0.530 0.000 1.000 0.000 0.000 0.000}
{AOEdgy 0.000 0.900 0.200 0.530 0.000 1.000 0.620 0.930 0.000}
{BlownGlass 0.040 0.340 1.000 1.000 0.000 0.100 0.000 0.000 1.000}
{GlassBubble 0.250 0.340 1.000 1.000 0.000 0.040 0.000 0.000 1.000}
{RTChrome 0.000 0.650 0.500 0.530 0.700 1.000 0.000 0.000 0.000}
} {
set i 1
foreach prop $properties { material change $prop [lindex $ele 0] [lindex $ele $i]; incr i }
unset i
}
}
# </materials>
}
# <custom>
# state : active
if { 1 } {
# <custom entry>
# Description: Pbcbox
pbc box
# </custom entry>
}
# </custom>
}
# End Theme File