VMD Preference 設定

# 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

http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node197.html

https://danlimerick.wordpress.com/2011/07/11/git-for-windows-tip-setting-home-and-the-startup-directory/

# 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
```