我使用的VMD初始化脚本

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#cr
#cr            (C) Copyright 1995-2007 The Board of Trustees of the
#cr                        University of Illinois
#cr                         All Rights Reserved
#cr
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# RCS INFORMATION:
#
#       $RCSfile: .vmdrc,v $
#       $Author: johns $        $Locker:  $                $State: Exp $
#       $Revision: 1.9 $      $Date: 2007/01/12 20:12:44 $
#
############################################################################
# DESCRIPTION:
#
# VMD startup script.  The commands here are executed as soon as VMD starts up
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# turn on lights 0 and 1
light 0 on
light 1 on
light 2 off
light 3 off

# position the stage and axes
axes location lowerleft
stage location off

# position and turn on menus
menu main     move 5   225
menu display  move 395 30
menu graphics move 395 500
menu color    move 125 225
menu files    move 125 325
menu labels   move 125 525
menu render   move 125 525

menu main      on
#menu display  on
#menu graphics on
#menu color    on
#menu labels   on
#menu render   on
#menu files    on

# start the scene a-rockin'
# rock y by 1

# User's default values for newly loaded molecules/reps, etc
#  mol default color {colorID 5}
#  mol default style {NewCartoon 0.300000 6.000000 4.100000 0}
#  mol default selection {name CA}
#  mol default material {Transparent}

display projection orthographic
after idle {
	foreach molid [molinfo list] {
		mol delrep 0 $molid

		set sel [atomselect $molid {protein}]
		if {[$sel num]} {
			mol selection {protein}
			mol representation newcartoon
			mol addrep $molid
			mol modcolor 0 $molid structure

			mol selection {protein and (name CA or not backbone)}
			mol representation lines
			mol addrep $molid
			mol modcolor 1 $molid resid
		}

		set sel [atomselect $molid {nucleic}]
		if {[$sel num]} {
			mol selection {nucleic}
			mol representation newribbons
			mol addrep $molid
			mol modcolor 0 $molid resid
		}

		set sel [atomselect $molid {water}]
		set num [$sel num]
		if {$num} {
			mol selection {water}
			if {$num <900 } {
				mol representation Lines
			} else {
				mol representation Points
			}
			mol addrep $molid
		}

		set txt "not(numbonds=0 or water or resname DA or resname DG or resname DT or resname DC or resname ALA or resname ARG or resname ASN or resname ASP or resname CYS or resname GLN or resname GLU or resname GLY or resname HIS or resname HOH or resname ILE or resname LEU or resname LYS or resname MET or resname PHE or resname PRO or resname SER or resname THR or resname TRP or resname TYR or resname VAL)"
		set sel [atomselect $molid "$txt"]
		set num [$sel num]
		if {$num} {
			if {$num <500 } {
				mol representation CPK
			} else {
				mol representation Lines
			}
			mol selection "$txt"
			mol addrep $molid
		}

		set txt "numbonds=0"
		set sel [atomselect $molid "$txt"]
		if {[$sel num]} {
			mol selection "$txt"
			mol representation VDW
			mol addrep $molid
		}
	}
	pbc box
}