The following are some small Tcl scripts for VMD, a program for visualizing molecular dynamics. These scripts demo some graphics and show the conformational change in hemoglobin when the heme is bound. The scripting syntax for VMD is poorly documented, so these scripts may be of use to people trying to get their scripts working.

Start VMD and do Extensions->Tk Console

In the console, CD to the working folder

Open Graphics->Representations to show graphics info

source 1.tcl

source 2.tcl

source 3.tcl

source 4.tcl

1.tcl

display resetview
display update on
display update ui
mol load pdb 1GZX.pdb
mol modstyle 0 0 NewCartoon
mol modcolor 0 0 Chain

2.tcl

mol selection heme
mol addrep 0
mol modstyle 1 0 licorice
mol modcolor 1 0 element

3.tcl

mol selection "oxygen within 4 of heme"
mol addrep 0
mol showrep 0 0 off
mol modstyle 2 0 VDW
mol modcolor 2 0 element

4.tcl

mol showrep 0 2 off
mol showrep 0 0 on
display resetview
mol selection polar
mol addrep 0
mol modstyle 3 0 dotted
mol modcolor 3 0 conformation

1GZX.pdb
1a3n-aligned.pdb

Screenshot