TCL script for VMD to generate primary or secondary structure.

# Set molnum to what VMD will make the next loaded molecule.
# If you've just started VMD and haven't loaded any molecules yet,
# then set this to one.
set molnum 23

# What we're doing here is setting up to run this over all the .coor
# files produced by a NAMD run.  In this case, the files we want 
# models (geometry) for are named 1ACC001.(timestep).coor.  Note
# that these files have to be in the current directory.
#
# Then, in the "for" loop, we generate two geometry files.  The first
# is a VRML file with the CPK geometry in it, and the second is an STL
# file with the secondary structure geometry in it.
#
for {set i 300} { $i <= 12000} { incr i 300} {
	# load the molecule and clear the default representation
	mol load pdb "1ACC001.$i.coor"
	mol delrep 0 $molnum

	# use these commands to setup the scene
	mol rep CPK
	mol color Type
	mol addrep $molnum

	# dump the file	
	render VRML-1 "CPK/1ACC.CPK.$i.stl"
	#	render PostScript "CPK/1ACC.CPK.$i.ps"

	# clear the representation
	mol delrep 0 $molnum	

	# use these commands to setup the scene
	mol rep Cartoon
	mol color Structure
	mol addrep $molnum

	# dump the file	
	render STL "SEC/1ACC.SEC.$i.stl"
	#	render PostScript "SEC/1ACC.SEC.$i.ps"

	# clear the molecule
	mol delete $molnum

	# setup for the next molecule
	incr molnum 1
}