VMD-L Mailing List

From: dwds gerge (mac140211_at_hotmail.com)
Date: Tue Sep 13 2011 - 12:06:10 CDT

Hi,
I have a little script attached that is supposed to simply load and render a molecule. 
However,

if the script below is copied and pasted into the VMD terminal, the cartoon representation of all protein residues changes to 'turn'. If the script is called from the command line using vmd -e script.vmd, it will work as expected.
If a for loop is build around the script, that is, if the the first line of the script is replaced by the following and if a closing bracket is appended at the last line,
foreach molecule [glob *.pdb] {...}
then all protein residues will be shown as 'turn' again, loosing secondary structure.

This is the script:
set molecule 1.pdb
mol new $moleculerotate x by -90rotate y by 135scale by 1.7translate by 0 -0.3 0
# representation of moleculemol modstyle 0 top Cartoon 2.100000 12.000000 5.000000mol modcolor 0 top ColorID 2mol modmaterial 0 top Transparentmol modselect 0 top chain A and not resid 121mol addrep topmol modselect 1 top chain B and not resid 121mol modstyle 1 top Cartoon 2.100000 12.000000 5.000000mol modcolor 1 top ColorID 2mol modmaterial 1 top Transparentmol addrep topmol modselect 2 top chain C and not resid 121mol modstyle 2 top Cartoon 2.100000 12.000000 5.000000mol modcolor 2 top ColorID 2mol modmaterial 2 top Transparentmol addrep topmol modselect 3 top chain D and not resid 121mol modstyle 3 top Cartoon 2.100000 12.000000 5.000000mol modcolor 3 top ColorID 2mol modmaterial 3 top Transparentmol showrep top 0 0
# rendering of moleculesource [file rootname $molecule].vmd
set sel [atomselect top {resid 121}]$sel set structure turn
set sel [atomselect top {resid 248 to 251}]$sel set structure turn
render TachyonInternal [file rootname $molecule].tga
# empty memory and start over with next moleculemol delete top

I'm using VMD1.9 on MacOSX 10.6.8. Is there are workaround?

Best,
Matthias