VMD-L Mailing List

From: Hoch,Jeffrey (hoch_at_uchc.edu)
Date: Thu Feb 19 2004 - 06:40:59 CST

Colleagues:

I created a "blank" molecule and fixed it, to serve as a canvas for drawing fixed labels.
However when I try to script the process I encounter errors creating the blank molecule.
Curiously, when I "log" the process, the "mol new" command gets translated to "mol rename",
and the log file doesn't "play" properly:

# VMD for MACOSX, version 1.8.2 (December 4, 2003)
# Log file 'junk.log', created by user jeffhoch
menu files off
menu files on
animate style Loop
display resetview
mol new {/Users/jeffhoch/mosart/ls3-1.pdb} type {pdb} first 0 last -1 step 1 waitfor 1
animate style Loop
menu files off
menu graphics off
menu graphics on
mol modstyle 0 0 Cartoon 2.100000 12.000000 5.000000
menu graphics off
animate style Loop
mol rename 1 {molecule1}
mol fix 1
# VMD for MACOSX, version 1.8.2 (December 4, 2003)
# end of log file.

I've also encountered difficulty scripting the "wait" command: it works fine when entered
into the terminal window interactively, but gets ignored when included in a script.

As is obvious from the log file, I am using version 1.8.2 on Mac OSX (10.2.8).

Suggestions?

Yours,

Jeff Hoch
University of Connecticut Health Center