From: Eric Smoll (
Date: Mon Dec 15 2014 - 14:20:04 CST

Hello VMD users,

I am trying to build a script for a workflow that I can carry out
completely with the GUI. I used the "Log Tcl commands to file" setting but
running the script with

vmd -e script.tcl

results in a few errors:

"illegal molecule specification '1'"
"illegal molecule specification '2'"
"illegal molecule specification '3'"

The scene is visible in the OpenGL window but not entirely correct. I have
a scene where I load 4 files with different molecule id's. Three molecule
id's have 1 representation, and one has 4 representations.

The GUI produced the file. I don't understand why it is not working. Any
assistance would be greatly appreciated. I am running version 1.9.1 on