From: Alison Grinthal (
Date: Fri Jun 19 2009 - 09:45:28 CDT

I'm having a minor issue and would like to know if anyone knows the
basis for it: for two coordinate files taken from the same trajectory and
loaded as separate molecules, if I try to align them using the rmsd
plugin, using "protein", I get a message saying "error: measure fit:
selections must have the same number of atoms". They do, and vmd thinks so
too based on the "VMD main" window". If I specify all the residues rather
than saying protein, it works fine.

This would be dealable, except I'm trying to use the coloring.tcl script
from the vmd tutorial file and that seems to be having a related problem
- it does a lot of the calculations and then stops at a number and says
"syntax error in expression "28.1843643188 - ": premature end of
expression" and the coloring turns out completely uniform. In this case,
changing the selection from protein to residues in the coloring script
doesn't help. The problems seems to go together - for two crd files that
don't give the "same number of atoms" message with alignment, the
coloring also works fine.

Does anyone know what could be causing this or how to get around it in the
coloring script? Thanks.