From: Axel Kohlmeyer (
Date: Fri Jun 19 2009 - 10:56:09 CDT


On Fri, 2009-06-19 at 10:45 -0400, Alison Grinthal wrote:
> 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.

that sounds like the files don't have identical residue or atom
names and thus the protein selection matches a different number
of atoms. you can check this easily on the command line , by creating
two selection and then querying them for the atom index and comparing
those. the ones that are in one selection, but not the other are
obviously the culprit.

without actually seeing the files, it is difficult to give any
advice beyond that.

> 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.

impossible to tell without an example to reproduce this.


Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.