From: John Stone (
Date: Tue Jul 20 2010 - 10:39:53 CDT


On Mon, Jul 19, 2010 at 01:10:16PM -0400, Ian Stokes-Rees wrote:
> 3 quick points/questions regarding VMD:
> 1. After rendering a movie with VMD (see parallel post on namd-l), I was
> unable to run the RMSD Traj Tool. Every attempt to do so resulted in the
> error:
> If I quit VMD, reloaded the structure, reloaded the frames, it would work
> OK. My best guess is that the movie renderer modifies the data in a way
> that stops the RMSD Traj Tool from working.

Most likely there is a bug in the behavior of the RMSDTT
plugin as related to the "current" trajectory frame or some
other global state, when other plugins update the active
frame, change the "top" molecule, or similar state changes.

I'll contact the author of RMSDTT, but he's on vacation for several
days currently (already had an email sent to him on an unrelated topic).

> 2. Is it possible to add a time index to each frame in the rendered
> movie? This would make it much easier to communicate with collaborators
> and colleagues on specific behavior at specific time points. A frame
> index may also be useful.

See Axel's excellent tutorial, which includes this and many other
useful examples:

I've also attached a trivial script that does this, you'll
want to edit it and customize it for your own purposes.

> 3. If I accidentally enter a directory name and try loading it, VMD
> crashes.

Can you be more specific? How do you try to load it, and on what
OS platform do you experience this behavior?

  John Stone

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078