VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 09 2006 - 17:08:46 CST

Hi Sergey,
  At the moment, there's not a built-in feature in the VMD movie maker
plugin to allow you to make movies by animating different structures, which
is a limitation that follows the general VMD assumption that animated
structures have a constant number of atoms. However, that said, it is
possible to make such an animation in VMD, but you'll need to edit one
of the trajectory movie scripts so it generates one frame for each of the
different structures you have loaded:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_movie/

The general idea is the same as the script above, but instead of stepping
through trajectory frames, you'll be stepping through loaded molecules.
Each of your different structures will have to be in a different molecule,
so what you'll do is load all of them up independently, but in the
right order (lots of calls to 'mol new'). Once loaded, you'll need to
change that movie script so that it loops over all molecule IDs that are
loaded, first setting them all hidden with "mol off N" where N is the
molecule ID. Once they are off, then you will loop through them again,
but this time you'll turn each mol on, one at a time, take your snapshot
image, and then turn them back off again before proceeding to the next one.

Let us know if you need more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 05, 2006 at 01:19:38PM +0300, Sergey Krishtal wrote:
> Dear VMD users,
>
> Happy New Year! May the use of VMD in your research be easier this year! :-)
>
> I'm trying to create a movie from multiple pdb files with VMD Movie Maker. My problem is that the number of atoms in pdb files differs from each other and therefore VMD reads in only the first frame and gives a message about incorrect number of atoms in following ones.
>
> I would be grateful for any help.
>
>
> Best regards,
>
> Sergey Krishtal 

-- 
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: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078