VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 04 2007 - 14:41:21 CDT

Hi,
  The VMD saved state feature only saves the manipulations
within VMD, and doesn't affect the atomic coordinate or trajectory
data loaded from the original files. If you want to align the frames
and reload the already aligned data next time, you'll need to save
it out to a new trajectory file using the File->Save Coordinates
menu. If you have an existing VMD saved state file based on the
unaligned trajectory, you can simply edit the text file and replace
the filename of the original unaligned trajectory with the name
of the aligned trajectory. Alternately, if you know that you're
going to do this sort of thing from the outset, you can rename the
original and new trajectories and not have to edit the saved state
file.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 04, 2007 at 11:56:36AM -0400, Stern, Julie wrote:
> When I do a load state to bring in previously saved trajectories, I notice that alignments are
> no longer saved. Is there anything I can do to save a current alignment into the save state request?
> Thanks for any suggestions. 

-- 
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