VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 13:40:07 CDT

Hi,
  The VMD saved state file only saves the viewing orientation of
the molecule. Due to the way the orientation matrices are updated
when the structure is loaded by the saved state script, the coordinate
axes will not necessarily remain in sync with the displayed structure(s),
since individual structures can be transformed differently. If you
reset the view however (e.g. Display->reset view), the axes will be
re-synced with the orientations of all of your structures.

If you want to change the actual atom coordinates, you must do this
using the Mouse->Move submenu items, atom selections, or other scripting
commands. If you change the actual atom coordinates and want them
reloaded, you will indeed need to save the structure out using the
save coordinates menu item. If you want the same saved state to load
the newly updated coordinates, you'll either have to save the coordinates
overwriting the original input file(s) or you'll need to edit the saved
state script to load the newly written coordinate files rather than the
original ones.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 14, 2007 at 01:21:53PM -0400, Subramanian Vaitheeswaran wrote:
> When I open a saved state (*.vmd file) for a molecule, the display opens correctly with the saved orientation of the molecule, but with the z-axis pointing directly out of the screen. Does a saved state also save the rotated coordinates or only the viewing angle? I thought it is the latter, but then why are the coord axes rotated?
>
> How can I save the rotated coords? I tried "Save coordinates" from the Main menu, but that only saves the original coords.
>
> thanks,
> Vaithee 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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