VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 12 2007 - 16:14:14 CDT

Carlos,
  You could try to use RMS alignment on a group of say 5 atoms, and
align all of your frames to a reference frame. That could likely
accomplish what you have in mind. Otherwise, you could transform
the molecule so a specific atom is at the origin, and then apply
rotations to bring one other atom along the X axis, and a third
into the yz plane, or something along these lines. You just need to be
able to construct a alignment coordinate frame and apply transformations
to get all frames to the same coordinate system. There are lots of ways
of accomplishing this. If you need help applying transformations, see
the atom selection "moveby" examples in the VMD User's Guide and
the tutorials.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 12, 2007 at 12:44:45PM -0400, carlos_at_avalon.umaryland.edu wrote:
>
> Hello, I have run various QM torsion scans and have extracted the final
> coordinates to xyz format. I would like to visualize (and produce a movie)
> of the scan in VMD. Unfortunately for each scan I have a xyz file, and the
> coordinates vary for each, so I do not get a clean view of the torsion
> scan, without the molecule flipping. I would like to see if one can fix the
> position of say two atoms, or a given atom, and have the molecule rotate,
> but maintain the selected atom always in that place (in the screen) and
> with the general orientation. I hope this makes sense.
>
> Thanks,
>
> Carlos A. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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