VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 14 2005 - 15:55:29 CDT

Jerry,
  Internally VMD uses cartesian coordinates for everything since this
greatly accelerates the graphics operations it performs when displaying
trajectories and large structures. At present there's not a convenient
way to alter the structure based on interpolation of internal coordinates,
though it should be possible to do this with some scripting. If you're
interested in doing operations like this, I can put you in touch with
Jan Saam who has done a significant amount of this sort of thing in the
process of his ongoing work on structure building plugins for VMD.
Let me know if you want to get into that further and I can hook you
up with a few people that are doing stuff that may be useful to you.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 13, 2005 at 11:21:32AM -0400, Jerry Parks wrote:
> How difficult would it be to generate a linear interpolation from one
> conformation to another in internal coordinates and then write out the
> coordinate snapshots? Such a script would be very useful to me. Sometimes
> cartesian interpolations just don't make physical sense.
>
> Thanks,
> Jerry Parks
>
> -----------------------------------------------------------------------
> Hi,
> If I understand correctly, what you're asking for is a script
> that will linearly interpolate the atom coordinates between two
> configurations of the same molecule? If I've misunderstood and
> you actually have more than two sets of coordinates (a trajectory for example)
> then you can use the Extensions->Visualization->Movie Maker tool to
> make trajectory animations of your simulation. If you indeed are
> asking for a script that does linear interpolation of atom coordinates,
> I don't have such a script handy but it would be easy to write if
> that's what you're actually after.
>
> John
>
> On Wed, Oct 12, 2005 at 01:58:55PM -0400, Mingliang Tan wrote:
> > Dear all,
> >
> > I would like to know how to show a movie from one static configuration
> > (pdb file available) of a protein to another (pdb file available too),
> > i.e., is there any way to have a movie showing the intermediate
> > structures in VMD?
> >
> > Thank you very much in advance,
> >
> > Mingliang
>
> --
> 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 

-- 
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