VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Tue Apr 09 2002 - 14:36:36 CDT

Here's another suggestion along those lines: rather than interpolating
the coordinates, you could interpolate the phi/psi angles. I haven't
actually tried this myself, but I'm curious and would be willing to help
you write a script if you need it.

Justin

On Tue, Apr 09, 2002 at 02:24:36PM -0500, John Stone wrote:
>
> Dear Paul,
> Yes, you should be able to use the atomselect "get" and "set"
> methods to manipulate the atom coordinates of a structure, to create
> any interpolation you like between two coordinate frames. You could
> load the coordinate frames in multiple times to give you a trajectory
> of the number of frames you want, then use the atomselect commands to
> modify the coordinates for the interpolated frames. Once they are
> all setup the way you want, you could write out the trajectory as
> a file (to make future re-loading or modifications easier/faster)
> and you could then use the vmd movie making scripts to process this
> animation for you. Here's an example of a script that does
> processing along these lines:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_smooth/
>
> Let us know if you have more questions,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Apr 09, 2002 at 02:12:49PM -0500, Paul Hubbard wrote:
> > Hi,
> >
> > I would like to make a short animation where a protein ligand undergoes
> > large torsion about 2 bonds. I have the before and after crystal
> > structures, but would like the inbetween ones. Strictly speaking, I'm
> > not trying to do a simulation, just interpolation. I was wondering if
> > VMD can do this - if so, could someone please give me some pointers as
> > to how to do this.
> >
> > Thanks
> >
> > AGS
> >
> > --
> > Paul Hubbard
> > Dept. of Biochemistry
> > Medical College of Wisconsin
> > Phone: 414-456 4305
> > Fax: 414-456 6510
> > URL: iris9.biochem.mcw.edu
> >
> >
>
> --
> 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 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D