VMD-L Mailing List

From: Paul Hubbard (phubbard_at_post.its.mcw.edu)
Date: Tue Apr 09 2002 - 15:09:40 CDT

Hello,

Thanks for the reponses. I have been thinking, if I interpolate the 2 molecules, the
correponding atoms would move in a straight line. This would be bad since they
actually move in arc (i.e., torsion about 2 bonds). I would like all bond lengths
(and most bond angles) fixed. If you could tell me what commands I need for
interpolation about multiple torsion angles, and some poniters/example scripts, that
would be great. I can send parts of the 2 PDB files if required.

Thanks

P.S: Just in-case there's a misundertanding, here's a similar example of what I'm
trying to do:
Torsion of ATP about the beta-gamma pyrophosphate linkage, such that the adenosine
moiety rotates about the gamma phosphate.

Thanks again

AGS

Justin Gullingsrud wrote:

> 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 

--
Paul Hubbard
Dept. of Biochemistry
Medical College of Wisconsin
Phone: 414-456 4305
Fax: 414-456 6510
URL: iris9.biochem.mcw.edu