VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Jul 16 2010 - 12:34:06 CDT

Hi John,

>draw the points as graphics objects with a script, with
>each frame in a different molecule

ok, so i create a series of different molecules using maybe 'mol new' each
time. into each molecule I draw the set of points for one frame.

>From there, you would animate
the movie using the multimolanim plugin.

ok, I found some brief web documentation for multimolanim, and found the gui
interface. but i can't find doc on how to store the movie that you can step
through with the gui.

Thx,
E

On Fri, Jul 16, 2010 at 11:23 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Edward,
> To accomplish what you have in mind, the easiest method would
> be to draw the points as graphics objects with a script, with
> each frame in a different molecule. From there, you would animate
> the movie using the multimolanim plugin. This would get you past
> the issue with varying particle counts, and treating the points as
> atoms, etc. Let me know if you need more guidance to get it going.
> Ultimately I intend to provide a means of rendering trajectories
> of arbitrary particle systems alongside normal molecules in VMD, but
> at present the method I describe above is the only thing that's currently
> feasible.
>
> Cheers,
> John Stone
>
>
>
> On Fri, Jul 16, 2010 at 10:54:47AM -0600, Edward Lyman wrote:
> > Hi all,
> >
> > I have a trajectory, but it is not a trajectory of a molecular system.
> > Rather it is a trajectory of a bunch of points in a plane that are
> > projections of the SASA of a molecular system. I have them stored in
> xyz
> > format, but each frame in my trajectory naturally has a different
> number
> > of points. Also, when I attempt to naively load the entire trajectory
> into
> > vmd, it fails on the second frame with lots of errors about too manty
> > bonds, as it tries to connect this points into a molecule.
> >
> > Is there a simple way to load a stack of, say, 200 snapshots of my
> points
> > and then stack them into an animation? All the scripts I see on the
> > website seem to work only for a trajectory that has the same number of
> > points in each frame.
> >
> > Thx,
> > Ed
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>