VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Jul 16 2010 - 13:09:09 CDT

ah, of course. Thanks to both of you for all the ideas. It seems like
disabling the bond warning and padding with dummy atoms is the simplest
solution...I can easily modify my script that writes the trajectory to pad
each snapshot with dummy atoms.

E

On Fri, Jul 16, 2010 at 12:05 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Jul 16, 2010 at 1:34 PM, Edward Lyman <edward.lyman_at_gmail.com>
> wrote:
> > 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.
>
> at the moment you would have to do that manually.
> using something like this (untested):
>
> set nm [molinfo num]
> for {set i 0} {$i < $nm} {incr i} {mol off $i}
>
> for {set i 0} {$i < $nm} {incr i} {
> mol on $i
> display update
> display update ui
> render snapshot [format "frame-%d.tga" $i]
> mol off $i
> }
>
> ...and then use whatever is needed to make a
> movie out of those files.
>
> cheers,
> axel.
>
> >
> > 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
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>