VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jul 16 2010 - 13:05:49 CDT

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/      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.