[chimerax-users] Smooth MD trajectory during moovie making

[Elaine Meng]

Hello,
There is a python script available from our website for ChimeraX trajectory smoothing, see this recent post:

<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-January/004741.html>

You can play trajectories with the ChimeraX "coordset" command.  However,  I don't know how this script would work together with the Molecular Dynamics Viewer GUI plugin (developed by 3rd party and available from the Toolshed). 

If it does not work directly, you may need to first run the python script, then save the smoothed trajectory as multimodel PDB with "save" command option "allCoordsets true"...
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>

... then use Molecular Dynamics Viewer to view the trajectory from the new PDB you just saved.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 6, 2023, at 8:39 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimera-X users!
> I am trying to make a movie using MD trajectory (in multi-model pdb file) by means of the Molecular Dynamics Viewer (v 1.2). is it possible to introduce smooth effects on the snapshots transition in the same way like it could be done via V*D ?
> Many thanks in advance
> Cheers
> Enrico