[chimerax-users] Smooth MD trajectory during moovie making

[Enrico Martinez]

Thank you very much Elaine!
In fact I've already tried this script directly with the Molecular Dynamics
Viewer GUI but I did not notice any differences in the smoothness.

I have also tried to load the ensemble of multi-pdb snapshots directly in
the Chimera-X in order that I could apply the python script on it, BUT it
seems that Chimera-X could not handle a big number of the snapshot in the
case of a long trajectory...


Il giorno sab 7 gen 2023 alle ore 00:58 Elaine Meng <meng at cgl.ucsf.edu> ha
scritto:

> 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
>
>
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