Dear Eric,

Thank you very much for your kind suggestions!

Actually my goal is to record the movie from the MD trajectory. Could we do it without the MD plugin e.g. using some built-in command of the Chimera-X assuming that I am dealing with a very long trajectory computed by AMBER and saved in multi-pdb format..

BTW I tried to follow the recommendations of Elaine: loading initial trajectory into the ChimeraX as multi-model pdb (it takes 30 minutes! :-) ) then applying the smooth script, saving it as a new PDB and then loading it directly to the MD viewer. So I tried to change the number of averaged snapshots in the script (either 2 or 25) and noticed that in both cases the new PDB was slightly bigger than the original trajectory (20 gb vs 14 gb). However, the results were almost the same regardless of the parameter used in the smooth script.

Many thanks in advance

Yours with thanks

Enrico

Il giorno lun 9 gen 2023 alle ore 19:32 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:

Hi Enrico,
Looking at the MD viewer code, I can see that it holds its own copy of the coordinates instead of storing them with the structure and therefore the script can't find them to do the smoothing. The structure effectively has a single coordinate set that is updated manually by the MD Viewer. Also, MD Viewer only reads/shows heavy atoms (i.e. it ignores hydrogens).
When you read your structure directly into ChimeraX, did you use the "coordsets true" option?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Jan 9, 2023, at 4:00 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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@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@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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