[chimerax-users] Smooth MD trajectory during moovie making

[Enrico Martinez]

Thank you very much Elaine ! 😇
Indeed I confirm that the default engine built-in Chimera-X coupled with
the MD smoothing script works much better for trajectory visualization and
movie making.

I also understood that the source of the lags in my case was related to the
initial PDB where I saved also the molecules of solvent (water) which
significantly increased size of each snapshot etc.

BTW would it be worth to try to make a MD movie based on the visualization
of protein surface (in the MD trajectory) instead of its cartoon
representation? Would the smooth script work for this case?
Yours sincerely 😘
Enrico


Il giorno mar 10 gen 2023 alle ore 18:15 Elaine Meng <meng at cgl.ucsf.edu> ha
scritto:

> Hello,
> You do not have to use the plugin from the toolshed to record a movie of
> your trajectory.  You can just use the built-in trajectory viewing options
> described below, and in that case you would also not need to save another
> file after smoothing.
>
> Without the plugin: If you open the trajectory in ChimeraX it will
> automatically show a slider interface with a red "record" button.  If the
> trajectory is in multi-model PDB format, you can open it with the "open"
> command and the "coordset true" option to tell ChimeraX that it is a
> trajectory (instead of showing all the models at once).  Other trajectory
> formats are also possible:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#slider>
>
> Clicking the red record button on the trajectory slider plays it from the
> current position to the end, and then saves it as a movie.  Or instead of
> using the graphical interface, to record a movie you can use a ChimeraX
> command script with the "coordset" command to play back the trajectory (and
> "movie" commands to start recording and stop recording and save a movie
> file).
>
> We talked about recording a trajectory yesterday.  That one was from a
> morph, but once you open your trajectory, it is the same thing:
> <
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-January/004767.html
> >
> <
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-January/004768.html
> >
>
> 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 10, 2023, at 7:25 AM, Enrico Martinez via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > 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 at 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 at 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 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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