[chimerax-users] Smooth MD trajectory during moovie making

Thu Jan 12 05:55:23 PST 2023

Thank you very much, Elaine!
Actually I've already tried to visualize the surface in each snapshot of
the trajectory processed via MD viewer plugin but the calculation of the
surface and its visualization were too slow. So I was wondering if I could
use some options to speed-up this type of the visualizations using direct
trajectory processing implemented in the Chimera-X.
Cheers,
Enrico

Il giorno mer 11 gen 2023 alle ore 18:29 Elaine Meng <meng at cgl.ucsf.edu> ha
scritto:

> It depends what you want to show in your movie.  You could try showing the
> molecular surface before playing the smoothed trajectory, and I don't see a
> reason why it would not work since it will just use the smoothed atomic
> coordinates to calculate the surface at each time.  It might take a little
> longer (just to calculate the surface as compared to ribbon only) but I
> don't know -- just try it and see.
>
> Elaine
>
> > On Jan 11, 2023, at 8:04 AM, Enrico Martinez via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > 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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