[chimerax-users] Smooth MD trajectory during moovie making

Thu Jan 12 08:01:20 PST 2023

Right, thank you very much Elaine! 😘
Enrico

Il giorno gio 12 gen 2023 alle ore 16:55 Elaine Meng <meng at cgl.ucsf.edu> ha
scritto:

> I don't know of any specific options.  However, if you are recording a
> movie file (e.g. mp4, quicktime, etc.) it will play back at whatever frame
> rate you specified when encoding the movie.  It may be much faster than
> when you actually recorded the movie, because when you use trajectory
> playback tool in ChimeraX (or Chimera) it has to calculate a new surface
> for each set of coordinates.  When you play back a movie file it does not
> need to recalculate surface, it just shows a series of images that you
> saved earlier.
> I hope this helps,
> Elaine
>
>
> > On Jan 12, 2023, at 5:55 AM, Enrico Martinez via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > 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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