You could just try these commands faster than to ask me, but yes, "coordset" is how you play an atomic trajectory, whether from input files or from morphing, etc. as described in the "trajectories" help:

<https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html>

I'm not aware of any specific netcdf limitations compared to other formats.

Elaine


> On Mar 7, 2024, at 9:28 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
>
> Okay, thank you very much Elaine !
>
> So basically I could load my netcdf trajectory using the following commands:
> open ./perfetto.pdb
> open ./stripped.nc structureModel #1
>
> This loaded trajectory VERY fast compared to the multiple pdb method.
>
> Do we have any limitations working with the netcdf trajectories (compared to multiple pdb) ?
> Does the coordset command work during recording movies e.g.
>
> movie record size 3840,2160
> # play movie from beginning to the end
> coordset #1 250,1250,1
> wait 1000
>
>
> I also tried to smooth the trajectory using smooth_md.py script that always works fine with the multiple PDB trajectory and got a crash (probably because of too many frames in the loaded trajectory ... )
>
> Many thanks in advance !
>
> Enrico
>
> Il giorno gio 7 mar 2024 alle ore 17:09 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
> As explained in the help,
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>
>
> ... for loading a netcdf trajectory you can either
>
> (1) open the netcdf file and a psf file in the same open command
>
> (2) ... or if you don't have a psf file, first you open a structure (like a single PDB) that has the correct topology and then in a second open command, you open the netcdf file specifying the already-open model with the "structureModel" option
>
> See the "open" help page for examples of the commands to use in either of these situations.  The examples show opening a trr file or a dcd file instead of netcdf, but it would be the same situation for netcdf.
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options>
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Resource for Biocomputing, Visualization, and Informatics
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Mar 7, 2024, at 2:30 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
> >
> > Right, thank you very much Eric !
> >
> > Could you please precise how I could load properly the netcdf trajectory in chimerax in the same way like i did it with multiframe pdb using
> > open ./my_trajectory.pdb coordset true
> >
> > Do I need to load at the same time a pdb file (with 1 snapshot) and the netcdf (.nc) file with the frames ? Will the coordset option be mandatory for such case?
> >
> > Many thanks in advance
> >
> > Enrico
>