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