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