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
Il giorno mar 5 mar 2024 alle ore 03:09 Eric Pettersen
Hi Enrico, PDB format, being ASCII, isn’t a particularly efficient format for storing trajectories. Is that really the original format of your data, or are you converting it from some other format? If you had your data in one of the dedicated trajectory formats that ChimeraX supports ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory), then you would be able to specify start and end frames and/or reading every Nth frame. To answer your question directly, ChimeraX’s PDB reader does not support restricting the frames it reads. I’m not strongly motivated to add such controls since PDB trajectory reading will always be inefficient due to its larger file size and the slowness of converting ASCII floating point representations into binary. I’d be more interested in adding support for whatever the native format of your trajectory is, assuming it’s at least somewhat widely used.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 4, 2024, at 6:15 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I have a question regarding the handling of a trajectory saved in multiple-pdb format. Loading such ensemble using dedicated open command typically load all frames at once:
open ./my_trajectory.pdb coordset true
Would it be possible to specify the range of the loaded frames to reduce the time for data loading e.g. i) to load first 3000 frames or ii) to load from 50 to 5000 frames?
Many thanks in advance !
Best wishes,
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/