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

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