Hi Enrico,

ChimeraX's PDB reader has no ability to skip MODELs in a multi-MODEL file.  So you would have to read the entire file into ChimeraX, but then with the help of a small bit of Python code you could write out your reduced PDB file.  The procedure would be:

1) Open the 3000-MODEL PDB file.

2) Run the following Python code:

s = session.models[0]

import numpy

s.add_coordsets(numpy.array([s.coordset(i).xyzs for i in s.coordset_ids[::5]]))

You would put the above code (but not indented) into a file with a ".py" suffix and open it in ChimeraX to run it.

3) Use the "save" command (with "allCoordsets true") to save the resulting 600-MODEL PDB file.

For convenience, I've attached a file with the Python code in it.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Oct 5, 2024, at 6:02 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimera-X users!

I am dealing with the visualization of a trajectory provided as the multi-model pdb contanained 3000 frames in multi-model format.

How can I extract every 5th frame from a multi-model PDB file and save the reduced set of frames into a new PDB file, such that the new file contains five times fewer frames ?

I've tried to do it like I did with the netcdf files but it does not work

open ./my.pdb structureModel #1 step 5

Many thanks in advance

Enriico

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