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