Hi Vincent,
in that case you would not use "combine" - just use the File... Save dialog, PDB format, choose all of the models you want in the file, specify filename.  Or, use the "save" command, e.g.

save blah.pdb models #1-3

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>

I hope this helps,
Elaine
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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 Apr 17, 2025, at 2:20 AM, Vincent CHAPTAL via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, 

using "combine #1-3" with 3 models having chain A only, it changes the chain Id to B and C for models #2-3, as described in the doc.

Is it possible to combine PDBs as a multimodel PDB, seperated by MODEL keywords in the PDB file? 

Thank you.
Vincent