Hi Tim,
Option "models" means the model containing those atoms:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>

To save part of a model you would need to do something else like select those atoms and then use option "selectedOnly true" (see link above for full description of that and other options relevant to PDB format). 

Also since your filename ends in .pdb I don't think you need the "format pdb" part; it's guessed from the filename suffix.

I hope this helps,
Elaine
-----
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 Jan 27, 2026, at 4:34 PM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> What am I doing wrong?
> save midas.pdb format pdb models #1/B:1101@MG
> saves the entire #1 structure rather than the single atom.
> I have a similar problem using combine.
>
> I issue a cd command in .cxc files. But at some point during sessions, the directory switches to my home directory. I have to frequently issue the cd command.
>
> - Tim
> Timothy A. Springer, Ph.D.
> Latham Family Professor, Harvard Medical School and Boston Children's Hospital
> Founder, Institute for Protein Innovation