That was very helpful, THANKS!

I just experimented and

delete #1 & ~ #1/B:1101@MG #1/A works

delete #1 & ~ #1/B:1101@MG ~#1/A does not work.

This command is similar to ones in pymol, but the NOT in chimera seems easier to use than in pymol.

I am still getting used to the order of the terms in chimera. One often does not need OR. Is there a link that explains the order of terms and the algebra? Is it meant to be more like how you would say it in a sentence?

- Tim

Timothy A. Springer, Ph.D.

Latham Family Professor, Harvard Medical School and Boston Children's Hospital

Founder, Institute for Protein Innovation

On Tue, Jan 27, 2026 at 8:10 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Tim,
Your question about "cd" in scripts was already answered, as well as how to stay in that directory. Please scroll down to see the bottom two responses in this thread:

<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/PFKUPP5LEWSZF4QEQIBCP4CG5WQGZATS/#XRURDVRE7WFPDMRBZZSFTJVEHMRHTRT5>

As for "combine," it combines the entire models. However, you can delete atoms from a model before combining (or saving it, for that matter), e.g.

select #1/B:1101@MG
delete #1 & ~sel

where the second says to delete #1 but not the selected part...or just doing that all in one command

delete #1 & ~ #1/B:1101@MG

I hope this helps,
Elaine

> On Jan 27, 2026, at 4:53 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> 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