You need to select the atom first with: sel #1/B:1101@MG and then save the PDB with: save midas.pdb selectedOnly true --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 27, 2026, at 5:42 PM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, For each command, a pdb file is saved, but it only has the header from #1 and not any coordinates.
save midas.pdb #1/B:1101@MG selectedOnly true save midasA.pdb #1/B:1101@MG #1/A selectedOnly true - 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 7:53 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@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 <mailto: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
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