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
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
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/...> 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
Thanks. How do I fix this: 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 On Tue, Jan 27, 2026 at 7:53 PM Elaine Meng <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> 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
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> 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
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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/...
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
In your second command, I think you're missing the "&" before the second "~" (... think "and not") Here's the documentation on combination symbols in command-line specification: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#combinations> The union may or may not be needed depending on the command and its context... but you can always try adding it or removing it if your first attempt doesn't seem to work. Elaine
On Jan 27, 2026, at 6:00 PM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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/...>
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
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Elaine Meng -
Eric Pettersen -
Timothy Springer