Hi Tony, (A) Yes, you could do it that way, with two zone selection commands, but you'd have to use "select add" on the second one or else it will simply replace the selection instead of adding to it: select /A & /C :<5.0 select add /C & /A :<5.0 See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html> But then you would still need to use "info residues" to report the selection. (B) If the goal is simply to get a list of the residues, a more direct single-command way is to use "contacts" to find all interchain atomic pairs within that distance and report only at the residue level (assuming you don't want to see all the atom-atom pairs in the results and you only care about the residues): contacts /A restrict /C distanceOnly 5.0 reveal true log true namingStyle residue See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html#options> (optionally with "saveFile" option if you want to write to a text file, not just the Log). This method bypasses selection. Of course, you can also use "select true" if you wanted to select the atom pairs meeting your contact criteria, and then "select up" to promote to whole residues if you wanted the whole residues selected. I like to use "reveal true" to make it clear what interactions were found, but it isn't necessary for writing the list. Both methods (A) and (B) above will use all residues with the specified chain IDs, which sometimes includes waters, ligands, etc. so you want to be aware of that, or combine with the "protein" specification, or delete nonprotein residues before using the commands if you don't want them in the results. I hope this helps, Elaine
On Aug 14, 2025, at 12:06 PM, Anthony Newcombe via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine
Many thanks for the help with the ChimeraX commands, these work great! Just to confirm, if I want residues within 5A distances between chains A and B, I would run:
select /A & /C :<5.0
Then the reverse:
select /C & /A :<5.0
Is this correct?
Thanks again for the help
Tony
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday 11 August 2025 16:35 To: Anthony Newcombe <http://anthony.newcombe@appliedbiopharm.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] ChimeraX support: Alphafold contacts
Hi Tony! There are lots of options in menu: Select... Contacts, so it rather depends on all of the specific settings that you chose. Here is the help for that GUI: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>
To summarize in regard to your questions...
If you are in the Chains tab, you have a choice to use atomic distance or buried surface area. If you chose atomic distance it is using all the atoms and doesn't care what is backbone or sidechain. It would be the minimum distance (closest pair).
At any point you can just simply list the residues in the current selection, e.g. command
info residues sel
... which will go to the Log but you could alternatively save to file, e.g.
info residue sel saveFile ~/Desktop/contacts.txt
If you are in the Atomic tab, then you have the choice to use VDW overlap (negative distance between VDW surfaces) or center-center distance as the main criterion. If using that tab, presumably you would have already selected one of the chains and then designate to limit the results to atom pairs where one of the atoms is selected.
You don't have to go through GUIs. If you just want to list residues in one chain with any atom within some distance of any atom in another chain, you could use commands like the following to select protein residues in chain A within 5.0 Angstroms of protein residues in chain C. The "protein" intersections are because some structures have water, ligand, ions with the same chain IDs as the protein chains, but I wanted to only consider the protein.
select (/A & protein) & (/C & protein) :<5.0 info residues sel
If the chains were only protein anyway, or you wanted to include any nonprotein residues, could be simpler
select /A & /C :<5.0
See command-line zone specification and combinations such as intersection (&): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones>
Again it is all atoms and the closest pair.
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 Aug 10, 2025, at 5:39 PM, Anthony Newcombe <http://anthony.newcombe@appliedbiopharm.com> wrote:
Hello Elaine
I have a commercial license of ChimeraX. Further to the email below, I have been using the menu and GUIs to select > contacts as described in your online message below
https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucs http://f.edu/message/MM3OC3GVF7XQGTDJEYYPAM7DRYSHXB5S/> This highlights the residues, and returns ' 267 atoms, 264 bonds, 32 residues, 1 model selected' between chains A and C
But is there a simple command to list the identified residues as an output that are within less than 5 Angstroms and may interact for chain A or chain C, ie
LEU264 SER265 ALA266
Also one question regarding the atomic distance used, is this a max distance between side chains, or the distance between the peptide backbones?
Thanks for the help and apologies if these are simple questions
Many thanks
Tony