Hi Nusrat, it depends on how you want to define a contact -- chain-chain buried surface area (use "interfaces") ? ...or atom-atom distance (use "contacts")? It might be easier for you to use the menu, Select... Contacts. Then you can choose the Chains tab if you only care about protein or nucleic acid chain-chain contacts (not ligands etc.). If you care about those other kinds of molecules, choose the Atomic tab. There are additional choices for parameter values in those tabs. See the help and links within: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html <mhttps://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>> Whatever you choose, when you click OK to do the calculation, the resulting command will be generated and shown in the Log. You can use that as an example if you want to use commands directly later. When I tried your molecule and Chains contacts between /A and /E (both chains), buried area >= 15 square angstroms, I got 26 residues selected, see image attached below after coloring them red, changing style to sticks, and zooming in on the selection. The Log showed that the command created by using the menu was: interfaces select /A & ::polymer_type>0 contacting /E & ::polymer_type>0 areaCutoff 0 bothSides true 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 Dec 2, 2025, at 10:32 AM, Nusrat Tazkia via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX developpers,
I hope you are doing well. I was trying to colour each amino acid present within a selected region of my model and couldn't figure out how to do it. Could you please guide me on how to do it? I ran these commands (for examples for chains A and E) and have attached my model in this email as well:
interfaces select /A contacting /E bothSides true color sel red
Please let me know at your earliest convenience.
Thank you,
Nusrat Tazkia<palchimera1_model.cif>_______________________________________________ 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/
