Thanks Tom, Is there a way to highlight which amino acids are involved in that area being measured? Geoff From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, January 7, 2026 4:21 PM To: Shimberg, Geoffrey (NIH/VRC) [C] <geoffrey.shimberg@nih.gov> Cc: chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Measuring contact area in a pdb file Hi Geoffrey, There is a new ChimeraX chat help<https://www.rbvi.ucsf.edu/chimerax/help_chat.html> system that uses all of the ChimeraX documentation and tutorials and mailing list questions to advise you that is worth a try on simple questions like this. The link is on the ChimeraX page under Documentation on the left. It told me "measure buriedarea /A with /B". Adapting that to the chain ids in PDB 7y0w which are R for the receptor and H and L for the heavy and light antibody I get 871 square Angstroms. measure buriedarea<help:user/commands/measure.html#buriedarea> /R with /H,L Buried area between /R and /H,L = 870.61 Tom Chat help question and answer: What is the command to measure the buried area between chains? The most common command to measure the buried surface area between two chains is measure buriedarea . To perform this measurement, you specify the two sets of atoms using the syntax measure buriedarea atom-spec1 withAtoms2 atom-spec2 . For example, the command measure buriedarea /A with /B calculates the total solvent-accessible surface area buried between chain A and chain B . On Jan 7, 2026, at 1:02 PM, Shimberg, Geoffrey (NIH/VRC) [C] via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX Developers, I was wondering if you could explain to me how to measure the contact residues/area in a pdb file containing an antibody and antigen? I have been trying to do either measure buriedArea or contactArea, but I get an error. I have been using the PDB file 7Y0W as a starter structure to then use for future structures. Let me know if you need anything else. Thank you for all your help. Geoffrey Shimberg _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.