...and then one way to see the help page is to click the "measure buriedarea" link in the Log after using the command. In the help page, you can see there is a "listResidues" option as well as additional examples of how to use the command. Here is the copy of the help page at our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> Elaine
On Jan 7, 2026, at 1:20 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Geoffrey,
There is a new ChimeraX chat help 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 /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> 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 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/
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