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 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

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