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.

Hi Geoff, Chat help is your friend. I asked it and followed its suggestion "measure buriedarea /R with /H,L color red" and hid extra antibody chains A,B (hide /A,B) and got this image. Tom  How to I color the buried residues? To color residues buried in the interface between two chains, use the measure buriedarea command with the color keyword . You can execute this by specifying the two chains and your chosen color, for example, measure buriedarea /A with /B color red, . This command identifies residues that bury solvent-accessible surface area and colors them in a single step , . By default, a residue is colored if it buries at least 1.0 Ų of area, though you can adjust this threshold using the cutoffArea option .

On Jan 7, 2026, at 1:25 PM, Shimberg, Geoffrey (NIH/VRC) [C] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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 <mailto:goddard@sonic.net>> Sent: Wednesday, January 7, 2026 4:21 PM To: Shimberg, Geoffrey (NIH/VRC) [C] <geoffrey.shimberg@nih.gov <mailto:geoffrey.shimberg@nih.gov>> Cc: chimerax-users@cgl.ucsf.edu <mailto: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 /Bcalculates 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.

_______________________________________________ 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/

Hi Geoff, I suggest you look at the help page, in which there is an example of using the "list" (aka "listResidues" option): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> Or, you could ask the chat how to do that, as Tom has suggested. Elaine

On Jan 7, 2026, at 1:48 PM, Shimberg, Geoffrey (NIH/VRC) [C] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks Tom, I was able to do what you suggested. Is there a way to show which amino acids are in red in the log? I tried doing the listResidues prompt, but got an error message. Geoff From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, January 7, 2026 4:32 PM To: Shimberg, Geoffrey (NIH/VRC) [C] <geoffrey.shimberg@nih.gov> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] [EXTERNAL] Re: Measuring contact area in a pdb file Hi Geoff, Chat help is your friend. I asked it and followed its suggestion "measure buriedarea /R with /H,L color red" and hid extra antibody chains A,B (hide /A,B) and got this image. Tom <image001.png> How to I color the buried residues? To color residues buried in the interface between two chains, use themeasure buriedarea command with the color keyword . You can execute this by specifying the two chains and your chosen color, for example,measure buriedarea /A with /B color red , . This command identifies residues that bury solvent-accessible surface area and colors them in a single step , . By default, a residue is colored if it buries at least 1.0 Ų of area, though you can adjust this threshold using the cutoffArea option .

On Jan 7, 2026, at 1:25 PM, Shimberg, Geoffrey (NIH/VRC) [C] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: 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 /Bcalculates 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/ 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. _______________________________________________ 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/ 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. _______________________________________________ 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/