Hi George, In the cavity list (the dialog with table of cavities) there are options for what to do when you choose a row in the table. See <https://rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html#cavitylist> - if you turn on the option "Show contacting residues" and then choose the row in that table for that cavity, it will display the residues contacting that cavity according to the kvfinder calculation. Then you can look in the Log for the "show" command that was used, which will list the residues. - or, if you prefer to use distance from cavity points, turn on the option "Select nearby atoms" with "nearby" distance also adjustable (default 3.5), then choose the row in the table for that cavity, then write a list of the selected residues or atoms to the Log, e.g. info residues sel - OR - info atoms sel I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 18, 2025, at 1:36 PM, George Tzotzos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I’ve opened 1PN9.pdb deleted all but chain A. I used kvfinder #1 probeIn 1.4 probeOut 4.0
The largest cavity has an ID 1.1.5. How does one identify the residues that line the cavity?
Thank you