Thanks. That worked. How do I remove the cavities that I am not interested in, when making figure? Miao From: Elaine Meng <meng@cgl.ucsf.edu> Date: Thursday, January 30, 2025 at 12:09 To: Zhang, Miao <zhang@chapman.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: finding protein pockets and tunnels External Message Hi Miao, You have good timing! We have a fairly new tool Find Cavities (in menu under Tools... Structure Analysis) and command "kvfinder" implementing the previously published KVFinder program from the Brazilian Biosciences National Lab. I don't know if the default settings would find your pocket, but you can adjust the probe radii and other parameters as described in the papers and (briefly) in the help pages. Not all of the features described in the help pages made it into the 1.9 release, so you might want to get a newer 1.10 daily build instead to match this documentation: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/kvfinder.html> Running it gives a list of cavities, their volumes, etc. and displays them as dots and/or surfaces. See screenshot attached. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2025, at 10:58 AM, Zhang, Miao via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine I read an old post in 2010 about the surfnet tool in Chimera. Is there anything similar to surfnet tool in ChimeraX? CASTp did not find the correct pocket in out apo protein. We want to refine manually and then measure the pocket. Miao
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