HI Miao, Depending on the options you checked in the tool, it should only display the pockets for the rows you highlighted with the mouse in the pocket list dialog. So it should be easy to just hide the ones you don't want to see by only highlighting the row(s) in the list for the one(s) you want to see. This is described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html#cavitylist> However if you really want to totally delete the other pockets, look in the Models list (you may need to click the disclosure triangle to expand to sub-models). Each set of dots for one cavity is one model. You can just close all the models for the pockets you don't care about, using the Close button in the Model Panel or with the "close" command. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html> Either way it would be a good idea to save a session so that if you need to re-make the figure later, it will be easy to restore the status/data. 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 4:24 PM, Zhang, Miao via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
NOTE: This email originated from outside Chapman’s network. Do not click links or open attachments unless you recognize the sender and know content is safe.<kvf-highlight.png> _______________________________________________ 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/