Hi James, This answer is for ChimeraX: If it is an enclosed surface (no openings, i.e. not a tunnel) you can use command "measure volume" <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume> For protein pockets/cavities in general see the new Find Cavities tool and "kvfinder" command (you need ChimeraX v1.9 release candidate or a newer daily build): <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/kvfinder.html> However, be aware that different adjustable parameters (and different pocket-finding methods, if you try comparing with other programs) will change the definitions of exactly where the molecular surface lies and where the "top" of a pocket is drawn, so it is best for only making comparisons among different pockets/tunnels calculated with the same set of parameters. 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 Nov 20, 2024, at 3:25 AM, Vitali James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimera support,

Is it possible to calculate the enclosed space, channel volume or void space with the x-ray structure in chimera or chimera x.

best,

James

I did not recommend using the CASTp recipe that you mention. Instead I recommended using the new Cavity Finder tool (in menu under Tools... Structure Analysis in ChimeraX version 1.9 and newer), which should be easier for you to use since it is a built-in, user-friendly tool instead of a recipe script.

<https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/kvfinder.html>

However, if you prefer to use CASTp pockets even though that process is less user-friendly: of course you can use the CASTp recipe ".py" file, which I believe should work for other structures. The specific commands in the example, however, are only for the example structure and would of course be different atoms/chains for different structures. As I understand it, however, you can just use "pocket 1" "pocket 2" etc. (not the specific atom names) for the pocket results of different structures. The .py script automatically uses the different atoms in the file to assign the pocket names. Also this process does not show you anything about the areas and volumes from CASTp in ChimeraX. It only colors and shows surfaces of the pocket atoms. That is why I suggested using Cavity Finder (KVFinder) instead, because you asked about getting the volume quantities, and then you do not have to run some separate calculation in some other program. 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 Nov 21, 2024, at 5:26 AM, Vitali James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Mr. Elaine Thanks for your helpful answer. I just download the read_castp.py from the following link and it works perfectly on the 3lbw example https://rbvi.github.io/chimerax-recipes/castp/castp.html

Do I have to modify the code for using on the other .poc files and add the pocket residues manually. I tried to run it on other examples and it create the surfaces and one can color it accordingly. In the example there is also mentioned to define the "name pocket1 /B:27@O/B:27@CG1…”. This has to do in the command line or int read_castp.py script.

best regards James

On Wed, Nov 20, 2024 at 5:57 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi James, This answer is for ChimeraX: If it is an enclosed surface (no openings, i.e. not a tunnel) you can use command "measure volume" <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume>

For protein pockets/cavities in general see the new Find Cavities tool and "kvfinder" command (you need ChimeraX v1.9 release candidate or a newer daily build): <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/kvfinder.html>

However, be aware that different adjustable parameters (and different pocket-finding methods, if you try comparing with other programs) will change the definitions of exactly where the molecular surface lies and where the "top" of a pocket is drawn, so it is best for only making comparisons among different pockets/tunnels calculated with the same set of parameters.

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 Nov 20, 2024, at 3:25 AM, Vitali James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimera support,

Is it possible to calculate the enclosed space, channel volume or void space with the x-ray structure in chimera or chimera x.

best,

James

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