The "name pocket1 ..." text in the CastP ChimeraX recipe page was describing what the script does. It is not something you need to type. I have clarified the description on that page. https://rbvi.github.io/chimerax-recipes/castp/castp.html Tom
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 <https://rbvi.github.io/chimerax-recipes/castp/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 <mailto: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 <mailto: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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