Hi Berenice, I'm told it is indeed 3.5 angstroms. I will add that to the help page. Best, Elaine
On Dec 15, 2025, at 1:42 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Berenice, The Help shows the initial default values for the cavity detection settings, <https://rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html>
...but I see it doesn't say the initial default distance for "Nearby" atoms, which is set on the "cavity list" results dialog. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html#cavitylist>
I believe the factory default of that was something smaller like 3.5 Angstroms; if it comes up with a different value, it may be remembering what you used last. Bear in mind that this distance will not affect what cavities are found or their measurements, only how you are displaying the results, so it is meant to be adjusted to whatever you think looks best.
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 Dec 15, 2025, at 12:32 PM, Berenice E Cowfer Chavez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, What is the default value of "Nearby" atoms are within X angstroms of cavity points in the Find Cavities tool? I remember it used to be 5.0 A but now when I use the tool it shows 6.0 A. Sincerely, Berenice E. Cowfer Chavez, M.S. Lab Manager, Profs. Johnson and Shoulders Labs Massachusetts Institute of Technology _______________________________________________ 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/
_______________________________________________ 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/