Dear all,

Thank you so much for the quick response. I confirm that I reported the bug via the official channel. Unfortunately, I cannot reverse the update to the MacOS version because the university forces these updates for security reasons. I will try to do what Dr. Meng suggested me as I need to quantify some cavities for some interaction comparisons. 

Thank you so much. 

Sincerely,
Claudia. 



From: Eric Pettersen <pett@cgl.ucsf.edu>
Sent: Monday, April 7, 2025 7:43:38 PM
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Elaine Meng <meng@cgl.ucsf.edu>
Cc: Marino, Claudia <clmarino@UTMB.EDU>
Subject: Re: [chimerax-users] Issues with find cavities tool
 
 
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Hi Claudia,
I just updated to 15.4 and also now get this error.  Before the update (on 15.1.1) it worked fine.  So I guess a word of warning to other Mac users that haven’t upgraded — if you use Find Cavities at all you might want to hold off on upgrading if you can.  I’ll put some kind of announcement here when we have more news about the problem (hopefully a fix!).
Claudia, I’ll be putting you on the ticket we have open for this (#17304 (pyKVFinder- missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)))

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Apr 7, 2025, at 5:28 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Claudia,
I could run it without problems in ChimeraX 1.9, but my Mac is at Sequoia 15.3.2.  So maybe it's something with 15.4 but I don't know exactly.

In general for problems like this, it may be better to use menu: Help... Report a Bug (instead of sending email to chimerax-users).  The bug report would automatically info about your platform and ChimeraX version, and what was in the Log.  Then you wouldn't need to screenshot it.

If this problem can be sorted out, I recommend using Find Cavities in a newer daily build because several improvements were added after the 1.9 release.  See the Change Log for more details, if you want them...
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>

Best,
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 Apr 7, 2025, at 5:07 PM, Marino, Claudia via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Greetings,
I am not sure why I recently cannot longer use the tool “find cavities”. My ChimeraX version is 1.9 and my MacOS is Sequoia 15.4. Please, find below the screenshot of the Error message.
Thank you very much in advance for your help.
Sincerely,
Claudia.

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