Dear all,

I am wondering if I can kindly ask you what the timeframe is usually for fixing these kinds of issues. I was going to complete a set of analyses for a collaborator and I would like to communicate a timeline.

Thank you very much in advance.

Sincerely,

Claudia.

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Monday, April 7, 2025 at 8:09 PM
To: Marino, Claudia <clmarino@UTMB.EDU>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Issues with find cavities tool

External Email Warning: Do not click links or open attachments unless you recognize the sender and expect the content. UTMB Email Phishing Awareness<https://www.utmb.edu/infosec/resources/phishawareness>

Hi Claudia,
Using a newer daily build is unlikely to solve the problem from Sequoia 15.4, sorry.  I only meant that if/when you can run Find Cavities, or if you could run it from some other computer, the newer version of ChimeraX's tool is better.

Note that the kvfinder method is also available as a website interface from the developers:
<https://kvfinder-web.cnpem.br/>

...  However, their web server uses different atomic radii than those in ChimeraX, so you cannot compare between results from previously running the tool in ChimeraX and what you get from the web server.  To really compare different structures, you'd need to run all the calculations using only the ChimeraX tool or only that web server.

Elaine

> On Apr 7, 2025, at 5:48 PM, Marino, Claudia <clmarino@UTMB.EDU> wrote:
>
> 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
>   External Email Warning: Do not click links or open attachments unless you recognize the sender and expect the content. UTMB Email Phishing Awareness
> 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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