I've found a quick workaround that works for different MacOS versions
Download MacOS Coot 9.8.1 standalone from CCP-EM
https://www.ccpem.ac.uk/download.php
In Phenix point it to coot-0.9.8.1/bin/coot
Real space refinement and the connection to Phenix works

Best
Ricardo

On Wed, Aug 10, 2022 at 8:38 PM Ricardo Padua <padua....@gmail.com> wrote:

> I had the same issue (MacOS Catalina 10.15.7 and the same phenix version).
> The fix was:
> In PHENIX Home screen, click on Preferences, then click on the graphics
> tab, in the Coot path box point it to the coot.app as in
> (/Applications/ccp4-8.0/coot.app) instead of
> (/Applications/ccp4-8.0/bin/coot)
>
> I must point that someone else in the lab has a similar issue using MacOS
> Mojave 10.14.6 and the fix above works for the restrain problem but the
> connection to Phenix is lost
>
> Best
> Ricardo
>
> On Sun, Aug 7, 2022 at 2:09 AM Cryo EM <cryoemfa...@gmail.com> wrote:
>
>> Hi everyone,
>>
>> I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. The
>> phenix version I am using is 1.20.1-4487.
>>
>> At the end of validation run or real space refinement for my cryo-EM map,
>> I want to fix the problems in the model interactively by the "open in coot"
>> button displayed in phenix. As soon as I click on the problems list in
>> phenix, coot takes me to that atom but I am not able to do any local real
>> space refinement in coot since it complains about the missing restrains for
>> even standard amino acids and nucleotides (screenshot attached).
>>
>> Please note that coot alone (when not connected to phenix) works for me
>> flawlessly. I guess it has something to do with missing monomer library
>> path in coot when connected to phenix but I am unable to fix this. Can
>> someone please redirect me to the solution?
>>
>> Regards and thanks!
>>
>>
>> [image: Mailtrack]
>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>  Sender
>> notified by
>> Mailtrack
>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;>
>>  07.08.22,
>> 07:51:32
>>
>> ------------------------------
>>
>> To unsubscribe from the COOT list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>>
>
>
> --
> Ricardo A. P. de Pádua
> HHMI Research Specialist
> Kern Lab
> Brandeis University, Waltham, MA
>
>

-- 
Ricardo A. P. de Pádua
HHMI Research Specialist
Kern Lab
Brandeis University, Waltham, MA

########################################################################

To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Reply via email to