[phenixbb] Phenix and Coot v0.9

[Billy Poon]

Hi Mirek,

I tracked down the problem. For ccp4-7.1 on macOS, the coot path should be
/Applications/ccp4-7.1/bin/coot, not the one in
/Applications/ccp4-7.1/coot.app/Contents/MacOS/coot. The current workaround
is to manually specify the path in the GUI preferences -> Graphics -> Coot
path. If you have ccp4-7.1 installed in another location, just replace
/Applications with that location. I have verified that this should work on
macOS 10.15.6 with ccp4-7.1 by restoring an old phenix.refine job and
displaying the model and maps in Coot 0.9 EL (ccp4). I'll be updating
Phenix to use /Applications/ccp4-7.1/bin/coot if it is available.

Let us know if you have any other questions. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org


On Thu, Sep 10, 2020 at 4:20 PM Billy Poon <BKPoon at lbl.gov> wrote:

> Hi Mirek,
>
> I think this is an issue with Coot 0.9 and it is something I am looking
> into. This is happening with other users as well.
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
>
> On Thu, Sep 10, 2020 at 12:34 PM Cygler, Miroslaw <
> miroslaw.cygler at usask.ca> wrote:
>
>> Hi,
>> I recently switched to Coot v0.9. When I start refinement now, the Coot
>> starts and window opens but the model and density are not uploaded there
>> and no phenix extensions show. I wonder is this is something that I can fix
>> on my mac laptop or a bigger issue requiring work of phenix developers?
>> Best,
>>
>> Mirek
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20200914/bbaea211/attachment.htm>