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


On Thu, Sep 10, 2020 at 4:20 PM Billy Poon <BKPoon@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


On Thu, Sep 10, 2020 at 12:34 PM Cygler, Miroslaw <miroslaw.cygler@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@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org