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 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 < [email protected]> 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]