Hi Chiara,
As a work around, you can have coot-1.X open and drag and drop the files directly from the phenix window into coot now.
Not really addressing the exact issue, but I find it useful.
Cheers,
eta
***
Eta A. Isiorho, Ph.D.
Research Assistant Professor/Macromolecular Crystallization Facility Manager
CUNY Advanced Science Research Center
85 Saint Nicholas Terrace, 3.352B/3.134
New York, NY 10031
Outreach Officer
NSLS-II UEC
[email protected]mailto:[email protected]
From: Rapisarda, Chiara /FR via phenixbb
Date: Wednesday, January 28, 2026 at 7:28 AM
To: [email protected]
Subject: [phenixbb] coot-1 linked to phenix
* External Sender - Proceed Cautiously with Links and Attachments. *
Hello,
I have a Mac that I upgraded to Tahoe, and now coot 0.9 isn’t working any more.
I would like to link phenix to coot-1. I can do that by adding:
/Applications/ccp4-9/coot_py3/bin/coot
To the coot path in preferences, but after a refinement when I open coot , it is open but it is not connected to the phenix refine job and no PDB nor map is open.
I am aware that I can manually open the map and pdf, I would like to know if coot-1 can be opened in a way that will allow me to navigate the structure using phenix.
When I ask gemini it tells me that I should point it to:
/Applications/ccp4-9/bin/coot-py3
But it doesn’t exist in my ccp4 installation.
Has anyone successfully managed to link coot-1 to phenix using a good bridge?
Any help will be greatly appreciated.
Best,
Chiara
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