[phenixbb] Phenix/Coot issue

[Xavier Brazzolotto]

> Dear Phenix and Coot users and developers
> 
> I've recently observed a kind of conflict between Phenix and Coot.
> 
> I am using Phenix v1.20.1-4487 and Coot 0.9.8.1 from thee CCP4 8.0 suite under macOS Monterey (v12.3.1).
> 
> If I launch Coot through Phenix via the « Open in Coot » of a refine job for example (the path to Coot has been defined in Phenix preferences), Coot opens correctly and displays the structure with the « Connected to Phenix tab". However if I wand to do some RSR then I get an error message stating "Refinement setup failure » : « Failed to find restraints for » and a list of the residues involved in RSR.
> 
> In parallel if I use Coot by itself (launched through the terminal), RSR works well… but upon opening Coot states that there is some "Nomenclature errors » with a list of different residues.
> 
> I wonder if there would be some conflict between residue libraries between Phenix and Coot ?
> 
> Just to leet you know I’ve also recently tried to install/comlplie the Coot v1 pre-version to have a loot at it and I do also have libccp4 installed in my Homebrew. Maybe everything comes from that ?

I’ve did some cleanup. Installed with Phenix and CCP4-8.0 many times.
I’ve removed my Homebrew to remove all traces of my tests with Coot v1-pre.

I did some Phenixbb archeology and a similar issue has been reported in 2014 and probably solved by changing the path of Coot.

Here I’ve changed multiple times using /Applications/CCP4-8.0/Coot.app or /Applications/CCP4-8.0/Coot.app/Contents/MacOS/coot
In this case Coot starts but does not automatically open model and maps and in find myself in a folder not related to the Phenix projet. No « connected to Phenix » appears.
If I load a model and maps, then RSR is functional meaning that Coot has has loaded its restraints library for the residues but no ligand cif is injected…

If I change the path to /Applications/CCP4-8.0/bin/coot or /Applications/CCP4-8.0/coot_py2/bin/coot, Coot starts with the « connected to Phenix » tab.
Coot automatically opens model and maps and works in the Phenix project folder. But the residues restraints library is not loaded, RSR does not work (only the RSR of an injected ligand works)…

The only solution I’ve found is to get back my old CCP4-7.1 folder containing Coot 0.9.6.
Declaring the new path /Applications/CCP4-7.1/bin/coot allowed me to get back a functional Coot linked to Phenix. Very strange….

I do have some questions :
Does Phenix write any configuration file in the Coot directory ? Maybe there is some conflict ?
Where is saved the preferences file of Phenix ?

Xavier