You can tell phenix where to find coot. Point coot to the ccp4 version, which 
has the libs. The stand alone version may not have the link to the lib that is 
maintained by ccp4.
kas



Kenneth A. Satyshur, M.S., Ph.D.

Senior Scientist, Retired From:

College of Ag and Life Sciences: Department of Bacteriology;

School of Medicine and Public Health:

Departments of Biomolecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center

(Small Molecule Screening Facility)

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

________________________________
From: Mailing list for users of COOT Crystallographic Software 
<COOT@JISCMAIL.AC.UK> on behalf of Cryo EM <cryoemfa...@gmail.com>
Sent: Sunday, August 7, 2022 12:58 AM
To: COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK>
Subject: Missing Restrains for standard amino acids

Hi everyone,

I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. The phenix 
version I am using is 1.20.1-4487.

At the end of validation run or real space refinement for my cryo-EM map, I 
want to fix the problems in the model interactively by the "open in coot" 
button displayed in phenix. As soon as I click on the problems list in phenix, 
coot takes me to that atom but I am not able to do any local real space 
refinement in coot since it complains about the missing restrains for even 
standard amino acids and nucleotides (screenshot attached).

Please note that coot alone (when not connected to phenix) works for me 
flawlessly. I guess it has something to do with missing monomer library path in 
coot when connected to phenix but I am unable to fix this. Can someone please 
redirect me to the solution?

Regards and thanks!


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