Hi Paul,
Thank you for your response!
I opened Coot from my terminal, and not seeing any diagnostic information, but
it just opens up coot.
When you mention I could try setting COOT_MONOMER_LIB_DIR or
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers… I’m not
sure as to what those files are or where I can find them.. are there
documentations to this that I can refer to? Thank you.
It’s strange that COOT starts having this issue for me all of a sudden. The
only thing I can think of is, over the weekend I had to do some mandatory
upgrades to my government computer that I’m using…do you think any updates to
the MacOS or something like that could have caused this issue for me?
Thank you for your help as always!
Best,
‘Kate’ Sun Kyung Kim
From: Paul Emsley
Date: Wednesday, February 21, 2024 at 9:35 AM
To: Kim, Sun Kyung , COOT@JISCMAIL.AC.UK
Subject: Re: How does COOT determine protonation states
On 21/02/2024 02:50, Kim, Sun Kyung wrote:
Thank you Paul for that information. I will look into Acedrg and Grade2!
Sounds good.
I have an unrelated question… I’ve never encountered this before, but all of a
sudden my COOT is complaining that it doesn’t have restraints for refinement…
(screenshot attached)… any idea why this error message is suddenly appearing?
Coot writes diagnostic information to the terminal/console/program from where
it was started. You need to get access to that information.
I would try to start Coot from a terminal and see what it says about
dictionaries and libraries as it starts up.
Before invoking coot, you could try setting COOT_MONOMER_LIB_DIR or
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers - how to
do that depends on your system.
Regards,
Paul.
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