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 <pems...@mrc-lmb.cam.ac.uk> Date: Wednesday, February 21, 2024 at 9:35 AM To: Kim, Sun Kyung <kim...@llnl.gov>, COOT@JISCMAIL.AC.UK <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. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/