I had the same issue (MacOS Catalina 10.15.7 and the same phenix version). The fix was: In PHENIX Home screen, click on Preferences, then click on the graphics tab, in the Coot path box point it to the coot.app as in (/Applications/ccp4-8.0/coot.app) instead of (/Applications/ccp4-8.0/bin/coot)
I must point that someone else in the lab has a similar issue using MacOS Mojave 10.14.6 and the fix above works for the restrain problem but the connection to Phenix is lost Best Ricardo On Sun, Aug 7, 2022 at 2:09 AM Cryo EM <cryoemfa...@gmail.com> wrote: > 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! > > > [image: Mailtrack] > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> > Sender > notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> > 07.08.22, > 07:51:32 > > ------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > -- Ricardo A. P. de Pádua HHMI Research Specialist Kern Lab Brandeis University, Waltham, MA ######################################################################## 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/
