I've found a quick workaround that works for different MacOS versions Download MacOS Coot 9.8.1 standalone from CCP-EM https://www.ccpem.ac.uk/download.php In Phenix point it to coot-0.9.8.1/bin/coot Real space refinement and the connection to Phenix works
Best Ricardo On Wed, Aug 10, 2022 at 8:38 PM Ricardo Padua <padua....@gmail.com> wrote: > 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 > > -- 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/
