Hi Dale, I recently updated Phenix and CCP4 on iOS had a similar issues with Phenix/Coot.
I fixed the issues with the restraint dictionary by directing Phenix to the new location for Coot (in the CCP4 program libraries) in the Phenix settings. This resolved the lack of restraints for every amino acid when opened through Phenix. This also resolved opening coot when clicked in Phenix. However, I was unable to get Phenix to actually open the file in Coot. I eventually gave up and have “manually” been opening the files in the Coot pop-up window when I click Phenix. This pop-up of Coot also does not have the “Connected to Phenix” status, similar to your issue. Maybe what I did will provide some information to someone familiar with how to resolve this Phenix issue. Alternatively, Coot and Phenix may just not “play well together” in the newer versions. The upgrade did not generate any issues for me in PyMOL, so I can’t be of assistance there. Best, Nick Clark On Tue, Jul 26, 2022 at 8:55 PM Dale C < [email protected]> wrote: > Hi all, > > I recently updated my ccp4 package to Program suite v8.0.002 and i have > now run into a few issues with other programs. The issues are highlighted > below... > > - When i click 'Open in Coot' on any output through Phenix (so far only > tested phenix.refine and phenix.phaser), i no longer see anything open. Nor > do i see the "Connected to Phenix" button in the toolbar on Coot. > > - The 'fetch' command in Pymol no longer works either (I have attached a > screenshot of the error message here) > > - Coot also seems to have an issue with not loading the amino acid > restraints so when i click real-space refine, i get the error 'unable to > find restraints for residue x,y,z'. > > I feel they may be all related and my first thought is that it has > something to do with my Python dependencies however I have no idea how to > fix this or reinstall them. > > Does anyone have an idea if they are all related? Or how i might fix this? > > fyi I am using > - ccp4 program suit v8.0.002 > - Coot 0.9.8.3 > - Phenix-1.20.1-4487 > > Thanks in advance. > > Dale. > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cbc214f0d9aa2402398d208da6f6ab3e7%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637944801472919679%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7C&sdata=DJJh5yNqVYgEWVYn251%2FLikUJZYbdbhIwVTAg4hJhj0%3D&reserved=0 > > This message was issued to members of > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cbc214f0d9aa2402398d208da6f6ab3e7%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637944801472919679%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7C&sdata=wU13PduKwZsJq5UBC9xg5EqU%2B%2Bg9CrVni94OYFgvNJc%3D&reserved=0, > a mailing list hosted by > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cbc214f0d9aa2402398d208da6f6ab3e7%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637944801472919679%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7C&sdata=VXWv9lZzPR9oGbk6%2FD4x%2Bt5Q3nwmsLz3OSX4Bb7G0WQ%3D&reserved=0, > terms & conditions are available at > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cbc214f0d9aa2402398d208da6f6ab3e7%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637944801472919679%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7C&sdata=w%2Byj8ur7y81BqZFA5WthakJyggriWmCnv9nKuRRZYJs%3D&reserved=0 > -- Nicholas D. Clark PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
