I had the same issue in the past. To resolve this issue, point Phenix (in settings -> Graphics, if I recall correctly) to the Coot location in CCP4. As you suspected, Coot does not know where the Restraint Library is when opened from Phenix.
Best, Nick Clark On Sun, Aug 7, 2022 at 2:00 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 the 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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailtrack.io%2F%3Futm_source%3Dgmail%26utm_medium%3Dsignature%26utm_campaign%3Dsignaturevirality11%26&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C1741bc4018624de3553f08da783a25de%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637954488531501533%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7C&sdata=aqUW%2BaOMn1rrpXLDUof7mLipiY82c7AzYS73O%2Fe%2BrTs%3D&reserved=0> > Sender > notified by > Mailtrack > <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailtrack.io%2F%3Futm_source%3Dgmail%26utm_medium%3Dsignature%26utm_campaign%3Dsignaturevirality11%26&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C1741bc4018624de3553f08da783a25de%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637954488531501533%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7C&sdata=aqUW%2BaOMn1rrpXLDUof7mLipiY82c7AzYS73O%2Fe%2BrTs%3D&reserved=0> > 07.08.22, > 07:59:09 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <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%7C1741bc4018624de3553f08da783a25de%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637954488531501533%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7C&sdata=k7wtzE6BDVcqcc1bLrm%2F0SvQFwrzGTT8QBHWUXYs%2B8Y%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/
