Hello, I can confirm that this happens in 0.9.8.7. The problem is intermittent and I have not been able to determine what causes it so far. Some residues just fall apart into atoms as a result of real space refinement.
Best, Yaroslav Yaroslav Tsybovsky, Ph.D. (contractor) Senior Scientist & Head Vaccine Research Center Electron Microscopy Unit Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. Post Office Box B Frederick, Maryland 21702 Phone: 301-846-7550 From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of David Lawson (JIC) Sent: Monday, July 17, 2023 6:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL? Hi All, Is it just me, but is real space refinement broken in COOT 0.9.8.8 EL? I am seeing this working through CCP4i2 (CCP4-8.0.012) and CCP4 cloud (v 1.7) on an M1 iMac (running Monterey 12.6.7). I am working on a protein-DNA complex and finding that often when I do real space refinement (well, I mostly use tandem refinement) the atoms just shoot off in one direction to give a very scrambled structure, even if I am just doing final tweaks on a close to final structure. I don't know if it has something to do with the DNA restraints, because refining the protein in regions distant from the DNA seems fine, whereas working on protein regions close to the DNA, or on the DNA itself, generally results in a mess. However, if I revert to COOT 0.9.6 EL (as distributed with CCP4-7) with the same input files, the problem goes away. Any help much appreciated, Dave ------------------------------- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk> ________________________________ To unsubscribe from the CCP4BB list, click the following link: Bad URL Removed - see why - https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=CCP4BB&A=1<Bad%20URL%20Removed%20-%20see%20why%20-%20https:/ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=CCP4BB&A=1> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. ######################################################################## 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/
