Hi! Yes, it's been broken for a long time, but it will be fixed in Coot very soon [https://pemsley.github.io/coot/blog/2023/06/05/AA-RNA.html]. A workaround is to downgrade to CCP4 v. 8.0.006 (Coot v. 0.9.8.5) through the CCP4 Update Manager.
Best, Eugene On Mon, Jul 17, 2023 at 1:45 PM David Lawson (JIC) <david.law...@jic.ac.uk> wrote: > 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 > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
