Hi Eugene, Many thanks – that’s sorted it!
Best wishes 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> From: Eugene Pichkur <eugene.pich...@gmail.com> Sent: Monday, July 17, 2023 11:59 AM To: David Lawson (JIC) <david.law...@jic.ac.uk> Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL? You don't often get email from eugene.pich...@gmail.com<mailto:eugene.pich...@gmail.com>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> 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<mailto: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<mailto: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/
