Hi, I can confirm that this happened to me now, using 0.9-pre build from CCPEM 1.4.1 (revision-count 855). I also tested some old binaries and the change was introduced sometime between revision-count 819 (does not try to connect across the gap) and revision-count 855 (if refining a single residue after a gap, coot tries to connect it to the residues before the gap).
Regards, Daniel > On 2019-12-09, at 17:50, Paul Emsley <[email protected]> wrote: > > On 05/12/2019 17:55, Xuewu Zhang wrote: >> >> The new version of Coot bundled with CCPEM seems behave differently >> for refinement near a gap. > > > Yes. > > >> In the past, if there is a gap, for example, a few residues missing >> between two beta-strands, refinement of one strand is independent from >> the other strand, as it is supposed to. However, in the new version, >> if the distance between the last residue of the first segment and the >> first residue of the second segment is small, refinement of one >> segment leads to "stretching" of the residue near the gap, as Coot >> tries to make a covalent linkage between the two segments, even though >> there is a gap and the residue numbers are not contiguous. Is there a >> way to change this back to the previous setting? >> > > I think I understand what you are describing - if the stretch is make to > a non-moving residue in refinement. That was fixed here: > > > commit c9f19a5b9b57a97c130907fa7b00ed6d9284615d > Author: Paul Emsley <[email protected]> > Date: Tue Dec 3 16:19:57 2019 +0000 > > > If you mean a stretch is made between two moving residues, then that is > a problem that I don't recognise (and according to my reading of the > code, shouldn't happen). > > > So, there is no setting - Coot should just do the right thing with gaps. > > > Paul. > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
