Dear All, Thank you so much for the suggestions. There was indeed a TER in my PDB file and removing it solved the problem. I was using Coot 0.8.9.2.
Best Regards, Nen On Thu, Feb 18, 2021 at 11:07 AM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > On 18/02/2021 15:21, Neno Vuksanovic wrote: > > > > I've been having an issue when manually adding C-terminal residue in > Coot (I add a terminal residue, then > > add OXT atom, and perform real space refinement). The residue links the > previous one properly and the > > density matches it well, but after refining in Phenix.refine, the > residue is unconnected from the rest of > > the chain. The log file does not mention having any issues with it. Do I > need to change the linking settings > > in Phenix.refine and what could be causing the issue? > > > > Why don't you tell us which version of Coot that you're using? > > Old Coots used to not properly handle TER records on chain extension. > Maybe it's that. > > Paul. > > ######################################################################## > > 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/ > ######################################################################## 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/
