Re: [ccp4bb] Coot/Phenix.refine C-terminus issue
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 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=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=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/
Re: [ccp4bb] Coot/Phenix.refine C-terminus issue
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=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/
[ccp4bb] Coot/Phenix.refine C-terminus issue
Dear All, 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? Best regards, Neno To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
