Hello, Thank you for your feedback. Yes, I meant those that appear in pdb validation report.
I will try to inspect surrounding residues as well as run with suggested keywords and let you know how it went. Thank you! Best regards, Vladyslav ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Keitaro Yamashita <kyamash...@mrc-lmb.cam.ac.uk> Sent: Thursday, August 17, 2023 5:03:00 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] How to fix ARG planarity outliers? Hi, I assume the planarity you mentioned is what is discussed in Moriarty et al (2020) https://doi.org/10.1107/S2059798320013534 As shown there, it is known to have some deviation. In Refmac (or in the CCP4 monomer library) it is restrained using a torsion angle with 5 degree sigma instead of the planarity restraint. You can tighten the restraint using an even smaller sigma. The keyword could be: restr tors include resi ARG name chi5 sigma 2.0 By the way, did you mean by "outliers" those from the PDB validation report? I have had a feeling that their criterion is a bit too strict. Could anyone from the PDB tell how the outlier of the ARG sidechain is calculated? Best regards, Keitaro On Thu, 17 Aug 2023 at 15:02, Vladyslav Yadrykhinsky <vladyslav.yadrykhin...@student.uib.no> wrote: > > Hello, > > I am refining a structure and I have ARG planarity outliers in the sidechain. > Could someone please tell me how should I set the planarity restraint in > REFMAC5 (version 5.8.0403) to correct them? > > Should I use: plane [value1] [value2] in the advanced settings? If so, what > values 1 and 2 should be? My current weight restraints are 0.128.... > > Please let me know if you need more information and I will appreciate any > assistance on the matter. > > Best regards, > Vladyslav > > ________________________________ > > 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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/
