Whatever it is worth, I agree with Dale. I see those "Major validation issues" all the time. Some structures at medium resolution (2-3A), and some are at high (1.1-1.4A). Not all Arg residues are "in violation". At low and medium resolution cases it is hard to argue. But high resolution electron density maps are showing correct fit, yet those Arg are called an "issue". Fixing restrains for all Arg is not right solution. Embracing the difference and understanding why those are different feels like scientific.
Thank you. Vaheh Oganesyan, Ph.D. [cid:image001.png@01D9D10E.4C64C4C0] R&D | Biologics Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Vladyslav Yadrykhinsky Sent: Thursday, August 17, 2023 11:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to fix ARG planarity outliers? 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<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Keitaro Yamashita <kyamash...@mrc-lmb.cam.ac.uk<mailto:kyamash...@mrc-lmb.cam.ac.uk>> Sent: Thursday, August 17, 2023 5:03:00 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto: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<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<mailto: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<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<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/<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<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/
