Vladyslav I would be very interested in seeing the PDB report that you received. If you wish to share, please send it directly to me.
Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Thu, Aug 17, 2023 at 10:25 AM Oganesyan, Vaheh < vaheh.oganes...@astrazeneca.com> wrote: > 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.* > > *R&D* *| Biologics Engineering* > > One Medimmune Way, Gaithersburg, MD 20878 > > T: 301-398-5851 > > *vaheh.oganes...@astrazeneca.com <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> 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, 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 > > ------------------------------ > > 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, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
