Dear Cyril and Paul, COVID struggles permitting, we will _very_ soon have Acedrg dictionaries for most pyranoses in the monomer library. These contain validated conformers, updated torsion restraints and, of course, modern geometry. Cyril: would you like to test these dictionaries with your structure? Best wishes, Jon
On Thu, 18 Mar 2021 at 08:56, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > The geometry targets for protein are well established (by which I mean > "agreed upon") and so the distribution > > > On 18/03/2021 07:19, Cyril Hamiaux wrote: > > Dear Jasmine (and all), > > > > Many thanks for the article. I have a question regarding the Z cutoffs > used to flag geometry outliers in the PDB validation reports: geometry > outliers are flagged with |Z|>2 for ligands (including carbohydrates), but > with |Z|>5 for proteins. What is the rational for using different criteria > for ligands vs proteins? After all isn’t this just one structure? > > > The geometry targets for protein are well established (by which I mean > "agreed upon") and so we can presume that the distribution for refinement > is similar to that of the validation. One cannot say as much for ligands at > the moment. the wwPDB wants to flag only what they have confidence are > wrong. In the CCP4 world, yes, it's all homogeneous (or that is the intent > (carbohydrates in particular need some attention in the monomer library > (I'd recommend that you just run Acedrg to update the dictionaries (or use > Coot, where this have been done for you))), but the wwPDB doesn't score > with CCP4 software (not today at least). > > > > > PS. I am refining a 2.4 A resolution structure of a N-glycosylated > protein and end up with a large number of geometry outliers for the sugars > when I generate PDB validation reports (especially angle outliers). > > Are you using/did you use the N-linked glycan builder in Coot? because > this really shouldn't happen if you are (it uses modern Acedrg-based > dictionaries). If not, you can still use "Refine Tree" and it should > (might?) do something helpful. > > > The huge majority of these outliers are flagged with |Z|<5 (ie they would > not be flagged if they were protein bonds or angles). The electron density > for the sugars is quite good and I made sure that correct LINKR records are > used during refinement in Refmac. I must admit that I’m a bit struggling to > improve this. > > > Refmac can report distance deviations, so you can see where the restraints > are fighting the density. > > You can do something similar in Coot too. > > > Paul. > > > > > > > > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> > <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *Jasmine Young > *Sent:* Thursday, 18 March 2021 2:46 am > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Enhanced Validation of Small-Molecule Ligands and > Carbohydrates > > > > A new article in *Structure* <https://doi.org/10.1016/j.str.2021.02.004> > describes new features, including branched representations and 2D SNFG > images for carbohydrates, identification of ligands of interest, 3D views > of electron density fit, and 2D images of small molecule geometry. > > These enhancements and processes for validation of 3D small-molecular > structures reflect recommendations from the wwPDB/CCDC/D3R Ligand > Validation Workshop and the adoption of software through community > collaborations. > > This manuscript also highlights enhancements made since the initial > implementation of Validation Reports as described in Validation of the > Structures in the Protein Data Bank (2017) Structure 25: 1916-1927 doi: > 10.1016/j.str.2017.10.009 <https://doi.org/10.1016/j.str.2017.10.009>. > > *Enhanced Validation of Small-Molecule Ligands and Carbohydrates in the > Protein Data Bank * > Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, Gérard > Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko F. > Aoki-Kinoshita, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. > Burley, and Jasmine Y. Young > (2021) Structure doi: 10.1016/j.str.2021.02.004 > <https://doi.org/10.1016/j.str.2021.02.004> > > [image: undefined] <https://doi.org/10.1016/j.str.2021.02.004> > > > <http://www.wwpdb.org/news/news?year=2021#top> > > -- > > Regards, > > > > Jasmine > > > > =========================================================== > > Jasmine Young, Ph.D. > > Biocuration Team Lead > > RCSB Protein Data Bank > > Research Professor > > Institute for Quantitative Biomedicine > > Rutgers, The State University of New Jersey > > 174 Frelinghuysen Rd > > Piscataway, NJ 08854-8087 > > > > Email: jasm...@rcsb.rutgers.edu > > Phone: (848)445-0103 ext 4920 > > Fax: (732)445-4320 > > =========================================================== > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > The contents of this e-mail are confidential and may be subject to legal > privilege. > If you are not the intended recipient you must not use, disseminate, > distribute or > reproduce all or any part of this e-mail or attachments. If you have > received this > e-mail in error, please notify the sender and delete all material pertaining > to this > e-mail. Any opinion or views expressed in this e-mail are those of the > individual > sender and may not represent those of The New Zealand Institute for Plant and > Food Research Limited. > > > ------------------------------ > > 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 > -- Dr Jon Agirre Royal Society Olga Kennard Research Fellow York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8252 Twitter: @glycojones ######################################################################## 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/
