Hi I think It may be worthwhile submitting your model and data to PDB-REDO to see if (inter alia) you have applied any unconscious bias to your building that has resulted in these outliers, or over- or under-interpreted the data. It’s quick and easy to submit and requires remarkably little effort on your part - another tool to your collection.
Harry > On 25 Sep 2023, at 07:00, Guillaume Gaullier <guillaume.gaull...@kemi.uu.se> > wrote: > > A good example of such expected outliers can be found in structures of > nucleosomes: the validation report always flags almost all DNA bases as > geometry outliers. But we have no end of evidence that these structures are > correct: for instance, the many ensemble and single-molecule FRET studies of > nucleosomes that relied on said structures to design their labeling scheme > and to formulate testable hypotheses. > > If your map insists on putting some residues in an uncomfortable > conformation, it’s possible that this is indeed what is going on in the > protein and not necessarily a modeling error. > > Cheers, > > Guillaume > >> On 23 Sep 2023, at 21:50, Eleanor Dodson >> <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> >> Well - some outliers are infix able! There are various reasons - floppy >> residues like arg or lys >> In multiple positions; strain due to protein folding constraints, etc. >> >> I use the validation report to check for obvious modelling errors but if you >> can’t find any, you have to just submit the results of your experiment... >> >> On Sat, 23 Sep 2023 at 02:29, Nitin Kulhar >> <00009dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote: >> Dear all >> >> We have refined (Refmac5) a crystallographic structure with Rw/Rf values >> 0.19/0.22 (Resln 2.67). However, the deposition has stalled on account of >> the wwPDB's preliminary validation report, which indicates map/model and >> geometry issues, with each criterion containing a few instances. We tried to >> correct these by varying overall geometry restraint weights, e.g. decreasing >> overall weights from default value of 1.0, incementally decreasing sigmas >> corresponding to the planarity restraint term. This did not resolve the >> issues. >> >> In another approach, real space refinement by hand (against 2fo-fc) in coot >> brought the geometry parameters within acceptable limits in addition to >> improved apparent agreement with electron density (2fo-fc, sigma=1), but >> uploading the resultant coordinates seems to undo the changes made in coot, >> as indicated by reappearance of same outliers in the subsequent validation >> report. >> >> I request your kind suggestions in this regard. Please also revert for any >> further information. >> >> Thanks >> Nitin Kulhar >> PhD student >> c/o Dr Rajakumara Eerappa >> Macromolecular Structural Biology Group >> Department of Biotechnology >> Indian Institute of Technology Hyderabad >> Kandi, Sangareddy >> Telangana, India 502284 >> >> Disclaimer:- >> >> This footer text is to convey that this email is sent by one of the users of >> IITH. So, do not mark it as SPAM. >> >> 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 >> >> >> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen >> avsändaren och vet att innehållet är säkert. >> CAUTION: Do not click on links or open attachments unless you recognise the >> sender and know the content is safe. > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det > att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan > du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. > For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > 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/
