Hello, unless it's changed over the last couple of years, the pdb rightly used to let you deposit a structure with outliers, hopefully not too many, though ;-0
I take it the stalling you reported probably comes from whoever is looking over your shoulder. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile -------- Original Message -------- On 23 Sept 2023, 02:29, Nitin Kulhar 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 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/
