Is the code publically available for the RSRZ calculation? Thanks,
Steve -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Tuesday, November 29, 2016 12:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports On Monday, 28 November 2016 08:35:44 PM Pavel Afonine wrote: > I find Lothar's comments regarding H and RSRZ excellent! I would think of > it as a pretty much bug report. I hope developers at that end listen. This > goes very well in line with Phoebe's comment earlier today. I guess I'm a bit surprised that adding or subtracting hydrogens from the model without re-refining or at least re-calculating Fc would affect RSRZ at all. I had thought that RSRZ was obtained by comparing density in an Fc map (or probably mFo-DFc) with the corresponding density in an Fo map. I thought that the coordinates were used only to determine the per-residue region of the map to be compared. Going back to the 2004 Kleywegt paper that the PDB cites for calculation of RSRZ I see that it's a bit ambiguous exactly what maps are being compared. So maybe I'm wrong and the current coordinates are used directly to get local "Fc density" by expanding 3D Gaussians without reference to a previously calculated map from refined phases. Can anyone clarify exactly what maps are being compared during wwPDB validation? Ethan > > Pavel > > On Mon, Nov 28, 2016 at 2:51 PM, Dale Tronrud <de...@daletronrud.com> wrote: > > > On 11/28/2016 12:52 PM, esse...@helix.nih.gov wrote: > > >> I found that one can get RSRZ to go way down by loosening the geometry > > >> restraints. The result is a crappy structure and I don't recommend > > doing > > >> that, but it does get all the atoms crammed into some sort of density. > > > > > > Your observation is quite interesting. I can add this: when we were > > working > > > with low to medium resolution structures, deleting the hydrogen atoms > > from > > > the model after refinement moved the very bad RSRZ statistic to about the > > > average in the given resolution range! Note, no re-refinement was done > > just > > > a simple deletion of the riding H-atoms. I find this to be odd given the > > > fact that, say the phenix developers favor the inclusion of H-atoms on > > > riding positions even in cases of low resolution structures. (I assume > > the > > > refmac5 and BUSTER-TNT developers have also a favorable opinion about > > > including H-atoms in the final model - and during refinement). > > > > > > In my mind, it may be tempting to delete H-atoms to improve this > > statistic but > > > when you use them in refinement they should be included regardless of the > > > outcome of the RSRZ analysis. > > > > Of course, if you trick a validation statistic like this you haven't > > accomplished anything. All you are saying is that one should rank RSRZ > > scores with and without hydrogen atoms separately. Perhaps you should > > suggest that to the PDB validation people. > > > > Dale Tronrud > > > > > >> > > >> RSRZ, in my most humble of opinions, seems like one of those statistics > > that > > >> is far more useful in theory than reality. Particularly for > > >> medium-resolution structures, the fit of each entire side chain to the > > density > > >> is likely to be imperfect because the density is imperfect, especially > > toward > > >> the tips of those side chains. > > >> > > >> Then again, it can be a good flag for bits of the structure worth a > > second > > >> look in rebuilding. > > > > > > The latter is certainly true. It may mean that the developers of RSRZ > > > analysis need to tune it a bit to make it fully useful. > > > > > > L. > > > > > >> > > >> ________________________________ > > >> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthew > > >> Bratkowski [mab...@cornell.edu] > > >> Sent: Tuesday, November 22, 2016 10:12 AM > > >> To: CCP4BB@JISCMAIL.AC.UK > > >> Subject: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports > > >> > > >> Hello all, > > >> > > >> I was wondering if anyone knew how the RSRZ score was calculated in the > > >> protein data bank validation reports and how useful of a metric this > > actually > > >> is for structure validation? I am trying to improve this score on a > > structure > > >> that I am working on, but I'm not really sure where to begin. From my > > >> understanding, the score is based on the number of RSRZ outliers with a > > score > > >>> 2. In my case, I have several residues with scores between 2 and 4, > > but at > > >> least by eye, fit to the electron density does not look that bad. > > Hence, I > > >> can't justify deleting them to try to improve the score. If the score > > is just > > >> based on percent of outlier residues, then for instance wouldn't a > > structure > > >> with say 20 residues modeled with no corresponding electron density > > have the > > >> same score as a structure with 20 residues with RSRZ values of say 2.5? > > >> > > >> > > >> I was also wondering how the resolution of the structure relates to the > > score? > > >> Glancing through several pdb validation reports, I noticed some > > structure > > >> with low resolution (3.5 A or lower) with relatively high scores, while > > others > > >> with high resolution (2 A or higher) getting low scores. It is > > reasonable to > > >> assume that a structure of lower than 3.5 A would be missing several > > side > > >> chains and may also have some ambiguous main chain electron density, > > which > > >> should in theory increase the RSRZ score. While of course every > > structure is > > >> different and the quality of it due to the rigor of the person building > > the > > >> model, I was wondering if there were any general trends related to > > resolution > > >> and RSRZ score. > > >> > > >> Thanks, > > >> Matt > > >> > > > > > -- mail: Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
