Dear all, I had this experience: going pedantically to the individual points the RSRZ and other validation statistics in the form were reporting - in a vast majority of the cases nothing was wrong at all. So it seems to be somewhat overdoing its job - not that this is bad on its own - but we are losing contrast quite a bit between the really serious issues on ... all the other.
Jan Dohnalek On Wed, Nov 30, 2016 at 2:33 AM, dusan turk <dusan.t...@ijs.si> wrote: > Guys, > > I have a two issues to add here: > > 1. RSZS validation does not tolerate chain IDs longer than 1 character, so > it kills one of the very essential reasons why mmCIF format was introduced > (to enable deposition of large structures in a single file). > > 2. I have noticed in validation report of my own structure (4PIA) that the > RSZS does not ALWAYS work right. For example, the "PHE 63" is well resolved > with a hole in the ring, yet the validation declares it as a density > outlier. Besides there are several other residues in this structure that > "sit" well in the density, but are considered outliers, whereas several, > for which side chains the density is missing, are not listed. > > Has anyone else had a similar experience? > > Taken all remarks together they suggest that something needs to be done > with RSZS software or density validation procedure to resolve these issues. > > ???? > > best, > dusan > > > On 30/11/16 01:00, CCP4BB automatic digest system wrote: > >> Date: Mon, 28 Nov 2016 20:35:44 -0800 >> From: Pavel Afonine<pafon...@gmail.com> >> Subject: Re: Calculation of RSRZ Score in PDB Validation Reports >> >> 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. >> >> 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 >>>>> >>>>> ------------------------------ >> >> Date: Mon, 28 Nov 2016 21:46:24 -0800 >> From: Ethan Merritt<merr...@u.washington.edu> >> Subject: Re: 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 >> >> > -- > Dr. Dusan Turk, Prof. > Head of Structural Biology Group http://bio.ijs.si/sbl/ > Head of Centre for Protein and Structure Production > Centre of excellence for Integrated Approaches in Chemistry and Biology of > Proteins, Scientific Director > http://www.cipkebip.org/ > Professor of Structural Biology at IPS "Jozef Stefan" > e-mail: dusan.t...@ijs.si > phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biol. > fax: +386 1 477 3984 Jozef Stefan Institute > Jamova 39, 1 000 Ljubljana,Slovenia > Skype: dusan.turk (voice over internet: www.skype.com > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758
