I started a ccp4 thread a few years ago about RSRZ score calculations favoring trimmed side chains because they produce better scores. Based on what I could find at that time, it looked like the density of your structure was compared to the density of that residue type in submitted PDBs of similar resolutions. However, I could be seriously mistaken.
Cheers, Katherine On Mon, Nov 28, 2016 at 11:46 PM, Ethan Merritt <merr...@u.washington.edu> wrote: > 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 > -- "Nil illegitimo carborundum"* - *Didactylos
