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 >> >
