Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports
> 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. > > 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 >
[ccp4bb] PDB Storage of Diffraction Images
Hello, for convenience I might ask the CCP4BB: does anyone know what the status of the PDB is with regard to the storage of diffraction images? I had the impression that this matter had been discussed as far back as ~15 years ago but what came out of it? Short of storing images, which is the ultimate preservation of primary information, I have always been puzzled by the fact that the PDB only stores unique reflections i.e. no Friedel pairs even when provided. Is this outdated perhaps ? I remember that my deposited SFs in the past where reduced to not contain Friedel pairs. If there had been a concern about increasing the storage space by actually less than twice the space for unique SFs, this may be invalid today and is still far less than the space required for images. However, it is possible that the information content in Friedel pairs is deemed insignificant compared to their extra costs. I for one would appreciate having access to Friedel pairs very much. Thanks, Lothar
Re: [ccp4bb] PDB Storage of Diffraction Images
Hi Nat, okay. Looks like I missed this. Perhaps the data sets that I wish had Fiedel pairs didn't and this solidified my incorrect assumption(s) about pdb policy. So Fiedel pairs are there when deposited. What about storage of images? Is it coming soon - it feels like that it is about time Lothar On Fri, May 16, 2014 at 7:12 AM, esse...@helix.nih.gov wrote: Short of storing images, which is the ultimate preservation of primary information, I have always been puzzled by the fact that the PDB only stores unique reflections i.e. no Friedel pairs even when provided. Is this outdated perhaps ? I remember that my deposited SFs in the past where reduced to not contain Friedel pairs. If there had been a concern about increasing the storage space by actually less than twice the space for unique SFs, this may be invalid today and is still far less than the space required for images. However, it is possible that the information content in Friedel pairs is deemed insignificant compared to their extra costs. I for one would appreciate having access to Friedel pairs very much. They definitely store Friedel pairs! Maybe you're confused by the layout of the mmCIF file, which (like MTZ) usually lists just the unique (non-anomalous) indices, but with separate values for F+/F- when they are available. I've been making extensive use of anomalous data depositions - unfortunately there aren't as many as we would like, either because many people do not realize that this is useful information even when the experiment was not specifically looking for anomalous signal, or because the complexity of PDB deposition discourages providing the most complete data. An even more useful improvement would be to make deposition of unmerged intensities straightforward - the JCSG does this somehow but it is non-trivial for the average user. Hopefully this will also change soon. -Nat
[ccp4bb] Job Opening: Postdoctoral Position at the NIH Bethesda
Job Position Type : Postdoctoral Position At the NIH NCI Bethesda, MD USA Position Title: Structural Mechanism of Multi-Drug Resistance Position Description: Applications are invited for a postdoctoral position to investigate the structures and functional mechanisms of the macromolecular machines that are involved in cellular multidrug resistance. The position is associated with the Crystallography Section (http://ccr.cancer.gov/staff/staff.asp?profileid=5719) in the Laboratory of Cell Biology, National Cancer Institute, NIH, which is located in the Bethesda Campus, Maryland. The successful candidate should have a recent Ph.D. and have practical experiences in both molecular biology and protein purification. Experience in membrane protein and protein crystallization is a plus, but not required. Applications, consisting of a CV, a statement of research, and three letters of recommendation, should be sent to: Dr. Di Xia via Email at x...@mail.nih.gov Employer Name: National Cancer Institute, NIH Position Location: Bethesda, MD 20892, USA Disclaimers: The NIH is dedicated to building a diverse community in its training and employment programs and this position is subject to a background investigation. [Sent on behalf of Dr. Di Xia by L. Esser]
