And again, has anyone seen the code to even know what's going on "under the hood"?
Thanks,
Steve
> On Nov 29, 2016, at 8:35 PM, dusan turk <[log in to unmask]> 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<[log in to unmask]>
>> 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<[log in to unmask]> wrote:
>>>
>>> On 11/28/2016 12:52 PM,[log in to unmask] 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 [[log in to unmask]] on behalf of Matthew
>>>>> Bratkowski [[log in to unmask]]
>>>>> Sent: Tuesday, November 22, 2016 10:12 AM
>>>>> To:[log in to unmask]
>>>>> 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<[log in to unmask]>
>> 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: [log in to unmask]
> 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
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