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
