Curiously enough, when I've recently submitted a coordinates file to RCSB with
this Molprobity summary (as remark 42; it is added onto the analyzed file by
the Molprobity program) it was deleted by the RCSB team.
Boaz
----- Original Message -----
From: "George M. Sheldrick" <[EMAIL PROTECTED]>
Date: Saturday, August 18, 2007 15:27
Subject: Re: [ccp4bb] The importance of USING our validation tools
To: CCP4BB@JISCMAIL.AC.UK
> There are good reasons for preserving frames, but most of all
> for the
> crystals that appeared to diffract but did not lead to a
> successful
> structure solution, publication, and PDB deposition. Maybe in
> the future
> there will be improved data processing software (for example to
> integrate
> non-merohedral twins) that will enable good structures to be
> obtained from
> such data. At the moment most such data is thrown away. However,
> forcing
> everyone to deposit their frames each time they deposit a
> structure with
> the PDB would be a thorough nuisance and major logistic hassle.
>
> It is also a complete illusion to believe that the reviewers for
> Nature
> etc. would process or even look at frames, even if they could
> download
> them with the manuscript.
>
> For small molecules, many journals require an 'ORTEP plot' to be
> submitted
> with the paper. As older readers who have experienced Dick
> Harlow's 'ORTEP
> of the year' competition at ACA Meetings will remember, even a
> viewer
> with little experience of small-molecule crystallography can see
> from the
> ORTEP plot within seconds if something is seriously wrong, and
> many
> non-crystallographic referees for e.g. the journal Inorganic
> Chemistry
> can even make a good guess as to what is wrong (e.g wrong
> element assigned
> to an atom). It would be nice if we could find something similar
> for
> macromolecules that the author would have to submit with the
> paper. One
> immediate bonus is that the authors would look at it carefully
> themselves before submitting, which could lead to an improvement
> of the
> quality of structures being submitted. My suggestion is that the
> wwPDB
> might provide say a one-page diagnostic summary when they
> allocate each
> PDB ID that could be used for this purpose.
>
> A good first pass at this would be the output that the
> MolProbity server
> http://molprobity.biochem.duke.edu/ sends when is given a PDB
> file. It
> starts with a few lines of summary in which bad things are
> marked red
> and the structure is assigned to a pecentile: a percentile of 6%
> means
> that 93% of the sturcture in the PDB with a similar resolution
> are
> 'better' and 5% are 'worse'. This summary can be understood with
> very
> little crystallographic background and a similar summary can
> of course be produced for NMR structures. The summary is
> followed by
> diagnostics for each residue, normally if the summary looks good
> it
> would not be necessary for the editor or referee to look at the rest.
>
> Although this server was intended to help us to improve our
> structures
> rather than detect manipulated or fabricated data, I asked it
> for a
> report on 2HR0 to see what it would do (probably many other
> people were
> trying to do exactly the same, the server was slower than
> usual).
> Although the structure got poor marks on most tests, MolProbity
> generously assigned it overall to the 6th pecentile, I suppose
> that
> this is about par for structures submitted to Nature (!).
> However there
> was one feature that was unlike anything I have ever seen before
> although I have fed the MolProbity server with some pretty ropey
> PDB
> files in the past: EVERY residue, including EVERY WATER
> molecule, made
> either at least one bad contact or was a Ramachandran outlier or
> was a
> rotamer outlier (or more than one of these). This surely would
> ring
> all the alarm bells!
>
> So I would suggest that the wwPDB could coordinate, with the
> help of the
> validation experts, software to produce a short summary report
> that
> would be automatically provided in the same email that allocates
> the PDB
> ID. This email could make the strong recommendation that the
> report file
> be submitted with the publication, and maybe in the fullness of
> time
> even the Editors of high profile journals would require this
> report for
> the referees (or even read it themselves!). To gain acceptance
> for such
> a procedure the report would have to be short and comprehensible
> to
> non-crystallographers; the MolProbity summary is an excellent
> first
> pass in this respect, but (partially with a view to detecting
> manipulation of the data) a couple of tests could be added based
> on the
> data statistics as reported in the PDB file or even better the
> reflection data if submitted). Most of the necessary software
> already
> exists, much of it produced by regular readers of this bb, it
> just needs
> to be adapted so that the results can be digested by referees
> and
> editors with little or no crystallographic experience. And most
> important,
> a PDB ID should always be released only in combination with such
> a
> summary.
>
> George
>
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-2582
>
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
