PS. A completely unimportant correction to my comment on the MolProbity
output for 2HR0: every residue is indeed an outlier in at least one test,
but in three cases it is only the CB-deviation test, not the other three
tests that I mentioned.
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
On Sat, 18 Aug 2007, George M. Sheldrick wrote:
> 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
>
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