Hi Boaz,
We were informed by an RCSB annotator in April 2006 that the
RCSB had suspended including REMARK 42 records in PDB files
pending the review of the process by the wwPDB.
In looking at the new annotation guidelines, it looks
like the result of that review was to reject the REMARK 42
record and the listing of additional validation items.
See page 23 of the July 2007 "wwPDB Processing Procedures
and Policies Document"
http://www.wwpdb.org/documentation/wwPDB-A-20070712.pdf
"REMARK 42 and use of other programs for validation Use of REMARK 42 is
discontinued.
If authors wish to indicate presubmission validation and other programs used before
deposition, the programs may be listed in a new remark, REMARK 40. This remark will
list the software name, authors and function of the program. Results of the software will
not be listed. Use of this remark is voluntary."
It seems that the wwPDB only allows the inclusion of validation
statistics output by the refinement program but not from additional
validation programs. So for additional statistics to be included
in the PDB header, they will either need to be implemented by the
refinement package or the wwPDB annotators.
Regards,
Mitch
________________________________
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Boaz Shaanan
Sent: Sunday, August 19, 2007 2:38 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] The importance of USING our validation tools
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" <[log in to unmask]>
Date: Saturday, August 18, 2007 15:27
Subject: Re: [ccp4bb] The importance of USING our validation tools
To: [log in to unmask]
> 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
