Hi Clemens,
Thanks for pointing out the table in the PDBpeep log file. It has the data I
need and since the issue only applies to deposited PDB entries it does the
trick quite nicely.
Cheers,
Robbie
> -----Original Message-----
> From: Clemens Vonrhein <vonrh...@globalphasing.com>
> Sent: Wednesday, June 3, 2020 14:18
> To: Robbie Joosten <robbie_joos...@hotmail.com>
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Completeness question
>
> Dear Robbie,
>
> On Sat, May 30, 2020 at 08:36:06AM +0000, Robbie Joosten wrote:
> > I've been looking at some recent PDB entries that have much lower
> > spherical) completeness than reported in the coordinate file. One
> > reason for this is that the data were anisotropicly truncated, another
> > reason is some mess-up with the deposition of the reflection data.
> > There is a lot of discussion about the former practice and I don't
> > want to go in to that, but the second one is obviously an error. Now
> > how do I distinguish these cases?
> >
> > Sometimes, you can look at the reported number of reflections and
> > compare that to the deposited reflection file and you will find that
> > something has clearly gone wrong. However, the reported number of
> > reflections is not entirely reliable because of other issues so I'd
> > rather not use it. If you use PDBpeep (e.g. for 6rjy) you can see
> > something is wrong, but that is completely visual. Is there a tool in
> > CCP4 that reports both spherical and ellipsoidal completeness (on
> > merged reflection data)? That would make it easy to distinguish such
> > cases.
>
> One needs a description of the anisotropy in a form that allows for a simple
> computation ("Is a reflection above a significance limit or
> not?") to relate this to the completeness of reflections above such a
> significance level. That model could e.g. be the ellipsoid fitted to the
> significance (local <I/sigI>) cutoff surface as done by STARANISO [1]. You can
> see that information e.g. at the PDBpeep server [2]:
>
> http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6rjy
>
> as
>
> Diffraction limits & principal axes of ellipsoid fitted to diffraction
> cut-off
> surface:
>
> 1.747 1.0000 0.0000 0.0000 a*
> 1.777 0.0000 1.0000 0.0000 b*
> 1.465 0.0000 0.0000 1.0000 c*
>
> Of course, if this information is already present in deposited PDB entries of
> interest, no additional computation is required. We are currently working
> with our colleagues from the PDBx/mmCIF working group on definitions and
> items that would extend the current PDBx/mmCIF dictionary so that the
> above information could be deposited to and retrieved from the PDB
> database.
>
> In any case, this information is then used for computation of the spherical
> and ellipsoidal completness e.g. within STARANISO - see link to the
> "complete log file" at the bottom of the page:
> http://staraniso.globalphasing.org/PDB/6rjy.log. It contains a table
> ("Statistics for isotropic, anisotropic & ellipsoidal diffraction
> cut-offs") where Cmeas_sph and Cmeas_ell should give the above
> information (showing clearly that for 6rjy something else went wrong during
> deposition).
>
> If there is unmerged data deposited, one could give that ellipsoid description
> e.g. to MRFANA [3] via
>
> mrfana -ell 1.747 1.0 0.0 0.0 1.777 0.0 1.0 0.0 1.465 0.0 0.0 1.0
> unmerged.mtz
>
> to get the same information (but maybe use different binning, limit
> resolution ranges etc).
>
> Cheers
>
> Clemens, Claus, Ian & Gerard
>
> [1] http://staraniso.globalphasing.org/
> [2] http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi
> [3] https://github.com/githubgphl/MRFANA, a result of the Data Quality
> Metrics Workshop organised by Global Phasing at the ESRF in April
> 2019
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