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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