Dear Colleagues,
Since the announcement of the STARANISO server in the message
included below, numerous groups have submitted datasets for anisotropy
characterisation and optional correction, and sent us feedback. A few
cases are illustrated on the "Gallery" at
http://staraniso.globalphasing.org/staraniso_gallery.html
and more will be posted.
One of these users, who saw substantial improvements in his maps,
has asked us the natural question: what should I put in Table I of my
manuscript concerning the resolution and the completeness of my data
after treatment with STARANISO?
As usual, anisotropy needs several numbers to describe it rather
than just one, and the problem is that Table I has only one cell for
resolution. Besides requiring up to three distinct numbers for the
resolution limits in several "principal" directions, it is necessary
to specify these directions themselves. At first sight one might think
that these will be the reciprocal cell axes, but as shown by the third
example in the Gallery, this may not be the case in low-symmetry space
groups.
There is "prior art" in this area, for instance in the AIMLESS
program that reports resolution limits in general reciprocal-space
directions if necessary, and we have checked that these agree with
those produced by STARANISO. The main point is: how can one fit all
this information into Table I without revisiting its format? And, by a
knock-on effect, whatever goes into Table I should end up in the PDB
entry for the published structure: how, then, should room be made so
that resolution can be upgraded from a scalar to at least a 2nd-order
tensor?
A related question is that of coming up with a meaningful
definition of completeness in the presence of anisotropy. A certain
notion of incompleteness still needs to be associated with that of
missing regions (e.g. angular wedges) of reciprocal space, simply
because they were not collected, and therefore to the idea of being
able to increase it through a better executed experiment (e.g taking
the trouble to "fill the cusp"). When anisotropy is present, one is
forced by the current conventions to declare completeness of the set
of unique reflections for which significant intensities are available
(rather than just "indices", to quote a famous witticism by Keith
Wilson) by reference to the resolution limit in the best direction(s).
This can result in alarmingly low values, even though everything worth
measuring has been measured.
Shouldn't there be a way in which a dataset containing all
significant data measurable on a crystal with anisotropic diffraction
limits would be credited as having 100% completeness, as there is no
way of measuring more? With the present definitions it is impossible
to tell whether one is missing indices for which intensities would
have no information content anyway (because of anisotropy) or indices
for which significant intensities would have been expected but didn't
get measured (because of a sub-optimal strategy or by lack of care).
At least two different numbers would therefore seem to be needed:
(1) completeness with respect to the resolution limit in the best
direction(s), so that a "data miner" doesn't get misled as to the
accuracy of the coordinates;
(2) completeness with respect to e.g. an ellipsoid-like region to
which anisotropy restricts measurable reflections, so that credit is
given to the experimentalist for having done his/her best, given the
circumstances.
Many of you will have thoughts on this: we look forward to
hearing them!
With best wishes,
Gerard, Ian & the Global Phasing developers.
--
On Thu, Jan 07, 2016 at 10:56:04AM +0000, Gerard Bricogne wrote:
> Dear Colleagues,
>
> We have been working for quite some time on new software (called
> STARANISO) to analyse the anisotropy of X-ray diffraction intensity
> data and investigate the appropriateness of various remedial measures,
> as well as to revisit subtleties in standard processing steps such as
> TRUNCATE where the existing treatment left something to be desired in
> the presence of significant anisotropy.
>
> We are pleased to invite you to test-drive this program via a Web
> server that offers access to it, and would greatly value your feedback
> on it. To do this, please connect to
>
> http://staraniso.globalphasing.org
>
> and peruse the material, links and buttons presented to you there.
>
> As it is the whole capability (including its user documentation)
> that is being submitted to your scrutiny, we will say no more, as any
> obscurity experienced by a first-time would-be user is part of what we
> are counting on you to report to us :-) .
>
> Thank you in advance for your time and attention in evaluating
> this server and the usefulness of what STARANISO produces for you. We
> very much look forward to your feedback and suggestions.
>
>
> While this request can be found at the bottom of the main server
> Web page, we expressly ask here again that you send your feedback to
>
> [log in to unmask]
>
> and not to individual developers that you might know. Thank you!
>
>
>
> Wishing you a Happy and more isotropic New Year,
>
> Ian Tickle & the Global Phasing developers.
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