Dear Khoa,
You are asking a very pertinent question, that will resonate in
(too) many people's minds.
Somehow anisotropy is very much "an inconvenient truth" in MX, as
many things have long been set up and operated on the basis of having
resolution be a single number and of all statistics being calculated
in spherical shells, throwing in everything that has an HKL associated
with it. We are repeatedly told that resolution *has* to be a single
number, because the title of a Nature paper only has room for one
number - if that isn't a case of the tail wagging the dog, I don't
know what is ;-) .
There are more serious contexts in which the requirement for a
single number can be a more complex issue, such as contractual
arrangements where the achievement of certain milestones and the
remuneration attached to them depend on reaching a certain resolution.
Here, whoever writes and/or accepts resolution criteria of this kind
will simply have to undergo further education and learn about that
inconvenient fact called anisotropy. Probably - especially in the case
of membrane protein structures - it is the highest resolution limit
that matters; but you can't have good completeness to that highest
resolution, by the very definition of anisotropy! Therefore, some
quality criteria that are compatible in the case of isotropic data can
become contradictory for anisotropic data, and force absurd decisions
to be made that result in the discarding of perfectly good data in
order to get back to a pseudo-isotropic situation.
Your question is very timely as well, as we are about to announce
a new version of the STARANISO server in which we have made an effort
to address these questions. You say you have used the UCLA server: it
is a fine resource, that has served the community for over a decade,
but there are limitations in its treatment of anisotropy, especially
in low-symmetry cases. Your structure is in C2, and if you look at the
example of a C2 structure at
http://staraniso.globalphasing.org/anisotropy_about.html
and especially at the picture at
http://staraniso.globalphasing.org/pereda.png
you will see that anisotropy can be such that it cannot be described
as separate effects along the individual crystallographic axes: in
this case, the principal directions are along the bisectors and not
along the axes, and a product of separate corrections along the two
axes would do a very bad job indeed. This is why I think you should
submit your data to the STARANISO server as well. You may also find
the interactive 3D display of the local average of I/sig(I) quite
informative about possible infelicities in your dataset.
Returning to a broader perspective, one thing should be clear:
there cannot be any good reason, based on downstream considerations
(such as what the PDB is prepared to accept, or there being room for
only a single number in manuscript titles and outsourcing contracts),
for throwing away data that are, as judged by a 3D local average of
I/sig(I), significantly above noise. The mission of data processing is
to capture every bit of information present in the raw images, without
any censorship originating from what may happen further downstream as
a result of anisotropy. All entities concerned (PDB, reviewers, legal
departments) will simply have to change their mental habits in order
to accommodate the inconvenient existence of anisotropy, as it is here
to stay :-) . In fact it has always been there, but has become harder
to ignore.
With best wishes,
Gerard.
--
On Sun, Jun 18, 2017 at 11:52:34AM +0000, Khoa Pham wrote:
> Dear Gerard,
>
> Thank you very much for your suggestions.
> We actually analyzed anisotropy of the data using UCLA-DOE LAB Diffraction
> Anisotropy Server https://services.mbi.ucla.edu/anisoscale/. The question is
> that if the data cut in the anisotropically way, should it be deposited to
> the pdb.
>
> Sincerely,
>
> Khoa Pham
--
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