Dear Matthew,
In my search for the validity of meta data, I went through several data
sets in SBGrid and proteindiffraction.org (IRRMC), especially those
where automatic processing did not succeed are gave different results
with different processing software. We reprocessed those data sets with
EVAL and located some issues with the meta data. Most of the problems
are related to wrong or absent primary beam positions.
SBGrid is very useful to find problematic data sets, since it lists four
attempts to re-process the data.
Some interesting cases could be:
SBGrid:
373 automatic processing failed to see the crystal is C (or I)-centered
monoclinic
254 unit cell no so easy to index and inaccurate (and therefore space
group wrong) because of presence of a second and third lattice
426 beam center very wrong (has to be manually set)
415 another beam center problem; caused large errors in unit cell
dimensions in automatic processing (only xia2-3dii has it right)
383 is a very challenging case; might be too complicated; at least two
lattices amd C-centered orthorombic (which none of the automatic
processing software found)
IRRMC
3m8t: apparent monoclinic C2 symmetry, but is in fact triclinic. Also a
second smaller fragment present.
4i08: wrong beam center. Rotation direction may have to be reversed.
Store.Synchrotron:
public data set https://store.synchrotron.org.au/experiment/view/1037/
: one long unit cell axis: quite a challenge combined with inaccurate
beam center.
Let me add: several initiatives exist or are on the way to publish and
describe raw data of which the structure could not be solved due to all
kinds of reasons: indexing fails, phase problem can not be solved, lots
of additional reflections present, diffuse scattering. See progress
report and references in there
(http://forums.iucr.org/viewtopic.php?f=21&t=396) of the IUCr working
group DDDWG, now continued as COMMDAT committee.
Best wishes,
Loes
On 09/20/18 02:15, Whitley, Matthew J wrote:
Dear colleagues,
For teaching purposes, I am looking for a small number (< 5) of
macromolecular diffraction datasets (raw images) that might be
considered 'difficult' for a beginning crystallography student to
process. By 'difficult' I generally mean not able to be processed
automatically by a common processing package (XDS, Mosflm, DIALS, etc)
using default settings, i.e., no black box "click and done" processing.
The datasets I am looking for would have some stumbling block such as
incorrect experimental parameters recorded in the image headers,
multiple lattices that cause indexing to fail, datasets for which
determining the correct space group is tricky, datasets for experiments
in which the crystal slipped or moved in the beam, or anything else you
can think of. The idea is for these beginning students to examine
several datasets that highlight various phenomena that can lead one
astray during processing.
A good candidate dataset would also ideally comprise a modest number of
images so as to keep integration time to a minimum. Factors that are
mostly irrelevant for my purpose: resolution (as long as better than
~3.5 Å), source (home vs synchrotron), presence/absence of anomalous
scattering, presence/absence of ligands, monomeric vs oligomeric
structures, etc. Also, to be clear, I am not looking for datasets that
have so many pathologies that they would require many long hours of work
for an expert to process correctly.
I have checked public repositories such as proteindiffraction.org and
SBGrid databank, but all of the datasets I acquired from these sources
process satisfactorily with little effort, and in any event I know of no
way to search for 'challenging' datasets. (I also wonder whether
anybody is in the habit of depositing, shall we say, less-than-pristine
images to public repositories?)
If you know of such a dataset that is already publicly available, or if
you have such a dataset that you are willing to share for solely
educational purposes, I would appreciate hearing from you, either on- or
off-list.
Thank you in advance for your suggestions.
Matthew
--
__________________________________________
Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands
E-mail : l.m.j.kroon-batenb...@uu.nl
phone : +31-30-2532865
fax : +31-30-2533940
__________________________________________
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