Hi,
While on the subject, a related matter that may be of relevance:
surprisingly many people do not remove the outliers after XDS
processing (via using the REMOVE.HKL file) and this, in certain
cases, has its effects on the intensity distribution and 'refinability'.
Petri
On Feb 21, 2008, at 11:44 AM, Kay Diederichs wrote:
Engin Ozkan schrieb:
Hi everyone,
I have been recently relying on XDS quite a bit, but at the same
time worrying about how XDS treats overlaps. We had one dataset
that both HKL2000 and Mosflm would show to have severe overlaps,
as expected due to unit cell parameters and the unfortunate
crystal orientation in the loop. We always ended up with
completeness percentages in the 70's.
XDS can find the same lattice, index and scale the data, but
yields a 100% complete mtz (and a nice structure). Without the HKL/
Mosflm-like GUI, it is difficult to assess the fate of the
overlapped observations in XDS. What I could see with VIEW was
that some observations were being divided into several ovals,
probably different reflections, but I'm not very certain.
So, the basic question is, how does XDS treat overlaps? I could
not find in the documentation an answer to this question; the
single mention of overlaps I could find tells me that XDS can
recognize overlaps, but does not tell me if it rejects them, or
divvies them up into separate reflections, and if that is the
case, how does it divide them, and how reliable is that? Depending
on how it divides the overlaps, could that affect commonly-used
intensity stats and distributions?
Thanks,
Engin
Engin,
the basic answer is:
a) each pixel of the detector is assigned to its nearest reflection
in reciprocal space
b) some of these pixels will mostly allow the background
estimation, others will mostly contribute to the integration area
(but as they are transformed into a local coordinate system there
is not a 1:1 relationship). At this step, pixels which should be
background but are higher than expected (due to overlap) are rejected.
c) for each reflection, the background is estimated, and the 3D
profile is assembled from the pixels contributing to it
d) a comparison is made: for a reflection, is the percentage of its
observed profile assembled in c) larger than some constant (called
"MINPK" in XDS.INP)? If the answer is no, this reflection will be
discarded (you could call this situation "overlap").
Among other things, this means that:
a) the program does _not_ look around each reflection to detect an
overlap situation, it just tries to gather the pixels for each
reflection
b) as a user, when your crystal-detector distance was chosen too
low or the reflections are very broad (resulting in generally
strong overlap), you may reduce MINPK down to 50. This will result
in more completeness, but you should monitor the quality of the
resulting data. Conversely, if you raise MINPK over its default of
75 you will discard more reflections, but the resulting dataset
will be a bit cleaner.
The reference is
W. Kabsch (1988) Evaluation of single-crystal X-ray diffraction
data from a position-sensitive detector. J. Appl. Cryst. 21,
916-924. (http://dx.doi.org/10.1107/S0021889888007903)
HTH,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
---
Petri Kursula, Ph.D.
Academy Research Fellow
Docent of Neurobiochemistry
Department of Biochemistry
University of Oulu
Oulu, Finland
[EMAIL PROTECTED]
cc.oulu.fi/~pkursula
www.biochem.oulu.fi/kursula
---
