Am 20:59, schrieb Sergei Strelkov:
...
I still tend to think that the best proof would be in the pudding,
i.e. trying to pool thin frames into thicker frames
(but I do not have an immediate means of doing this... )
Sergei,
try to locate 2pck and 2pck.man which were part of former XDS
distribu
Dear All,
first of all, I would like to thank the many
good people who have responded to my query.
Yet another truly interesting discussion on this BB!
As a partial summary, two points:
1. Few people suggested that our high Rmerge problem
could be caused by experimental troubles
like phi angle
Dear Ronnie,
we are working with weak diffracting crystals. Many tests (and taking
into account Marcus Muellers results) showed that 0.3-0.5 of XDS
mosaicity, (very) low dose, and high redundancy give the best results.
Our crystals diffract between 7 and 4 A. At low dose I do not check
diffra
Hi All
Both Martin and Kay ( in a later message) have misinterpreted what I
wrote - what I meant was that it seems normal in using XDS with
Pilatus data, not the normal thing to do with data from other detectors.
I had found a number of scripts on the web that deal specifically
with proce
Am 20:59, schrieb Harry Powell:
...
I think there may be issues with collecting data too finely with a
Pilatus, even in shutterless mode. I don't know where the problems arise
(can't be shutter/rotation axis synchronisation), but it seems to be the
normal thing in XDS (which should have no proble
Compensating like this is of course not the best (go and recollect!)
but still way better than unusable data in the meantime. In the case
Sergei originally described it would at least indicate what the
problem may be. Sergei did not say which detector was used for the
data collection so we don't k
Hi Harry,
On Nov 5, 2010, at 5:45 PM, Harry Powell wrote:
>
> I think there may be issues with collecting data too finely with a Pilatus,
> even in shutterless mode. I don't know where the problems arise (can't be
> shutter/rotation axis synchronisation), but it seems to be the normal thing
>
Hello Tassos,
the data you are missing are available from XDS_ASCII.HKL and can e.g. be
generated with Kay Diederichs xdsstat, see
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSSTAT
According to the web site, it prints Rmeas instead of Rmerge, but since Rmeas
should anyhow be promo
Hi
I'd read Jim Pflugrath's 1999 paper in Acta D for a discussion on fine phi
slicing - in general, if memory serves me correctly, he suggested using an
oscillation angle ~0.5x the mosaic spread.
I think there may be issues with collecting data too finely with a Pilatus,
even in shutterless mo
In the Pilatus mode these are "open-shutter" experiment, where the
Pilatus integrates over different times
- all these exposure times are slower than the frequency of the
detector, as far as I understand the setup.
So, the crystal gets the 'full blast' in all cases, and the blast is
the sam
On Nov 5, 2010, at 16:57, Ronnie Berntsson wrote:
Dear Tassos,
I'm interested in your third point. Do you have any explanation for
why 0.5-1 degrees oscillation gave better data? Purely due to the
fact that the crystals survived longer and thus yielded higher
redundancy data, or also oth
3. making too fine slices of too weak diffraction images ends up with
either too weak counting statistics or inability to 'lock' the
refinement.
we did that for one crystal form, collecting 0.1, 0.2, 0.35, 0.5, 0.7,
1.0 from various crystals (with the same dose per degree, at SLS using a
PILAT
Dear Tassos,
I'm interested in your third point. Do you have any explanation for why 0.5-1
degrees oscillation gave better data? Purely due to the fact that the crystals
survived longer and thus yielded higher redundancy data, or also other
parameters?
Also do anyone know where the threshold li
three additional points:
1.
OTOH, if "The diffraction is quite weak", one may be limited by
counting
statistics. This also cannot be overcome by processing.
As JIm suggests above then, maybe you should look if the 15% Rmerge is
almost reasonable given the specific I/sigI at low resolutio
mailto:ccp...@jiscmail.ac.uk] On Behalf Of Sergei
Strelkov
Sent: Friday, November 05, 2010 3:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] High Rmerge with thin frames
Dear All,
I am processing a dataset collected (not by me) with 0.1 degree
oscillations.
The diffraction is quite weak even though there
Hi Sergei,
such fine slicing during data collection would suggest a large cell. How many
reflections are you merging? And what is the redundancy (in the expected
symmetry)? Rmerge tends to go up with more reflections added.
Peter
On 5 Nov 2010, at 08:40, Sergei Strelkov wrote:
> Dear All,
>
the ESRF. Unfortunately the pages are no longer available,
but I might have a backup if you are interested.
Cheers,
Bill
De: CCP4 bulletin board de la part de Sergei Strelkov
Date: ven. 05/11/2010 09:40
À: CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] High Rmerge with thi
Dear Sergei,
Did you check the "mean intensity as function of spindle position" statistics
in the CORRECT.LP file?
Any (even minute) shutter problems will affect these thin frames significantly.
If this is indeed the problem, you could then try to set:
PATCH_SHUTTER_PROBLEM=TRUE
for the CORRECT
Dear Sergei
how much do the refined unit cell parameters (given a fixed detector distance)
vary as a function of frame number? We have been using such initial diagnostic
approach to trace radiation damage issues (among other problems) for a number
of crystal forms that maximally diffracted in th
Dear Sergei,
since your Rmerge is high at low resolution even in P1, my guess is,
that there was a problem either with the crystal or with the data
collection. Fine slicing should improve the data quality, because your
get a better description of the reference profiles and reduce the
backgrou
Dear Sergei,
with only 3A data and 0.1 deg frame width my first guess would be radiation
damage.
In that case there is little you can do - the Rmerge might just be realistic.
XDS has not problem dealing with thin frames (on the contrary!) and it won't
help pooling frames together.
Check out the s
Dear All,
I am processing a dataset collected (not by me) with 0.1 degree
oscillations.
The diffraction is quite weak even though there is a clean diffraction
pattern to about 3A.
Either Mosflm or XDS processes the data readily with +/- default settings
but both yield a high overall Rmerge of
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