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 other parameters?
No, x-ray beam survival had nothing to do with this. The dose was the
same per degree, so the damage was the same in all, at least on
principle, and from what I see in practice.
I simply think that the very low partiality of all reflections ends up
with counts that are just above the noise (even for a well set up
experiment and an excellent detector). The diffracting volume of these
crystals in some orientation was really small! 1x40x70 microns, only,
so the signals were very low. I think that the end integration goes
wrong because images cannot be well refined with so low-count data. As
soon as the reflections were stronger, things 'catch up'.
Also do anyone know where the threshold lies for when not to use
fine phi slicing on the PILATUS? ie, at what level of diffraction
would one need to increase the exposure (and oscillation in order to
still get redundant data)?
In general, the slicing of the Pilatus works great for us. My only
negative experience was really really small crystals.
We'll be in a similar position in the coming weeks with data
collection using PILATUS detectors, and would like to maximize the
potential data quality from our weak diffracting crystals. Any input
on this would be greatly appreciated!
I would aim to be able to see nice spots, to at least 3.5 A: these
would be enough to 'lock' the orientations, and I would expect either
XDS or MOSFLM to integrate even very low signals.
A.
Cheers,
Ronnie Berntsson
On Nov 5, 2010, at 16:16, Anastassis Perrakis wrote:
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 resolution?
2. If there is one thing I do not like in XDS, is that there is no
(or I have failed to find) statistics of I/sigI and Rmerge as
function of image.
Have a look at the SCALA output. Maybe some images are bad?
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 PILATUS, mosaicity 0.4-0.6) in an attempt to get better
Se signal. We miserably failed to get any useful signal at the end,
but learned that for these very weak diffracting plates (submicron)
collecting 0.5-1.0 degrees was actually giving at the end better
data.
A.
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
