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
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
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
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
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,
It is difficult to say without looking at XDS or MOSFLM logfiles, but this sort
of problem (high flat Rsym in all resolution bins) sounds like the crystal
vibrating wildly in the cryostream. You could ask the data collector the
following questions: 1) Was the cryostream
Dear CCP4ers,
sorry for this off-topic question, but maybe, somebody can answer this:
I want to refine some self-defined dummy-atoms (scatter.lib, topology,
parameter: all copypaste from water and modified) with CNS and get the
following enigmatic error message:
%CONNE2 error encountered:
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,
Dear All,
We have a fully funded position open for postdoctoral researchers to study
the mechanism and regulation of mobile DNA with Structural Biology
(crystallography) and Biochemistry.
The successful applicant will join the Barabas group at the Structural and
Computational Biology Unit,
In general, if the Rmeas or Rmerge is high in the low resolution shells,
then something is not optimal with the data collection.
Bill Shepard has already mentioned the loop vibrating or moving in the
cryogenic gas flow. Other problems could be the goniometer head was loose,
the magnet was loose,
Refmac doesn't output mFo as such, however it does output DFc: that's
what is in the columns FC PHIC, or FC_ALL PHIC_ALL if you want the
total DFc including solvent contribution.
You could obviously get mFo by multiplying the FP FOM columns, or
you could do it using the fact that mFo =
Dear CCP4ers,
After I make Molecular replacement with Phaser and combine the resulting mtz
and the anomalous .mtz using CAD, I obtain an anomalous map which shows me
good anomalous signal. I'm displaying this map in coot by choosing in the
expert mode the labels DANO and PHWT (or PHIC together
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
Hi Maiclo,
After I make Molecular replacement with Phaser and combine the resulting
mtz and the anomalous .mtz using CAD, I obtain an anomalous map which shows
me good anomalous signal. I'm displaying this map in coot by choosing in the
expert mode the labels DANO and PHWT (or PHIC together
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
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
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 same
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
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
OK you could be right, it's not an issue for me because I never use
the FC/PHIC columns anyway, since it's not clear why you *wouldn't*
want to include the solvent contribution, as opposed to any of the
other contributions to the SF (what's so special about the solvent?).
In fact it's not clear
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
in
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
Hi,
I have been trying to download the program nucplot from
http://www.biochem.ucl.ac.uk/bsm/nucplot/avail.html but the files are no longer
available there. Could somebody tell me where I can download the program, or if
there is an equivalent program I could use to make a schematic of
Dear all,
I'm working on a protein which starts to precipitate after 3-4 days of storage
at 4 degrees or room temperature. The storage buffer contains 300 mM NaCl
because at lower salt concentrations it also tends to precipitate. Different
buffers and adding glycerol did not help although this
Hello Eric,
Does your protein also precipitate at lower protein concentrations? In
isolated cases, we've had protein stocks precipitate overnight at 4 degrees,
and the only way around it was to store them diluted, and concentrate right
before any experiments/crystallization trials. In two
Dear Joyce,
PDBsum/EBI also produces Nucplot output. You can also upload you own file
for analysis.
also this might help you http://monster.northwestern.edu/
If you find any other alternatives, I am happy to hear them.
HTH,
Juha
On 5 November 2010 21:06, Joyce wrou...@yahoo.com wrote:
Hi,
Hello Eric,
I would try not to store a protein for 3-4 days and set up drops as quickly as
possible. 3-4 days can be a long time for a sensitive protein. If you expressed
too much, add 15% glycerol and store the protein at -80deg. Gel-filtrate the
solution and re-concentrate before the next use.
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