Dear Annette,
I suspect that a trivial error like confusing F and intensity is the
cause of your problem. You would probably get a better response if you
sent your message to the very informative Bruker mailing list or asked
one of the Bruker applications scientists. If you wish to send me your
data in confidence I would be happy to try to sort it out for you. I
suggest that you send me the .raw files produced by the Bruker
integration program SAINT after gzipping them, please do not send the
frames(!). Note that the Bruker control software can also write
'unwarped' frames if you really need them, however we get excellent data
with the normal Bruker procedure (SAINT, SADABS, XPREP and then F2mtz
etc.). As Tim says, XPREP is not an integration program but it does
determine the space group and provide a lot of useful statistics.
My other strong recommendation, irrespective of which beamline or
in-house system you are using, is to collect a quick cubic insulin or
lysozyme dataset from time to time. This will tell you if all the
hardware and software is functioning correctly, and incidentally
provides you with a accurate X,Y beam position which can be invaluable
for indexing problem datasets.
Best wishes, George
On 06/25/2012 06:25 PM, Annette Medina Morales wrote:
Hi,
We collected data using our in-house Bruker Proteum X8 diffractometer
and after using Xprep to integrate the images the output HKL file was
converted to an mtz using CCP4's Scalepack2mtz. The prp file
generated by Xprep shows good statistics with completeness and good
data for 2.4 angstrom resolution. Mean intensity/sigma, Rsym, and
Rsigma have good values. Pointless indicates space group is P212121.
Later we used molecular replacement and obtained a good model and
Refmac to refine the structure. The electron density maps show the
correct density for the amino acids, waters, and other metals in the
structure and refinement with coot improves the electron density
around the atoms.
However, after multiple rounds of refinement the R value drops to 0.25
but Rfree does not go below 0.35! Also, the structure factors are
very low. We have tried all the obvious reasons as not having the
correct space group which is not the case, and have included NCS
restraints as well as TLS parameters to improve the refinement. None
of this has helped in helping the Rfree value go down. Since we never
have this problem with data collected from other detectors (like at
SSRL), and this problem repeats with other datasets from collected
in-house, we suspect that the original integration of the images using
Xprep might be a problem and might be doing something to the
reflection data. Does anyone have any experience with this?
Also, I have recently tried using iMosflm to refine the data but using
the .sfrm images from the Bruker detector is problematic since I get
an Application error that reads "invalid command name" and an "Image
read error" that reads "Error reading image header. Message from
Mosflm is error reading record 33: check image is correct size". Does
anyone have any advice on how to correct this since I understand that
iMosflm is supposed to be able to read Bruker .sfrm images? Thanks!
Annette
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
