Dear all,
technically, the ccp4bb (especially Conn Mallett and Jim Pflugrath)
helped to resolve the problem: The procedure to get ccp4-readable data
from the .ref files uses dtreflnmerge (provided as part of CrystalClear
/ d*trek from Rigaku) from the command line, for example:
dtreflnmerge.exe dtprofit.ref dtprofit_ascii.ref -ascii
These .ref files could be converted by dtrek2scala to an mtz file in ccp4.
These mtz files (one for every scan) were merged with sortmtz.
The sorted multibatch mtz file was scaled with aimless.
The structure was not solvable, though, which is a bit puzzling to me,
because the diffraction pattern is clean to better than 1 A resolution,
the unit cell only ca. 1000 cubic Angstrom (small molecule) and the
crystals contain Pd with an organic ligand. I am thus still wondering,
if something gets messed up in this procedure. I have also tried
processing with xds, mosflm and xia2 dials, they failed at indexing. I
don't have the resources to figure this out soon, but anybody, who is
curious to try the processing is welcome. Contact me directly in
December, success will be duly acknowledged.
Greetings
Gottfried
original post:
Problem with ref format (Rigaku)
Dear all,
this is a question about scaling data integrated in CrystalClear
(Rigaku data processing gui based on d*trek) in ccp4.
Since scaling dtprofit.ref files from different scans is sometimes poor
or even failing within CrystalClear (i.e. with dtscaleaverage after
merging them), I used to try scaling them with scala. I am facing this
problem mainly with high resolution / small molecule data collection,
where I need up to 20 scans, each 90-180 degrees, for complete low and
high resolution.
The procedure, that worked, was using
dtrek2scala for each scan (with scan1.ref and output_scan1.head, then a
second run of dtrek2scala for scan2.ref and output_scan2.head, etc.) to
create scan1.mtz, scan2.mtz, etc.
sortmtz with scan1.mtz, scan2.mtz, ... to create a multibatch mtz file
scala with the multibatch.mtz file to create the final scaled mtz file
Some time ago Rigaku changed the format of the .ref files, so
dtrek2scala is not working any more.
Is there a possibility to change the new .ref format to the old one? Or
can I read the new .ref files in scala or better aimless directly?
The alternative to process the images in xds hits a similar problem: The
format of the images has also changed and the new .img files (from the
Saturn92 detector) are not read anymore (whereas they used to be
processable in xds before).
Greetings
Gottfried
Dr. Gottfried Palm
Ernst-Moritz-Arndt-UniversitÀt
Inst. für Biochemie (MNF)
Abt. Biochemie I
Felix-Hausdorff-StraÃe 4
17489 Greifswald
