Hi Almu, some other pointers that might be useful in your case:
* Check the list of known beamline configurations (and particulars) at [1] and [2] to see if there is something you need to tell the processing software about. * If you have multiple lattices, split spots or ice rings (or combinations of these), something like "iterative indexing" can ensure that subsequent integration starts from a good, initial orientation matrix [3,4]. * Finally a note about damaged/unmasked pixels: these can greatly confuse COLSPOT when it comes to classifying so-called "weak spots" with odd results [5,6,7]. As Kay said, there are very few datasets where XDS indexing is genuinely stuck - as long as (a) there are spots with a hint of a spotlike shape and (b) the processing is told about beamline and detector specifics. Cheers Clemens [1] https://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings [2] https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP [3] https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_IterativeIndexing [4] https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Indexing [5] https://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings#hotpixels [6] https://www.globalphasing.com/autoproc/wiki/index.cgi?AnalyseDataForDamagedPixels [7] https://www.globalphasing.com/autoproc/wiki/index.cgi?DataProcessingHdf5Eiger16bit201910 On Sat, Nov 30, 2019 at 11:06:42AM +0100, Almudena Ponce Salvatierra wrote: > Hi Raphael, > > Thank you very much. I tried yesterday with different origins and I have > changed the REFINE(IDXREF) keyword several times as to refine BEAM, > POSITION, DISTANCE... I have to keep trying because fo far I didn't succeed. > > I will get back to you once I find what the problem is. > > Thank you once again! > > Best, > > Almudena > > El vie., 29 nov. 2019 a las 12:56, R. Gasper-Schönenbrücher (< > raphael.gas...@mpi-dortmund.mpg.de>) escribió: > > > Hi Almu, > > > > this is most often the case, when your beam center is not assigned > > correctly. Try to find out the beam center: > > > > > > https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Finding_out_ORGX_ORGY > > Another possibilty is that the distance that you get from the > > header/machine is not very accurate. You can try to slightly adjust your > > distance and see, whether this improves your indexing (e.g. instead of 50 > > start from 52). > > > > In XDS.INP you can enable distance refinement (as well as beam center > > refinement) throughout all steps. Just remove the "!" in "Refine" > > > > Hope this helps, > > > > Best wishes, > > > > Raphael > > > > > > On 29.11.19 12:48, Almudena Ponce Salvatierra wrote: > > > > Dear all, > > > > I have some data sets that don't want to be processed :p > > > > In one of them, when I look at IDXREF.LP I see virtually none of the found > > spots were indexed and the reason is that they are "too far from the > > expected position". The spots are smeary and elongated, so not the > > prettiest. > > > > I have managed to process so far only one data set with decent statistics > > from another crystal harvested from the same drop, where the diffraction > > spots look better. > > > > I am trying to find in the xds wiki the keyword I should fine tune in > > order to make those spots indexable. > > > > Could you help me please? > > > > Thank you very much in advance. > > > > Best wishes, > > > > Almu > > > > ------------------------------ > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > > Dr. Raphael Gasper-Schönenbrücher > > Crystallography and Biophysics Facility > > Max-Planck-Institute of Molecular Physiology > > Room F0.92 > > Otto-Hahn-Str. 11 > > 44227 Dortmund, Germany > > Tel +49 (0)231-133 2729 > > > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
