Hi LU, the reason why IDXREF is not indexing smoothly is that the spot positions in your SPOT.XDS are not very meaningful - you pick up a lot of noise! I plotted your SPOT.XDS using
%%:-/tmp/luo% gnuplot gnuplot> set size square gnuplot> set out "tmp.png" gnuplot> set term png nocrop medium size 1280,960 Terminal type set to 'png' Options are 'nocrop medium size 1280,960 ' gnuplot> plot 'SPOT.XDS' us 1:2 w dots gnuplot> quit and got the attached file tmp.png. This shows: - ice rings - streaks parallel to the x-axis - some modules of the detector behave very differently from others Poor IDXREF tries to make sense of all of this and still somehow manages to come up with something that may be useful for further processing. But the real remedy of the problems would be to properly set the parameters influencing the COLSPOT step. These are documented at http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html (load the page into your browser, and search for occurrences of COLSPOT). The most important ones in this case are probably MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=6 ! this is the default STRONG_PIXEL=3 ! this is the default INCLUDE_RESOLUTION_RANGE =50 0 ! no default, but you could try 50 4 to exclude the ice rings I don't know which values you used (you forgot to post XDS.INP), so I would try with the above first, run COLSPOT, inspect with the gnuplot technique I described, and then modify the parameters until the plot looks more meaningful, at which point IDXREF will most likely happily index. No, this is not fully automatic, but at least it's a logical way forward. good luck, Kay On Mon, 11 May 2015 19:56:33 +0800, luzuok <luzuo...@126.com> wrote: > Dear Karine and Jürgen, > > The XDS terminated in IDXREF with error message: > > > !! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS > > > In the COLSPOT, I can see > > NUMBER OF DIFFRACTION SPOTS LOCATED 53669 > > IGNORED BECAUSE OF SPOT MAXIMUM OUT OF CENTER 174 > > IGNORED BECAUSE OF SPOT CLOSE TO UNTRUSTED REGION 450 > > WEAK SPOTS OMITTED 11753 > > NUMBER OF DIFFRACTION SPOTS ACCEPTED 41292 > > > It seems that the accepted spots are enough. But I don't know why there > are so many spots which cannot be indexed. > > > Best wishes! > > > LU >
