Dear Kay,
I've tune these parameter for many times, and I got best results . :SPOT_RANGE=1 100 INCLUDE_RESOLUTION_RANGE=50 4.2 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=20 but still got the same error message! The SPOT.XDS file was ploted (see attachment "spot_15.png" ), it seems that the ice ring and beam stop shadow was excluded. But the result is still frustrating. Best wishes! LU zuokun -- 卢作焜 南开大学新生物站A202 At 2015-05-11 23:20:55, "Kay Diederichs" <kay.diederi...@uni-konstanz.de> wrote: >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 >> > > >
XDS.INP
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IDXREF.LP
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