-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Natalie,
I usually look at the first frame with adxv and estimate the ORGX ORGY (which can be different from the direct beam position) by eye based on shadows (as Kay mentioned before) or ice rings and copy the values into XDS.INP. Regards, Tim On 05/12/2015 03:08 PM, Natalie Tatum wrote: > Dear Lu, > > Just last week I faced an almost identical problem: iMoslfm had no > problem but XDS failed. I discovered, as Kay has suggested, the > ORGX and ORGY values were incorrect in XDS.INP. In fact, they had > essentially been swapped. If you have AUTOINDEX.INP from fast_dp, > you can compare the values. For me, they were correct in > AUTOINDEX.INP but incorrect in XDS.INP. I'd suggest (because it > fixed the problem for me) simply swapping the values of ORGX and > ORGY back, and rerunning XDS. > > HTH > > Natalie > > > On 12 May 2015 at 13:54, Kay Diederichs > <kay.diederi...@uni-konstanz.de> wrote: > >> Dear LU, >> >> yes, your spot_15.png looks good. What worries me now is the >> table >> >> INDEX_ QUALITY DELTA XD YD X Y Z >> DH DK DL ORIGIN >> >> 0 0 0 1.7 0.1 997.7 1020.9 0.0010 0.0005 >> 1.0219 0.38 0.51 0.25 0 -1 0 3.0 0.4 1002.5 >> 1000.4 0.0026 -0.0063 1.0219 0.36 0.27 0.16 0 0 -1 >> 3.3 0.4 972.7 1021.8 -0.0073 0.0009 1.0219 0.30 0.42 >> 0.19 0 -1 -1 4.0 0.5 977.6 1001.3 -0.0057 -0.0059 >> 1.0219 0.34 0.32 0.15 1 -1 0 5.2 0.4 1012.8 >> 1027.9 0.0060 0.0029 1.0219 0.48 0.64 0.30 1 -1 -1 >> 5.4 0.2 988.2 1028.8 -0.0022 0.0032 1.0219 0.58 0.75 >> 0.38 0 0 1 6.0 0.5 1022.8 1019.9 0.0094 0.0002 >> 1.0219 0.48 0.63 0.31 1 0 0 6.2 0.6 1008.1 >> 1048.3 0.0045 0.0097 1.0219 0.28 0.53 0.15 1 0 -1 >> 6.7 0.6 983.3 1049.2 -0.0038 0.0100 1.0219 0.36 0.56 >> 0.19 0 -1 1 7.7 0.7 1027.5 999.4 0.0109 -0.0066 >> 1.0219 0.38 0.26 0.18 0 1 0 7.9 0.4 992.8 >> 1041.6 -0.0006 0.0074 1.0219 0.61 1.05 0.46 0 1 -1 >> 9.6 0.7 967.7 1042.5 -0.0090 0.0077 1.0219 0.50 0.91 >> 0.40 0 -1 -2 10.5 0.8 952.9 1002.3 -0.0139 -0.0056 >> 1.0218 0.35 0.40 0.17 ... >> >> That table is based on the assumption of ORGX=994.64 ORGY=1019.22 >> (the values from the header), so IDXREF puts the origin of the >> reciprocal lattice closest to these given values. However, as the >> table indicates, choosing the origin at other places (columns XD >> YD) would result in much lower DH DK DL, so it may well be the >> case that the values of ORGX ORGY are not correct. From the frame >> hg6_L1_1_00001.mccd you posted, I would rather (visually, based >> on beamstop shadow) estimate ORGX ORGY to be at 980 1060 or so. >> If I run (using the SPOT.XDS you posted yesterday) IDXREF with >> e.g. ORGX=994.64 ORGY= 1035 then I get better indexing, and a >> rather clear indication that the space group is orthorhombic: >> INDEX_ QUALITY DELTA XD YD X Y Z >> DH DK DL ORIGIN >> >> 0 0 0 1.8 0.2 998.4 1022.2 0.0015 -0.0050 >> 1.2019 0.25 0.35 0.15 0 -1 0 2.5 0.1 994.3 >> 1040.4 -0.0001 0.0021 1.2019 0.38 0.57 0.25 0 0 1 >> 3.3 0.4 977.2 1020.4 -0.0068 -0.0057 1.2019 0.21 0.37 >> 0.14 0 -1 1 4.0 0.4 973.1 1038.5 -0.0084 0.0014 >> 1.2019 0.32 0.52 0.22 0 0 -1 4.7 0.5 1019.7 >> 1024.1 0.0098 -0.0043 1.2019 0.35 0.35 0.18 0 -1 -1 >> 5.3 0.4 1015.5 1042.3 0.0082 0.0029 1.2019 0.45 0.62 >> 0.28 and LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS >> (ANGSTROEM & DEGREES) CHARACTER LATTICE OF FIT a b >> c alpha beta gamma >> >> * 44 aP 0.0 64.5 93.3 116.4 90.2 90.0 >> 90.0 * 31 aP 0.4 64.5 93.3 116.4 89.8 >> 90.0 90.0 * 35 mP 1.0 93.3 64.5 116.4 >> 90.0 90.2 90.0 * 33 mP 4.0 64.5 93.3 >> 116.4 90.2 90.0 90.0 * 34 mP 4.1 64.5 >> 116.4 93.3 90.2 90.0 90.0 * 32 oP 4.5 >> 64.5 93.3 116.4 90.2 90.0 90.0 37 mC 249.9 >> 241.6 64.5 93.3 90.0 90.2 74.5 >> >> I would hypothesize that the beam position is incorrect. >> Personally, I'd use JOB= DEFPIX INTEGRATE CORRECT ORGX=994.64 >> ORGY= 1035 for a tentative round of integration, maybe together >> with SPACE_GROUP_NUMBER=19 UNIT_CELL_CONSTANTS= 64.5 93.3 >> 116.4 90. 90.0 90.0 and then inspect the result. If the >> statistics look reasonable (ISa > 10 or so), you should optimize >> it (see XDSwiki). If it looks very bad (ISa < 5), you can run >> echo CENTRE | pointless XDS_ASCII.HKL afterwards, which will tell >> you whether an offset in one of the indices has to be applied. In >> that case, you should inspect the "INDEX ORIGIN" table of >> IDXREF.LP again, to see which ORGX ORGY this corresponds to. >> After this, re-integrate, optimize ... >> >> If you are not successful, compress your frames, upload them to >> some Dropbox-like directory, and send me the link. I'll look at >> your data, treating them confidentially of course, and tell you >> what I find. >> >> best, Kay >> >> >> >> >> >> >>> 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 >> > > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iD8DBQFVUgApUxlJ7aRr7hoRAlptAKDxJWKkEk9/hKwjnlr3DJWAdTmESQCgjfW1 dyjZMKntxpWgCuKIKYYZKW8= =LaUJ -----END PGP SIGNATURE-----
