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
