Dear Natalie,
I try to run my images with fast_dp, but got the error message:
Fast_DP installed in: /home/lu/bin/fast_dp_20141205
Starting image: /home/lu/Documents/hg6l3/Hg6_L3_1_00002.mccd
Number of jobs: 1
Number of cores: 0
Processing images: 1 -> 360
Phi range: 112.50 -> 472.50
Template: Hg6_L3_1_#####.mccd
Wavelength: 0.97853
Working in: /home/lu/bin/fast_dp_20141205/bin
Autoindexing error: 'sensor'
I cannot find any relative document about fast_dp or autoindexing.
Do you have any idea?
Best!
Lu
--
卢作焜
南开大学新生物站A202
在 2015-05-12 21:08:42，"Natalie Tatum" <nataliejta...@gmail.com> 写道：
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
--
Natalie J. Tatum
PhD Researcher
Durham University
http://about.me/n.j.tatum
