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2VB1: Difference between revisions
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ORGX=3130 ORGY=3040 ! for ADSC, header values are subject to interpretation; these values from visual inspection | ORGX=3130 ORGY=3040 ! for ADSC, header values are subject to interpretation; these values from visual inspection | ||
! the following is for masking the beamstop shadow in sweeps c-d | ! the following is for masking the beamstop shadow in sweeps c-d | ||
UNTRUSTED_RECTANGLE | UNTRUSTED_RECTANGLE=0 3189 2960 3087 ! use XDS-viewer of ADXV to find the values | ||
! the following is for sweeps e-h | ! the following is for sweeps e-h | ||
UNTRUSTED_RECTANGLE=1 3160 3000 3070 | UNTRUSTED_RECTANGLE=1 3160 3000 3070 | ||
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INCLUDE_RESOLUTION_RANGE=30 0.65 | INCLUDE_RESOLUTION_RANGE=30 0.65 | ||
=== XSCALE.LP | === XSCALE.LP tables === | ||
The error model is adjusted by XSCALE: | |||
a b ISa ISa0 INPUT DATA SET | |||
7.094E+00 1.294E-04 33.00 38.03 ../a/XDS_ASCII.HKL | |||
7.476E+00 1.170E-04 33.81 38.95 ../b/XDS_ASCII.HKL | |||
7.453E+00 1.598E-04 28.98 38.00 ../c/XDS_ASCII.HKL | |||
6.539E+00 1.640E-04 30.54 39.08 ../d/XDS_ASCII.HKL | |||
7.304E+00 1.342E-04 31.94 37.69 ../e/XDS_ASCII.HKL | |||
8.201E+00 1.574E-04 27.83 35.58 ../f/XDS_ASCII.HKL | |||
8.182E+00 1.759E-04 26.36 27.60 ../g/XDS_ASCII.HKL | |||
7.717E+00 3.694E-04 18.73 21.93 ../h/XDS_ASCII.HKL | |||
and there are about 1500 rejected reflections. It is reassuring to note that the error model works well; the ISa goes down toward sweep h probably because the crystal degrades. But see also the "a posterior remarks" below - sweep h is the one that is most affected by a shadow on the detector. | |||
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION | SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION | ||
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total 1435805 190032 191232 99.4% 3.1% 3.3% 1434290 33.42 3.3% 3.1% 3% 0.801 170264 | total 1435805 190032 191232 99.4% 3.1% 3.3% 1434290 33.42 3.3% 3.1% 3% 0.801 170264 | ||
If two more resolution shells are added, they look like - | |||
0.64 23276 7411 9155 81.0% 35.0% 40.6% 22324 2.90 41.7% 47.9% 3% 0.683 3204 | |||
0.63 18044 6488 9647 67.3% 42.2% 49.7% 16630 2.22 50.7% 60.9% -5% 0.643 2437 | |||
So there is still useful signal beyond 0.65 A. | |||
== Some ''a posteriori'' remarks == | |||
* For sweeps e-h one should use TRUSTED_REGION= 0 1.2 since that already gives 0.626 A in the corners. | |||
* The first and last frames of sweeps g and h show a shadow in one corner of the detector. Nothing was done by me to exclude this shadow from processing (but one should do so at least if the resolution should be expanded beyond 0.65 A which the XSCALE statistics suggest to be possible). <br> One could experiment with MINIMUM_VALID_PIXEL_VALUE= 40 (or so) instead of 1 - I'd probably try that, but of course one does not want to exclude valid pixels so the result has to be carefully checked. <br> Anyway, there is no general facility in XDS to exclude bad areas of ''specific'' frames in a dataset; one needs to chop the dataset into parts and deal with each shadow separately. | |||
== Comparison of data processing: published (2006) ''vs'' XDS results == | == Comparison of data processing: published (2006) ''vs'' XDS results == | ||
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</table> | </table> | ||
== Availability of data from XDS processing == | |||
I changed XSCALE.INP to have | |||
!FRIEDEL'S_LAW=TRUE ! by commenting it out XSCALE will use FRIEDEL'S_LAW=FALSE | |||
! since this is how the data were processed | |||
RESOLUTION_SHELLS=2.91 2.06 1.68 1.45 1.30 1.19 1.10 1.03 0.97 0.92 0.88 0.84 0.80 0.76 0.73 0.70 0.67 0.65 0.64 0.63 | |||
and ran XSCALE again, to get a file with reflections to 0.63 A. | |||
Conversion to other program systems is performed with XDSCONV. XDSCONV.INP for producing a MTZ file with intensities and anomalous signal is: | |||
INPUT_FILE= lys-xds.ahkl | |||
OUTPUT_FILE=temp.hkl CCP4_I | |||
After running xdsconv, I cut-and-paste the screen output: | |||
f2mtz HKLOUT temp.mtz<F2MTZ.INP | |||
cad HKLIN1 temp.mtz HKLOUT output_file_name.mtz<<EOF | |||
LABIN FILE 1 ALL | |||
END | |||
EOF | |||
and obtain output_file_name.mtz which I mv to [https://{{SERVERNAME}}/pub/xds-datared/2vb1/xds-hewl-I.mtz xds-hewl-I.mtz]. SFCHECK statistics for this file are [https://{{SERVERNAME}}/pub/xds-datared/2vb1/sfcheck_XXXX.pdf here]. | |||
Similarly, using OUTPUT_FILE=temp.hkl CCP4 I obtained a file with amplitudes, [https://{{SERVERNAME}}/pub/xds-datared/2vb1/xds-hewl-F.mtz xds-hewl-F.mtz] | |||