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SSX: Difference between revisions
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This article deals with how to process serial synchrotron crystallography (SSX) data. | This article deals with how to process serial synchrotron crystallography (SSX) data. | ||
http://bl831.als.lbl.gov/ | |||
The particular data we are processing are artificial and were prepared by James Holton. The files Illuin_microfocus_minimal_00[1-3].tar.bz2 can be [http://bl831.als.lbl.gov/example_data_sets/tarballs downloaded] and the data and problem are described on his [http://bl831.als.lbl.gov/~jamesh/challenge/microfocus microfocus challenge page]. | |||
The challenges are | The challenges are | ||
# strong radiation damage | # partial data sets: each of the 100 data sets has only 3 frames of 1° oscillation | ||
# the b and c axes are the same length, but the crystals are orthorhombic. This makes it difficult to index them consistently - it is | # strong radiation damage: the crystals decay to about 1/2 within these 3 frames | ||
# the b and c axes are the same length, but the crystals are orthorhombic. This makes it difficult to index them consistently - it is wrong to just merge them, because that yields a pseudo-tetragonal merged data set. | |||
== Round 1: processing the data, and determining the space group == | == Round 1: processing the data, and determining the space group == | ||
In order to be able to merge the data in XSCALE, we must ensure that they are all processed in the same space group, with similar cell parameters. Some exploratory processing (not shown) and averaging of cell parameters reveals that IDXREF finds a primitive lattice with one axis of 38.3 Å, and two with 79.1 Å; angles are 90°. The data go to 1.8 Å; beyond that, the intensities suddenly drop to 0 - presumably because James Holton simulated them only that far. | |||
Using the following as the processing script integrate.rc: | Using the following as the processing script integrate.rc: | ||
<pre> | <pre> | ||
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FRIEDEL'S_LAW=TRUE | FRIEDEL'S_LAW=TRUE | ||
eof | eof | ||
find $PWD/../wedge* -name XDS_ASCII.HKL | awk '{print "INPUT_FILE=",$0;print "NBATCH=1 CORRECTIONS= | find $PWD/../wedge* -name XDS_ASCII.HKL | awk '{print "INPUT_FILE=",$0;print "NBATCH=1 CORRECTIONS=ALL"}' >> XSCALE.INP | ||
</pre> | </pre> | ||
we obtain in P1 | we obtain in P1 | ||
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cluster: 2 center: 6 elements: 49 core: 49 halo: 0 | cluster: 2 center: 6 elements: 49 core: 49 halo: 0 | ||
</pre> | </pre> | ||
and prepares XSCALE.1.INP (and XSCALE.2.INP for further use. | and prepares XSCALE.1.INP (and XSCALE.2.INP) for further use. | ||
coot iso.pdb | coot iso.pdb | ||
shows | shows | ||
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== Round 2: using the REFERENCE_DATA_SET == | == Round 2: using the REFERENCE_DATA_SET == | ||
The processing script integrate.rc is changed a bit: | The processing script integrate.rc is changed a bit, to a) use the REFERENCE_DATA_SET, b) prevent adjustment of variances by CORRECT (this should be done by XSCALE) , c) allow some radiation damage compensation: | ||
<pre> | <pre> | ||
#!/bin/bash -f | #!/bin/bash -f | ||
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total 256288 42935 43227 99.3% 13.4% 14.0% 255575 11.63 14.6% 99.6* 21* 0.975 19321 | total 256288 42935 43227 99.3% 13.4% 14.0% 255575 11.63 14.6% 99.6* 21* 0.975 19321 | ||
</pre> | </pre> | ||
The substructure (locating 4 Se with anom data to | The substructure (locating 4 Se with anom data to 3Å) and structure (198 residues) can now easily be solved with [[ccp4com:SHELX C/D/E|hkl2map]]: | ||
[[File:Cc12ano.png]] | [[File:Cc12ano.png]] | ||
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[[File:Ribbon.png]] | [[File:Ribbon.png]] | ||
Further optimization of processing may be possible, but is left as an exercise to the reader. | |||