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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. | ||
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 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], and in a [http://journals.iucr.org/d/issues/2019/02/00/ba5297/index.html paper]. | ||
The challenges are | The challenges are | ||
# partial data sets: each of the 100 data sets has only 3 frames of 1° oscillation | # partial data sets: each of the 100 data sets has only 3 good frames of 1° oscillation; later frames have 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. | # the b and c axes are the same length, but the simulated crystals are orthorhombic. This makes it difficult to index them consistently - it is wrong to just merge them in a orthorhombic space group without resolving the indexing ambiguity, because that yields a pseudo-tetragonal twinned merged data set. | ||
== Round 1: processing the data, and determining the space group == | == Round 1: processing the data, and determining the space group == | ||
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REIDX=0 1 0 0 0 0 1 0 1 0 0 0 | REIDX=0 1 0 0 0 0 1 0 1 0 0 0 | ||
</pre> | </pre> | ||
where the last line takes care of the shuffling of axes into the order k,l,h, , and obtain | where the last line takes care of the shuffling of axes into the order k,l,h, (after all, the XDS_ASCII.HKL are in P1 with a,b,c of 38.3,79.1,79.1) , and obtain | ||
<pre> | <pre> | ||
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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[[File:1g1c-94.png]] | [[File:1g1c-94.png]] | ||
(If the space group were correct, the result of xscale_isocluster should look similar to this: | (If the space group were correct, the result of [[xscale_isocluster]] should look similar to this: | ||
[[File:Lyso-xscale-isocluster.png]] | [[File:Lyso-xscale-isocluster.png]] | ||
| Line 184: | Line 184: | ||
[[File:Coot.png]] | [[File:Coot.png]] | ||
and thus reveals two well separated clouds, corresponding to the two possible indexing modes of the data in space group | and thus reveals two well separated clouds, corresponding to the two possible indexing modes of the data in an orthorhombic space group. | ||
Using XSCALE.1.INP with its 51 XDS_ASCII.HKL, and FRIEDEL'S_LAW=TRUE, we get | Using XSCALE.1.INP with its 51 XDS_ASCII.HKL, and FRIEDEL'S_LAW=TRUE, we get | ||
| Line 218: | Line 218: | ||
and find that data sets 1 and 17 are wrongly included in the cloud of 51 data sets. Thus they are removed manually from XSCALE.INP. | and find that data sets 1 and 17 are wrongly included in the cloud of 51 data sets. Thus they are removed manually from XSCALE.INP. | ||
After xscale_isocluster -dim 2 -clu 1 , | After <code>xscale_isocluster -dim 2 -clu 1</code> , | ||
coot iso.pdb | coot iso.pdb | ||
now reveals a single cloud: | now reveals a single cloud: | ||
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thus we now know the spacegroup. | thus we now know the spacegroup. | ||
== Round 2: using the REFERENCE_DATA_SET == | == Round 2: using the REFERENCE_DATA_SET obtained from one cluster== | ||
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 correction in XSCALE: | 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 rather be done by XSCALE) , c) allow some radiation damage correction in XSCALE: | ||
<pre> | <pre> | ||
#!/bin/bash -f | #!/bin/bash -f | ||
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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]]: | 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]]: | ||
== Result == | |||
=== SHELXC: anomalous CC<sub>1/2</sub> === | |||
[[File:Cc12ano.png]] | [[File:Cc12ano.png]] | ||
=== SHELXD: CCall ''versus'' CCweak, and histogram === | |||
[[File:Ccallcsccweak.png]] | [[File:Ccallcsccweak.png]] | ||
[[File:Histcfom.png]] | [[File:Histcfom.png]] | ||
=== SHELXE: contrast versus cycle, and PDB with structure === | |||
[[File:Contrastvscycle.png]] | [[File:Contrastvscycle.png]] | ||