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Analysis with | Analysis with | ||
xscale_isocluster -dim 2 -clu 2 temp.ahkl | xscale_isocluster -dim 2 -clu 2 temp.ahkl | ||
yields a iso.pdb which is not at all a single cluster; it is a severely elongated single cloud. We must now investigate whether the data have lower than tetragonal symmetry. | yields a iso.pdb which is not at all a single cluster; it is a severely elongated single cloud: | ||
[[File:1g1c-94.png]] | |||
(If the space group were correct, the result of xscale_isocluster should look similar to this: | |||
[[File:Lyso-xscale-isocluster.png]] | |||
which is from a lysozyme SSX data collection performed at the SLS; outliers are labelled. In this case, the data are truely tetragonal.) | |||
We must now investigate whether the data have lower than tetragonal symmetry. | |||
XSCALEing with | XSCALEing with | ||
SPACE_GROUP_NUMBER=16 | SPACE_GROUP_NUMBER=16 | ||
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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 (these two files collect the differently, but internally-consistently indexed XDS_ASCII.HKL files). | ||
coot iso.pdb | coot iso.pdb | ||
shows | shows | ||
| Line 174: | Line 184: | ||
[[File:Coot.png]] | [[File:Coot.png]] | ||
and thus reveals two well separated clouds. | and thus reveals two well separated clouds, corresponding to the two possible indexing modes of the data in space group 19. | ||
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 | ||
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xdscc12 -w XSCALE.1.HKL | grep ^a | sort -nk6 | xdscc12 -w XSCALE.1.HKL | grep ^a | sort -nk6 | ||
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. | ||
We then re-run XSCALE with MERGE=TRUE. The resulting XSCALE.1.HKL is then used as REFERENCE_DATA_SET for a second round of integration with XDS. | |||
After xscale_isocluster -dim 2 -clu 1 , | |||
coot iso.pdb | |||
now reveals a single cloud: | |||
[[File:1g1c-19.png]] | |||
We then re-run XSCALE with MERGE=TRUE. The resulting reflection output file XSCALE.1.HKL is then used as REFERENCE_DATA_SET for a second round of integration with XDS. | |||
pointless xdsin XSCALE.1.HKL | pointless xdsin XSCALE.1.HKL | ||
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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, 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 | 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: | ||
<pre> | <pre> | ||
#!/bin/bash -f | #!/bin/bash -f | ||