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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]] | |||
We must now investigate whether the data have lower than tetragonal symmetry. | |||
XSCALEing with | XSCALEing with | ||
SPACE_GROUP_NUMBER=16 | SPACE_GROUP_NUMBER=16 | ||
| Line 175: | Line 179: | ||
and thus reveals two well separated clouds. | and thus reveals two well separated clouds. | ||
(It 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) | |||
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 207: | Line 217: | ||
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 | ||