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XSCALE ISOCLUSTER: Difference between revisions
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xscale_isocluster [ | xscale_isocluster [https://{{SERVERNAME}}/pub/linux_bin/xscale_isocluster (Linux binary)][https://{{SERVERNAME}}/pub/mac_bin/xscale_isocluster (Mac binary)] is a program that clusters datasets stored in a single unmerged reflection file as written by [[XSCALE]]. It implements the method of [https://doi.org/10.1107/S1399004713025431 Brehm and Diederichs (2014)] and theory of [https://doi.org/10.1107/S2059798317000699 Diederichs (2017)]. | ||
The help output (obtained by using the <code>-h</code> option) is | The help output (obtained by using the <code>-h</code> option) is | ||
<pre> | <pre> | ||
xscale_isocluster KD | xscale_isocluster KD 2020-07-27. -h option shows options | ||
Licensed for academic use only; no redistribution. | Licensed for academic use only; no redistribution. | ||
Please cite Assmann,Wang and Diederichs (2020) Acta Cryst D76, 636. | |||
usage: xscale_isocluster -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -dim <dim> -clu <#> -cen <#,#,#,...> -<aAisw> XSCALE_FILE_NAME | usage: xscale_isocluster -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -dim <dim> -clu <#> -cen <#,#,#,...> -<aAisw> XSCALE_FILE_NAME | ||
highres, lowres and nbin (default=1 for low, and 10 for high multiplicity) have the usual meanings. | highres, lowres and nbin (default=1 for low, and 10 for high multiplicity) have the usual meanings. | ||
| Line 19: | Line 20: | ||
-w: no weighting of intensities with their sigmas | -w: no weighting of intensities with their sigmas | ||
The XSCALE.?.INP output files have angles [deg] w.r.t. cluster centers | The XSCALE.?.INP output files have angles [deg] w.r.t. cluster centers | ||
</pre> | </pre> | ||
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Furthermore, a file iso.pdb is produced that may be loaded into coot. Then use Show/Cell and Symmetry/Show unit cell (to see the origin, which coot marks with "0"), and visualize the relations between data sets. Systematic differences are related to the angle (with the tip of the angle at the origin) between the vectors that represent the data sets; ideally, in the case of isomorphous data sets all vectors point into the same direction. Random differences are related to the lengths of the vectors (starting at the origin; short vectors correspond to weak/noisy data sets). With the -i option, individual iso.x.pdb files can be written for each cluster. For an example, see [[SSX]]. | Furthermore, a file iso.pdb is produced that may be loaded into coot. Then use Show/Cell and Symmetry/Show unit cell (to see the origin, which coot marks with "0"), and visualize the relations between data sets. Systematic differences are related to the angle (with the tip of the angle at the origin) between the vectors that represent the data sets; ideally, in the case of isomorphous data sets all vectors point into the same direction. Random differences are related to the lengths of the vectors (starting at the origin; short vectors correspond to weak/noisy data sets). With the -i option, individual iso.x.pdb files can be written for each cluster. For an example, see [[SSX]]. | ||
=== Resolving indexing ambiguity === | |||
A useful set of options for resolving an indexing ambiguity is shown in the following example: | |||
xscale_isocluster -i -dim 2 -clu 2 -dmin 20 -dmax 2.5 XSCALE.HKL | |||
coot iso.1.pdb iso.2.pdb | |||
Specifying dmin and dmax is often needed because a) the high resolution is often weak and noisy, and should be excluded, and b) the default of the program is to choose the resolution range that is covered by all datasets, which may be quite narrow. | |||
In coot, use Draw->Cell-&-Symmetry->Show Unit Cells->Yes and use the Display Manager to switch the pseudo-PDB files on/off. In this 2-dimensional analysis, all pseudo-atoms are in the AB plane. The two clusters may be situated at a right angle; one of these corresponds to one (internally consistent) way of indexing, the other to the other way of indexing. This means that after each INPUT_FILE= line of one of the two XSCALE.?.INP files, a re-indexing line such as | |||
REIDX_ISET= -1 0 0 0 0 -1 0 0 0 0 1 0 | |||
should be added which would be valid for spacegroups 150, 152 and 154 (and 143-145 for which there are also other possibilities), or | |||
REIDX_ISET= 0 1 0 0 1 0 0 0 0 0 -1 0 | |||
which would be valid for spacegroups 75-80, 149, 151, 153, 168-173, and 195-199 (and 143-146 for which there are other also other possibilities) (see [[Space_group_determination#Table_of_space_groups_by_Laue_class_and_Bravais_type]] and https://www.ccp4.ac.uk/html/reindexing.html). | |||
== Output == | == Output == | ||
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The console output gives informational and error messages. Each file XSCALE.x.INP enumerates the contributing INPUT_FILEs in the order of increasing angular distance. Example: | The console output gives informational and error messages. Each file XSCALE.x.INP enumerates the contributing INPUT_FILEs in the order of increasing angular distance. Example: | ||
<pre> | <pre> | ||
UNIT_CELL_CONSTANTS= | UNIT_CELL_CONSTANTS= 88.740 88.740 104.930 90.000 90.000 120.000 | ||
SPACE_GROUP_NUMBER= | SPACE_GROUP_NUMBER= 152 | ||
OUTPUT_FILE=XSCALE.1.HKL | OUTPUT_FILE=XSCALE.1.HKL | ||
SAVE_CORRECTION_IMAGES=FALSE | SAVE_CORRECTION_IMAGES=FALSE | ||
WFAC1=1 | PRINT_CORRELATIONS=FALSE | ||
WFAC1=1.25 ! XDS/XSCALE defaults are 1.0/1.5 | |||
INPUT_FILE=../xds_ss091d3chip/1501_1506/XDS_ASCII.HKL | |||
!new, old ISET= 1 134 length=CC*,angle,cluster= 0.120 0.4 1 | |||
INPUT_FILE=../ | |||
!new, old ISET= | |||
!INCLUDE_RESOLUTION_RANGE=00 00 | !INCLUDE_RESOLUTION_RANGE=00 00 | ||
INPUT_FILE=../ | WEIGHT= 1.000 | ||
!new, old ISET= | INPUT_FILE=../xds_ss091c10chip/2281_2286/XDS_ASCII.HKL | ||
!new, old ISET= 2 96 length=CC*,angle,cluster= 0.922 1.9 1 | |||
!INCLUDE_RESOLUTION_RANGE=00 00 | !INCLUDE_RESOLUTION_RANGE=00 00 | ||
INPUT_FILE=../ | WEIGHT= 1.001 | ||
!new, old ISET= | INPUT_FILE=../xds_ss091b11chip/751_756/XDS_ASCII.HKL | ||
!new, old ISET= 3 46 length=CC*,angle,cluster= 0.556 2.1 1 | |||
!INCLUDE_RESOLUTION_RANGE=00 00 | !INCLUDE_RESOLUTION_RANGE=00 00 | ||
INPUT_FILE=../ | WEIGHT= 1.001 | ||
!new, old ISET= | INPUT_FILE=../xds_ss091a11chip/121_126/XDS_ASCII.HKL | ||
!new, old ISET= 4 14 length=CC*,angle,cluster= 0.602 22.8 1 | |||
!INCLUDE_RESOLUTION_RANGE=00 00 | !INCLUDE_RESOLUTION_RANGE=00 00 | ||
... | |||
</pre> | </pre> | ||
Each INPUT_FILE line is followed by a comment line. In this, the first two numbers (''new'' and ''old'') refer to the numbering of datasets in the resulting XSCALE.#.INP, ''versus'' that in the original XSCALE.INP (which produced XSCALE_FILE). Then, '' | Each INPUT_FILE line is followed by a comment line. In this, the first two numbers (''new'' and ''old'') refer to the numbering of datasets in the resulting XSCALE.#.INP, ''versus'' that in the original XSCALE.INP (which produced XSCALE_FILE). Then, ''length=CC*,angle,cluster'' refers to vector length which is inversely proportional to the random noise in a data set, to the angle (in degrees) to the center of the cluster (the lower the better/closer), and to ''cluster'', which if negative, identifies a dataset that is outside the core of the cluster. To select good datasets and reject bad ones, the user may comment out INPUT_FILE lines which refer to datasets that are far away in angle or outside the core of the cluster. Furthermore, resolution ranges may be specified, possibly based on the output of [[XDSCC12]]. | ||
== Notes == | == Notes == | ||