XSCALE ISOCLUSTER: Difference between revisions

xscale_isocluster [ftp://turn5.biologie.uni-konstanz.de/pub/xscale_isocluster_linux.bz2 (Linux binary)][ftp://turn5.biologie.uni-konstanz.de/pub/xscale_isocluster.osx (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)].

Academic use only; no redistribution. Expires 2019-07-31

dmax, dmin and nbin (default 1) have the usual meanings. The default

  of dmax, dmin is the common resolution range of all datasets in XSCALE_FILE.

For dataset analysis, the program uses the method of [https://dx.doi.org/10.1107/S1399004713025431 Brehm and Diederichs (2014) ''Acta Cryst'' '''D70''', 101-109] ([https://kops.uni-konstanz.de/bitstream/handle/123456789/26319/Brehm_263191.pdf?sequence=2&isAllowed=y PDF]) whose theoretical background is in [https://doi.org/10.1107/S2059798317000699 Diederichs (2017) ''Acta Cryst'' '''D73''', 286-293] (open access). This results in segmentation, i.e. an arrangement of the N datasets represented by N vectors in a low-dimensional space. Typically, the dimension of that space may be chosen as n=2 to 4, but may be higher if N is large.  

n=1 would be suitable if the datasets only differ in their random error (i.e. they are highly isomorphous).  One more dimension is required for each additional systematic property which may vary between the datasets, e.g. n=2 is suitable if they only differ in their indexing mode (which then only should have two alternatives!), or in some other systematic property, like the length of a cell axis. Higher values of n (e.g. n=4) are appropriate if e.g. there are 4 indexing possibilities (which is the case in P3_x), or more systematic ways in which the datasets may differ (like significant variations in the a, b and c axes), or conformational or compositional differences. In cases where datasets differ e.g. with respect to the composition or conformation of crystallized molecules, it is ''a priori'' unknown which value of n should be chosen, so several values need to be tried, and the results inspected (see [[Xscale_isocluster#Notes]]).

After segmentation of data sets in n-dimensional space, the program may be used (by specifying the -clu <m> option; default m=1) to try and identify <m> clusters of datasets. The program writes files called XSCALE.1.INP with lines required for scaling the datasets of cluster 1, and similarly XSCALE.2.INP for cluster 2, and so on. Typically, one may want to create directories cluster1 cluster2 ..., and then establish symlinks (called XSCALE.INP) in these to the XSCALE.#.INP files. This enables separate scaling of each cluster.

Furthermore, a file iso.pdb is produced that may be loaded into coot. Then use Show/Cell and Symmetry/Show unit cell, and visualize the relations between datasets. With the -I option, individual iso.x.pdb files can be written for each cluster. For an example, see [[SSX]].

UNIT_CELL_CONSTANTS= 91.490 91.490  68.790   90.000  90.000  120.000

SPACE_GROUP_NUMBER= 145

WFAC1=1

INPUT_FILE=../x4/XDS_ASCII.HKL

!new, old ISET=      1     3 strength,dist,cluster=    0.855    0.035      1

INPUT_FILE=../x3/XDS_ASCII.HKL

!new, old ISET=     2      2 strength,dist,cluster=    0.861    0.045     1

!new, old ISET=     3      7 strength,dist,cluster=    0.852     0.112      1

!new, old ISET=      4     6 strength,dist,cluster=    0.902    0.155     1

INPUT_FILE=../x1/XDS_ASCII.HKL

!new, old ISET=      5      1 strength,dist,cluster=    0.749     0.173     1

INPUT_FILE=../x5/XDS_ASCII.HKL

!new, old ISET=      6      4 strength,dist,cluster=    0.678     0.223     1

INPUT_FILE=../x6/XDS_ASCII.HKL

!new, old ISET=      7      5 strength,dist,cluster=    0.788    0.406     1

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, ''dist'' refers to arccosine of the angle (e.g. a value of 1.57 would mean 90 degrees) to the center of the cluster (the lower the better/closer), ''strength'' refers to vector length which is inversely proportional to the random noise in a data set, and ''cluster'', 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]].