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Xds nonisomorphism: Difference between revisions
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[ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/xds_nonisomorphism xds_nonisomorphism][ftp://turn5.biologie.uni-konstanz.de/pub/sources/xds_nonisomorphism.f90] is a program that | [ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/xds_nonisomorphism xds_nonisomorphism][ftp://turn5.biologie.uni-konstanz.de/pub/sources/xds_nonisomorphism.f90] is a program that analyzes data sets stored in unmerged reflection files (typically called XDS_ASCII.HKL) as written by [[XDS]]. 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)]. Its purpose is the identification of non-isomorphous (i.e. dissimilar or less well related) data sets among other, more similar data sets. As a consequence of running xds_nonisomorphism, one may choose to only merge the most isomorphous (similar) data sets, and to discard the non-isomorphous ones - or to analyze these separately. | ||
The assumption is that several data sets exist, and that these should be merged with [[XSCALE]]. The program therefore reads the names of the XDS_ASCII.HKL files from XSCALE.INP . The latter file, and the XDS_ASCII.HKL listed after each INPUT_FILE= line in XSCALE.INP must exist. The program reads the files in the order given, and produces tables with pairwise statistics. | |||
In particular, for each pair it determines | |||
* the CC* values (Karplus & Diederichs (2012). Science 336, 1030–1033) from the [[CC1/2]] of the data sets (using the σ-τ method of Assmann ''et al.'', J. Appl. Cryst. (2016). 49, 1021–1028), and | |||
* the pairwise (Pearson's) correlation coefficients. | |||
As given by equation 2 of [https://doi.org/10.1107/S2059798317000699 Diederichs (2017)], the ratio between the latter quantity and the product of the CC* values of a pair is a measure of the non-isomorphism - for isomorphous data, that ratio is 1. | |||
The method requires data sets with internal multiplicity, and mutual overlap (common reflections). Angles (calculated as the inverse cosine of the ratio) are expressed in degrees. Less than 10° may be considered good isomorphism, 90° means highly non-isomorphous (i.e. completely unrelated) datasets. After the analysis, the program produces a 3D representation of the arrangement of data sets such that their distances in 3D try to reproduce the angles (please note that this is a completely different representation from that of [[xscale_isocluster]]!). | |||
xds_nonisomorphism prints a short help text if the -h option is used. | |||
== Usage == | |||
** | |||