ctruncate - Intensity to amplitude conversion and data statistics.
ctruncate
-hklin filename
-hklout filename
-seqin sequence file name
-colin column label
-colano column label
-colout column label
-nres number of residues
-no-aniso
-amplitudes
[Keyworded input]
Conversion of measured intensities to structure factors is complicated by the fact that background subtraction can result in negative intensities for weak reflections. CTRUNCATE is a new CCP4 program, intended ultimately to replace the original TRUNCATE program, which uses Bayesian statistics to calculate positive structure factors from negative input intensities. Small positive intensities are also boosted by the conversion process. The algorithm used is that of French and Wilson.
In addition, CTRUNCATE calculates a number of statistics from the intensity data, such as moments, cumulative intensity distributions and the Wilson plot. When output in graphical form, these can be used to assess data quality and to check for possible twinning.
CTRUNCATE looks for anisotropy in the data and performs anisotropy correction. A test for translational NCS is also performed. Two methods are used to test for twinning: Yeates' H test and Padilla and Yeates L test. The twinning tests, as well as the moments and cumulative intensity plots are done using data which has been corrected for anisotropy. However the output structure factors and the Wilson plot use uncorrected data.
-hklin filename
(Compulsory) Input mtz file name. '-mtzin' is accepted as an alternative to '-hklin'.
-hklout filename
Output mtz file name. Default 'ctruncate_out.mtz'. '-mtzout' is accepted as an alternative to '-hklout'.
-seqin sequence file name
Input sequence file in any common format (e.g. pir, fasta), used for scaling.
-colin column label
Column names for mean intensity data. Default '/*/*/[IMEAN,SIGIMEAN]'.
-colano column label
Column names for anomalous data. Both positive and negative names need to be specified e.g. '/*/*/[I(+),SIGI(+),I(-),SIGI(-)]'. If column names for anomalous data are not specified, the program will only consider mean data.
-colout column label
Identifier to be appended to output column names.
-nres number of residues
Specifies the number of residues in the asymmetric unit for scaling purposes. If not used and an input sequence file is not provided, the number of residues will be estimated assuming 50% solvent content.
-no-aniso
Anisotropy correction will not be performed.
-amplitudes
Input data is structure factors rather than intensities.
Norman Stein, Daresbury Laboratory.