CIF2MTZ (CCP4: Supported Program)

NAME

cif2mtz - Convert an mmCIF reflection file to MTZ format

SYNOPSIS

cif2mtz hklin foo.cif hklout foo.mtz
[Keyworded input]

DESCRIPTION

CIF2MTZ is a program to convert an mmCIF reflection file to MTZ format.

KEYWORDED INPUT

Possible keywords are:

TITLE, LABOUT, CELL, SYMMETRY, PNAME, DNAME, ANOMALOUS, END

All keywords are optional. The program will read in data, such as symmetry, from the mmCIF file if it is there. The keywords can be used to provide missing information, or to override existing information.

TITLE <title>

Put a suitable title in the output MTZ file.

CELL <a> <b> <c> [ <alpha> <beta> <gamma> ]

Followed by the cell lengths and angles.

SYMMETRY <spacegroup>

Followed by the standard space group name or number, or explicit symmetry operators.

LABOUT <program label>=<file label> ...

The program currently recognises the following mmCIF item names for reflection data:


     _refln.index_h                H             h index
     _refln.index_k                K             k index
     _refln.index_l                L             l index
     _refln.status                 FREE          free R flag
     _refln.F_meas_au              FP            structure factor
     _refln.F_meas_sigma_au        SIGFP         sigma(F)
     _refln.F_calc                 FC            calculated structure factor
     _refln.phase_calc             PHIC          sigma(FC)
     _refln.phase_meas             PHIB          experimental phase
     _refln.fom                    FOM           figure of merit
     _refln.intensity_meas         I             intensity
     _refln.intensity_sigma        SIGI          sigma(I)

An MTZ column is output for each mmCIF item found. The default column name <program label> is given in the middle column above, but the LABOUT keyword can be used to rename these columns.

With the ANOMALOUS option, there are additional columns F(+) SIGF(+) F(-) SIGF(-) which can be renamed by LABOUT.

Note: the mmCIF file may contain alternative labels, e.g. _refln.F_meas rather than _refln.F_meas_au. In such cases, it is sufficient to edit the label name directly in the mmCIF file to one of the above labels.

PNAME <projectname>

[default: 'unknown']
<projectname> is taken from _entry.id if present in the mmCIF file
Project Name used for Data Harvesting. A dataset, as listed in the MTZ header, is specified by a project-name/dataset-name pair. The project-name specifies a particular structure solution project, while the dataset-name specifies a particular dataset contributing to the structure solution. An entry in the PNAME keyword should therefore be accompanied by a corresponding entry in the DNAME keyword.

DNAME <datasetname>

[default: 'unknownddmmyy' where ddmmyy is the date]
<datasetname> is taken from _diffrn.id if present in the mmCIF file
Dataset Name used for Data Harvesting. A dataset, as listed in the MTZ header, is specified by a project-name/dataset-name pair. The project-name specifies a particular structure solution project, while the dataset-name specifies a particular dataset contributing to the structure solution. An entry in the DNAME keyword should therefore be accompanied by a corresponding entry in the PNAME keyword.

ANOMALOUS

If this keyword is given, the program will attempt to recover F(+) and F(-) columns from hkl / -h-k-l pairs in the input mmCIF file. Any hkl singletons will be treated as F(+) data. Columns FP/SIGFP will also be output as mean of the input F(+) and F(-).

Warning: this option will work with mmCIF such as are output by MTZ2VARIOUS, where the -h-k-l reflection immediately follows the corresponding hkl, and where hkl reflections are in the CCP4 asymmetric unit. It will fail in other cases. Without the ANOMALOUS option, all reflections will be passed unchanged to HKLOUT.

END

End keyworded input.

AUTHOR

Martyn Winn