NAME

       cif_mark_disorder - mark disorder in CIF files judging by distance and occupancy.

SYNOPSIS

       cif_mark_disorder --options input1.cif input*.cif

DESCRIPTION

       Mark disorder in CIF files judging by distance and occupancy.

OPTIONS

       -d, --distance-sensitivity  0.000001
                         Specify maximum distance between two atoms that should
                         be perceived as belonging to the same atom site.
                         Default: 0.000001.

       --occupancy-sensitivity  0.01
                         Set maximum deviation for the sum of occupancies of
                         the atoms from the same atom site from 1.
                         Default: 0.01.

       -h, --add-cif-header
                         Comments from the beginning of this file will be
                         prepended to the output.

       --exclude-zero-occupancies
                         Ignore atoms with an occupancy of 0 in the calculations.
                         Default.

       --no-exclude-zero-occupancies,

       --dont-exclude-zero-occupancies
                         Use atoms with an occupancy of 0 in the calculations.

       --ignore-occupancies
                         Do not require occupancies of atoms in the same
                         atom site to sum up to 1.

       --no-ignore-occupancies,

       --dont-ignore-occupancies
                         Require occupancies of atoms in the same atom site
                         to sum up to 1 to be recognised as a disordered site.
                         Default.

       --reconstruct-symmetry
                         Reconstruct crystal symmetry before searching for
                         possible unmarked disorder.

       --no-reconstruct-symmetry,

       --dont-reconstruct-symmetry
                         Do not reconstruct symmetry, act on asymmetric unit
                         cell only. Default.

       --output-dot-assemblies
                         Use dot ('.') assembly names. With this option on,
                         already existing dot assemblies in the input CIF
                         will be preserved. If no assemblies have existed in
                         the input file, but the script found a single new
                         assembly, it will be named '.'.

       --no-output-dot-assemblies,

       --dont-output-dot-assemblies
                         Rename dot ('.') assemblies in the input and do not
                         name new assemblies '.'. Default.

       --report-marked-disorders
                         Print each of the marked disorder assemblies to
                         stderr, listing atom labels. Default.

       --no-report-marked-disorders,

       --dont-report-marked-disorders
                         Do not print marked disorder assemblies to stderr.

       --add-depositor-comments
                         Append reports about newly marked disorder assemblies
                         together with the signature of this script to the
                         '_cod_depositor_comments' value. Default.

       --no-add-depositor-comments,

       --dont-add-depositor-comments
                         Do not append anything to the value of
                         '_cod_depositor_comments'.

       --brick-size  1
                         Brick size parameter for the 'AtomBricks' algorithm.

       --uniquify-atoms
                         Makes unique the labels of atoms.

       --no-uniquify-atoms, --dont-uniquify-atoms
                         Do not makes unique labels for atoms,
                         exclude duplicates. Default.

       --continue-on-errors
                         Do not terminate script if errors are raised.

       --die-on-errors
                         Terminate script immediately if errors are raised.
                         Default.

       --continue-on-warnings
                         Do not terminate script if warnings are raised. Default.

       --die-on-warnings
                         Terminate script immediately if warnings are raised.

       --continue-on-notes
                         Do not terminate script if notes are raised. Default.

       --die-on-notes
                         Terminate script immediately if notes are raised.

       --use-perl-parser
                         Use Perl parser for CIF parsing.

       --use-c-parser
                         Use Perl & C parser for CIF parsing. Default.

       --help, --usage
                         Output a short usage message (this message) and exit.

       --version
                         Output version information and exit.

REPORTING BUGS

       Report cif_mark_disorder bugs using e-mail: cod-bugs@ibt.lt

                                                                                            CIF_MARK_DISORDER(1)