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.

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

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

       --exclude-zero-occupancies
                         Do not use atoms with 0 occupancies in calculations (default).

       --no-exclude-zero-occupancies

       --dont-exclude-zero-occupancies
                         Use atoms with zero (0) occupancies in the calculations.

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

       --no-ignore-occupancies

       --dont-ignore-occupancies
                         Require the occupancies of the atoms in the same atom site
                         to sum up to 1 to be recognised as disorder (default).

       --report-marked-disorders
                         Print each of the marked disorder assemblies to
                         the standard error, listing atom labels (default).

       --no-report-marked-disorders

       --dont-report-marked-disorders
                         Do not print marked disorder assemblies to the
                         standard error.

       --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 'AtomBricks' algorithm.

       --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)