.TH CIF_MARK_DISORDER 1
.SH NAME
cif_mark_disorder \- mark disorder in CIF files judging by distance and occupancy.

.SH SYNOPSIS
cif_mark_disorder \-\-options input1.cif input*.cif

.SH DESCRIPTION
Mark disorder in CIF files judging by distance and occupancy.

.SH 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.

.SH "REPORTING BUGS"
Report cif_mark_disorder bugs using e\-mail: cod\-bugs@ibt.lt