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CIF_MARK_DISORDER(1) General Commands Manual CIF_MARK_DISORDER(1)

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