---
name: "cif_mark_disorder"
section: "1"
platform: "linux"
package: "cod-tools"
version: "3.11.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cif_mark_disorder"
---

# cif\_mark\_disorder(1)

mark disorder in CIF files judging by distance and occupancy.

## 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