CIF_MARK_DISORDER(1)

✨ CIF_MARK_DISORDER ✨

okay bestie, welcome to section 1 of the general commands manual, this is cif_mark_disorder and she is that girl 💅

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🌸 NAME 🌸

cif_mark_disorder — mark disorder in CIF files judging by distance and occupancy. yes that's the whole job. she looks at how close atoms are and how full their little seats are, and she flags the messy ones. iconic behaviour honestly 🎀

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🦋 SYNOPSIS 🦋

cif_mark_disorder --options input1.cif input*.cif

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💖 DESCRIPTION 💖

Mark disorder in CIF files judging by distance and occupancy.

like, that's it. that's the vibe. distance + occupancy = disorder detection. no cap 🔥

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✨ 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. cute little header moment 💌
• --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. she's doing the whole glow-up first ✨
• --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.

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🫶 REPORTING BUGS 🫶

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

fr fr if something's acting up, tell the cod people, they wanna know 💀

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and that's a wrap on the CIF_MARK_DISORDER(1) manual page, general commands manual edition — thanks for reading, bestie, go mark some disorder 💜✨🎀