CIF_P1(1)

💖 CIF_P1 — bestie's guide to expanding your CIF 💖

okay so welcome to cif_p1, a manual page from the General Commands Manual section of your friendly neighbourhood Unix. grab a boba, we're doing crystallography 💅

✨ NAME ✨

cif_p1 — expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).

🌸 SYNOPSIS 🌸

cif_p1 --options input1.cif input*.cif

🦋 DESCRIPTION 🦋

Expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).

That's literally the whole vibe: it takes your CIF, blows it up into P1, and keeps your molecules intact the whole time — meaning the atoms it spits out are actually bonded to each other at bond distances. no cap. 🫶

👑 OPTIONS 👑

pick your fighter, bestie. every single one is here, i'm not gatekeeping:

• --always-continue — keep going and still return a successful return status, even if errors get diagnosed. she's unbothered. 💅
• -c-, --always-die — stop and return error status the second errors are diagnosed.
• -1, --one-datablock-output — dump all the molecules AND all the alternative conformations into a single output data block.
• -1-, --multiple-datablocks-output — the opposite energy: every molecule and every example of an alternative conformation gets its own separate data block.
• -c, --covalent-sensitivity — set a new covalent sensitivity value (default: 0.35).
• --simplify-formula — simplify the chemical formula and output only a minimal stoichiometric set of molecules instead of the whole P1 cell. should give you the same result as 'cif_molecule --preserve-stoichiometry'.
• --dont-simplify-formula, --no-simplify-formula — don't simplify the formula, output the whole P1 cell (this is the default).
• --exclude-zero-occupancies — don't use atoms with 0 occupancies in calculations (default).
• --dump-atoms — dump atoms (including symmetry-equivalent ones) in CIF format so you can go stare at them in some graphics program. 🔥
• --dont-dump-atoms, --no-dump-atoms — don't dump atoms (default).
• -i, --ignore-bumps — detect close atom "bumps" and warn about them, but don't stop processing.
• --dont-ignore-bumps, --no-ignore-bumps — stop processing immediately if bumps are detected (default). she does NOT play about bumps. 💀
• --bump-distance-factor 0.75 — a fraction of the covalent bond radii sum, used to figure out when atoms are too close and count as a bump.
• --max-polymer-span 4 — a span, in +/- unit cells, in which polymeric molecules (repeating units) will be constructed.
• --max-polymer-atoms 100 — the max allowed count of polymer example atoms. more than this amount of symmetry (translational) equivalent atoms, for each AU atom, will not be written to the output file:
  • using --max-polymer-span=0 --max-polymer-atoms=1 essentially switches off the polymer detection.
• --split-disorder-groups, --dont-merge-disorder-groups — put examples of disorder group conformations into separate data blocks (default).
• --merge-disorder-groups, --dont-split-disorder-groups — put all disorder groups into one data block.
• --use-perl-parser — use the development CIF parser written in Perl.
• --use-c-parser — use the faster C/Yacc CIF parser (default).
• --debug — print some human-readable debug output.
• --no-debug — suppress any debug output (default).
• --format "%8.6f" — use the specified format for output coordinate printout.
• --audit — print audit information to the generated CIF file (default).
• --no-audit — do not print audit information to the generated CIF file.
• --continue-on-errors — do not terminate the script if errors like unrecognised atoms show up.

⚠️ the output may be incorrect and missing some atoms if you use this option! like, for real. 🙈

• --die-on-errors, --dont-continue-on-errors, --no-continue-on-errors — terminate the script immediately if errors are raised (default).
• --continue-on-warnings — do not terminate the script if warnings are raised (default).
• --die-on-warnings — terminate the script immediately if warnings are raised.
• --continue-on-notes — do not terminate the script if notes are raised (default).
• --die-on-notes — terminate the script immediately if notes are raised.
• --verbose — print warning messages in long format.
• --no-verbose — print warning messages in concise format (default).
• --help, --usage — output a short usage message (this message) and exit.
• --version — output version information and exit.

🎀 REPORTING BUGS 🎀

found a bug? spill the tea, bestie — report cif_p1 bugs using e-mail: cod-bugs@ibt.lt

and that's the whole page, periodt. this little guide lives under the manual name CIF_P1 in section 1 — the one and only, CIF_P1(1) — and it's giving very much read me before you run me energy. now go expand those atoms, main character. 🌈✨👑