COOT(1)

okay so bestie, this is the manual page for coot-mini-rsr, and it lives in section 1 of the General Commands Manual — that's the big book of "type a command, get a result" tools, iykyk 🫶

also there's literally a lone q chillin' at the very top of this page. we don't know her, we don't question her, she stays. 💀

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✨ NAME ✨

coot-mini-rsr — real space Refinement using X-ray data 💖

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🌸 SYNOPSIS 🌸

coot-mini-rsr [OPTIONS] ...

that's it. that's the whole vibe. you feed her options, she does her thing. no cap. 🌈

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🦋 DESCRIPTION 🦋

coot-mini-rsr does real-space refinement of structures — and the whole point, the moment, the slay — is that you do not need interactive molecular graphics. no clicking. no dragging little molecules around with your mouse at 2am. just options, bestie. periodt. 💅

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👑 OPTIONS 👑

here's the full menu, and yes we're doing all of them, we don't skip:

• --pdbin <coordinates-file-name> — hand her the coordinates file name. this is the one she's working on. 🎀
• ---hklin <mtz-file-name> — yes it really is three dashes, that is not a typo, that is canon, we do not "fix" it 👑 — it takes the mtz file name.
• --dictionary <mmCIF/pdbx dictionary file-name> — the mmCIF/pdbx dictionary file name. your dictionary. your rules. 💜
• --chain-id chain-id — which chain id you're about.
• --weight weight — the weight value.
• --radius radius — the radius value.
• --rama — the rama flag. takes no argument, just vibes.
• --torsions — the torsions flag. also no argument.
• --no-planar-peptide-restraints — the flag literally named no-planar-peptide-restraints. no argument.
• --no-trans-peptide-restraints — the flag literally named no-trans-peptide-restraints. no argument.
• --tabulate-distortions — tabulate distortions. no argument.
• --correlations — correlations. no argument.
• --version — version. no argument. she'll tell you who she is. ✨

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🎀 specify residues 🎀

pick your fighter, bestie — you got a range, one single residue, or everything around a residue:

• --resno-start res_no_low and --resno-end res_no_high — the low end and the high end, together, as a pair 🫶
• or --residue-number res_no — just the one residue number.
• or --residues-around res_no — the residues around a residue number.

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🍓 specify map 🍓

two ways to tell her about your map:

• --mapin <CCP4-format-map-file-name> — the CCP4-format map file name. 🧚
• or --f f_col_label plus --phi phi_col_label — an f column label and a phi column label.

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💜 AUTHOR 💜

Paul Emsley 🌸

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okay that's the whole page, we ate and left no crumbs 🔥 — this was the COOT(1) manual page from the General Commands Manual, and the footer down there just reads COOT(1), so like, that's all she wrote. go refine something, bestie, you're the main character now ⭐💖