FINDLIGAND(1)

💖 FINDLIGAND(1) 💖

okay bestie, so this is findligand, a manual page from the General Commands Manual section of the Unix world. sit down, grab a strawberry 🍓, and let's get you fluent in ligand-hunting.

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✨ NAME ✨

findligand — find ligands in a protein structure 🔍🧬

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🦋 SYNOPSIS 🦋

findligand [options]

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🌸 DESCRIPTION 🌸

so like, findligand is literally a part of the Coot suite of programs. that's the whole vibe. it's one of the gang. 💅

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👑 OPTIONS 👑

findligand serves up a whole bunch of command line arguments so you can have increased flexibility, and honestly? we love options. these follow the usual GNU command line syntax, and just so you know, long options start with two dashes (--, yes, two of them, not one, iykyk). here's the full rundown, bestie:

• --pdbin=file — the name of the input PDB file 📄
• --hklin=file — the MTZ file that's holding your structure factors
• --f=label — the label of the MTZ file column with the structure factor amplitudes in it
• --phi=phi_col_label — the label of the MTZ file column with the structure factor phases in it
• --clusters=nclust — how many density clusters (aka potential ligand sites 👀) you want it to search for
• --sigma=level — the density level (in sigma) above which the map gets searched for ligands [default 2.0]
• --fit-fraction=frac — the minimum fraction of atoms in density that's allowed after the fit [default 0.75]
• --flexible — use the torsional conformation ligand search 🌀 (flexible queen behavior)
• --samples=nsamples — how many flexible conformation samples to take [default 30]
• --dictionary=file — the name of the file containing the CIF ligand dictionary description
• --absolute=level — set the absolute density level above which to search for ligands
• --script=file — the file name of a helper script that's suitable for use in Coot [default: coot-ligands.scm]
• --pos-x
• --pos-y
• --pos-z

not me listing three options that are literally just flags with no description attached 🙈 but fr fr, they're in the original, so here they are, exactly as-is. no cap.

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🎀 EXAMPLE 🎀

okay so the way you actually use findligand is like this:

$ findligand various-args ligand-pdb-file-name(s)

i.e. — and this is the important bit, bestie — the example ligand pdb files that you wish to search for go at the end of the command line. 🫶

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🌈 SEE ALSO 🌈

bfactan(1), coot(1), density-score-by-residue(1), findwaters(1), fix-nomenclature-errors(1), lidia(1).

go read those too, they're iconic in their own right 💜

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⭐ AUTHOR ⭐

findligand is written by Paul Emsley. 👑

This manual page was written by Morten Kjeldgaard <mok@bioxray.dk>.

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and that's the whole page, bestie 💖 this version was living its January, 2011 era, straight out of the General Commands Manual — slay, periodt. 🎀✨