CSB-PRECISION(1)

✨ csb-precision(1) ✨

okay bestie, welcome to the csb-precision manual page, which lives in section 1 of the manual (User Commands, if you were wondering 💅). this is your girl's guide to measuring how good your fragment library actually is. spoiler: it's giving science, and we're obsessed.

🎀 NAME 🎀

csb-precision — measure the precision and coverage of a fragment library

like. literally that's the whole thing. it measures precision AND coverage. of a fragment library. no cap.

🌸 DESCRIPTION 🌸

okay so first things first, here's the usage, verbatim, don't @ me:

usage: csb-precision [-h] -p PDB -n NATIVE [-c CHAIN] [-t TOP] [-C CPU]

[-r RMSD] [-o OUTPUT] [-s]
       library

so what does it actually do? it measures the precision and coverage of a fragment library that's stored in Rosetta NNmake format. that's it. that's the job. it's not complicated, it's just thorough, which honestly? same.

🦋 positional arguments: 🦋

• library — the fragment library file, and yes it has to be in Rosetta NNmake format. this is your main character. give her what she needs.

💖 optional arguments: 💖

• -h, --help — shows this help message and then dips. the classic. exits immediately after.
• -p PDB, --pdb PDB — the PDB database. that means a directory that contains all your PDB files, not a single file, bestie, don't get it twisted.
• -n NATIVE, --native NATIVE — the native structure of the target. this one IS a PDB file. your reference point, your blueprint, your blueprint-iest blueprint.
• -c CHAIN, --chain CHAIN — chain identifier. if you don't specify it, it just uses the first chain. lowkey convenient, highkey worth knowing.
• -t TOP, --top TOP — reads the top N fragments per position. default is 25. so if you're silent about it, you're getting 25. periodt.
• -C CPU, --cpu CPU — maximum degree of parallelism. default is 4. yes, it multithreads, she's efficient like that 💅.
• -r RMSD, --rmsd RMSD — the RMSD cutoff for precision and coverage. default is 1.5. this is the threshold that decides what counts, so pick it with intention, okay?
• -o OUTPUT, --output OUTPUT — output directory. default is . — i.e. right here, right now, in your current working directory. iconic.
• -s, --save-structures — creates a PDB file for each fragment, superimposed over the native. default is False, so it's opt-in. this one can generate a LOT of files, so know what you're signing up for before you flip this switch 👑

💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. shoutout Andreas, absolute legend, we love a manpage author who documents things properly 🫶

friendly reminder bestie: -p wants a directory full of PDBs and -n wants one PDB file. mixing those up is a rite of passage but you don't have to go through it. 💀

csb-precision version 1.2.5, dated November 2017 — that's the tea, that's the source, that's the version, and that's a wrap. go measure something gorgeous ✨🎀🦋💖