SUPERPOSE(1)

👑 SUPERPOSE(1) — like, the whole vibe

okay bestie, welcome to superpose from the User Commands section, and no, this is not a makeup tutorial, it's Protein Structure Superposition and it eats every single time 💅✨

🌸 NAME 🌸

superpose — Protein Structure Superposition 🧬💖

✨ USAGE ✨

here's the group chat receipt, copy it exactly bestie:

superpose q.pdb [-s CIDQ] t1.pdb [-s CID1] ... tN.pdb [-s CIDN]
[-o foo_out.pdb]

so, breaking it down like it's a fit check:

• q.pdb is the Query structure, aka the one the transformation gets applied to 👑
• ti.pdb is the ith fixed Target structure — the one that stays put, main character energy only for the query fr
• [-s CIDi] are optional selection strings in MMDB convention (iykyk, if you don't, it's MMDB convention, that's the whole tea)
• [-o foo_out.pdb] is the optional output file specification, so you can decide where the glow-up gets saved 🎀

and lowkey the important part: if more than one target is specified, multiple structure alignment is calculated. not a single alignment, a multiple one. periodt.

🦋 the asterisk thing (this is the fun bit) 🦋

instead of using asterisks '*' for selecting all atoms, '-all' may be used, such that

superpose q.pdb -s * t.pdb -s * foo_out.pdb

and

superpose q.pdb -s -all t.pdb -s -all foo_out.pdb

are equivalent. like, literally the same thing, two different outfits, same slay 💀✨

📚 REFERENCES 📚

because we cite our sources in this house, no cap:

• Collaborative Computational Project, Number 4. 2011. "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242. — as well as any specific reference in the program write-up.
• E. Krissinel and K. Henrick (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst. D60, 2256-2268.
• http://www.ebi.ac.uk/msd-srv/ssm/papers/ssm_reprint.pdf 🫶

bestie reminder: the -all thing and the * thing are equivalent, so don't come for me saying one is better, they're the same, I checked, it's in the page 💖

and that's the whole page!! this was superpose, version vibes from May 2018, living in section 1 of the manual under superpose, and honestly? iconic. go align some proteins, you're doing amazing sweetie 🌈⭐👑

💜 bye bestie, structure superposition is your moment 💜