TMALIGN(1)

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💖 TMalign 💖

Okay bestie, this is the manual page for TMalign from the TMALIGN(1) entry in the General Commands Manual (section 1) 📖✨. It's the tool for protein structure alignment, so let's get into it 🧬

🎀 NAME 🎀

TMalign is all about protein structure alignment 🦋

🌸 SYNOPSIS 🌸

TMalign structure.pdbtarget.pdb[options]

✨ DESCRIPTION ✨

Okay so TMalign lines up proteins structurally, and the score it gives comes from the TM-score algorithm 💅 It's giving precision, no cap 🔥

👑 OPTIONS 👑

Okay this part is literally the main character 💜 If you run TMalign with no options, it just shows you a summary of commands. If you give it two protein structures, the TM-score normalises by the length of the second protein 🫶 And the final structural alignment is the same no matter which options below you use, so the alignment itself is totally stable 🧚

  • -L number — lets you normalise the TM-score by a length you pick yourself, measured in aa (amino acids) 🍓
  • -a — normalises the TM-score by the average length of the two structures ✨
  • -b — normalises the TM-score by the length of the shorter of the two structures 🌈
  • -c — normalises the TM-score by the length of the longer of the two structures 🦋
  • -o filename — runs TM-align and writes the superposition to filename.sup and filename.sup_all 🎀 Those output files double as scripts for rasmol 💖 To see the superimposed structures of just the aligned regions, run:
rasmol -script TM.sup

To see the superimposed structures of all regions, run:

rasmol -script TM.sup_all

🦋 SEE ALSO 🦋

Check out http://zhang.bioinformatics.ku.edu/TM-align/ and rasmol(1) 💜 And if you want the deep dive, go read the publication in NucleicAcidsRes. (2005) Volume 33 page 2303ff. by Zhang and Skolnick 📚 Iconic citation, periodt ✨

🧚 AUTHOR 🧚

tm-align was written by Zhang and Skolnick 👑

This manual page was written by Steffen Moeller <moeller@debian.org>, for the Debian project (but it's totally fine for others to use it too) 🫶

Manual page wrapped up with love 💖 TMALIGN(1), dated October 21, 2007 🌈 Stay iconic, bestie 💅✨

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