MICAN on PyMOL 🍊

MICAN is a protein structure alignment software. Most notable feature of Mican is that it can align two proteins in non-sequential manners.

I often use mican as a commandline tool, but visualizing the results with pymol needs parsing mican’s output file like below.

mican protein1.pdb protein2 -o output.pdb
extract_models_all.sh output.pdb # My own script to parse NMR-like model
pymol output.model1.pdb output.model2.pdb

Pymol wrapper

So I wrote a wrapper script to run mican on pymol.

micanpymol

Using this, you can interactively run mican. It’s fun. This will be beneficial since mican has many alignment modes or parameters.

How to use

Launch pymol

pymol protein1.pdb protein2.pdb

Load the script (or give it in pymolrc if you want it every pymol session)

run micanpymol.py

Run mican. Third argument is the option given to mican.

mican protein1, protein2, -s -m matrix.txt

You need mican executable in your PATH. Launching pymol from GUI sometimes fail to load PATH (in my environment). It’s a good choice to change “mican” in the script to the full path to the executable.

Reference

• MICAN website
  • http://www.tbp.cse.nagoya-u.ac.jp/MICAN/
  • You need a Mican executable. Let’s compile it for MAC.
• MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments
  • http://www.biomedcentral.com/1471-2105/14/24/abstract
• MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers
  • https://academic.oup.com/bioinformatics/article-abstract/34/19/3324/4992143?redirectedFrom=fulltext

🍊 MIKAN is a kind of Japanese orange, the software is named after it.