This is a wrapper to run mican from pymol.
- micanpymol.py / for python3-based pymol
- micanpymol_python2.py / for python2-based pymol
Auto-zooming after loading the dummy structures, which had made the camera-focus move unwantedly, was suppressed.
You need mican binary in your PATH.
If you launch pymol from GUI, PATH variable may differ from ones launched from CUI.
So it's better to give the full-path for mican inside the script.
First, load this script:
run micanpymol.py
Then run mican on pymol: basic usage
mican protein1, protein2
With options (check Mican's help for options)
mican protein1, protein2, -R -i 3 -m matrix.txt -a align.txt
Something around temporary directories differs between python3 and python2.
For older pymol running on python2, use micanpymol_python2.py instead.
- Selections are output into two temp files.
- Mican superposes them.
- Script load mican-output pdb as dummy.
- Script aligns the original object to the dummy pdb.
- Dummies are deleted.
Copyright (c) 2020 Koya.S Released under the MIT license https://opensource.org/licenses/mit-license.php
Mican is a protein structure alignment program by Dr. Shintaro Minami et al.
http://www.tbp.cse.nagoya-u.ac.jp/MICAN/
Reference
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MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments
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MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers
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https://academic.oup.com/bioinformatics/article-abstract/34/19/3324/4992143?redirectedFrom=fulltext