Super: Difference between revisions
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<source lang="python"> | <source lang="python"> | ||
super p1 & alt A+'', p2 & alt B+'' | super p1 & alt A+'', p2 & alt B+'' | ||
</source> | |||
== Write rmsd to file == | |||
'''pymol_rmsd_test.pml''' | |||
<source lang="python"> | |||
reinitialize | |||
fetch 1F9J, async=0 | |||
fetch 1YX5, async=0 | |||
extract 1F9J_A, 1F9J and chain A | |||
extract 1YX5_B, 1YX5 and chain B | |||
test=cmd.super("1F9J_A","1YX5_B") | |||
python | |||
writefile=open("rmsd_file.txt","a") | |||
writefile.write(' '.join('%s' % x for x in test)) | |||
writefile.write('\n') | |||
writefile.close() | |||
python end | |||
</source> | |||
In terminal | |||
<source lang="bash"> | |||
pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt | |||
</source> | </source> | ||
Revision as of 10:38, 23 January 2014
super aligns two selections. super is more robust and accurate than align. For syntax, see align.
Algorithm Details
super does a sequence-independent structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (e.g. >2 standard deviations from the cycle's mean deviance).
Caveats
- If super ever tells you no matched atoms, then instead of
super p1, p2
try
super p1 & alt A+'', p2 & alt B+''
Write rmsd to file
pymol_rmsd_test.pml
reinitialize
fetch 1F9J, async=0
fetch 1YX5, async=0
extract 1F9J_A, 1F9J and chain A
extract 1YX5_B, 1YX5 and chain B
test=cmd.super("1F9J_A","1YX5_B")
python
writefile=open("rmsd_file.txt","a")
writefile.write(' '.join('%s' % x for x in test))
writefile.write('\n')
writefile.close()
python end
In terminal
pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt