Difference between revisions of "Super"
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| Line 15: | Line 15: | ||
<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 11:38, 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