Super

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

See Also

• align
• Cealign