super aligns two selections. super is more robust and accurate than align. For syntax, see align.
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).
- If super ever tells you no matched atoms, then instead of
super p1, p2
super p1 & alt A+'', p2 & alt B+''
Write rmsd to file
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
pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt