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i have two protein pdb files and want to calculate the backchain RMSD between them. As far as I know the GUI of Pymol can use align to calculate the RMSD (but I don't know if it is the backchain RMSD).I want to use the python code to use pymol to calculate the backchain RMSD. I know how to align them but don't know how to calculate the RMSD.

import pymol2
with pymol2.PYMOL() as pymol:
    pymol.cmd.load('foo.pdb', 'foo')
    pymol.cmd.load('bar.pdb', 'bar')
    pymol.cmd.align('foo', 'bar')
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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Feb 9 at 10:00

1 Answer 1

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The backbone can be specified using a selector for the names of these, which are N, CA (Cα) and C (C-prime).

out = pymol.cmd.align('foo and name N+CA+C and polymer', 'bar and name N+CA+C and polymer')
rmsd, n_atoms, n_cyles, n_rmsd_pre, n_atom_pre, score, n_res = out

If you do not wish the proteins to be moved you can use rms_cur, which is just the rmsd.

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  • $\begingroup$ Thank you for your answer! It works well! however,i want to further learn related knowledge about pymol like this. Can you provide some web/cook book name? $\endgroup$
    – chengyun zhang
    Feb 13 at 1:51

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