Hi,
I'm trying to compute the interface RMSD (iRMSD) between two protein pairs
that are highly similar (might have a few missing residues, but are
otherwise identical). Right now, my code does something like the following
for protein pairs "gold" and "test" (receptor has chains A+B and ligand has
chains C):
PyMOL>select contact_rec, (gold & chain A+B) & all within 10 of (gold &
chain C) & n. ca
PyMOL>select contact_lig, (gold & chain C) & all within 10 of (gold & chain
A+B) & n. ca
PyMOL>align gold & contact_rec + contact_lig, test, cycles=0
Match: read scoring matrix.
Match: assigning 82 x 445 pairwise scores.
MatchAlign: aligning residues (82 vs 445)...
MatchAlign: score 257.500
ExecutiveAlign: 67 atoms aligned.
Executive: RMS = 14.161 (67 to 67 atoms)
This seems to suggest that, even with cycles=0, 82-67=15 atoms were not
included in the alignment. When I look at the alignment (object=aln), it
appears that most of the "missing" residues from this alignment have the
same residue name, are matches in the sequence alignment, and are in a
nearby location.
Is it possible to force align to give the full RMSD calculation? super has
the same issue, and I'm concerned that using something like rms or fit
won't work because the "gold" and "test" have different residue numbering
(and might be missing residues so it's not always possible to give them an
equivalent numbering).
Does anybody have any suggestions?
Thanks in advance,
Nathan
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