[phenixbb] C-alpha r.m.s.d. calculation before and after structural alignment

Bret Wallace bretw319 at gmail.com
Thu Apr 4 07:00:15 PDT 2013

Dear All,

I have solved a complex structure of two proteins, and a reviewer has asked
to compare the altered interface binding of one particular binding partner
(protein2) in this complex to various other similar deposited PDBs through
r.m.s.d. calculations and rotation/translation matrices.

After aligning ~4 structures from the PDB (specifically aligning 1 chain to
the other binding partner, protein1) to my structure, I want to calculated
the rmsd before and after re-aligning the deposited structures (containing
protein2) to my complexed protein2.

I have used the superpose utility in phenix to align the C-alphas, however,
I am getting very large rmsd values after alignment (~3.3). This is rather
strange as the aligned proteins are essentially the exact same, both in
sequence and secondary structure.  Using various different programs such as
SSM, Coot, and others give me an rmsd value of ~1, which is far more
reasonable, but they do not output a "start" rmsd value.

Any suggestions on what the cause of this large rmsd value? Or possibly
another program that could provide start and final rmsd values along with
rotation/translation matrices for alignment?

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