[phenixbb] C-alpha r.m.s.d. calculation before and after structural alignment
pafonine at lbl.gov
Thu Apr 4 09:38:03 PDT 2013
phenix.superpose_pdbs reports both rmsd values: before and after. Also,
if I remember correctly, it uses all matching atoms to compute rmsd (and
not only those used to perform superposition). This may explain the
difference. Also, it reports rotation/translation matrices.
On 4/4/13 7:00 AM, Bret Wallace wrote:
> 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
> 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?
> phenixbb mailing list
> phenixbb at phenix-online.org
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