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

Pavel Afonine pafonine at lbl.gov
Thu Apr 4 09:38:03 PDT 2013

Hi Bret,

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.

More information:


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 
> 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?
> Thanks,
> Bret
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130404/e45ccaa7/attachment.htm>

More information about the phenixbb mailing list