[phenixbb] How does phenix.fmodel treat isotropic and anisotropic B?

zhangh1 at umbc.edu zhangh1 at umbc.edu
Tue Sep 14 16:48:21 PDT 2010


I am doing a phenix.fmodel calculation for a PDB structure containing
anisotroipc B. If I understand it correctly, the B factor is composed of
both the isotropic B for ATOM line (Biso) and the anisotropic B from
ANISOU line (Uani):

Fc=sigma ( fi * exp (-Biso*s*s) * exp (-st*Uani*s) * exp (i*r*s) )

Please correct me if the above equation is wrong. I also noticed that in
PDB, the Uani (after scaling by 10^-4) is generally much smaller than
Biso. So I assume that Biso has a much bigger contribution than Uani, the
latter only implying the vibrational anisotropicity.

However, I did a test calculation by setting all Bio to 0 whereas keeping
Uani unchanged. Due to the above assumption, I expected the results should
be very different from the native structure; however, coot told me they
were just so close...

Maybe I am wrong somewhere...

Best Regards, Hailiang

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