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

Pavel Afonine pafonine at lbl.gov
Wed Sep 15 09:19:31 PDT 2010

  Hi Hailiang,

> Then, I think phenix.fmodel should consider only Uani in ANISOU line
> (since Biso in ATOM line can be just derived, or redudant).

correct, and this is exactly what I wrote in my previous reply. Here is 


all phenix.fmodel uses from input PDB file are:

- CRYST1 record;
- Coordinates, occupancies and scattering types from ATOM records;
- ADPs defined in ANISOU records (if ANISOU records are available) or it
takes isotropic equivalent from ATOM records.


> However, as I
> mentioned before, I set all Biso in ATOM lines to be 0 while keeping
> ANISOU line unchanged. Now I think the results should be identical, but
> numerically the output Fc is still different,

The results must be identical, it not, then I can't explain it without 
having more information.

> Finally, if Biso is just derived from Uiso, how is the residual B (say
> after TLS refinement) considered?

The answers are here:


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