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

zhangh1 at umbc.edu zhangh1 at umbc.edu
Wed Sep 15 10:22:21 PDT 2010

Hi Pavel:

I just found that the PDB structure I tested has very small part isotropic
B, and my program set them to 0 as well. Now I am clear that phenix.fmodel
check each atom for anisotropic B: if has, ignore the isoB, if not, take
the isoB.

Sorry for the confusion due to my careless about the small part isotropic
B (hard to find though:(

Best Regards, Hailiang

>   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
> copy-paste:
> """
> 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:
> http://journals.iucr.org/j/issues/2002/04/00/ks0128/index.html
> http://www.phenix-online.org/newsletter/
> Pavel.
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