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

[Pavel Afonine]

  Hi Hailiang,

ok, great! I'm glad you sorted this out.

Pavel.


  On 9/15/10 10:22 AM, zhangh1 at umbc.edu wrote:
> 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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>>
>
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