# [phenixbb] B factor

Jianghai Zhu jzhu at idi.harvard.edu
Sat May 10 18:38:32 PDT 2008

```Hi, Pavel,

Thanks for the answer.  If I compare the isotropic equivalent B-factor
after TLS refinement to the isotropic B-factor without TLS refinement,
will they have the same trend?  I want to use the B-factor
distribution to describe the ordered and disordered region in the
structure, will the TLS refinement skew that?  Thanks.

-- Jianghai

On May 10, 2008, at 10:47 AM, Pavel Afonine wrote:

> Hi Jianghai,
>
> here is the copy from phenix.refine manual
> (http://phenix-online.org/documentation/refinement.htm):
>
> " When refining TLS, the output PDB file always has the ANISOU records
> for the atoms involved in TLS groups. The anisotropic B-factor in
> ANISOU
> records is the total B-factor (B_tls + B_individual). The isotropic
> equivalent B-factor in ATOM records is the mean of the trace of the
> ANISOU matrix divided by 10000 and multiplied by 8*pi^2 and represents
> the isotropic equivalent of the total B-factor (B_tls +
> B_individual)."
>
> If ANISOU records are present then the equivalent isotropic B-
> factors in
> ATOM records are always derived from ANISOU as described above (in
> accordance with PDB format).
>
> I do not know if it is the same as TLSANL.
>
> Pavel.
>
>
> On 5/10/2008 7:09 AM, Jianghai Zhu wrote:
>> Hi,
>>
>> When TLS is used, phenix.refine gives 6 ANISOU B factors for each
>> atoms.  But we also get a number at the normal isotropic B factor
>> position.  If that number is the isotropic B factor, how was it
>> calculated?  Did you use something like the following?
>>
>> Uiso(e)^2=U11*e1^2+U22*e2^2+U33*e3^2+2U12*e1e2+2U13*e1e3+2U23*e2e3
>>
>> Is it the same as the output from tslanl if using refmac5?
>>
>> -- Jianghai
>>
>>
>>
>>
>>
>>
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```