[phenixbb] B factor

Pavel Afonine pafonine at lbl.gov
Sat May 10 07:47:43 PDT 2008

Hi Jianghai,

here is the copy from phenix.refine manual 

" 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.


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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