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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