Hi Jianghai,
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?
yes, only if: 1) the choice of TLS groups is correct; 2) the restraints on isotropic individual B-factors are not too tight.
I want to use the B-factor distribution to describe the ordered and disordered region in the structure, will the TLS refinement skew that?
I'm not sure what exactly you want to do here. But anyway, by using TLS model you better describe atomic ADP: TLS models global domain motion and individual B-factors model local atomic vibrations; that is each kind of motion receives dedicated parameterization (which is good). However, if you model everything with individual B-factors (no TLS) the similarity restraints are always used and they tend to remove TLS contribution making final B-factors less adequate. Pavel.