Hi Martin,
> 2) in the context of PX, only the total "B factor" contribution to Fcalc needs to be positive definite, the TLS component might not be (though it is satisfying if it is)
>
Please correct me if I'm wrong.... My understanding was that the T and L
matrices must be positive definite, otherwise they do not have physical
sense. Yes, I understand that what's in the end important for the actual
calculations is the positive definiteness of the total B-factor (since
it goes as sqrt(det(B)) into denominator in electron density and
gradients calculation).
> The PDB entries should contain the origin of the coordinate system to which the TLS parameters refer, and thus it is something you choose not something you calculate.
>
OK, this partially the deviations I observe. Although, I'm still a bit
puzzled about why some differences are so large? Isn't it true that the
computed center of mass of a group should be pretty close to the
"chosen" one (at least for large groups)?
Cheers,
Pavel.
---
Pavel V. Afonine, Ph.D.
Lawrence Berkeley National Lab, Berkeley CA, USA (http://www.lbl.gov/)
CCI: Computational Crystallography Initiative (http://cci.lbl.gov/)
PHENIX (http://phenix-online.org/)
|