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/)
