On Wednesday 12 March 2008 18:30, Pavel Afonine wrote:
> 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)
Correct (if I understand what you mean).
Note that the PDB header may also contain an overall B correction that
also contributes to the net individual ADPs.
> 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.
Not quite correct. If the tensors are NPD, then the rigid body assumption
is violated. This does not necessarily mean that the description is
nonsensical (although it could be). For instance, if you swing a normal
wooden baseball bat[*] the motion can be described by TLS. Now imagine
that the bat is made of rubber, and can bend as you swing it. In this
case the tip of the bat will lag the grip and the body during the first
part of your swing. This is still describable using TLS, but the L
vector will go NPD.
In the case of a protein stucture, such a model was probably not what
the depositor intended. But I don't see an a priori reason to say that
the description is invalid. The TLS model may correctly describe the
distribution of individual ADPs in the structure, even if the physical
interpretation diverges from a small set of truly rigid bodies.
Of course, non-positive definite tensors may also be the result of a
refinement that has simply gone bad. I'm not saying the model should be
accepted without further inspection!
Ethan Merritt
[*]
American readers: s/wooden/aluminum/
British readers: s/baseball/cricket/
> 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/)
>
--
Ethan A Merritt Courier Deliveries: 1959 NE Pacific
Dept of Biochemistry
Health Sciences Building
University of Washington - Seattle WA 98195-7742
