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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