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On Wed, 2008-03-12 at 18:30 -0700, 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) > > > > 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). I suppose that is what I mean by "satisfying" ! If you have non-positive definite T and L, then you still have a valid mathematical model for the Fs, but the interpretation in terms of a simple rigid body model is flawed. This is not good, but I would say that you shouldn't take the rigid body model too literally even in the case of positive definite T and L. > > 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)? I am unsure how you are computing the TLS origins. My point was that that is a choice, and you didn't say what your choice was. Refmac chooses the (occupancy-weighted) centroid. This should be pretty much the same as the centre of mass. And at least for large groups, it is likely to be close to the centre of reaction, but you may get larger discrepancies for smaller groups. Cheers Martyn > > 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/) > > -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: [log in to unmask] * * Fax: +44 1925 603825 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************