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Quoting Ethan Merritt <[EMAIL PROTECTED]>: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > On Wednesday 10 January 2007 13:18, [EMAIL PROTECTED] wrote: > > > > Quoting Ethan Merritt <[EMAIL PROTECTED]>: > > > > > > If this concept is taken further, one could ask why we are not > > > > explicitly refining hydrogen atoms ? > > > > > > We are. > > > At least, those who correctly use available options in refmac or shelx > are. > > > The best results (R, Rfree, geometry) are obtained by explicit inclusion > > > of hydrogens via the riding-hydrogen model. This is also a basis for the > > > Molprobity validation tools. > > > > This misses the point. In the riding hydrogen model, the positions of the > > hydrogens are NOT explicitly refined but extrapolated in each refinement > cycle > > from knowledge of the positions of the other protein atoms and by assuming > ideal > > geometry. > > It does not miss the point. It illustrates the point exactly. > Because we know the hydrogens must be there (they are covalently attached) > we should make our best effort at including that knowledge in the model. > The correctness of our knowledge and the success of our effort is reflected > by > the observed improvement in objective measures like R and Rfree. > > The same holds for disordered sidechains. We know they must be there, > and we should make our best effort to include that knowledge in the model. These two issues are entirely different. To "model" something is one thing. To refine something is another. In the riding-hydrogen model, there are NO explicit X Y Z B parameters for the hydrogen atoms that are refined. It is merely an improved model for the scattering atoms (just as a 5-term Gaussian expansion of the atomic formfactors might give better results than a 2-term expansion, or just as the correct inclusion of f' for the S or other heavier atoms might improve the fit etc), but it does not introduce additional parameters in the refinement. What I was objecting against, is the suggestion that was made earlier on this bulletin board to explicitly refine X Y Z B parameters for atoms of disordered side-chains. This DOES introduce additional parameters in the refinement process and, worse, it introduces parameters for which there is little or nothing in the experimental data to refine against. As a result, the refined X Y Z values run the risk of being close to meaningless. Non-crystallographers who use a PDB file are unlikely to look at OCCUP or B columns in the file, but the data which they certainly will use (either directly or indirectly by displaying the structure on a screen) are the X Y Z values. It is not because we know that "something must be there" that we are entitled to refine it. > Because it is not necessary to do so. Storing every H coordinate generated > by the > riding model adds no information to the PDB file that is not already present > in the > parsimonious description provided by the header record: > REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS Exactly what I am saying: the riding-hydrogen model does not explicitly refine the positions of the hydrogen atoms, but just puts them in idealized positions with respect to the non-hydrogen atoms.
