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Nicholas M Glykos <[EMAIL PROTECTED]> wrote: > To give a semi-philosophical argument, the best model is the one that > maximises the product (likelihood * prior). A model for which all surface > exposed lysines, arginines, etc, have all atoms after Cbeta missing should > be given an extremely low prior probability (based purely on chemical- > biological grounds :-) I strongly agree with this viewpoint. We should not be discussing _whether_ to include these atoms in the model, but how _best_ to include these atoms in the model. : Marc Delarue <[EMAIL PROTECTED]> wrote: > One possibility is indeed to put all possible rotamers coordinates, only I > would not recommand 1/Nrot occupancy, but, instead, Boltzmann-like weights > with an Energy taking into account both the Corr. coeff. of that > particular rotamer in the electron density (E-1-CC) and a penalty given by > some oracle called Ms_Bump. I like this idea, but you would have to watch out for a proliferating number of parameters to implement it. If you want separate occupancy, weights, and B factors for each rotamer, that is a suspiciously large number of parameters in the case of Arg or Lys. On Wednesday 10 January 2007 09:01, Marc SCHILTZ wrote: > > So the criterion of atoms that should be modelled because they "are in > the crystal" has now been narrowed down to atoms that should be modelled > because they are "covalently connected to the rest of the protein". > > 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. > But we are not refining hydrogen atoms because the experimental data > does not warrant this ! (unless we got very high-resolution data). Not true. In fact the hydrogen scattering contribution falls off with resolution just like the normal scattering from any other atom type.
