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On 12/18/2008 8:23 AM, Ed Pozharski wrote: >>> Riding hydrogens are *not* part of your model, >>> >> The fact that you don't see H in your fo-fc map due to limited >> resolution and high level of noise does not mean that H atoms are not >> present in actual real structure -:) >> >> > > Let me ask you this - are bond length restraints part of the *model*? > Obviously not, they are part of refinement target. In the same way > riding hydrogens are used to calculate the refinement target, but they > do not increase the number of parameters of your model. So I guess my > definition of the "model" excludes deduced parameters. > - "bond length restraints" do not contribute to the scattering and hence do not affect the R-factors, while H atoms do contribute to scattering and therefore R-factors computed from the model with or without hydrogens can be different (I spent a couple of months implementing it in PHENIX and I can say for sure that the difference is well noticeable). - the (slightly) different geometry library values for hydrogens will obviously lead to different positions for H atoms which has a great potential to yield different validation results (for example, clash scores in Molprobity). >> Not all programs and their versions place H atoms the exact same way >> (using same geometry values, same rules for B-factors assignment: in >> some programs H inherit the B-factors of the atom it's attached to, in >> some it is multiplied by the factor from 1.1... to 1.5, etc. What >> about occupancies, especially for alternate conformations?). >> > > But as I said, (if) the program and version is included in the PDB file, > riding hydrogens can always be reconstructed. > What about 50 years from now? Are you sure you will be able to dig out that xxx.zzz.aaa version of that program, install it and run? I would assume it will be much easier to take a complete model from data base. Pavel.