On Thursday 18 December 2008, 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.
The riding-hydrogen treatment is definitely part of the model. But the number of parameters associated with it is not derived from the number of individual hydrogen atoms and their coordinates, it is limited to the number of parameters needed to describe the riding model itself. I.e. what is the C-H bond length and assigned geometry for each class of C and N atom for which hydrogens are generated. On the order of a dozen parameters total, I would guess, though I have not inspected this part of the code in refmac. > > 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. If you can find that particular version of the program! This is relevant also for regenerating the treatment of bulk solvent, particularly if a mask is involved. The K/B values for a bulk solvent model stored in the PDB header records are not sufficient by themselves to reproduce the calculation made by a particular program. Perhaps there should be a registry of the parameters associated with each version of each refinement program, and the PDB file could refer to the appropriate parameter set by name rather than including it in-line in each individual PDB entry. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
