HI James,
Obviously, this depends a bit on which refinement program you use, and I am > not familiar with all of them. However, I have had some conversations with > Garib "refmac" Murshudov and Pavel "phenix.refine" Afonine about this, and > the shocking answer appears to be "no". > wow, I've got a middle name -:) > Personally, I think that "something should be done" about disordered > aliphatic hydrogens (particularly since I don't have to code it). I'm doing this right now... Next version of phenix.refine will be smarter about it. But what about MolProbity? and all those neat inter-digitating hydrogens? > Should it not be possible for the refinement program to be "smarter" about > where it puts riding hydrogens? Well, that is always possible, but I don't > think MolProbity is exactly built into refmac. You can, however, run > MolProbity before you put your model into refinement! > In fact, phenix.refine uses MolProbity to add H atoms (well, it uses Reduce to add hydrogen atoms), and it updates their positions every macro-cycle! MolProbity uses Reduce too to add H. > The problem, of course, is if you have a 4.5 A structure with all the > hydrogens built in you will get hateful comments containing the word > "parameters" from undereducated reviewers. I say "undereducated" because > getting the electron count right is actually MORE important for low-angle > structure factors than it is for high-angle ones (the extreme case of this > being F000 itself). Yes, explicit hydrogen atoms do slow down the > refinement, and clutter the graphics, but they do not really add much by way > of "free parameters". Not if the geometric restraints are sensible. In > fact, the central lesson of MolProbity is that hydrogens do introduce (at > least potentially) better geometric restraints. Sort of like what an > elastic network model can do (ahem). Agree. That's what I keep saying over and over. Yes, H atom is a weak scatterer, and it contributes to low resolution more than to high (similarly to bulk-solvent). In fact its contribution to high resolution reflections approaches zero. Pavel.
