Dear James, I did once write a refinement program so I should try to answer your question. All hydrogen atoms attached to C and N in standard proteins and almost all in DNSs and RNAs can be calculated geometrically with no ambiguities. This has been standard practice in SHELX for about 35 years and I believe that Refmac and Phenix_refine do so too. The bond lengths to hydrogen are set to values about 0.1 shorter than the neutron diffraction values to best fit the electron density. Methyl groups attached to sp3 atoms are staggered. For other methyls SHELX has a facility to calculate the electron density around a circle and does 3-fold averaging to find the best torsion angle. H on O can either be found in this way or the torsion angle chosen that makes the best H-bond. For macromolecular refinements I recommend including hydrogens at any resolution but leaving out H on O unless (at very high resolution) they can be seen in the difference map. Adding the electrons to the C, N or O atoms is not a good idea.
Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 7 Jan 2011, James Holton wrote: > 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". Carbon has six electrons, even if it is a > methyl carbon with three unmodeled hydrogens stuck to it. Yes, this does > introduce a 33% error in the number of electrons at every CH3! I am also > suspicious that free ions like "Cl" are often modeled as free elemental Cl, > and not the Cl- ion, which has 1 more electron. But this is only a 3% error. > > Personally, I think that "something should be done" about disordered aliphatic > hydrogens (particularly since I don't have to code it). I suggest that simply > adding "3" to the "constant" coefficient of the "C" form factor to make a "CH3 > form factor" might just do the trick. Not only are the electrons brought in > by the H atoms generally delocalized into the carbon's electron cloud anyway, > but at most MX resolutions, the whole CH3 group is just one big fat lump of 9 > electrons. Mathematically, this is equivalent to saying that the B-factor > Gaussian (1.5 A FWHM when B=30) dominates the 5 much narrower Gaussians of the > atomic form factor. > > That said, I should also add that our illustrious refinement program authors > have good reasons for doing things the way they do. Mostly because users can > say some very unkind things if the new version makes their R factors go up. > It is true that riding hydrogens "count" as one electron each, but it is not > always clear where to put them, and in situations like methyl group hydrogens > they could be anywhere in the "doughnut of uncertainty" traced out by rotating > the X-CH3 about its X-C bond. It is tempting to say that this doughnut should > be modeled in somehow, but an important caveat to remember is that putting an > atom in the wrong place is twice as bad as leaving it out. That is, you get > one difference feature if the atom is missing, but two (one positive, one > negative) if it is wrong. So, a "doughnut atom" is expected to at best cancel > itself out. One could call this a corollary of of the general principles of > model building: "When it doubt, don't". > > 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! > > 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). > > -James Holton > MAD Scientist > > On 1/6/2011 8:15 PM, Kenneth A. Satyshur wrote: > > Persons of interest: > > > > I understood that refinements in refmac of low res structures without > > hydrogens includes a component of the Hydrogen atom attached to the > > carbon in the carbon scattering factors. Or is this just if the Hydrogen > > atoms > > are in the riding position. If so, why bother to add hydrogens in the > > riding > > position. > > > > Thanks > > kas > > > > > > -- > > Kenneth A. Satyshur, M.S.,Ph.D. > > Associate Scientist > > University of Wisconsin > > Madison, Wisconsin 53706 > > 608-215-5207 > >
