 |
 |
On Thu, 2008-12-18 at 10:15 -0800, Ethan A Merritt wrote: > 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. It is part of the model, but riding hydrogen positions are not refined (or am I missing something?). Thus, there is no formal omission. If I skip all the sidechain atoms, now that would be an omission. > 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. Exactly! I think if this issue of incomplete deposition is to be resolved, one has to determine first why is it necessary (and it's fine if it's just a matter of principle) and what additional information is needed. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /