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Hi Phil,
My question with this approach is that is there any potential to have a negative effect on refining the structure, given that one is introducing a number of bonds with relatively high average deviations from the mean ? The rest of the bonded (covalent) geometry has an rms in the range 0.004 - 0.015 (-ish) but this is one to two orders of magnitude tighter than a hydrogen bond. Is the target function sophisticated enough to handle this or is there a problem with treating hbonds and covalent bonds as peers ?
I think the L-BFGS algorithm we're using is smart enough to handle this situation, but I haven't investigated this question systematically. Note that e.g. most dihedral restraints are also much weaker than the bond restraints. Ralf