[phenixbb] solvent model in phenix.refine

Weiergräber, Oliver H. o.h.weiergraeber at fz-juelich.de
Thu Dec 1 01:50:03 PST 2011


the ordered_solvent option in phenix.refine apparently uses these parameters by default:

    min_model_peak_dist = 1.8
    max_model_peak_dist = 6.0
    min_peak_peak_dist = 1.8

I was wondering about the justification for this (extremely relaxed) set of limits. As far as I know, the shortest hydrogen bonds (if defined as donor-acceptor distance) are about 2 A, and even these are considered exceptional and rare. Similarly, anything in excess of 3.5 A is quite unlikely to be significant energetically, so why use 6 A as an upper limit? Even if  max_model_peak_dist was only meant to limit the extent of the outer solvent shell, there is no such thing as max_peak_peak_dist to avoid unreasonably long individual bonds.
My personal suggestion would be a range of about 2.3 - 3.2 A for a significant hydrogen bond, with the lower limit exemplified by charged interactions (carboxyl-water or oxonium-water), which tend to be shorter - and stronger - than average.

On the other hand, I do frequently observe elongated densities which, in accordance with the default parameters, are typically interpreted by phenix.refine as two water molecules about 2 A apart. So the question arises whether this is a realistic assumption, compared to a "sliding water" model in which the position of a single molecule is just ill-defined in a certain direction (due to a competition of adjacent binding sites for example)?

Best regards,

  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-1448

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