Add --no-bss flag to optionally turn off bulk-solvent scaling in phenix.refine
#28
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Note - this PR does not change the default behavior. The default behavior is still to try and produce the "best" phases, which means including bulk-solvent scaling. If this ever changes in the future, I will be sure to make that clear.
The new feature is implemented as an optional flag,
--no-bss, which takes no argument. Including this flag will tellmatchmapsto skip the bulk solvent scaling step of phenix refinement for both off and on data. The rationale is that in some cases, there is interesting signal (e.g. a bound ligand) that is far away from the protein model. This signal is susceptible to be altered by BSS in a way that is undesirable. In at least one case (not shown), turning off BSS leads to significant improvement of map quality.In the limiting, isomorphous case, this
--no-bssflavor ofmatchmapsis much closer to mathematically equivalent to an isomorphous difference map. Additionally, and unsurprisingly,matchmapsruns much faster when BSS is skipped.