[phenixbb] difference map peaks
krahn at niehs.nih.gov
Wed Oct 7 08:47:30 PDT 2009
Pavel Afonine wrote:
>> I suspect that negative peaks are from the bulk-solvent mask, as you
> The bulk solvent is flat... at least phenix.refine uses Flat Bulk
> solvent model (mask based). If bulk solvent is guilty for this, why
> would you observe peaks ?
> I repeat once again: looking at Average Kick map may resolve this puzzle.
Sometimes there are voids just big enough for a tiny bit of solvent mask
to fill. This results in negative difference density. Even though the
mask is flat, the B-factor adjustment will convert small , isolated
fragments of bulk mask into an approximately gaussian sphere, producing
a well-defined negative peak.
However, this situation is fairly rare. Voids big enough for the bulk
mask to enter are usually big enough for a water. A true hydrophobic
void deters from protein folding stability, and normally only occur if
it pertains to the protein's function. So, a simple noise peak probably
is more likely.
The only way to know for sure is to make a bulk-solvent map. Is it
possible to write out bulk solvent coefficients?
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