[phenixbb] difference map peaks

Joe Krahn 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 
>> suspected. 
> 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.
> Pavel.
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?

Joe Krahn

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