Well yes, The bulk solvent model can distort the density, especially if the ligand is large. But it usually isnt too serious - try doing "SIMPLE" scaling and see if that has any effect on the appearance of the density Eleanor
On 22 July 2014 10:16, <herman.schreu...@sanofi.com> wrote: > Dear Armando, > Is 1.9Å really the diffraction limit of your crystals, or do they diffract > further and is 1.9Å just a convenient resolution cutoff? In the latter case > you might be looking at truncation effects. > Best, > Herman > > > > -----Ursprüngliche Nachricht----- > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > Armando Albert > Gesendet: Freitag, 18. Juli 2014 18:04 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [ccp4bb] Negative electron density in the Fo-Fc map at the > binding site > > Dear all, > I am screening a small library of ligands against my protein crystals. > Following a soaking with different ligands, I collect datasets to 1.9A > resolution and refine them against an empty model without any problem. > What is the meaning of a rather large negative electron density in the > Fo-Fc map at the binding site?. Could it be related to an incorrect bulk > solvent model? > Thank you in advance > Armando >
