Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if & when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor
On 9 January 2015 at 20:13, Roberts, Sue A - (suer) <s...@email.arizona.edu> wrote: > I always try both methods - usually there is little difference. However, > > For CueO (multicopper oxidase) where there are about 25 disordered > (unseen) residues in a loop, using Babinet scaling instead of the default > refmac scaling reduced the R factors by about 2% (both R and Rfree) and > improved the quality of the maps substantially. > > From Dirk's comment, I'd guess this is because the mask-based solvent > model is putting solvent where there is (disordered) protein, which is > different from real bulk solvent. > > Sue > > Dr. Sue A. Roberts > Dept. of Chemistry and Biochemistry > University of Arizona > 1306 E. University Blvd, Tucson, AZ 85721 > Phone: 520 621 4168 > s...@email.arizona.edu > > > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Armando Albert > Sent: Friday, January 09, 2015 12:56 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Bulk solvent > > Dear all, > Is there any reason for using Babinet scaling for bulk solvent correction > instead of mask based scaling? > Armando >
