What still evades me is, why exactly is the Babinet immune to these effects of excluding/masking-out unmodelled parts?
The Babinet correction is also a function of the MODELLED part, just the opposite sign. So an incomplete model de facto equals an over-estimated solvent. Is it just the high effective dampening of this correction (B ~200) as Pavel said that makes it less susceptible because the higher resolution reflections are less affected and therefore have a chance to correct/overcome the inadequate (implicit) masking? Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Sonntag, 11. Januar 2015 17:05 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Bulk solvent 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 <tel:520%20621%204168> 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
