On 12 Jan 2015, at 10:09, Bernhard Rupp <b...@ruppweb.org<mailto:b...@ruppweb.org>> wrote:
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? I have the feeling that this might be the case. More details on the two bulk-solvent correction methods available in Refmac (with formulae) are in Murshudov et al (2011) Acta Cryst D67, 355-367 - Section 2.4 Best wishes Roberto 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<mailto: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<mailto: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<mailto:s...@email.arizona.edu> -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UK<mailto: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 Roberto A. Steiner, PhD Randall Division of Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk> Phone 0044 20 78488216 Fax 0044 20 78486435 Room 3.10A New Hunt's House Guy's Campus SE1 1UL London
