Dear Alaistair, this sound a little like the SQUEEZE command in Platon (with dummies placed at the spurious regions), although I am not an expert about what SQUEEZE does in detail. If your structure is not too large, you could give it a try. The Polymerase is too large for Platon, but it works with insulin ;-)
best, Tim On 01/11/2015 08:05 PM, Alastair Fyfe wrote: > A related/follow-on question, hopefully on the same topic: > > When mask-based solvent modeling leads to problems caused by calculation > of an inappropriate mask (eg inclusion of disordered loops or > inaccessible pockets as bulk-solvent volume) it seems that a feasible > workaround is to (a) output the calculated mask via MSKOUT (b) edit it > to remove spurious regions (c) calculate partial structure factors for > the new solvent region using refmac's previous kSol, bSol estimates (d) > include the partial structure factors in a second round of refinement by > specifying "SOLVENT NO", FPART and SCPART. > > However, this does not re-calculate kSol and bSol to reflect the > modified mask. Is there a way to simply supply the mask to be used > rather than have refmac calculate it ? > Thanks, > Alastair Fyfe > > > On 01/11/2015 08:04 AM, Eleanor Dodson wrote: >> 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 >>> > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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