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
