Dear all,
a follow-up to yesterday's question about map sharpening. The problem
was that the sharpened maps aren't displayed in coot, but this is not
coot's fault, as can be seen from the output:
regular map:
making conventional map from MTZ filename unsharp.mtz using FWT PHWT
Number of OBSERVED reflections: 34725
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 128, 128, 384)
INFO:: 0.086 seconds to read MTZ file
INFO:: 0.002 seconds to initialize map
INFO:: 0.305 seconds for FFT
INFO:: 0.013 seconds for statistics
Map mean: ........ -1.4987e-06
Map sigma: ....... 0.0957995
Map maximum: ..... 0.629714
Map minimum: ..... -0.606727
INFO:: 0.026 seconds for contour map
INFO:: 0.432 seconds in total
sharpened map:
(as above, except:)
Map mean: ........ 0
Map sigma: ....... 0
Map maximum: ..... 0
Map minimum: ..... 0
These mtz files are generated identically, zero rounds of refinement in
Refmac 5.7 (from ccp4 6.3.0) with sharpening disabled or enabled (B
value = 5, 20, 60, 200). There are no features in the sharpened maps. Why?
When I don't specify a B value for map sharpening, it is calculated to
61 and the resulting map displays just fine.
Andreas
On 25/09/2012 11:52, Robert Nicholls wrote:
Hi Andreas,
In your case, it sounds like a reasonable strategy would be to use external
restraints for a few rounds of refinement (as you have done), but then release
them and instead use jelly-body restraints. This two-stage process will help to
initially hold your model in a sensible conformation using external restraints,
but then gently release the structure in order to reduce further bias in later
rounds. The immediate subsequent use of jelly-body restraints after external
restraints will ensure that the model won't deviate too far from that sensible
conformation, unless the data suggests otherwise.
Of course, if certain regions lose their sensible conformations in subsequent
rounds of refinement, you can continue to use external restraints just in these
regions.
I substantially rebuilt a surface loop that I don't want to restrain by the
model.
In this case, I would recommend re-generating the external restraints, this
time telling ProSMART not to generate restraints for these particular
residues/regions. This can be done using the -restrain and -restrain_rm
keywords, as described in the documentation (let me know off-board if you want
help with this).
If you enable map sharpening then the single output MTZ file should be the
sharpened map… I'm not sure why you are finding that the map is not displayed…
do you see any difference between enabling/disabling map sharpening?
Cheers,
Rob
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
