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[ccp4bb]: CNS composite SA omit - summary



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And the verdict is ... general disillusionment?

individual comments:
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In my opinion, SA refinement and maps are never any better than those that I
get from the normal minimization runs in CNS.  This is for structures where I
have data to roughly 2A, and also to higher resolution.  SA refinement tends
to randomize well-built structures, and does as well, but not better than
simple minimization on structures that have errors.

So you're not the only one.
---------------------------------------------------------------
I'm interested as my observations have been similar to
yours.  Basically, very little differences and I've
stopped doing the omit maps.  Did anyone suggset a
magic variable that we've got set incorrectly?
-------------------------------------------------------------------
In my opinion, SA-omit maps are quite useless because:
1- they take too long to compute;
2- in your case you are using the "wrong" coefficients (2mFo-DFc).

Much more interesting are modified SIGMAA maps (3mFo-2DFc for acentrics
and 2mFo-DFc for centrics) and Bhat's OMIT maps computed using these
coefficients. Also reduces calculation time, the maps clearly indicate
where errors are.
----------------------------------------------------------------
It is my (our) experience as one moves towards the end of a refinement that
composite
omit maps calculated via the sa_omit script in CNS and "normal" cross
validated
2mfo-dfc maps tend to track each other quite well.   The only potential issue
is that
the composite omit maps may be a bit more noisy than the 2mfo-dfc maps which
means
that some care should be taken in adding solvents based on peaks in the omit
maps or perhaps
in dealing with disordered regions in structures which give rise to broken
density in the
normal 2mfo-dfc map.  In fact most differences we have noticed have involved
regions
of weak density in the 2mfo-dfc map where the composite omit maps sometimes
tend
to be a bit more broken (at a given contour level) than the sigmaa weighted
map.
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..... anyway, if you load both maps into mapman you can at
least check *how* similar the they are. if they are
*identical* i suggest that something has gone awry
with the map files at some stage
.....
 > I get a correlation coefficient of 0.998.
.....
not sure if that
is good news or not. well, it saves running eternal
composite sa omit map jobs



Phoebe A. Rice
Asst. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://molbiol.bsd.uchicago.edu/faculty/pRice/index.html
http://bmb.bsd.uchicago.edu/