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[ccp4bb]: Omit maps in Xtalview

Eleanor J. Dodson ccp4 at ysbl.york.ac.uk
Wed Aug 9 04:35:19 EST 2000

Paul Hubbard wrote:
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> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> Hi,
> Yet another semi-related CCP4 question, but if there's a more suitable
> news group please let me know...
> I have been playing around with Xtalview as it can make omit maps "on the
> fly" which seems a pretty useful thing to do. However I have noticed a few
> things which I want to check before I really start using it. Mainly, the
> omit maps which seem a little different to those I normally make. It
> seems as though when I omit waters in Xtalview, the resulting density
> suggests that some of them should be moved a few tenths of an Angstrom
> (almost 1A in some cases), whereas when doing this in CNS (the S.A. omit
> map way), and looking at the map in O, these waters seem spot on.
> To make the map I initally calculate phases in CCP4i using current refined
> coordinates, switching the "scale input Fp to the Fcalc" toggle on. I
> make sure the working set used to make the model in CNS/O is flagged the
> same in the mtz file. Next I run the following script to make the phs
> file:
> mtz2various HKLIN phased.mtz HKLOUT out.phs << eof OUTPUT USER -
>     '(3I4,x,F7.2,x,F7.2,x,F7.2)'
> end

 You can probably use REFMAC for this step; or are you using CNS for
> In Xtalview I make a mFo-Fc map with cubic splines, applying bulk solvent
> correction. Finally, to make the omit map, I select the waters to be
> ignored and recalulate the map with the shake option turned on.
> Does the shake routine work as well as true S.A., and can I get
> reliable omit map; or am I missing something which is causing this density
> shift problem.
> Again, profuse apologies for such an unrelated CCP4/CNS question...
> (though they are both involved in this problem).

 I strongly suspect that the "shift" is real; you dont say what
resolution you are working at, but "water" peaks are often a mixture of
true signal; diffraction ripples due both to truncated data and scaling
vagaries, and once a site is given the VDW repulsion restraints come
into play to keep it at reasonable distances from the rest of the

 We have noticed for a long time; back in the pre automated structure
days when you really examined your maps in detail, that using omit maps
to verify HOH positions made you depressed..at least 50% of them were as
you say embarrassingly far from the assigned site.

 In my opinion SA is no better than the shake option for removing bias -
it is very powerful for exploring alternate conformations for protein
etc, but not much use for examining HOH.

 If we were realistic we would accept that many many of our HOH sites
are partially occupied and until we can build such models, and software
can take that into account all checking procedures will throw up such

 Eleanor Dodson 
Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65


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