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Omit maps in Xtalview

Paul Hubbard phubbard at post.its.mcw.edu
Tue Aug 8 23:39:19 EST 2000


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

mtz2various HKLIN phased.mtz HKLOUT out.phs << eof OUTPUT USER -

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).



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