Dale Tronrud recently said ' I always like controls.’ in the discussion
concerning water molecules.
So do I but I prefer an alternative to his suggestion, which is the profile of
how the average carbonyl oxygen would look in an F11 map. This is absolute in
the sense that it is full occupancy and it is something truly integral to the
molecule of interest. My original implementation built a 3D profile based on
the local density of 50 carbonyl oxygens that had been chopped from the phases
(the water commands in ‘A-Z of O’ from my home page if you are interested in
details). There is a much simpler variation on this theme that works with any
refinement program and any graphics program where you set zero occupancy to
three consecutive carbonyl oxygens ( I use residues in a b-strand) at the
beginning of the refinement and keep them like that until you are finished (is
one ever finished?). If you go through multiple rebuilding rounds, it pays to
regularise the segment every cycle or two, since the C can move towards the
correct position of the O, otherwise it is easy to do. Just remember to reset
the occupancies before submitting coordinates to the PDB and then carry out a
final refinement run.
The peak height is, of course, resolution dependent but any graphics program
should allow you to change a slider to see what is realistic.
Although this gives an absolute value for what you are looking for, the
crystallographer still has to decide what fraction of the average carbonyl
oxygen shall I use for adding waters :)
Seeing three gleaming beacons in your F11 map focuses your mind and may dampen
unrealistic expectations.
Sorry for the long post...
Alwyn Jones
al...@xray.bmc.uu.se
http://xray.bmc.uu.se/alwyn
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