Re: [ccp4bb]: water picking

[Laurence Pearl <l.pearl@icr.ac.uk>]

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I guess I am beginning to show my age here, but I'm not so fond of these
automated methods for 'water' assignment. I've always found it well worth
while going through the list of positive peaks in the Fo-Fc map from the
highest down, and examining them by hand using the PEKPIK (or equivalent)
routines in O (for example). Lots of these peaks will actually be due to
rotomer mistakes and other defects in the protein model rather than actual
bound solvent. Of course the clever automatic programs won't put waters in
these peaks because they wont look round enough or be at the correct distance
to make hydrogen bonds, but (unless I really have missed some major
breakthroughs due to encroaching senility) they don't sort out the mistakes
either.

Laurence Pearl

Anastassis Perrakis wrote:

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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> > So, my question - what is the consensus out there for the best method of
> > picking waters.
>
> arp_warp 5.1 of course ;-)
>
>                 Tassos
>
> P.S. is that un-biased opinion ? hmmmm...
> P.S.2 The arp_warp included in ccp4 4.1a will do the
> solvent building job as well.

---------------------------------------------------------------------------
  Laurence H. Pearl

  Section of Structural Biology, Institute of Cancer Research
  Chester Beatty Laboratories,  237 Fulham Road
  London SW3 6JB, UK

  Phone +44-207-970 6045 : Secretary +44-207-970 6046
  FAX   +44-207-970 6051 : E-Mail l.pearl@icr.ac.uk
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