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Is ignorant rambling, was: DNA Structure: An Age of Refinement...

Harry Powell hrp1000 at cus.cam.ac.uk
Wed Feb 3 06:10:51 EST 1999

I really should know better than to rise to the bait again, but this guy
takes the cake.

On Wed, 3 Feb 1999, Clive Delmonte wrote:

> It would not matter whether heavy atoms were used, or MAD, or synchrotron
> sources, or the use of allegedly ab inititio methods, or whatever; since
> only one structural outcome would be possible.

Of course it matters. Although the refinement programs used often used
pretty heavy restraints, the ab initio solution programs don't (note that
ULTIMA isn't an ab initio program - it's a "blobby" molecular replacement
program). The beauty of ab initio methods (e.g. MAD) is that they _aren't_
biased by a molecular model. 

> Many algorithms have been used to determine oligonucleotide structure, such
> example.  Doubtless it would be unfair merely to assume that all these
> programs, or the context of their use, incorporated directly or indirectly,
> explicitly or implicitly, an a priori acceptance of the DNA double helix,
> but, unfortunately, explicit details of the working of the algorithms, and
> the
> context of their use, do not seem to be widely and publicly available.

I'll say it's unfair! If you want explicit details of the workings of
those programs, try READING THE LITERATURE. Alternatively, if you want to
be really rigorous in your analysis, the source code of many of the above
is available from the authors so you can go through it and work it out
for yourself. 

Dr Harry Powell, MRC Laboratory of Molecular Biology,
MRC Centre, Hills Road, Cambridge, CB2 2QH

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