Hello Andrew !
I'm not a crystallographer either, but I do appreciate how complicated and
mathematical crystallography is. I have done a lot of programming in
FORTRAN, and I also appreciate exactly how hard it would be to follow
someone else's algorithm (if I haven't been given the logic flow chart
behind the
algorithm) in a program with many variables designed to accommodate a very
wide range of possible atoms, symmetries, symmetry operations, temperature
factors, atomic masses, diffraction coefficients, linked atoms, etc., etc.
If someone gave me a text in Arabic, Hebrew, Cuneiform, Greek, etc., even
with a dictionary, I'd be just as totally lost as having to follow the logic
behind
a complicated crystallographic package in source code which has been
developed and
elaborated over many years.
Moreover, any suggestion that I, or others, should address ourselves to such
an analysis of a dozen or so different crystallographic refinement packages
in order to spot, in maybe hundreds of lines of mathematics, whether the
outcomes have been predetermined in any way (consciously or otherwise) could
even give the impression that it was intended to be obstructive.
This is why, in my opinion, we really do need a very clear statement,
intended for easy comprehension by non-crystallographic scientific
colleagues, setting out the philosophical foundation of the algorithms in
use in each oligonucleotide refinement program, and focussing on the
geometric relationship between the strands.
I have read the crystallographic literature on oligonucleotides fairly
conscientiously and I have a copy of SHELX, courtesy of Professor Sheldrick.
It is my experience, though perhaps not yours, that explicit statements of
the philosophical approach being adopted towards the prior acceptance of
plectonaemic winding in DNA in an algorithm is extremely rare. In one
important exception, the Cambridge meeting in 1989, it was made explicit
that plectonaemic winding was fully incorporated into the algorithms used by
the participants.
In every other field of biophysics and biochemistry, researchers usually lay
out each main stage of their work in explicit, comprehensible experimental
detail, and explain the philosophical development underlying their work, as
well as the way they carried it out.
In the Puzzles we see with stark clarity exactly what problems we have
induced for ourselves by an uncritical acceptance of strident assertions
that high polymer DNA is a double helix even when that model does not give
us any helpful clue as to how to resolve the Puzzles, and when AFM & STM
have revealed a different DNA structure in a number of studies.
Why does it have to become such big deal when a scientist has the temerity
to ask an oligonucleotide crystallographer to explain exactly in clear
English the philosophical foundation underpinning his or her work ?
Could it be that the crystallographic outcomes are not actually as secure as
the strident claims made for them might induce us to believe ?
It would be so unfortunate if any ferocious and unhelpful responses from
oligonucleotide crystallographers came to be seen as deliberately
intimidatory, wouldn't it ?
Clive Delmonte
E-mail: clived at ndirect.co.uk
or: clivedelmonte at c-i-delmonte.freeserve.co.uk
-----Original Message-----
From: Andrew Dalke <dalke at bioreason.com>
Newsgroups: bionet.biophysics,bionet.xtallography
Date: 08 February 1999 00:57
Subject: Re: Is ignorant rambling, was: DNA Structure: An Age of
Refinement...
>On Wed, 3 Feb 1999, Clive Delmonte wrote:
>> Many algorithms have been used to determine oligonucleotide structure,
>> such as, CORELS, DBLHLX, HELIX, NEWHELIX, NUCLSQ, SHELX93 and ULTIMA,
>> for 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'm not a crystallographer, but I just did a quick search for SHELX93
>on Altavista. The page:
>http://www.esrf.fr/computing/expg/asciidoc/shelx.doc>>states:
>> SHELXL-93 is provided in source form as well as precompiled PC
>> versions. An application form is reproduced in Appendix F.
>>>> The program is available free to academics (and for a modest license
>> fee to commercial institutions) subject to the condition that it is
>> acknowledged in all publications which report structures refined with
>> it.
>>You can't get much better details of how something works than the
>source code. So why do you say this isn't "widely and publicly
>available"?
>> Andrew
>dalke at acm.org
Andrew Dalke wrote in message <36BE3682.977F323B at bioreason.com>...
>On Wed, 3 Feb 1999, Clive Delmonte wrote:
>> Many algorithms have been used to determine oligonucleotide structure,
>> such as, CORELS, DBLHLX, HELIX, NEWHELIX, NUCLSQ, SHELX93 and ULTIMA,
>> for 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'm not a crystallographer, but I just did a quick search for SHELX93
>on Altavista. The page:
>http://www.esrf.fr/computing/expg/asciidoc/shelx.doc>>states:
>> SHELXL-93 is provided in source form as well as precompiled PC
>> versions. An application form is reproduced in Appendix F.
>>>> The program is available free to academics (and for a modest license
>> fee to commercial institutions) subject to the condition that it is
>> acknowledged in all publications which report structures refined with
>> it.
>>You can't get much better details of how something works than the
>source code. So why do you say this isn't "widely and publicly
>available"?
>> Andrew
>dalke at acm.org
