From owner-biophysics@net.bio.net Sun Feb 07 22:00:00 1999 From: "Clive Delmonte" Newsgroups: bionet.biophysics,bionet.xtallography References: <36b81714.0@news.netdirect.net.uk> <36BE3682.977F323B@bioreason.com> Subject: Re: Is ignorant rambling, was: DNA Structure: An Age of Refinement... Date: Mon, 8 Feb 1999 15:36:34 -0000 Lines: 137 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 195.7.225.210 Message-ID: <36beffa3.0@news.netdirect.net.uk> X-Trace: 8 Feb 1999 15:15:47 GMT, 195.7.225.210 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.tli.de!newsfeed.nacamar.de!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.210 Xref: biosci bionet.biophysics:4763 bionet.xtallography:4586 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@ndirect.co.uk or: clivedelmonte@c-i-delmonte.freeserve.co.uk -----Original Message----- From: Andrew Dalke 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@acm.org Andrew Dalke wrote in message <36BE3682.977F323B@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@acm.org .