From sklenar@mdc-berlin.de
Date: Sun, 01 Jun 2003 18:45:01 +0200
From: Heinz Sklenar <sklenar@mdc-berlin.de>
To: David Beveridge <dbeveridge@wesleyan.edu>,
     Zippi Shakked <zippi.shakked@weizmann.ac.il>,
     Remo Rohs <mail@remo-rohs.de>, Thomas Cheatham <cheatham@chpc.utah.edu>,
     Stephen Neidle <stephen.neidle@ulsop.ac.uk>,
     Victor Zhurkin <zhurkinv@exchange.nih.gov>,
     martin.egli <martin.egli@vanderbilt.edu>, ponzy <ponzy@sas.upenn.edu>,
     Juan.A.Subirana <Juan.A.Subirana@ups.es>,
     Karolin.Luger <Karolin.Luger@colostate.edu>, schlick <schlick@nyu.edu>,
     loren.williams <loren.williams@chemistry.gatech.edu>,
     sklenar <sklenar@mdc-berlin.de>, e.westhof <e.westhof@ibmc.u-strasbg.fr>,
     xiangjun <xiangjun@rutchem.rutgers.edu>,
     Krystyna.Zakrzewska <Krystyna.Zakrzewska@ibpc.fr>, sponer <sponer@ibp.cz>,
     m.zacharias <m.zacharias@iu-bremen.de>, agor <agor@ornl.gov>,
     heinemann <heinemann@mdc-berlin.de>, olson <olson@rutchem.rutgers.edu>,
     haim.rozenberg <haim.rozenberg@weizmann.ac.il>
Cc: Rama Sarma <rhs07@albany.edu>, Richard Lavery <Richard.Lavery@ibpc.fr>,
     Richard E. Dickerson <red@mbi.ucla.edu>
Subject: Albany workshop

Dear colleagues,

in the view of the forthcoming Albany workshop, where on standard
definition of nucleic acid parameters will be discussed, the well
known problem of mean frame definition is of particular importance.
This issue affects almost all parameters that have been considered
by the Cambridge conventions and, therefore, should play a central
role in our discussions.

Under the pressure of preparing for the workshop, I came across this
problem again, since I still missed a satisfying solution. I wanted
to include some different approaches, developed in the last ten 
years, as options in the CURVES program, but ended up with a new
definition.

In the attached Word file (frames.doc), I give a detailed analysis
of the problem from my point of view, explain the suggested solution,
and come to the conclusion that this approach should be a candidate
for the envisaged standard definition.

I would be very grateful to you if you could have a look at the draft,
before we will meet in Albany and, particularly, if you could inform
me about any drawback or inconsistency you might detect.

Because, in the last weeks, I was very busy with the development of
this concept (including comparison with other approaches), I was not
yet able to included it in the parameter calculation routines of the
revised CURVES program, that I had promised to send you last week.

I apologize for this delay and hope, you will not consider it as an
excuse, when I think that a consistent concept seems to be even more
important than program implementations. Thank you for your
understanding.

I will now focus on implementations in the revised CURVES program
and hope you will obtain it still before the workshop, and will have
some possibility for your own testing.


With best regards,

Heinz Sklenar
    [ Part 2, Application/MSWORD  112KB. ]
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