From sklenar@mdc-berlin.de
Date: Tue, 06 May 2003 11:43:12 +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>,
     John.A.Subirana <John.A.Subirana@ups.es>, olson <olson@utchem.rutgers.edu>,
     csrozen <csrozen@ray4.weizmann.ac.il>,
     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>
Cc: Richard Lavery <Richard.Lavery@ibpc.fr>, Rama Sarma <rhs07@albany.edu>
Subject: Workshop at Albany

Dear colleagues,

Prof. Sarma has asked me to arrange a workshop on the use
of the revised CURVES program that now is scheduled as a
pre-workshop of the 13th Albany conversation.

I have agreed, but had to realize that there are still
some open questions that are not yet decided by the
Cambridge-Tsukuba conventions. As you know, the parameters
calculated by currently available programs (Newhelix, 3DNA,
CompDNA, CURVES etc.) do not fully agree due to
slightly different definitions of rotations and projections.
The disagreement becomes particularly visible when largely
distorted structures are analyzed.

For local step and intra-strand parameters, the projections
of the single rotation axis, proposed by Wilma Olson's
group, solve the problem of independence of direction
most elegantly, without defining a mid-plane, but make
it more difficult to understand the rotations about
the respective axes. Although I tend to this definition
as a possible 'standard', one should perhaps re-consider
the alternative before making a decision.

Since local step parameters are not very useful for
curvature analysis, another important issue is the
definition of the curved global helical axis and the
calculation of easily understandable curvature parameters.
Also this requires some conventions to be agreed upon
before deciding on the proposed standard for curvature
analysis.

I will include some options in the Curves program for
the comparison of alternative definitions, and I am
very grateful to you for your willingness to run
some tests with your structures.

In my opinion, an agreement on the detailed definitions
is more important than declaring one of the programs as
the 'standard' for nucleic acid structure analysis. In
fact, if different programs calculate the same values
of parameters, the most user-friendly program will be
preferred.

I am sorry for still needing some time to finish the
program, but hope that I can send you the program
including a preliminary manual and sample I/O files
until May 25. 

I am sure that your comments will be very
helpful for the final CURVES version and hopefully
for a final agreement on the 'standard', too.

Looking forward to seeing you in Albany and having
a successful workshop, resulting in the 'Cambridge-
Tsukuba-Albany' conventions.

With best regards,


Heinz Sklenar