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--></style><title>SedAnal: Sedimentation Velocity Analysis package
calle</title></head><body>
<div>Dear RASMBers;<br>
</div>
<div><x-tab> </x-tab>A new
software package called<b> SedAnal</b> has been developed at BBRI and
has been made available on the RASMB FTP archive site.</div>
<div><br></div>
<div>SedAnal will perform curve fits to sedimentation velocity data
obtained from interacting (and non-interacting) systems. It can fit
for sedimentation coefficients, molecular weight. loading
concentrations and equilibrium constants. It is capable of
fitting up to 3 thermodynamic components, and up to 7 species
related by up to 6 chemical reactions. It can fit globally data from
up to 5 cells, simultaneously. It runs under Windows98 and has
an easy to use graphical user interface. It is accompanied by a User's
Manual.</div>
<div><br>
It fits to time difference data to eliminate time-independent,
radially-dependent systematic noise completely. It has a preprocessor
section that allows choice of the meniscus and base positions as well
as the radial range of data to use for fitting. The preprocessor
allows essentially complete removal of radially-independent,
time-dependent optical "jitter" and correction for
integral fringe shifts associated with interference data.<br>
<br>
The package contains a Model Editor that allows the user to develop a
database of reaction schemes which can be used to fit the data.<br>
<br>
The fitting section ( Control Screen) allows the user to choose one of
the models, select and enter initial values for the parameters to be
fit (or held) and select the cells to be combined for global
fitting.<br>
<br>
The model editor allows one to create various reaction schemes ranging
from a single-component, single-species system (i.e. no interactions)
to a single-component, 2 species system (e.g.. simple monomer, n-mer
self-association, 2A=A2), to a 3 component, 3 species system (i.e.
simple complex formation of the type A + B = C), a 2 component, 4
species system (i.e. simple complex formation with self association of
one of the reactants or the complex (e.g. A+B=C; 2A=A2), a 2
component, 4 species system like an antigen-antibody reaction (e.g.
A+B=C;C+B=D) and so on.<br>
</div>
<div>The current version of SedAnal can handle up to 3 components, 7
species and 6 chemical reactions in any combination consistent
with the constraint that Number_of_components = number_of_species -
number_of_chemical_reactions, of course. (This is probably more than
one should ever dare to use without some prior knowledge). Isodesmic
self-association will be handled in a future version.</div>
<div><br>
The Control Screen also allows the user to generate synthetic data
using any of the models.<br>
</div>
<div>The internal routine uses numerical solutions to the Lamm
equation solved using Claverie's finite-element method. Mass action is
accounted for by various kinetic schemes and is solved internally by
the Bulirsch-Stoer differential equation solver routine. Least squares
minimization is done by the Simplex method of Nelder and Mead.</div>
<div><br>
There is an user's manual in PDF format. The manual is fairly
extensive and still evolving.<br>
<br>
The software/documentation package can be downloaded from the RASMB
FTP archives at<br>
<br>
ftp://rasmb.bbri.org/rasmb/spin/ms_dos/sedanal-stafford/<br>
</div>
<div>The zip archive contains the user manual, the model editor, an
example Model database file, Sedanal.exe, which is the interface to
the Preprocessor and the Fitter Control Screen. Please read the README
file and the user's manual first. AND take note of the mandatory
directory structure. The unzipping process should put everything into
the correct directory tree structure.</div>
<div><br></div>
<div>There is a separate email discussion group at
http://www.rasmb.bbri.org/mailman/listinfo/sedanal</div>
<div>for those who want to discuss the more arcane aspects of using
SedAnal without cluttering up the RASMB email list.</div>
<div><br></div>
<div><br>
<br>
<br>
<br>
<br>
</div>
<div><font color="#0000FF">-- <br>
---------------------------------------------------------------------<span
></span>----------------------------------</font></div>
<div><font color="#0000FF">Walter Stafford</font></div>
<div><font color="#0000FF">mailto:stafford@bbri.org</font></div>
<div><font color="#0000FF">direct dial:
617-658-7808</font></div>
<div><font color="#0000FF">receptionist: 617-926-8040</font></div>
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