[RASMB] Release of SEDNTERP version 3

[John Philo]

After more than a year of work, a new version of SEDNTERP is now available
for download at http://www.jphilo.mailway.com/download.htm

This version has been re-built from the ground up, with a new user
interface.  Among other new features (see more details below), it now
computes hydrodynamic results based on diffusion experiments, and can derive
sample molar masses from combining separate sedimentation velocity and
diffusion experiments.  It also now calculates the refractive index of
buffers from their composition, the refractive increments (dn/dc values) for
proteins (including PEGylated and glycoproteins), and includes tools for
fitting sedimentation or diffusion coefficients measured at multiple
concentrations to extrapolate to zero concentration and measure ks or kD.

Version 3 uses a new database structure, but it can import your old database
from either versions 1 or 2.

As is true after any major program change, this first release will almost
surely still have some bugs. Therefore 

(1) I urge the many users who have not yet asked me to add them to my "known
users" list to do so now so you will be informed when updates are released.

(2) Please, if you encounter a bug, tell me how to reproduce it, and if
possible also send a copy of any error message you received.  

Best regards to all, and stay safe.

John

 

What's new in version 3?

*	A new user interface, drawing on some elements of the version 2
interface, but with better separation of sample and experimental properties
(and full separation of sedimentation equilibrium and sedimentation velocity
experiments)
*	Support for diffusion experiments (and diffusion coefficients
determined from sedimentation velocity)
*	Calculation of protein refractive increments and the refractive
index of your buffers (features which will be useful to the light scattering
community as well as in AUC)
*	Concentrations of buffer components can now optionally be entered in
molal, mg/mL, g/mL, or weight % units (or volume % for liquid solutes).
Different components also can use different concentration units.
*	Values for sedimentation (or diffusion) coefficients at multiple
concentrations can be entered, fitted to evaluate ks and s020,w (or kD and
D020,w), and stored in the database
*	Experimental molar masses can now be calculated by combining
sedimentation and diffusion experiments (which can be in different buffers)
*	Hydrodynamic results may now be based on either sedimentation or
diffusion data, and may now combine data from experiments run in different
buffers (e.g. equilibrium and velocity done in different buffers)
*	Partial specific volumes calculated from amino acid composition may
now optionally include corrections for the volume of the N- and C-terminal
residues and the Traube covolume term (refs. 94
<file:///C:/Users/jphil/Documents/HelpStudio%20Projects/Sednterp%203%20Help%
20Source/Reference94.html> , 95
<file:///C:/Users/jphil/Documents/HelpStudio%20Projects/Sednterp%203%20Help%
20Source/Reference95.html> ), which should give more accurate results,
particular for peptides.
*	Disk (short cylinder) shape models are now supported, and cylinder
models are now accurate for length/diameter ratios from 0.01 to 100 (vs.
only 2 to 20 for versions 1 and 2)
*	Hydration can now be calculated for rod and disk models when the
asymmetry (L/d or d/H ratio) is known
*	The displayed numeric values are now all color-coded to indicate
whether the value is a user input (black), calculated (blue), or a user
"override" input of a value that is normally calculated (green)
*	The graphs of hydrodynamic shape models and of sample properties
(titration curves and extinction spectra) are now generated automatically
and shown within the main program form.
*	Both viscosity and refractive index can now be calculated for
buffers containing D2O
*	53 tables of refractive index vs. concentration for existing solutes
were fitted to polynomials and the resulting polynomial coefficients added
to the database.  Six new solutes of particular interest to the
biotechnology community were also added (L-arginine, L-alanine, L-histidine,
L-glycine, sorbitol, and Tween-80), all of which have both density and
viscosity data (and all but sorbitol and L-glycine have refractive index
data also).
*	The default pKa values for the amino acids and the N- and C-terminus
have been updated to reflect newer experimental values from Thurkill et al.
(2006).
*	The equations for the density and viscosity of water have been
updated to reflect current "recommended" values and changes to the
International Practical Temperature Scale.  The values of the fundamental
constants have also been updated to current recommended values. (Yes these
things do change over the ~25 years since SEDNTERP was created!)
*	The Help file has been completely revised and re-formatted, and 28
additional references added.


What's missing?


*	"Loosely-bound" conjugates ("non-covalent" conjugates) are no longer
supported.  All conjugates are assumed to be fully bound (either covalently
or non-covalently) and therefore are included when computing the total molar
mass, overall partial specific volume, overall refractive increment, etc.
*	Pasting or entering amino acid sequences in 3-letter AA codes is no
longer supported.
*	Saving or reading sample composition or buffer composition files
(.smp and .buf files) is no longer supported.  (Those features were a
hold-over from pre-release versions that did not use a database.)

 

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