[RASMB] Release of SEDNTERP version 3

[Lake Paul]

Thank you John.

Serendipitously, you just saved us from digging into the literature for
some density and buffer calculations.

Lake

On Thu, Feb 11, 2021, 7:43 PM John Philo <jphilo at mailway.com> wrote:

> 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, 95), 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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