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SEDNTERP 3

Revision history

What is the purpose of SEDNTERP?

The SEDNTERP program is a general purpose tool for the interpretation of sedimentation equilibrium, sedimentation velocity, and diffusion experiments. It collects many diverse functions into a single program. SEDNTERP is useful both for computing molecular structural estimates from experimental data and for calculation of physical parameters of common buffers used in sedimentation experiments. It is also useful to create a database of:

bulletThe properties of samples (proteins) you work with (molar mass, partial specific volume, hydration, UV extinction coefficients, dn/dc)
bulletThe properties of buffers that you use in your lab (density, viscosity, refractive index, pH, composition)
bulletExperimental results (sedimentation coefficients, diffusion coefficients, sedimentation equilibrium results)
bulletThe derived hydrodynamic properties of your samples (maximum possible sedimentation and diffusion coefficients, f/f0 ratio, Perrin P, Stokes radius, computed shape and dimensions from ellipsoidal or cylindrical models)

Importantly, storing this information in the program database allows you to document and reproduce any calculated values you will be using in reports or publications.

What's new in version 3?

bulletA 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)
bulletSupport for diffusion experiments (and diffusion coefficients determined from sedimentation velocity)
bulletCalculation 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)
bulletConcentrations 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
bulletValues 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
bulletExperimental molar masses can now be calculated by combining sedimentation and diffusion experiments (which can be in different buffers)
bulletHydrodynamic 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)
bulletPartial 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, which should give more accurate results, particular for peptides.
bulletDisk (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)
bulletHydration can now be calculated for rod and disk models when the asymmetry (L/d or d/H ratio) is known
bulletThe 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)
bulletThe 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
bulletBoth viscosity and refractive index can now be calculated for buffers containing D2O
bullet53 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)
bulletThe equations for the density and viscosity of water have been updated to reflect current "best" 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!)
bulletThe Help file (manual) has been completely revised and re-formatted, and 28 additional references added.

What's missing?

bullet"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, etc.
bulletPasting or entering amino acid sequences in 3-letter AA codes is no longer supported
bulletSaving 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.)