[RASMB] Release of SEDNTERP version 3

Thu Feb 11 16:56:14 PST 2021

Thank you John!  This is most welcome!

Mike Fried

Sent from my iPhone

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

CAUTION: External Sender

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<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jphilo.mailway.com%2Fdownload.htm&data=04%7C01%7Cmichael.fried%40uky.edu%7C61df63dd0c6a4008b75e08d8ceef47d6%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C637486874389741063%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=piXM0OzeyCf%2BZyr6Uia5poL3pAj9pzaNfyDdne7ns2I%3D&reserved=0>
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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