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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link="#0563C1" vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal style='margin-bottom:6.0pt'>After more than a year of work, a new version of SEDNTERP is now available for download at <a href="http://www.jphilo.mailway.com/download.htm">http://www.jphilo.mailway.com/download.htm</a><o:p></o:p></p><div style='mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;padding:0in 0in 1.0pt 0in'><p class=MsoNormal style='margin-bottom:6.0pt;border:none;padding:0in'>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 (<i>dn/dc</i> 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 <i>k<sub>s</sub></i> or <i>k<sub>D</sub></i>.<o:p></o:p></p><p class=MsoNormal style='margin-bottom:6.0pt;border:none;padding:0in'>Version 3 uses a new database structure, but it can import your old database from either versions 1 or 2.<o:p></o:p></p><p class=MsoNormal style='margin-bottom:6.0pt;border:none;padding:0in'>As is true after any major program change, this first release will almost surely still have some bugs. Therefore <o:p></o:p></p><p class=MsoNormal style='margin-bottom:6.0pt;border:none;padding:0in'>(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.<o:p></o:p></p><p class=MsoNormal style='margin-bottom:6.0pt;border:none;padding:0in'>(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. <o:p></o:p></p><p class=MsoNormal style='margin-bottom:6.0pt;border:none;padding:0in'>Best regards to all, and stay safe.<o:p></o:p></p><p class=MsoNormal style='margin-bottom:6.0pt;border:none;padding:0in'>John<o:p></o:p></p><p class=MsoNormal style='margin-bottom:6.0pt;border:none;padding:0in'><o:p> </o:p></p></div><p class=MsoNormal><span style='font-size:13.0pt;font-family:"Segoe UI Historic",sans-serif;color:#222222'>What's new in version 3?<o:p></o:p></span></p><ul type=disc><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>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)<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>Support for diffusion experiments (and diffusion coefficients determined from sedimentation velocity)<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>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)<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>Concentrations of buffer components can now optionally be entered in <span class=dxmisspelled>molal</span>, mg/mL, g/mL, or weight % units (or volume % for liquid solutes). Different components also can use different concentration units.<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>Values for sedimentation (or diffusion) coefficients at multiple concentrations can be entered, fitted to evaluate k<sub>s</sub> and s<sup>0</sup><sub>20,w</sub> (or k<sub>D</sub> and D<sup>0</sup><sub>20,w</sub>), and stored in the database<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>Experimental molar masses can now be calculated by combining sedimentation and diffusion experiments (which can be in different buffers)<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>Hydrodynamic results may now be based on either sedimentation or diffusion data, and may now combine data from experiments run in different buffers (<i>e.g.</i> equilibrium and velocity done in different buffers)<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>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 <span class=dxmisspelled>Traube</span> <span class=dxmisspelled>covolume</span> term (refs. <a href="file:///C:/Users/jphil/Documents/HelpStudio%20Projects/Sednterp%203%20Help%20Source/Reference94.html">94</a>, <a href="file:///C:/Users/jphil/Documents/HelpStudio%20Projects/Sednterp%203%20Help%20Source/Reference95.html">95</a>), which should give more accurate results, particular for peptides.<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>Disk (short cylinder) shape models are now supported, and cylinder models are now accurate for length/diameter ratios from 0.01 to 100 (<em><span style='font-family:"Segoe UI Historic",sans-serif'>vs.</span></em> only 2 to 20 for versions 1 and 2)<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>Hydration can now be calculated for rod and disk models when the asymmetry (<em><span style='font-family:"Segoe UI Historic",sans-serif'>L/d</span></em> or <em><span style='font-family:"Segoe UI Historic",sans-serif'>d/H</span></em> ratio) is known<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>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)<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>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.<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>Both viscosity and refractive index can now be calculated for buffers containing D<sub>2</sub>O<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>53 tables of refractive index <em><span style='font-family:"Segoe UI Historic",sans-serif'>vs.</span></em> 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-<span class=dxmisspelled>arginine</span>, L-<span class=dxmisspelled>alanine</span>, L-<span class=dxmisspelled>histidine</span>, L-<span class=dxmisspelled>glycine</span>, <span class=dxmisspelled>sorbitol</span>, and <span class=dxmisspelled>Tween</span>-80), all of which have both density and viscosity data (and all but <span class=dxmisspelled>sorbitol</span> and L-<span class=dxmisspelled>glycine</span> have refractive index data also).<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>The default <em><span style='font-family:"Segoe UI Historic",sans-serif'>pKa</span></em> values for the amino acids and the N- and C-terminus have been updated to reflect newer experimental values from <span class=dxmisspelled>Thurkill</span> <em><span style='font-family:"Segoe UI Historic",sans-serif'>et al.</span></em> (2006).<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>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!)<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1'><span style='font-family:"Segoe UI Historic",sans-serif'>The Help file has been completely revised and re-formatted, and 28 additional references added.<o:p></o:p></span></li></ul><h3><span style='font-size:12.0pt'>What's missing?<o:p></o:p></span></h3><ul type=disc><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo2'><span style='font-family:"Segoe UI Historic",sans-serif'>"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, <em><span style='font-family:"Segoe UI Historic",sans-serif'>etc.</span></em><o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo2'><span style='font-family:"Segoe UI Historic",sans-serif'>Pasting or entering amino acid sequences in 3-letter AA codes is no longer supported.<o:p></o:p></span></li><li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo2'><span style='font-family:"Segoe UI Historic",sans-serif'>Saving or reading sample composition or buffer composition files (.<span class=dxmisspelled>smp</span> and .<span class=dxmisspelled>buf</span> files) is no longer supported. (Those features were a hold-over from pre-release versions that did not use a database.)<o:p></o:p></span></li></ul><p class=MsoNormal style='margin-bottom:6.0pt'><o:p> </o:p></p></div></body></html>