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Thank you John! This is most welcome!
<div><br>
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<div>Mike Fried<br>
<br>
<div id="AppleMailSignature" dir="ltr">Sent from my iPhone</div>
<div dir="ltr"><br>
On Feb 11, 2021, at 7:43 PM, John Philo <<a href="mailto:jphilo@mailway.com">jphilo@mailway.com</a>> wrote:<br>
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--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
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<div><span style="background-color:#FFEB9C; border-style: solid; border-color:#9C6500; border-width:1pt; padding:2pt; font-size:11pt; line-height:12pt; font-family:'Calibri'; color:Black; text-align: left; font-weight:bold;"><span style="color:#9C6500;">CAUTION:</span>
External Sender</span></div>
<br>
<div>
<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="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" originalsrc="http://www.jphilo.mailway.com/download.htm" shash="tojc8gReIASsbXVjt5hjoUUNK+REX6mnu53WtJ5uku24Uiu+4t7xS/CFejrFvUbKCdCNJJxKNnVUhBQrpmQ5LsRkHYxhzZeiDqgMdarm2e03ZJHflAtDG479nfj3GOzfQO30wtSOp2kjsyB+J6RU1Px7LIhTDW8S4ZOBz4CApwo=">
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>
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