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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thank you for the clarification Walter. I had misunderstood this and had thought that if vbar and DCDT had been run the fitted values returned were the s20w values. This still does not explain the behavior of the BETA version and Web version of SEDNTERP, but is important for me to realize nonetheless.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>John Sumida<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Analytical Biopharmacy Core<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>University of Washington.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> rasmb-bounces@list.rasmb.org [mailto:rasmb-bounces@list.rasmb.org] <b>On Behalf Of </b>Walter Stafford<br><b>Sent:</b> Saturday, August 10, 2013 3:30 AM<br><b>To:</b> Laue, Thomas<br><b>Cc:</b> alex.wied@unh.edu; Hurton, Thomas; rasmb@rasmb.org<br><b>Subject:</b> Re: [RASMB] s20w calculation<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>SEDANAL does the conversion to s(20,w) only in DCDT and the only if the v-vbar and density have been entered into the database though the Preprocessor. All other values of s* are the raw value. I.e. s(t,b).<br><br>Sent from my iPad Mini<o:p></o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><br>On Aug 9, 2013, at 5:25 PM, "Laue, Thomas" <<a href="mailto:Tom.Laue@unh.edu">Tom.Laue@unh.edu</a>> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>Hi-<br>Sorry to be late replying... I am out of town... and sorry there is a problem with Sednterp.<br>I've forwarded this thread to the gang to see what the problem might be. <br>One thing they might try is to see if the desktop and web version give the same error. The calculations are identical, but the rendering engines are different.<br>Again, sorry for any trouble.<br>Tom<o:p></o:p></span></p><div><div class=MsoNormal align=center style='text-align:center'><span style='color:black'><hr size=2 width="100%" align=center></span></div><div id=divRpF101953><p class=MsoNormal style='margin-bottom:12.0pt'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <a href="mailto:rasmb-bounces@list.rasmb.org">rasmb-bounces@list.rasmb.org</a> [<a href="mailto:rasmb-bounces@list.rasmb.org">rasmb-bounces@list.rasmb.org</a>] on behalf of David Hayes [<a href="mailto:drdavidbhayes@yahoo.com">drdavidbhayes@yahoo.com</a>]<br><b>Sent:</b> Friday, August 09, 2013 5:04 PM<br><b>To:</b> <a href="mailto:rasmb@rasmb.org">rasmb@rasmb.org</a><br><b>Subject:</b> Re: [RASMB] s20w calculation</span><span style='color:black'><o:p></o:p></span></p></div><div><div><div><p class=MsoNormal style='background:white'><span style='font-family:"Arial","sans-serif";color:black'>Hi John,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>I sent some off list response with extra information and opinion I am not sure about and don't want to be on list.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>I am also waiting for Walter or Peter Sherwood to answer about SEDANAL questions, but I suspect that you are thinking SEDANAL is doing s20w corrections that it really is not, but I don't know if that is the problem.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>Everyone should know that the Web SEDNTERP and the desktop beta share the exact same calculation source code, so if they are the same version, they better agree on everything, feature for feature, bug for bug.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>But also, basically trust the by hand calculations as was posted previously, ask the programmers which numbers are s20w and which are not, and thank you for posting the problems so the developers of SEDNTERP can work out the bugs. Due to John Philo's incredible and meticulous work, SEDNTERP 1.2 was incredibly reliable and calculated things to 5 decimal places reliably and exactly the same as the published equations. the new version of SEDNTERP will take a lot of sweat to get to that level of excellence.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>David Hayes<o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p></div><div><div><div><div class=MsoNormal align=center style='text-align:center;background:white'><span style='color:black'><hr size=1 width="100%" align=center></span></div><p class=MsoNormal style='background:white'><b><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>From:</span></b><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> John Sumida <<a href="mailto:jpsumida@u.washington.edu">jpsumida@u.washington.edu</a>><br><b>To:</b> <a href="mailto:drdavidbhayes@yahoo.com">drdavidbhayes@yahoo.com</a> <br><b>Cc:</b> <a href="mailto:rasmb@rasmb.org">rasmb@rasmb.org</a> <br><b>Sent:</b> Friday, August 9, 2013 1:44 PM<br><b>Subject:</b> Re: [RASMB] s20w calculation</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='color:black'><o:p> </o:p></span></p><div id=yiv1626916188><div><div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>Hi David,</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>Thanks for taking the time to respond. I’m attempting to respond to your post. Apologies if I’m committing some type of etiquette violation in responding to the group, but as you requested some clarification as to my process I thought to respond publicly.</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>To answer your questions.</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>I’ve been trying to understand why this particular polymer material produces a large s20w value when another material with different surface charge properties produces an s20w of 7.9s and sediments very differently.</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>So the back calculation, going from s20w to s*, was me playing with the data to see if I could go from the 17.3 s20w back to s* which I would have hoped – as you point out – would not have been much different from 17.3s.</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>My initial calculation using the s20w correction equation (equation 19) was comforting in that the calculated s* was 16.4s. I used SEDFIT to perform the same calculation just to check that all was in order – and as I stated SEDFIT returned the 16.4s value as had the calculation and the analysis in SEDANAL. Note that vbar and solvent parameters had been entered in into the experiment file and gOfs files had been generated by running DCDT. So I believe the s values returned in SEDNAL are s20w values.</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>The problem arose when I used the Experiment page in SEDNTERP (version 20120828 BETA). Using the calculated value of s*, SEDNTERP did not return the same value for s20w that SEDANAL output. </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>I also attempted the same operation using the web version of SEDNTERP which resulted in the same result, namely calculating an s20w of 27.8s when the experimentally observed s20w was17.3s.</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>I had not thought to turn off the s20w calculation (in order to do so do I just remove vbar from the experiment info?) and attempt to fit for s*. Will try that next.</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>Best regards,</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>John Sumida, Ph.D.</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'><a href="http://depts.washington.edu/cidb4bio/index.shtml" target="_blank"><span style='color:windowtext'>Analytical Biopharmacy Core Facility</span></a></span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>University of Washington</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'><a href="http://www.moles.washington.edu/" target="_blank"><span style='color:windowtext'>Molecular Engineering & Sciences Institute, G22</span></a></span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>3946 West Stevens Way NE</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>Seattle WA 98195-1653</span><span style='color:black'><o:p></o:p></span></p></div></div></div></div><p class=MsoNormal style='margin-bottom:12.0pt;background:white'><span style='color:black'><o:p> </o:p></span></p></div></div></div></div></div></div></div></div></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>_______________________________________________<br>RASMB mailing list<br><a href="mailto:RASMB@list.rasmb.org">RASMB@list.rasmb.org</a><br><a href="http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org">http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org</a><o:p></o:p></p></div></blockquote></div></body></html>