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<div class="moz-cite-prefix">On 08/10/13 06:41, Walter Stafford
wrote:<br>
</div>
<blockquote
cite="mid:BEA8FE13-5DF8-4157-B9B2-D7AE157127FB@walterstafford.com"
type="cite">
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<div>SEDANAL does the conversion to s(20,w) only in DCDT and the
only if the v-vbar and density<u><font class="Apple-style-span"
color="#ff2d26"> and viscosity ratio </font></u>have been
entered into the database though the Preprocessor. All other
values of s* are the raw value. I.e. s(t,b). <font
class="Apple-style-span" color="#ff2521">The equation used is
the standard equation used by Svedberg in "The
Ultracentrifuge" and hasn't changed since then.</font></div>
<div><font class="Apple-style-span" color="#ff2521"><br>
</font></div>
<div><font class="Apple-style-span" color="#ff2521">In the Fitter
the correct value of density increment must be entered to get
the correct molar mass. So in the fitter only the buoyancy
correction is made since the correction from s*(t,b) to
s(20,w) and from D(t,b) to D(20,w) is the same and cancels
out. The values used by the fitter are the raw values, i.e.
the actual values that pertain to solution conditions being
fitted.</font><br>
<br>
Sent from my iPad Mini</div>
<div><br>
On Aug 9, 2013, at 5:25 PM, "Laue, Thomas" <<a
moz-do-not-send="true" href="mailto:Tom.Laue@unh.edu">Tom.Laue@unh.edu</a>>
wrote:<br>
<br>
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">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<br>
<div style="font-family: Times New Roman; color: #000000;
font-size: 16px">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF101953"><font
face="Tahoma" color="#000000" size="2"><b>From:</b> <a
moz-do-not-send="true"
href="mailto:rasmb-bounces@list.rasmb.org">rasmb-bounces@list.rasmb.org</a>
[<a moz-do-not-send="true"
href="mailto:rasmb-bounces@list.rasmb.org">rasmb-bounces@list.rasmb.org</a>]
on behalf of David Hayes [<a moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:rasmb@rasmb.org">rasmb@rasmb.org</a><br>
<b>Subject:</b> Re: [RASMB] s20w calculation<br>
</font><br>
</div>
<div>
<div style="color:#000; background-color:#fff;
font-family:arial,helvetica,sans-serif;
font-size:12pt">
<div><span>Hi John,</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span><br>
</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span>I sent some off list response with extra
information and opinion I am not sure about and
don't want to be on list.</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span>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.</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span><br>
</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span>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.</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span><br>
</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span>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.</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span><br>
</span></div>
<div style="color:rgb(0,0,0); font-size:16px;
font-family:arial,helvetica,sans-serif;
background-color:transparent; font-style:normal">
<span>David Hayes</span></div>
<div><br>
</div>
<div style="font-family:arial,helvetica,sans-serif;
font-size:12pt">
<div style="font-family:'times new roman','new
york',times,serif; font-size:12pt">
<div dir="ltr">
<hr size="1">
<font face="Arial" size="2"><b><span
style="font-weight:bold">From:</span></b>
John Sumida <<a moz-do-not-send="true"
href="mailto:jpsumida@u.washington.edu">jpsumida@u.washington.edu</a>><br>
<b><span style="font-weight:bold">To:</span></b>
<a moz-do-not-send="true"
href="mailto:drdavidbhayes@yahoo.com">drdavidbhayes@yahoo.com</a>
<br>
<b><span style="font-weight:bold">Cc:</span></b>
<a moz-do-not-send="true"
href="mailto:rasmb@rasmb.org">rasmb@rasmb.org</a>
<br>
<b><span style="font-weight:bold">Sent:</span></b>
Friday, August 9, 2013 1:44 PM<br>
<b><span style="font-weight:bold">Subject:</span></b>
Re: [RASMB] s20w calculation<br>
</font></div>
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<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">Hi David,</span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">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></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">To answer
your questions.</span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">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></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">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></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">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></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">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></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">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></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">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></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">Best regards,</span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">John Sumida,
Ph.D.</span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"><a
moz-do-not-send="true"
rel="nofollow"
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style="color:windowtext">Analytical
Biopharmacy Core Facility</span></a></span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">University of
Washington</span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt"><a
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rel="nofollow"
href="http://www.moles.washington.edu/"
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Engineering & Sciences
Institute, G22</span></a></span></div>
<div class="yiv1626916188MsoNormal"><span
style="font-size:14.0pt">3946 West
Stevens Way NE</span></div>
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style="font-size:14.0pt">Seattle WA
98195-1653</span></div>
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<br>
<br>
</div>
</div>
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</blockquote>
<blockquote type="cite">
<div><span>_______________________________________________</span><br>
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</blockquote>
Can I be so cruel as to suggest to the questioner that a firm
understanding of what s and s20,w is before one blindly uses a
computer program on dc/dr/dt data. Given that s is a function of
rho, vbar, t and frictional coefficient, it might just be necessary
to have known rho, vbar, viscosity and temperature to translate a
measured s at that condition to s at 20C in water. The computer
program can't know what solvent, temperature and vbar to use unless
you supply it, I suspect. <br>
<br>
2 cents from a retired former Model E user! <br>
<br>
<pre class="moz-signature" cols="72">--
Kirk C Aune, Ph.D.
16289 Cambridge Court
Granger, IN 46530
(574)277-8589
Linux User #1720
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