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So I agree with Steve:<br>
<br>
Those data may not be recordable, especially near the bottom at higher
speeds, but one must know those positions accurately to do the curve
fitting properly (for two more components) because the best fit must
match the observable part of the data (i.e. that range over which the
data are being compared to the model for computation of the rms
residuals), and the proper best fit (i.e. the model) is computed
assuming those positions are known. For a self-associating system
(which is a single component, albeit multi-species) it is not so
important since the only error in that case would be the loading
concentration - which we're not especially interested in. But for a
hetero-associating system, say A+B=AB, the relative loading
concentrations of the two components do matter in the fitting and in
getting accurate values of the equilibrium constants. <br>
<br>
Since I do most of my runs using interference optics and always do a
blank run both before and after the main run in that case, at the speed
of the run, I can use those scans to get the positions of the bases of
the channels. And SEDANAL will do an interpolated blank subtraction.<br>
<br>
Walter<br>
<br>
Stephen Harding wrote:
<blockquote
cite="mid:44005B520511CA40807C5D097783A29123393B4A63@EXCHANGE2.ad.nottingham.ac.uk"
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<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">I also
disagree with John and agree almost 100% with Walter, i.e. meniscus and
base positions have to be identifiable (and not just for SEDANAL) but I
don’t think its possible to record (reliable) concentration data at the
solution boundaries, particularly for heterogeneous systems.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Steve<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal" style="margin-left: 36pt;"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US"> <a class="moz-txt-link-abbreviated" href="mailto:rasmb-bounces@rasmb.bbri.org">rasmb-bounces@rasmb.bbri.org</a>
[<a class="moz-txt-link-freetext" href="mailto:rasmb-bounces@rasmb.bbri.org">mailto:rasmb-bounces@rasmb.bbri.org</a>] <b>On Behalf Of </b>Walter
Stafford<br>
<b>Sent:</b> 09 December 2010 23:14<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:jphilo@mailway.com">jphilo@mailway.com</a><br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:rasmb@rasmb.bbri.org">rasmb@rasmb.bbri.org</a><br>
<b>Subject:</b> Re: [RASMB] radial scans 6 sector cells<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-left: 36pt;"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;">I disagree with John.
<br>
<br>
For example, my software (SEDANAL) needs to have both the menicus and
the base positions identifiable in order to do consrevation of mass
calculations for multi-compnent systems. For an equilibrium run - since
time is not of the essentce here - is to collect enough data to include
the solution boundaries.<br>
<br>
actually, I usually collect all three channels of data in one scan and
process it afterward - once for each channel. Less muss and less fuss.<br>
<br>
<o:p></o:p></p>
<pre style="margin-left: 36pt;"><o:p> </o:p></pre>
<pre style="margin-left: 36pt;">===============================================<o:p></o:p></pre>
<pre style="margin-left: 36pt;">Walter F. Stafford, Ph.D.<o:p></o:p></pre>
<pre style="margin-left: 36pt;">Senior Scientist<o:p></o:p></pre>
<pre style="margin-left: 36pt;">Boston Biomedical Research Institute<o:p></o:p></pre>
<pre style="margin-left: 36pt;">64 Grove Street<o:p></o:p></pre>
<pre style="margin-left: 36pt;">Watertown, MA 02472<o:p></o:p></pre>
<pre style="margin-left: 36pt;">617-658-7808<o:p></o:p></pre>
<pre style="margin-left: 36pt;">skype: w.stafford3<o:p></o:p></pre>
<pre style="margin-left: 36pt;">----------------------<o:p></o:p></pre>
<pre style="margin-left: 36pt;">"Be kind, for everyone you meet is fighting a hard battle." -Plato<o:p></o:p></pre>
<pre style="margin-left: 36pt;">------------------------------------ <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
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<hr align="center" size="2" width="100%"></span></div>
<p class="MsoNormal"
style="margin-right: 0cm; margin-bottom: 12pt; margin-left: 36pt;"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US"> <a moz-do-not-send="true"
href="mailto:rasmb-bounces@rasmb.bbri.org">rasmb-bounces@rasmb.bbri.org</a>
[<a moz-do-not-send="true" href="mailto:rasmb-bounces@rasmb.bbri.org">mailto:rasmb-bounces@rasmb.bbri.org</a>]
<b>On Behalf Of </b>Lake Paul<br>
<b>Sent:</b> Thursday, December 09, 2010 1:26 PM<br>
<b>To:</b> 'Roy Hantgan'; <a moz-do-not-send="true"
href="mailto:rasmb@rasmb.bbri.org">rasmb@rasmb.bbri.org</a><br>
<b>Subject:</b> Re: [RASMB] radial scans 6 sector cells</span><span
style="font-size: 12pt; font-family: "Times New Roman","serif";"
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="color: rgb(31, 73, 125);">Roy,</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="color: rgb(31, 73, 125);">Funny you should mention this, I did
my first 6-sector experiment yesterday. The 5.7 default might not cover
the inside sector, so you might have to adjust it to 5.65. I did this
by trial and error and by getting help from Dr. John Burgner. The 5.65
worked well I get alittle of the top of the cell and both menisci. Hope
this helps.</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="color: rgb(31, 73, 125);">Lake</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<div>
<div
style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal" style="margin-left: 36pt;"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> <a
moz-do-not-send="true" href="mailto:rasmb-bounces@rasmb.bbri.org">rasmb-bounces@rasmb.bbri.org</a>
[<a moz-do-not-send="true" href="mailto:rasmb-bounces@rasmb.bbri.org">mailto:rasmb-bounces@rasmb.bbri.org</a>]
<b>On Behalf Of </b>Roy Hantgan<br>
<b>Sent:</b> Thursday, December 09, 2010 3:42 PM<br>
<b>To:</b> <a moz-do-not-send="true"
href="mailto:rasmb@rasmb.bbri.org">rasmb@rasmb.bbri.org</a><br>
<b>Subject:</b> [RASMB] radial scans 6 sector cells</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal" style="margin-left: 36pt;"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;">Dear colleagues:<o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;">Can you please
remind me how you set the radial distance for sed eq runs in 6-sector
cells?<br>
I’ve only run sed eq in double sector cells. <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;">Thanks for your
advice,<o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;">Roy <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";">Roy R.
Hantgan, Ph.D.</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";">Associate
Professor of Biochemistry / Associate in Molecular Medicine</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";">Director,
Macromolecular Interactions Core Laboratory (MICL)</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";">Wake
Forest University School of Medicine</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";">3058 Hanes
Bldg / TEL 336-716-4675</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 36pt;"> <o:p></o:p></p>
<pre style="margin-left: 36pt;"><o:p> </o:p></pre>
<pre style="margin-left: 36pt;"><o:p> </o:p></pre>
<pre style="margin-left: 36pt;">_______________________________________________<o:p></o:p></pre>
<pre style="margin-left: 36pt;">RASMB mailing list<o:p></o:p></pre>
<pre style="margin-left: 36pt;"><a moz-do-not-send="true"
href="mailto:RASMB@rasmb.bbri.org">RASMB@rasmb.bbri.org</a><o:p></o:p></pre>
<pre style="margin-left: 36pt;"><a moz-do-not-send="true"
href="http://rasmb.bbri.org/cgi-bin/mailman/listinfo/rasmb">http://rasmb.bbri.org/cgi-bin/mailman/listinfo/rasmb</a><o:p></o:p></pre>
<pre style="margin-left: 36pt;"> <o:p></o:p></pre>
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<pre class="moz-signature" cols="72">
--
===============================================
Walter F. Stafford, Ph.D.
Senior Scientist
Boston Biomedical Research Institute
64 Grove Street
Watertown, MA 02472
617-658-7808
skype: w.stafford3
----------------------
"Be kind, for everyone you meet is fighting a hard battle." -Plato
------------------------------------ </pre>
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