<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" color="#950f0b" size="4">Hi Frank</font><div><font class="Apple-style-span" color="#950f0b" size="4"><br></font></div><div><font class="Apple-style-span" color="#950f0b" size="4">I wonder why you are running so unusually long a column? I calculate it to be 6.2 mm in length, which will inevitably mean the distribution takes a very long time indeed to attain equilibrium. Using a little Excel utility I wrote a while back, which among other things computes using the old formulae the "time to equilibrium within 0.1%", if your trimer has a MW of 200,000 then it will take at least 147 hours to get there! Although if it is a trimer of a 30 kDa monomer, then a mere 108 hours might suffice. That assumes your trimer to be more or less globular - if the frictional ratio is > ~1.2, then the time to equilibrium increases. Of course with half the column length - and a 3.1 mm column gives you lots of data points - then the time to equilibrium goes down 4-fold! And a 3.1 mm column is quite long by most standards, and gives you lots of data points (OK - that applies to fringe optics, less to absorption).</font></div><div><font class="Apple-style-span" color="#950f0b" size="4"><br></font></div><div><font class="Apple-style-span" color="#950f0b" size="4">Doing matching of successive scans, then you would hope to see the rmsd between successive to be of the same order as what we find when we <b><i>know</i> </b>the two scans to be identical, which is around 0.007 fringe*. I mean, if two successive scans differ by no more (judged by rmsd) than would two identical scans, you are home and dry.</font></div><div><font class="Apple-style-span" color="#950f0b" size="4"><br></font></div><div><font class="Apple-style-span" color="#950f0b" size="4">Best of luck!</font></div><div><font class="Apple-style-span" color="#950f0b" size="4"><br></font></div><div><font class="Apple-style-span" color="#950f0b" size="4">Arthur</font></div><div><font class="Apple-style-span" color="#950f0b" size="4"><br></font></div><div><font class="Apple-style-span" color="#950f0b" size="4">*f</font><span class="Apple-style-span" style="color: rgb(149, 15, 11); font-size: large; ">or a discussion of the nature and magnitude of noise in interference/absorption signals see Ang & Rowe (2010) "</span><font class="Apple-style-span" color="#950f0b" size="4">Evaluation of the
Information Content of Sedimentation Equilibrium Data in Self-Interacting
Systems". Macromolecular Bioscience 10 798-807</font></div>
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Template>Normal.dotm</o:Template>
<o:Revision>0</o:Revision>
<o:TotalTime>0</o:TotalTime>
<o:Pages>1</o:Pages>
<o:Words>23</o:Words>
<o:Characters>135</o:Characters>
<o:Company>Biosciences - NCMH</o:Company>
<o:Lines>1</o:Lines>
<o:Paragraphs>1</o:Paragraphs>
<o:CharactersWithSpaces>165</o:CharactersWithSpaces>
<o:Version>12.0</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:WordDocument>
<w:Zoom>0</w:Zoom>
<w:TrackMoves>false</w:TrackMoves>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:DrawingGridHorizontalSpacing>18 pt</w:DrawingGridHorizontalSpacing>
<w:DrawingGridVerticalSpacing>18 pt</w:DrawingGridVerticalSpacing>
<w:DisplayHorizontalDrawingGridEvery>0</w:DisplayHorizontalDrawingGridEvery>
<w:DisplayVerticalDrawingGridEvery>0</w:DisplayVerticalDrawingGridEvery>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:DontGrowAutofit/>
<w:DontAutofitConstrainedTables/>
<w:DontVertAlignInTxbx/>
</w:Compatibility>
</w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" LatentStyleCount="276">
</w:LatentStyles>
</xml><![endif]-->
<!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-parent:"";
mso-padding-alt:0cm 5.4pt 0cm 5.4pt;
mso-para-margin:0cm;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:12.0pt;
font-family:"Times New Roman";
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"Times New Roman";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;
mso-ansi-language:EN-US;}
</style>
<![endif]-->
<!--StartFragment-->
<!--EndFragment--><div><br><div><div>On 11 Oct 2013, at 15:23, Frank Niesen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hello everybody,<div><br></div><div>I was hoping for advice on what rmsd between successive scans at one speed I should be aiming for to determine if equilibrium is achieved? Below 0.01? Below 0.005? Or dependent on how the residuals are distributed?</div>
<div>To give an example, I am spinning samples of a protein that forms trimers in 2-sector cells (190 ul/cell). The highest concentrated sample is 200 uM and I waited for about 90 hours, seeing gradual improvement, to currently 0.019 rmsd (I use Sedfit to match, thanks Peter & Co. for the excellent tool!). The differences toward the meniscus and the bottom are about -0.03 and 0.04, respectively. So, the distribution is still "developing"...</div>
<div>But, how good is good enough, having in mind the demand for answers by my collaborators and my desire to proceed to the next speed for the weekend? ;o)</div><div><br></div><div>Many thanks for any help you can give, and a great weekend for all!</div>
<div><br></div><div>Frank</div></div>
_______________________________________________<br>RASMB mailing list<br><a href="mailto:RASMB@list.rasmb.org">RASMB@list.rasmb.org</a><br>http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org<br></blockquote></div><br><div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Arthur J Rowe<br>125 Uplands Road<br>Oadby<br>Leicester<br>LE2 4NW<br><br>Tel: +44 116 2714502<br><a href="mailto:arthur.rowe@connectfree.co.uk">arthur.rowe@connectfree.co.uk</a><br><br></div>
</div>
<br></div></body></html>