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<div><font size="2" face="Tahoma">Mark</font></div>
<div><font size="2" face="Tahoma"><font face="tahoma"></font></font> </div>
<div><font size="2" face="Tahoma"><font face="tahoma">Not clear how you get s1<a></a><a></a> and s2<a></a><a></a> from a single sample analysis for an interacting system? If cs<a></a><a></a> gives you two peaks its because the trailing edge of a monomer dimer<a></a><a></a>
reaction boundary gets turned into a peak. But its not a species if its truly<a></a> an interacting system. You must do a wide concentration range, show a shift in Sw<a></a> and extrapolate the end points<a></a>. Then choose a model and fit to it.</font></font></div>
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<font color="#000000" size="2" face="Tahoma"><b>From:</b> rasmb-bounces@rasmb.bbri.org [rasmb-bounces@rasmb.bbri.org] On Behalf Of Mark Agacan [M.Agacan@dundee.ac.uk]<br>
<b>Sent:</b> Tuesday, April 26, 2011 10:36 AM<br>
<b>To:</b> RASMB@rasmb.bbri.org<br>
<b>Subject:</b> Re: [RASMB] error estimates and F-statistics in Sedphat<br>
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<div>Thanks Patrick and Chad for the information about error estimates from F-statistics.</div>
<div> </div>
<div>My problem now is that the apparent errors for the binding constants derived from the analysis of F-statistic appear to be very large. When I make a change to e.g. log10Ka12, by any value from 0.1 - 3.0, there is no change (or only a very small change)
in chi squared, so I can never reach the critical chi squared. </div>
<div> </div>
<div>Each dataset looks good and gives low rmsd values when processing with the c(s) model in sedfit. I'm using the monomer-dimer self-association model in sedphat, with the values for S1 and S2 taken from c(s) analysis. I have tried to fit to other models
with only worse results.</div>
<div> </div>
<div>The fit looks very poor (see screenshots attached). I don't think I need to repeat the experiment because the data looks good, at least to my eye, but the fit to the monomer-dimer model seems very bad.
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<div>Any further suggestions or advice would be very welcome.</div>
<div> </div>
<div>Many Thanks,</div>
<div> </div>
<div>Mark</div>
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<div>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery,<br>
Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH
<br>
Tel: +44 1382 386095 Fax: +44 1382 345764 Mobile: 07525 451 117<br>
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<div><font color="#666666">Please consider the environment. Do you really need to print this email?</font>
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<br>
<br>
>>> Chad Brautigam <Chad.Brautigam@UTSouthwestern.edu> 4/23/2011 15:02 >>><br>
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Hi, Mark,<br>
<br>
The F-statistics in SEDPHAT are meant to allow you to construct a "do-it-yourself" error interval. Check out the statistics help page. Under the heading "Error Analysis" there is a procedure for how to use the output "critical chi-square" from the Statistics
Menu to find an error interval.<br>
<br>
Cheers,<br>
Chad<br>
<br>
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<div style="DIRECTION: ltr" id="divRpF398298"><font color="#000000" size="2" face="Tahoma"><b>From:</b> rasmb-bounces@rasmb.bbri.org [rasmb-bounces@rasmb.bbri.org] on behalf of Mark Agacan [M.Agacan@dundee.ac.uk]<br>
<b>Sent:</b> Friday, April 22, 2011 6:36 AM<br>
<b>To:</b> rasmb@rasmb-email.bbri.org<br>
<b>Subject:</b> [RASMB] error estimates and F-statistics in Sedphat<br>
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<div>Hello,</div>
<div> </div>
<div>I'm calculating errors in the binding constants in sedphat as instructed in the statistics help page, but I don't appear to get an output for the F-statistics. Are the F-stats output only as (changes in) chi-squared values? e.g. the error associated with
the binding constants is clearly given in the covariance matrix.</div>
<div> </div>
<div>Best Wishes,</div>
<div> </div>
<div>Mark</div>
<div> </div>
<div> </div>
<div>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery,<br>
Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH
<br>
Tel: +44 1382 386095 Fax: +44 1382 345764 Mobile: 07525 451 117<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</div>
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