[RASMB] error estimates and F-statistics in Sedphat

[Mark Agacan]

Thanks Patrick and Chad for the information about error estimates from F-statistics.
 
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.  
 
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.
 
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.  
 
Any further suggestions or advice would be very welcome.
 
Many Thanks,
 
Mark
 

 
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery,
Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH 
Tel: +44 1382 386095    Fax: +44 1382 345764    Mobile: 07525 451 117
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
************************************************************ 
Please consider the environment. Do you really need to print this email? 


>>> Chad Brautigam <Chad.Brautigam at UTSouthwestern.edu> 4/23/2011 15:02 >>>
Hi, Mark,

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.

Cheers,
Chad

From: rasmb-bounces at rasmb.bbri.org [rasmb-bounces at rasmb.bbri.org] on behalf of Mark Agacan [M.Agacan at dundee.ac.uk]
Sent: Friday, April 22, 2011 6:36 AM
To: rasmb at rasmb-email.bbri.org
Subject: [RASMB] error estimates and F-statistics in Sedphat

Hello,
 
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.
 
Best Wishes,
 
Mark
 
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery,
Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH 
Tel: +44 1382 386095    Fax: +44 1382 345764    Mobile: 07525 451 117
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 
************************************************************ 
Please consider the environment. Do you really need to print this email? 


The University of Dundee is a registered Scottish charity, No: SC015096 


UT Southwestern Medical Center
The future of medicine, today.

The University of Dundee is a registered Scottish charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://list.rasmb.org/pipermail/rasmb-rasmb.org/attachments/20110426/8f14e48b/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Slide1.JPG
Type: image/jpeg
Size: 140379 bytes
Desc: not available
URL: <http://list.rasmb.org/pipermail/rasmb-rasmb.org/attachments/20110426/8f14e48b/attachment.jpeg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Slide2.JPG
Type: image/jpeg
Size: 106696 bytes
Desc: not available
URL: <http://list.rasmb.org/pipermail/rasmb-rasmb.org/attachments/20110426/8f14e48b/attachment-0001.jpeg>