[RASMB] Equilibrium runs with small peptides, high offset values

[John Correia]

How many data sets are you globally fitting?  What centerpiece, ie. what
column height is the data?  Sigma's below 1 are hard to fit, and without
multi-channel, in this case multi concentration with offset floating,
and 3 mm data sets,  you have no hope of good fits.



-------------------------------------------------------------------
 Dr. John J. "Jack" Correia
 Department of Biochemistry
 University of Mississippi Medical Center
 2500 North State Street
 Jackson, MS  39216
 (601) 984-1522                                 
 fax (601) 984-1501                             
 email address: jcorreia at biochem.umsmed.edu     
 homepage location: http://biochemistry.umc.edu/correia.html  
 dept homepage location:    http://biochemistry.umc.edu
-------------------------------------------------------------------
 
 


>>> Erin Matthews <erin.matthews at yale.edu> 12/09/02 06:34PM >>>
----------------------------------------------------------------------------------
The older archived RASMB emails can be found at:
http://rasmb-email.bbri.org/rasmb_archives 
and current archives at
http://rasmb-email.bbri.org/pipermail/rasmb/ 
Search All the Archives at:
http://rasmb-email.bbri.org/rasmb_search.html 
----------------------------------------------------------------------------------

Thanks everyone for suggestions on my last question about data with
negative slopes!  I have yet another question on a different system.

I did an equilbrium (absorbance optics) run on a water   
soluble  peptide of 1290 Daltons.  I had to spin at 60K rpm 
to get any reasonble data (data at lower speeds showed virtually no 
curvature).  My problem now is this: using Nonlin,  the best fit to
the
data gives a lower than expected sigma (.35 instead of .46 with both
the 
offset and the second virial coefficent set to 0).  There doesn't
appear 
to be a higher order association.  When I fix sigma to the 'known'
value, the fit is poor, but when I then let the offset float I get a
good fit, but the offset is .1332.  Very high!  I obviously can't do
an
overspeeding experiment to get an experimental measure of the depleted
meniscus absorbance.  As well, I imagine that the calculated partical
specific volume (from Durchschlag and Zipper, 1994) could be
inaccurate.
Is there something more I can be doing to get an accurate fit?  Which
would be considered a more physically reasonble fit to the data--a fit
using a lower than expected sigma value or a high offset? 

Thanks,

Erin Matthews
Graduate Student, Engelman Lab, Yale University
_______________________________________________
RASMB mailing list
RASMB at rasmb-email.bbri.org 
http://rasmb-email.bbri.org/mailman/listinfo/rasmb