[RASMB] NONLIN

Neil Errington neil.errington at nottingham.ac.uk
Wed May 8 09:40:00 PDT 2002


Hi Daryl

with regard to your NONLIN questions:

>
>First question:
>
>Can anyone tell me explicitly where I may find a comprehensive manual
>for NONLIN?  I have been on the web and found useful material (including
>past emails to RASMB), but not a manual.  For example, I was not able to
>find how to plot the residuals under the plot menu.  (?)

I don't know of a Manual Per se: perhaps the guys at Storrs could help you
there. In order to plot residuals you go under the plot menu and plot
"deviations", it's the same thing.

>
>Second more detailed question (for those who have the time):
>
>I set up the NONLIN fitting procedure according to the instructions for
>self association in the README file that accompanied NONLIN.  First I
>read in 8 files (one speed, one detected wavelength, 8 concentrations).
>Set the value for LnK2 to 0 (allow to converge).  Delta y is 0 (b/c this
>is absorbance),

firstly, are you sure that deltaY is actually zero? this can easily be
checked by over-speeding the run once data at equilibrium have been
captured. You then clear at least the meniscus region of solute and can read
any excess absorbance value. it should be very small ().02 or so, if you
have dialysed the sample) but is not often exactly zero. Secondly I usually
set lnK2 to be 1 and then float, shouldn't make a difference but I dislike
converging from zero.

>LnA refers to the lowest concentration and so I set this
>to -12 (for 7 uM)--allow to converge.  Set sigma to 0.8 (calculated with
>SEDNTERP) and allow to converge.

If you're fitting for self-association you shouldn't allow the sigma value
to float, as this is the set value for e.g. monomer. If sigma is allowed to
float then you're fitting for the Ka for an n-mer of the floated sigma
value.

  Do not put anything in for
>concentration and speed factors b/c only one speed used here and one
>wavelength detected. 

fine

LnK2 is calculated by NONLIN as -13.  I assume
>this means the Ka in absorbance is 3.1 e-6 

I make it 2.26 x 10^-6, don't know what this will convert to in per molar
terms but it will be somewhere well below zero unless you have a very high
extinction coefficient. this would give a Kd in the tens of molar range, and
I guess that this is WAY too weak an interaction! This situation would
improve if you didn't allow sigma to float.

I hope this helps you out (and If I've got it all wrong will someone tell
me?)

Neil

(in Beckman I get Ka in
>absorbance of 0.151).  I know the accuracy will improve by using another
>speed, but I am first trying to get a handle on the program and hope to
>get something that is reasonable (Ka of 3.1 e-6 is not reasonable).  If
>the more experienced NONLIN user can already see a fatal error in my
>fitting approach, would you please let me know?
>
>Your responses are greatly appreciated, thank you
>
>Daryl Bosco
>
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