[RASMB] NONLIN

[Daryl Bosco]

Hello

I have recently started using NONLIN in an effort to calculate Kd's for
a self associating system (comparing WT and mutants).

I first used the Beckman/ Origins software to calculate a Ka in
absorbance units which I converted to a Kd.  I then went to NONLIN and
found that the Ka in absorbance units (I assume that is what I am
calculating) is many orders of magnitude off.  I assume this is because
I am not experienced with the program and how it is working.

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.  (?)

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), 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.  Do not put anything in for
concentration and speed factors b/c only one speed used here and one
wavelength detected.  LnK2 is calculated by NONLIN as -13.  I assume
this means the Ka in absorbance is 3.1 e-6 (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