[SciPy-user] scipy.optimize.leastsq and covariance matrix meaning
Mon Nov 10 12:23:15 CST 2008
Bruce Southey wrote:
> What are the actual parameters that you think you are trying to estimate
persistent length and contour length (Lo and P in the script).
> What is y and x relative to the equation? In particular is y=F*P or just
> F or P?
I don't understand that. y is a force, x is a distance.
> Your parameter therm is a constant so I would first compute Y/therm
> before doing anything else or just ignore it.
This is a nice idea, thanks.
> Also, you probably need to rescale both x and y because these are either
> very small or very large.
Why? Is there any numerical error waiting, you mean?
> Perhaps even standardize x to mean 0 and
> variance 1. However, you do need to be very careful here. Getting
> nonlinear models to converge to 'correct' parameters is often an art
> than a science.
I think I have been misunderstood. The nonlinear model converges *very
correctly*, and the parameters I find are in *excellent agreement* with
expected values in practically all cases.
What I am asking is for a way to estimate the sigma I have on these
parameters on a single fit.
The covariance matrix gives me what, in my naivety, look like
unreasonably enormous covariance values. This to me seems very odd,
given that I can estimate the correct length of an about 30-nm protein
module, as measured on several peaks, with a 1.5 nm sigma.
> However, I still don't think you have the data to estimate this function
> as there are no clear 'high' and 'low' points. I also don't think this
> model will describe the patterns provided by the links (not even clear
> how your data relates to these images).
The model describes peaks on force spectroscopy curves very well -it's
the standard model used in the literature for that. The model does not
describe the *whole* sawtooth curve, but only *each* rising portion of
The data I put in the script is just an interval where I fit the whole
dataset. I have curves with lots of peaks. In the software, I have a
function that allows me to click two points on the curve and have the
WLC fitted to the data interval between two points. I just pasted that
interval and put it in a small script to give the mailing list actual
stuff to help me.
Massimo Sandal , Ph.D.
University of Bologna
Department of Biochemistry "G.Moruzzi"
Via Irnerio 48, 40126 Bologna, Italy
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