So (see previous email) this fitting method is now checked into the update
server. See below for details about how to interpret the parameters. Let
me know of any problems (I don't have any data to test this on!).
Wayne
On Mon, 2 Jun 2008, Wayne Boucher wrote:
> Hello,
>
> On the fitting equation front, in fact up until 7 August 2007 that was the
> formula we were fitting. But somehow I was convinced (and I can't
> remember why or how) that we should instead be using the formula that is
> in there now (which is similar to the below, but not the same). I think
> what I'll do is add the below in as well.
>
> Well, in the C world, this becomes simplified somewhat to:
>
> y = A ((B+x)-sqrt((B+x)^2 - 4x))
>
> where y = ChemShiftChange, A = maxChemShiftChange/2, B = 1 + Kd/[protein].
> Somehow in the Python world we'll have to allow these parameters to be
> converted to the form you want. (That probably won't be done until the
> next release, so once the above is in, for now it will require an Excel
> spreadsheet or similar to do the calculation converting A, B to
> maxChemShiftChange, Kd, given [protein].)
>
> I'll have to look into the other issues.
>
> Wayne
>
> On Sun, 1 Jun 2008, Lisa Rose Warner wrote:
>
> > Hello all,
> >
> > I am having the same issues as Conny. As an additional note, I ran into this problem after I performed an update on Friday. I hadn't downloaded updates since February and prior to updating, I had no problems grouping peaks and fitting.
> >
> > As for the fitting equation, it would be very useful to have a prompt for protein concentration and use the following equation to fit to a ligand concentration titration series.
> >
> > ChemShiftChange= (Kd + [ligand] + [protein] - Sqrt[(Kd + [ligand] + [protein])^2 - 4*[ligand]*[protein]])/(2*[protein]) *maxChemShiftChange
> >
> > (For an example, see PNAS 2008 vol. 105 (2) pp. 506-11)
> >
> > Thanks -- Lisa
> >
> > On Sun, Jun 1, 2008 at 10:21 AM, Conny Johanssin
> > <[log in to unmask]> wrote:
> > > I've been making some titrations lately and have run into some trouble
> > > analysing the data.
> > >
> > > 1) When I make histograms of resonance1 vs shift dist The resonances are not
> > > displayed on the x axis, but they are for other people in the lab. Still we
> > > are all using the same installation of Analysis. See attachment for screenshot.
> > >
> > > 2) When I try to fit my titration to the saturation curve function in
> > > analysis (the longest function, 2nd from bottom) and then press group peaks
> > > I get a error (see screen dump). The annoying thing is that I got it to work
> > > with another titration 2 weeks ago, but not this time. I've tried both
> > > ligand ratio and ligand conc.
> > >
> > > 3) When I managed to fit the function 2 weeks ago I got a really nice
> > > fitting curve and equation (with the variable values). Theoretically, I
> > > should be able to derive the Kd from this function. It would be really nice
> > > to be able to do that right away in Analysis rather than using some other
> > > program. Anyhow, I don't recognize the equation and I find it strange that
> > > it doesn't need the protein concentration, just the ligand. Do you have some
> > > kind of reference on this equation where I can read about it, or where does
> > > it come from? Do you know how I can get the Kd from the equation?
> > >
> > > Thanks
> > > Conny
> > >
> >
> >
> >
> > --
> > Lisa R. Warner
> > Graduate Student
> > Dept. of Biochemistry
> > University of Colorado, Boulder
> > 215 UCB
> > Boulder, CO 80309-0215
> > 303.492.8085
> >
> >
> >
> > --
> > Lisa R. Warner
> > Research Assistant
> > Dept. of Biochemistry
> > University of Colorado, Boulder
> > 215 UCB
> > Boulder, CO 80309-0215
> > 303.492.8085
> >
>
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