<HTML>
<HEAD>
<TITLE>Re: [RASMB] HELP!</TITLE>
</HEAD>
<BODY>
<BLOCKQUOTE>Hi Chris<BR>
<BR>
Looking at your graph, there is enough indication of where the peaks are for fitting to be stable and possible. Given, of course, software that is appropriate.<BR>
<BR>
The problems are<BR>
<BR>
(1) there seem to be 8 peaks present, which means that you have to float 8 x 3 = 24 parameters (assuming that you fix the baseline - see below). {3 parameters, area, location along x axis and SD, per peak}<BR>
<BR>
(2) most curve-fitting packages have a multi-gaussian fitting option - but use with care! They may use unfriendly* parameters such as 'peak height' and what they mean by SD can sometimes turn out to be the variance!<BR>
<BR>
(3) even having got the option that you want for fitting, entering some vague guesses for the parameters and then calling up Marquadt-Levenberg for fitting (and major packages such as ORIGIN give you no choice) then you will probably get nothing but error messages. Agreed that lots of times fitting in that way poses no problems, but with multi-gaussian fits it is unstable<BR>
<BR>
(4) the baseline - is it really level, or does it go up? Obviously I am not saying that the elevation at the RHS is not real, very possibly it is. But I find that if a baseline gradient is present for real, then stripping it off gives a much better and more valid fit.<BR>
<BR>
<FONT SIZE="2">*OK - these parameters may be very friendly for other purposes<BR>
</FONT><BR>
<B>Suggestions:<BR>
</B><BR>
<B>Option A. You have access to an Apple Mac<BR>
</B><BR>
Download Pro Fit from http://www.quansoft.com/ - you will have to pay for the key, but this software at $95 is many times lower in price than ORIGIN. And it is better in lots of ways - e.g. you have a choice of <U>three</U> alternative fitting algorithms selectable, a lovely simple programming language if you want to use it (not just C !), interface to any compiled language allowed, and so on . . . .<BR>
<BR>
I <U>still</U> do not like the way their multi-guassian fitter module is set up, but I can mail you our own locally written one. <FONT COLOR="#800000"><B>If you would like a demo of what it does - just mail me the textfile of your data. </B></FONT>The way I use it, ROBUST fitting (see - if need be - http://www.clecom.co.uk/science/autosignal/help/Robust_Fitting.htm for what I am talking about) is indeed ROBUST, and gets me very near the answer, and yields excellent first guesses for final Levenberg-Marquadt fitting. NO crashes.<BR>
<BR>
<B>Option B. You have only WINDOWS software available<BR>
</B><BR>
Leaving aside the obvious point that you can buy an inexpensive Mac <I>plus</I> Pro Fit software for around the price of 1 copy of ORIGIN, there is a decent alternative available in the cross-platform Sigma Plot ($495 academic rate - still expensive!): (http://www.rockware.com/catalog/pages/sigmaplot.html). I cannot, I am afraid, remember what their multi-gauss fitter is like, but assuming it is set up with the parameters you want, the general approach is as follows:<BR>
<BR>
(i) make the very best guesses you can for the position of the center of each peak<BR>
(ii) assuming this is an input parameter, FIX it for each gaussian, but FLOAT the areas & SDs<BR>
(iii) using the estimates for the latter as first guesses, float everything and pray!<BR>
(iv) if all that fails, then back to (i) with better initial guesses<BR>
<BR>
Only general problem with Sigma Plot - otherwise a nice if overpriced utility - is that plotting user-defined functions is klunky beyond belief.<BR>
<BR>
Hope all this helps. And mail me your data if you like.<BR>
<BR>
All best<BR>
<BR>
Arthur<BR>
<BR>
</BLOCKQUOTE>--<BR>
*******************************************************<BR>
Arthur J Rowe<BR>
Professor of Biomolecular Technology<BR>
NCMH Business Centre<BR>
University of Nottingham<BR>
School of Biosciences<BR>
Sutton Bonington<BR>
Leicestershire LE12 5RD UK<BR>
<BR>
Tel: +44 (0)115 951 6156<BR>
+44 (0)116 271 4502<BR>
Fax: +44 (0)115 951 6157<BR>
email: arthur.rowe@nottingham.ac.uk<BR>
arthur.rowe@connectfree.co.uk (home)<BR>
Web: www.nottingham.ac.uk/ncmh/business<BR>
*******************************************************<BR>
<BR>
<BR>
<BLOCKQUOTE><BR>
</BLOCKQUOTE><BR>
<BLOCKQUOTE><FONT SIZE="2"><FONT FACE="Arial">Dear RASMB colleagues,<BR>
</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">Does anyone know of a software program that can deconvolute mutiple peaks that are not well separated? (Please see the attachment)<BR>
Your help in above regard is greatly appreciated.<BR>
Many thanks in advance.<BR>
</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">Regards,<BR>
</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">Chris<BR>
</FONT></FONT> <BR>
<BR>
<BR>
<FONT SIZE="2"><FONT FACE="Arial">--------------------------------------------------------------------------</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">Christopher Chin</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">Manager, XLA-Analytical Ultracentrifugation facility</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">Sealy Center for Structural Biology</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">HBC&G, 5.134 MRB.UTMB, Galveston,Tx 77555-1055</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">cchin@utmb.edu, 409-772-1693, efax 708-585-1920</FONT></FONT> <BR>
<FONT SIZE="2"><FONT FACE="Arial">---------------------------------------------------------------------------</FONT></FONT> <BR>
<BR>
<BR>
</BLOCKQUOTE><BR>
</BODY>
</HTML>