From owner-btk-mca@hgmp.mrc.ac.uk Thu Aug 9 16:57:31 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3362B17D04 for ; Thu, 9 Aug 2001 16:57:21 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 02C0617CFD; Thu, 9 Aug 2001 16:56:41 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5AD7D17D03; Thu, 9 Aug 2001 16:38:28 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA14930; Thu, 9 Aug 2001 16:30:12 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Jim Reid X-Newsgroups: bionet.molbio.methds-reagnts,bionet.metabolic-reg Subject: Re: fitting with dynafit? Date: Thu, 09 Aug 2001 16:28:39 +0100 Organization: Sheffield University Lines: 50 Message-ID: <3B72AC27.684B541F@sheffield.ac.uk> References: <7fcc7.34584$jA2.2726200@news20.bellglobal.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Complaints-To: usenet@shef.ac.uk X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en To: btk-mca@hgmp.mrc.ac.uk.methods@hgmp.mrc.ac.uk Sender: owner-btk-mca@hgmp.mrc.ac.uk Precedence: bulk Hi, I've cc'd this to bionet.matabolic-reg as it seems to be the closest to a "numerical modeling in enzymology" newsgroup. Anyway I suppose it very much depends on what you are trying to do. I've fitted binding data without too many problems but that isn't very tricky. When I've tried to fit more demanding data sets (e.g. progress curves at varied ligand and enzyme concs.) I've had more problems. On the basis of _very_ little experience (you have been warned!) these can be due to problems analogous to determining Vmax when [S] << Km. These are easy to spot when an analytical equation describing the model is available but harder when you are only dealing with progress curves. Perhaps a good safety net would be to simulate curves for your fitted parameters in concentration regions that are far from your experimentally explored ones. This is a bit off topic now but might get a discussion going. As for the initial value problem, I have suffered from this when trying to simulate the first few minutes of the time course of an enzyme with a long lag phase in an attempt to get a steady state rate. I am not convinced that this is anything to do with the program (similar problems with kin/fitsim), but that there are a lot of local minima and picking good starting values is just essential. Looking back over this it doesn't look very helpful but I'd also be interested in hearing about the success stories or problems that people are having with these numerical methods. Are they worth the effort? Always? Sometimes - It depends? Never, just design expts. to avoid them? All the best, Jim ricnews wrote: > > Hi, > > I'm wondering if anyone successfully used dynafit to fit their data to a > model? I tried but even with a simple test I couldn't get it to fit unless I > gave it starting values that were basically the answer. Using starting > values that converge easily in sigmaplot or excel dynafit still couldn't get > the answer. > > I received no response from the author so I was hoping someone else might > use the software and be able to help me out. > > Thanks, > Ric .