From geoff at compbio.dundee.ac.uk Thu Jul 17 18:53:22 2003 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Thu Jul 17 17:51:33 2003 Subject: [Discuss] Re: Regarding STAMP In-Reply-To: References: Message-ID: Hi Kiran, Stamp wasn't really designed for simple superposition of short fragments, though in principle it should be able to cope with "domain definitions" that are only four residues long. You certainly can't do anything of less than 3 residues as you need a minimum of three points to define a plane and so get a unique solution in any superposition. Stamp works from C-alpha atoms, so points=residues. Stamp may have some internal limitation due to the dynamic programming step that is stopping it going below 5 if this is the case. I have never tried anything that short. For general superposition where you already know which residues to superimpose, then try Andrew Martin's program for this (I forget the name, but a web search should turn it up). Alternatively, there will be parts of the CCP4 package that will do this. Geoff. Hope this helps, On Wed, 16 Jul 2003, Ch.Kiran Kumar wrote: > Dear Geoff, > I am using your STAMP program for structural superimposition. I have > one doubt regarding superimposition. Can I superimpose fragments of length > less than 5 ? If so, Please help me out in giving me the procedure. > > Sorry for bothering you. > > Yours sincerely, > Kiran Kumar > > > > Ch.Kiran Kumar > Project Assistant, > Bioinformatics Center, > Indian Institute of Science, > Bangalore-560012. > > ------------------ Prof. Geoff Barton, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK. http://www.compbio.dundee.ac.uk geoff@compbio.dundee.ac.uk, Tel:+44 1382 345860, Fax: +44 1382 345764