From bryanlepore at mail.utexas.edu Fri Dec 14 03:04:57 2007 From: bryanlepore at mail.utexas.edu (Bryan W. Lepore) Date: Fri Dec 14 03:10:06 2007 Subject: [Discuss] stamp and center of mass Message-ID: i was under the impression that stamp rotates/translates the reference structure to the center of mass - is that right? can't seem to find it in the manual. thanks -bryan From geoff at compbio.dundee.ac.uk Fri Dec 14 09:30:23 2007 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Fri Dec 14 09:29:47 2007 Subject: [Discuss] stamp and center of mass In-Reply-To: References: Message-ID: Hi Bryan, No, stamp does not use the centre of mass. The rotation and translation is based on the superposition obtained from the alignment and so will differ depending on the alignment. For two proteins that are roughly the same shape and length, and which structurally align over most of their length, the centre of mass for the two proteins will be close in the superimposed structures, but is unlikely to be exactly coincident. Geoff. On Thu, 13 Dec 2007, Bryan W. Lepore wrote: > i was under the impression that stamp rotates/translates the reference > structure to the center of mass - is that right? can't seem to find it in > the manual. > > thanks > > -bryan > _______________________________________________ > Discuss mailing list > Discuss@compbio.dundee.ac.uk > http://www.compbio.dundee.ac.uk/mailman/listinfo/discuss > -- Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 385860/388731 (Fax:385764) www.compbio.dundee.ac.uk