________________________________ > From: ccp4...@hotmail.com > To: pymol-users@lists.sourceforge.net > Date: Fri, 8 Nov 2013 19:53:50 -0600 > Subject: [PyMOL] alignment of metal coordination > > Hi, > > Is it possible to align two structure based on metal coordination or > metal-coordinating residues? What is good way to do it?
Is this a 1-D alignment or spatial ? There are conserved sequence DB's and of course if you want to check there are things like citeseer and pubmed as well as google scholar for finding algorithms if nothing exists in pymol. Maybe someone can comment on how to do this in pymol but you can always define your own figure of merit and optimize that as a function of relative orientation. I suppose you can define an ordering of residues based on interactions with metals. I actually downloaded several orderings from ( hotmail makes it almost impossible any more to insert links into plain text messages.... now thinking I must mean html ) http://www.expasy.org/tools/protscale.html\ for exampl,e, Hphob.Argos.tr KDRENQPHYSWTGCAVMILF > I appreciate your guidance. > > Thanks > SDY > > > ------------------------------------------------------------------------------ > > November Webinars for C, C++, Fortran Developers Accelerate application > performance with scalable programming models. Explore techniques for > threading, error checking, porting, and tuning. Get the most from the > latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk > _______________________________________________ PyMOL-users mailing > list (PyMOL-users@lists.sourceforge.net) Info Page: > https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
