*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Tea and Tim, This may be a stupid idea, but what about this: 1. Superpose the proteins of interest 2. Compute their molecular surfaces with msms/Grasp or generate a mask with an appropriated probe 3. Take one of these surfaces and "invert it" over a cube defined from a clipping plane behind your region of interest (so the surface is put "inwards out" locally; for obvious reasons you cannot do this with all the surface) 4. Measure their complementarity with Michael Lawrence's "sc" program (in ccp4). You might need to translate stepwise if sc doesn't work on surfaces with clashes. Perhaps one of the tools to work with maps/mask could do the inversion? Or perhaps it's indeed a stupid idea, after all. Cheers, Miguel En/na Tim Gruene ha escrit: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > You can use grasp or msms/Raster3D to calculate and visualise protein > surfaces. > But how would you _compare_ surfaces quantitatively? > > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > On Wed, 21 Jun 2006, Tea Pavkov wrote: > >> *** For details on how to be removed from this list visit the *** >> *** CCP4 home page http://www.ccp4.ac.uk *** >> >> >> Dear ccp4bb, >> >> I would like to compare surfaces (not only ligand binding sites) of the >> proteins within the same family. Do you know if there is a program doing >> that or do you know people who are involved in developing something like >> that? >> >> Thank you in advance! >> >> Tea >> >> >> --------------------------------------------------------- >> Mag. Pavkov Tea >> Institute of Chemistry - Structural Biology >> Karl-Franzens-University Graz >> Heinrichstrasse 28, 8010 Graz, Austria >> >> Phone: ++43 316 380 5414 >> Fax: ++43 316 380 9850 >> http://PhysChem.kfunigraz.ac.at/sb >> --------------------------------------------------------- >> > - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: [EMAIL PROTECTED] - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Darwin) iD8DBQFEmnZBF6oOrDvhbQIRAjIaAJ4qOxFxPbNovZbGyc7XRheQGzkb8wCgp4+2 9OUG+U3Wqiz+gK3vNW8aURQ= =3wVY -----END PGP SIGNATURE-----
