*** 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 Sure, but with the plugin you have very little control on parameters such as pH for the calculations, ionic strength, etc. Also, it tends to be slightly behind the latest apbs version, but this is a minor problem. However, the biggest problem I see with it is that it works as a black box, so people could be not aware of the type of calculations they are doing. Might be all right if you just want to have an idea... Cheers, Miguel En/na Donnie Berkholz ha escrit: > Miguel Ortiz Lombardia wrote: >> You can use pdb2pqr/propKa (http://pdb2pqr.sourceforge.net/) to generate >> a coordinates file with the atom radii in the "occupancy" column and the >> partial charge in the "B-factor" column. You can ask for different pHs >> (if using the appropriate force-field) >> >> Whith this modified pdb you can run Apbs (http://apbs.sourceforge.net/) >> and get an electrostatic potential map. >> >> Chimera (http://www.cgl.ucsf.edu/chimera/) or pymol >> (http://www.pymol.org) can read the apbs maps in ".dx" format and map >> them onto the surface. > > There's an apbs plugin for pymol that will take care of all this for you > -- all you need to do is install apbs. It's linked from the main plugins > page on the pymol homepage. > > Thanks, > Donnie > - -- 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) iD8DBQFEpYidF6oOrDvhbQIRAp5wAJoDu+s6zlit0SiVSd+jT02JaJFKYgCggH8G JJxNnr8mwaA0X/cReyyh0KI= =nmgd -----END PGP SIGNATURE-----
