> 1- calculation of surface potentials- will this be coming soon? Creation of a Possion-Boltzman solver is a bit of work, so this will not happen very soon -- probably not until we accumulate enough sponsorship to contract with someone to perform the task. But perhaps someone might volunteer to write an open-source Python PB module in the meantime? [sounds like a good summer project for a graduate student in computational chemistry : )]
In the meantime, I recommend using Grasp to calculate the potential, saving the potential as a ".phi" file, and then loading the potential into PyMOL for visualization. Delphi should work too in theory, but we're currently working to resolve a few problems with the approach... > 2- Are you thinking of including any kind of sequence viewer and > sequence alignment tools to tie in with the fitting - as seen with > swissPDB? This would be verh high on my wishlist. It is high on my list as well. > 3- Will you be including any more NMR biased features like a quick > fitting and RMSD calculation for ensembles of structures? This is currently possible using "intra_fit" if the ensemble is loaded as a single object. Between objects, you can do pair-wise fits using "fit" or "align", but that gets tedious with a lot of structures. The sequence viewer will hopefully make multi-object fitting easier. > 4- Is there any chance you will be able to include non-continuous > selections ie select (resi 10-20,30-40) rather than just 10-20 and > ignore residues 30-40? This is already possible using the selection macros: 10-20,30-40/ which is equivalent to resi 10-20 or resi 30-40 Please see the new "Command Syntax and Atom Selections" chapter in the User's Manual for more information on selections. http://pymol.sourceforge.net/newman/user/S0220commands.html#7 Cheers, Warren
