> 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:
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.