[PyMOL] Further functionality

[Jules Jacobsen]

Hi Warren,

I was just wondering about a few features that pymol is currently 
lacking and if/when you were planning on implementing them.


1- calculation of surface potentials- will this be coming soon?
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.
3- Will you be including any more NMR biased features like a quick 
fitting and RMSD calculation for ensembles of structures?
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?


many thanks

Jules

Re: [PyMOL] Further functionality

[NICHOLAS FITZKEE]

 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?
 

Jules,
 It's a little more cumbersome, but one way to
do the above selection would be:

select resi 10-20 or resi 30-40
select chain A and (resi 10-20 or resi 30-40)

It's not quite as convenient, but it gets the job done.

Regards,
Nick

-- 
Nicholas Fitzkee
nickfitz...@jhu.edu

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RE: [PyMOL] Further functionality

[Warren L. DeLano]

 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