Re: [PyMOL] Electrostatic potential surface

[James S. <jms...@gm...>]

As I understood the APBs plugin which already exist in PyMol is the
very efficient device for electrostatic potential calculations.

2 questions have been arisen:


1- How I could change cut-off distances for the electrostatic? E.g I'd
like to consider only interactions within 5 A between any charged
groups.


2- What advantages has the usage of pdb2pqr plugin? Also in the
pdb2pqr tools options I've found some options for force fields. As I
know Poisson-Boltzmann equation on which APBS is based doesnt need any
force fields (charge calculation from ab initio principles). Why force
fields used here ?

3- IS there other plugins for the electrostatic surface calculation
with (1) possibility to change cut-offs and (2) charge assignment from
the force fields or ab initio calculations ?


Thanks for help,
James

2013/3/27 Mike Marchywka <mar...@ho...>:
>
>
>
> I have a similar requirement, taking density and potential dstriutbutions from
> jdftx which are written as plain binarry doubles. I use a script and
> some code to create an xplor file which seems to work but I have
> to adjust the position and scale to let it
> overlay the ion positions that I read from an xyz file.
>
> AFAICT xplor is about the only easy format that pymol takes
> but I was debating about trying to find others. i think
> I dug through my older version of pymol, went to the
> effort of changing it all to c++/extern c and then dropped it.
> The xplor approch seems to work well enough for now.
>
>
> Is there an easier way?
> Thanks.
>
>
> ----------------------------------------
>> Date: Wed, 27 Mar 2013 13:41:24 +0400
>> From: jms...@gm...
>> To: pym...@li...
>> Subject: [PyMOL] Electrostatic potential surface
>>
>> Dear PyMol users!
>>
>>
>> I wounder to know about built-in PyMol option for electrostatic
>> potential visualisation.
>>
>> For example I have pdb coordinates of my protein as well as its
>> electrostatic potential distribution (calculated by another software).
>> Using MolMol with both of that files I can visualize the electrostatic
>> potential surface by means of "PaintSurface" option. Can I do the same
>> with the PyMOl?
>>
>>
>>
>> Thanks for help,
>>
>>
>> James
>>
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>