The problem with pdb2pqr have been solved :)

Another question which I have  is the calculation of the potential maps from the ensemble of the conformers (for example I want to compare potential distribution from the ensemble of the x-ray structures of one protein which were solved in different condition).

In the visualization tab I found that APBS-2 can align maps. But what is the most suitable way to provide such ensemble for the calculations ? Should it be in NMR-like format or each conformer should be loaded by means of poadDir for instance ? How I can calculate maps from all conformers at once ?

James

2013/3/28 James Starlight <jmsstarlight@gmail.com>
by the way have someone had problems with the pdb2pqr usage with APBS in pymol?


I've tried to install pdb2pqr from source as well as via packages
then I've add usr/bin/pdb2pqr to the APBs plugin window

and when I've started APBS I obtained error like

Error: 5
<type 'exceptions.UnboundLocalError'> Exception in Tk callback
  Function: <function <lambda> at 0x333fcf8> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py",
line 153, in <lambda>
    command=lambda self=self, name=name: self._doCommand(name))
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py",
line 132, in _doCommand
    return command(name)
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
line 1036, in execute
    good = self.generatePqrFile()
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
line 1007, in generatePqrFile
    good = self._generatePdb2pqrPqrFile()
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
line 1615, in _generatePdb2pqrPqrFile
    if retval != 0:
<type 'exceptions.UnboundLocalError'>: local variable 'retval'
referenced before assignment

If I launch pdb2pqr from the terminal I've obtained

own@starlight ~/Desktop $ pdb2pqr
Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH

pdb2pqr.py: error: Incorrect number (0) of arguments!
argv: ['/usr/share/pdb2pqr/pdb2pqr.py'], args: []

should I provide some addition paths to the bash?
James

2013/3/27 James Starlight <jmsstarlight@gmail.com>:
> 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 <marchywka@hotmail.com>:
>>
>>
>>
>> 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: jmsstarlight@gmail.com
>>> To: pymol-users@lists.sourceforge.net
>>> 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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>>