Re: [PyMOL] APBS plugin woes

FYI, that worked for me.  I just copied the binary to /usr/local/lib.

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Mon, Nov 30, 2009 at 2:56 PM, Michael Lerner <mgl...@gm...> wrote:
> Can you go to the "Program Locations" tab and find out which version of APBS
> you're using? There's a problem with the one in
> /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.
>
> I've added instructions for fixing this problem to
> http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the
> top of the page, under "APBS Plugin FAQ". Could you try them out and see if
> they work for you?
>
> Thanks,
>
> -Michael
>
> On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi <dga...@ni...>
> wrote:
>>
>> I download and install macpymol-1_2r2.tgz.
>>
>> I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
>> up.
>>
>> Load a pdb file after removing HETATM lines.
>>
>> Open APBS Tools and set grid:
>> Log:
>> Maximum number of grid points exceeded.  Old grid dimensions were
>> [129, 97, 129]
>> Fine grid points rounded down from [117, 87, 117]
>> New grid dimensions are [97, 65, 97]
>>  APBS Tools: coarse grid: (76.908,61.259,77.489)
>>  APBS Tools: fine grid: (65.240,56.035,65.582)
>>  APBS Tools: center: (-22.620,-1.106,-3.967)
>>  APBS Tools: fine grid points (97,65,97)
>>
>> Click "Run APBS", see hydrogens appear, see residues being selected
>> and unselected, then the display says:
>>
>> Log:
>> ObjectMapLoadDXFile-Error: Unable to open file!
>> ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
>>
>>
>> Help?
>> PowerBook, PPC, 10.4.11
>>
>> Dave
>>
>>
>> --
>> David N. Garboczi, PhD
>> Phone: 301-496-4773
>> Head, Structural Biology Section (SBS)
>> Research Technologies Branch (RTB)
>> National Institute of Allergy and Infectious Diseases (NIAID)
>> National Institutes of Health (NIH)
>> Twinbrook 2/Room 110
>> 12441 Parklawn Drive
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>> Fax:    301-402-0284
>> Email: dga...@ni...
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>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
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