Re: [PyMOL] Fwd: Help setting apbs tools2 on Mac

Hi Daniel,

The version on the wiki (http://pymolwiki.org/index.php/User:Mglerner)
should handle the fink (apbs-mpi-openmpi and apbs-mpi-lammpi) and macports
(apbs-mpi) versions of MPI-enabled APBS.

Please note that the PyMOL-APBS plugin doesn't go out of its way to take
advantage of parallel features; it just calls the MPI-enabled versions of
APBS.

Because I test the non-parallel versions more frequently, it checks for the
normal APBS first. If you want it to find the MPI by default, you can 1)
uninstall the non-MPI version, 2) set the APBS_BINARY variable in the plugin
directly, or 3) set the APBS_BINARY_DIR environment variable.

It's worth noting that the environment variables weren't working in some
previous versions of the plugin.

Cheers,

-Michael

On Wed, Jul 21, 2010 at 2:56 PM, Michael Lerner <
mgl...@gm... <mglerner%2Bs...@gm...>> wrote:

> Hi Daniel,
>
> Sorry for the delay! I wasn't actually aware of that talk page; you'll get
> a faster response if you email the PyMOL list.
>
> The version that you can download from pymolwiki.org will fix the problems
> you had with the temp path. I've never used the openmpi version of APBS on
> the mac before, so I want to do a few more tests before I put up a version
> of the plugin that finds it by default. In the meantime, you can type the
> binary location into the APBS Location box and it should work. You don't
> need to worry about APBS's psize.py for the vast majority of systems.
>
> I'll let you know when I've updated the plugin fully deal with this.
>
> Note that the plugin will still run things using the same input files it
> would with a single-processor APBS.
>
> -Michael
>
>
> On Tue, Jul 20, 2010 at 7:15 PM, RaDaniel Christian 성준 <
> ren...@gm...> wrote:
>
>> I want to bring to your attention the wiki entry I posted in pymolwiki
>> regarding the default loading paths for apbs:
>> After installing with fink, none of the default paths work.
>>
>>
>> http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F
>>
>> If someone knows what is going on, please drop a line!
>> Many thanks in advance,
>> Daniel Ra
>>
>> ---------- Forwarded message ----------
>> From: RaDaniel Christian 성준 <ren...@gm...>
>> Date: Mon, Jun 7, 2010 at 7:07 PM
>> Subject: Help setting apbs tools2 on Mac
>> To: su...@de...
>>
>>
>> Can I get help with setting configuration files on pymol (cvs fink
>> version1.2r3pre)?
>> [ snip ]
>
>


-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)