Dear Michael,
With help of Andreas I got apbs plugin 2 working on my pymol and I must say
that's beautiful and I believe it's a 'must have' functionality to add to
your plugin, the ability to show field lines easily.
Another suggestion I have is considering the use of apbs with mpi.
Putting simply, e.g., apbs-mpi-openmpi in pymol apbs plugin configuration
will not take advantages, e.g., of a dual-core computer. 'pdime' need to be
setup properly in pymol-generated.in (see
http://www.poissonboltzmann.org/documentation/parallel-electrostatics-calculations-actin-dimer
)
I wonder if there would be a clever way of setting 'pdime' according to the
number of cpus available.
For a dual-core, 'pdime 2 1 1' should work.
Many thanks for your plugin.
Alan
On Mon, Feb 15, 2010 at 10:42, Alan <alanwil...@gmail.com> wrote:
> Dear Michael,
>
> I am using Pymol 1.2r3pre and APBS 1.2, all installed via FINK in my Mac
> (10.6.2).
>
> I start pymol, build a TRP, call apbs plugin, set grid, run apbs and I can
> see surface and all, but when trying your commands below, pymol-generated
> doesn't exist for me.
>
> Either I am doing something wrong or I don't have the right version of
> Pymol and/or Apbs.
>
> May you clarify me here? This addition to the plugin would be very welcome.
>
> Thanks in advance,
>
> Alan
>
> On Sat, Feb 13, 2010 at 04:55,
> <pymol-users-requ...@lists.sourceforge.net>wrote:
>
>> Message: 3
>> Date: Wed, 10 Feb 2010 20:26:47 -0500
>> From: Michael Lerner <mgler...@gmail.com>
>> Subject: [PyMOL] Showing electric field lines
>> To: pymol mailinglist <pymol-users@lists.sourceforge.net>
>> Message-ID:
>> <e4c539ed1002101726k30ae7cbcm2482f11fe09dc...@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi all,
>>
>> Someone recently asked me if there was a way to display field lines with
>> PyMOL or with an external plugin. Here's what I wrote:
>>
>> It turns out that PyMOL recently grew the ability to display field lines.
>> After you've run APBS, you'll have a map object called pymol-generated.
>> Try
>> this series of commands from the PyMOL prompt:
>>
>> gradient my_grad, pymol-generated
>> ramp_new my_grad_ramp, pymol-generated
>> color my_grad_ramp, my_grad
>>
>
>
>
> --
> Alan Wilter Sousa da Silva, D.Sc.
> PDBe group, PiMS project http://www.pims-lims.org/
> EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
> +44 (0)1223 492 583 (office)
>
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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