Re: [apbs-users] Control APBS Tool 2 in PyMOL by command line

[Ooker <gan...@gm...>]

Oops, I mean the author of APBS Tool, sorry.


On Tue, Jul 22, 2014 at 1:25 AM, Thomas Holder <
tho...@sc...> wrote:

> On 19 Jul 2014, at 01:02, Ooker <gan...@gm...> wrote:
> > Shouldn't we ask the author of the plugin about this?
>
> I'm the author of PSICO.
>
> --Thomas
>
> > On Saturday, July 19, 2014, Thomas Holder <tho...@sc...>
> wrote:
> > Hi Nathan,
> >
> > unfortunately, no documentation has been written for the apbs features
> in PSICO. Also it's long overdue to include those as core commands into
> PyMOL to not depend on additional module installations. It's on my plate...
> >
> > Best,
> >   Thomas
> >
> > On 17 Jul 2014, at 20:32, Baker, Nathan <Nat...@pn...> wrote:
> >
> > > Hi All --
> > >
> > > This sounds like a great resource.  Thomas, is there a basic tutorial
> or other documentation that we could include on the APBS website in case
> others have similar questions?
> > >
> > > Thanks,
> > >
> > > --
> > > Nathan Baker
> > > Laboratory Fellow and Technical Group Manager
> > > Applied Statistics and Computational Modeling
> > > Pacific Northwest National Laboratory
> > > +1-509-375-3997 ● http://nabaker.github.io
> > >
> > > -----Original Message-----
> > > From: Ooker [mailto:gan...@gm...]
> > > Sent: Wednesday, July 16, 2014 08:50
> > > To: Thomas Holder
> > > Cc: Baker, Nathan; apb...@li...; Jurrus,
> Elizabeth R; Monson, Kyle E
> > > Subject: Re: [apbs-users] Control APBS Tool 2 in PyMOL by command line
> > >
> > > Hi Thomas,
> > >
> > > Thanks for your module, it's great. Now I can put it on the script so
> that I can save images automatically.
> > >
> > > I have some more questions.
> > > 1. Why is the potential from -4.587 to 4.587 kT/e? Is there any way to
> manipulate it, say from -1 to 1 kT/e?
> > > 2. If I have already run APBS for my protein and have a potential map,
> can I load it and see the surface without running it again?
> > > 3. I'm not really sure what the map_new_apbs command do. Is it save a
> potential map? I couldn't see where it saves.
> > >
> > > Thank you so much for a great tool.
> > >
> > >
> > > On 7/16/14, Thomas Holder <tho...@sc...> wrote:
> > >> Hi Ooker and Nathan,
> > >>
> > >> the APBS Tools PyMOL Plugin doesn't provide command line access.
> > >> However, the "psico" python module for PyMOL provides the commands
> > >> "apbs_surface" and "map_new_apbs", maybe those work for you? You can
> > >> download the module from http://pymolwiki.org/index.php/Psico
> > >>
> > >> Cheers,
> > >>  Thomas
> > >>
> > >> On 16 Jul 2014, at 08:41, Baker, Nathan <Nat...@pn...>
> wrote:
> > >>
> > >>> Hi –
> > >>>
> > >>> I don’t know; have you asked on the PyMOL mailing list as well?
> > >>>
> > >>> Kyle, have you looked at Python control of PyMOL at all?
> > >>>
> > >>> Sorry I don’t have more information,
> > >>>
> > >>> --
> > >>> Nathan Baker
> > >>> Laboratory Fellow and Technical Group Manager Applied Statistics and
> > >>> Computational Modeling Pacific Northwest National Laboratory
> > >>> +1-509-375-3997 ● http://nabaker.github.io
> > >>>
> > >>> From: Ooker [mailto:gan...@gm...]
> > >>> Sent: Tuesday, July 15, 2014 22:17
> > >>> To: apb...@li...
> > >>> Subject: [apbs-users] Control APBS Tool 2 in PyMOL by command line
> > >>>
> > >>> Hello,
> > >>>
> > >>> Is there a way to control APBS Tool 2 in PyMOL by using command line?
> > >>> Say I want to visualize the molecule surface colored by potential on
> > >>> SAS from
> > >>> -5 to 5 by using keyboard, not mouse. If it is possible, then you can
> > >>> easily put it on a script to run it.
> > >>>
> > >>> Thank you.
> > >>
> > >> --
> > >> Thomas Holder
> > >> PyMOL Developer
> > >> Schrödinger, Inc.
> >
> > --
> > Thomas Holder
> > PyMOL Developer
> > Schrödinger, Inc.
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>