Re: [apbs-users] Control APBS Tool 2 in PyMOL by command line
Biomolecular electrostatics software
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From: Baker, N. <Nat...@pn...> - 2014-07-20 03:30:29
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Ok, please let me know if there's anything we can do to bel Sent from my iPhone > On Jul 18, 2014, at 12:05, "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. > |