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

[Ooker]

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.

[Baker, Nathan]

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

[Thomas Holder]

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

--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

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[Ooker]

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.

[Thomas Holder]

Hi Ooker,

1. the range is picked automatically. You can pass maximum and minimum to the apbs_surface function if you want:

PyMOL> apbs_surface yoursele, 1, -1

2. If you already have the dx map file, then you can use core PyMOL commands to do everything:

PyMOL> load yourstructre.pdb
PyMOL> load yourmap.dx
PyMOL> ramp_new yourramp, yourmap, [-5, 0, 5], [red, white, blue]
PyMOL> set surface_color, yourramp, yourstructure
PyMOL> set surface_ramp_above_mode

See also:
http://pymolwiki.org/index.php/Ramp_new
http://pymolwiki.org/index.php/Surface_ramp_above_mode

3. "map_new_apbs" is used by "apbs_surface", it's the low level command which runs apbs to create the map. The dx map file is deleted instantly by default, but you can pass the preserve=1 argument to keep it. Learn about available command arguments by calling the command with a question mark:

PyMOL> map_new_apbs ?

Hope that helps.

Cheers,
Thomas

[Baker, Nathan]

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

[Ooker]

You missed

 

PyMOL> show surface

 

to show it. Thanks for your help :D

Ooker.

[Thomas Holder]

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

[Ooker]

Shouldn't we ask the author of the plugin about this?

[Jurrus, Elizabeth R]

Haresh,

See this form:
https://lists.sourceforge.net/lists/listinfo/apbs-users


It will send you a password reminder.

- liz



On 7/18/14, 8:20 AM, "Haresh More" <htm...@nyu.edu> wrote:

>How do I unsubscribe from the email list. I don't remember my password as
>well.
>
>Sent from my iPhone
>
>> On Jul 17, 2014, at 8:37 PM, "Baker, Nathan" <Nathan...@pnnl.gov>
>>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:ganuo...@gmail.com]

>> Sent: Wednesday, July 16, 2014 08:50
>> To: Thomas Holder
>> Cc: Baker, Nathan; apbs-...@lists.sourceforge.net; Jurrus, Elizabeth
>>R; Monson, Kyle E

[Baker, Nathan]

Ok, please let me know if there's anything we can do to bel

Sent from my iPhone

[Thomas Holder]

On 19 Jul 2014, at 01:02, Ooker <ganuo...@gmail.com> wrote:
> Shouldn't we ask the author of the plugin about this?

I'm the author of PSICO.

--Thomas

[Ooker]

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

[Michael Lerner]

On Tue, Jul 22, 2014 at 5:44 AM, Ooker <ganuo...@gmail.com> wrote:

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

That's me, but apparently my email filters are a bit too aggressive, and I missed this. I'll start taking a look at (finally) updating APBS Tools as part of my pre-tenure sabbatical this term.

 

[Ooker]

Great news. Thank you so much for your help.

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