Re: [apbs-users] visualizing the electrostatic potential of each atom from a flat format

[Thomas H. <tho...@tu...>]

Hi Davide,

the spectrum command in PyMOL takes a color palette and has "minimum" 
and "maximum" arguments to define the value to color mapping. Example:

spectrum b, red_white_blue, minimum=-10, maximum=10

This will map -10: red, 0: white, 10: blue

For available color palettes, see:
http://pymolwiki.org/index.php/Spectrum

I don't think that potential values at atom positions provide enough 
information for calculating an isosurface.

Cheers,
   Thomas

Davide Mercadante wrote, On 05/05/12 06:04:
> Dear Jason,
> 
> Thank you for your prompt response. So do you suggest that a script that
> automatically substitute the field of the B-factors with the electrostatic
> potential calculated by atompot could do the trick? At that stage taking
> snapshots of the colored protein and creating a movie wouldn't be
> difficult. However, I was wondering what color would be used by the
> program for electrostatic potential values that are negative as the
> B-factors are never negative I imagine.
> 
> Could I also define a scale on how to treat the values of the B-factors
> depending from the potential that I get from atompot (APBS)?.
> That's for atom coloring depending on the electrostatic potential. What
> about the possibility to visualize the potential in a 3D way using for
> example Isosurface representation?
> 
> Thank you again for your help. Much appreciated.
> 
> Cheers,
> Davide
> 
> On 5/05/12 3:20 AM, "Jason Vertrees" <jas...@sc...>
> wrote:
> 
>> Hi Davide,
>>
>> This might be easier in VMD -- I'm not sure.
>>
>> You could easily assign the b-factor values to each atom and then
>> color by atom. This is frequently done
>> (http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Colori
>> ng);
>> however, PyMOL only supports reading b-factors across multiple states
>> not writing. So, to create a movie you'd have to re-assign the
>> b-factors at each step or split your trajectory into multiple objects.
>> Both of those solutions would be painfully slow. We'll soon allow
>> writing to b-factors across multiple states to make this painless.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Fri, May 4, 2012 at 1:05 AM, Davide Mercadante
>> <dm...@au...> wrote:
>>> Dear Prof. Baker,
>>>
>>> Thank you for your quick reply. That sounds good.!
>>>
>>> Regards,
>>> Davide
>>> From: "Baker, Nathan" <Nat...@pn...>
>>> Date: Thu, 3 May 2012 19:23:26 -0700
>>> To: Davide Mercadante <dm...@au...>,
>>> "apb...@li..." <apb...@li...>
>>> Cc: "jas...@sc..." <jas...@sc...>,
>>> "jo...@ks..." <jo...@ks...>
>>> Subject: RE: [apbs-users] visualizing the electrostatic potential of
>>> each
>>> atom from a flat format
>>>
>>> Hi Davide ­
>>>
>>>
>>>
>>> Great question!
>>>
>>>
>>>
>>> This should be possible with VMD ­ and probably PyMOL.  I know VMD a bit
>>> better:  you should be able to create a script that renders each scene
>>> to an
>>> image file.  I would recommend starting by saving the VMD scene and
>>> editing
>>> the resulting Tk script.  I¹m Cc¹ing John Stone to see if he has
>>> additional
>>> suggestions about VMD.  I¹m also Cc¹ing Jason Vertrees for the PyMOL
>>> perspective.
>>>
>>>
>>>
>>> Thanks!
>>>
>>>
>>>
>>> __________________________________________________
>>> Nathan Baker
>>> Pacific Northwest National Laboratory
>>> Tel:  +1-509-375-3997
>>> http://nabaker.me
>>>
>>>
>>>
>>> From: Davide Mercadante [mailto:dm...@au...]
>>> Sent: Thursday, May 03, 2012 3:38 PM
>>> To: apb...@li...
>>> Subject: [apbs-users] visualizing the electrostatic potential of each
>>> atom
>>> from a flat format
>>>
>>>
>>>
>>> Dear APBS users,
>>>
>>>
>>>
>>> I have performed a series of APBS calculations on MD trajectories of a
>>> complex and I wanted to follow the evolution of the electrostatic
>>> potential
>>> of a series of specific atoms of the complex, along the time.
>>>
>>> To do this I have written the atompot for each atom but in a flat format
>>> instead of .dx as reported in the user's manual.
>>>
>>>
>>>
>>> How I can visualize the electrostatic potential of the atoms I am
>>> interested
>>> in, using a visualization software such as Pymol or VMD? I suppose that
>>> having the potential written for the complex in the .dx format I could
>>> isolate only the atoms I am interested in and visualize them using
>>> different
>>> visualization modes (isosurface, field lines, surf etcŠ.), therefore
>>> using
>>> only the visualization software. However is there another way starting
>>> from
>>> the flat format of the atompot output?
>>>
>>>
>>>
>>> Thank you in advance for your time.
>>>
>>>
>>>
>>> Cheers,
>>>
>>> Davide
>>
>>
>> -- 
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrödinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen