[chimera-dev] FW: [Chimera-users] Electrostatics

[Eric Pettersen]

On Jun 18, 2009, at 3:55 PM, Gawronski, Alexander wrote:

> Hello,
>
> I sent an email to Eric Pettersen about automating coloring by  
> electrostatics (see below). He told me to direct further questions  
> to the chimera-dev list. So my question is, in the function  
> colorESP(surf, rgbas, potVals) what should rgbas and potVals be  
> specifically?
>
Hi Alex,
	Well, as I said in the initial mail:

> Given a surface, RGBA values,
> and corresponding potential values, something like:
>
> from ESP import colorESP
> colorESP(surf, rgbas, potVals)
>
'rgbas' would be a list of RGBA tuples (red-green-blue-alpha; Google  
'rgba' for more info).  'potVals' would be a list of floating-point  
electrostatic potential values corresponding to the given RGBAs.
> Is there additional information on this functionality that I can  
> look at?
>

You can look at the ESP module, included in your Chimera (daily build)  
distribution in <chimera installation>/share/ESP -- specifically the  
__init__.py file.  The colorESP function is defined there.

There is user-oriented documentation here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

>
> Thanks!
> Alex Gawronski
>
>
> -----Original Message-----
> From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
> Sent: Thu 6/18/2009 2:50 PM
> To: Gawronski, Alexander
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Electrostatics
>
> Hi Alex,
>         In theory this is doable.  In practice, this will not work  
> for some
> of structures in the PDB until our next release.  This is because the
> MSMS surfacing library that we're currently using will fail for a
> small fraction of the structures in the PDB.  Of course, a "small
> fraction" of the entire PDB is still probably hundreds of structures.
> Our next release (1.4) will include a new surfacing library that will
> be more stable -- though it might not be as fast as MSMS.  My best
> guesstimate of when the 1.4 release will be available is September,
> though there's a slight chance it could be earlier.
>         Do you intend to compute electrostatics using some Poisson- 
> Boltzmann
> solver?  If so, then doing that for the entire PDB seems like a
> Herculean task.  Certainly Chimera can show the output once you've
> computed it, but it won't be much help in automating the computation.
> An alternative is that the current daily build includes the Coulombic
> Surface Coloring tool, which unsurprisingly performs the somewhat
> cruder coulombic electrostatics computation for a structure and then
> colors a surface appropriately.  Although Poisson-Boltzmann is a more
> accurate computation it has been our experience that qualitatively the
> results are quite similar.  You can see an informal comparison  
> here:  http://tinyurl.com/mzopva
>         There is no command line version of Coulombic Surface  
> Coloring, so
> you would have to use the Python API.  Given a surface, RGBA values,
> and corresponding potential values, something like:
>
> from ESP import colorESP
> colorESP(surf, rgbas, potVals)
>
> and to get a surface object (assuming exactly one is open):
>
> import chimera, _surface
> surf = chimera.openModels.list(modelTypes=[_surface.SurfaceModel])[0]
>
>         As to how to call Chimera commands from a Python script:
>
> from chimera import runCommand
> runCommand("surf")
>
>         To run a Python script without bringing up the Chimera GUI,  
> look at
> the --nogui and --script arguments documented here:
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html
>
>         Further questions should probably be sent to the chimera-dev  
> mailing
> list rather than the chimera-users list.
>
> --Eric
>
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          http://www.cgl.ucsf.edu
>
>
> On Jun 18, 2009, at 7:02 AM, Gawronski, Alexander wrote:
>
> > Hello,
> >
> > I'm a student at Carleton University and I need to create meshes
> > with electrostatic coloring for all the proteins in the pdb. I need
> > a way of automating this process with scripts but I can't figure out
> > how. Is this possible to do this through command line? How do I call
> > chimera commands from a script?
> >
> > Any help would be greatly appreciated!
> >
> > Thanks,
> > Alex Gawronski
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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