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? Is there additional information on this functionality that I can look at? Thanks! Alex Gawronski -----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Thu 6/18/2009 2:50 PM To: Gawronski, Alexander Cc: chimera-users@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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