Hi Marco, It is already possible, Chimera can read the open dx files generated by APBS. You can represent them with the Volume Viewer and/or map them on surfaces. In the latter case, it is preferable to use solvent accessible surfaces and not molecular surfaces and to use lower thresholds (such as 2 kT/e, equivalent to ~ 50 mV at 298 K ) to avoid a bias towards local features. Of course, this depends on the purpose of your representation. While it is not possible with the current implementation of Chimera surfaces (MSMS) to produce solvent accessible surfaces, it can be approximated by adding 1.4 A to all van der Waals radii ( vdwdefine +1.4) and then set the probe radius to its minimum allowed value ( it should be 0 A, because you included the probe in the previous command, but at the moment it must be 0.5 A ) It will be great to have solvent accessible surfaces in the next 1.4 release of chimera :-) Best, Miguel Le 20 juin 09 à 11:42, sette@uniroma2.it a écrit :

Hi,

do you think it is possible in future versions of Chimera to read the results of APBS calculation for electrostatic properties?

Thanks, Marco

Def. Quota "Eric Pettersen" <pett@cgl.ucsf.edu>:

...

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

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328

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