Lots of options nowadays! Just to clarify what you can or can't do with PyMOL, here are the choices:
1) PyMOL has an automated menu action that generates a "local protein contact potential" with a constant dielectric screening function. If all you want is a GRASP-like surface image to get a qualitative idea of what regions of your protein surface are relatively positive, neutral, or negative, this is a trivially easy way to access that information. However, as Nathan Baker correctly points out, it is best to simply think of this as a "charge-smoothed" surface representation rather than a true electrostatic potential. To generate this view of any protein object consisting of ONLY the standard 20 amino acids, follow the "A" (action) pop-up menu to "generate", "vacuum electrostatics", and "protein contact potential (local)". You might want the latest beta for this. Builds for Win & Mac can be found at: http://delsci.com/beta and http://delsci.com/macbeta. Recent additions: sequence viewer, easier mouse actions, perspective rendering, right-click menu, animated scenes & transitions, and more. As usual, beta cautions apply... 2) PyMOL comes with an APBS Tools plugin written by Michael Lerner that can call upon an external copy of Nathan's APBS to calculate true Possion-Boltzmann electrostatic potentials. This can require a little bit more manual intervention, but the resulting potential is much more correct and can be used for quantitative analysis. 3) You can use MEAD, GRASP, or ZAP to calculate potentials externally and then read them into PyMOL for realtime visualization and photorealistic rendering. As with any volumetric data in PyMOL, the resulting 3D field can be used to color molecular objects, to create solid or mesh isosurfaces, or to color a slice-plane or height-map that intersects the grid. http://www.pymol.org Cheers, Warren PS. I am proud to announce that even though DeLano Scientific LLC has become a successful company, PyMOL *remains* unrestricted open-source software. Despite the naysayers, with open source you can have your cake and eat it too -- and that's great news. Thanks to everyone who continues to make this possible through your sponsorship of the project! -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: owner-ccp...@dl.ac.uk [mailto:owner-ccp...@dl.ac.uk] On > Behalf Of Eleanor Dodson > Sent: Friday, December 03, 2004 1:20 AM > To: voganes...@lbl.gov > Cc: ccp...@dl.ac.uk; o-i...@o-info.bioxray.dk > Subject: Re: [ccp4bb]: GRASP > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > The CCP4MG graphics offers a GRASP alternative and certainly > runs on Linux OS > > Go to the CCP4 main page > > > http://www.ccp4.ac.uk/main.html > > nd click CCP4MG from the top tool bar > > Eleanor > > > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > Dear colleagues, > > > > > > Is there a version of GRASP that works on linux OS? > > or > > Are there other programs that create an electrostatic > potential of the > > macromolecule suitable for publication? > > > > Thanks. > > > -- > Eleanor Dodson > Structural Biology Laboratory > Department Of Chemistry > University of York > Heslington > YORK > UK > YO10 5YW > Telephone: +44 1904 328259 > Fax: +44 1904 328266 > Electronic email : e.dod...@ysbl.york.ac.uk > > >
