PyMOLers, Electrostatics purists will undoubtedly question the wisdom of this action, but in the latest Windows beta version of PyMOL, I have added an experimental and as-yet-unvalidated automatic way to calculate and display vacuum electrostatic potentials (computed with a constant homogenous dielectric everywhere) around protein atoms.
http://delsci.com/beta (pymol-0_96beta16-bin-win32) Usage: for any protein-containing molecular object, from its Action (A) menu, select generate, vacuum electrostatics, and then choose either an absolute or relative protein surface potential. The calculation runs quickly for small proteins, and is still quite managable for 5-15k atom systems... WARNING: Please don't misuse this feature -- these potentials may look enticing, but THEY'RE NOT REALISTIC due to an absence of solvent dielectric screening. This means that surface charges will have an exaggerated impact on surrounding potentials. Thus, you should only use this feature for QUALITATIVE ASSESSMENT of surface potentials in regions of interest. Also, since this code is currently unvalidated, you should treat the results with extra skepticism. Nevertheless, it is definitely a step up from coloring GLU & ASP red and ARG & LYS blue, and that is my primary justification for making it available now. It is a step in the right direction, even it if isn't quite as far as some of us might like ; ). For publication figures or for quantitative analysis, ALWAYS PLEASE use an external Poisson-Boltzmann electrostatics solver such as Grasp, Delphi, APBS, Zap, or Mead and then load those potential maps into PyMOL for display. We're working to make such integrated usage easier too. Perhaps someday we will even have PB available from directly within PyMOL, with no end-user-integration/multiple-packages/file-manipulation required... Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
