Chimera electrostatic potential
Hi, I've been unable to figure out how to colour the electrostatic surface of a protein red/white/blue. I'm assuming that you have to some how assign electrostatic potential before colouring but how is this done? I'm using a Mac and I've tried to use apbs with pymol but it will not recognise my pqr file generated on the pdb2pqr server or generate it itself. Thanks, Kate
An excellent question, one we have tried wrestling with along the way, so far unsuccessfully. John On 9/7/07 3:07 AM, "Kate Hardie" <kate@flamerock.com> wrote:
Hi,
I've been unable to figure out how to colour the electrostatic surface of a protein red/white/blue. I'm assuming that you have to some how assign electrostatic potential before colouring but how is this done? I'm using a Mac and I've tried to use apbs with pymol but it will not recognise my pqr file generated on the pdb2pqr server or generate it itself.
Thanks,
Kate
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Dear Kate, John, et al. Currently there is no way to calculate the electrostatic potential in Chimera. The separate (not included in Chimera) programs APBS, DelPhi, Grasp, or UHBD can be used to calculate a potential map and write it out to a file, which can then be read into Chimera. Chimera does have a "DelPhiController" tool that interfaces with the academic version of DelPhi, but you still have to get that program separately from its authors. See this page for links to the Web sites for APBS, DelPhi, Grasp, and UHBD: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp While I don't think there are web servers to run such calculations (perhaps due to their complexity and the frequent need to edit the structure beforehand), some of those programs are available free of charge for academic use. Once you have generated an electrostatic potential file, you can open it and the corresponding structure (PDB file) in Chimera, show the surface, and use Chimera's "Electrostatic Surface Coloring" tool to color the surface based on the values. You can also display isopotential surfaces using the "Volume Viewer" tool. I don't know what the issue is with Pymol, but I hope this clarifies the Chimera situation. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Sep 7, 2007, at 4:46 AM, Patton, John (NIH/NIAID) wrote:
An excellent question, one we have tried wrestling with along the way, so far unsuccessfully. John
On 9/7/07 3:07 AM, "Kate Hardie" <kate@flamerock.com> wrote:
Hi, I've been unable to figure out how to colour the electrostatic surface of a protein red/white/blue. I'm assuming that you have to some how assign electrostatic potential before colouring but how is this done? I'm using a Mac and I've tried to use apbs with pymol but it will not recognise my pqr file generated on the pdb2pqr server or generate it itself. Thanks, Kate
participants (3)
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Elaine Meng -
Kate Hardie -
Patton, John (NIH/NIAID)