From: Michael L. <mgl...@gm...> - 2006-12-19 01:23:10
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Hi, I want to show the electrostatic potential surface 10A away from a protein. I used to do this by setting all of the vdw radii to 10A, but I'm wondering if there's a better way these days. The surface I got by altering the vdw radii always looked really choppy and not so smooth. Thank you, -Michael Lerner -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net |
From: Andreas F. <doc...@gm...> - 2006-12-19 11:05:21
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Hi Michael, try to set a low resolution in addition to the increased VdW radii. Play around with the following set of commands: set gaussian_resolution, 9.0 # or whatever looks best map_new mapName, gaussian, 3.0, object # number is separation between grid lines, 1 is way too detailed for low resolution isosurface surfaceName, mapName, 1.0 # contour level, 3 looks good This is what Warren helped me with when I tried to create an EM-like figure. Andreas On 12/19/06, Michael Lerner <mgl...@gm...> wrote: > > Hi, > > I want to show the electrostatic potential surface 10A away from a > protein. I used to do this by setting all of the vdw radii to 10A, > but I'm wondering if there's a better way these days. The surface I > got by altering the vdw radii always looked really choppy and not so > smooth. > > Thank you, > > -Michael Lerner > |