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[PyMOL] Showing the surface

From: Michael Lerner <mglerner@gm...> - 2006-12-19 01:23

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

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Thread	Author	Date
[PyMOL] Showing the surface	Michael Lerner <mglerner@gm...>

Re: [PyMOL] Showing the surface

From: Andreas Forster <docandreas@gm...> - 2006-12-19 11:05

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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 <mglerner@...> 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
>