Re: [PyMOL] Showing the surface

2006-12-19 Thread Andreas Forster 

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 mgler...@gmail.com 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

[PyMOL] Showing the surface

2006-12-18 Thread Michael Lerner 

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