RE: [PyMOL] EMizing an xray structure

[Warren D. <wa...@de...>]

Try a command sequence like this:

alter all,b=3D10
set gaussian_resolution, 9.0
map_new dcalc, gaussian, 3.0
map_double dcalc
isosurface dsurf, dcalc, 1.0

Cheers,
Warren

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Warren L. DeLano, Ph.D.                    =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Andreas F=F6rster
> Sent: Wednesday, November 30, 2005 1:32 PM
> To: pym...@li...
> Subject: [PyMOL] EMizing an xray structure
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> Hey all,
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> I'm trying to make a figure from a pdb that's supposed to=20
> look like an EM structure.  According to an older post from=20
> Warren I should increase solvent_radius and alter vdw.
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> For most combinations of the two, artefacts appear all over=20
> the place, like missing surface and surface floating about. =20
> I succeeded in making a figure without artifacts (high vdw=20
> increase, minimal solvent_radius increase), but it looks more=20
> like a lychee than a protein.
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> Has anyone found numbers that work well?  Or a different=20
> approach to creating an EM reconstruction-like figure.
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> Merci bien.
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> Andreas
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> --=20
>     -->       Andreas F=F6rster       <--
> Institut de Biologie Structural, Grenoble
>        www.biochem.utah.edu/~andreas
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