pymol-users

[PyMOL] EMizing an xray structure

[<an...@bi...>]

Hey all,

I'm trying to make a figure from a pdb that's supposed to look like an=20
EM structure.  According to an older post from Warren I should increase=20
solvent_radius and alter vdw.

For most combinations of the two, artefacts appear all over the place,=20
like missing surface and surface floating about.  I succeeded in making=20
a figure without artifacts (high vdw increase, minimal solvent_radius=20
increase), but it looks more like a lychee than a protein.

Has anyone found numbers that work well?  Or a different approach to=20
creating an EM reconstruction-like figure.

Merci bien.


Andreas



--=20
    -->       Andreas F=F6rster       <--
Institut de Biologie Structural, Grenoble
       www.biochem.utah.edu/~andreas

Re: [PyMOL] EMizing an xray structure

[Sabuj P. <sab...@va...>]

You can create an mrc map from a PDB using the pdb2mrc program in the
EMan package (http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/ and
http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/doc/progs/pdb2mrc.html).

Pdb2mrc allows you to specify parameters that would affect what a
theoretical cryo EM 3D reconstruction would look like. If you are
looking for a theoretical negative stain EM image, EMan can create
flattened projections of the mrc from multiple angles as well.

I don't know if pymol can read MRC though (I know Chimera can).

Andreas F=F6rster wrote:
> Hey all,
>=20
> I'm trying to make a figure from a pdb that's supposed to look like an
> EM structure.  According to an older post from Warren I should increase
> solvent_radius and alter vdw.
>=20
> For most combinations of the two, artefacts appear all over the place,
> like missing surface and surface floating about.  I succeeded in making
> a figure without artifacts (high vdw increase, minimal solvent_radius
> increase), but it looks more like a lychee than a protein.
>=20
> Has anyone found numbers that work well?  Or a different approach to
> creating an EM reconstruction-like figure.
>=20
> Merci bien.
>=20
>=20
> Andreas
>=20
>=20
>=20