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 Förster wrote: > Hey all, > > 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. > > 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. > > Has anyone found numbers that work well? Or a different approach to > creating an EM reconstruction-like figure. > > Merci bien. > > > Andreas > > >
