Crystallography‎ > ‎Molecular graphics‎ > ‎Pymol‎ > ‎

Electron density maps

To load map and let pymol infer the type from the extension (xplor in this case):

load 2fofc.xplor,map1

To explicitly provide the type:


Display an isosurface‚ as mesh at level 1.0 over the entire map object "map1":

isomesh msh1,map1,1.0

Display isosurface‚ as mesh at 1.0 in a brick about chain A with a border of 3.0 Angstroms:

isomesh msh2,map1,1.0,(chain A),3.0

Pymol can read DSN6 or shelx maps also. 
No need of mapman conversion. 
Just make sure to name the map file xx.dsn6, then use:

isomesh m1, xx.dsn6, 1.0, (residue or mol) carve=2


isomesh m4, map1, 1.0, resi 25, carve=3

This command should nicely put the map around the residue or the inhibitor and no background density!! if you do not want to carve the density of interest, then simply remove the "carve" command and may add say 6.0 (which means that density for six angstrons will be drawn).
To nicely render maps use:

set mesh_radius = 0.016

Last command is to make very thin density representation to have a better effect, but supersample map is betterTo increase the number of lines in a mesh use:
map_double, -1

About carve

from message on ccp4bb from Dirk Kostrewa:

The parameter "carve=1.6" means that density is only shown within a radius of 1.6 A around atoms. This is usually done for clarity, but may give an unrealistic impression of the density quality. A radius that shows the density similar as in a plot without any "carve" parameter, while cutting away the density from the surrounding atoms that you don't want to show, 
should be carefully choosen. Good advice: choosing a radius similar to the maximum resolution of your data as a starting point. The "carve"-radius should then be reported in the figure.


PyMOL>map_double 2mFo-DFc, -1
PyMOL>isomesh msh1, 2mFo-DFc, 1.0, resi 7-27 and chain A, carve=2.2
PyMOL>create 7-27, (resi 7-27 and chain A)
PyMOL>set mesh_radius, 0.025
PyMOL>set opaque_background, off