Electron density maps (from X-ray crystallographic structures) and CryoEM maps are the final piece of information from the experiments, that has been used to build the atomic model, we are interpreting and using for the generation of molecular models. The atomic model is an interpretation of the experimental maps and in many cases it is useful to analyze these to conclude, how well the modeled conformation is supported by the experiment.
In the newly opened GUI window enter the PDB ID and tick 2Fo-Fc
map and Fo-Fc map.
The electron density maps are not displayed directly. If you activate the object (by clicking on its name in the object menu), the unit cell is shown. You can display the complete map of the unit cell via (A)ction, mesh, @level ... For 2Fo-Fc maps use level 1.0 and for Fo-Fc maps level 3.0. The molecule, or part of it may be outside of the unit cell and display of the whole map of the unit cell may slow down the computer or even led PyMOL to crash due to memory shortage.
Center on the region of interest (e.g. the ligand) and activate the Density Wizard: Menu: Wizard, Density. Now only a region around the center is shown and you can adjust the radius and contour level of the map or activate the Fo-Fc map via the menus below the object menu. If the region of interest is outside of the unit cell, you need to click "Next Res." followed by a click on an atom to center the map on the clicked atom.
A shortcoming of the Density Wizard is that one cannot fine tune the density level, which is required in many cases. You can change the density level by the command cmd.get_wizard().set_level(0,1.3) which will set the contour level to 1.3 σ. The corresponding command for the difference density is cmd.get_wizard().set_level(1,2.0). This assumes that map 1 is the 2Fo-Fc map and map 2 the Fo-Fc map.
For many cases you might want to paste the following commands. This will
only work after map 1, map 2 and map 3 have been activated in the menus of
the Density Wizard.
cmd.get_wizard().set_level(0,1.3)
cmd.get_wizard().set_level(1,3.0)
cmd.get_wizard().set_level(2,-3.0)
cmd.color_deep("blue", 'w1_*', 0)
cmd.color_deep("green", 'w2_*', 0)
cmd.color_deep("red", 'w3_*', 0)
This will provide a common coloring of electron density maps in that
positive difference density is shown in green and negative difference
density in red.
Maps can also be read in via the GUI from local files: Menu: File, Open...
Using the file browser, you can select a pdb or cif coordinate file. For loading a map, you can select an mtz or cif reflection data file.
The following script loads our example structure 4eiy, centers on the ligand and displays the normal and difference electron density maps:
reinitialize
fetch 4eiy
fetch 4eiy, type=2fofc, 2fofc
fetch 4eiy, type=fofc, fofc
hide all
show sticks
select ligand, resn ZMA
zoom ligand
isomesh mesh2fofc, 2fofc, 1.3, ligand, carve=8.0
isomesh mesh+fofc, fofc, 3.0, ligand, carve=8.0
isomesh mesh-fofc, fofc, -3.0, ligand, carve=8.0
set mesh_width, 0.5
color grey70, mesh2fofc
color green, mesh+fofc
color red, mesh-fofc
show mesh, mesh*
The isomesh command generates the mesh according to the loaded
electron density map. The numbers specify the contour level. "ligand" ist
the selection around which the map is drawn with a carving
distance of 8.0 Angstrom in this example. This means that electron
density at 8 Angstrom distance around the atom selection is shown. For
showing just the density of the ligand, a smaller carving distance of 2
Angstrom might be optimal.
Loading cryoEM density maps into PyMOL
XXX
|