Hi Lina,At present I have problem created the map.
1] do I need generate the map from ccp4
(I have already installed the ccp4i, but seems not easy to know how
to get the map)
The CCP4 file is a map. Once the map is loaded into PyMOL you can choose how you want to represent the data: isomesh, isosurface, slice, gradient, or the new volumes. To make a new representation for the map choose one of those from the "A" (Action) button.
2] For small molecular (ligand), the ccp4 is the best way to obtain
its electron density map?
PyMOL natively reads these maps, so you don't need ccp4i or any special plugins.
Jason Vertrees, PhD
PyMOL Product Manager
(o) +1 (603) 374-7120