Hi Lina,

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

Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120