Phenix

Calculate electron densities using Phenix

Here are a couple of useful phenix commands to calculate electron densities. In docking, it is often useful to have a look at electron densities, especially for proteins and ligands determined at low resolution. Also, you may want to display them in Pymol: here[link] is described how you generate a electron density map in CCP4 format map, which is required for Pymol.

Calculate electron densities from deposited structure factors

You can download structure factors (Miller indices and measured intensities) from the PDB.