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.

1. Download PDB coordinates and structure factors from PDB.ORG

To calculate a electron density, you need to download PDB coordinates and structure factors (Miller indices and measured intensities) from the PDB. On pdb.org, there is a dropdown menu on the right top corner of each entry site where PDB and structure factors can be downloaded (see image on the right).

2. Calculate electron densities from deposited structure factors

You can calculate an electron density (in CCP4 and mtz format) using a PDB and structure factors using Phenix. Simply type:

phenix.maps 4DJH.pdb 4djh-sf.cif