Home > PyMOL > Electron density map

This article explains how to download an electron density map from PDB(Protein Data Bank) , display it in PyMOL, and output images.

Electron density map display

  1. Overall
    fetch (PDB ID), type=2fofc
    Load the electron density map.
    isomesh (any name), (electron dinsity map), (sigma)
    Read the PDB and electron density map and display the whole. If sigma is not entered, it defaults to 1.
    fetch 2BU4
    fetch 2BU4, type=2fofc
    isomesh mesh_all, 2BU4_2fofc, 1.1


  2. Partial and Peripheral Display
    isomesh (any name), (electron density map), (selection), buffer=2, (sigma)
    A map of the lattice enlarged by 2 Å is displayed with buffer=2. In this example, a ligand is selected.
    isomesh mesh_ligand, 2BU4_2fofc, selection=(resn 2GP), buffer=2, 1.1


  3. Partial Display
    isomesh (any name), (electron density map), (selection), carve=2, (sigma)
    carve=2 displays a map within 2 Å.
    isomesh mesh_ligand_carved, 2BU4_2fofc, selection=(resn 2GP), carve=2, 1.1


For changing mesh width and color, see Display CCP4 Maps.