Getting Structures from the PDB and Viewing Density Maps

TL;DR

1. Find the structure you're interested in. Here we use 5D8V, currently the highest-resolution structure (0.48 Å) in the database, as an example.

2. Download the model and density:

   1. The model in PDB format
   2. The Validation 2Fo-Fc coefficients file — decompress it to get a CIF file
   3. The Validation Fo-Fc coefficients file — decompress it to get a CIF file
   4. You now have 3 files:
      1. 5d8v.pdb
      2. 5d8vvalidation2fo-fcmapcoef.cif
      3. 5d8vvalidationfo-fcmapcoef.cif

3. Convert the format:

   1. Use cif2mtz from the CCP4 suite:

      BASHCopy

      cif2mtz hklin 5d8v_validation_2fo-fc_map_coef.cif hklout 2fo-fc.mtz << EOF
      EOF
      
      cif2mtz hklin 5d8v_validation_fo-fc_map_coef.cif hklout fo-fc.mtz << EOF
      EOF
      

   2. Use the standalone Python package gemmi:

      BASHCopy

      pip3 install gemmi
      
      gemmi cif2mtz 5d8v_validation_2fo-fc_map_coef.cif 2fo-fc.mtz
      gemmi cif2mtz 5d8v_validation_fo-fc_map_coef.cif fo-fc.mtz
      

4. Load the PDB model along with 2fo-fc.mtz and fo-fc.mtz into COOT, and that's all you need.

Reference

1. X-ray Electron Density Maps