Jayden

TL;DR#

1. Find a structure of interest, taking the currently highest resolution structure (0.48 Å) 5D8V as an example.

2. Download the model and density

   1. Model in PDB format
   2. Validation 2fo-fc coefficients file, extract to obtain cif format file
   3. Validation fo-fc coefficients file, extract to obtain cif format file
   4. Obtain 3 files:
      1. 5d8v.pdb
      2. 5d8v_validation_2fo-fc_map_coef.cif
      3. 5d8v_validation_fo-fc_map_coef.cif

3. Convert format:

   1. Use cif2mtz from the CCP4 suite

      Copy

      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

      Copy

      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 and 2fo-fc.mtz as well as fo-fc.mtz in COOT

Reference#

1. X-ray Electron Density Maps

This article is synchronized and updated by Mix Space to xLog. The original link is https://xxu.do/posts/structure/Retrieve-structure-from-PDB-and-view-density