Obtain structure from PDB and view density

Jan 14, 202513

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The document discusses finding an interesting structure, specifically the highest resolution structure (0.48 Å) in the database, identified as 5D8V. It outlines the steps to download the model and density, which includes obtaining a PDB format model and two validation coefficient files in CIF format. The three resulting files are: 5d8v.pdb, 5d8v_validation_2fo-fc_map_coef.cif, and 5d8v_validation_fo-fc_map_coef.cif. It also describes converting the CIF format to MTZ format using the CCP4 suite's cif2mtz tool.

TL;DR#

Find a structure of interest, taking the currently highest resolution structure (0.48 Å) 5D8V as an example.
Download the model and density
1. Model in PDB format
2. Validation 2fo-fc coefficients file, unzip to obtain cif format file
3. Validation fo-fc coefficients file, unzip 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

Convert format:

Use cif2mtz from the CCP4 suite

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

Use the standalone python package gemmi

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

Load the PDB model and 2fo-fc.mtz as well as fo-fc.mtz in COOT

Reference#

X-ray Electron Density Maps

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The original link is https://xxu.do/posts/structure/Retrieve-structure-from-PDB-and-view-density