N U C P L O T manual

Appendix A - PDB file format

NUCPLOT reads the atomic coordinates from standard PDB format files only.

In particular, NUCPLOT may not produce coherent outputs if the following are not observed:

• Chain ID
  - all protein and nucleic acid chains must be labelled with a chain ID.
  
  
• Protein residue and nucleic acid base names
  - protein residues must be named by their three-letter codes and bases by their one-letter codes. Some crystallographic programs generate PDB files with three-letter base names but unfortunately some of these codes are already taken up as HETATM codes (eg. GUA = glutaric acid).
  
  
• Water names
  - water should be labelled HOH.
  
  
• Atom names
  - all atoms should be named according to the standard PDB format eg. sugar atoms in the nucleic acid backbone should be named C5*, C4* etc not C5', C4'.
  
  

For complete details of the PDB format please see:

N U C P L O T manual