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Coot

Inserting missing residues into PDB files

  • Load PDB file
  • Load MTZ file
    • An MTZ file is the electron density map for the given molecule. This can sometimes be obtained from the electron density server. If the map can't be obtained simply load any MTZ file for any molecule.
  • Find the carbon atom on the residue you wish to continue the backbone from.
    • This is not the alpha carbon, it's the one connected to the oxygen
  • Click on the add residue tool then on the carbon atom
    • Coot attempts to add a new residue that fits the electron density map. This initial placement is usually junk because the reason the author didn't include the residue in the first place is because the electron density here is too spread out. Also, refinement steps may have removed the electron density here completely.
    • Move the residue close enough to bond to the carbon atom
  • Click on the regularize zone tool then on the new residue
    • This idealizes the residue's geometry while ignoring the electron density map
  • Choose File → Save Coordinates to save

Duplicating a portion of a molecule onto another molecule

Suppose you've got two PDB files and each are missing the last few residues. You want to insert the residues into both & have them match exactly.

  • Load both PDB files into Coot
  • Insert residues into one of the proteins and get them looking how you want
  • Save and close this protein
  • In PyMol load the protein with the new residues. Make a new PDB file that is just the newly inserted residues and the residue they connect to. Load this PDB file into Coot.
  • In Coot choose Calculate → LSQ superpose and align the molecule and the fragment using the residue right before the new residues
  • Delete the connecting residue
  • Choose Calculate → Merge Molecules to merge the two into one molecule
  • Choose File → Save Coordinates to save this new molecule

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