[PyMOL] save sequence in FASTA format

We use PyMOL to display beautiful structures of biomolecules. We could also extract sequence information from PyMOL directly. Thus, no need to go to PDB site to obtain sequence information.

The usage argument is: save file_name.fasta, object, selection

Here is the example, using human glutamine synthetase 2QC8 (assuming PyMOL object name is 2QC8).

  • save all chains: save file_name.fasta (if you have more than 1 object, it will save all chains).
  • save all chains from one object: save file_name.fasta, 2QC8
  • save one chain from one object: save file_name_chainX.fasta, 2QC8 and chain B
  • save two chains from one object: save file_name_chainXY.fasta, 2QC8 and chain A+B

The saved sequence files in FASTA format can found at default PyMOL path or in your manually defined $HOME path (in your pymolrc file).