Remove PDB disordered atoms
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You have a PDB with disordered atoms, i.e. different atomic positions with occupancies that add up to 100%. From this PDB you want to create a new one having only one set of the disordered atoms. This can be necessary if you want to perform RMSD calculations or Molecular Dynamics simulations. | You have a PDB with disordered atoms, i.e. different atomic positions with occupancies that add up to 100%. From this PDB you want to create a new one having only one set of the disordered atoms. This can be necessary if you want to perform RMSD calculations or Molecular Dynamics simulations. | ||
== Solution == | == Solution == | ||
| − | [[Bio.PDB]] is proficient in dealing disordered atoms. Each disordered atom has a property indicating its alternative positions: atom.altloc. Usually there are only two alternative positions labelled 'A' and 'B' | + | [[http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc118 |Bio.PDB]] is proficient in dealing disordered atoms. Each disordered atom has a property indicating its alternative positions: atom.altloc. Usually there are only two alternative positions labelled 'A' and 'B' |
[[Category:Cookbook]] | [[Category:Cookbook]] | ||
Revision as of 15:23, 15 July 2009
Problem
You have a PDB with disordered atoms, i.e. different atomic positions with occupancies that add up to 100%. From this PDB you want to create a new one having only one set of the disordered atoms. This can be necessary if you want to perform RMSD calculations or Molecular Dynamics simulations.
Solution
[|Bio.PDB] is proficient in dealing disordered atoms. Each disordered atom has a property indicating its alternative positions: atom.altloc. Usually there are only two alternative positions labelled 'A' and 'B'
