Remove PDB disordered atoms

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
 
== Problem ==
 
== 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.
 
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'
  
  
 
  [[Category:Cookbook]]
 
  [[Category:Cookbook]]

Revision as of 15:18, 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'

Personal tools
Namespaces
Variants
Actions
Navigation
Toolbox