BioJava:CookBook:PDB:mutate

From BioJava

How can I mutate a residue

 // mutate a protein structure
 // and save to file
 
 String filename   =  "5pti.pdb" ;
 String outputfile =  "mutated.pdb" ;
 
 PDBFileReader pdbreader = new PDBFileReader();
 
 try{
     Structure struc = pdbreader.getStructure(filename);
     System.out.println(struc);
 
 
     String chainId = " ";
     String pdbResnum = "3";
     String newType = "ARG";
 
     // mutate the original structure and create a new one.
     // lets side chain point into the same direction, but only uses Cb atom
      Mutator m = new Mutator();
 
      Structure newstruc = m.mutate(struc,chainId,pdbResnum,newType);
 
      FileOutputStream out= new FileOutputStream(outputfile); 
      PrintStream p =  new PrintStream( out );
 
      p.println (newstruc.toPDB());
 
      p.close();
 
 
  } catch (Exception e) {
      e.printStackTrace();
  }