Tutorial::Mutating Residues

This is an example on how to make mutations and add conformations (rotamers) in MSL. This tutorial explains functions in the PDBTopology and others.

Complete source of example_mutation_rotamers.cpp

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Mutation and rotamers built by this example

To compile

% make bin/example_mutation_rotamers

To run the program

Go to the main directory and run the command (note, the location of the exampleFiles subdirectory needs to be provided as an argument)

% bin/example_mutation_rotamers exampleFiles library/rotlib/balanced/rotlib-balanced-200.txt

Program description

	// Read pdb file into a System object
	System sys;
	sys.readPdb(pdbFile);

	// Get one of the residues : chain B position 4
	Residue &res = sys.getIdentity("B,1");

	// Create a PDBTopology object
	PDBTopology pdbTop;

	// Set a rotamer library and use atoms defined in the rotamer library to build
	pdbTop.readRotamerLibrary((string)argv[2]);
	pdbTop.setAddAtomsFromRotLib(true);

	// Get backbone atoms  
	AtomPointerVector backboneAtoms = pdbTop.getBackboneAtoms(res);
	
	// *********  MUTATE *************** //
	//    B,2,ASP to B,2,ASN and get 3 ASN rotamers
	AtomContainer newAtoms = pdbTop.getResidue("B,1,ASN",backboneAtoms,3);

	// Add atoms to the system
	sys.getPosition("B,1").addIdentity(newAtoms.getAtomPointers(),"ASN");
	sys.getPosition("B,1").setActiveIdentity("ASN");

	// Write out new pdb with an Asn at position 1, chain B.  instead of Asp.
	sys.writePdb("/tmp/example00005_withAsn.pdb");
	cout << "Wrote file /tmp/example00005_withAsn.pdb , has Asn instead of Asp\n";

	// Change conformation , First conformation is 2.  Write out conformation 0 and 1.
	sys.getResidue("B,1,ASN").setActiveConformation(0);
	sys.writePdb("/tmp/example00005_withAsn_rotamer0.pdb");
	cout << "Wrote file /tmp/example00005_withAsn_rotamer0.pdb , has Asn (alternate rotamer) instead of Asp\n";

	sys.getResidue("B,1,ASN").setActiveConformation(1);
	sys.writePdb("/tmp/example00005_withAsn_rotamer1.pdb");
	cout << "Wrote file /tmp/example00005_withAsn_rotamer1.pdb , has Asn (alternate rotamer) instead of Asp\n";

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