Tutorial::Mutating Residues - Revision history

Dwkulp: /* Program description */

2010-08-31T04:02:28Z

‎Program description

Dwkulp at 04:25, 15 July 2010

2010-07-15T04:25:39Z

Dwkulp at 04:25, 15 July 2010

2010-07-15T04:25:27Z

Dwkulp at 04:22, 15 July 2010

2010-07-15T04:22:54Z

Dwkulp at 04:21, 15 July 2010

2010-07-15T04:21:54Z

Dwkulp: Created page with 'Tutorial writing in progress This is an example on how to make mutations and add conformations (rotamers) in MSL. This tutorial explains functions in …'

2010-07-15T04:18:51Z

Created page with '<font color="red">Tutorial writing in progress</font> This is an example on how to make mutations and add conformations (rotamers) in MSL. This tutorial explains functions in …'

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<font color="red">Tutorial writing in progress</font>

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

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/example_mutation_rotamers.cpp?view=markup Complete source of example_mutation_rotamers.cpp]

[[Image:coils.png|500px|center|thumb|Mutation and rotamers built by this example]]

=== To compile ===
<source lang="text">
% make bin/example_mutation_rotamers
</source>

=== 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)
<source lang="text">
% bin/example_mutation_rotamers exampleFiles library/rotlib/balanced/rotlib-balanced-200.txt
</source>

=== Program description ===

<source lang="cpp">
// 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";
</source>

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

← Older revision		Revision as of 04:25, 15 July 2010
Line 1:		Line 1:

−		+	This is an example on how to make mutations and add conformations (rotamers) in MSL. There are multiple ways to do this in MSL, here we describe the simplest way (only needing a rotamer library). This tutorial explains functions in the '''[[MSL Objects:PDBTopology\|PDBTopology]]''' and others.
−	This is an example on how to make mutations and add conformations (rotamers) in MSL. There are multiple ways to do this in MSL, here we describe the simplest way (only needing a ~~rotaer~~ library). This tutorial explains functions in the '''[[MSL Objects:PDBTopology\|PDBTopology]]''' and others.

← Older revision		Revision as of 04:25, 15 July 2010
Line 1:		Line 1:


−		+	This is an example on how to make mutations and add conformations (rotamers) in MSL. There are multiple ways to do this in MSL, here we describe the simplest way (only needing a rotaer library). This tutorial explains functions in the '''[[MSL Objects:PDBTopology\|PDBTopology]]''' and others.
−	This is an example on how to make mutations and add conformations (rotamers) in MSL. This tutorial explains functions in the '''[[MSL Objects:PDBTopology\|PDBTopology]]''' and others.

← Older revision		Revision as of 04:22, 15 July 2010
Line 1:		Line 1:
−	~~<font color="red">Tutorial writing in progress</font>~~	+

← Older revision		Revision as of 04:21, 15 July 2010
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−	[[Image:~~coils~~.png\|500px\|center\|thumb\|Mutation and rotamers built by this example]]	+	[[Image:rotamers.png\|500px\|center\|thumb\|Mutation and rotamers built by this example]]

@@ Line 30: / Line 30: @@
 	sys.readPdb(pdbFile);
-	// Get one of the residues : chain B position 4
+	// Get one of the residues : chain B position 1
 	Residue &res = sys.getIdentity("B,1");
@@ Line 44: / Line 44: @@
 	// *********  MUTATE *************** //
-	//    B,2,ASP to B,2,ASN and get 3 ASN rotamers
+	//    B,1,ASP to B,1,ASN and get 3 ASN rotamers
 	AtomContainer newAtoms = pdbTop.getResidue("B,1,ASN",backboneAtoms,3);