Tutorial::CoiledCoils Bundles - Revision history

Dwkulp at 16:12, 16 May 2010

2010-05-16T16:12:35Z

Dwkulp at 16:10, 16 May 2010

2010-05-16T16:10:48Z

Dwkulp at 16:08, 16 May 2010

2010-05-16T16:08:05Z

Dwkulp: Created page with 'Tutorial writing in progress, code may not be checked into SVN yet This is an example on how to generate a coiled coil bundle (coiled-coil generation +…'

2010-05-16T15:51:46Z

Created page with '<font color="red">Tutorial writing in progress, code may not be checked into SVN yet</font> This is an example on how to generate a coiled coil bundle (coiled-coil generation +…'

New page

<font color="red">Tutorial writing in progress, code may not be checked into SVN yet</font>

This is an example on how to generate a coiled coil bundle (coiled-coil generation + symmetric bundle creation) in MSL. This tutorial explains functions in the '''[[MSL Objects:CoiledCoils|CoiledCoils]]''' and the '''[[MSL Objects:Symmetry|Symmetry]]''' objects.

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

In MSL the program [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/generateCoiledCols.cpp?view=markup generateCoiledCoils] utilizes the type of code in this tutorial to iterate over the parameter space of coiled coils and generate large numbers of coiled coil structures.

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

=== Program description ===

<source lang="cpp">

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

[[Category:Tutorial]]

← Older revision		Revision as of 16:12, 16 May 2010
Line 10:		Line 10:
	In MSL the program [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/generateCoiledCols.cpp?view=markup generateCoiledCoils] utilizes the type of code in this tutorial to iterate over the parameter space of coiled coils and generate large numbers of coiled coil structures.		In MSL the program [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/generateCoiledCols.cpp?view=markup generateCoiledCoils] utilizes the type of code in this tutorial to iterate over the parameter space of coiled coils and generate large numbers of coiled coil structures.

−	[[Image:coils.png\|~~800px~~\|~~frame~~\|C4 Coiled coil bundle generated by this tutorial]]	+	[[Image:coils.png\|500px\|center\|thumb\|C4 Coiled coil bundle generated by this tutorial]]

← Older revision		Revision as of 16:10, 16 May 2010
Line 10:		Line 10:
	In MSL the program [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/generateCoiledCols.cpp?view=markup generateCoiledCoils] utilizes the type of code in this tutorial to iterate over the parameter space of coiled coils and generate large numbers of coiled coil structures.		In MSL the program [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/generateCoiledCols.cpp?view=markup generateCoiledCoils] utilizes the type of code in this tutorial to iterate over the parameter space of coiled coils and generate large numbers of coiled coil structures.

−	[[~~Media~~:coils.png]]	+	[[Image:coils.png\|800px\|frame\|C4 Coiled coil bundle generated by this tutorial]]

← Older revision		Revision as of 16:08, 16 May 2010
Line 9:		Line 9:

	In MSL the program [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/generateCoiledCols.cpp?view=markup generateCoiledCoils] utilizes the type of code in this tutorial to iterate over the parameter space of coiled coils and generate large numbers of coiled coil structures.		In MSL the program [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/generateCoiledCols.cpp?view=markup generateCoiledCoils] utilizes the type of code in this tutorial to iterate over the parameter space of coiled coils and generate large numbers of coiled coil structures.
		+
		+	[[Media:coils.png]]
		+


Line 26:		Line 29:

	<source lang="cpp">		<source lang="cpp">
		+	// CoiledCoils object used to create a coiled helix (by a number of algorithms)
		+	CoiledCoils cc;
		+
		+	// A super-helical radius
		+	double sr = 6.5;
		+
		+	// An alpha-helical phase angle
		+	double aph = 0.0;
		+
		+	// A super-helical pitch angle, and pitch distance
		+	double shpa = 190;
		+	double shPitch = (2M_PIsr)/tan(M_PI*shpa/180);
		+
		+	// Hard code values of h (rise/residue) = 1.51, r1 (alpha-helical radius), and theta (alpha helical frequency)
		+	double risePerResidue = 1.51;
		+
		+	// Use observed medians by Gevorg Grigoryan (Probing Deisgnability via a Generalized Model of Helical Bundle Geometry, JMB 2010)
		+	double alphaHelicalRadius = 2.26;
		+	double alphaHelicalFrequency = 102.8;
		+
		+	// Number of residues in coil ( lets do 4 heptads = 28 residues )
		+	double numberOfResidues = 28;
		+
		+	// Generate a coiled coil, using specified parameters
		+	cc.northCoiledCoils(sr, risePerResidue, shPitch, alphaHelicalRadius, numberOfResidues, alphaHelicalFrequency, aph);
		+
		+	// Get the atoms from the CoiledCoils object back (this is a single coiled-coil helix)
		+	AtomPointerVector coil = cc.getAtomPointers();
		+
		+	cout << "Writing /tmp/singleHelixCoil.pdb"<<endl;
		+	PDBWriter pout;
		+	pout.open("/tmp/singleHelixCoil.pdb");
		+	pout.write(coil);
		+	pout.close();
		+
		+	// Create a symmtery object to generate a coiled bundle ( C4 symmetric )
		+	Symmetry sym;
		+
		+	// Apply C4 to "coil"
		+	sym.applyCN(coil,4);
		+	cout << "Writing /tmp/C4HelixCoil.pdb"<<endl;
		+	pout.open("/tmp/C4HelixCoil.pdb");
		+	pout.write(sym.getAtomPointers());
		+	pout.close();
		+	</source>