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alpha() -- make an $ \alpha $ -helix

This makes restraints enforcing an $ \alpha $ -helix (mainchain conformation class ``A'') for the residue segment specified by residues (which can be created using the model.residue_range() function). The helix is restrained by $ \Phi,\Psi$ binormal restraints, N-O hydrogen bonds, $ {C}_\alpha$ - $ {C}_\alpha$ distances for $ i-j \in \{2-9\}$ , $ {C}_\alpha$ -O distances for $ i-j \in \{2-9\}$ , and O-O distances for $ i-j \in \{2-6\}$ 6.1. Note that this requires all heavy atoms to be present to work properly, so will not work with the $ {C}_\alpha$ -only topology.

To actually add the restraints, pass the new object to restraints.add(). See Section 2.2.9 for an example.

Ben Webb 2007-01-19