... alignment.^2.1

If the residue type is defined in 'modlib/restyp.lib' you can use the 1-letter code that is specified there, but if in doubt use '.', since that matches everything.

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... restraints^2.2

The restraints include bond, angle and dihedral angle restraints. The SG -- SG atom pair also becomes an excluded atom pair that is not checked for an atom-atom overlap. The $\chi_i$ dihedral angle restraints will depend on the conformation of the equivalent disulfides in the template structure, as described in [Š ali & Overington, 1994].

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... ^6.1

The target distances were all obtained from a regular $\alpha$ -helix in one of the high-resolution myoglobin structures.

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...http://www.ks.uiuc.edu/Research/vmd/. ^6.2

Note that binary trajectory files are machine dependent; it is up to the visualization software to do any necessary byte-swapping.

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