Footnotes
Keywords: manual

... 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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... restraints2.2
  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 dihedral angle restraints will depend on the conformation of the equivalent disulfides in the template structure, as described in [Šali & Overington, 1994].

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... exception5.1
  MODELLER can raise the following Python exceptions: `ZeroDivisionError`, `IOError`, `MemoryError`, `EOFError`, `TypeError`, `NotImplementedError`, `IndexError`, and `ValueError`.

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... scores6.1
  The mean and standard deviation of the DOPE score of a given protein is estimated from its sequence. The mean score of a random protein conformation is estimated by a weighted sum of protein composition over the 20 standard amino acid residue types, where each weight corresponds to the expected change in the score by inserting a specific type of amino acid residue. The weights are estimated from a separate training set of 1,686,320 models generated by MODPIPE.

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... 6.2
  The target distances were all obtained from a regular -helix in one of the high-resolution myoglobin structures.

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...http://www.ks.uiuc.edu/Research/vmd/. 6.3
  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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