... 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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... assigned^2.2

After uppercase letters A-Z are used, chain IDs 0 through 9 are assigned, then lowercase letters a-z. If your protein contains more than 62 chains, the remaining chains are given no IDs.

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... restraints^2.3

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 [Šali & Overington, 1994].

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... exception^5.1

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

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... special.^5.2

On Unix/Linux systems, MODELLER assumes that your filesystem also stores filenames in UTF-8. This is usually the case on modern systems; however, you can change the encoding by setting the G_FILENAME_ENCODING environment variable.

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... communication)^6.1

Fractional surface area of a residue X is given as the calculated surface area divided by that of the residue in an extended tripeptide Ala-X-Ala conformation.

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... scores^6.2

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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... ^6.3

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/. ^6.4

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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