... 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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... name^5.2

All MODELLER Python classes are named using CamelCase, such as Model, Alignment, or AutoModel. Previous versions of MODELLER used lowercase names, such as model, alignment, or automodel. These lowercase names are still available but are deprecated.

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... special.^5.3

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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... numbers^6.1

for mmCIF format, author-provided residue numbers (_atom_site.auth_seq_id) are used if available rather than the canonical sequence id (_atom_site.label_seq_id)

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... library^6.2

If no atoms in the first chain have coordinates, internal coordinate generation is seeded by placing the first atom at the origin, the second along the x axis, and the third in the xy plane. If no atoms in subsequent chains have coordinates, the first atom is placed 2 angstroms along each of the x, y and z axes from the last atom in the previous chain, and the second and third atoms placed in the same way as for the first chain.

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... communication)^6.3

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^6.4

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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... ^6.5

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

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...http://www.ks.uiuc.edu/Research/vmd/. ^6.6

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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... files^6.7

This won't work in combination with write_whole_pdb = False for structures that were added to the alignment with Alignment.append_model(), since such inputs may not have an atom file to extract the directory from. In this case the outputs will end up in the current directory.

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... out^6.8

Any structures that were added with Alignment.append_model() will need to have their corresponding atom files available, so that the originals can be reread at this point.

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... files^6.9

This won't work in combination with write_whole_pdb = False for structures that were added to the alignment with Alignment.append_model(), since such inputs may not have an atom file to extract the directory from. In this case the outputs will end up in the current directory.

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... out^6.10

Any structures that were added with Alignment.append_model() will need to have their corresponding atom files available, so that the originals can be reread at this point.

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... model^6.11

residue numbers in mmCIF refer to author-provided values, if available (e.g. atom_site.auth_seq_id), otherwise to label_seq_id.

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...'m'^6.12

Note that 'm.chains['A'].residues['10']' in most cases is the same as 'm.residues['10:A']'. However, if there are multiple chains in the model called 'A' the first syntax will return residue 10 in the first chain called A (and so will fail if that chain does not contain this residue) whereas the second will look for the first residue numbered 10 in any of the A chains. (Generally speaking, you should avoid having duplicate chain IDs or residue numbers!)

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... code^B.1

for PDB format, this is a 1-letter chain ID; for mmCIF format, this is the author-provided chain/asym ID (_atom_site.auth_asym_id) if available, otherwise the canonical asym ID (_atom_site.label_asym_id), both of which can be multiple characters in length

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