... 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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... 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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...'m'^6.11

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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