- ... 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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