... Release 6¹

This version of the manual is not up to date.

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... residue.^1.1

There are several small differences between the ``CHARMM'' IUPAC definitions here and those actually used by PDB (e.g., Ile CD1 in PDB is CD in CHARMM, Leu CD1 and CD2 atoms are swapped, and the PDB carboxy terminal atoms O and OXT are OT1 and OT2 in CHARMM, respectively). These differences are handled internally by MODELLER.

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... is.^2.1

This has not been implemented for all the output yet.

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... command.^2.2

The 'default' substitution will be phased out because it is a subset of the ${DEFAULT} substitution.

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