6.3.1 Advanced Options
- 6.3.1.1 planarAniline option

6.3 Using WriteDict

Activating the ``Make Dictionary...'' menu option openes up the writedict dialog:

**Figure 6.3:** writedict dialog

To use the writedict dialog, simply select the protein or ligand from the pull-down menu and click ``ok''. Coot will automatically open up the resulting dictionary and pdb files generated by writedict.

Note that new ``.pdb'' files are generated when using writedict, this is because (as mentioned in Chapter 2.4.1) hydrogen bonds may have been renumbered and covalent LINK records may have been inserted into the pdb file.

6.3.1 Advanced Options

Flynn's coot interface includes access to some of the advanced options contained in the application.

6.3.1.1 planarAniline option

Similar to flynn's mmff94s option, this enforces planar aniline nitrogen configurations. Note that since this is an approximation of the MMFF94s forcefield using planar constraints, it is not called MMFF94s.

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