Using WriteDict

Activating the “Make Dictionary...” menu option opens up the WriteDict dialog:

../../_images/writedict.png

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 hydrogen may have been relabeled and covalent LINK records may have been inserted into the pdb file.

WriteDict Advanced Options

FLYNN’s coot interface includes access to some of the advanced options contained in the application.

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. See the WriteDict writedictOutputOptions command line flags for more details.