(Modeling proteins)

Graphical User Interfaces

A GUI is absolutely essential for working with proteins.  There are many good GUIs.  If the MOPAC keyword HTML is used, a web-page will be written that would allow details of a protein to be examined using JSmol, and some simple geometric operations (optimizing the positions of small sets of atoms).  This GUI is fast and simple to use, and is useful for exploring mechanisms.

What to look for in a GUI

A GUI must be able to read and write files that MOPAC can read and write.  These include the <name>.mop and <name>.pdb, as well as <name>.arc files.

The GUI should allow structures to be manipulated (edited).

If the GUI can handle and edit residue sequences and backbone ribbons (alpha helices and beta sheets, etc.) that would be a bonus.

Other considerations

A good GUI can make working with proteins much easier.  If you are planning on buying a GUI, try working with it for a week or two.  Make sure that you can perform all, or at least most, of the following operations:

Some functions of GUIs that are utterly useless, and, if they cannot be disabled, make the GUI unacceptable for use in modeling proteins:

These faults, if not detected, can invalidate weeks of work.