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.
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:
Read in a structure in one format, and write it out in another format,
and verify that atom 1 has not moved.
Move an atom in the middle of the data-set, then verify that atom 1 has
Select a few (2 to 6) residues, and hide all the rest of the system.
Measure distances between pairs of atoms.
Somewhere in the structure, change a H to a C and, in one step (a few
clicks) convert the C into a normal methyl group.
Some functions of GUIs that are utterly useless, and, if they cannot be
disabled, make the GUI unacceptable for use in modeling proteins:
Automatic rectification of atoms by the addition of hydrogen atoms to
satisfy valence requirements. Adding hydrogen atoms requires several
steps, and any process that does it automatically is certain to make
Automatic optimization of the positions of hydrogen atoms. This
"one size fits all" approach usually fails because there are many exceptions to
rules. For example, if a hydrogen atom of a carboxylic acid group is
near to a water molecule that is near to a sulfate ion, the electrostatic
field of the sulfate polarizes the water which, in turn, might pull the
proton off the carboxylic acid group. Even if it does not pull the proton
off, the O-H bond-length in the carboxylic acid will be increased.
These faults, if not detected, can invalidate weeks of work.