View Partition Molecule Dialog Box

Partition Molecule Dialog Box

Atoms...: push button; This push button calls up an "Atom Select" dialog box wherein the molecules, substructures, and atoms for the partition operation can be chosen. In most cases choosing "All" atoms is the appropriate option.
Partition Method: option menu: {Calculate|Dictionary}; HINT offers two methods of partitioning the molecule on this option menu: "Calculate" or "Dictionary". The Calculate method uses the molecule's atom types (Sybyl) and bond connections as input data to the partition algorithm. The Dictionary method relies on a predefined set of predefined data for regularly occurring substructures such as amino acid residues and nucleic acid bases. In this case the input data is the atom names and substructure names/types.
Partition File: check box and field; The Partition File check box designates whether or not you want to write a file of the molecule partition data as it is calculated. The default is Off. The Partition File field parameter is the name of the disk file to be written of molecule partition data if the check box is set to On. Any valid unix file name may be used, but the HINT convention is for the extension to be .par.
Direction Vectors/Parameters...: check box and push button; Use these options to activate directionality vectors for the molecule partition. These vectors can focus the interactions/hydropathy along bond or electronic density axes. Pressing the Parameters button calls the Direction Vector dialog box.
Hydrogen Treatment: option menu: {United|Essential|All}; This menu describes how the Partitioning will treat hydrogens; there are three options: "United" (using an approach the treats all hydrogens implicitly as part of their parent heavy atom), "Essential" (using an approach that treats (only) polar hydrogens explicitly), and "All". Note that the selection of this parameter has implications in following interaction calculations. For example, hydrogen bonding will be incorrectly modeled by HINT if the United option is chosen. In general the Essential option is best for most applications. The All option appears to "dilute" the hydrophobic density, but treats aromatic hydrogens as potential hydrogen bond donors.
Solvent Condition: option menu: {Inferred|Neutral|Acid|Base}; This option menu is active only if the "Dictionary" method is chosen. The menu lists four options: "Inferred", "Neutral", "Base", "Acid". The latter three represent the pH conditions under which the molecule is to be partitioned. Inferred represents a special case where each substructure (e.g., residue) will be partitioned based on its hydrogen count. For example, if one aspartic acid in a protein is believed to be protonated while other acidic and basic residues are to remain at neutral pH, using the Inferred Solvent Condition is the appropriate approach. Note that all essential hydrogens must be present in the entire model, not just in the "special" residues.
Polar Proximity: option menu: {Off|Via_Bond|Through_Space}; This option menu is only active if the "Calculate" method is chosen. When two or more polar groups are in "in proximity" within a molecule, their effects are cumulatively diminished -- this is termed the polar proximity effect and is dealt with by the Leo method of LogP estimation and by HINT as corrective factors to the hydrophobic atom constants. HINT offers three options for Polar Proximity: "Off", "Via_Bond", and "Through_Space". The Via_Bond method is most compatible with the Leo system, and is the option recommended. Through_Space may be appropriate for some larger molecules that have significant intramolecular non-covalent interactions between polar groups. It uses a through-space distance function to estimate the polar proximity effect.
Through Space Function...: push button; This button, which is only active if Polar Proximity is chosen to be Through_Space, calls the Polar Prox. Dist. dialog to define the specific through-space distance function to be applied to the polar proximity correction.