View HINTMAP MSS Dialog Box
HINTMAP MSS Dialog Box

- Calculation Type
- radios: {InterMolecular [with Prototype Conformer]|IntraMolecular
[requires Prototype]|Molecule [requires Prototype]|Complement
[requires Prototype]}
- These four options refer to the different maps the HINTMAP MSS function
can calculate:
- InterMolecular [with Prototype Conformer] will take each row as a
conformation of the same molecule (i.e., Prototype) and
calculate an InterMolecular Interaction map for it, against a
common rigid receptor.
- IntraMolecular [requires Prototype] will calculate an IntraMolecular
Interaction map for each conformation of the Protoype in the Molecular
Spreadsheet.
- Molecule [requires Prototype] will calculate a Hydropathic Molecule
property map for each conformation of the Protoype in the Molecular
Spreadsheet.
- Complement [requires Prototype] will calculate a Hydropathic Molecule
property map for the presumed Complementary species for each conformation
of the Protoype in the Molecular Spreadsheet.
- Partition Receptor
- push button
- Two components are necessary for the InterMolecular HINTMAP Function:
a Macromolecule in a Sybyl Molecular area, and a Molecular
Spreadsheet of ligand conformers oriented for interaction with the
common receptor (Macromolecule). Pressing this button
calls the HINT Partition Molecule
dialog to Partition the Macromolecule.
- Partition Prototype
- push button
- This button Partitions a prototype of the molecule whose conformations
are stored in the MSS. Pressing this button calls the HINT
Partition Molecule dialog.
- Distance Function...
- push button
- Select this button to describe the mathematical distance behavior
of hydropathy for the current calculation. This button calls the
Distance Function dialog box.
- Map File Root
- text
- Enter a text file name to be used as the "root" of each Hint Map
created by this command. Each individual file will be named as a
derivative of this root name.
- Grid Calculation: Interactions
- option menu: {All|Hydrophobic|Polar}
- The Interaction parameter allows you to choose the types of
interactions to be recorded by the calculation. The options are:
- All records all interactions in the HintTable or map. Positive
values represent favorable binding situations such as
hydrophobic-hydrophobic, acid-base, hydrogen bonding, Coulombic,
etc. Negative values in the HintTable or map represent
unfavorable binding situations such as hydrophobic-polar,
repulsive (like charge) Coulombic interactions, etc.
- Hydrophobic records only interactions involving hydrophobic atoms
in the HintTable or map. Positive values generally represent
hydrophobic-hydrophobic interactions and negative values generally
represent hydrophobic-polar interactions.
- Polar records all interactions that do not involve hydrophobic
atoms. Positive values generally represent acid-base and hydrogen
bonding and negative values generally represent acid-acid and
base-base unfavorable interactions.
- Grid Calculation: IntraMonomer
- check box
- The IntraMonomer parameter specifies whether IntraMolecular
interactions within the same monomer or substructure are to
be recorded by the HintTable or map.
- Grid Calculation: Grid Types
- option menu: {Hydrophobic/Polar|Acid/Base}
- The Grid Types parameter allows the specification of the
information to be calculated by the map command. Alternately,
you can calculate a map where the positive grid values represent
hydrophobic regions and negative grid values represent polar
regions or a map where the polar information has been categorized
into acidic regions and polar regions (at the expense of the
hydrophobic information which is lost). If all three types of
infomation are desired, you will have to run two HINT map
calculations. The available Grid Type options are:
- Hydrophobic/Polar where positive map values represent hydrophobic
regions of space and negative map values represent polar regions
of space.
- Acid/Base where positive map values represent acidic regions of
space and negative map values represent basic regions of space.
Note that this option requires the selection of an Acid Base
Definition.
- Grid Calculation: Acid Base Definition
- option menu: {Coulombic|Bronsted|Lewis}
- The Acid Base Definition parameter specifies what model for
acids and bases will be used by HINT if Grid Type is set to
Acid/Base. These definitions are static; they are based on
the SYBYL atom types and are not dynamically reevaluated.
Three models are available as options:
- Coulombic is a formal charge-based model. Atoms with formal
positive charges are considered to be acids and atoms with
formal negative charges are considered to be bases.
- Bronsted uses the Bronsted-Lowry theory of acids and bases.
An acid is a proton donor while a base is a proton acceptor.
- Lewis uses the Lewis theory of acids and bases. An acid is
an electron pair acceptor and a base is an electron pair
donor.
- Region Definition...
- push button
- Select this button to define the spatial extents of the map
region. The Region Definition
dialog box appears when this button is selected.
- Grid Control: Volume Averaging
- check box
- Turning On the Volume Averaging parameter produces smoother
HINT maps, but at a cost of approximately an eight-fold
increase in calculation time. The algorithm surrounds each
actual grid point with a box whose corners are at (+/-) 1/3
grid spacing along each cartesian axis. The map is evaluated
for each corner of the box and the resulting values averaged
to yield the map value at the original grid point.
- Grid Control: Inside Mol Cut Off
- check box
- The Inside Mol Cut Off parameter specifies whether grid points
inside the Van der Waals radius of any atom are to be set to
predefined constant values.
- Low Limit
- field
- The Low Limit parameter is the constant that will be assigned
to negative-valued grid points inside the Van der Waals radius
of any atom if Inside Mol Cut Off is set to On.
- High Limit
- field
- The High Limit parameter is the constant that will be
assigned to positive-valued grid points inside the Van der
Waals radius of any atom if Inside Mol Cut Off is set to On.
- Grid Control: Cut Off Radius
- field
- The Cut Off Radius parameter represents a method to reduce
calculation time for HINT calculations. If the distance
between two atoms (for HintTable calculations) or between
a grid point and an atom (for map calculations) exceeds the
cutoff-radius that interaction is ignored. Cut Off Radius
values of greater than 6.0 Angstroms appear to have minimal
effect on the calculation quality but can save considerable
calculation time.
- Grid Control: Van der Waals Limit
- field
- The Van der Waals Limit parameter allows limited user control
of the HINT Van der Waals radii set. The Van der Waals Limit
is a multiplicative factor (default = 1.00) that adjusts the
predefined radii set. A value of less than 1 would allow
more "bump" between atoms, while a value greater than one
would allow less.