View Map Molecule Dialog Box

Map Molecule Dialog Box

Molecule...: push button; Select this button to identify the Molecular Area containing the Molecule to be used for the command. The selected molecule must have been previously "Partitioned".
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.
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.
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.
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.
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.
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.
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.
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.
Map File: field; Enter the desired filename for the map. In order for the map to be properly recognized by SYBYL for contouring, use .cnt as the filename extension.
Job Name: field; Enter a Job Name for the calculation if this is to be a SYBYL Netbatch background job.
Batch: check box; Turn this check box on if you wish the calculation to be a background (Netbatch) job. HINT calculations can take from a few seconds to several hours depending on the size of the molecule and the type of calculation.