View Map InterMolecular Dialog Box

Map InterMolecular 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".
Molecule2...: push button; Select this button to identify the Molecular Area containing the second Molecule to be used for the command. InterMolecular HINT calculations require two distinct molecules in two separate Molecular Areas. The selected molecule must have been previously "Partitioned".
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.
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.
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.