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 "Indexed".
Grid Types: option menu: {EState|H EState (Heavy)|H EState (Protons)}; The Grid Types parameter allows the specification of the information to be calculated by the map command. There are two options: using the EState paradigm where all information is localized on the Heavy atoms, or the H EState paradigm where all information is localized on the hydrogens. Both sets of data can be represented on one contour map by running the two calculations concurrently or sequentially and saving the results in separate SYBYL .cnt files.
Cut Off Radius: field; The Cut Off Radius parameter represents a method to reduce calculation time for Molconn-Z calculations. If the distance 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 Molconn-Z 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 or 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 Molconn-Z 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.