Description:
create: | create a new grid. |
delete: | delete the current grid. |
compute: | compute new function values in current grid. |
contour: | generate iso-surface for current grid function |
box: | change display attributes (on/off, linewidth, color) of grid box. |
read: | read a grid from file. |
write: | write the current grid to file. |
end: | keep current grid, return to Surface menu. |
Generating surfaces from grids:
1. create a new grid:
The new grid will be centered around the given atomselection (or around the point specified by x,y,z). Resolution defines the distance between grid points. Keep in mind that the number of grid points grows with the third power of 1/resolution. Small values of resolution will result in better quality surfaces, at the (considerable) expense of CPU time. The default of 0.5 Å is reasonable for small to medium sized molecules, but for large proteins, a larger value should be used. Margin defines the amount by which the grid extends beyond the atomselection. For grids that are to be converted so solvent accessible surfaces it is necessary to add a margin of largest vdW radius + probe radius (the default of 3.5 Å should work fine for most cases).
Currently, Wit!P can not handle multiple grids. Therefore, if a grid already exists when you try to create a new one, the program will ask you if you want to delete the old grid, before creating the new one. Answer yes to delete the old grid, no to keep the old grid (and not create the new one).
You may use the box option do make the extent of
the current grid visible
or
compute vdwdist atomselection
This will compute for each point in the current grid (an approximation of the distance of the point from the solvent accessible surface (solvent probe radius probe_radius) of the atoms selected in the atomselection. The second form of the command will compute the distance of grid points to the van der Waals surface of the atomselection. Distances of points that are "outside" of the solvent accessible (or van der Waals) volume are negative, distances of points that are "inside" are positive.
Computing the distances may take a while, depending on the size of the grid and the number of atoms involved.
(The grid/compute menu offers to compute other grid functions,
which are not generally useful, and which are not documented here).
This will contour the current grid function at the preset contour level, and add the resulting surface to the named display_object (usually a molecule). The new surface will receive the name surface_name, which should be unique (otherwise, it will be difficult to change surface attributes, like display status, color, transparency,... later on). The new surface will become the current surface, which may be saved to file by the surface/write command.
The contour add
command uses preset values for attributes of the surface that it generates.
The initial values of these attributes are