Points can be generated on one or more surface levels or in a rectangular box defined by maximum and minimum x, y, and z values.
POINTS INITIALIZE APPEND SURFACE REENTRANT CONTACT ( ALL = CONTACT + REENTRANT ) ACCESSIBLE VOLUME PLANE 3*realx/y/z, 3*real (sx/sy/sz), 3*inte (x/y/z) SELECT ... END RADIUS real (1.4) DENSITY real (4.0) RANGE real real STEP real
... SELECT ... END
Two SELECTIONS are required for generation of a Connolly SURFACE. The first one is the one on which atoms points are generated and the second one serves to cut away the inner points, that wouldn't be generated if the whole molecule would have been chosen. For syntax see SELECT.
... SURFACE REENTRANT CONTACT ALL (= CONTACT + REENTRANT ) ACCESSIBLE
Calculates the Connoly surface ( by the Connoly algorithm ). The atomic radii should be specified by the SET RADII. Three kinds of SURFACES can be calculated: CONTACT, REENTRANT and ACCESSIBLE. Points of CONTACT and REENTRANT surfaces lie for the atomic RADII far away from atoms, while points of the solvent ACCESSIBLE surface represent the boundary to which the centers of solvent atoms can still approach. The ACCESSIBLE surface is mathematically the same as the CONTACT surface, only the atomic radii are enlarged for the solvent radius.
... RADIUS real
Defines the RADIUS of the solvent molecules.
Defines the DENSITY of points. Default value is 4.0 point per square A. Higher number means more points. 4.0 is well enough when the protein as whole is suppose to be inspected. For smaller parts it is reasonable to increase it.
... RATIO real
RATIO is the real number with which atomic radii are multiplied.
... RANGE real1 real2
RANGE is the distance from VdW radii of atoms out in space in which the surface points are generated.
... STEP real
When surfaces are generated in a RANGE then STEP is the distance between the 2 consecutive layers of SURFACE.
... PLANE 3*real x/y/z, 3*real sx/sy/sz, 3*inte x/y/z
The PLANE command words offers a possibility to generate points in a 3-D lattice. From the origin (3*real x/y,z), step size in each direction (3*real sx/sy/sz) and number of steps (3*inte x/y/z) the 3-D lattice is generated.
The VOLUME points options are more than replaced with the MAP operations.
MAIN> point surface all ratio 1.2 select all end select all end
MAIN> point surface all select activ_site end - MAIN> select protein end dens 7.0 initialize
MAIN> point plane -2. -2. -2. 1. 1. 1. 5 5 5