SURFNET Operating Manual
8. Planes, paraboloids and boxes
i. Planes
The PLANE program generates a surface corresponding to a given
equation of a plane within a given region of space. Like the SURFNET
surfaces, the plane is stored as a 3D array of grid-points having high
values on one side of the plane and low values on the other side. The
values are chosen such that a contour level of 100.0 will display
the plane in the contouring routines of the standard molecular graphics
packages.
To run the program, type:-
You will then be asked for the following parameters:-
- Parameters defining plane: A, B, C, D - where the equation of
the plane is given by:-
- Coordinates of centre of box - defining the centre of the box
within which the surface is to be generated. Enter three numbers,
separated by spaces, corresponding to the x-, y- and
z-coordinates of the box's centre.
- Size of box in each direction - defining the length of box in
each direction. Enter three numbers, separated by spaces.
- Grid separation - defining the separation of the grid-points in
the generated box. A standard grid-spacing is usually around 0.8Å.
- Map-format required: (Q)uanta, (C)CP4, (S)ybyl, (I)nsightII or
(N)one - defining which output format the plane is to be written out
in.
You can use the PRINCIP program (described next) to compute the
equation of a best-fit plane to any set of coordinates.
Best-fit planes
The program PRINCIP computes a best-fit plane through any set
of atoms in a PDB-format file. It uses principal-component analysis
to compute the principal axes of the object represented by the set of
coordinates in the PDB file. The axes, in turn, give the equation of
the best-fit plane which is written out to a file called plane.in.
This file can be used as input to the program PLANE as follows:-
Note that the default output format written to plane.in is
QUANTA (given by the Q in the last line of the file). To have
the plane written out in any other format, edit the plane.in file
before running PLANE as above.
Transform
You can also use the results of the principal components analysis performed
by PRINCIP to transform a PDB-format molecule so as to place the
principal axes along the x-, y- and z-directions.
This is achieved using a program called TRANSFORM which simply
applies the transformation matrix in the transform.in (created by
program PRINCIP) to a given PDB file.
To run TRANSFORM, just type:-
and supply the names of the input and output PDB files when
asked. Respond with a N to the question: Back-transform
coordinates for SURFPLOT - (Y/N)?.
To apply any other transformation, just edit the transform.in file
to give the required transformation.
ii. Paraboloids and cubics
The CURVE program generates a surface corresponding to a given
equation of a plane, paraboloid or cubic surface within a given region of
space. As in the SURFNET and PLANE programs,
the surface is stored as a 3D array of grid-points having high
values on one side of the surface and low values on the other side. The
values are chosen such that a contour level of 100.0 will display
the surface in the contouring routines of the standard molecular graphics
packages.
To run the program, type:-
You will then be asked for the following parameters:-
- Type of surface to be generated - being one of
- Plane
- Paraboloid
- Cubic
- Parameters defining the surface - where the parameters depend on
the type of surface chosen
- For a plane there are 4 parameters - A, B, C, D -
in the equation:
- For a paraboloid there are 6 parameters - A to
F - in the equation:
- For a cubic there are 10 parameters - A to
J - in the equation:
- Coordinates of centre of box - defining the centre of the box
within which the surface is to be generated. Enter three numbers,
separated by spaces, corresponding to the x-, y- and
z-coordinates of the box's centre.
- Size of box in each direction - defining the length of box in
each direction. Enter three numbers, separated by spaces.
- Grid separation - defining the separation of the grid-points in
the generated box. A standard grid-spacing is usually around 0.8Å.
- Map-format required: (Q)uanta, (C)CP4, (S)ybyl, (I)nsightII or
(N)one - defining which output format the surface is to be written out
in.
iii. Boxes
The GENBOX program generates a surface corresponding to a given
box of a given size and at a given point in space. Like the SURFNET,
PLANE and CURVE surfaces, the box is stored as a 3D array of
grid-points having high values inside it and low values outside. The
values are chosen such that a contour level of 100.0 will display
the box in the contouring routines of the standard molecular graphics
packages.
To run the program, type:-
You will then be asked for the following parameters:-
- Coordinates of centre of box - defining the centre of the box
within which the surface is to be generated. Enter three numbers,
separated by spaces, corresponding to the x-, y- and
z-coordinates of the box's centre.
- Length of box in x-, y- and z-directions - defining the length
of box in each direction. Enter three numbers, separated by spaces.
- Grid separation - defining the separation of the grid-points in
the generated box. A standard grid-spacing is usually around 0.8Å.
- Map-format required: (Q)uanta, (C)CP4, (S)ybyl, (I)nsightII or
(N)one - defining which output format the box is to be written out
in.
A box is useful for defining a region of a molecule, say round the region
occupied by a binding site, for use with the related program X-SITE.
SURFNET Operating Manual
iii. Boxes