Volume 2 Chapter 3 3D-Constrain Sub-menu PARAMETER

Function

PARAMETER is used to define distances, angles and torsion angles :

Remarks

The parameters which can be defined are as follows:

distance between two points
distance (perpendicular) from a point to a plane
angle at point 2 made by points 1 and 3
angle between two vectors
angle between a vector and the normal to a plane
angle between the normals to two planes ie. the dihedral angle
torsion angle about vector 2...3 from point 1 to point 4

The points can be either

atoms of the search fragment
or: centroids already set up
or: dummy points already set up

Any vectors or planes used in the parameter definition must have already been setup.

By default, the parameter names are

Bn for distances
An for angles
Tn for torsion angles.

However, the user is allowed to assign alternative parameter names, each with a maximum of six characters.

The values of parameters defined with the PARAMETER command will be saved in the output parameter table, if the test succeeds.

However, if a parameter is to be transformed (see DEFINE TRANSFORM) and not saved in the output parameter table then the name of this intermediate parameter must begin with ?

Example

Select PARAMETER

Select or type items for PARAMETER. If necessary reselect
PARAMETER to end input.
Select CANCEL to cancel command.

Select N atom

8 appears in the dialogue area

Select or type items for PARAMETER. If necessary reselect PARAMETER to end
input.
Select CANCEL to cancel command.

Select O atom

Dialogue area now has

8 7

Select or type items for PARAMETER. If necessary reselect PARAMETER to end
input.
Select CANCEL to cancel command.

Select PARAMETER

Dialogue area now has

DEFINE   [B1]   8   7
Enter new parameter name (<7 chars.) or <RETURN> for the default [B1]
Intermediate parameter names beginning with ? will not be tabulated

Type N...O <RETURN>
In the summary area we now have:
```
N...O   8   7
```
This line is displayed in green to indicate that it is a DEFINE command.
N and O atoms in the fragment are linked by a green line labelled N...O
In the dialogue area we now have the "home" prompt:
```
Search for ALL crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.
```
The resultant command in the instruction document is:
```
DEFINE  N...O  8  7
```

Note: In the above example if you type a name longer than 6 characters then:

Type DIST-NO <RETURN>
Select PARAMETER

Beep

Dialogue area now has

ERROR - Maximum number of characters allowed = 6
Enter new parameter name (<7 chars.) or <RETURN> for the default [B1]
Intermediate parameter names beginning with ? will not be tabulated

Note that, when a torsion angle is defined, after the fourth atom is selected or typed there is no need to reselect PARAMETER. The default parameter name is automatically displayed.

Back to Table of Contents

Volume 2 Chapter 3 3D-Constrain Sub-menu DEFINE-STRUCTURE .