Activated OBJECT are defined in order to interactively (by dials) manipulate conformations of models without actually changing the coordinates data. The OBJECTS are supposed to be defined via MENU commands, though they can be changed and also manipulated manually via command sentences. Each OBJECT obtains a KEYED SELECTION. The SELECTIONS can be changed also after the OBJECTS have been already defined. Up to 30 activated OBJECTS are allowed to be set simultaneously. The SYMMETRY OBJECTS have to be defined manually.
OBJECT inte SELECT ... END
BOND atom-num atom-num (atom-num) DISTANCE atom-num1 atom-num ANGLE atom-num atom-num atom-num DIHEDRAL atom-num atom-num atom-num atom-num TRANSLATE ROTATE atom-num SYMMETRY MATRIX inte TRANSLATION inte inte inte SET TRUE FALSE INITIAL BOND real ANGLE real DISTANCE real DIHEDRAL real TRANSLATION 3*real ROTATION 9*real
FROM int2 AUTO
OBJECT inte ...
Defines the identity number of the OBJECT on which to following function is activated.
... SELECT ... END
Defines the SELECTION on which the specified function acts. The name of the OBJECT'S KEY is a 4 character string ``ob__''. The ``__'' are replaced with the OBJECT identity number.
... BOND atom-num1 atom-num2 [atom-num3]
Activates rotation around the BOND atom-num1 atom-num2. The atom-num3 is optional. Usually it is chosen from the neighbours of atom-num2 by the program itself.
... DISTANCE atom-num1 atom-num2
Activates translation of the SELECTION along the vector atom-num1 atom-num2.
... ANGLE atom-num1 atom-num2 atom-num3
Activates rotation of the SELECTION around axes that goes through atom atom-num2 and is perpendicular to the plane defined by the 3 atoms.
... DIHEDRAL atom-num1 atom-num2 atom-num3 atom-num4
Activates rotation of the SELECTION around bond atom-num2 atom-num3.
Activates TRANSLATION of the SELECTION in X Y and Z components.
... ROTATE atom-num
Activates ROTATION of the SELECTION around X Y and Z axes. The CENTER of ROTATION is at the position of atom atom-num.
... SYMMETRY MATRIX inte TRANSLATION inte inte inte
Activates crystallographic SYMMETRY operations on the given object. It acts only with a link to an activated parent OBJECT. When the parent is moved (ROT_TRAN) also the children are following its rotations and translations with the chosen SYMMETRY operations plus the additional TRANSLATIONS in whole number fractional coordinates. The SYMMETRY operation MATRIX inte is the sequential number taken from the list of SYMMETRY MATRICES that should be already read before.
OBJECT inte FROM int0
The changes of the activated OBJECTS can be dependent from each other. The OBJECT int0 is the parent of the OBJECT inte. That means, that whatever happen to the parent OBJECTS, happen to the children as well. The command word AUTO tells the program to find the parents, if they exist, from the SELECTIONS of the activated OBJECTS. An OBJECT is a child, when a parent OBJECT can be found. A parent OBJECT includes the complete SELECTION of its' child.
... SET TRUE FALSE INITIAL BOND real ANGLE real DISTANCE real DIHEDRAL real TRANSLATION 3*real ROTATION 9*real
The values of activated OBJECTS' functions are normally defined interactively with DIALS. They can be checked with a SHOW OBJECT command. In the case of restarts or since the user would like to do it manually, The values can be set directly. For BOND, ANGLE, DISTANCE and DIHEDRAL it is enough to specify 1 value, while for the TRANSLATION the whole vector is is required and for ROTATION the whole 3x3 matrix. The values can be any moment INITIALIZED - set to starting point, the current OBJECT definition can be accepted (SET TRUE) (the coordinates are accordingly changed) or rejected (SET FALSE). Either rejection or confirmation of the current OBJECT'S status, eliminates the OBJECT'S definition and the KEY connected to it.