The modeling functions ("MOV_SELE", "RT_CHAIN", "RT_BETWEE", "MOV_ATOM", "MOV_RESI", "TRANSLATE", "MOV_DIST", "MOV_RT_6", "RT_ANGLE") activate OBJECTS for interactive spatial modifications of molecular geometry and assign DIALS to them. After the geometry has been changed using mouse or dials, the change has to be accepted using "OBJ_ACCE" or rejected "OBJ_REJE".
Remember first to pick the atoms and afterwards pick an ITEM. The last picked atoms may be used any number of times.
All these commands can be applied in any combination on various or the same group of atoms. The order in which they are applied does matter - eroneous combinations may result in eroneous results (first defien bodn rotation and the a rigid body bovement of the moving atoms by "MOV_RESI" or "MOV_SELE".
(See also DIAL_SAV and DIAL_RST regarding DIAL set storage end retrivial.)
The "INV_CHIR" and "CONNECT" act instantaneously and do not need any DIAL action or aproval ("OB_ACCEPT").
See also MAIN_MENU:history.html and MAIN_MENU:nice_sel.html.
Does rigid body movement (combines "ROTATION" and "TRANSLATION") of the selected atoms (key "active") using the last PICKED atom as the center of rotation. The simplest way of selecting atoms is using the functions of the menu block nice_sel.html. Shortcut is "x.
Does rigid body movement (ROTATES and TRANSLATES) of the residue disregarding the connectivities of that particular residue. (You don't have to break bonds as in the case of the "ROT_TRAN" command.) The center of rotation is the last picked atom.
ROTATE the molecule of the last PICKED atom. Useful if you do not want to move a molecule but only adjust its orientation.
TRANSLATES the molecule of the last PICKED atom. Useful if you do not want to change orientation of a molecule but only adjust its position
TRANSLATES the last PICKED atom disregarding its connectivities. (You don't have to break bonds as in the case of the TRANSLAT command.)
Does not save the DIAL set automatically.
RT_CHAIN activates rotation of all BONDS between the last 2 PICKED atoms. MAIN is only capable of checking each separate bond rotation. When there are more bonds to be rotated in the chain and one is a part of a ring, an error message will appear. In such case you should hit "OB_REJECT" and pick a different pair of atoms.
The menu item "RT_CHAIN" calls within a loop a variety of command files, one for each rotatable bond. After each 8th bond, the DIAL WRITE sentence is automatically done.
Rotate all atoms, which are part of covalent bond network, between the last two picked atoms. The command was created to enable adjustments of a peptide bond orientation by clicking on two neighboring CA atoms and then activation the function.
Takes the last 3 atoms from the HISTORY list ($3, $2, $1) and modifies angle between them. Atoms on the $2 atom side of the bond ($3 - $2) are rotated about the axis perpendicular to the plane defined by the last three atoms and going through the atom $2.
Moves (translates) the molecule of the last PICKED atom in the direction of the vector connecting the last two PICKED atoms. When the atoms are connected via a covalent bond, then on the atoms on the side $2 (first picked) atom is moved.
Activates 3 BOND and 2 ANGLE rotations and 1 DISTANCE movement. This is an INTERNAL (relative) coordinate way of ROTATION and TRANSLATION (ROT_TRAN) function that is applied in absolute (cartesian) coordinate space. The last 6 PICKED history atoms are required.
This is an internal coordinate alternative to ROT_TRAN function. It also includes 6 degrees of freedom.
Automatically saves the DIAL set.
Interchanges the positions of the two side chains attached to a single atom. In other words: inverts the chirality of the common neighbour of the last 2 PICKED atoms.
Moves the first picked molecule into a reasonable binding geometry against to the second picked molecule and forms a covalent bond between the last two picked atoms. You may wish to rotate about the newly formed bond to improve its' dihedral conformation (see "RT_CHAIN").
OB_START
> OBJECT int SET INIT
OB_REJEC
> OBJECT int SET TRUE
OB_ACCEP
> OBJECT int SET FALSE
These commands affect all activated OBJECTS. The objects are either returned to their initial position ("OB_START"), rejected (OB_REJEC) or accepted ("OB_ACCEP"). Only "OB_ACCEPT" changes atom coordinates. After "OB_REJEC" and "OB_ACCEP" the complete image is redrawn.