Overview of Grab Commands (980216)
The Grab commands allow the user to change a model by moving bits of it around. These commands differ from the Move commands in that they do not use dials (whether real or fake ones) to control the movement of the affected atoms. Instead, the mouse controls all manipulations. The translation that is applied to the atom(s) is also different. In the Grab commands, the mouse pointer is the position to which the affected atoms are moved. In Grab_atom, for example, an atom is identified, the mouse button is kept depressed, and the mouse moved. The identified atom, then follows the moving mouse pointer until the mouse button is released. The rotational component is also controlled by the mouse, when the keyboard Ctrl-key is depressed. Mouse movement with right button and Ctrl-key depressed is then mapped into horizaontal and vertical rotations (as for the viewing transformation). Depressing the middle and right mouse buttons with the Ctrl-key depressed is mapped into a rotation around an axis perpendicualr to the screen.
There is no Grab_zone command, just break a few bonds.
grab_atom <id>
This command allows the user to move an atom around in space. All movement is controlled by the mouse. The atom must be identified, and the left mouse button must be kept down. As the mouse moves, so will the atom. When the mouse is released, the atom stops moving. The same atom or another atom can then be identified and moved around. Activating No, returns the present moving atom to its position when it was last identified. The command can be cleared with the Yes or Clear_flag commands.
To be accurate about the use of the No flag, lets say that there is an atom at point A. It is identified, the mouse left button kept down, and moved so that the atom is moved to point B. The mouse is now released, and lets say that the view is changed (to see what has happened). The same atom is now ID'ed again, and moved to point C. If the No command is now activated, the grabbed atom goes back to point A. Now lets say we move it from, A to C via a mouse release at B. Then we release the mouse and grab a different atom. After a while we come back to our starting atom and grab it again, shifting it to point D. What happens when we say No? It goes back to point C.
grab_group <id>
This command allows the user to move a group of connected atoms around in space as a rigid body. All movement are controlled by the mouse. An atom must be identified, and if the left mouse button is kept down., the group of connected atoms will be translated as the mouse is moved. If the ctrl-key is depressed, then pressing the right button will rotate the fragment. Pressing the middle and right buttons with ctrl-key depressed, rotates the fragment clockwise/anti-clockwise about an axis perpendicualr to the screen. The identified atom is the pivot point for the rotations. When the mouse is released, the group of atoms stops moving. The command stays active so that when another atom in the fragment is identified, this atom becomes the pivot point. Only atoms within the fragment are affected.
Activating No, returns the moving fragment to its position when it was first identified. The command can be cleared with the Yes or Clear_flag commands.
Unlike the grab_atom command, if an atom not in the moving group is identified, a new moving group is not defined.
Fragments can be created by changing the connectivity with the Bond_break or Bond_make commands, or by making suitable objects. The new bonds do not have to make chemical sense but just used to create a suiyble group of connected atoms
This action is clearly different from the move_zone or move_fragment commands. For example, if a fragement corresponding to a portion of Ca is grab_goup'ed, the rest of the atoms in the zone are not affected.
grab_resikdue <id>
This command allows the user to move atoms in one residue around in space as a rigid body. All movement are controlled by the mouse. An atom must be identified, and if the left mouse button is kept down., the group of connected atoms will be translated as the mouse is moved. If the ctrl-key is depressed, then pressing the right button will rotate the fragment. Pressing the middle and right buttons with ctrl-key depressed, rotates the fragment clockwise/anti-clockwise about an axis perpendicualr to the screen. The identified atom is the pivot point for the rotations. When the mouse is released, the group of atoms stops moving. The command stays active so that when another atom in the residue is identified, this atom becomes the pivot point. Only atoms within the residue are affected.
Activating No, returns the moving residue to its position when it was first identified. The command can be cleared with the Yes or Clear_flag commands.
Unlike the grab_atom command, if an atom not in the moving resdiue is identified, a new moving resdiue is not defined.
grab_fragment <id>
This command allows the user to move a fragment of connected atoms around in space as a rigid body. The atoms making up the fragment are defined in a database entry for that particular residue type. For example, atoms within a PHE residue are defined
.RSR_dict_phe T 2 70
CA C O N+
CB CG CD1 CD2 CE1 CE2 CZ
and define 2 fragments. Identifying any atom in the phenol ring would allow one to move the whole ring. Likewise identifying the CA atom would allow one to grab the atoms defing the peptide plane.
All movement are controlled by the mouse. An atom must be identified, and if the left mouse button is kept down., the fragment of connected atoms will be translated as the mouse is moved. If the ctrl-key is depressed, then pressing the right button will rotate the fragment. Pressing the middle and right buttons with ctrl-key depressed, rotates the fragment clockwise/anti-clockwise about an axis perpendicualr to the screen. The identified atom is the pivot point for the rotations. When the mouse is released, the group of atoms stops moving. The command stays active so that when another atom is identified it is used to define a new fragment. This atom becomes the pivot point. Only atoms within the fragment are affected.
Activating No, returns the moving fragment to its position when it was first identified. The command can be cleared with the Yes or Clear_flag commands.
Like the grab_atom command, if another atom is identified, a new moving fragment of atoms is defined.
Fragments can be created by changing the connectivity with the Bond_break or Bond_make commands, or by making suitable objects. The new bonds do not have to make chemical sense but just used to create a suiyble group of connected atoms
This action is clearly different from the move_zone or move_fragment commands. For example, if a fragement corresponding to a portion of Ca is grab_goup'ed, the rest of the atoms in the zone are not affected.