Picking

    This menu specifies what action should be taken when the user picks an object. To pick an object, place cursor on it, and click the left mouse button. The middle mouse button may also be used to pick, but it will only pick surface vertices. Vertices can not picked by the left button.   If spock is currently displaying unrealized symmetry-related molecules (§ 6.7.11), then picking any object will also identify which symmetry replicate that object is in. Replicate 0 is the original molecule; others are numbered sequentially. Since the symmetry replicates are not realized, most picking operations actually refer to the corresponding objects in the original molecule. For example, helix-sheet distance picking will return the distance between the helices or sheets in the original molecule, not the distance of the replicates in the unit cell. However, since it's a common operation to look for close contacts between molecules in the lattice, the Atom distance picking command is programmed to apply the symmetry transformation to the atoms picked, and will return the distance in the unit cell.  

Identify object

These options provide information about atoms when they are picked.

   
• Identify object Prints out a string identifying the an object when it is picked. Note that for CA traces, each segment is owned by the first CA in the connected pair. The format of the atom information displayed is: residue name (3 chars), icode (1 char), residue number (4 chars), chain name (1 chars), alternate location indicator (1 char), atom name (4 chars). Note that many proteins don't have named chains, alternate location indicators, or insertion code specifiers, and those fields will be filled with spaces. Picking an atom also identifies the symmetry replicate number, if unrealized symmetry is displayed. (See below).    
• Command Prompts for a command to be executed when an atom is picked. This command is limited by the atom number of the picked atom. For example if the command is bc=0, and atom 4 is picked, bc=0,an=0 is sent to the command processor as if it had been typed on the command line. Ignores symmetry.  
• Projected Command This also prompts for a command to be executed when an object is picked, but it uses the ``projection'' mechanism as described in § 5.4.1 to make the command apply to an entire residue. For instance entering the command bc=0, and picking atom 4 sends the command bc=0,(an=4)->r to the command processor. The projection syntax makes the selection apply to all atoms in a residue, so that in this case, all bonds in whichever residue contains atom 4 would be hidden. Ignores symmetry.  
• Distance Calculate the distance between successive picked atoms. If displaying unrealized symmetry-related molecules, and atoms on two different symmetry replicates are picked, the distance is the distance between the atoms with the symmetry applied, not the distance between the atoms in the original molecule.  
• Angle Calculate the angle between three successive picked atoms. Ignores symmetry.  
• Torsion Angle Calculates the torsion angle between four successive picked atoms. Ignores symmetry.

   

Helix/Sheet Information

        These options provide information about helices and sheets when the helix or sheet axis cylinder is selected. See §6.4.8 and 6.4.9 for more information about helices and sheets.

• Helix/Sheet Distance Prints the distance at the closest point of approach of the axes of two successive helices or sheets. Ignores symmetry.
• Helix/Sheet Angle Prints the distance between successively selected helices or sheets. Ignores symmetry.

 

Labels

  These options allow editing and positioning of labels and annotations, § 6.4.11. If ``Move annotation'' is selected, and an annotation is picked, the placement of the annotation on the screen is tied to mouse movement. If ``Edit label/annotation'' is selected and a label or annotation is picked, a prompt is displayed which allows the label or annotation to be edited. If a standard label is picked and edited in this manner, it becomes a custom label.  

Interactions

        These options allow for the dynamic creation, deletion and editing of interactions. See §6.4.12 for more information. In short, for the ``Add interaction'' mode, picking two atoms in succession will create an interaction between them. For ``Delete interaction'', picking an interaction will remove it from the interaction list. Finally, for ``Set interaction style'', picking an interaction will cause it to inherit the current style set in the Alter Interactions menu.  

Modeling

  This option simply indicates that picking is set to one of the modeling functions described in the modeling menu §6.7.