Pick Item Mode Submenu

   

The mouse can also be used to select things from the screen. As with many molecular graphics programs, an  atom can be picked by moving the cursor over it and clicking the left mouse button. When an atom is picked for the first time, a text label appears which shows the atom residue name and number, and the atom name. Clicking on the atom again turns the label off.

          Picking atoms with the mouse is used to turn on or off various types of labels, to query for information about an object, or to move items around on the screen. You can label an atom (and display the atom name), or you can label geometric values such as the distance between two atoms (a bond label), an angle between three atoms (an angle label), or the dihedral angle formed by four atoms (a dihedral label). This is done by setting the mouse into the proper picking mode and then selecting the relevant atoms with the mouse.

You first select the proper picking mode by using the popup menu, and choosing the mode required to perform the desired action. The available actions when in pick item mode are:

• Pick Item Mode Query 
  Clicking with the left or middle mouse button on an item will print out the name of the item (e.g. the atom name) to the text console window. The hot key to set this mode is `0'.
• Pick Item Mode Center 
  This mode is used to change the point about which a molecule rotates when the molecule is rotated. To cause a molecule to rotate about a specific atom, select this mode and then click on that atom. The rotation point may be restored to its default position (the center of volume of the molecule) by executing the `Reset View' option from the popup menu (see below). The hot key to set the mouse to Pick Item Mode Centering mode is `c'.
• Pick Item Mode Atom 
  Clicking on an atom will toggle on/off a label for the atom. The hot key to set this mode is `1'.
• Pick Item Mode Bond 
  Clicking on two atoms in a row will toggle on/off a bond distance label between the two atoms (a dotted line with the distance printed at the midpoint). The hot key to set this mode is `2'.
• Pick Item Mode Angle 
  Clicking on three atoms in a row will toggle on/off a label showing the angle formed by the three atoms. The hot key to set this mode is `3'.
• Pick Item Mode Dihedral 
  Clicking on four atoms in a row toggles on/off a label showing the dihedral angle formed by the four atoms. The hot key to set this mode is `4'.
• Pick Item Mode MoveAtom 
  In this mode, the position of an atom can be changed by clicking on the desired atom, and dragging with the mouse while the button is still pressed. This will change the atom coordinates. The hot key to set this mode is `5'.
• Pick Item Mode MoveResidue 
  This mode may be used to move all the atoms in a selected residue at the same time. Select an atom in a residue, and move it to a new position while keeping the mouse button pressed. All the atoms in the same residue as the selected one will be moved the same amount. This will change the atome coordinates. The hot key to set this mode is `6'.
• Pick Item Mode MoveFragment 
  A fragment is a set of atoms all connected by a series of covalent bonds. This mode acts just like MoveResidue, except that the atoms which are moved are all in the selected fragment rather than in the selected residue. This will change the atom coordinates. The hot key to set this mode is `7'.
• Pick Item Mode MoveMolecule 
  This mode may be used to move all the atoms in a selected molecule at the same time. Select an atom in a molecule, and move it to a new position while keeping the mouse button pressed. All the atoms in the same molecule as the selected one will be moved the same amount. This will change the atom coordinates. The hot key to set this mode is `8'.

When a label is added to a molecule (say, for a bond, or just to show the name of an atom), a new entry will be added to the list of current labels which is available via the Labels form, or from the Labels popup menu commands. These controls also contain options to turn the labels on or off, or to delete them entirely from memory.  

  Since atom and bond picking is a very common action, these two types of labels can be added without having to set the mouse to a picking mode. To just add an atom label, click on and release the left mouse button while pointing to an atom, without moving the mouse during the click and release. To add a bond label, click on and release the middle mouse button on first one, and then the other, of the two atoms involved. Again, make sure not to move the mouse while the button is pressed down.