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.
options provide information about atoms when they are picked.
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.
- 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
- 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
- Angle Calculate the angle between three successive
picked atoms. Ignores symmetry.
- Torsion Angle Calculates the torsion angle between four
successive picked atoms. Ignores symmetry.
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.
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.
This option simply indicates that picking is set to one of the modeling
functions described in the modeling menu §6.7.
- 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.
Tue Sep 14 16:44:48 CDT 1999