Subsets

  Spock allows the user to define subsets of atoms and surfaces and give those subsets names. Those subsets can later be referenced by the given name. The command subdef= discussed in § 5.2.7 may be used to create a subset, and the selection string sub=NAME (§5.3.2) may be used to select a subset. For vertex subsets, the corresponding commands are vsubdef and vsub=. Note that in spock, atom and vertex subsets are entirely separate, and do not share the same name space. You may define an atom and a vertex subset with the same name, but the vertex subset will refer only to vertices and the atom subset will refer only to atoms. Subset definitions are static, in that once defined, a subset remains constant, even if the values on which the defining expression depend change.

The subset menu expands on the subset commands and provides a more convenient user interface for subsetting commands. Up to 28 user-defined atom subsets may be active at one time. (The upper limit is because subsets are stored internally as one bit of a 32-bit integer array, and bits 0 through 3 are reserved for internal use.) Up to 26 surface subsets may be defined. (Bits 0 through 5 are reserved.) An individual atom or vertex may belong to any number of subsets. Subsets may also be referred to by number in a selection string (e.g. bc=0,sub=1). Subsets are numbered sequentially starting with 1. Again, atom and vertex subsets are separate, so there is a atom subset numbered 1 and a distinct vertex subset numbered 1 if they have been created. If you delete a subset, all following subsets are renumbered so that there are no gaps in the numbering sequence.         It is also possible to graphically define vertex (surface) subsets via the ``Surface selection'' commands of the ``Graphics Mouse bindings'' menu, as described in §6.11.3. There are two names that are reserved for graphically defined vertex subsets, vsub=MARKED and vsub=FILLED. These names should not be used for any other user-defined surface subsets.

The menu options to control subsets are similar for atoms and surfaces, and are described in general terms below:

• Define Define a new subset. Prompts for a subset name and a selection string (§5.3) of atoms to be included in the subset. As a safety feature, you can not re-define a subset from this option.
• Redefine Replace the definition of a subset with a new selection string. Spock will prompt for the old subset and a new selection string to use for that subset name.
• Broaden Add some new atoms into a subset. Spock prompts for a new selection string and a subset name. The selected atoms are added to the definition of the subset.
• Narrow Restrict a subset by a new selection string. Only atoms in both the original subset and the new selection string are included in the new subset.
• Delete Remove a subset from memory.
• Set subset origin This sub-menu allows the user to set the origin of rotation for a particular subset. ``To atom selection'' prompts for a selection string of atoms. The center-of-mass of these atoms is then used for the subset's origin of rotation. ``To center of subset'' sets the subset's center of rotation to its center of mass. ``To coordinates'' prompts for the x,y,z coordinates of the point to be used as the subset's center of rotation, and ``To world center'' sets the subset's center of rotation to be the center of mass of all defined atoms.        
• Attach motion This submenu specifies to which group of objects mouse movement or dial changes (§6.11.5) should be attached. ``World'', the default, means movement should apply to all objects. Other standard options are ``TOR'', and ``FBRT'' described in §6.7.13. Finally, all currently defined atom subsets are listed. If a subset, TOR or FBRT is selected, motion is restricted to that subset (or rotation about the TOR bond/FBRT atom). Note that the internal coordinates of a subset are updated as a subset is rotated, not just the viewing projection, so that if you perform a subset rotation and then save a PDB file, or list the coordinates, they will be changed from the original coordinates. Subset rotations may be ``undone'' by choosing the ``Undo subset rotation'' option. Note that for efficiency, not all objects are re-built updated with every redraw. Bonds and circle de atoms will always reflect the current coordinates, however. To update the other objects, toggle them off and on again in the Display menu. Note that pressing and holding shift, alt, or control before any mouse buttons, will temporarily re-attach the mouse to the world view, making it easier to switch back and forth between manipulating a subset and the global view.
• Lock subset rotation This option makes resets the subset undo matrix to the identity matrix, making the subset rotation permanent. Subsequent invocations of ``Undo subset rotation'' will revert to this point.  
• Undo subset rotation This option removes the all rotations applied to a subset, since the last time the rotations were locked. Performing rotations on overlapping subsets (subsets which share atoms with other subsets) is allowed, but undo cannot be fully supported in this case. For an atom which is shared between subsets, if more than one subset which contains that atom has been rotated without an intervening call to undo, undo will have unpredictable results.
• Update bonds only/Update all objects These options control which objects are updated when motion is attached to a subset. The default is for only the bonds to be updated, which reasonably fast. However, users can choose that all objects be updated when moving subsets, which can be slow depending on which objects are currently turned on in the Display menu. Note that surfaces can only be rebuilt manually.