Picking and Additional Mouse Functionalities
Basics
How to pick:
- Picking is done by either LEFT-hand or
MIDDLE mouse button clicks. In addition,
the Ctrl-key has to be held pressed down,
because otherwise the mouse only causes changes of the view.
- The ALT key may be pressed down in addition
to enable exclusive active-entry picking.
Several types of objects can be picked:
- Atoms (or vertices of objects stored as entries, e.g. hierarchical trees)
- Bonds (or edges)
- Surface dots
- Surface edges (net representation)
When is picking enabled?
- By default only atoms can be picked to toggle
label display on and off.
- If a menu item requires picking, choosing it results in
highlighting the item letter.
- With a highlighted menu item, picking addresses the corresponding
menu context, i.e. label toggling is turned off.
- The menu context may require picking an atom, or a bond, or either.
If a whole entry needs to be specified, it can be picked on any atom
or bond.
- Some menu items may require picking surface objects (vertices, edges).
Additional Mouse Functionality
In an appropriate context, to:
- change the position of an atom, of a set of atoms or of a whole entry
- modify the value of torsion angles
- etc.
is achieved by operating the mouse with either SHIFT
keys pressed down.
This is illustrated by the following
Exercise in Forging (Changing Atomic Coordinates)
- Start Moloc with our project
by typing the command: mx my_project.ils
- Enter the display menu '...'
to make mtx the only visible entry 'a'
and center it 'z'.
- Exit from 'display' and enter the forge menu frg
- Move a single atom:
- Click menu item 'a' (move single atom); the letter
'a' becomes highlighted to indicate that
atom picking is now required.
- Pick any atom of 'mtx'. The corresponding atom label will appear.
- Press SHIFT, the MIDDLE mouse
button and move the mouse. The atom will move in the screen plane,
while the rest of the molecule stays in place.
- To move the atom in z-direction, also press the
LEFT-hand mouse button.
All reactions to mouse movments are analogous
to adjusting the view.
- Perform bond rotation:
- Click 't'
- Pick a rotatable bond (if the bond is within a ring the program
will issue the message 'NOT a cut-bond!')
- Press SHIFT, the LEFT-hand mouse
button and move the mouse sideways: The smaller end of the bond will
rotate.
- The MIDDLE mouse button causes the larger end to rotate.
- To reset to the original orientation press LEFT-hand
and MIDDLE mouse button.
- Define a SET of atom:
For that purpose you have to specify the set of atoms first.
Option 's' throws you into the 'set' menu.
The menu header reads 'u0: forge' to indicate
that you are about to define user set 0 calling from the forge menu.
- To specify the GLU substituent of benzene as our set choose
's' (substituents).
- Pick the benzene atom first, then the adjacent atom of the substituent
The atoms of GLU will now be marked by small rings as belonging to the set.
- To remove the peptide group from the set choose 'a'
and pick the three atoms C, O, N with the middle mouse button.
This will cause the corresponding rings to disappear.
- Other options of this general menu will be treated in an
appropriate context.
- Exit from the set menu.
The rings disappear, but the set is now known in 'frg' and will
only be removed upon leaving the 'frg' menu.
- Move the SET of atom:
- Choose 'm' (move set) which will be highlighted
to indicate that the SHIFT key has to be pressed to
switch the mouse action from adjusting the view to moving the set.
- Move the set around as you please: LEFT = rotate x, y;
MIDDLE = translate x, y; LEFT and MIDDLE = translate/rotate z.
- Option 'd' (drag set) in addition moves
atoms adjacent to the set by distance-dependent reduced amounts.