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Drawing Overview


To draw a molecule, first select 'Draw' if it isn't already active by selecting the 'Draw' button at the lower left corner of the Toolbox, and then select a palette structure such as the benzene ring.  Move the cursor into the drawing region and click the mouse button to draw the structure.  If the item you are adding is a ring, you can press and hold the button while moving the cursor and an outline of the ring will follow the cursor movement.  When the button is released, the ring will be drawn at its current location (or moved as necessary to merge with its closest atomic neighbors - see below).  As the structure is created, the current molecular weight and elemental composition are continuously updated in the two boxes at the bottom of the screen.

* IMPORTANT *   The default is for each successive structure or atom to merge with its nearest atomic neighbors.  For example, when you move a ring near the current structure and release the mouse button the new ring will move and merge with the neighboring structure.  If a merge would cause a valence violation then the program will not add the ring and a 'Valence Violation' error message will display briefly in the lower left portion of the main window.  If you want to add a separate structure that is not connected to the current molecule, then hold down the <shift> key while releasing the mouse button.  That will lock the new structure in its current position without merging.  Valence restrictions also can be overridden if needed.  See Valence   
   
Separate structures can be linked by drawing a bond between them.  If the termination point of the bond is in close proximity (about 2-3 mm) to another atom, the bond will be attached to that atom.  If the valence would be exceeded, MSC will abort the addition.  However, if the termination point of a bond is not in close proximity to another atom, then a new methyl group will be added.  You can add new structures such as a methyl or amino group to a current atom by just clicking on the atom.  The new atom(s) and bond will be drawn automatically.  If the positioning is not what you want, then click the Undo arrow and add the group again by drawing the bond to the position that you want before releasing the mouse button.  Note that it is sometimes quicker to undo the last step by right clicking and choosing Undo from the Popup menu.  However, the toolbar buttons can always be used as well.

To replace one atom with another, select the element to add then click on the atom in the structure that you want to replace.   To make changes to the molecule you can use the Undo and Redo buttons as needed.  The Select function (F2 or right-click for the popup menu) will let you make more extensive changes such as move the entire molecule or a group of atoms, or delete one or more atoms in the structure.