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Tutorial 02 -- Editing Structures


If nicotine is not already present on screen from the previous tutorial, please click File | Open (or click the Speed Button) and load it from the Data folder before continuing. 

1  Make sure you are in 'Draw' mode and right-click to display the Popup menu and click on the 'Select' option.  Select can also be accessed from the Edit menu, or by pressing the accelerator key (hot key) F2.  When Select is activated,  the cursor changes form to a crosshair.

2  Move the mouse pointer to a position above and to the left of the nicotine structure.  Press and hold the left mouse button and, while continuing to hold the button, move the mouse down and to the right.   As the mouse is moved, a 'box' will appear on screen which is continuously updated as the mouse moves.  Use the mouse to draw a box surrounding just the pyridine ring and release the button.  Each of the (non-hydrogen) atoms in the enclosed pyridine structure will be drawn with a superimposed red dot to indicate that they have been 'selected'.

3  Move the mouse pointer to a location inside the box (the exact location is not important), press and hold the left mouse button, and drag the box upward about 2 cm.  As the mouse is moved up, the box outline will track it on screen.  When the button is released, the selected atoms will all be moved as indicated by the current location of the selection box.

This is one of the functions of Select.  You can select one or several atoms of a structure to be moved relative to the remainder of the structure.  You can also outline the entire molecule to move it, but that is more easily done by clicking on the Move Structure button (it has the appearance of 4 dots on it) which will select the molecule in one step.  Substructure movements can be used to adjust the relative position of substituents.

      MSC Pro default structures do not use normal ring bond angles by default; they are deliberately drawn to facilitate fragmenting on screen.  However, you can at any time convert them into more "normal" structures with standard bond lengths and angles by clicking Edit | Clean.  If you try that now a more typical nicotine structure will be drawn.  However, for optimum performance in the main drawing and fragmentation routines, it is best to use only the default ring structures which will automatically 'fit together' properly when merged on screen.  If you have used Clean, click on Undo to revert to the default  structure.

4  Another function of Select is to delete subregions of a molecule.  Press F2 to activate Select again.  Draw a box around the top two ring carbons of the pyrrolidine ring; they will be highlighted as before to indicate that they have been selected.  Now press the <Del> key on the keyboard.  The selected atoms, their valence H, and any associated bonds will be removed, and the remainder of the molecule will reorganize itself as necessary.  You can click on  'Show Atoms'  to confirm the proper valences of each atom.

Try repeating this operation by selecting one of the carbons of the pyridine ring.  In this case, when one of the ring atoms is deleted, the aromatic ring is destroyed and the remaining atoms are revised as (saturated) acyclic atoms.  To abort any of the editing modes press the Escape key.

5  Select works on atoms (and their associated bonds).  To remove only a bond, or to reduce it one level, click on 'Reduce Bonds' on the Edit menu  or Press F10.   Each nonaromatic bond in the molecule will be drawn with a marker dot.  Click on one of the bonds in the structure; it will be removed and its associated atoms will each have their valence H adjusted.  If the bond order is greater than 1, then it will be reduced by 1 (e.g. double to single bond, etc.)  Note: 'Bonds' works only on nonaromatic bonds

6  MSC normally maintains the proper valence of a structure by default.  However, this can be overridden if desired by using the Valence option.  To incorporate atoms at other than their default valence state (e.g. S in sulfonic acids or P in phosphate), you would use the Valence option.  Click on 'Valence/Add' on the Edit menu, or press F4.  The mouse pointer will change shape to a '+H' symbol.  Move the pointer over an atom and press the left mouse button.  The number of hydrogens on that atom will be incremented by one.  Press the left mouse button twice more and two more H will be added.  You can continue to add H to this or other atoms as desired in this way.

7    To decrement H, click on Valence | Subtract (or press F5)  The cursor will then appear as '-H' and clicking on an atom will decrement the H by 1.  If there are no H remaining on the atom, then this operation will have no effect.  If you are working with ring carbons, you will probably want to turn on Show to view the effect of adding or removing H from the atom.  To quit Valence  mode, either click on the Valence menu selection  again to turn it off, or press the <Esc> key.

8  You can completely remove a structure from the screen by using the New function.  Select 'New' (the first option on the main File menu) to remove the remainder of this structure from the screen.

Goto Tutorial #3

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