Modifying Angles
Bond angles and dihedral angles are modified with Angle and Dihedral SmartSlides.
The Angle and Dihedral SmartSlides
Once you have modified a parameter using the SmartSlide, the button must be pressed before any of the changes made on any SmartSlide are actually applied to the molecule. Clicking the close box will discard any changes; it is equivalent to selecting the button.
The figure following illustrates some of the combinations of various
settings for bond angles (they work in the same way for dihedral angles). The possible choices for each popup menu are:
![]() Original Molecule |
![]() 1,2=Fixed, 3=Rotate Atom |
![]() 1,2=Fixed, 3=Rotate Group |
![]() 1,2=Fixed, 3=Translate Group |
![]() 1,3=Rotate Atom, 2=Fixed |
![]() 1,3=Rotate Group, 2=Fixed |
![]() 1,3=Translate Group, 2=Fixed |
Bond Angle Modification Options
All six of these structures result from increasing the 1-2-3 bond angle. In the top row, atoms 1 and 2 are both held fixed. Compare the results of increasing the bond angle to the same value in the three cases (keeping in mind the “normal” position for the ring atoms and the methyl groups). The movement of the methyl group attached to atom 3 ranges from substantial in the first frame to a little in frame 2 to almost none in frame 3. In the second row, atom 2 is held fixed while other choices are used for atoms 1 and 3. Comparison of these illustrations as well as experimentation will make the differences between the choices clear and familiar.
The Dihedral SmartSlide dialog allows you to reposition the molecule using a Newman projection along the 2,3 internuclear axis or the 3,2 internuclear axis.
popup menu in the lower left corner of the
Viewing a Dihedral along the 2,3 Internuclear Axis
You may choose to reposition the molecule so
that the 1,2 or 3,4 axis is vertical.