Summary of Scigress commands

Practical 1

Task Scigress command Shortcut Comments/notes

Change- use bar at top
of window
Draw  Atom type
atoms  Bond type
 Hybridisation
 Charge
Arrow = Select Atom

Arrow + ring = Select

Select Molecule
atoms
Arrow + 3 atoms =
select Group

Allows you to:

-delete hydrogens
-check valence and
hybridisation
 Valence
- adds
hydrogen to
fill bonds
 Rings
- gives ring
Beautify Action | Beautify | Comprehensive Ctrl B
structures
accurate
shapes
 Geometry
- adjust the
position of
the selected
atom to
match their
hybridizatio
n

1
 Rotate: Click and drag
to rotate the molecule

Translate: appears as a
hand. Click and drag
the mouse to move the
molecule around.

Translate Zoom: magnifying

, Rotate, glass. Click and drag
and the magnifying glass up
Zoom or down to zoom in or
out.

Ctrl + f
-Re positions the
structure
-centers the structure
and scale the molecule
to fit the window.

View | Styles | Atoms The options in the atom

attribute box allow you
to change the way
atoms and bonds are
Change displayed.
the way
atoms
and
bonds are
displayed

Modifyin Clean up the valence,

g Action | Beautify | Comprehensive hybridisation, rings and
structure geometry for the
s selected objects.
Measure 1. Click on an atom and hold down ctrl Record the distance and
the Bond key while you click on another atom click cancel.
Lengths 2. Select Action | Geometry Labels |
and Atom Distance... Bond angle between the
Angles 3. Choose Action | Geometry Labels | atoms in degrees.
Bond Angle...

Fragment Window | show explorers | library Collection of

2
 window compounds, ions,
functional groups…
which can be used
when building
molecules.

library

1. Open the molecule A calculation window

Optimize 2. Select Experiment | run appears, information
a 3. Choose category... about the progress of
molecule 4. Choose property... the optimization scrolls
5. Choose procedure... in the window.
6. Click start
1. Click in the molecule window to Using the calculations,
Generate
activate it we can create pictures
MOs and
2. Select of the molecule
Other
Analyse | Electronic structure | surfaces and individual
Surfaces
HOMO & LUMO MO’s.

Energy 1. Shift click on all atoms

maps 2. Select Action | Geometry
Labels | Dihedral Angle
3. Click Define Geometry Label
and Search between -180 and
+180 using 24 steps.
4. Click ok. A search label
reading appears on the
molecule.
-now we can calculate the energy for each of
the angles specified by the label.
5. Select Experiment | Run
6. Select category:
conformations
7. Property: potential energy
map
8. Procedure: standard
procedure
9. Click Start

3
4