Stereographic (3D):

Atom Colors

Cations:

Na

Mg

Ca

Co

Zn

Cd

Cs

Anions:

O

F

Cl

S

Br

Note: the atom colors are:
B	C	N	O	F	S	Br	I	P	Te	Xe	H

Load Structure You can load any single molecule in the lists.
The ESP surfaces show the charge distribution in the molecule. The surface corresponds to the 95% electron density surface (the electrons are found with in this surface 95% of the time). Red indicates areas of high electron denisty and blue low areas.

Organic:
Inorganic:
Biological:
Animations:
ESP Surfaces:

Molecular Display This allows you to change the visual display of the moleucle.
Spacefilling: changes the radius of the atoms
Ball & Stick: atomic spheres connected by tubes
Tube: bonds are tubes
Wireframe: thin lines connect atoms
Proteins: backbone trace, 2° structures as ribbons or rockets highlight water or ligands in proteins
3D: display using anaglyphic glasses (colored) or crossed-eyed
Axes: display the cartesian coordinate system.
VDW: displays the Van der Waals surface for a molecule. Note this will be VERY time consuming for large moleucles.
Point Group: displays the symmetry elements and Point Group of the molecule.

Atomic Size:
Schemes:
Proteins:
Highlight:
Stereographic (3D):
Axis:
VDW:
Point Group:
MEP
PAC

Measure Measure a distance, angle or torsion angle by clicking on 2, 3 or 4 atoms respectively.
Distance is in Angstrom, angles in degrees.

    

Spin, Translate & Zoom Rotate about the cartesian X, Y or Z axis, or pick any two atoms to define a rotating axis, Translate the molecule in the X - Y plane, or Zoom in or out

Spin about an Axis		Translate				Zoom

Center & Label Center the display on a selected atom. Unchecking the box recenters the molecule. Label atoms by atom type.

   

Molecular Dipole & Hydrogen Bonding Display the molecular dipole moment or hydrogen bonds.

   

Load Structure Bravais Lattices: are used to show some of the different lattice types in a larger structure.
Other Compounds: are crystal structures of interest.

Bravais Lattices:		Other Compounds:

Spacefill Spacefill: adjusts the size of the ions as a percentage of the van der Waals radii.
(Note: the ionic radii is a more accurate representation of the size of ions).

Measure Measure: will allow you to measure bond distance, angle or torsion angles by clicking on 2, 3 or 4 atoms respectively.
Clear will remove all measurements.

   

Single Unit Cell Single Unit Cell: when a structure is loaded by choosing one of the compounds from the "Load Structures" lists only the unique atoms in the unit cell are displayed.
To display all atoms in a single unit cell use the "All Atoms" button.

       

Multiple Unit Cells Multiple Unit Cells: are used to display larger representations of the crystal structure.

Rotate Rotate about the X, Y Z axes or pick a pair of atoms to define your own axis of rotation.

Center Center the structure with the specified atom in the center.

Miller Indices Miller Indices: display some of the Miller Indices (planes of atoms) of the unit cell.

Extras Extras:
Unit Cell Parameters turns on/off the unit cell parameters displayed in the upper left corner of the Jmol.Jmol applet.
Polyhedra turns on/off a polyhedra showing the coordination of the ions in the structure.
Connect Atoms turns on/off bonding between atoms in the crystal structure.
Boundary Box turns on/off a box around the entire group of unit cells displayed.
Unit Cell turns on/off the box and axes for the unit cell.

Load Geometric Structures See the common 3D geometric structures

Load Example Molecules See Examples of VSEPR 3D structures

Linear

Trigonal Planar

Tetrahedral

Trigonal Bypyramidal

Trigonal Bypyramidal

Pentagonal Bypyramidal

Extras Extras:
Spin: rotate about the Y axis
Display Lone Pair Electrons
Measure: bond lenghts or bond angles by clicking on two or three atoms
View the structure in 3D

Measure:

Stereographic (3D):  

Load Structure You can load any single molecule in the lists. The Klotho data base contains over 400 biologically based chemicals. They have been subdivided into main groups for easier access.
source: www.biocheminfo.org
Note: Amines are not generally depicted correctly in this database. A trivalent nitrogen atom adjacent to an sp² center will generally become sp² itself.

Molecular Display This allows you to change the visual display of the moleucle.
Spacefilling: changes the radius of the atoms
Ball & Stick: atomic spheres connected by tubes
Tube: bonds are tubes
Wireframe: thin lines connect atoms
Proteins: backbone trace, 2° structures as ribbons or rockets highlight water or ligands in proteins
3D: display using anaglyphic glasses (colored) or crossed-eyed
Axes: display the cartesian coordinate system.
VDW: displays the Van der Waals surface for a molecule. Note this will be VERY time consuming for large moleucles.
Point Group: displays the symmetry elements and Point Group of the molecule.

Atomic Size:
Schemes:
Proteins:
Highlight:
Stereographic (3D):
Axis:
VDW:
Point Group:

Measure Measure a distance, angle or torsion angle by clicking on 2, 3 or 4 atoms respectively.
Distance is in Angstrom, angles in degrees.

    

Spin, Translate & Zoom Rotate about the cartesian X, Y or Z axis, or pick any two atoms to define a rotating axis, Translate the molecule in the X - Y plane, or Zoom in or out

Spin about an Axis		Translate				Zoom

Center & Label Center the display on a selected atom. Unchecking the box recenters the molecule. Label atoms by atom type.