Viewing Small Organic Molecule

(Download urea.pdb)

The following skill will be taught here:

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Once you open up a ".pdf" file, e.g. a urea molecule, it will look like this:

¡@(Download human amylase.pdb)

You can change the appearance of the molecule by clicking the 'Display' menu from the toolbar. The default display mode is 'wireframe'. You can also choose the following display: 

Display

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Wireframe(default) Only bond between atoms are shown
Backbone

Representation of a polypeptide backbone as a series of bonds connecting the adjacent carbons of each amino acid in a chain
Sticks Atoms are represented by thick lines
Spacefill Atoms are represented by spheres with size dependent on their atom type
Ball & Stick Atoms are represented by spheres and bonds are represented by thicker lines
Ribbons  Structures are represented by a smooth solid "ribbon" surface passing along the backbone
Strands Structures are represented by parallel strands of depth-cued curves passing along the backbone 
Cartoons Display of the cartoon version of the 'ribbons' display

(Examples can be seen by clicking the name of the display in the above table.)

There is an assigned colour for each atom. In the default colour setting, hydrogen atoms are white, nitrogen atoms are blue and oxygen atoms are red. Other colours of the atoms can be found in the following periodic table:

By using the mouse, you can do the following: