Introduction to molecular visualization: Difference between revisions

 

 

 

Atomic representations include '''ball-and-stick, stick (wireframe), and spacefilling'''. The 20 amino acids are [http://biomodel.uah.es/en/model3/aa.htm here represented in each of these 3 ways], and also illustrated in this [[Glycine|page about Glycine]]. These representations show positions of atoms and covalent bonds. Such representations are useful for looking at atomic detail, but become too cluttered to be useful for visualizing [[peptides]] or [[chains|protein chains]].

Simplified representations such as '''[[Backbone_representations|backbone traces or ribbons/cartoons]]''' are very helpful in understanding structure when it comes to large molecules such as proteins, DNA, RNA and their complexes. These representations are available under the ''representations'' tab in Proteopedia's [[Scene Authoring Tools]], as well as in the ''Views'' tab in [[FirstGlance in Jmol]].

A set of standard color schemes for macromolecules, called [[DRuMS]], was released in 2000. These color schemes are offered on buttons in Proteopedia's [[Scene Authoring Tools]]. They derive in part from physical ball and stick models (called [[CPK|Corey-Pauling-Kolton or CPK]] models) that [[History of Macromolecular Visualization|pre-dated computer visualization]]. Those early colors for chemical elements were incorporated into early [[Molecular modeling and visualization software|Molecular Visualization Software]] such as [[Kinemages%2C_Mage_and_KiNG|Kinemages]], [[RasMol]], and [[Chime]]. The [[CPK]] colors for chemical elements, and the [[DRuMS]] color schemes were incorporated into the [http://jmol.sourceforge.net/jscolors/ color schemes] built into [[Jmol]], the visualization engine used in Proteopedia.