Introduction to molecular visualization: Difference between revisions

Atomic representations (displays, renderings) 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]].

Methods for searching the [[Protein Data Bank]] for published empirical 3D models are [[Practical_Guide_to_Homology_Modeling#Do_you_need_a_homology_model.3F|explained here]]. ''Empirical models'' are those determined by experimentation, notably [[X-ray diffraction]], [[solution nuclear magnetic resonance]], or cryo-electron microscopy. Empirical models are far more reliable than [[theoretical models]], but one must pay attention to the [[Quality assessment for molecular models|quality of an empirical model]] since some are more reliable than others.

Empirical models are available for only a small fraction of all proteins, probably <10%. If an empirical model is not available, the next best thing would be a [[homology model]]. About one third of all proteins can be reliably homology modeled, but homology models have [[Practical_Guide_to_Homology_Modeling#Limitations_of_Homology_Modeling|more uncertainties]] than do empirical models.