Introduction to molecular visualization: Difference between revisions
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''Molecular visualization'' means looking at molecular models in order to explore and understand them. Molecular visualization does not necessarily involve ''molecular modeling'', which means creating molecular models, or changing the composition or configurations of existing models. Here we will be dealing primarily with models of macromolecules (protein, DNA, RNA, or their complexes). | ''Molecular visualization'' means looking at molecular models in order to explore and understand them. Molecular visualization does not necessarily involve ''molecular modeling'', which means creating molecular models, or changing the composition or configurations of existing models. Here we will be dealing primarily with models of macromolecules (protein, DNA, RNA, or their complexes). | ||
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==Representations of Molecular Models== | ==Representations of Molecular Models== | ||
Molecular models can be represented (displayed, rendered) in various ways. | Molecular models can be represented (displayed, rendered) in various ways. | ||
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*Distances between any two atoms, and angles or dihedral angles defined by 3 or 4 atoms, using ''Distances/Angles'' in the ''Tools'' tab. | *Distances between any two atoms, and angles or dihedral angles defined by 3 or 4 atoms, using ''Distances/Angles'' in the ''Tools'' tab. | ||
*[[Crystal contacts]]. | *[[Crystal contacts]]. | ||
==Obtaining Molecular Models== | |||
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. | |||
==See Also== | ==See Also== | ||