View source for Introduction to molecular visualization

''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).

==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.

==Representations of Molecular Models==
Molecular models can be represented (displayed, rendered) in various ways.

===Atomic Representations===
Atomic representations are illustrated in the [[Glycine|page about Glycine]]. These 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]].

''Ball and stick'' is one option in the ''representations'' tab of Proteopedia's [[Scene Authoring Tools]]. Another is ''stick'', also called ''wireframe''.

In [[FirstGlance in Jmol]], you can isolate a small portion of a large structure, and then display it as sticks (''Vines/Sticks'' in the ''Views'' tab). Or, rather than isolating it, which hides everything else, you can center it and then turn on slabbing.

===Slabbing===
A useful way to see atomic details of a small part of a large macromolecular model is to center the moiety of interest, and then cut away the front and back portions of the molecule. This is called ''slabbing'' since one is, in effect, looking at a slab cut out of the larger model. Slabbing can be done using [[FirstGlance in Jmol]]: In the ''Views'' tab, use ''Center Atom'' to center the region of interest, and then click the ''Slab'' button. Further instructions will appear automatically.

===Simplified Schematic Representations===
For large molecules such as proteins, DNA, RNA and their complexes, simplified representations such as [[Backbone_representations|backbone traces or ribbons/cartoons]] are very helpful in understanding structure. 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]].

==Color Schemes for Macromolecules==
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 schems were incorporated into the [http://jmol.sourceforge.net/jscolors/ color schemes] built into [[Jmol]], the visualization engine used in Proteopedia.

==Visualizing Structural Features==
===Overall Features===
Combinations of representations and color schemes are useful to highlight
# [[Protein primary, secondary, tertiary and quaternary structure|Secondary, tertiary, and quaternary structure]]
# N- and C-terminal ends of protein chains; 5' and 3' ends of nucleic acid chains.
# Distribution of polar (charged or uncharged: hydrophilic) vs. hydrophobic amino acids on the surface and in the core (using slabbing).
# The distribution of positive and negative charges on the surface of a protein.
# [[Introduction to Evolutionary Conservation|Evolutionary conservation]] to identify functional regions of proteins.
# [[Lipid bilayer boundaries]] for integral membrane proteins.

The above features can be most easily displayed in the ''Views'' tab of [[FirstGlance in Jmol]]. Evolutionary conservation can sometimes be seen with [[How to see conserved regions|one click in Proteopedia]], or in other cases requires [[ConSurf Quick Analysis Procedure|submitting a job to the ConSurf server]]. For a specific protein, such features can be displayed by using Proteopedia's [[Scene Authoring Tools]] and then attached to green links when authoring a page.

===Covalent and Non-Covalent Interactions===
[[FirstGlance in Jmol]] provides "one-click" routines, in its ''Tools'' tab, to highlight
*Disulfide bonds
*[[Salt bridges]]
*[[Cation-pi interactions]]
*Non-covalent interactions with any sub-structure that you select, using ''Contacts & Non-Covalent Interactions'' 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]].

==See Also==
*[[Help:Getting Started in Proteopedia]]
*[[Help:Contents]] -- a list of many Help pages in Proteopedia.
*[[History of Macromolecular Visualization]]
*[[Molecular Sculpture]]