Introduction to molecular visualization: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) No edit summary |
||
| Line 8: | Line 8: | ||
==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. | ||
===Atomic Representations=== | ===Atomic Representations=== | ||
Atomic representations are illustrated in the [[Glycine|page about Glycine]]. These show positions of atoms and covalent bonds. Such representations are too cluttered to be useful for visualizing [[peptides]] or [[chains|protein chains]]. | Atomic representations are illustrated in the [[Glycine|page about Glycine]]. These show positions of atoms and covalent bonds. Such representations are too cluttered to be useful for visualizing [[peptides]] or [[chains|protein chains]]. | ||
===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 from the larger model. Slabbing can be done using [[FirstGlance in Jmol]]: In the ''Views'' tab, use ''Center Atom'', and then click the ''Slab'' button. Further instructions will appear automatically. | |||
===Simplified Schematic Representations=== | ===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. | 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. | ||
==Color Schemes for Macromolecules== | ==Color Schemes for Macromolecules== | ||
