Introduction to molecular visualization: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 24: | Line 24: | ||
==Color Schemes for Macromolecules== | ==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 pre-dated computer visualization. Those early colors for chemical elements were incorporated into the color schemes built 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 elements were incorporated into the [http://jmol.sourceforge.net/jscolors/ color schemes] built into [[Jmol]], the visualization engine used in Proteopedia. | 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 pre-dated computer visualization. Those early colors for chemical elements were incorporated into the color schemes built 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 elements were incorporated into the [http://jmol.sourceforge.net/jscolors/ color schemes] built into [[Jmol]], the visualization engine used in Proteopedia. | ||
==Visualizing Structural Features== | |||
Combinations of representations and color schemes are useful to highlight | |||
* 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. | |||
* Evolutionary conservation to identify functional regions of proteins. | |||
The above features can be most easily displayed | |||
==See Also== | ==See Also== | ||