Scene authoring tools: Difference between revisions
Eran Hodis (talk | contribs) No edit summary |
Eran Hodis (talk | contribs) No edit summary |
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=='colors' tab== | =='colors' tab== | ||
The first area is the 'all and halo toggle' area. This provides a button to select all atoms, and a checkbox to turn selection halos on or off. | |||
The 'color' area first lets you choose whether you would like to change the color of the current selection, or of the background. The color palette is clickable and as soon as you click on a color, either your selection or the background (as was previously selected) will change to the clicked color. Hover over a color to view its name. There is a series of buttons below the color palette, each representing a specific color scheme. | |||
CPK is the standard CPK coloring scheme. Amino and amino2 color each amino acid as a different color. Chain colors each chain different colors. Spectrum colors protein and nucleic acids from blue to red on a spectrum with the N or 5' terminus as blue and the C or 3' terminus as red. Structure colors according to secondary structure. Fixed and relative temperature color according to temperature and formal and partial charge according to charge. DRuMS composition colors according to the DRuMS scheme (http://www.umass.edu/molvis/drums/). Hydrophobic/polar colors hydrophobic amino acids grey and polar (charged or uncharged) residues pink. Charge colors hydrophobic residues grey, polar-uncharged residues pink, cationic residues blue, anionic residues red, and backbone atoms purple whether charged or uncharged. More information on Jmol colors is available at http://jmol.sourceforge.net/jscolors/. | |||
The 'transparency' area allows you to render your selection transparent. Zero percent transparent will be opaque, 100 percent transparent will be invisible, and anywhere in between will be transparent to a degree. | |||
==Manipulating Jmol with your mouse== | ==Manipulating Jmol with your mouse== | ||