(red = oxygen = C-terminal = end of chain = 3') (blue = nitrogen = N-terminal = start of chain = 5') Backbone displays (such as ribbons, cartoons, etc.) are rendered in the color of alpha carbons for proteins, phosphorus for nucleic acids.ĭefault element colors, by periodic table: Hover over any element to see more information.Ĭlick on an element to move to the same information in the Atomic Numbers table below. Related commands: color object cpk, set defaultColors Jmol, set defaultColors RasmolĪpplies color to each atom of the object according to element, as shown in the tables below. Atoms ('CPK' colors, default element colors) Many of the following coloring patterns apply only to PDB and mmCIF files for biomacromolecules. Information on RasMol colors is included for those who are adapting RasMol and Chime-based materials for use in Jmol. if the object is omitted, atoms is assumed.object can be atoms, bonds, backbone, cartoon, stars, rockets, ribbon, dots, label, echo, hbonds, ssbonds, axes, boundbox, measure, polyhedra, isosurface, pmesh, unitcell.color scheme is specified using pre-defined terms detailed on this page.(For the default colors and color values used in Jmol, see table below.) It can also be a JavaScript color name, a RasMol color name, or a Jmol color name. color is specified as decimal or hexadecimal triplets.A full list of Jmol commands can be found here.Objects can be custom colored in Jmol using the color (or colour) command: color object color or color scheme The results and error messages (if any) are displayed at the top, and in the Jmol window. At the bottom, users can write Jmol commands. Console: this option opens another window that is divided into two parts.Choose delete measurements to remove all measurements from the screen. To display torsion angles, choose click for torsion (dihedral) measurement. To display bond angle, choose click for angle measurement. Click on the same two atoms to delete the bond length. The bond length will appear on the screen. Note that the chosen atoms are displayed on the status bar of the html page. To display bond length, choose click for distance measurement. Measurement: use this sub-menu to display bond lengths, bond angles and torsion angles.Spin: rotates molecule automatically around the Z-axis.Size can also be changed using the mouse wheel. Zoom: changes the molecule size on the Jmol screen.Atom colors are specified on the Jmol website help site. This scheme was developed by Corey and Pauling and later enhanced by Koltun (hence the name CPK), and initially used to mark atoms in plastic models. Color: this menu controls the color scheme of atoms, bonds and other items on the screen.Select the thickness of bonds from 0.10Å to 0.30Å. Bonds - choose on or off to show or hide chemical bonds.Labels - select the appropriate option to display atom symbols and serial numbers.Control the size of balls in all atoms, using the van der Waals 15%-100% option. Atoms - choose show hydrogens to show or hide hydrogen atoms.Sticks - sticks represent chemical bonds and vertices represent atoms.Wireframe - lines represent chemical bonds and vertices represent atoms.Ball & Stick - sticks represent chemical bonds and balls represent atoms.Scheme - several display formats are available.Style: opens a sub-menu containing the following items:.Select an atom or atoms to change the color, to display labels, or to execute other options with respect to part of the molecule. Select: use this option to select all atoms or a specific atom.Use this option to toggle between models or display them together. Model: this option is active when the file contains more than one molecular model.Select Script with state to save the molecule as a three-dimensional model that can be viewed in Jmol. Select JPG Image to save a molecule as a picture. Save: this option can be used to save molecules from the Jmol window.A detailed explanation of Jmol commands can be found here. Some of the menu options are listed below. Jmol provides its own menu that enables users to toggle between different molecular display options. Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.
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