Sets the amount of "ambient" light filling the shadows created by the apparent light source. These lines can either be between the two sidechain sulfur atoms (the default) or between the two backbone alpha-carbon atoms, depending upon the desired effect. Sulfur-sulfur bonds in cysteine bridges of proteins are displayed as lines. These lines can be displayed whether or not the H atoms are present in the file, and can be drawn either between the two non-hydrogen atoms involved in the bond (O or N, typically, the default) or, alternatively, between the two backbone alpha-carbon atoms, depending upon the desired effect. Hydrogen bonds between protein amino acid residues or nucleic acid base pairs are displayed as lines. Set this flag off if you want all bonds to appear as single bonds. The bonds flag determines whether or not multiple bonds are displayed. In some file formats (.mol files, for example) the connection data may indicate the bond type-single, double, triple, or quadruple. When script commands affect a set of atoms, EITHER atom may be in the set for the bonds also to be affected. When script commands affect a set of atoms, BOTH atoms must be in the set for the bonds between them to also be affected. This TENDS to indicate secondary structure, but is not perfect.The correlation between color and offset are as follows:ColorOffsetgreen-4cyan-3white+2magenta+3 (turns)red+4 (alpha-helix)orange+5yellowother (e.g. The colors assigned are based on the number of basepairs between the interacting H atoms. Note that to get this effect, one must first execute "hbonds ON" and then issue "color hbonds TYPE". Sets the color of the molecular surface dots.Ĭolors hydrogen bonds specifically in proteins based on how many residues one end is from the other. Sets selected atom colors to the default "cpk" color scheme (either Jmol or Rasmol). Sets the selected atom set to a color based on a particular color scheme. Using a relative scale (parameter "temperture" or "relativeTemperature") sets the blue-red range to match the range of varibility in the model itself. Using a fixed scale (parameter "fixedTemperature") allows direct comparison between two structures. Colors range from blue (least positional variability within the crystal) through white to red (most positional variability). Sets the color of atom-related objects based on a previously selected atom set to a specific color, a color scheme, or back to its default color (NONE).Ĭolor atoms based on a crystallographic B-factor or "temperature" scale. Sets the color of the specified Rasmol object based on a color scheme.Ĭolor This will help us prioritize future development.Įxamples color Please give us feedback on what features you would use and would like to Larger vanderWaals percentages (such as 50% or more). Finally, Jmol does not haveĪ true 3D graphics engine, so renderings of intersecting surfacesĪre not handled properly. Specular and specpower are not available. Jmol does not perform lightingĪnd surface rendering on the fly, so settings such as ambient, shadows, Things that explicitly do *not* work are protein rendering formats suchĪs ribbons, cartoons, strands, etc. In this release most movement, selection, atom expression and That supports a larger number of file formats on a wider variety of This will provideĪ migration path for those who wish to move to an open source solution
#COLOR RESIDUES JMOL FULL#
Goal is to eventually provide full script support. Jmol currently supports many of RasMol/Chime scripting commands. The current URL for extended chime scripting commands is: Various extensions were added, including additional scriptingĬommands. The Chime web browser plug-in was based upon the RasMol source code. The current URL for full RasMol documentation is: Jmol supports the RasMol scripting language defined by RasMol. You can do this through the jmol home page Supply feedback in case of bugs and/or unexpected behavior and/or As of this writing it should be considered *alpha test* code. The scripting engine has been completely rewritten for Jmol ReleaseĦ.
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