None of Jmol's smooth-style backbone representations (cartoon, trace, ribbon, etc.) is a trace of the alpha carbons of a protein. Would it be possible to add to Jmol a smooth representation that follows that alpha carbons quite faithfully? In the Jmol scripting documentation, the descriptions of how the smoothed representations relate to the backbone are different and should probably be standardized. 'Ribbons' is clearly incorrect in saying: "Ribbons offer a representation the protein backbone or nucleic acid helix using a flat band that smoothly traces the midpoints of adjacent alpha carbon atoms..." In contrast, 'trace' reads: "A "trace" is a smooth curve through the center of the carbonyl carbon-alpha carbon bonds of a peptide or the ribose 1-O-P bond. " Is that the correct description? Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
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