(was part of [Jmol-users] feature request- alpha carbon trace,and documentation correction )
> Frieda Reichsman wrote: > > > In the Jmol scripting documentation, the descriptions of how the > > smoothed representations relate to the backbone are different and > > should probably be standardized. What I have understood or assumed is that these renderings are drawn as inherited from Rasmol, and all use the same trajectory: * backbone Consecutive straight lines joining alpha carbons in protein, or phosphates in nucleic. * trace, ribbons, strands, cartoons > > "through the center of the nitrogen - carbonyl carbon bonds of a peptide" I just checked: it's correct, right through the middle of the peptide bonds. > > or the ribose 1-O-P bond. " This is not correct. First, "ribose 1" makes no sense to me. C1' has no involvement in the backbone. Second, in DNA I see the trace passes close to the P, sometimes close to O3', others to 5', but not quite through any bond midpoint. Third: drawing trace together with backbone, I would say that on DNA trace is just a smoothed backbone; that's why it doesn't reach the P atoms, but stays slightly inside the helix. A look into Z-DNA (2zna.pdb) reinforces this idea: the trace passes through the midpoints of the zig-zag backbone. Same with several RNAs. In summary, trace, ribbons, strands, are a smoothed curve (spline? hermite?) whose nodes are: - for proteins, the midpoint of the peptide bonds (N - C carbonyl) - for nucleics, the midpoint of the P-P line (segment of backbone) ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
