Bob wrote: > Neither of these solutions is impossible. I propose we implement the > second -- a ribbon associated with carbohydrates. Jmol already identifies > chains of carbohydrates and can show a trace through the anomeric carbon > atoms.
Wow, I didn't know that ribbons were already implemented for carbohydrates! This makes my efforts to draw curves unneccesary. On models with straight amylose helix (30 to 100 residues), ribbons are already quite adequate, at least in this PDB model where all the C1 atoms are correctly labeled. Some funny effects at seen at spots, but I need to check if the atoms are properly labeled before I complain. > What is needed to make ribbons would be to identify the second > atom. This could be easy or difficult, depending upon how that is defined. > Can you tell us what you would use to define the ribbon? Once we have > that, it is possible that this could be implemented very easily. Right now the orientation of the ribbon is OK (tangent to the helix). I will have to look at other models that are not so regular and have other monosaccharides than glucose. Will come back to this when I have some hints. (I'm leaving for vacation this afternoon) > If you will work with me and have a good idea of This can be a promising starting point. Some people have published two nice algorithms for cartoon-type rendering of carbohydrates, implemented in their own software and on the way to get implemented in VMD. I have already talked to them about the possibility to add that to Jmol. If we have a simple ribbon already worked out, it will help future work for the more sophisticated renderings. ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
