Well, actually, Jmol isn't supposed to be rendering ribbons with carbohydrates -- that's a bug. (trace, yes; ribbon, no), and the trace also is too crude -- we aren't checking for connected monomers yet. A good example of how this does NOT work correctly is with
load =1uh3;display carbohydrate;ribbon on Bob Angel Herraez wrote: >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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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
