Bugs item #1097575, was opened at 2005-01-06 20:14 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1097575&group_id=23629
Category: Algorithms Group: None Status: Open Resolution: None Priority: 5 Submitted By: Miguel (migueljmol) Assigned to: Miguel (migueljmol) Summary: single residue chains Initial Comment: ---------------------------- Mensaje original ---------------------------- Asunto: [Jmol-users] Single-residue chains invisible in backbone? De: "Eric Martz" <[EMAIL PROTECTED]> Fecha: Jue, 6 de Enero de 2005, 13:35 Para: [email protected] -------------------------------------------------------------------------- The discussion of invisible unbonded atoms in wireframe display reminded me: A related issue is one-residue "chains". In other words, if a single residue is given a unique chain name, then the "backbone" display leaves that residue invisible in RasMol 2.6/Chime. In Protein Explorer's firstview backbone trace rendering, I work around this by displaying all alpha carbons and nucleotide phosphorus atoms as spheres the same diameter as the backbone rods. These spheres don't change backbone connectors because they are hidden inside the backbone rods for connected residues, but they appear as single isolated spheres for unconnected single-residue "chains". Examples: 1B07 has a single-residue chain named B containing one HIS residue (a histidine tag engineered onto the molecule to assist in purification prior to crystallization). The HIS is chemically part of chain B, but was given a separate chain name because it is not coded for by the gene. In PE's FirstView, "chain" B appears as a small purple sphere. http://molvis.sdsc.edu/protexpl/pe.htm?id=1b07 1ARJ has a single-residue chain P containing one ARG residue bound to an RNA chain. "Chain P" appears as an isolated small cyan sphere in PE's FirstView. http://molvis.sdsc.edu/protexpl/pe.htm?id=1arj PROPOSAL for Jmol For Jmol, I suggest that all backbone displays (backbone, trace, cartoon, etc.) show the alpha-carbon or phosphorus atoms of single-residue chains as small spacefilled spheres. -Eric ---- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1097575&group_id=23629 ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
