Feature Requests item #1588916, was opened at 2006-11-01 21:56 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1588916&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: friedar (friedar) Assigned to: Nobody/Anonymous (nobody) Summary: alpha carbon smooth trace/ribbon/etc. Initial Comment: Jmol should have an option (and actually IMO it should be the default) of smooth backbone representations that follow the alpha carbon position rather than the current default of the peptide bond. Since the work to accomplish this is not trivial, I'd like to justify the need for this rather strongly. There are two compelling reasons. One is that it is simply the standard in crystallography and NMR representations of proteins, so it is hard to understand why Jmol should execute this very standard representation differently. An alpha carbon trace has a characteristic look and feel that protein structure people expect to see, because it is more reflective of the true path of the backbone. The muted curves of the backbone in Jmol's sheets, turns and loops are actually quite different from the undulations of an alpha carbon trace/ribbon/cartoon. Second, in proteins there is a frequent need to display a few key side chains as sticks (or ball and stick) protruding from a smooth trace or cartoon at an active or binding site. This type of display is used in almost every structure representation of a ligand binding site. With the current Jmol representations, the alpha carbons of these key side chains are hanging in space, unconnected to the backbone tracing. This looks odd and is, of course, incorrect. Using a strict "backbone" display that connects the alpha carbons with straight rods is insufficient, since the straight rods echo the stick nature of the sidechains, and it is harder for the eye to discern the side chains. The smooth representations are important in this context. Thanks for listening. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1588916&group_id=23629 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
