Feature Requests item #1588916, was opened at 2006-11-01 22:56 Message generated for change (Comment added) made by aherraez 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: Bob Hanson (hansonr) 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. ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2006-11-02 11:37 Message: Logged In: YES user_id=1065324 I agree with Frieda, and I vote for having this as the default (if not the only one; we are getting things complicated with so many nice options; it's great for authors to have the options, but I think the program should not offer two ways of tracing, will be confusing to users). Yes, the wavy sheets don't look too good, but in the end they are *pleated* sheets, right? The backbone is zig-zag, so that's what we (must) see. I checked Rasmol (2.7.3.1) and the "wavyness" is there, more than with Jmol's set traceAlpha OFF but less than with set traceAlpha ON; the trace/ribbon does not go right through the center oh the alphaC atoms, but slightly to one side, making very little distance in helices but noticeable in sheets and turns. Maybe someone can check the code used in Rasmol. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-11-02 05:30 Message: Logged In: YES user_id=1082841 done now for all secondary renderings: cartoons, meshRibbons, ribbons, rockets, strands, trace HOWEVER -- while I agree that helices look terrific with an alpha trace, I'm not sure you will say the same about beta-pleated sheets. They are awefully wavy. I notice that RasMol does not do this. Kinemage does not do this. (Protein Workshop's sheet representation is pretty messed up, so let's not compare that.) I suspect that you do not really want it, either. What do you really want for sheets? Bob ---------------------------------------------------------------------- Comment By: friedar (friedar) Date: 2006-11-02 00:43 Message: Logged In: YES user_id=1190355 OK so is this the right form box to use for response? I hope so! 1 - thanks for implementing trace, I look forward to checking it out. 2 - Yes, I think this is needed for cartoons and ribbons. Again, the path of the backbone looks quite different and I think we should be able to display it correctly. Rockets - I am not sure we need it for this, I can't quite imagine the difference in the rocket position, but I suspect it would not be a very big or meaningful difference. I have asked Eric (Martz) for his thoughts on the rockets aspect. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-11-02 00:07 Message: Logged In: YES user_id=1082841 trace is easy and is now (10.9.90) enabled by set traceAlpha which can be toggled back and forth to see the difference. Are you saying that you need this as well for cartoons? I can see what it is about in terms of the trace; what would be implied in terms of rockets or cartoons? Bob ---------------------------------------------------------------------- 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? 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