[Jmol-developers] [ jmol-Feature Requests-1588916 ] alpha carbon smooth trace/ribbon/etc.

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Feature Requests item #1588916, was opened at 2006-11-01 15:56
Message generated for change (Comment added) made by hansonr
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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.




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>Comment By: Bob Hanson (hansonr)
Date: 2006-11-01 22:30

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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

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Comment By: friedar (friedar)
Date: 2006-11-01 17:43

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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.

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Comment By: Bob Hanson (hansonr)
Date: 2006-11-01 17:07

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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


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