[Jmol-developers] [ jmol-Feature Requests-1539252 ] Need better cartoon renderings

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Feature Requests item #1539252, was opened at 2006-08-12 12:10
Message generated for change (Comment added) made by hansonr
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Category: None
Group: v10
>Status: Closed
Priority: 5
Submitted By: Eric Martz (emartz)
Assigned to: Bob Hanson (hansonr)
Summary: Need better cartoon renderings

Initial Comment:
I would like to request that Jmol's rendering of 
secondary structure 
cartoons be improved. In my opinion, its 'cartoon' 
rendering is very 
important but unsatisfactory. With increased exposure 
(Nature is working on 
installation of FirstGlance in Jmol), the present 
rendering may diminish 
Jmol's acceptance/reputation.

Presently, Jmol draws beta planks as absolutely 
straight. In reality, beta 
strands are often curved and usually somewhat twisted.

In some cases, Jmol's beta strand planks not only 
largely miss the correct 
positions, but end up crossing through each other. 
This happens for 1APM 
(restrict 42-75 to see the relevant portion).

Similarly, many alpha helices are curved, and Jmol's 
rockets need to 
reflect this.

Also, the cone-heads of Jmol's rockets (very nice) 
sometimes "flap" 
annoyingly when the molecule is rotating. Though less 
important, it would 
be great if this could be fixed.

I have put an MS Word 2002 file, ss-cartoon.doc, 
containing snapshots of 
some cases where Jmol's rendering is unsatisfactory at:
http://www.umass.edu/microbio/chime/beta/jmol/
 and I have also uploaded it here as an attachment. 
Snapshots there compare the renderings of Jmol, Chime, 
and Protein Workshop.
(If anyone has trouble displaying the .doc file, let 
me know.)


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>Comment By: Bob Hanson (hansonr)
Date: 2006-08-22 19:01

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cartoonRockets 
 

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Comment By: Bob Hanson (hansonr)
Date: 2006-08-14 22:59

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10.x.42c This is pretty much complete. See
http://www.stolaf.edu/people/hansonr/jmol/test/proto

Arrow head wiggling is fixed. It was really a problem with
all parts of all cylinders. It's still not absolutely
perfect, but it's pretty close. 

I'll leave this open for additional comments/suggestions.


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Comment By: Bob Hanson (hansonr)
Date: 2006-08-14 04:25

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A first attempt is at
http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm

10.x.42 includes the command

set cartoonRockets on|off

A hybrid of cartoons and rockets. I'm dissatisfied with the
renderings, though, and have tracked this down to a bug in
the line drawing rasterizer. I will look at it when I have
more time.

Basically, the beta sheets are fine; the alpha helix rockets
show undesireable characteristics, though, including
flapping cones and undesireable line breaks. This has been a
problem since the inception of rockets; I will see what I
can do. 




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