better way to draw cartoon sheets

Case number:845833-990660
Topic:Game: Display
Opened by:jlangsdo
Status:Open
Type:Suggestion
Opened on:Saturday, October 1, 2011 - 14:25
Last modified:Saturday, October 22, 2011 - 06:39

In the Cartoon view, which shows sheets, each sheet is drawn from quadrilateral plates with donor and acceptor atoms on the 4 corners, with the sidechain coming out of the center. I think this is misleading.

The flex point in each amino acid is on the C-alpha that has the sidechain coming out of it. That's what is special about the peptide bond; the 3 bonds along the backbone between two C-alpha atoms are coplanar. This is why we can't draw bands between adjacent amino acids - the bands connect C-alpha atoms, and none of the bonds between them flex relative to one another. This stiffness is shown nicely in the Trace Tube view, where the joints are the C-alpha atoms with fixed length tubes between them.

So I suggest that the cartoon sheets be drawn differently, shifting the meaning of the plates.

The sheet should be built out of chevron shaped plates (see below) that are drawn from C-alpha to C-alpha, with a donor and acceptor on the side of the plate. As in the Trace Tube view, you would select the C-alpha and it would highlight as a joint along with and half of each of the two attached plates. At the ends of the sheet (where it connects to a loop), the sheet should be closed with a triangle, so selecting the last amino acid of the sheet would highlight the triangle and half of one plate.

That way the stiffness of the peptide bond and it planarity would be visualized in the Cartoon sheet. Bending of the sheet would be accurately represented as a rotation at a joint between two stiff plates, rather than like a flexing of the plates themselves.

Proposed:
|
---R -------
/ / |
O==C |
\ \ Inflexible plate
\ N--H |
\/ \ |
R--- ----- Joint at C-alpha
\ \ |
C==O |
/ / Inflexible plate
H--N / |
/ \/ |
---R -------

Present:
R
/
O==C O___
\ \
N--H N
/
R Flexible plate, joint in the center
\
C==O ___O
/ /
H--N N
\
R

(Sat, 10/01/2011 - 14:25  |  4 comments)


Joined: 09/24/2011
Groups: None

Aw, nuts, it collapsed my carefully drawn character picture.
If you view it in a fixed type font like courier it will show what I meant.

infjamc's picture
User offline. Last seen 2 years 41 weeks ago. Offline
Joined: 02/20/2009
Groups: Contenders

Unfortunately that didn't work either since "extra spaces" are automatically removed... You might want to draw the diagram on another program, save a screenshot, then upload the image as a PNG...

Joined: 09/24/2011
Groups: None

Picture of proposal attached

spmm's picture
User offline. Last seen 37 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers

This is interesting - how would it affect our ability to visually match sheeets to each other?

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