Part Type:Coding:Icon Discussion

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possible enzyme icon? Part icon enzyme1.png...basic idea is a box binding two substrates in it...(--mel)

  • I like the little shapes in the box, but it would be better to omit the top of the box (make it a trough instead). That's more realistic for most enzymes. Also, could the box sides be extended to convey the notion that the enzyme is usually much bigger than the substrate(s)? [SCM - 3/12/07]
  • OK, I made a few "open trough" format enzymes....closer? I'm still not sure what the metabolism ones should be like Enzyme open.pngI rounded the bottom to align better with the stuff inside it
    • This one looks very nice. I like the shape complementarity -- perhaps you can work with it a little more (use a triangle rather than a ball for one of the substrates? Also, rounding the ends of the open box would be good (proteins are rounded and irregular -- with no square corners. [SCM 3/28/07]
  • Another image, this one more symbolic with the protein coding parts, but the coding regions aren't necessarily substrates, so it could be misleading Enzyme open2.png
    • I agree about the possible confusion of using the arrow (which we should restrict to icons for DNA.) Let's discard this one. [SCM - 3/28/07]
  • An alternative suggestion from Reshma: Make little curved arrows and put several of them in a row, all pointing in the same direction (reminiscent of a metabolic pathway). [SCM - 3/14/07]
  • Metabolism
  • would metabolism really represent the action of an enzyme? I don't think I've ever seen the curved arrows before...are those the ones indicating electron-arrow pushing? That idea with the trough sounds good to me. --Smelissali 15:29, 26 March 2007 (EDT)
    • Well, enzyme catalysis always causes a chemical change and "metabolism" constitutes the sum total of all (biologically programmed) chemical changes in the cell/organism. But I agree about the lack of familiarity of most people with presentations that have curved arrows (they are generally used in diagrams where the process is shown vertically, not horizontally). [SCM 3/28/07]
  • Possible repressor protein icon? Part icon inhibitor2.png, Part icon inhibitor3.png?
  • Repressor icon should be an inverted T, as in circuit diagrams. Activator icon should be an arrow pointing up. [SCM - 3/12/07]
  • Here's a simple repressor bar, is this what you were thinking of? Repressor bar.png --Smelissali 08:41, 27 March 2007 (EDT)
    • Yes, that's a good step in the right direction. Could you put the little "T" upside down on **top** of the bar? Also, if you can add a short horizontal handle, that would be perfect. The activator icon could just be a little arrow (again with a horizontal handle).
  • Reshma and Mack favor a slightly more elaborate symbol for each of these, along the lines of the circuit-component interaction lines. each would have a short vertical bar, a horizontal bar starting at the top end of that, then from the end of the horizontal bar a second, equal-sized vertical bar going downward. For activation the tip of the second bar would be an arrowhead, and for repression it would be another horizontal bar. [SCM - 3/14/07]