Post by R Smith on May 15th, 2012 at 1:51pm
I would like to know how to customize/add/edit/change the color scheme. The current ones don't work for me.
I have attached a color scheme that I think makes better sense, although if there suggestions or corrections, I would appreciate them.
Here is my rationale:
1. Basic amino acids, R and K, are litmus blue with R being more basic and thus more blue
2. Acidic amino acids, E and D, are litmus red, with D being slightly more acidic and thus more red (in the figure, unfortunately, I show E more red than D)
3. Hydrophobic/aliphatic amino acids I, L, V, and A are shown as yellow, with intensity of the yellow color showing more hydrophobic character; I am working from memory so I may need to shade them differently
4. Sulfur-containing amino acids C and M were shaded green. Since M is slightly more hydrophobic, I sought a combination between yellow and green, with a greater color intensity.
5. Histidine H can be basic and aromatic, I suppose, so I give it a bluer color but also wanted to de-emphasize its basicity
6. The polar amino acids I include as the amides N and Q and S and T. Being in between red and blue, shades of magenta/purple were reasonable. The intensity of the color--lighter for less polarity, darker for more polarity---should be reflective of that.
7. The aromatics got a special color scheme--tending to coloring of the gray. Yellowing a gray color was suitable for F to reflect its lower hydrophilicity, and the "purpling" of Y seemed okay given its hydroxyl group. Perhaps W is too much of a bluing of the grey.
8. Glycine G should get full gray, since it inhabits a gray zone somewhat.
9. And proline P being in a distinctive special class should be easily discerned in an off-white. Many biologists will want to pick it out readily particularly if they are running analyses on epitope-shaping domains.
I welcome criticism of this color scheme
AAColorScheme.png (8 KB | )
I have attached a color scheme that I think makes better sense, although if there suggestions or corrections, I would appreciate them.
Here is my rationale:
1. Basic amino acids, R and K, are litmus blue with R being more basic and thus more blue
2. Acidic amino acids, E and D, are litmus red, with D being slightly more acidic and thus more red (in the figure, unfortunately, I show E more red than D)
3. Hydrophobic/aliphatic amino acids I, L, V, and A are shown as yellow, with intensity of the yellow color showing more hydrophobic character; I am working from memory so I may need to shade them differently
4. Sulfur-containing amino acids C and M were shaded green. Since M is slightly more hydrophobic, I sought a combination between yellow and green, with a greater color intensity.
5. Histidine H can be basic and aromatic, I suppose, so I give it a bluer color but also wanted to de-emphasize its basicity
6. The polar amino acids I include as the amides N and Q and S and T. Being in between red and blue, shades of magenta/purple were reasonable. The intensity of the color--lighter for less polarity, darker for more polarity---should be reflective of that.
7. The aromatics got a special color scheme--tending to coloring of the gray. Yellowing a gray color was suitable for F to reflect its lower hydrophilicity, and the "purpling" of Y seemed okay given its hydroxyl group. Perhaps W is too much of a bluing of the grey.
8. Glycine G should get full gray, since it inhabits a gray zone somewhat.
9. And proline P being in a distinctive special class should be easily discerned in an off-white. Many biologists will want to pick it out readily particularly if they are running analyses on epitope-shaping domains.
I welcome criticism of this color scheme
AAColorScheme.png (8 KB | )