General Category >> Help and How-to >> Amino Acids Color Scheme

Message started by R Smith on May 15th, 2012 at 1:51pm

Title: Amino Acids Color Scheme
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 | )

Title: Re: Amino Acids Color Scheme
Post by Olga Golosova on May 16th, 2012 at 11:59am
I've created a new issue to allow one to customize a multiple alignment's color scheme. So you would be able to set up the specified scheme as well as any other required scheme as soon as this issue is implemented.

You can track the issue status here:

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