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desc of "blue is for basic" - seq app color file

Finn Drablos drablos at marvin.mr.sintef.no
Thu Jun 24 00:50:58 EST 1993

ahouse at hydra.rose.brandeis.edu (Jeremy John Ahouse) writes:

(... some text deleted ...)

>Red for acidic amino acids; Glu, Asp 
>(since red is a common danger signal and acids are dangerous
>(well maybe not amino acids, but it's a start))
Also : Oxygen is a key feature here, and in organic chemistry you
usually use red for oxygen.

>Blue for basic amino acids; Lys, Arg, His
>(blue and basic both start with "b")
Here too : You normally use blue for nitrogen.

(... more text deleted ...)

So I find these colors very reasonable. But they lead to an interesting
question. How do you color electrostatic surfaces? Let me explain:

In our lab we do a lot of calculations of electrostatic properties of
macromolecules, and display the results as grids or surfaces, colored
in red and blue. But there are two opposite views with respect to how
red and blue colors are used. The "chemistry school" prefer to use
red for negative charges, as negative charges often are at oxygens,
and blue for positive charges, because positive charges often are
found at nitrogens. The "physics school" prefer to use blue for negative
charges, because blue often is associated with negative temperature,
negative potential etc, and red for positive charges for similar
reasons. This can be quite confusing.

Is there any consensus on this?


Finn Drablos                drablos at marvin.mr.sintef.no
MR-Center, SINTEF UNIMED    phone +47 7 99 77 10
N-7034 TRONDHEIM, NORWAY    fax   +47 7 99 77 08

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