Virtual colors for atom representation?

In summary, the conversation discusses the standard colors used to represent different atoms in molecules, particularly in chemistry and biology. While there is no set standard, some sources, such as Atkins' Molecules and PyMol, use specific colors for certain elements, such as white for hydrogen and red for oxygen. The conversation also mentions the colors used for potassium and sodium in flame tests and in crystal structures.
  • #1
somasimple
Gold Member
766
5
Hi there,

I suppose there is a standard palette for atoms representation?
i.e. white for hydrogen, red for oxygen?

Is there a site or a link that provides such information?
 
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  • #2
No such standard as far as I am aware.
 
  • #3
If you're interested in precedent, Atkins uses in Atkins' Molecules white/gray for H, black for C, blue for N, red for O, light blue for F, orange for P, yellow for S, and green for Cl.
 
  • #4
That's a beginning! Nothing about K and Na?
 
  • #5
Sodium was purple. He didn't write about any molecules with potassium!
 
  • #6
Thanks, I'll find a color for potassium.
 
  • #7
Carbon black, chlorine green - these are colors more or less related to the elements. You may think about colors potassium and sodium give in the flame test.
 
  • #8
In biology, programs that display crystal structures of protein and nucleic acids generally use yellow for carbon, white for hydrogen, red for oxygen, blue for nitrogen, orange for sulfur or phosphorus, and green for things like metal ions, halogens, or other small ions that may be in the structure. (the specific program I'm referring to is PyMol [www.pymol.org][/URL])
 
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  • #9
thanks for information.
 

1. What are virtual colors for atom representation?

Virtual colors for atom representation are artificial colors that are assigned to atoms in a molecule for visualization purposes. These colors are not based on the actual colors of the atoms, but rather on their physical properties such as atomic number or electronegativity.

2. How are virtual colors chosen for atom representation?

Virtual colors are chosen based on a color scheme or color map, which assigns specific colors to different ranges of atom properties. These colors can also be customized by the user according to their preference.

3. Why are virtual colors used for atom representation?

Virtual colors are used to make it easier to distinguish between different atoms in a molecule and to highlight specific features or patterns. They also make it easier to visualize and interpret complex molecular structures.

4. Are virtual colors accurate representations of atoms?

No, virtual colors are not meant to accurately represent the actual colors of atoms. They are used purely for visualization purposes and do not affect the chemical properties of the atoms in any way.

5. Can virtual colors be used for all types of atoms?

Yes, virtual colors can be used for all types of atoms, including atoms from different elements and isotopes. They can also be used for atoms in different states, such as ions or radicals.

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