Molecular Key

[toma1990]

I am an A-Level chemistry student and was trying to work out what the proteins were made up of. The only problem is i dont know what all the colours for the molecules are on the ball and stick diagram. I wondered if there was a key i could use to help me. I presume that the grey atoms are carbons, the dark blue are nitrogen, yellow is sulphur, light blue are hydrogen and red is oxygen. This is fine until i found different shades of colours, for example some white atoms. I wondered what the significance of the changes in shade was. I was particularly stuck on a molecule section that appeared to be a carbon bonded to two oxygens and another carbon and from my understanding of chemistry i could not understand how this works unless the molecule has lost the hydrogen atom from an acid group. Can anyone help????

[susato]

The color code may vary according to the machine you're viewing on.

If you switch back and forth between the backbone and the ball-and-stick model, you'll be able to pick out the carbon and nitrogen molecules of the peptide backbone. You should see a carbon attached to the amino acid's functional group, a second carbon attached to an oxygen, and then a nitrogen. (ok, there are exceptions for some aromatic aa)

Yes, yellow is sulfur, and those atoms should be pretty uncommon.
Are you looking at a ribosome project? The mystery molecule may be a phosphorus, especially if it appears in the backbone of the nucleic acid.

In the space around the protein, look for water molecules (H2O) and urea.

Most of the projects have pictures which can be viewed here at the jmol site thanks to NicoV.

[uncle_fungus]

The colours for atoms should match this:

Code: Select all

    /* Carbon - dark grey*/
    /* Hydrogen - grey*/
    /* Nitrogen - blue*/
    /* Oxygen - red*/
    /* Sulfur - yellow*/
    /* any heavy atoms - purple*/

Beware however, that GROMACS has the ability to convert hydrogens (and aromatics) into virtual sites, which won't appear in the protein display.