Now you can clearly see the position of the secondary structure elements. Combine this coloring with rocking the structure and you will have a good idea of how the linear primary sequence folds into the final tertiary structure. This is effective at showing the start and stop of the polypeptide chain. Plain Colors – simple colors that affect all selected atoms.Structure – Uses six different colors to distinguish four types of protein secondary structures and DNA vs.Shapely – colored according to the ‘Shapely’ coloring scheme.Monomer – a reverse rainbow gradient used to color according to position along a chain starting with blue and finishing with red.Relative Charge – colors atoms based on their partial charge, or electron density.Formal Charge – colors atoms based on their formal charge, or ionic state.Chain – assigns each macromolecular chain a unique color.Amino Acid – colored according to traditional amino acid properties.Relative temperature – relative to the lowest and highest temperature factor values.Fixed temperature – according to the temperature factor, a measure of the mobility or uncertainty of a given atom’s position referred to an absolute scale of 0-100.Default (CPK) – industry standard scheme representing atoms by specific colors.

Gently rocking the structure back and forth will allow you to more easily see which parts are at the back and which at the front. This is a well known visual effect and is commonly used to help show depth on a 2D display. One thing you might notice is that when you are rotating the structure, it looks more three-dimensional than when it is static. Try all of these and get used to moving the structure around. Now as you move the mouse around the structure will pan in the window. Moving the mouse left or right will rotate the structure in the appropriate direction.įinally, you can pan the structure by holding the Shift key down and double clicking in the window and holding the mouse button down. Moving the mouse down will make the structure grow as your point of view moves towards it. Moving the mouse up will make the structure appear smaller as your point of view moves away. You can also zoom the structure in and out by clicking in the window and holding both the left mouse button and Shift key on your keyboard down. This isn’t a static image and the molecule can be moved around by clicking in the window and dragging the mouse while holding the left mouse button down.

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