The problem is that you are not visualising the backbone nitrogens. You only show the side chains as sticks and the backbone is shown as cartoons.These schematic representations of secondary structure are drawn using Calpha atom positions and (typically) inherit the colour of the Calphas.  If you show the backbone as sticks, the nitrogens will be visible and they will have colour. Same goes for backbone oxygens which are similarly hidden in your image, but are coloured in the side chain at the bottom of the image.

hth, Marko

On 23/07/2018 18:17, Santrupti Nerli wrote:
Hi,

I want to color backbone nitrogen atoms together with side-chain nitrogen atoms. The side-chain nitrogens get the color, however the backbone nitrogens don’t (see below; I have selected backbone nitrogens). I tried some options such as

select bb, name n
color by element 


But, the backbone nitrogens aren’t getting colored. Is there a way to color them without showing them as spheres?

Thanks a lot.


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-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
mh...@cam.ac.uk
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