[Chimera-users] << Rendering proteins with Chimera >>

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 23 11:18:10 PST 2007

Hi Hatuey,
It may not be problem.  You did not give very much information, but I  
am guessing you are using the ribbons preset and different proteins.   
If a protein just has one chain, that chain is rainbow-colored from  
blue at the N-terminus to red at the C-terminus.  If there are  
multiple chains, each chain is instead its own color.  Or, if you  
have more than one model, each model is instead its own color.  It  
probably does not matter what programs were used to prepare the  
structure file.

The preset tries to adapt to the situation to make it easy to see  
your structure(s) in a single step.

For example, if you had 12 chains in 3 different models, it would be  
too confusing if each chain was rainbow-colored, but when you only  
have one, it helps you understand the structure.

Of course, if you don't like how anything is shown, just change it.   
There are many different ways to change colors, display styles, what  
is displayed, etc. (using Select and Actions menus, commands, other  
Tools).  The presets are just meant to be quick and convenient but of  
course cannot cover every possible way you might want to show the  

We have beginner tutorials included with Chimera, see "getting started":

and there is an expanded, more detailed "getting started" tutorial at  
our web site:
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 23, 2007, at 10:52 AM, Hatuey Hack wrote:

> Hi all,
> As a Chimera new users, I notice that the proteins are rendering
> different depending on the program they where prepared.
> I used the preset to render them. I have a protein with all residues
> in different color and the other protein is rendered in a single
> color.
> My question is: this is a problem of Chimera or it is a problem with
> the protein file?
> Regards,
> Hatuey
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> Chimera-users at cgl.ucsf.edu
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