[Chimera-users] color changes

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 17 14:23:28 PST 2009

On Feb 17, 2009, at 1:15 PM, Jean-Paul Armache wrote:

> hello,
> i have one question concerning color manipulation in chimera.
> every pdb file one opens gets a specific color (if set so). so,  
> having a few of them open, one can distinguish
> between them color-wise.
> now, when one selects the files, it is possible to change the color  
> via actions->color. this indeed changes all
> of the things selected, and if the whole pdb was selected, all the  
> chains there. when one looks then into the
> model panel, the old colors are still there - untouched. this would  
> be reasonable in the case when only parts
> of the pdb were selected and re-colored. however if one selects  
> whole files and changes the colors - is it
> possible to have these colors changed also in the model panel? and  
> is it possible to revert to the old color
> once changed through this action menu?
> best regards,
> jean-paul armache

Hi Jean-Paul,
It is because there is a coloring hierarchy:  the Model Panel shows  
the model color, but you can also set atom colors, whichoverrule and  
hide the model color.  As you found, Actions... Color and the "color"  
command set the atom colors (otherwise you would not be able to make  
different parts of the same model different colors).

If you already colored the atoms of a model, you can "uncolor" some or  
all of them to reveal the model color using the command "~color".   
Another way is to choose "Actions... Color... from editor" and then  
click the "No Color" button in the Color Editor.  (The Color Editor  
can be found in the menu under Tools... Utilities)

You can change the model color with the command "modelcolor" or by  
clicking on the square color wells in the Model Panel to call up the  
Color Editor.


I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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