[Chimera-users] Changing default element colors

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 17 13:57:02 PDT 2009

Some additional clarification:

Opening a Chimera command file executes the commands in it, so you  
could simply open the file every time you wanted to set up those  
element colors. *.com or *.cmd is the standard filename extension for  
a Chimera command file.

Using the Command Line preferences as described in my previous  
message is just a way to avoid having to open it yourself every  
time.  If you do change preferences, remember to click Save in each  
category (Command Line, Tools) to make them apply to future uses of  


On Mar 17, 2009, at 9:32 AM, Elaine Meng wrote:

> Hi Thomas,
> It is easy to do so with a series of colordef commands, where the name
> of the color being defined is an element symbol. For example:
> colordef C green
> colordef Zn hot pink
> If you have a very recent daily build, you can also specify colors
> with R,G,B components or as a Tk color code:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html>
> List of color names:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html>
> Subsequent coloring by element will use those colors.  The definitions
> are saved in session files, but if you want them to apply in all later
> uses of Chimera (not necessarily starting from a saved session), make
> a Chimera command file, simply a text file including all those
> commands.  Then, in the preferences (Favorites... Preferences, Command
> Line category, only shown when you are showing the Command Line),
> specify the command file as a "file to read at startup", which
> actually means as soon as the Command Line is shown.  To make the
> Command Line always shown when you start Chimera, change to the Tools
> category of preferences and check the "Auto Start" column for the
> Command Line tool.
> I hope this helps,
> Elaine
> On Mar 17, 2009, at 5:57 AM, Dipl.-Ing. Thomas Mitterfellner wrote:
>> Hello!
>> Can the default element colors be changed easily and if so, how?
>> Thank you,
>> Tom
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