[Chimera-users] configuration file for chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 17 09:31:24 PST 2009

Dear Bala,

(1) which tools (Command Line, etc.) automatically start at Chimera  
startup:  use Preferences, Tools category.  You can choose  
"Favorites... Preferences" and then go to the Tools category, or go to  
it directly by choosing "Tools... Add to Favorites/Toolbar".  Either  
way you will want to check the "Auto Start" column for "Command Line"  
and any other tools you want to appear at startup.  Remember to click  
Save if you want the settings to apply to later uses of Chimera.

(2) initial molecule appearance: use Preferences, New Molecules  
category. It sounds like you already saw this, and have found that the  
options there are somewhat limited.  There is no way in this dialog to  
say carbons should be green, for example.  However, at least the  
things you mentioned can be done by combining some of these New  
Molecules preference settings with a startup command script.  In the  
New Molecules preferences, change "per-atom coloring" to "by element"  
and click Save.  Then make a Chimera command script that defines your  
various macros (I imagine you could do this with the "alias" command)  
and changes the carbon element color to green.  You specify the name/ 
location of any startup scripts in Preferences, Command Line category  
(again remember to click Save).

Note that since the script is read at startup, it will not do any good  
to insert commands that do things to structures such as color carbons  
green, because there will not be any structures right at startup.   
Instead you must literally redefine the carbon element-coding color as  
green with the command:

colordef C green

I just tried this whole procedure to make sure it works.  Each element  
color is simply named with the element symbol, see
The default hydrogen color is already white.

I should say that the longer-term goal is to allow people to define  
their own presets as well as which settings should apply to new  
molecules -- a more complete and flexible approach than is available  
currently -- so how one would go about this is expected to change.   
However, all of the above is how you would do it in today's Chimera.   

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

On Feb 17, 2009, at 2:48 AM, Bala subramanian wrote:

> Dear chimerians,
> Sorry if this question has been asked before. Where can i fix the  
> default parameters for chimera. I explored the preferences option in  
> favourites menu and set chose some preferences. In addition to that  
> I want to the following like
> setting the color of carbon atoms as green as default
> setting the color of hydrogen atoms as white as default
> setting some macros
> setting the command line option when the chimera starts up (every  
> time i go to favourites and click command line to invoke it)
> and other settings something like the configuration file used for  
> vmd (.vmdrc ).
> Thanks in advance,
> Bala

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