[Chimera-users] Maintaining Color and Formatting Selections for New Molecules

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 8 10:07:10 PST 2008

Hi Eric,
There is no automatic way to apply everything you have done to the  
display of one molecule to others opened later.  However, here are a  
few ways to avoid repetition:

(a) the New Molecules category in Preferences ("Favorites...  
Preferences" in the menu) controls how you want structures to look  
when they are opened.  The main limitation of this approach is that  
not everything you might want is in this panel.  After changing  
settings, remember to click Save if you want them to apply to later  
uses of Chimera.

(b) make a Chimera command file that sets up display how you want.  If  
you used commands for the first molecule, you could open the Command  
History and save those set of commands to a file.  Otherwise, you  
could just create it with a text editor.  Then simply opening the  
command file named *.com or *.cmd automatically executes all the  
commands.  The drawback to this approach is needing to learn how to  
use commands:

(c) there are a few choices in the Presets menu to automatically  
change several display parameters at once.  In the future we would  
like to allow users to make custom presets that would also appear in  
this menu, but unfortunately that is not yet possible.

I hope this helps,

On Dec 8, 2008, at 9:39 AM, Eric Ganz wrote:

> Now that I have formatted and colored one molecule, I would like to  
> maintain
> the color and formatting selections for a series of new molecules.   
> How
> should I do this?

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