[Chimera-users] configuration file for chimera
meng at cgl.ucsf.edu
Tue Feb 17 09:31:24 PST 2009
(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,
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