[Chimera-users] Customizing Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 25 10:08:20 PST 2014

The link in Eric’s mail for information on startup command files was supposed to go here:


See also: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>

On Dec 25, 2014, at 9:59 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> On Dec 22, 2014, at 1:08 AM, Michał Kadlof wrote:
>> Hello,
>> I'm currently work on proteins with disulfide bonds. I'm very often do the same sequence of tasks in Chimera:
>> 1. open structure
>> 2. Select -> chemistry -> functional group -> disulfide
>> 3. extend selection to have selected all atoms of Cys-Cys bridge
>> 4. Show selected atoms
>> Is there any way to wrap it into one-click button on toolbar?
> Hi Michał,
> 	While it is literally possible to put what you want on the toolbar, it's a bit easier to make a menu item instead.  To do that, you create a command alias for the actions, and put that in a file that Chimera reads at startup so that it is always available.  Details:
> The alias would be
> 	alias ^showbridge sel disulfide; sel up; disp sel
> This creates an alias named "showbridge" which is only expanded if typed at the beginning of a line -- that's what the ^ indicates.  Such beginning-of-line aliases are also placed in an Aliases menu that appears after the Favorites menu (if you have any such aliases).
> 	To get the alias read by Chimera at startup you would put it in any of the files listed in the "Files to read at startup" section of the Command Line preferences (Favorites->Preferences).  This is also described in more detail here:  Command Line.
> 	Finally, if you really want it on the toolbar instead, that will involve making your own (simple) plug-in in Python.  I can provide more detail about that if you like.
> --Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
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