[Chimera-users] How to "Align" two atoms

Thomas Goddard goddard at cgl.ucsf.edu
Thu Oct 4 14:37:28 PDT 2007

Hi Matt,

   Many Chimera commands are defined in


They are sometimes a pain to call from Python.  Here is some code for 
the align command.


from chimera import openModels, selection
m = openModels.list()[0]
sel = selection.ItemizedSelection()
from Midas import align

Matthew Baker wrote:
> I'm writing a module.  I've created a model and added it to the open 
> models.  How can I reproduce the command-line function
>     align #1:1 #1:2
> The variable names for my two atoms are newModel.atoms[0] and 
> newModel.atoms[1].
> Thanks,
> Matt

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