[Chimera-users] Getting an extension handle

[Charles Moad]

Elaine Meng wrote:
>>How would I get get a handle on a running instance of an extension? 
>>Specifically, I want to be able to associate my own structures to 
>>sequences in the MultAlignViewer.
> 
> 
> Hi Charlie,
> If I understand you correctly, this is something you
> can do this in the user interface (without dealing with code).
> Your structures should automatically associate with the
> sequences when opened in Chimera, if the structure's sequence
> and the sequence in the alignment match well enough.  Even
> if they don't, you can "force" the structure to associate
> using Multalign Viewer's menu option
>   Structure... Associations
> This option brings up a dialog in which you can specify
> which of the structures open in Chimera should be
> associated with  a sequence in the alignment.
> 

I am working on a plugin so I do want to be able to do this 
programatically.  Thanks for the hint on the auto-association.  The 
problem I have now is matching too well.  Both sequences are matching 
the second model loaded.  I see I can fix this in the interface, but any 
clue on how to access this for scripting?

Thanks again,
	Charlie