[Chimera-users] Getting an extension handle

Charles Moad cmoad at indiana.edu
Mon Feb 7 10:50:41 PST 2005

Charles Moad wrote:
> 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?

I think I found my answer by looking at some sources.  The following 
works given my list of models, mdls:

for mdl,mseq in map(lambda x,y: (x[0],y), mdls, mav.seqs):
         mav.associate(mdl.sequences()[0], seq=mseq, force=1)


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