[Chimera-users] How are chains paired in morphing?

Eric Pettersen pett at cgl.ucsf.edu
Tue Feb 23 15:00:59 PST 2010

The sequences are in input order unless you ask for the return value  
to be a dictionary (with the 'asDict' keyword).


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Feb 22, 2010, at 11:25 AM, Conrad Huang wrote:

> There's a comment in Segment.py:
> 	# Get the chains from each model.  If they do not have the
> 	# same number of chains, we give up.  Otherwise, we assume
> 	# that the chains should be matched in the same order
> It uses molecule.sequences() to get the chains.  Eric, does  
> sequences() return the chains in input order, or is it random (eg  
> hash order)?
> Conrad
> On 2/22/2010 10:26 AM, Thomas Goddard wrote:
>> Bobby Laird showed me a homo-tetramer with chains A, B, C, D that  
>> when
>> morphed between two states with the Chimera morph conformations tool
>> swapped two of the monomers. In other words the 4 chains from one  
>> state
>> weren't correctly paired with the 4 chains from the other state so  
>> two
>> monomers exchanged positions during the morph. The tetramers were  
>> built
>> from dimers 1pfk and 2pfk by using the symmetry of the unit cell with
>> other software (coot?).
>> How does morph conformations decide which chains to pair?
>> Tom
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>> Chimera-users at cgl.ucsf.edu
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