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

Thomas Goddard goddard at cgl.ucsf.edu
Mon Mar 1 11:57:21 PST 2010

Hi Eric,

   So either the morphing is pairing chains according to the order in 
the PDB file or maybe it is random.  I think it would be better if Morph 
Conformations paired chains with the same chain ID.  Since the two 
conformations may use different chain identifiers a more general rule 
might be to order the chains alphabetically by chain ID and pair them in 
that order.  That would be the behavior for the dialog interface.  For 
the "morph" command it would be good to allow the above alphabetical 
pairing or an explicit ordering of chains given on the command-line such 
as :.A,.C,.B,.D for one conformation, :.P,.Q,.S,.R for the next.


> The sequences are in input order unless you ask for the return value to
> be a dictionary (with the 'asDict' keyword).
> --Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
> 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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