Hi All,

I have two structures that are homologous.  One structure #1 contains 100 states and structure #2 contains only one state.  I would like to align each state of structure #1 to structure #2 based upon some selection.  From what I can understand, if I say:

align struct1, struct2

This will align state #1 of structure #1 to state #1 of structure #2. 

align struct1, struct2, mobile_state=50

This will align state #50 of structure #1 to state #1 of structure #2.  I believe that if I follow the first alignment command above with this one then I lose the first alignment.  That is, state #1 of structure #1 will no longer be aligned to state #1 of structure #2.

I understand that there is an "intra_fit" command but this only aligns all states of one structure with respect to one of the states in the same structure.  This is not good enough for me.  I want all states of one structure to be aligned with respect to another independent structure, structure #2.  As well, I know that I could in theory split the states, align each structure, and group the structures back together but this seems extremely clumsy.

Can this be done?  Any suggestions would be greatly appreciated.

Sean


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