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.