Eric looked at the code and said the changechains command can’t change the blank chain id because it won’t accept a quoted space character as the chain letter. It could be done with Python code, or as you mention you can do it with the change chain ids gui.

On Oct 20, 2015, at 2:07 PM, Broyde, Joshua E. <wrote:

Dear Tom,
Hope you are well. I am having an issue with redefining the chains in a pdb open in Chimera. If a model has two chains (A and B) then it is easy to reassign the chain ids using:
changechains A,B B,A

However, if one of the chains does not have a chain id already, (what Chimera calls, the "principle chain"), how do I assign a chain id? This is easy to do in the GUI, but I cannot find a command for doing so.

Sincerely,
Joshua Broyde