you can set the number of cycles of refinement on the command line. change this:
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca to this: > align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca, 0, 0 I forget what the first 0 means; the second means "don't refine." It'll use all matching atoms this way.
