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improve_alignment （尚未明白，还在查询）：
There are several possibilities as to the final orientation of the input coordinates. If fit_on_first is True, all the coordinate sets are superposed on the first structure, using the final multi-feature multiple alignment. If fit_on_first is False, and position feature was used, and fit was True, the coordinates will be superposed in the progressive manner guided by the tree, by the routine that calculates the inter-molecular distance matrices; this superposition is based only on the positions of the selected atoms (feature 2), not on other features such as residue type, secondary, structure, etc. If improve_alignment is False, it does not make much sense to have fit = True (use fit_on_first = True). |
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