After running Phase Shape I noticed that two columns are returned: "Shape Sim" and "Shape Sim Pure". Could you explain the difference and when and why to use one or the other?

These are the reported similarities from both with and without atom typing. Shape Sim is computed directly from the alignments obtained using atom typing. The idea that when atom typing is used to compute similarities and optimize the alignments, one may wish to confirm whether there is high similarity between the pure, generic shapes when aligned in the same manner.

Keywords: Phase, Shape Screening, Shape Sim Pure, atom typing

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