Using version 1.3 (so maybe this is fixed in 1.4 already), if you manually move a molecule using Action -> deprotect and [shift]+clicking to drag one molecule around, cealign stops working. The RMSD reported by cealign appears to be correct, but the view is not updated (i.e. the molecule does not visually move in space). If you save a PDB of the altered coordinates, delete the object, and re-load the coordinates, then cealign works as expected.
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