steps to reproduce:
PyMOL>fetch 1ake 4ake, async=0 PyMOL>super 1ake and chain A, 4ake and chain A, object=aln PyMOL>count_atoms aln and name N count_atoms: 0 atoms
Tested with PyMOL 1.1r1 to 1.5.0.2
The problem is a forward search over atoms in SelectorCreateAlignments. This works fine if a residue is represented by its first atom, but "super" passes the CA atom as representative, which is sorted after the N atom.
Patch: https://github.com/speleo3/pymol/commit/fa53f1ad7ec61aec28aabcbcc5043f94c4207153
fixed in rev 4006
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The problem is a forward search over atoms in SelectorCreateAlignments. This works fine if a residue is represented by its first atom, but "super" passes the CA atom as representative, which is sorted after the N atom.
Patch:
https://github.com/speleo3/pymol/commit/fa53f1ad7ec61aec28aabcbcc5043f94c4207153
fixed in rev 4006