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Bug report: the oxygen coordinates of peptide bond predicted by PepFlow is incorrect. #4

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yangxiufengsia opened this issue Nov 14, 2024 · 1 comment

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@yangxiufengsia
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yangxiufengsia commented Nov 14, 2024

Hi, thanks for such interesting paper. I played around your method, but found the generated backbone oxygen coordinate is not correct, could you please tell me the reason or help fix this bug? Thank you again.
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@yangxiufengsia yangxiufengsia changed the title But report: the oxygen coordinates of peptide bond predicted by PepFlow is incorrect. Bug report: the oxygen coordinates of peptide bond predicted by PepFlow is incorrect. Nov 14, 2024
@Guo-Stone
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To my way of thinking, this may arribute to the wrong standard position of O atom. In the dict rigid_group_heavy_atom_positions, the standard position of O is ['O', 3, (0.627, 1.062, 0.000)]. But I think it should be ['O', 3, (0.627, -1.062, 0.000)], because I have calculated it into detail.

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