RNA training omits O2' atom — predicted 2'-OH positions are non-physical #4

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Open
RNA training omits O2' atom — predicted 2'-OH positions are non-physical#4

Description

@Buddha7771
Buddha7771
opened on Apr 29, 2026

Summary

rnapro/data/rna_dataset_allatom.py:75-103 defines ATOM_NAMES with 26 RNA atoms, but the docstring on line 140 says "Supports 27 standard RNA atoms". The missing atom is O2' (the ribose 2'-OH oxygen). Because this list is used to extract ground-truth coordinates from the training CSV (lines 401-417), the model receives no supervision for O2'. As a result, predicted O2' positions in inference output are non-physical and far from their parent ribose.

This affects all-atom geometric quality of every RNAPro RNA prediction.

Visualization

The image below shows the R1107(PDB id: 7QR3) prediction : backbone as gray sticks (cartoon overlay), all O2' atoms as red spheres. Many O2' atoms float far from any ribose:

Image

Root cause

rnapro/data/rna_dataset_allatom.py:75-103:

ATOM_NAMES= [
"P", "OP1", "OP2", "O5'", "O3'",
"C1'", "C2'", "C3'", "C4'", "O4'", "C5'", # ← O2' missing here"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6", "O4",
"N9", "N7", "C8", "N6", "N2", "O6"
]
# len(ATOM_NAMES) == 26 but the docstring on line 140 says "Supports 27 standard RNA atoms"

Used to construct the per-residue GT coordinate tensor (lines 401-417):

coord_cols= [f"{atom_name}_x_1"foratom_nameinATOM_NAMES] + ...
coords_matrix=group[coord_cols].values.astype(np.float32)
coords_reshaped=coords_matrix.reshape(n_residues, n_atoms, 3) # n_atoms = 26

Atoms not in ATOM_NAMES are never loaded as GT, so the loss never penalises wrong O2' positions.

Impact

  • All-atom lDDT, all-atom RMSD, and any downstream task sensitive to 2'-OH positioning (ribozyme catalysis modelling, ligand docking, sugar pucker analysis) are unreliable.
  • Visual inspection of any prediction shows clearly unphysical O2' positions.

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      Skip to content
      RNA training omits O2' atom — predicted 2'-OH positions are non-physical #4
      Open
      Open
      RNA training omits O2' atom — predicted 2'-OH positions are non-physical#4
      Description
      @Buddha7771
      Buddha7771
      opened on Apr 29, 2026
      Summary
      rnapro/data/rna_dataset_allatom.py:75-103 defines ATOM_NAMES with 26 RNA atoms, but the docstring on line 140 says "Supports 27 standard RNA atoms". The missing atom is O2' (the ribose 2'-OH oxygen). Because this list is used to extract ground-truth coordinates from the training CSV (lines 401-417), the model receives no supervision for O2'. As a result, predicted O2' positions in inference output are non-physical and far from their parent ribose.
      This affects all-atom geometric quality of every RNAPro RNA prediction.
      Visualization
      The image below shows the R1107(PDB id: 7QR3) prediction : backbone as gray sticks (cartoon overlay), all O2' atoms as red spheres. Many O2' atoms float far from any ribose:
      Image
      Root cause
      rnapro/data/rna_dataset_allatom.py:75-103:
      ATOM_NAMES= [
"P", "OP1", "OP2", "O5'", "O3'",
"C1'", "C2'", "C3'", "C4'", "O4'", "C5'", # ← O2' missing here"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6", "O4",
"N9", "N7", "C8", "N6", "N2", "O6"
]
# len(ATOM_NAMES) == 26 but the docstring on line 140 says "Supports 27 standard RNA atoms"
      Used to construct the per-residue GT coordinate tensor (lines 401-417):
      coord_cols= [f"{atom_name}_x_1"foratom_nameinATOM_NAMES] + ...
coords_matrix=group[coord_cols].values.astype(np.float32)
coords_reshaped=coords_matrix.reshape(n_residues, n_atoms, 3) # n_atoms = 26
      Atoms not in ATOM_NAMES are never loaded as GT, so the loss never penalises wrong O2' positions.
      Impact
      • All-atom lDDT, all-atom RMSD, and any downstream task sensitive to 2'-OH positioning (ribozyme catalysis modelling, ligand docking, sugar pucker analysis) are unreliable.
      • Visual inspection of any prediction shows clearly unphysical O2' positions.
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(function(){
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          Skip to content
          RNA training omits O2' atom — predicted 2'-OH positions are non-physical #4
          Open
          Open
          RNA training omits O2' atom — predicted 2'-OH positions are non-physical#4
          Description
          @Buddha7771
          Buddha7771
          opened on Apr 29, 2026
          Summary
          rnapro/data/rna_dataset_allatom.py:75-103 defines ATOM_NAMES with 26 RNA atoms, but the docstring on line 140 says "Supports 27 standard RNA atoms". The missing atom is O2' (the ribose 2'-OH oxygen). Because this list is used to extract ground-truth coordinates from the training CSV (lines 401-417), the model receives no supervision for O2'. As a result, predicted O2' positions in inference output are non-physical and far from their parent ribose.
          This affects all-atom geometric quality of every RNAPro RNA prediction.
          Visualization
          The image below shows the R1107(PDB id: 7QR3) prediction : backbone as gray sticks (cartoon overlay), all O2' atoms as red spheres. Many O2' atoms float far from any ribose:
          Image
          Root cause
          rnapro/data/rna_dataset_allatom.py:75-103:
          ATOM_NAMES= [
"P", "OP1", "OP2", "O5'", "O3'",
"C1'", "C2'", "C3'", "C4'", "O4'", "C5'", # ← O2' missing here"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6", "O4",
"N9", "N7", "C8", "N6", "N2", "O6"
]
# len(ATOM_NAMES) == 26 but the docstring on line 140 says "Supports 27 standard RNA atoms"
          Used to construct the per-residue GT coordinate tensor (lines 401-417):
          coord_cols= [f"{atom_name}_x_1"foratom_nameinATOM_NAMES] + ...
coords_matrix=group[coord_cols].values.astype(np.float32)
coords_reshaped=coords_matrix.reshape(n_residues, n_atoms, 3) # n_atoms = 26
          Atoms not in ATOM_NAMES are never loaded as GT, so the loss never penalises wrong O2' positions.
          Impact
          • All-atom lDDT, all-atom RMSD, and any downstream task sensitive to 2'-OH positioning (ribozyme catalysis modelling, ligand docking, sugar pucker analysis) are unreliable.
          • Visual inspection of any prediction shows clearly unphysical O2' positions.
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(function(){
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var __re = new RegExp('^' + ".*" + '

              Skip to content
              RNA training omits O2' atom — predicted 2'-OH positions are non-physical #4
              Open
              Open
              RNA training omits O2' atom — predicted 2'-OH positions are non-physical#4
              Description
              @Buddha7771
              Buddha7771
              opened on Apr 29, 2026
              Summary
              rnapro/data/rna_dataset_allatom.py:75-103 defines ATOM_NAMES with 26 RNA atoms, but the docstring on line 140 says "Supports 27 standard RNA atoms". The missing atom is O2' (the ribose 2'-OH oxygen). Because this list is used to extract ground-truth coordinates from the training CSV (lines 401-417), the model receives no supervision for O2'. As a result, predicted O2' positions in inference output are non-physical and far from their parent ribose.
              This affects all-atom geometric quality of every RNAPro RNA prediction.
              Visualization
              The image below shows the R1107(PDB id: 7QR3) prediction : backbone as gray sticks (cartoon overlay), all O2' atoms as red spheres. Many O2' atoms float far from any ribose:
              Image
              Root cause
              rnapro/data/rna_dataset_allatom.py:75-103:
              ATOM_NAMES= [
"P", "OP1", "OP2", "O5'", "O3'",
"C1'", "C2'", "C3'", "C4'", "O4'", "C5'", # ← O2' missing here"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6", "O4",
"N9", "N7", "C8", "N6", "N2", "O6"
]
# len(ATOM_NAMES) == 26 but the docstring on line 140 says "Supports 27 standard RNA atoms"
              Used to construct the per-residue GT coordinate tensor (lines 401-417):
              coord_cols= [f"{atom_name}_x_1"foratom_nameinATOM_NAMES] + ...
coords_matrix=group[coord_cols].values.astype(np.float32)
coords_reshaped=coords_matrix.reshape(n_residues, n_atoms, 3) # n_atoms = 26
              Atoms not in ATOM_NAMES are never loaded as GT, so the loss never penalises wrong O2' positions.
              Impact
              • All-atom lDDT, all-atom RMSD, and any downstream task sensitive to 2'-OH positioning (ribozyme catalysis modelling, ligand docking, sugar pucker analysis) are unreliable.
              • Visual inspection of any prediction shows clearly unphysical O2' positions.
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var __re = new RegExp('^' + "youtube\\.com" + '

                  Skip to content
                  RNA training omits O2' atom — predicted 2'-OH positions are non-physical #4
                  Open
                  Open
                  RNA training omits O2' atom — predicted 2'-OH positions are non-physical#4
                  Description
                  @Buddha7771
                  Buddha7771
                  opened on Apr 29, 2026
                  Summary
                  rnapro/data/rna_dataset_allatom.py:75-103 defines ATOM_NAMES with 26 RNA atoms, but the docstring on line 140 says "Supports 27 standard RNA atoms". The missing atom is O2' (the ribose 2'-OH oxygen). Because this list is used to extract ground-truth coordinates from the training CSV (lines 401-417), the model receives no supervision for O2'. As a result, predicted O2' positions in inference output are non-physical and far from their parent ribose.
                  This affects all-atom geometric quality of every RNAPro RNA prediction.
                  Visualization
                  The image below shows the R1107(PDB id: 7QR3) prediction : backbone as gray sticks (cartoon overlay), all O2' atoms as red spheres. Many O2' atoms float far from any ribose:
                  Image
                  Root cause
                  rnapro/data/rna_dataset_allatom.py:75-103:
                  ATOM_NAMES= [
"P", "OP1", "OP2", "O5'", "O3'",
"C1'", "C2'", "C3'", "C4'", "O4'", "C5'", # ← O2' missing here"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6", "O4",
"N9", "N7", "C8", "N6", "N2", "O6"
]
# len(ATOM_NAMES) == 26 but the docstring on line 140 says "Supports 27 standard RNA atoms"
                  Used to construct the per-residue GT coordinate tensor (lines 401-417):
                  coord_cols= [f"{atom_name}_x_1"foratom_nameinATOM_NAMES] + ...
coords_matrix=group[coord_cols].values.astype(np.float32)
coords_reshaped=coords_matrix.reshape(n_residues, n_atoms, 3) # n_atoms = 26
                  Atoms not in ATOM_NAMES are never loaded as GT, so the loss never penalises wrong O2' positions.
                  Impact
                  • All-atom lDDT, all-atom RMSD, and any downstream task sensitive to 2'-OH positioning (ribozyme catalysis modelling, ligand docking, sugar pucker analysis) are unreliable.
                  • Visual inspection of any prediction shows clearly unphysical O2' positions.
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(function(){
try {
var __m = "*";
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                      Skip to content
                      RNA training omits O2' atom — predicted 2'-OH positions are non-physical #4
                      Open
                      Open
                      RNA training omits O2' atom — predicted 2'-OH positions are non-physical#4
                      Description
                      @Buddha7771
                      Buddha7771
                      opened on Apr 29, 2026
                      Summary
                      rnapro/data/rna_dataset_allatom.py:75-103 defines ATOM_NAMES with 26 RNA atoms, but the docstring on line 140 says "Supports 27 standard RNA atoms". The missing atom is O2' (the ribose 2'-OH oxygen). Because this list is used to extract ground-truth coordinates from the training CSV (lines 401-417), the model receives no supervision for O2'. As a result, predicted O2' positions in inference output are non-physical and far from their parent ribose.
                      This affects all-atom geometric quality of every RNAPro RNA prediction.
                      Visualization
                      The image below shows the R1107(PDB id: 7QR3) prediction : backbone as gray sticks (cartoon overlay), all O2' atoms as red spheres. Many O2' atoms float far from any ribose:
                      Image
                      Root cause
                      rnapro/data/rna_dataset_allatom.py:75-103:
                      ATOM_NAMES= [
"P", "OP1", "OP2", "O5'", "O3'",
"C1'", "C2'", "C3'", "C4'", "O4'", "C5'", # ← O2' missing here"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6", "O4",
"N9", "N7", "C8", "N6", "N2", "O6"
]
# len(ATOM_NAMES) == 26 but the docstring on line 140 says "Supports 27 standard RNA atoms"
                      Used to construct the per-residue GT coordinate tensor (lines 401-417):
                      coord_cols= [f"{atom_name}_x_1"foratom_nameinATOM_NAMES] + ...
coords_matrix=group[coord_cols].values.astype(np.float32)
coords_reshaped=coords_matrix.reshape(n_residues, n_atoms, 3) # n_atoms = 26
                      Atoms not in ATOM_NAMES are never loaded as GT, so the loss never penalises wrong O2' positions.
                      Impact
                      • All-atom lDDT, all-atom RMSD, and any downstream task sensitive to 2'-OH positioning (ribozyme catalysis modelling, ligand docking, sugar pucker analysis) are unreliable.
                      • Visual inspection of any prediction shows clearly unphysical O2' positions.
                      Metadata
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                      Assignees
                      No one assigned
                        Labels
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                        Type
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                          Skip to content
                          RNA training omits O2' atom — predicted 2'-OH positions are non-physical #4
                          Open
                          Open
                          RNA training omits O2' atom — predicted 2'-OH positions are non-physical#4
                          Description
                          @Buddha7771
                          Buddha7771
                          opened on Apr 29, 2026
                          Summary
                          rnapro/data/rna_dataset_allatom.py:75-103 defines ATOM_NAMES with 26 RNA atoms, but the docstring on line 140 says "Supports 27 standard RNA atoms". The missing atom is O2' (the ribose 2'-OH oxygen). Because this list is used to extract ground-truth coordinates from the training CSV (lines 401-417), the model receives no supervision for O2'. As a result, predicted O2' positions in inference output are non-physical and far from their parent ribose.
                          This affects all-atom geometric quality of every RNAPro RNA prediction.
                          Visualization
                          The image below shows the R1107(PDB id: 7QR3) prediction : backbone as gray sticks (cartoon overlay), all O2' atoms as red spheres. Many O2' atoms float far from any ribose:
                          Image
                          Root cause
                          rnapro/data/rna_dataset_allatom.py:75-103:
                          ATOM_NAMES= [
"P", "OP1", "OP2", "O5'", "O3'",
"C1'", "C2'", "C3'", "C4'", "O4'", "C5'", # ← O2' missing here"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6", "O4",
"N9", "N7", "C8", "N6", "N2", "O6"
]
# len(ATOM_NAMES) == 26 but the docstring on line 140 says "Supports 27 standard RNA atoms"
                          Used to construct the per-residue GT coordinate tensor (lines 401-417):
                          coord_cols= [f"{atom_name}_x_1"foratom_nameinATOM_NAMES] + ...
coords_matrix=group[coord_cols].values.astype(np.float32)
coords_reshaped=coords_matrix.reshape(n_residues, n_atoms, 3) # n_atoms = 26
                          Atoms not in ATOM_NAMES are never loaded as GT, so the loss never penalises wrong O2' positions.
                          Impact
                          • All-atom lDDT, all-atom RMSD, and any downstream task sensitive to 2'-OH positioning (ribozyme catalysis modelling, ligand docking, sugar pucker analysis) are unreliable.
                          • Visual inspection of any prediction shows clearly unphysical O2' positions.
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                              RNA training omits O2' atom — predicted 2'-OH positions are non-physical #4
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                              RNA training omits O2' atom — predicted 2'-OH positions are non-physical#4
                              Description
                              @Buddha7771
                              Buddha7771
                              opened on Apr 29, 2026
                              Summary
                              rnapro/data/rna_dataset_allatom.py:75-103 defines ATOM_NAMES with 26 RNA atoms, but the docstring on line 140 says "Supports 27 standard RNA atoms". The missing atom is O2' (the ribose 2'-OH oxygen). Because this list is used to extract ground-truth coordinates from the training CSV (lines 401-417), the model receives no supervision for O2'. As a result, predicted O2' positions in inference output are non-physical and far from their parent ribose.
                              This affects all-atom geometric quality of every RNAPro RNA prediction.
                              Visualization
                              The image below shows the R1107(PDB id: 7QR3) prediction : backbone as gray sticks (cartoon overlay), all O2' atoms as red spheres. Many O2' atoms float far from any ribose:
                              Image
                              Root cause
                              rnapro/data/rna_dataset_allatom.py:75-103:
                              ATOM_NAMES= [
"P", "OP1", "OP2", "O5'", "O3'",
"C1'", "C2'", "C3'", "C4'", "O4'", "C5'", # ← O2' missing here"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6", "O4",
"N9", "N7", "C8", "N6", "N2", "O6"
]
# len(ATOM_NAMES) == 26 but the docstring on line 140 says "Supports 27 standard RNA atoms"
                              Used to construct the per-residue GT coordinate tensor (lines 401-417):
                              coord_cols= [f"{atom_name}_x_1"foratom_nameinATOM_NAMES] + ...
coords_matrix=group[coord_cols].values.astype(np.float32)
coords_reshaped=coords_matrix.reshape(n_residues, n_atoms, 3) # n_atoms = 26
                              Atoms not in ATOM_NAMES are never loaded as GT, so the loss never penalises wrong O2' positions.
                              Impact
                              • All-atom lDDT, all-atom RMSD, and any downstream task sensitive to 2'-OH positioning (ribozyme catalysis modelling, ligand docking, sugar pucker analysis) are unreliable.
                              • Visual inspection of any prediction shows clearly unphysical O2' positions.
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