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Fix: Prevent AlphaFold 1x1x1 dummy cell crashes #21

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Fix: Prevent AlphaFold 1x1x1 dummy cell crashes #21

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2b3caec
Fix: Prevent AlphaFold 1x1x1 dummy cell crashes using Gemmi to sync M…
KevinBattaile Jun 12, 2026
14e4d78
Fix: Update pre-processor to handle list of inputs and ignore web dow…
KevinBattaile Jun 13, 2026
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31 changes: 31 additions & 0 deletions main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import os
import sys
import argparse
import gemmi
if __name__ == '__main__' and __package__ is None:
sys.path.insert(1, os.path.dirname(os.path.dirname(os.path.abspath(__file__
))))
Expand Down Expand Up @@ -47,6 +48,36 @@
GOOD_FINAL_RFREE = 0.4

def dimple(wf, opt):

# --- START ALPHAFOLD PRE-PROCESSOR FIX ---
for i, pdb_path in enumerate(opt.pdbs):
if os.path.isfile(pdb_path):
try:
pdb_st = gemmi.read_structure(pdb_path)

# Check for the AlphaFold dummy cell (a-axis <2)
if pdb_st.cell.a < 2.0:
# Assign a safe, massive dummy cell
# Volume = 1,000,000 A^3. rwcontents won't crash
# It will NOT match the MTZ, forcing dimple to use the phaser-mr path
pdb_st.cell = gemmi.UnitCell(100.0, 100.0, 100.0, 90.0, 90.0, 90.0)
pdb_st.spacegroup_hm = 'P 1'

# Write to the absolute path of the output directory
new_filename = "fixed_AF_" + os.path.basename(pdb_path)
absolute_out_dir = os.path.abspath(opt.output_dir)
fixed_path = os.path.join(absolute_out_dir, new_filename)
pdb_st.write_pdb(fixed_path)

# Update Dimple's internal list to use the new patched file
opt.pdbs[i] = fixed_path

except Exception as e:
# If gemmi fails for any reason, print a warning but don't crash
print(f"[*] Pre-processor warning: Could not read PDB with Gemmi ({e}). Proceeding...")
# --- END ALPHAFOLD PRE-PROCESSOR FIX ---


comment(' ### Dimple v%s. Problems and suggestions:'
' ccp4.github.io/dimple ###' % __version__)
mtz_meta = wf.read_mtz_metadata(opt.mtz)
Expand Down