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openmm / pdbfixer

PDBFixer fixes problems in PDB files
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CONNECT records lost in processing #139

Closed spadavec closed 8 years ago

spadavec commented 8 years ago

After processing a PDB, the CONNECT records appear to have been deleted for a ligand in a PDB:

Recipe to recreate (Using the web interface): 1) Download 4djw 2) Select only items for Chain A to be kept (e.g. Protein and TLA/0KP) 3) Select None additional residues to be built in 4) Keep all heterogens 5) Add hydrogrens for pH 7 and don't add Water 6) Save and look at file. Residue 0KP (imatinib) will appear to not have any bonds, but the atoms are present

Screenshot of output in PyMOL

peastman commented 8 years ago

I just sent a PR with the fix: #140. Could you test it and verify it works for you?