MantisBT - Rosetta
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0000162Rosetta[All Projects] Incorrect Resultspublic2012-12-11 14:412012-12-12 22:13
All platformsAnyAny
Any which read PDBs
score_jd2 -s input.pdb
Confirmed As Bug
0000162: Incorrect TER card handling in input/output
If you have a PDB with a single PDB chain ID, but with TER records between the residues, Rosetta will split the chain and make the residues on either side of the TER into terminus variants.

However, upon output those TER cards are lost, so the next time Rosetta inputs the file it will treat them as a single chain.
Take a protein structure. Add TER records between residue with the same PDB chain ID (with or without removing intervening residues). Then pass the result through Rosetta twice. e.g.

score_jd2 -s input.pdb -out:pdb
score_jd2 -s input_0001.pdb -out:pdb

Compare the input_0001.pdb and input_0001_0001.pdb files - particularly note the differences in the patch information in the scoring block on the residues next to the original TER records and the OXT and 1H, 2H, and 3H atoms in the coordinates section.

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Issue History
2012-12-11 14:41rmorettiNew Issue
2012-12-11 14:45rmorettiNote Added: 0000133

2012-12-11 14:45   
BTW, hat tip to robren in the forums ( [^]) for getting me thinking about this.