0000162: Incorrect TER card handling in input/output

MantisBT - Rosetta
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ID	Project	Category	View Status	Date Submitted	Last Update
0000162	Rosetta	[All Projects] Incorrect Results	public	2012-12-11 14:41	2012-12-12 22:13

Reporter	rmoretti
Assigned To
Priority	normal	Severity	minor	Reproducibility	always
Status	new	Resolution	open
Platform	All platforms	OS	Any	OS Version	Any
Product Version	Trunk
Fixed in Version
Application(s) Affected	Any which read PDBs
Command Line Used	score_jd2 -s input.pdb
Developer Options	Confirmed As Bug
Fixed in SVN Version

Summary	0000162: Incorrect TER card handling in input/output
Description	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.
Steps To Reproduce	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
Date Modified	Username	Field	Change
2012-12-11 14:41	rmoretti	New Issue
2012-12-11 14:45	rmoretti	Note Added: 0000133

Notes