0000236: Rosetta crashes on missing atoms in unrecognized SUCK residues

MantisBT - Rosetta
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ID	Project	Category	View Status	Date Submitted	Last Update
0000236	Rosetta	[All Projects] Crash	public	2013-03-29 19:16	2013-04-01 12:39

Reporter	amelie
Assigned To	amelie
Priority	normal	Severity	crash	Reproducibility	always
Status	assigned	Resolution	open
Platform	All platforms	OS	Any	OS Version	Any
Product Version	Trunk
Fixed in Version
Application(s) Affected	all, presumably
Command Line Used	rosetta_source/bin/score.macosgccrelease -database rosetta_database/ -ignore_unrecognized_res -s 3itb_clean.pdb
Developer Options
Fixed in SVN Version

Summary	0000236: Rosetta crashes on missing atoms in unrecognized SUCK residues
Description	This PDB contains several non-canonical residues. Rosetta doesn't discard them, but then fails to identify them properly, and finally exits with "too many tries in fill_missing_atoms!". This might be because one of the residues has the 3-letter-code SUC, which is close to the internally used SUCK. protocols.jobdist.JobDistributors: Looking for an available job: 1 1 local_scratch/clean/3itb_clean.pdb 1 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6400 residue types core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 347 in file local_scratch/clean/3itb_clean.pdb. Best match rsd_type: GLY core.io.pdb.file_data: [ WARNING ] discarding 23 atoms at position 349 in file local_scratch/clean/3itb_clean.pdb. Best match rsd_type: SUCK core.io.pdb.file_data: Adding undetected upper terminus type to residue 347 core.io.pdb.file_data: Adding undetected lower terminus type to residue 349 core.conformation.Residue: WARNING: Residue connection id changed when creating a new residue at seqpos 349 core.conformation.Residue: WARNING: ResConnID info stored on residue 350 is now out of date! core.io.pdb.file_data: Adding undetected upper terminus type to residue 350 core.conformation.Conformation: [ WARNING ] missing heavyatom: ORIG on residue SUCK 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: ORIG on residue SUCK 348 [... very many repeats of the line above ... ] ERROR: too many tries in fill_missing_atoms! ERROR:: Exit from: src/core/conformation/Conformation.cc line: 2664 Error: Must call shutdown() when finished using job distributor! caught exception [ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/Conformation.cc line: 2664 ERROR: too many tries in fill_missing_atoms!
Steps To Reproduce	see command line below
Additional Information
Tags	No tags attached.
Relationships
Attached Files	3itb_clean.pdb (215,434) 2013-03-29 19:16 https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=23&type=bug

Issue History
Date Modified	Username	Field	Change
2013-03-29 19:16	amelie	New Issue
2013-03-29 19:16	amelie	File Added: 3itb_clean.pdb
2013-04-01 12:39	smlewis	Note Added: 0000230
2013-04-01 12:39	smlewis	Assigned To	=> amelie
2013-04-01 12:39	smlewis	Status	new => assigned

Notes