0000236: Rosetta crashes on missing atoms in unrecognized SUCK residues

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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

Any

OS Version

Any

Product Version

Trunk

Fixed in 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core.conformation.Residue: WARNING: ResConnID info stored on residue 350 is now out of date!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

Tags

No tags attached.

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

Attached Files

3itb_clean.pdb [^] (215,434 bytes) 2013-03-29 19:16

Relationships

Notes
(0000230) smlewis (Administrator) 2013-04-01 12:39	SUCK has no business being active by default. Remove it from the default ResidueTypeSet (by #commenting it out in residue_types.txt) and this should go away.

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