0000028: 1L2Y produces warnings in fixbb integration test

View Issue Details [ Jump to Notes ]

[ Issue History ] [ Print ]

Project

Category

View Status

Date Submitted

Last Update

0000028

Rosetta

[All Projects] Bad Coding

public

2012-06-26 08:38

2012-06-27 17:18

Reporter

smlewis

Assigned To

momeara

Priority

low

Severity

minor

Reproducibility

always

Status

resolved

Resolution

fixed

Platform

All platforms

Any

OS Version

Any

Product Version

Fixed in Version

Summary

0000028: 1L2Y produces warnings in fixbb integration test

Description

1L2Y produces warnings in the fixbb integration test:

core.io.pdb.file_data: [ WARNING ] discarding 7 atoms at position 1 in file 1l2y.pdb. Best match rsd_type: ASN_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 2 in file 1l2y.pdb. Best match rsd_type: LEU
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 3 in file 1l2y.pdb. Best match rsd_type: TYR
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 4 in file 1l2y.pdb. Best match rsd_type: ILE
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 5 in file 1l2y.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 6 in file 1l2y.pdb. Best match rsd_type: TRP
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 7 in file 1l2y.pdb. Best match rsd_type: LEU
core.io.pdb.file_data: [ WARNING ] discarding 11 atoms at position 8 in file 1l2y.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 9 in file 1l2y.pdb. Best match rsd_type: ASP
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 10 in file 1l2y.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 11 in file 1l2y.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 12 in file 1l2y.pdb. Best match rsd_type: PRO
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 13 in file 1l2y.pdb. Best match rsd_type: SER
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 14 in file 1l2y.pdb. Best match rsd_type: SER
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 15 in file 1l2y.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 10 atoms at position 16 in file 1l2y.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 17 in file 1l2y.pdb. Best match rsd_type: PRO
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 18 in file 1l2y.pdb. Best match rsd_type: PRO
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 19 in file 1l2y.pdb. Best match rsd_type: PRO
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 20 in file 1l2y.pdb. Best match rsd_type: SER_p:CtermProteinFull

Steps To Reproduce

integration.py fixbb

Additional Information

Suggested fixes: replace 1l2y with a rosetta-output PDB, or grep -v the hydrogens

Tags

No tags attached.

Application(s) Affected

fixbb integration test

Command Line Used

integration.py fixbb

Developer Options

Fixed in SVN Version

49635

Attached Files

Relationships

Notes
(0000017) momeara (Attentive Developer) 2012-06-27 11:56	This is really a problem with Rosetta's hydrogen naming convention. Until it is made standards compliant the solution is to use rosetta_tools/convert_hatm_names.py

Issue History
Date Modified	Username	Field	Change
2012-06-26 08:38	smlewis	New Issue
2012-06-27 11:56	momeara	Fixed in SVN Version	=> 49635
2012-06-27 11:56	momeara	Note Added: 0000017
2012-06-27 11:56	momeara	Status	new => closed
2012-06-27 11:56	momeara	Assigned To	=> momeara
2012-06-27 11:56	momeara	Resolution	open => fixed
2012-06-27 17:18	delucasl	Status	closed => resolved