Opened 4 years ago

Closed 4 years ago

#4810 closed defect (fixed)

AddH: name 'chain' is not defined

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202106210544 (2021-06-21 05:44:33 UTC)
Description
AddH broken for PDB files...

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color bychain; color byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3.dev202106210544 (2021-06-21)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open working.pdb

Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> dssp

> save working.pdb #1

> close #1

> open working.pdb

Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close #1

> open
> /run/media/tic20/storage/structure_dump/aus/melb/mcconville/4w8i/working.pdb
> format pdb

Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> cbc

> close #1

> open
> /run/media/tic20/storage/structure_dump/aus/melb/mcconville/4w8i/working.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/aus/melb/mcconville/4w8i/working.pdb  
---  
warning | PDB SEQRES record for chain B is incomplete. Ignoring input sequence
records as basis for sequence.  
  
Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> show /B:150

> select /B:150

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:150

24 atoms, 23 bonds, 1 residue, 1 model selected  

> cbc

> delete /B:150

> select clear

> save working.pdb

> isolde start

> set selectionWidth 4

Chain information for working.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  
Done loading forcefield  

> dssp

(CLIPPER) NOTE: No symmetry information found in model. Using symmetry from
MTZ file.  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 60,44,44, pixel
0.602,0.591,0.602, shown at level 0.323, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 60,44,44, pixel
0.602,0.591,0.602, shown at level -0.132,0.132, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_3 as #1.1.1.4, grid size 60,44,44, pixel
0.602,0.591,0.602, shown at level 0.312, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 60,44,44, pixel
0.602,0.591,0.602, shown at level 0.29, step 1, values float32  

> ui tool show Shell

> isolde write phenixRefineInput #1 numProcessors 12

> save working.pdb_for_phenix.cif #1.2 selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> save working.pdb_for_phenix.mtz #1.1.1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  
A phenix.refine input file refine.eff with settings recommended for ISOLDE
models has been written to
/run/media/tic20/storage/structure_dump/aus/melb/mcconville/4w8i along with a
current snapshot of your model (working.pdb_for_phenix.cif) and reflections
(working.pdb_for_phenix.mtz). Note that the reflections file only contains
amplitudes - if you have a MTZ file with intensities you may wish to edit
refine.eff to substitute that. You can start a refinement job by running the
following command in the working directory:  
phenix.refine refine.eff.  

> view /B:151

No objects specified.  

> view /B:152

No objects specified.  

> view /B:149

> select clear

> open
> /run/media/tic20/storage/structure_dump/aus/melb/mcconville/4w8i/Q5X3A8.fasta

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/aus/melb/mcconville/4w8i/Q5X3A8.fasta  
---  
note | Alignment identifier is Q5X3A8.fasta  
  
Opened 1 sequences from Q5X3A8.fasta  

> sequence chain /A

Alignment identifier is 1.2/A  

> isolde write phenixRefineInput #1 numProcessors 12

> save working.pdb_for_phenix.cif #1.2 selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> save working.pdb_for_phenix.mtz #1.1.1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  
A phenix.refine input file refine.eff with settings recommended for ISOLDE
models has been written to
/run/media/tic20/storage/structure_dump/aus/melb/mcconville/4w8i along with a
current snapshot of your model (working.pdb_for_phenix.cif) and reflections
(working.pdb_for_phenix.mtz). Note that the reflections file only contains
amplitudes - if you have a MTZ file with intensities you may wish to edit
refine.eff to substitute that. You can start a refinement job by running the
following command in the working directory:  
phenix.refine refine.eff.  

> close #1

Deleting Crystallographic maps (4w8i_for_phenix.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_3  
Deleting (LIVE) MDFF potential  

> open
> /run/media/tic20/storage/structure_dump/aus/melb/mcconville/4w8i/working.pdb_for_phenix_refine_001.pdb

Chain information for working.pdb_for_phenix_refine_001.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for working.pdb_for_phenix_refine_001.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  

> dssp

> set bgColor white

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 60,44,44, pixel
0.602,0.591,0.602, shown at level 0.371, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 60,44,44, pixel
0.602,0.591,0.602, shown at level -0.188,0.188, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_3 as #1.1.1.4, grid size 60,44,44, pixel
0.602,0.591,0.602, shown at level 0.356, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 60,44,44, pixel
0.602,0.591,0.602, shown at level 0.34, step 1, values float32  

> addh

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2854, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 168, in hbond_add_hydrogens  
_prep_add(session, structures, unknowns_info, template, **prot_schemes)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 423, in _prep_add  
real_N, real_C, fake_N, fake_C, fake_5p = determine_termini(session,
structures)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/util.py", line 73, in determine_termini  
rn, rc, fn, fc, f5p = guess_termini(chain)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/util.py", line 140, in guess_termini  
if chain.polymer_type == Residue.PT_AMINO:  
NameError: name 'chain' is not defined  
  
NameError: name 'chain' is not defined  
  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/util.py", line 140, in guess_termini  
if chain.polymer_type == Residue.PT_AMINO:  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        7.8G         42G        340M         11G         54G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.7
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.23
    ChimeraX-AtomicLibrary: 3.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202106210544
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev8
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.3
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.6
    ChimeraX-PDB: 2.4.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.10
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
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    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.2.1
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
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    line-profiler: 3.3.0
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    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.20.3
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
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    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
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Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → AddH: name 'chain' is not defined

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Only affects structure lacking SEQRES information. Fixed in tomorrow's build.

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