Opened 4 years ago

Closed 4 years ago

#5685 closed defect (fixed)

Fixing unparameterized residue: cannot unpack non-iterable builtin_function_or_method object

Reported by: roberto.diaz@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Trying to model build a crystallographic model with ligands N-acetyl-Glucosamine,  di-NAG,  and tri-NAG.  Missing MD parameters error thrown

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/rediaz/Downloads/Refine_6/G07_QCR005_p04_1_refine_6-coot-0.pdb
> format pdb

Chain information for G07_QCR005_p04_1_refine_6-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Drag select of 11 atoms, 10 residues, 8 bonds  

> select clear

Drag select of 2 atoms, 1 bonds  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for G07_QCR005_p04_1_refine_6-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  
Done loading forcefield  

> open 1a0m structureFactors true

Summary of feedback from opening 1a0m fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 437 free from 9264 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Fetching compressed mmCIF 1a0m from
http://files.rcsb.org/download/1a0m.cif  
Fetching compressed 1a0m structure factors from
http://files.rcsb.org/download/1a0m-sf.cif  
Resolution: 1.0944213038232693  
  
Opened (LIVE) 2mFo-DFc as #2.1.1.2, grid size 72,70,74, pixel
0.347,0.347,0.326, shown at level 2.35, step 1, values float32  
Opened (LIVE) mFo-DFc as #2.1.1.3, grid size 72,70,74, pixel
0.347,0.347,0.326, shown at level -0.328,0.328, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_27 as #2.1.1.4, grid size 72,70,74, pixel
0.347,0.347,0.326, shown at level 0.908, step 1, values float32  
1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m  
---  
Chain | Description  
2.2/A 2.2/B | α-conotoxin [TYR15]-epi  
  
Non-standard residues in 1a0m #2.2  
---  
NH2 — amino group  
  

> open 1a0m structureFactors true

Summary of feedback from opening 1a0m fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 521 free from 9264 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 1.0944213038232693  
  
Opened (LIVE) 2mFo-DFc as #3.1.1.2, grid size 72,70,74, pixel
0.347,0.347,0.326, shown at level 2.47, step 1, values float32  
Opened (LIVE) mFo-DFc as #3.1.1.3, grid size 72,70,74, pixel
0.347,0.347,0.326, shown at level -0.302,0.302, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_27 as #3.1.1.4, grid size 72,70,74, pixel
0.347,0.347,0.326, shown at level 0.908, step 1, values float32  
1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m  
---  
Chain | Description  
3.2/A 3.2/B | α-conotoxin [TYR15]-epi  
  
Non-standard residues in 1a0m #3.2  
---  
NH2 — amino group  
  
Opened (LIVE) MDFF potential as #2.1.1.5, grid size 72,70,74, pixel
0.347,0.347,0.326, shown at level 0.933, step 1, values float32  

> save /Users/rediaz/Desktop/1a0m.mtz #1

You need to specify at least one crystallographic map set to save!  

> save /Users/rediaz/Desktop/1a0m.mtz #1

You need to specify at least one crystallographic map set to save!  

> close #1

> close #2

Deleting Crystallographic maps (1a0m-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_27  
Deleting (LIVE) MDFF potential  

> close #3

Deleting Crystallographic maps (1a0m-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_27  

> open /Users/rediaz/Downloads/Refine_6/G07_QCR005_p04_1_refine_6-coot-0.pdb
> format pdb

Chain information for G07_QCR005_p04_1_refine_6-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #1

12742 atoms, 11957 bonds, 1724 residues, 1 model selected  

> ~select #1

Nothing selected  
running convert_amber_files  
/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/parmed/utils/netcdf.py:770: SyntaxWarning: "is not" with a literal.
Did you mean "!="?  
if typecode is not 'c':  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for G07_QCR005_p04_1_refine_6-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  
Done loading forcefield  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 60,58,58, pixel
0.423,0.425,0.425, shown at level 0.998, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 60,58,58, pixel
0.423,0.425,0.425, shown at level -0.244,0.244, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_20 as #1.1.1.4, grid size 60,58,58, pixel
0.423,0.425,0.425, shown at level 0.626, step 1, values float32  
Opened (STATIC) (Model-structure-factors-(bulk-solvent-and-all-scales-
included)) F-model, PHIF-model as #1.1.1.5, grid size 60,58,58, pixel
0.423,0.425,0.425, shown at level -1.29,1.29, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6,
grid size 60,58,58, pixel 0.423,0.425,0.425, shown at level 1.02, step 1,
values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.7, grid size 60,58,58, pixel 0.423,0.425,0.425, shown at level 1.01,
step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid
size 60,58,58, pixel 0.423,0.425,0.425, shown at level -0.415,0.415, step 1,
values float32  
Opened (LIVE) MDFF potential as #1.1.1.9, grid size 60,58,58, pixel
0.423,0.425,0.425, shown at level 0.652, step 1, values float32  

> isolde restrain ligands #1

> addh

Summary of feedback from adding hydrogens to
G07_QCR005_p04_1_refine_6-coot-0.pdb #1.2  
---  
notes | No usable SEQRES records for G07_QCR005_p04_1_refine_6-coot-0.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for G07_QCR005_p04_1_refine_6-coot-0.pdb (#1.2) chain
B; guessing termini instead  
Chain-initial residues that are actual N termini: /A TYR 22, /B TYR 22  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A SER 390, /B HIS 397  
3379 hydrogen bonds  
/A SER 390 is not terminus, removing H atom from 'C'  
/B HIS 397 is not terminus, removing H atom from 'C'  
2053 hydrogens added  
  

> hide HC

> hide HC

> select #1

14795 atoms, 14010 bonds, 1724 residues, 43 models selected  

> isolde sim start sel

Loading residue template for CHB from internal database  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Fetching CCD CHB from http://ligand-expo.rcsb.org/reports/C/CHB/CHB.cif  
Fetching CCD GLC from http://ligand-expo.rcsb.org/reports/G/GLC/GLC.cif  
Fetching CCD A2G from http://ligand-expo.rcsb.org/reports/A/A2G/A2G.cif  
Fetching CCD NGA from http://ligand-expo.rcsb.org/reports/N/NGA/NGA.cif  
Fetching CCD BM3 from http://ligand-expo.rcsb.org/reports/B/BM3/BM3.cif  
Fetching CCD BM7 from http://ligand-expo.rcsb.org/reports/B/BM7/BM7.cif  
Fetching CCD NDG from http://ligand-expo.rcsb.org/reports/N/NDG/NDG.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  

> open /Users/rediaz/Downloads/chitooligos/chitobiose.cif
> /Users/rediaz/Downloads/chitooligos/chitotriose.cif
> /Users/rediaz/Downloads/chitooligos/glcnac.cif

Summary of feedback from opening
/Users/rediaz/Downloads/chitooligos/chitobiose.cif  
---  
warning | Skipping chem_comp category: Missing column 'type' near line 19  
  
Summary of feedback from opening
/Users/rediaz/Downloads/chitooligos/chitotriose.cif  
---  
warning | Skipping chem_comp category: Missing column 'type' near line 19  
  
Summary of feedback from opening
/Users/rediaz/Downloads/chitooligos/glcnac.cif  
---  
warning | Skipping chem_comp category: Missing column 'type' near line 19  
  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro13,2
      Processor Name: Dual-Core Intel Core i7
      Processor Speed: 3.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 429.140.8.0.0
      SMC Version (system): 2.37f25

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 7 days 15:25

Graphics/Displays:

    Intel Iris Graphics 550:

      Chipset Model: Intel Iris Graphics 550
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1927
      Revision ID: 0x000a
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    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: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    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: 2.0.1
    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-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Fixing unparameterized residue: cannot unpack non-iterable builtin_function_or_method object

comment:2 by Tristan Croll, 4 years ago

Resolution: → fixed
Status: assigned → closed

This will be fixed in the coming release (which was planned for this week, but my daughter testing positive for COVID put the brakes on that). New target date is the middle of next week.

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