id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5685 Fixing unparameterized residue: cannot unpack non-iterable builtin_function_or_method object roberto.diaz@… Tristan Croll "{{{ 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 }}} " defect closed normal Third Party fixed all ChimeraX