Opened 4 years ago
Closed 4 years ago
#6428 closed defect (duplicate)
name 'critera' is not defined
Reported by: | Owned by: | pett | |
---|---|---|---|
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: Windows-10-10.0.19044 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6m5p format mmcif fromDatabase pdb 6m5p title: A class C beta-lactamase [more info...] Chain information for 6m5p #1 --- Chain | Description | UniProt A | Beta-lactamase | Q9XB24_KLEPN Non-standard residues in 6m5p #1 --- MER — (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid (Meropenem, bound form) > close > open 6i1i Summary of feedback from opening 6i1i fetched from pdb --- notes | Fetching compressed mmCIF 6i1i from http://files.rcsb.org/download/6i1i.cif Fetching CCD JPP from http://ligand-expo.rcsb.org/reports/J/JPP/JPP.cif 6i1i title: Crystal structure of TP domain from Escherichia coli penicillin-binding protein 3 in complex with penicillin [more info...] Chain information for 6i1i #1 --- Chain | Description | UniProt A | Peptidoglycan D,D-transpeptidase FtsI,Peptidoglycan D,D-transpeptidase FtsI | FTSI_ECO57 Non-standard residues in 6i1i #1 --- JPP — Piperacillin (Open Form) > select /A:523 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > style sphere Changed 2534 atom styles > select clear > style sphere Changed 2534 atom styles > show atoms > hide cartoons > style stick Changed 2534 atom styles > show cartoons > hide atoms > select /A:523 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ASN rotLib Dynameomics /A GLN 523: phi -158.1, psi 92.2 trans Changed 90 bond radii > swapaa #1/A:523 ASN criteria 1 rotLib Dynameomics Using Dynameomics library 6i1i #1/A GLN 523: phi -158.1, psi 92.2 trans Applying ASN rotamer (chi angles: -179.8 -106.8) to 6i1i #1/A ASN 523 > select /A:373 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > style sphere Changed 2533 atom styles > show atoms > style stick Changed 2533 atom styles > select /A:372@CD 1 atom, 1 residue, 1 model selected > view sel > ui mousemode right clip > select clear > style sphere Changed 2533 atom styles > hide cartoons > hide atoms > show cartoons > select /A:373 6 atoms, 5 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel PRO rotLib Dynameomics /A SER 373: phi -53.4, psi -33.4 trans Changed 10 bond radii > swapaa #1/A:373 PRO criteria 1 rotLib Dynameomics Using Dynameomics library 6i1i #1/A SER 373: phi -53.4, psi -33.4 trans Applying PRO rotamer (chi angles: 8.7) to 6i1i #1/A PRO 373 > select clear > style sphere Changed 2534 atom styles > show atoms > hide cartoons > select /A:397@CB 1 atom, 1 residue, 1 model selected > view sel > ui mousemode right clip > show sel cartoons > select clear > show cartoons > style stick Changed 2534 atom styles > ui tool show Rotamers > swapaa interactive sel SER rotLib Dynameomics /A ARG 397: phi -101.0, psi 0.1 trans Changed 9 bond radii > swapaa #1/A:397 SER criteria 1 rotLib Dynameomics Using Dynameomics library 6i1i #1/A ARG 397: phi -101.0, psi 0.1 trans Applying SER rotamer (chi angles: -49.7) to 6i1i #1/A SER 397 > view > select clear > style sphere Changed 2529 atom styles > style stick Changed 2529 atom styles > ui tool show Rotamers > swapaa interactive sel LYS rotLib Dynameomics /A ARG 324 (alt loc A): phi -112.5, psi 172.1 trans Changed 486 bond radii > swapaa #1/A:324 LYS criteria 1 rotLib Dynameomics Using Dynameomics library 6i1i #1/A ARG 324 (alt loc A): phi -112.5, psi 172.1 trans 6i1i #1/A ARG 324 (alt loc B): phi -115.5, psi 174.8 trans Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer run(self.session, cmd) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2856, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\cmd.py", line 45, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: NameError: name 'critera' is not defined NameError: name 'critera' is not defined File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: See log for complete Python traceback. > swapaa #1/A:324 LYS criteria 1 rotLib Dynameomics Using Dynameomics library 6i1i #1/A ARG 324 (alt loc A): phi -112.5, psi 172.1 trans 6i1i #1/A ARG 324 (alt loc B): phi -115.5, psi 174.8 trans Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer run(self.session, cmd) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2856, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\cmd.py", line 45, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: NameError: name 'critera' is not defined NameError: name 'critera' is not defined File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: See log for complete Python traceback. > swapaa #1/A:324 LYS criteria 2 rotLib Dynameomics Using Dynameomics library 6i1i #1/A ARG 324 (alt loc A): phi -112.5, psi 172.1 trans 6i1i #1/A ARG 324 (alt loc B): phi -115.5, psi 174.8 trans Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer run(self.session, cmd) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2856, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\cmd.py", line 45, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: NameError: name 'critera' is not defined NameError: name 'critera' is not defined File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: See log for complete Python traceback. > swapaa interactive sel LYS rotLib Dynameomics /A ARG 324 (alt loc A): phi -112.5, psi 172.1 trans Changed 486 bond radii > swapaa #1/A:324 LYS criteria 1 rotLib Dynameomics Using Dynameomics library 6i1i #1/A ARG 324 (alt loc A): phi -112.5, psi 172.1 trans 6i1i #1/A ARG 324 (alt loc B): phi -115.5, psi 174.8 trans Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer run(self.session, cmd) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2856, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\cmd.py", line 45, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: NameError: name 'critera' is not defined NameError: name 'critera' is not defined File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: See log for complete Python traceback. > swapaa #1/A:324 LYS criteria 1 rotLib Dynameomics Using Dynameomics library 6i1i #1/A ARG 324 (alt loc A): phi -112.5, psi 172.1 trans 6i1i #1/A ARG 324 (alt loc B): phi -115.5, psi 174.8 trans Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer run(self.session, cmd) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2856, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\cmd.py", line 45, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: NameError: name 'critera' is not defined NameError: name 'critera' is not defined File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa if len(critera) > 1: See log for complete Python traceback. OpenGL version: 3.3.0 - Build 27.20.100.8730 OpenGL renderer: Intel(R) HD Graphics 620 OpenGL vendor: Intel Manufacturer: SAMSUNG ELECTRONICS CO., LTD. Model: 900X3J OS: Microsoft Windows 10 家用版 (Build 19044) Memory: 8,499,580,928 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz OSLanguage: zh-TW Locale: ('zh_HK', 'cp950') 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: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 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: 1.6.1 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: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
Component: | Unassigned → Structure Editing |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → name 'critera' is not defined |
comment:2 by , 4 years ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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Hi Kelvin,
--Eric