Opened 4 years ago
Closed 4 years ago
#6428 closed defect (duplicate)
name 'critera' is not defined
| Reported by: | 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: 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