Opened 5 years ago

Closed 5 years ago

#3847 closed defect (duplicate)

Various bugs after "rename" command

Reported by: sitins07@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open X:/Work/Projects/EF-G/g3/finalmaps/70S_tRNA/70S_AP_v2.cif-coot-2.pdb
> X:/Work/Projects/EF-G/g3/finalmaps/70S_tRNA/70S_APtRNA_job536_3d512_235A_sharpened_a.mrc

Summary of feedback from opening
X:/Work/Projects/EF-G/g3/finalmaps/70S_tRNA/70S_AP_v2.cif-coot-2.pdb  
---  
warning | Ignored bad PDB record found on line 147610  
END  
  
Chain information for 70S_AP_v2.cif-coot-2.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
y | No description available  
z | No description available  
  
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc, grid size 512,512,512,
pixel 0.652, shown at level 5.08, step 2, values float32  

> style stick

Changed 147609 atom styles  

> show cartoons

> rename #1-2 id 3

> rename #3 id 1

Traceback (most recent call last):  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py",
line 275, in execute  
cmd.run(cmd_text)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\rename.py", line 34, in rename  
change_model_id(session, models, id, new_name = nname)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\rename.py", line 54, in change_model_id  
ml.add(models, parent = p)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 645, in add  
self._reparent_model(model, parent, minimum_id = minimum_id)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 737, in _reparent_model  
self._update_child_ids(model)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 744, in _update_child_ids  
del mt[child.id]  
KeyError: (3, 2)  
  
KeyError: (3, 2)  
  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 744, in _update_child_ids  
del mt[child.id]  
  
See log for complete Python traceback.  
  

> close #1

> close session

Traceback (most recent call last):  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py", line
914, in <lambda>  
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py", line
633, in file_close_cb  
run(session, 'close session')  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session  
session.reset()  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\session.py",
line 502, in reset  
sm.reset_state(container, self)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 568, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 886, in close  
self.remove(mopen)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 862, in remove  
del self._models[model_id]  
KeyError: (1, 1)  
  
KeyError: (1, 1)  
  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 862, in remove  
del self._models[model_id]  
  
See log for complete Python traceback.  
  

> close session

Traceback (most recent call last):  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py", line
914, in <lambda>  
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py", line
633, in file_close_cb  
run(session, 'close session')  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session  
session.reset()  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\session.py",
line 502, in reset  
sm.reset_state(container, self)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 568, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 886, in close  
self.remove(mopen)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 850, in remove  
mlist.sort(key=lambda m: len(m.id), reverse=True)  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 850, in <lambda>  
mlist.sort(key=lambda m: len(m.id), reverse=True)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "X:\Soft\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\models.py",
line 850, in  
mlist.sort(key=lambda m: len(m.id), reverse=True)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GE73VR 7RF
OS: Майкрософт Windows 10 Pro (Build 19041)
Memory: 17,059,950,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-Phenix: 0.1
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 5 years ago

Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Various bugs after "rename" command

comment:2 by Tom Goddard, 5 years ago

Resolution: → duplicate
Status: assigned → closed

These errors are due to a bug in the rename command that was fixed a couple weeks ago (bug #3812). Get the ChimeraX daily build if you want to use the rename command.

Note: See TracTickets for help on using tickets.