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
(Describe the actions that caused this problem to occur here)
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/sheiny/Desktop/SEN6.pdb
Summary of feedback from opening /Users/sheiny/Desktop/SEN6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALAU1 71
LEUU1 84 1 14
Start residue of secondary structure not found: HELIX 2 2 SERU1 356 TYRU1 360
1 5
Start residue of secondary structure not found: HELIX 3 3 ASNE2 493 ARGE2 505
1 13
Start residue of secondary structure not found: HELIX 4 4 LEUE2 526 ALAE2 528
1 3
Start residue of secondary structure not found: HELIX 5 5 ASNE2 529 SERE2 535
1 7
97 messages similar to the above omitted
Chain information for SEN6.pdb
---
Chain | Description
1.1/A4 | No description available
1.2/D | No description available
1.1/E2 | No description available
1.1/F2 | No description available
1.1/G2 | No description available
1.3/U | No description available
1.1/U1 | No description available
1.1/U3 | No description available
> hide atoms
> hide cartoons
> style stick
Changed 7659 atom styles
> show cartoons
> hide #!1.3 models
> show #!1.3 models
> ui mousemode right select
> select #1.1/F2:1790
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1.1/F2:449
11 atoms, 9 bonds, 2 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> color sel byhetero
> ui mousemode right bond
> show sel cartoons
> hide sel atoms
> ui mousemode right select
> select clear
> select #1.1/U1:880
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.1/G2:1488
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.1/U1:880
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1.1/U1:881
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel cartoons
> select #1.1/G2:1488
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> color sel byhetero
> select #1.1/G2:1487
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel atoms
> color sel byhetero
> select #1.1/G2:1487@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> ui mousemode right "select fragment"
> select clear
> hide sel atoms
> show sel cartoons
> select clear
> ui mousemode right select
> select #1.1/U1:880
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1.1/G2:1488
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1.1/G2:1488
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.1/U1:880
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> select #1.1/G2:1488
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> delete atoms sel
> delete bonds sel
> select #1.1/G2:1487
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> ui mousemode right "select fragment"
> ui mousemode right bond
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> ui mousemode right select
> ui mousemode right "select fragment"
> show sel cartoons
> hide sel atoms
> style sel stick
Changed 241 atom styles
> color sel byhetero
> hide sel atoms
> show sel atoms
> hide sel cartoons
> ui mousemode right "structure eraser"
> ui mousemode right bond
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel cartoons
> ui mousemode right "structure eraser"
> ui mousemode right bond
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/sheiny/Library/Application Support/ChimeraX/1.2/site-
packages/SEQCROW/mouse_modes.py", line 356, in mouse_up
new_bond = atom.structure.new_bond(atom, self._atom1)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1577, in new_bond
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)
IndexError: map::at: key not found
IndexError: map::at: key not found
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1577, in new_bond
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/sheiny/Library/Application Support/ChimeraX/1.2/site-
packages/SEQCROW/mouse_modes.py", line 356, in mouse_up
new_bond = atom.structure.new_bond(atom, self._atom1)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1577, in new_bond
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)
IndexError: map::at: key not found
IndexError: map::at: key not found
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1577, in new_bond
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 11.6 (20G165)
Kernel Version: Darwin 20.6.0
Time since boot: 6 days 23:01
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
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
biopython: 1.79
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-Phenix: 0.3
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-StrudelScore: 0.1.10
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
mrcfile: 1.3.0
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
pandas: 1.3.4
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
recordtype: 1.3
requests: 2.24.0
scipy: 1.5.2
Send2Trash: 1.8.0
SEQCROW: 1.3
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
threed-strudel: 0.9.13
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Would need more info to reproduce. If the atoms being bonded weren't in the same structure, the error would be different.