The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/elena/Desktop/Ring1b-BMI1-models-coot/refined-coot-5.pdb
refined-coot-5.pdb title:
Molrep --- /vers 11.9.02; 28.02.2022/ [more info...]
Chain information for refined-coot-5.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> show atoms
> show cartoons
> hide atoms
> lighting simple
> open /Users/elena/Desktop/figures_TAC/ranked_0.pdb
Chain information for ranked_0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker refined-coot-5.pdb, chain L (#1) with ranked_0.pdb, chain B (#2),
sequence alignment score = 474.6
RMSD between 95 pruned atom pairs is 0.917 angstroms; (across all 101 pairs:
1.217)
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:335
18 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/C:1-335
5299 atoms, 5359 bonds, 335 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki
> select clear
> select #2/B:340
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #2/B:91-340
3885 atoms, 3917 bonds, 250 residues, 1 model selected
> select #2/B:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:1-260
3984 atoms, 4013 bonds, 260 residues, 1 model selected
> select #2/B:340
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #2/B:1-340
5277 atoms, 5320 bonds, 340 residues, 1 model selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel cadet blue
> select clear
> select #2/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:1-162
2554 atoms, 2591 bonds, 162 residues, 1 model selected
> ui tool show "Color Actions"
> color sel rosy brown
> select clear
[Repeated 1 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain #1/K
Alignment identifier is 1/K
> sequence chain #1/L
Alignment identifier is 1/L
> select #1/L:115
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/L:15-115
787 atoms, 801 bonds, 101 residues, 1 model selected
> select #1/K:98
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/K:5-98
754 atoms, 769 bonds, 94 residues, 1 model selected
> delete sel
> select #1/L:115
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/L:15-115
787 atoms, 801 bonds, 101 residues, 1 model selected
> delete sel
> combine #1 #2
Remapping chain ID 'A' in ranked_0.pdb #2 to 'K'
Remapping chain ID 'B' in ranked_0.pdb #2 to 'L'
Remapping chain ID 'C' in ranked_0.pdb #2 to 'M'
> save /Users/elena/Desktop/figures_TAC/xl-ms-alphafold.cxs
> ui tool show XMAS
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Downloads/20220909_EXPL6_NiKr_LC12-16_SA_Orbi4324_Sample02_fractionation_Crosslinks.txt
Unique peptide pairs: 108 out of 108
Unique peptide pairs with pseudobonds: 60
Pseudobonds are stored in
/Users/elena/Downloads/20220909_EXPL6_NiKr_LC12-16_SA_Orbi4324_Sample02_fractionation_Crosslinks_1,2,3.pb
Mapping information is stored in
/Users/elena/Downloads/20220909_EXPL6_NiKr_LC12-16_SA_Orbi4324_Sample02_fractionation_Crosslinks_1,2,3.tsv
Please select pseudobonds
Please select pseudobonds
> select clear
Traceback (most recent call last):
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 1763, in <lambda>
self.show_slider(checked, s))
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2113, in show_slider
slider.within_range(slider.value_type, None, slider.function)
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in within_range
distance_range = [float(s.text()) for s in distance_slider.setters]
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in <listcomp>
distance_range = [float(s.text()) for s in distance_slider.setters]
ValueError: could not convert string to float: ''
Populating font family aliases took 336 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
ValueError: could not convert string to float: ''
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in
distance_range = [float(s.text()) for s in distance_slider.setters]
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 1763, in <lambda>
self.show_slider(checked, s))
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2113, in show_slider
slider.within_range(slider.value_type, None, slider.function)
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in within_range
distance_range = [float(s.text()) for s in distance_slider.setters]
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in <listcomp>
distance_range = [float(s.text()) for s in distance_slider.setters]
ValueError: could not convert string to float: ''
ValueError: could not convert string to float: ''
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in
distance_range = [float(s.text()) for s in distance_slider.setters]
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 1763, in <lambda>
self.show_slider(checked, s))
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2113, in show_slider
slider.within_range(slider.value_type, None, slider.function)
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in within_range
distance_range = [float(s.text()) for s in distance_slider.setters]
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in <listcomp>
distance_range = [float(s.text()) for s in distance_slider.setters]
ValueError: could not convert string to float: ''
ValueError: could not convert string to float: ''
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in
distance_range = [float(s.text()) for s in distance_slider.setters]
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 1763, in <lambda>
self.show_slider(checked, s))
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2113, in show_slider
slider.within_range(slider.value_type, None, slider.function)
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in within_range
distance_range = [float(s.text()) for s in distance_slider.setters]
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in <listcomp>
distance_range = [float(s.text()) for s in distance_slider.setters]
ValueError: could not convert string to float: ''
ValueError: could not convert string to float: ''
File "/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 2394, in
distance_range = [float(s.text()) for s in distance_slider.setters]
See log for complete Python traceback.
OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2,4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
Boot ROM Version: 1554.50.3.0.0 (iBridge: 18.16.12561.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H15)
Kernel Version: Darwin 19.6.0
Time since boot: 3 days 19:09
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
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-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 1.1.0
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
et-xmlfile: 1.1.0
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openpyxl: 3.0.10
openvr: 1.16.802
packaging: 21.0
pandas: 1.5.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
seaborn: 0.12.0
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed with newest release of XMAS (1.1.3)