The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4rc202205060510 (2022-05-06 05:10:33 UTC)
Description
Hello, I'm trying to import SIM-XL results (mzIdentML 1.2 format) and it does not work. I notice the problem is in the line 104 of mzidentml.py and you are expecting a <cvParam> into <DBSequence> tag. However this parameter is not mandatory and SIM-XL results provide this information in <Seq> tag. Could you fix it please? Please find attached an example of SIM-XL results stored in PSI github. Thank you very much
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.4rc202205060510 (2022-05-06)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open /Users/diogobor/Downloads/Results_SIMXL.mzid
Unrecognized file suffix '.mzid'
> open /Users/diogobor/Downloads/ChimeraX_XMAS-1.1.1-py3-none-any.whl
Unrecognized file suffix '.whl'
> ui tool show "Side View"
> ui tool show Meeting
> toolshed show
Downloading bundle ChimeraX_XMAS-1.1.1-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages
sysconfig: /Users/diogobor/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages
sysconfig: /Users/diogobor/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application
Support/ChimeraX/include/python3.9/pandas
sysconfig: /Users/diogobor/Library/Python/3.9/include/pandas
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application Support/ChimeraX/bin
sysconfig: /Users/diogobor/Library/Python/3.9/bin
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application Support/ChimeraX
sysconfig: /Users/diogobor/Library/Python/3.9
WARNING: Additional context:
user = True
home = None
root = None
prefix = None
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application
Support/ChimeraX/include/python3.9/et-xmlfile
sysconfig: /Users/diogobor/Library/Python/3.9/include/et-xmlfile
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application
Support/ChimeraX/include/python3.9/seaborn
sysconfig: /Users/diogobor/Library/Python/3.9/include/seaborn
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application
Support/ChimeraX/include/python3.9/qtrangeslider
sysconfig: /Users/diogobor/Library/Python/3.9/include/qtrangeslider
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application
Support/ChimeraX/include/python3.9/openpyxl
sysconfig: /Users/diogobor/Library/Python/3.9/include/openpyxl
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-XMAS
sysconfig: /Users/diogobor/Library/Python/3.9/include/ChimeraX-XMAS
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/diogobor/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN
sysconfig: /Users/diogobor/Library/Python/3.9/include/UNKNOWN
WARNING: You are using pip version 21.3.1; however, version 22.0.4 is
available.
You should consider upgrading via the
'/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/MacOS/ChimeraX
-m pip install --upgrade pip' command.
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/diogobor/Downloads/ChimeraX_XMAS-1.1.1-py3-none-any.whl
Requirement already satisfied: ChimeraX-Core~=1.3 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.1) (1.4rc202205060510)
Collecting qtrangeslider
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)
Collecting seaborn
Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
Collecting openpyxl
Downloading openpyxl-3.0.9-py2.py3-none-any.whl (242 kB)
Requirement already satisfied: ChimeraX-UI~=1.3 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.1) (1.18.2)
Collecting pandas
Downloading pandas-1.4.2-cp39-cp39-macosx_10_9_x86_64.whl (11.1 MB)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.1) (1.1)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.1) (1.1)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.1) (1.0)
Collecting et-xmlfile
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
Requirement already satisfied: python-dateutil>=2.8.1 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.1) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.1) (2022.1)
Requirement already satisfied: numpy>=1.18.5 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.1) (1.22.1)
Requirement already satisfied: scipy>=1.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from seaborn->ChimeraX-XMAS==1.1.1) (1.7.3)
Requirement already satisfied: matplotlib>=2.2 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from seaborn->ChimeraX-XMAS==1.1.1) (3.5.1)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.1)
(1.0)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.1)
(1.2)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.1) (1.0)
Requirement already satisfied: packaging>=20.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=2.2->seaborn->ChimeraX-XMAS==1.1.1) (21.0)
Requirement already satisfied: kiwisolver>=1.0.1 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=2.2->seaborn->ChimeraX-XMAS==1.1.1) (1.4.2)
Requirement already satisfied: pillow>=6.2.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=2.2->seaborn->ChimeraX-XMAS==1.1.1) (9.0.1)
Requirement already satisfied: pyparsing>=2.2.1 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=2.2->seaborn->ChimeraX-XMAS==1.1.1) (3.0.8)
Requirement already satisfied: cycler>=0.10 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=2.2->seaborn->ChimeraX-XMAS==1.1.1) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=2.2->seaborn->ChimeraX-XMAS==1.1.1) (4.33.3)
Requirement already satisfied: six>=1.5 in
/private/var/folders/hq/k7z38pss1pjbn956c872rnlw0000gn/T/AppTranslocation/645642DC-91E0-49F4-BD88-D135050F57A0/d/ChimeraX-1.4-rc2022.05.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from python-dateutil>=2.8.1->pandas->ChimeraX-XMAS==1.1.1) (1.16.0)
Installing collected packages: pandas, et-xmlfile, seaborn, qtrangeslider,
openpyxl, ChimeraX-XMAS
Successfully installed ChimeraX-XMAS-1.1.1 et-xmlfile-1.1.0 openpyxl-3.0.9
pandas-1.4.2 qtrangeslider-0.1.5 seaborn-0.11.2
\---
Successfully installed ChimeraX-XMAS-1.1.1 et-xmlfile-1.1.0 openpyxl-3.0.9
pandas-1.4.2 qtrangeslider-0.1.5 seaborn-0.11.2
Installed ChimeraX-XMAS (1.1.1)
> ui tool show XMAS
> open /Users/diogobor/Downloads/chimeraX/AF-Q16543-F1-model_v2.pdb
AF-Q16543-F1-model_v2.pdb title:
Alphafold monomer V2.0 prediction for HSP90 Co-chaperone CDC37 (Q16543) [more
info...]
Chain information for AF-Q16543-F1-model_v2.pdb #1
---
Chain | Description | UniProt
A | HSP90 Co-chaperone CDC37 | CDC37_HUMAN
Traceback (most recent call last):
File "/Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 285, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 443, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py", line 456, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "/Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/read_evidence.py", line 51, in __init__
self.peptide_pairs = parse_xl_peptides(evidence_file)
File "/Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/mzidentml.py", line 166, in parse_xl_peptides
dbs = parse_sequence_dbs(mzidentfile)
File "/Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/mzidentml.py", line 104, in parse_sequence_dbs
sq.ProteinDescription = cv_param[0].getAttribute("value")
IndexError: list index out of range
Populating font family aliases took 1330 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
IndexError: list index out of range
File "/Users/diogobor/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/mzidentml.py", line 104, in parse_sequence_dbs
sq.ProteinDescription = cv_param[0].getAttribute("value")
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.5.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel 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: MacBookPro15,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.7 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0)
OS Loader Version: 540.100.7~23
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 34 days 4:37
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
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
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: 1.4rc202205060510
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
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: 1.18.2
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: 1.1.1
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: 3.6.0
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: 3.0.9
openvr: 1.16.802
packaging: 21.0
pandas: 1.4.2
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: 3.0.8
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: 22.3.0
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: 0.11.2
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
File attachment: ResultsSIMXL.mzid
ResultsSIMXL.mzid
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
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