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
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d
Current thread 0x0000542c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xc0000374
Thread 0x0000224c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Current thread 0x0000542c (most recent call first):
File "", line 5 in unique
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\molarray.py", line 357 in unique_ordered
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\molarray.py", line 256 in unique
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\pbgroup.py", line 392 in hidden_structures
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\pbgroup.py", line 245 in _shown_pbonds
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\pbgroup.py", line 213 in _update_graphics
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\pbgroup.py", line 63 in pbg_update
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 134 in invoke
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 217 in _activate
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 186 in activate
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 354 in activate_trigger
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\changes.py", line 43 in check_for_changes
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 58 in draw_new_frame
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 139 in _redraw_timer_callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show XMAS
> open "C:/Users/zeman/Documents/MassSpec/__RQT
> results/HADDOCK_run2/cluster11_1.pdb"
Summary of feedback from opening C:/Users/zeman/Documents/MassSpec/__RQT
results/HADDOCK_run2/cluster11_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_343w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_343.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
30 messages similar to the above omitted
Chain information for cluster11_1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 341 out of 412
Unique peptide pairs with pseudobonds: 203
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.pb
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.tsv
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 341 out of 412
Unique peptide pairs with pseudobonds: 203
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.pb
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.tsv
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 134 out of 154
Unique peptide pairs with pseudobonds: 98
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5_1.pb
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5_1.tsv
> close #3
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #4 models
> color #4 #d4d400 models transparency 0
> color #4 #9bd400 models transparency 0
> color #4 #a3d400 models transparency 0
> show #4 models
> color #4 #00d419 models transparency 0
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> log metadata #1
The model has no metadata
> log chains #1
Chain information for cluster11_1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> show #2 models
> open "C:/Users/zeman/Documents/MassSpec/__RQT
> results/HADDOCK_run2/cluster19_1.pdb"
Summary of feedback from opening C:/Users/zeman/Documents/MassSpec/__RQT
results/HADDOCK_run2/cluster19_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_405w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_405.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
30 messages similar to the above omitted
Chain information for cluster19_1.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #1 models
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 341 out of 412
Unique peptide pairs with pseudobonds: 203
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.pb
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.tsv
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 134 out of 154
Unique peptide pairs with pseudobonds: 98
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.pb
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.tsv
> hide #2 models
> hide #4 models
> hide #5 models
> show #5 models
> hide #6 models
> show #1 models
> hide #3 models
> show #3 models
> hide #1 models
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 341 out of 412
Unique peptide pairs with pseudobonds: 203
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.pb
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.tsv
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 134 out of 154
Unique peptide pairs with pseudobonds: 98
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.pb
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_5PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.tsv
Traceback (most recent call last):
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks
evidence = Evidence(evidence_file)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 106, in __init__
self.engines[engine][1](df)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 132, in parse_pd_xi_seqs_scores
function(peptide_pairs, df, xi_alternative)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 231, in parse_xi_pos_ids
residues = [res for res in seq if res.isupper()]
TypeError: 'float' object is not iterable
TypeError: 'float' object is not iterable
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 231, in parse_xi_pos_ids
residues = [res for res in seq if res.isupper()]
See log for complete Python traceback.
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 341 out of 412
Unique peptide pairs with pseudobonds: 203
Traceback (most recent call last):
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 522, in map_crosslinks
self.align_peptides(peptide_pairs, checked_models)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 674, in align_peptides
self.create_pseudobonds(peptide_pairs)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 738, in create_pseudobonds
self.create_files(pbonds, info_file_path)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 751, in create_files
created_model = self.create_pseudobonds_model(pbonds,
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 785, in create_pseudobonds_model
group = self.get_pseudobonds_model(name)
File "C:\Users\zeman\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 857, in get_pseudobonds_model
self.session.models.add([group])
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\models.py", line 647, in add
raise ValueError('Attempted to add model %s to scene twice' % model)
ValueError: Attempted to add model
RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1,3(1).pb #7 to scene
twice
ValueError: Attempted to add model
RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1,3(1).pb #7 to scene
twice
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\models.py", line 647, in add
raise ValueError('Attempted to add model %s to scene twice' % model)
See log for complete Python traceback.
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-
SDA/SBP/results_HiError/RQT_SBP_HigherError_Results_5PercentLinkFDR_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 51 out of 52
Unique peptide pairs with pseudobonds: 24
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-
SDA/SBP/results_HiError/RQT_SBP_HigherError_Results_5PercentLinkFDR_CSM_xiFDR2.1.5.5_1,3.pb
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-
SDA/SBP/results_HiError/RQT_SBP_HigherError_Results_5PercentLinkFDR_CSM_xiFDR2.1.5.5_1,3.tsv
> hide #8 models
> hide #7 models
> hide #5 models
> show #1 models
> hide #3 models
> close #7-8
> close #2,4
> hide #9 models
> show #5 models
> show #9 models
> color #9 #1100ff models transparency 0
> color #9 #003cff models transparency 0
> color #9 #0073ff models transparency 0
> color #9 #0062ff models transparency 0
> color #5 #00ffbf models transparency 0
> color #5 #00ff40 models transparency 0
> color #5 #ff00e6 models transparency 0
> set bgColor white
> set bgColor black
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting simple
Please select pseudobonds
Venn diagrams can only be plotted for two or three groups
C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py:301:
UserWarning: Attempted to set non-positive left xlim on a log-scaled axis.
Invalid limit will be ignored.
self.exec_()
> hide #5 models
> hide #9 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> close #2
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #4 models
> hide #5 models
> show #4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> close #4
> show #3 models
> hide #1 models
Distances updated in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-
SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.tsv
Distances updated in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-
SDA/SBP/results_HiError/RQT_SBP_HigherError_Results_5PercentLinkFDR_CSM_xiFDR2.1.5.5_1,3.tsv
Distances updated in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-
SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1,3.tsv
Distances updated in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-
SDA/SBP/results_HiError/RQT_SBP_HigherError_Results_5PercentLinkFDR_CSM_xiFDR2.1.5.5_1,3.tsv
> show #1 models
> hide #1 models
> show #1 models
> hide #3 models
> show #5 models
> select clear
> hide #5 models
> show #9 models
> hide #9 models
> show #5 models
Please select pseudobonds
> select #1/A#3/A
38678 atoms, 39330 bonds, 733 pseudobonds, 3934 residues, 5 models selected
> ui tool show "Color Actions"
> color sel tan
> color sel pink
> color sel deep pink
> color sel tan
> undo
> ui tool show "Color Actions"
> color sel rosy brown
> color sel tan
> color sel goldenrod
> color sel sandy brown
> color sel dark goldenrod
===== Log before crash end =====
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
OpenGL version: 3.3.0 NVIDIA 457.49
OpenGL renderer: GeForce GTX 1060 3GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP EliteDesk 800 G4 TWR
OS: Microsoft Windows 10 Education (Build 19044)
Memory: 16,948,436,992
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
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-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-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-XMAS: 1.1.1
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
et-xmlfile: 1.1.0
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
openpyxl: 3.0.9
openvr: 1.16.801
packaging: 21.3
pandas: 1.4.2
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
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
seaborn: 0.11.2
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
First XMAS bug report!