The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
When using the package XMAS to analyse crosslinking mass spectrometry data, closing the visualisation window associated with XMAS leads to a crash of ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x0000000205218600 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 1000000,
"procLaunch" : "2023-05-30 12:23:47.3510 +0200",
"procRole" : "Foreground",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 24376130944884,
"coalitionID" : 11277,
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"captureTime" : "2023-05-30 12:49:33.7457 +0200",
"incident" : "E8CC473D-AD6B-44D3-8209-73260D81EABE",
"bug_type" : "309",
"pid" : 65032,
"procExitAbsTime" : 24413243206087,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "B19A06E3-DCCD-D801-C243-0206CF6237B0",
"wakeTime" : 2451,
"sleepWakeUUID" : "333A7E28-59A7-4771-9438-F6257EB54601",
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"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000fdeea89bf708","rawCodes":[1,279201472837384],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000fdeea89bf708 -> 0x00007deea89bf708 (possible pointer authentication failure)"},
"vmregioninfo" : "0x7deea89bf708 is not in any region. Bytes after previous region: 32907646990089 Bytes before following region: 2195966920952\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 6000b8000000-6000c0000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> GAP OF 0x1fed32700000 BYTES\n MALLOC_TINY 7fedf2700000-7fedf2800000 [ 1024K] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/bram_1/Documents/ChimeraSessions_and_PDBs/Candida_Spc72_CM1/analysingcrosslinks.cxs
Log from Tue May 23 16:40:28 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/Model_building/relion_locres_filtered_correcthandedness.mrc
Opened relion_locres_filtered_correcthandedness.mrc as #1, grid size
512,512,512, pixel 1.07, shown at level 0.00797, step 2, values float32
> open /Users/bram_1/Downloads/AF-A0A1D8PTZ8-F1-model_v4.pdb
Summary of feedback from opening
/Users/bram_1/Downloads/AF-A0A1D8PTZ8-F1-model_v4.pdb
---
warning | Ignored bad PDB record found on line 39
DBREF XXXX A 1 924 UNP A0A1D8PTZ8 A0A1D8PTZ8_CANAL 1 924
AF-A0A1D8PTZ8-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (A0A1D8PTZ8)
[more info...]
Chain information for AF-A0A1D8PTZ8-F1-model_v4.pdb #2
---
Chain | Description
A | uncharacterized protein
> open /Users/bram_1/Downloads/AF-Q5AGV5-F1-model_v4.pdb
AF-Q5AGV5-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (Q5AGV5) [more
info...]
Chain information for AF-Q5AGV5-F1-model_v4.pdb #3
---
Chain | Description | UniProt
A | uncharacterized protein | Q5AGV5_CANAL
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select #2
7107 atoms, 7206 bonds, 924 residues, 1 model selected
> select clear
Drag select of 1930 residues
> view matrix models
> #2,1,0,0,277.73,0,1,0,373.35,0,0,1,151.33,#3,1,0,0,277.73,0,1,0,373.35,0,0,1,151.33
> select #3
8143 atoms, 8240 bonds, 1006 residues, 1 model selected
Drag select of 41 residues
> view matrix models
> #2,1,0,0,278.77,0,1,0,373.73,0,0,1,153.12,#3,1,0,0,278.77,0,1,0,373.73,0,0,1,153.12
> select clear
> select #3
8143 atoms, 8240 bonds, 1006 residues, 1 model selected
> view matrix models #3,1,0,0,347.44,0,1,0,371.06,0,0,1,304.16
> select clear
> open
> /Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/Model_building/ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6.pdb
Chain information for
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6.pdb
#4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> open
> /Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/Model_building/ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
Chain information for
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> open
> /Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/Model_building/ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
Chain information for
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> select #5
18332 atoms, 18685 bonds, 16 pseudobonds, 2245 residues, 2 models selected
> view matrix models #5,1,0,0,-30.62,0,1,0,-20.768,0,0,1,-93.434
> fitmap #5 inMap #1
Fit molecule
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
(#5) to map relion_locres_filtered_correcthandedness.mrc (#1) using 18332
atoms
average map value = 0.02539, steps = 428
shifted from previous position = 22.7
rotated from previous position = 55.5 degrees
atoms outside contour = 1429, contour level = 0.0079731
Position of
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
(#5) relative to relion_locres_filtered_correcthandedness.mrc (#1)
coordinates:
Matrix rotation and translation
0.88678512 -0.45979150 0.04694587 118.00662024
0.26819206 0.59464114 0.75794125 -203.20672829
-0.37641089 -0.65954052 0.65063135 303.84489223
Axis -0.85972026 0.25677113 0.44153105
Axis point 0.00000000 261.20494053 401.20296012
Rotation angle (degrees) 55.52623624
Shift along axis -19.47334687
> select #6
18332 atoms, 18685 bonds, 16 pseudobonds, 2245 residues, 2 models selected
> view matrix models #6,1,0,0,37.65,0,1,0,-21.416,0,0,1,109.99
> fitmap #6 inMap #1
Fit molecule
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
(#6) to map relion_locres_filtered_correcthandedness.mrc (#1) using 18332
atoms
average map value = 0.02699, steps = 480
shifted from previous position = 53.2
rotated from previous position = 55.5 degrees
atoms outside contour = 1278, contour level = 0.0079731
Position of
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
(#6) relative to relion_locres_filtered_correcthandedness.mrc (#1)
coordinates:
Matrix rotation and translation
0.88699567 0.26763785 -0.37630926 64.24733202
-0.45934136 0.59497451 -0.65955352 375.32066495
0.04737293 0.75787552 0.65067695 -49.31136068
Axis 0.85989947 -0.25703162 -0.44103021
Axis point 0.00000000 261.24509907 401.03491506
Rotation angle (degrees) 55.50574727
Shift along axis -19.47523374
> hide #!1 models
> show sel cartoons
> hide sel atoms
Drag select of 4175 residues, 55042 atoms, 47 pseudobonds
> hide sel atoms
> show sel cartoons
> select clear
> color /F deep pink
> color /E deep pink
> color /B orange
> color /A gold
> color /D cornflower blue
> color /C aquamarine
> select clear
> select #3/A:664
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1026 atoms, 1031 bonds, 125 residues, 1 model selected
> select up
8143 atoms, 8240 bonds, 1006 residues, 1 model selected
> color sel deep pink
> select clear
[Repeated 1 time(s)]
> select #2/A:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
62 atoms, 61 bonds, 9 residues, 1 model selected
> select up
7107 atoms, 7206 bonds, 924 residues, 1 model selected
> color sel white
> select clear
> close #1
> combine #2-6
Remapping chain ID 'A' in AF-Q5AGV5-F1-model_v4.pdb #3 to 'B'
Remapping chain ID 'A' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6.pdb
#4 to 'G'
Remapping chain ID 'B' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6.pdb
#4 to 'H'
Remapping chain ID 'A' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#5 to 'I'
Remapping chain ID 'B' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#5 to 'J'
Remapping chain ID 'C' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#5 to 'K'
Remapping chain ID 'D' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#5 to 'L'
Remapping chain ID 'E' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#5 to 'M'
Remapping chain ID 'F' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#5 to 'N'
Remapping chain ID 'A' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#6 to 'O'
Remapping chain ID 'B' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#6 to 'P'
Remapping chain ID 'C' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#6 to 'Q'
Remapping chain ID 'D' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#6 to 'R'
Remapping chain ID 'E' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#6 to 'S'
Remapping chain ID 'F' in
ISOLDEafterRealSpaceRefine46_twodihedraloutliersfixedbycoot_angleoutliersfixedbycoot_pluscablam_ISOLDEfixedallfromchecklist_cootfixedbondlengthangleoutliers_round6_nohydrogens.pdb
#6 to 'T'
> close #2-3#4-6
> save
> /Users/bram_1/Documents/ChimeraSessions_and_PDBs/Candida_Spc72_CM1/analysingcrosslinks.cxs
——— End of log from Tue May 23 16:40:28 2023 ———
opened ChimeraX session
> ui tool show XMAS
Traceback (most recent call last):
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/core/indexes/base.py", line 3652, in get_loc
return self._engine.get_loc(casted_key)
File "pandas/_libs/index.pyx", line 147, in
pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 176, in
pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in
pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in
pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'PSMID'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 457, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 105, in __init__
self.engines[engine][1](df)
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores
function(peptide_pairs, df, xi_alternative)
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 218, in parse_xi_pos_ids
params[key] = df[col_name].tolist()
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/core/frame.py", line 3761, in __getitem__
indexer = self.columns.get_loc(key)
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/core/indexes/base.py", line 3654, in get_loc
raise KeyError(key) from err
KeyError: 'PSMID'
KeyError: 'PSMID'
File "/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/core/indexes/base.py", line 3654, in get_loc
raise KeyError(key) from err
See log for complete Python traceback.
Peptide pair mapping of XlinkX evidence file:
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks.txt
Unique peptide pairs: 768 out of 768
Unique peptide pairs with pseudobonds: 457
Pseudobonds are stored in
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks_1.pb
Mapping information is stored in
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks_1.tsv
/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
using color= is deprecated and will be removed in version 0.13. Set
`palette='dark:gray'` for same effect.
warnings.warn(msg, FutureWarning)
> select clear
> hide #2 models
> split #1
Split combination (#1) into 20 models
Chain information for combination A #1.1
---
Chain | Description
A | No description available
Chain information for combination B #1.2
---
Chain | Description
B | No description available
Chain information for combination C #1.3
---
Chain | Description
C | No description available
Chain information for combination D #1.4
---
Chain | Description
D | No description available
Chain information for combination E #1.5
---
Chain | Description
E | No description available
Chain information for combination F #1.6
---
Chain | Description
F | No description available
Chain information for combination G #1.7
---
Chain | Description
G | No description available
Chain information for combination H #1.8
---
Chain | Description
H | No description available
Chain information for combination I #1.9
---
Chain | Description
I | No description available
Chain information for combination J #1.10
---
Chain | Description
J | No description available
Chain information for combination K #1.11
---
Chain | Description
K | No description available
Chain information for combination L #1.12
---
Chain | Description
L | No description available
Chain information for combination M #1.13
---
Chain | Description
M | No description available
Chain information for combination N #1.14
---
Chain | Description
N | No description available
Chain information for combination O #1.15
---
Chain | Description
O | No description available
Chain information for combination P #1.16
---
Chain | Description
P | No description available
Chain information for combination Q #1.17
---
Chain | Description
Q | No description available
Chain information for combination R #1.18
---
Chain | Description
R | No description available
Chain information for combination S #1.19
---
Chain | Description
S | No description available
Chain information for combination T #1.20
---
Chain | Description
T | No description available
> close #2-3
Peptide pair mapping of XlinkX evidence file:
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks.txt
Unique peptide pairs: 768 out of 768
Unique peptide pairs with pseudobonds: 141
Pseudobonds are stored in
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks_1.1.pb
Mapping information is stored in
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks_1.1.tsv
Please select pseudobonds
/Users/bram_1/Library/Application Support/ChimeraX/1.3/site-
packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
using color= is deprecated and will be removed in version 0.13. Set
`palette='dark:gray'` for same effect.
warnings.warn(msg, FutureWarning)
Distances updated in
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks_1.1.tsv
Distances updated in
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks_1.1.tsv
> hide #2 models
> show #2 models
> hide #2 models
> close #3
> show #2 models
Peptide pair mapping of XlinkX evidence file:
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks.txt
Unique peptide pairs: 768 out of 768
Unique peptide pairs with pseudobonds: 30
Pseudobonds are stored in
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks_1.2.pb
Mapping information is stored in
/Users/bram_1/Documents/Papers/Candida_small_complex_Spc72_Stu2/XL-
MS_solutionanalysis_byZMBHfacility/23-67_Q25070-23-67and68-XlinkX_XLonly_Crosslinks_1.2.tsv
> hide #2 models
===== 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: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2,4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 16 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 15 days 38 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
U32P2WG6:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, '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
blockdiag: 2.0.1
certifi: 2021.5.30
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: 1.1.2
ChimeraX-Zone: 1.0
colorama: 0.4.4
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: 3.1.2
openvr: 1.16.801
packaging: 21.0
pandas: 2.0.1
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
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: 0.12.2
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
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
tzdata: 2023.3
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Bram,
--Eric