![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 2 years ago
#9009 closed defect (can't reproduce)
Crash running save dialog
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000002043d1b40 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 39 in display
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 27 in _file_save
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 45 in run_provider
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/__init__.py", line 37 in run_provider
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1289 in run_provider
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 165 in callback
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.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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"version" : 2,
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"captureTime" : "2023-05-13 15:00:32.3487 -0700",
"incident" : "AC69BC21-9B97-4588-9519-881510F8D40E",
"pid" : 73161,
"translated" : false,
"cpuType" : "ARM-64",
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"bug_type" : "309",
"procLaunch" : "2023-05-13 14:01:44.2329 -0700",
"procStartAbsTime" : 15995785120057,
"procExitAbsTime" : 16080454690811,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "FF382F5F-F05C-8036-7639-09BFBDA00407",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"wakeTime" : 528773,
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"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105556740145128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 6000d8000000-6000e0000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/carriepartch/Desktop/5hwv.pdb
5hwv.pdb title:
Crystal structure of PAS1 complexed with toluene [more info...]
Chain information for 5hwv.pdb #1
---
Chain | Description | UniProt
A B | sensor histidine kinase tods | TODS_PSEP1 43-168
Non-standard residues in 5hwv.pdb #1
---
MBN — toluene
> set bgColor white
> open /Users/carriepartch/Desktop/5hwv.pdb format pdb
5hwv.pdb title:
Crystal structure of PAS1 complexed with toluene [more info...]
Chain information for 5hwv.pdb #2
---
Chain | Description | UniProt
A B | sensor histidine kinase tods | TODS_PSEP1 43-168
Non-standard residues in 5hwv.pdb #2
---
MBN — toluene
> select /B:43-167
1952 atoms, 1980 bonds, 250 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
Drag select of 14 atoms, 14 bonds
> hide sel atoms
> select clear
> select #1/A:42
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:43
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add #1/A:44
25 atoms, 23 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select clear
> hide #2 models
Drag select of 16 residues
> hide sel cartoons
> select :MBN
28 atoms, 28 bonds, 4 residues, 2 models selected
> style sel & #1 sphere
Changed 14 atom styles
> ui tool show "Color Actions"
> color sel light gray
> lighting soft
> select #2/A:42-165
964 atoms, 978 bonds, 124 residues, 1 model selected
> color sel cadet blue
> select #2/A:42-165
964 atoms, 978 bonds, 124 residues, 1 model selected
> select #2/A:42-165
964 atoms, 978 bonds, 124 residues, 1 model selected
> select add #2
2262 atoms, 1982 bonds, 559 residues, 1 model selected
> select subtract #2
Nothing selected
> color cadet blue
> select :MBN
28 atoms, 28 bonds, 4 residues, 2 models selected
> color sel light gray
> select clear
> save /Users/carriepartch/Desktop/5HWV-cartoon.cxs
> save /Users/carriepartch/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/carriepartch/Desktop/movie1.mp4
Movie saved to /Users/carriepartch/Desktop/movie1.mp4
> close #2
> close
> open /Users/carriepartch/Desktop/4jgp.pdb
4jgp.pdb title:
The crystal structure of sporulation kinase D sensor domain from bacillus
subtilis subsp In complex with pyruvate At 2.0A resolution [more info...]
Chain information for 4jgp.pdb #1
---
Chain | Description | UniProt
A B | sensor histidine kinase D | KIND_BACSU 37-250
Non-standard residues in 4jgp.pdb #1
---
PYR — pyruvic acid
> select /B:40-245
1621 atoms, 1648 bonds, 206 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 7 atoms, 5 bonds
> hide sel atoms
> close
> open /Users/carriepartch/Desktop/4r38.pdb
4r38.pdb title:
Lov domain from erythrobacter litoralis EL346 blue-light activated histidine
kinase [more info...]
Chain information for 4r38.pdb #1
---
Chain | Description | UniProt
A B C D | blue-light-activated histidine kinase 2 | LVHK2_ERYLH 1-134
Non-standard residues in 4r38.pdb #1
---
RBF — riboflavin (riboflavine; vitamin B2)
> select /B:40-245
1337 atoms, 1351 bonds, 84 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 16 atoms, 21 residues, 12 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 1 residues
Drag select of 16 atoms, 1 residues, 11 bonds, 2 pseudobonds
> hide sel cartoons
> hide sel atoms
Drag select of 75 atoms, 52 residues, 69 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 268 atoms, 161 residues, 221 bonds, 3 pseudobonds
> hide sel cartoons
> hide sel atoms
Drag select of 124 atoms, 104 bonds, 7 pseudobonds
> hide sel atoms
Drag select of 31 atoms, 26 bonds
> hide sel atoms
Drag select of 1 atoms
Drag select of 3 residues
> hide sel cartoons
> hide sel atoms
> select /D:16-123
1687 atoms, 1704 bonds, 108 residues, 1 model selected
> hide sel atoms
> select :RBF
188 atoms, 196 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 188 atom styles
> color sel light gray
> color sel byhetero
> select clear
> select ::name="HOH"
145 atoms, 145 residues, 1 model selected
> hide sel atoms
> select /D:16-123
1687 atoms, 1704 bonds, 108 residues, 1 model selected
> color sel medium aquamarine
> color sel light sea green
> lighting soft
> select clear
> save /Users/carriepartch/Desktop/4R38-cartoon.cxs
> save /Users/carriepartch/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/carriepartch/Desktop/movie1.mp4
Movie saved to /Users/carriepartch/Desktop/movie1.mp4
> close
> open /Users/carriepartch/Desktop/4wn5.pdb
4wn5.pdb title:
Crystal structure of the C-terminal per-ARNT-sim (pasb) of human hif- 3Α9
bound to 18:1-1-monoacylglycerol [more info...]
Chain information for 4wn5.pdb #1
---
Chain | Description | UniProt
A B | hypoxia-inducible factor 3-α | HIF3A_HUMAN 237-347
Non-standard residues in 4wn5.pdb #1
---
MVC — monovaccenin (11.7 mag)
P6G — hexaethylene glycol (polyethylene glycol PEG400)
SO4 — sulfate ion
> select :P6G
225 atoms, 220 bonds, 5 residues, 1 model selected
> hide sel atoms
> select :SO4
10 atoms, 8 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /B:238-342
1579 atoms, 1596 bonds, 105 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select ::name="HOH"
295 atoms, 295 residues, 1 model selected
> hide sel atoms
> select clear
Drag select of 27 atoms, 26 bonds
> hide sel atoms
> select /B:238-342
1579 atoms, 1596 bonds, 105 residues, 1 model selected
> close
> open /Users/carriepartch/Desktop/4wn5.pdb
4wn5.pdb title:
Crystal structure of the C-terminal per-ARNT-sim (pasb) of human hif- 3Α9
bound to 18:1-1-monoacylglycerol [more info...]
Chain information for 4wn5.pdb #1
---
Chain | Description | UniProt
A B | hypoxia-inducible factor 3-α | HIF3A_HUMAN 237-347
Non-standard residues in 4wn5.pdb #1
---
MVC — monovaccenin (11.7 mag)
P6G — hexaethylene glycol (polyethylene glycol PEG400)
SO4 — sulfate ion
> select /A:235-343
1629 atoms, 1646 bonds, 1 pseudobond, 108 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
Drag select of 95 atoms, 72 bonds
> hide sel atoms
> select :P6G
225 atoms, 220 bonds, 5 residues, 1 model selected
> hide sel atoms
> select :SO4
10 atoms, 8 bonds, 2 residues, 1 model selected
> hide sel atoms
> select ::name="HOH"
295 atoms, 295 residues, 1 model selected
> hide sel atoms
> select /B:238-342
1579 atoms, 1596 bonds, 105 residues, 1 model selected
> hide sel atoms
> select clear
> select :MVC
130 atoms, 128 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 130 atom styles
> color sel light gray
> color sel byhetero
> select clear
> lighting soft
> save /Users/carriepartch/Desktop/4WN5-cartoon.cxs
> select /B:238-342
1579 atoms, 1596 bonds, 105 residues, 1 model selected
> color sel dark sea green
> select clear
> save /Users/carriepartch/Desktop/4WN5-cartoon.cxs
> save /Users/carriepartch/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/carriepartch/Desktop/movie1.mp4
Movie saved to /Users/carriepartch/Desktop/movie1.mp4
> close
> open /Users/carriepartch/Desktop/1p0z.pdb
1p0z.pdb title:
Sensor kinase cita binding domain [more info...]
Chain information for 1p0z.pdb #1
---
Chain | Description | UniProt
A B C D E F G H I J | sensor kinase cita | CITA_KLEPN 5-135
Non-standard residues in 1p0z.pdb #1
---
FLC — citrate anion
MO7 — bis(Μ4-oxo)-bis(Μ3-oxo)-octakis(Μ2-oxo)-dodecaoxo-heptamolybdenum (VI)
(heptamolybdate [Mo(VI)7O24]6-)
NA — sodium ion
OMO — Mo(VI)(=O)(oh)2 cluster
> hide cartoons
> hide surfaces
> show cartoons
> hide atoms
> select :FLC
130 atoms, 120 bonds, 10 residues, 1 model selected
> style sel sphere
Changed 130 atom styles
> select :FLC
130 atoms, 120 bonds, 10 residues, 1 model selected
> style sel sphere
Changed 130 atom styles
> close
> open /Users/carriepartch/Desktop/2pd7.pdb
2pd7.pdb title:
2.0 angstrom crystal structure of the fungal blue-light photoreceptor vivid
[more info...]
Chain information for 2pd7.pdb #1
---
Chain | Description | UniProt
A B | hypothetical protein NCU03967.1 | Q9C3Y6_NEUCR 37-184
Non-standard residues in 2pd7.pdb #1
---
FAD — flavin-adenine dinucleotide
> select /A:36-184
1187 atoms, 1210 bonds, 149 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 57 atoms, 58 bonds
> hide sel atoms
> select /B:71
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 24 residues
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
> select /B:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /B:43-184
1130 atoms, 1150 bonds, 142 residues, 1 model selected
> hide sel atoms
> select ::name="HOH"
313 atoms, 313 residues, 1 model selected
> hide sel atoms
> select :FAD
106 atoms, 116 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 106 atom styles
> color sel light gray target cspf
> color sel byhetero target cspf
> color sel light gray target cspf
> select :FAD
106 atoms, 116 bonds, 2 residues, 1 model selected
> color sel light gray target cspf
> select /A:36-184
1187 atoms, 1210 bonds, 149 residues, 1 model selected
> select /B:43-184
1130 atoms, 1150 bonds, 142 residues, 1 model selected
> color sel light steel blue target cspf
> color sel dark cyan target cspf
> color sel cornflower blue target cspf
> color sel dark goldenrod target cspf
> color sel peru target cspf
> color sel sandy brown target cspf
> select clear
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 1 model selected
> color sel light gray target cspf
> color sel gray target cspf
> color sel dark gray target cspf
> select /B:7202@C2B
1 atom, 1 residue, 1 model selected
> select clear
> lighting soft
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 1 model selected
> color sel light gray
> color sel byhetero target cspf
> color sel byhetero
> select clear
> save /Users/carriepartch/Desktop/2PD7-cartoon.cxs
> save /Users/carriepartch/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/carriepartch/Desktop/movie1.mp4
Movie saved to /Users/carriepartch/Desktop/movie1.mp4
> close
> open /Users/carriepartch/Desktop/5f5y.pdb
5f5y.pdb title:
WT drosophila melanogaster cycle pas-B with bound ethylene glycol [more
info...]
Chain information for 5f5y.pdb #1
---
Chain | Description | UniProt
A | protein cycle | CYCL_DROME 311-412
Non-standard residues in 5f5y.pdb #1
---
EDO — 1,2-ethanediol (ethylene glycol)
> select /A:310-412
861 atoms, 884 bonds, 103 residues, 1 model selected
> hide sel atoms
> select :EDO
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 4 atom styles
> color sel light gray
> color sel byhetero
> lighting soft
> select /A:310-412
861 atoms, 884 bonds, 103 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue target cspf
> select clear
> save /Users/carriepartch/Desktop/5F5Y-cartoon.cxs
> save /Users/carriepartch/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/carriepartch/Desktop/movie1.mp4
Movie saved to /Users/carriepartch/Desktop/movie1.mp4
> close
> open /Users/carriepartch/Desktop/3by8.pdb
3by8.pdb title:
Crystal structure of the E.coli dcus sensor domain [more info...]
Chain information for 3by8.pdb #1
---
Chain | Description | UniProt
A | sensor protein dcus | DCUS_ECOLI 42-181
Non-standard residues in 3by8.pdb #1
---
LMR — (2S)-2-hydroxybutanedioic acid (L-malate)
> close
> open /Users/carriepartch/Desktop/3eeh.pdb
3eeh.pdb title:
The crystal structure of the domain of the putative light and redox sensing
histidine kinase from haloarcula marismortui [more info...]
Chain information for 3eeh.pdb #1
---
Chain | Description | UniProt
A | putative light and redox sensing histidine kinase | Q5UZS4_HALMA 1-125
Non-standard residues in 3eeh.pdb #1
---
PG5 — 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane
Drag select of 12 residues
> hide sel cartoons
> select ::name="HOH"
108 atoms, 108 residues, 1 model selected
> hide sel atoms
> select :PG5
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 12 atom styles
> color sel light gray target cspf
> color sel light gray
> color sel byhetero
> select /A:10-125
940 atoms, 957 bonds, 116 residues, 1 model selected
> color sel crimson target cspf
> color sel orchid target cspf
> color sel medium orchid target cspf
> color sel medium purple target cspf
> color sel pale violet red target cspf
> color sel magenta target cspf
> color sel dark turquoise target cspf
> color sel dark magenta target cspf
> color sel purple target cspf
> color sel violet target cspf
> color sel dark magenta target cspf
> select clear
> lighting soft
> save /Users/carriepartch/Desktop/3EEH-cartoon.cxs
> save /Users/carriepartch/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/carriepartch/Desktop/movie1.mp4
Movie saved to /Users/carriepartch/Desktop/movie1.mp4
> close
> open /Users/carriepartch/Desktop/3mqo.pdb
3mqo.pdb title:
The crystal structure of the pas domain In complex with isopropanol of A
transcriptional regulator In the luxr family from burkholderia thailandensis
to 1.7A [more info...]
Chain information for 3mqo.pdb #1
---
Chain | Description | UniProt
A B | transcriptional regulator, luxr family | Q2SVC5_BURTA 2-121
Non-standard residues in 3mqo.pdb #1
---
EDO — 1,2-ethanediol (ethylene glycol)
IPA — isopropyl alcohol (2-propanol)
NA — sodium ion
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
> close
> open /Users/carriepartch/Desktop/2j80.pdb
2j80.pdb title:
Structure of citrate-bound periplasmic domain of sensor histidine kinase cita
[more info...]
Chain information for 2j80.pdb #1
---
Chain | Description | UniProt
A B | sensor histidine kinase CITA periplasmic domain | CITA_KLEPN 2-133
Non-standard residues in 2j80.pdb #1
---
FLC — citrate anion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NA — sodium ion
SO4 — sulfate ion
> select /B:6-129
919 atoms, 930 bonds, 124 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 26 atoms, 3 pseudobonds, 17 bonds
> hide sel atoms
Drag select of 13 residues
Drag select of 21 atoms, 14 residues, 6 pseudobonds, 17 bonds
> select clear
> close
> open /Users/carriepartch/Desktop/2v0u.pdb
2v0u.pdb title:
N- and C-terminal helices of oat LOV2 (404-546) are involved In light-induced
signal transduction (cryo dark structure of LOV2 (404-546)) [more info...]
Chain information for 2v0u.pdb #1
---
Chain | Description | UniProt
A | LOV2 | O49003_AVESA 404-546
Non-standard residues in 2v0u.pdb #1
---
FMN — flavin mononucleotide (riboflavin monophosphate)
GOL — glycerol
> select /A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:413
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:411
17 atoms, 15 bonds, 2 residues, 1 model selected
Drag select of 5 residues
> select subtract /A:409
47 atoms, 15 bonds, 6 residues, 1 model selected
> select add /A:409
56 atoms, 23 bonds, 7 residues, 1 model selected
> select subtract /A:409
47 atoms, 15 bonds, 6 residues, 1 model selected
> select add /A:404
55 atoms, 22 bonds, 7 residues, 1 model selected
> select add /A:403
66 atoms, 33 bonds, 8 residues, 1 model selected
> select add /A:402
75 atoms, 41 bonds, 9 residues, 1 model selected
> select add /A:401
79 atoms, 44 bonds, 10 residues, 1 model selected
> hide sel cartoons
> select /A:412
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:408
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add /A:409
26 atoms, 23 bonds, 3 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /A:401-546
1186 atoms, 1205 bonds, 146 residues, 1 model selected
> hide sel atoms
> select ::name="HOH"
173 atoms, 173 residues, 1 model selected
> hide sel atoms
Drag select of 6 atoms, 5 bonds
Drag select of 5 atoms, 5 bonds
Drag select of 6 atoms, 5 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> select ::name="GOL"
36 atoms, 30 bonds, 6 residues, 1 model selected
> hide sel atoms
> select :FMN
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 31 atom styles
> color sel light gray target cspf
> color sel light gray
> color sel byhetero
> ui tool show "Color Actions"
> select /A:401-546
1186 atoms, 1205 bonds, 146 residues, 1 model selected
> color sel slate gray target cspf
> color sel dark orange target cspf
> color sel coral target cspf
> select clear
> lighting soft
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,2
Model Number: Z14L000UULL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.100.650
OS Loader Version: 8422.100.650
Software:
System Software Overview:
System Version: macOS 13.3.1 (22E261)
Kernel Version: Darwin 22.4.0
Time since boot: 10 days, 3 hours, 59 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash running save dialog |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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