![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8556 closed defect (can't reproduce)
Crash in molarray.LookupTable._delete_table
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Nothing special: I was changing colors to a model based on sequence selection. Model around 750 kDa, sleections around 250.
Fatal Python error: Aborted
Thread 0x000070000d6da000 (most recent call first):
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000011cf7a600 (most recent call first):
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 302 in _delete_table
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 296 in __del__
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py", line 510 in cast
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_internal.py", line 282 in data_as
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 322 in pointer
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 197 in get_prop
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 1774 in _update_graphics_if_needed
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 283 in check_for_drawing_change
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/s5/6_ctjry574s9mp33rrzjf3z40000gr/T/AppTranslocation/A964E6BB-5F6F-45C1-B53E-2C90E671AD06/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-02-24 12:41:52.00 +0100","app_version":"1.5.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.6.3 (21G419)","incident_id":"FFB81FBA-9969-4664-ABD2-BA22392C68D7","name":"ChimeraX"}
{
"uptime" : 580000,
"procLaunch" : "2023-02-24 11:15:47.6856 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "iMac16,2",
"procStartAbsTime" : 577110622609857,
"coalitionID" : 13776,
"osVersion" : {
"train" : "macOS 12.6.3",
"build" : "21G419",
"releaseType" : "User"
},
"captureTime" : "2023-02-24 12:36:10.8543 +0100",
"incident" : "FFB81FBA-9969-4664-ABD2-BA22392C68D7",
"bug_type" : "309",
"pid" : 40700,
"procExitAbsTime" : 581933683924682,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"74FA844B-17B2-51C5-B489-9F7F67C83E90","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3C7A34AF-7825-EEFA-DB16-895E42E776EF",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":2419955,"threadState":{"r13":{"value":80},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":6},"rsi":{"value":6},"r8":{"value":140360767856456},"cr2":{"value":140360797960832},"rdx":{"value":0},"r10":{"value":4780959232,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":11769733039800880539},"r15":{"value":22},"rbx":{"value":4780959232,"symbolLocation":0,"symbol":"_main_thread"},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703524065294,"matchesCrashFrame":1},"rbp":{"value":140360767855232},"rsp":{"value":140360767855192},"r12":{"value":259},"rcx":{"value":140360767855192},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":32782,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":0},{"imageOffset":25087,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":1},{"imageOffset":279256,"symbol":"raise","symbolLocation":26,"imageIndex":2},{"imageOffset":15869,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":3},{"imageOffset":0,"imageIndex":4},{"imageOffset":531748,"symbol":"abort","symbolLocation":123,"imageIndex":2},{"imageOffset":62295,"symbol":"malloc_vreport","symbolLocation":551,"imageIndex":5},{"imageOffset":75051,"symbol":"malloc_report","symbolLocation":151,"imageIndex":5},{"imageOffset":153174,"symbol":"std::__1::__tree, 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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ivercell/Desktop/manuscripts/SCs_tissues/figures_V1/A_respirasome_box_rsr1_002_rsr.pdb
> /Users/ivercell/Desktop/manuscripts/SCs_tissues/figures_V1/C_respirasome_box_rsr1_001_rsr-
> morph-coot_rsr2_002_rsr.pdb
> /Users/ivercell/Desktop/manuscripts/SCs_tissues/figures_V1/SC_respirasome_box_rsr1_002_rsr-
> coot-0.pdb
Summary of feedback from opening
/Users/ivercell/Desktop/manuscripts/SCs_tissues/figures_V1/A_respirasome_box_rsr1_002_rsr.pdb
---
warnings | Ignored bad PDB record found on line 922
SSBOND 8 CYS X1 35 CYS X1 65
Ignored bad PDB record found on line 923
SSBOND 9 CYS X1 45 CYS X1 55
Ignored bad PDB record found on line 924
SSBOND 10 CYS X1 77 CYS X1 109
Ignored bad PDB record found on line 925
SSBOND 11 CYS X1 87 CYS X1 99
Ignored bad PDB record found on line 926
SSBOND 12 CYS Y1 17 CYS Y1 74
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 9 9 SERC1 15 PROC1 34 1
20
Start residue of secondary structure not found: HELIX 10 10 GLYC1 56 HISC1 67
1 12
Start residue of secondary structure not found: HELIX 11 11 ALAC1 126 PHEC1
138 1 13
Start residue of secondary structure not found: HELIX 37 37 LYSF1 16 ARGF1 20
1 5
Start residue of secondary structure not found: HELIX 38 38 ARGF1 32 GLYF1 40
1 9
207 messages similar to the above omitted
Summary of feedback from opening
/Users/ivercell/Desktop/manuscripts/SCs_tissues/figures_V1/C_respirasome_box_rsr1_001_rsr-
morph-coot_rsr2_002_rsr.pdb
---
warnings | Ignored bad PDB record found on line 915
SSBOND 1 CYS X1 35 CYS X1 65
Ignored bad PDB record found on line 916
SSBOND 2 CYS X1 45 CYS X1 55
Ignored bad PDB record found on line 917
SSBOND 3 CYS X1 77 CYS X1 109
Ignored bad PDB record found on line 918
SSBOND 4 CYS X1 87 CYS X1 99
Ignored bad PDB record found on line 919
SSBOND 5 CYS Y1 17 CYS Y1 74
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 9 9 SERC1 15 PROC1 34 1
20
Start residue of secondary structure not found: HELIX 10 10 GLYC1 56 HISC1 67
1 12
Start residue of secondary structure not found: HELIX 11 11 ALAC1 126 PHEC1
138 1 13
Start residue of secondary structure not found: HELIX 37 37 LYSF1 16 ARGF1 20
1 5
Start residue of secondary structure not found: HELIX 38 38 ARGF1 32 GLYF1 40
1 9
207 messages similar to the above omitted
Summary of feedback from opening
/Users/ivercell/Desktop/manuscripts/SCs_tissues/figures_V1/SC_respirasome_box_rsr1_002_rsr-
coot-0.pdb
---
warnings | Ignored bad PDB record found on line 1021
SSBOND 1 CYS X1 35 CYS X1 65
Ignored bad PDB record found on line 1022
SSBOND 2 CYS X1 45 CYS X1 55
Ignored bad PDB record found on line 1023
SSBOND 3 CYS X1 77 CYS X1 109
Ignored bad PDB record found on line 1024
SSBOND 4 CYS X1 87 CYS X1 99
Ignored bad PDB record found on line 1025
SSBOND 5 CYS Y1 17 CYS Y1 74
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 ARG 1 35 SER 1 54 1
20
Start residue of secondary structure not found: HELIX 2 2 ALA 1 63 PRO 1 75 1
13
Start residue of secondary structure not found: HELIX 3 3 ASP 1 78 GLY 1 83 1
6
Start residue of secondary structure not found: HELIX 4 4 ASN 1 104 MET 1 117
1 14
Start residue of secondary structure not found: HELIX 5 5 GLY 1 127 GLY 1 132
1 6
410 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (359 )
Cannot find LINK/SSBOND residue CYS (365 )
Cannot find LINK/SSBOND residue CYS (405 )
Cannot find LINK/SSBOND residue CYS (362 )
Cannot find LINK/SSBOND residue CYS (103 )
40 messages similar to the above omitted
Chain information for A_respirasome_box_rsr1_002_rsr.pdb #1
---
Chain | Description
1 | No description available
A | No description available
B M | No description available
B1 | No description available
C N | No description available
D | No description available
D1 | No description available
E P | No description available
E1 | No description available
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G | No description available
H S | No description available
H1 | No description available
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J1 | No description available
K | No description available
K1 | No description available
L | No description available
L1 | No description available
M1 | No description available
O | No description available
Q | No description available
R | No description available
R1 | No description available
T | No description available
T1 | No description available
V | No description available
V1 | No description available
W1 | No description available
Y1 | No description available
a1 | No description available
b1 | No description available
d1 | No description available
f1 | No description available
g1 | No description available
h1 | No description available
i1 | No description available
j1 | No description available
k1 | No description available
l1 | No description available
m1 | No description available
n | No description available
n1 | No description available
o | No description available
o1 | No description available
p | No description available
p1 | No description available
q | No description available
q1 | No description available
r | No description available
r1 | No description available
s | No description available
s1 | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
Chain information for C_respirasome_box_rsr1_001_rsr-morph-
coot_rsr2_002_rsr.pdb #2
---
Chain | Description
1 | No description available
A | No description available
A1 | No description available
B M | No description available
B1 | No description available
C N | No description available
D | No description available
D1 | No description available
E P | No description available
E1 | No description available
F | No description available
G | No description available
H S | No description available
H1 | No description available
J U | No description available
J1 | No description available
K | No description available
K1 | No description available
L | No description available
L1 | No description available
M1 | No description available
O | No description available
Q | No description available
R | No description available
R1 | No description available
T | No description available
T1 | No description available
V | No description available
W1 | No description available
Y1 | No description available
a1 | No description available
b1 | No description available
d1 | No description available
f1 | No description available
g1 | No description available
h1 | No description available
i1 | No description available
j1 | No description available
k1 | No description available
l1 | No description available
m1 | No description available
n | No description available
n1 | No description available
o | No description available
o1 | No description available
p | No description available
p1 | No description available
q | No description available
q1 | No description available
r | No description available
r1 | No description available
s | No description available
s1 | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
Chain information for SC_respirasome_box_rsr1_002_rsr-coot-0.pdb #3
---
Chain | Description
1 | No description available
A | No description available
A1 | No description available
B M | No description available
B1 | No description available
C N | No description available
D | No description available
E P | No description available
E1 | No description available
F | No description available
G | No description available
H S | No description available
H1 | No description available
I | No description available
J U | No description available
J1 | No description available
K | No description available
K1 | No description available
L | No description available
L1 | No description available
M1 | No description available
N1 | No description available
O | No description available
Q | No description available
R | No description available
R1 | No description available
T | No description available
T1 | No description available
V | No description available
W1 | No description available
Y1 | No description available
Z1 | No description available
a n | No description available
a1 | No description available
b o | No description available
b1 | No description available
c p | No description available
c1 | No description available
d q | No description available
e r | No description available
f s | No description available
g t | No description available
h u | No description available
h1 | No description available
i v | No description available
i1 | No description available
j1 | No description available
k x | No description available
l y | No description available
m z | No description available
q1 | No description available
r1 | No description available
s1 | No description available
w | No description available
> hide atoms
> hide cartoons
> show surfaces
> set bgColor white
> set bgColor #ffffff00
> hide #!1 models
> hide #!2 models
> hide #!3 models
> open /Users/ivercell/Downloads/7o3c.pdb
7o3c.pdb title:
Murine supercomplex CIII2CIV In the mature unlocked conformation [more
info...]
Chain information for 7o3c.pdb #4
---
Chain | Description | UniProt
A L | cytochrome B-C1 complex subunit 1, mitochondrial | QCR1_MOUSE
B M | cytochrome B-C1 complex subunit 2, mitochondrial | QCR2_MOUSE
C N | cytochrome B | CYB_MOUSE
D O | cytochrome C1, heme protein, mitochondrial | CY1_MOUSE
E P | cytochrome B-C1 complex subunit rieske, mitochondrial | UCRI_MOUSE
F Q | cytochrome B-C1 complex subunit 7 | Q9CQB4_MOUSE
G R | cytochrome B-C1 complex subunit 8 | QCR8_MOUSE
H S | cytochrome B-C1 complex subunit 6, mitochondrial | QCR6_MOUSE
I | COX7A2L protein | Q99KD6_MOUSE
J U | cytochrome B-C1 complex subunit 9 | QCR9_MOUSE
K V | cytochrome B-C1 complex subunit 10 | QCR10_MOUSE
T | cytochrome B-C1 complex subunit 9 | UCRI_MOUSE
a | cytochrome C oxidase polypeptide I | COX1_MOUSE
b | cytochrome C oxidase polypeptide II | COX2_MOUSE
c | cytochrome C oxidase polypeptide III | COX3_MOUSE
d | cytochrome C oxidase subunit 4 isoform 1, mitochondrial | COX41_MOUSE
e | cytochrome C oxidase polypeptide VA | COX5A_MOUSE
f | cytochrome C oxidase polypeptide VB | COX5B_MOUSE
g | cytochrome C oxidase subunit 6A2, mitochondrial | CX6A2_MOUSE
h | cytochrome C oxidase subunit 6B1 | CX6B1_MOUSE
i | cytochrome C oxidase polypeptide VIC | COX6C_MOUSE
k | cytochrome C oxidase polypeptide VIIB | COX7B_MOUSE
l | cytochrome C oxidase polypeptide VIIC | COX7C_MOUSE
m | cytochrome C oxidase subunit 8B, mitochondrial | COX8B_MOUSE
Non-standard residues in 7o3c.pdb #4
---
3PE — 1,2-distearoyl-Sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
CUA — dinuclear copper ion
FES — FE2/S2 (inorganic) cluster
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NA — sodium ion
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
TGL — tristearoylglycerol (triacylglycerol)
ZN — zinc ion
> hide #!4 atoms
> lighting full
> show #!4 surfaces
> select #4/A-K
17377 atoms, 17796 bonds, 22 pseudobonds, 2159 residues, 2 models selected
> color (#!4 & sel) orange red
> color (#!4 & sel) yellow
> select #4/I
838 atoms, 860 bonds, 111 residues, 1 model selected
> color (#!4 & sel) blue
> color (#!4 & sel) medium blue
> select #4/L-Z
17069 atoms, 17477 bonds, 23 pseudobonds, 2125 residues, 2 models selected
> color (#!4 & sel) orange
> select #4/a-z
14086 atoms, 14510 bonds, 31 pseudobonds, 1724 residues, 2 models selected
> color (#!4 & sel) cyan
> color (#!4 & sel) #74faedff
> color (#!4 & sel) #73f7ebff
> color (#!4 & sel) #71f2edff
> color (#!4 & sel) #70eeeeff
> color (#!4 & sel) #6ce0edff
> color (#!4 & sel) #6bdfecff
> color (#!4 & sel) #69d8ebff
> color (#!4 & sel) #62bee7ff
> color (#!4 & sel) #518de3ff
> color (#!4 & sel) #5798e3ff
> color (#!4 & sel) #84e4e5ff
> color (#!4 & sel) #91e4e0ff
> color (#!4 & sel) #93e4deff
> color (#!4 & sel) #99e6e2ff
> color (#!4 & sel) #99e6dcff
> color (#!4 & sel) #9fe6d9ff
> color (#!4 & sel) #9fe5d9ff
> color (#!4 & sel) #a2e6daff
> color (#!4 & sel) #ade8deff
> color (#!4 & sel) #b5eae2ff
> color (#!4 & sel) #c1ece5ff
> color (#!4 & sel) #c8eee8ff
> select #4/A-K
17377 atoms, 17796 bonds, 22 pseudobonds, 2159 residues, 2 models selected
> color (#!4 & sel) #cdefe8ff
> color (#!4 & sel) #e0f1d3ff
> color (#!4 & sel) #ebf1cfff
> color (#!4 & sel) #eef0c9ff
> color (#!4 & sel) #edeec1ff
> color (#!4 & sel) #f1f0c9ff
> color (#!4 & sel) #f2f0cfff
> color (#!4 & sel) #f4f2d7ff
> color (#!4 & sel) #f4f1d8ff
> color (#!4 & sel) #f5f2daff
> color (#!4 & sel) #f6f3dfff
> color (#!4 & sel) #f8f6e7ff
> color (#!4 & sel) #f9f8edff
> color (#!4 & sel) #faf9f1ff
> color (#!4 & sel) #f8f7ebff
> color (#!4 & sel) #eeeab6ff
> color (#!4 & sel) #e9e691ff
> color (#!4 & sel) #e8e682ff
> color (#!4 & sel) #e8e578ff
> color (#!4 & sel) #e8e574ff
> color (#!4 & sel) #e9e667ff
> color (#!4 & sel) #e8e46eff
> color (#!4 & sel) #e8e38aff
> color (#!4 & sel) #eae5a4ff
> color (#!4 & sel) #ede9b6ff
> color (#!4 & sel) #f0ecc5ff
> color (#!4 & sel) #f1edccff
> color (#!4 & sel) #f2efd2ff
> color (#!4 & sel) #f4f2d7ff
> color (#!4 & sel) #eaedbaff
> color (#!4 & sel) #e7eaa9ff
> color (#!4 & sel) #e2e898ff
> color (#!4 & sel) #e2e897ff
> select #4/I
838 atoms, 860 bonds, 111 residues, 1 model selected
> color (#!4 & sel) #d9e796ff
> color (#!4 & sel) #9f92e4ff
> color (#!4 & sel) #8a85e2ff
> color (#!4 & sel) #4c57e0ff
> color (#!4 & sel) #5765e0ff
> color (#!4 & sel) #5a68e0ff
> color (#!4 & sel) #5b6ae0ff
> color (#!4 & sel) #5c6ae0ff
> color (#!4 & sel) #616edfff
> color (#!4 & sel) #6870e0ff
> color (#!4 & sel) #6b74e0ff
> color (#!4 & sel) #6e75e0ff
> color (#!4 & sel) #6d71e0ff
> color (#!4 & sel) #6d70e0ff
> color (#!4 & sel) #6f70e0ff
> color (#!4 & sel) #7773e1ff
> color (#!4 & sel) #8079e1ff
> color (#!4 & sel) #8385e2ff
> color (#!4 & sel) #6a7de0ff
> color (#!4 & sel) #6079e0ff
> color (#!4 & sel) #536fe1ff
> color (#!4 & sel) #4766e1ff
> color (#!4 & sel) #4262e2ff
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.1 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 16 GB
System Firmware Version: 476.0.0.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.32f21
Software:
System Software Overview:
System Version: macOS 12.6.3 (21G419)
Kernel Version: Darwin 21.6.0
Time since boot: 6 days 17:53
Graphics/Displays:
Intel Iris Pro Graphics 6200:
Chipset Model: Intel Iris Pro Graphics 6200
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1622
Revision ID: 0x000a
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
24MB65:
Resolution: 1200 x 1920
UI Looks like: 1200 x 1920 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 610NTKF5M253
Mirror: Off
Online: Yes
Rotation: 90
iMac:
Display Type: Built-In Retina LCD
Resolution: 4096 x 2304 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 5A0210B908424
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
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
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: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in molarray.LookupTable._delete_table |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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ChimeraX crashed trying to release some memory. This was probably because some ChimeraX code that ran earlier corrupted memory. The crash report does not give any clues about what caused that. I see from the log that you just opened some large PDB structures, selected and colored. If you see similar crashes, please report again and maybe we will get some additional clue.
Eric, the crash was in our C++ deleting a std::map<>, which happened during garbage collection while evaluating StructureData.graphics_changeds. Some numpy operation triggered the garbage collection. I don't think any of this is the bug -- something earlier corrupted the memory. But the log shows only simple operations coloring, selecting on open .pdb files, also surface calculation, were done. So it must have been some basic operation that led to the problem.