Opened 3 years ago

Closed 3 years ago

#8556 closed defect (can't reproduce)

Crash in molarray.LookupTable._delete_table

Reported by: irene.vercellino@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Eric Pettersen
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  
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  
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 Eric Pettersen, 3 years ago

Cc: Eric Pettersen added
Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in molarray.LookupTable._delete_table

comment:2 by Tom Goddard, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed

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.

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