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#8673 closed defect (fixed)

Crash in garbage collection

Reported by:	chimerax-bug-report@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	UI	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-13.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202303162359 (2023-03-16 23:59:45 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 0x00000001f4283a80 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 362 in _cleanup
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 402 in cb
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
  File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 29000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,2",
  "coalitionID" : 4322,
  "osVersion" : {
    "train" : "macOS 13.1",
    "build" : "22C65",
    "releaseType" : "User"
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  "captureTime" : "2023-03-20 10:30:34.9304 +0100",
  "incident" : "BCFE68A6-D3A5-4DE4-BD9C-4CA0268AB98D",
  "pid" : 75594,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-03-20 10:15:55.4580 +0100",
  "procStartAbsTime" : 696226755603,
  "procExitAbsTime" : 717334011253,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"61411086-A479-529F-8E04-7671DA2A7CFF","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D87A52A5-9748-9A31-24F8-BF6246639123",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 2621,
  "sleepWakeUUID" : "B38BFC1D-1F04-46FE-B8FB-C245AA25B1C5",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 105559424499543\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO              600178000000-600180000000 [128.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\n",
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 105559424499543\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO              600178000000-600180000000 [128.0M] rw-\/rwx SM=PRV  ",
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  "faultingThread" : 0,
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===== Log before crash start =====
Startup Messages  
---  
notes | 2023-03-20 10:16:09,354:INFO:OpenGL_accelerate module loaded  
2023-03-20 10:16:09,375:INFO:Using accelerated ArrayDatatype  
  
UCSF ChimeraX version: 1.6.dev202303162359 (2023-03-16)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/simonaamodeo/Downloads/4v88.cif

Summary of feedback from opening /Users/simonaamodeo/Downloads/4v88.cif  
---  
warnings | Ignoring microheterogeneity for label_seq_id 3 in chain  
Ignoring microheterogeneity for label_seq_id 4 in chain BO  
Ignoring microheterogeneity for label_seq_id 11 in chain BO  
Ignoring microheterogeneity for label_seq_id 13 in chain BO  
Ignoring microheterogeneity for label_seq_id 16 in chain BO  
35 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /A5:420  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /A5:420  
notes | Fetching CCD OHX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/OHX/OHX.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
4v88.cif title:  
The structure of the eukaryotic ribosome at 3.0 A resolution. [more info...]  
  
Chain information for 4v88.cif #1  
---  
Chain | Description | UniProt  
A1 A5 | 25S rRNA |  
A2 | 18S RIBOSOMAL RNA |  
A3 A7 | 5S rRNA |  
A4 A8 | 5.8S rRNA |  
A6 | 18S rRNA |  
AA CA | 40S ribosomal protein S0-A | RSSA1_YEAST 1-252  
AB CB | 40S ribosomal protein S1-A | RS3A1_YEAST 1-255  
AC CC | 40S ribosomal protein S2 | RS2_YEAST 1-254  
AD CD | 40S ribosomal protein S3 | RS3_YEAST 1-240  
AE CE | 40S ribosomal protein S4-A | RS4A_YEAST 1-261  
AF CF | 40S ribosomal protein S5 | RS5_YEAST 1-225  
AG CG | 40S ribosomal protein S6-A | RS6A_YEAST 1-236  
AH CH | 40S ribosomal protein S7-A | RS7A_YEAST 1-190  
AI CI | 40S ribosomal protein S8-A | RS8A_YEAST 1-200  
AJ CJ | 40S ribosomal protein S9-A | RS9A_YEAST 1-197  
AK CK | 40S ribosomal protein S10-A | RS10A_YEAST 1-105  
AL CL | 40S ribosomal protein S11-A | RS11A_YEAST 1-156  
AM CM | 40S ribosomal protein S12 | RS12_YEAST 1-143  
AN CN | 40S ribosomal protein S13 | RS13_YEAST 1-151  
AO CO | 40S ribosomal protein S14-A | RS14A_YEAST 1-137  
AP CP | 40S ribosomal protein S15 | RS15_YEAST 1-142  
AQ CQ | 40S ribosomal protein S16-A | RS16A_YEAST 1-143  
AR CR | 40S ribosomal protein S17-A | RS17A_YEAST 1-136  
AS CS | 40S ribosomal protein S18-A | RS18A_YEAST 1-146  
AT CT | 40S ribosomal protein S19-A | RS19A_YEAST 1-144  
AU CU | 40S ribosomal protein S20 | RS20_YEAST 1-121  
AV CV | 40S ribosomal protein S21-A | RS21A_YEAST 1-87  
AW CW | 40S ribosomal protein S22-A | RS22A_YEAST 1-130  
AX CX | 40S ribosomal protein S23-A | RS23A_YEAST 1-145  
AY CY | 40S ribosomal protein S24-A | RS24A_YEAST 1-135  
AZ CZ | 40S ribosomal protein S25-A | RS25A_YEAST 1-108  
Aa Ca | 40S ribosomal protein S26-A | RS26A_YEAST 1-119  
Ab Cb | 40S ribosomal protein S27-A | RS27_YEAST 1-82  
Ac Cc | 40S ribosomal protein S28-A | RS28A_YEAST 1-67  
Ad Cd | 40S ribosomal protein S29-A | RS29A_YEAST 1-56  
Ae Ce | 40S ribosomal protein S30-A | RS30A_YEAST 1-63  
Af Cf | 40S ribosomal protein S31 | RS27A_YEAST 1-152  
Ag Cg | Guanine nucleotide-binding protein subunit beta-like protein (ASC1,
RACK1) | GBLP_YEAST 1-319  
Ah | Suppressor protein STM1 | STM1_YEAST 1-273  
BA DA | 60S ribosomal protein L2-A | RL2A_YEAST 1-254  
BB DB | 60S ribosomal protein L3 | RL3_YEAST 1-387  
BC DC | 60S ribosomal protein L4-A | RL4A_YEAST 1-362  
BD DD | 60S ribosomal protein L5 | RL5_YEAST 1-297  
BE DE | 60S ribosomal protein L6-A | RL6A_YEAST 1-176  
BF DF | 60S ribosomal protein L7-A | RL7A_YEAST 1-244  
BG DG | 60S ribosomal protein L8-A | RL8A_YEAST 1-256  
BH DH | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
BI DI | 60S ribosomal protein L10 | RL10_YEAST 1-221  
BJ DJ | 60S ribosomal protein L11-A | RL11A_YEAST 1-174  
BL DL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199  
BM DM | 60S ribosomal protein L14-A | RL14A_YEAST 1-138  
BN DN | 60S ribosomal protein L15-A | RL15A_YEAST 1-204  
BO DO | 60S ribosomal protein L16-A, 60S ribosomal protein L16-B | RL16A_YEAST
1-199  
BP DP | 60S ribosomal protein L17-A | RL17A_YEAST 1-184  
BQ DQ | 60S ribosomal protein L18-A | RL18A_YEAST 1-186  
BR DR | 60S ribosomal protein L19-A | RL19A_YEAST 1-189  
BS DS | 60S ribosomal protein L20-A | RL20A_YEAST 1-172  
BT DT | 60S ribosomal protein L21-A | RL21A_YEAST 1-160  
BU DU | 60S ribosomal protein L22-A | RL22A_YEAST 1-121  
BV DV | 60S ribosomal protein L23-A | RL23A_YEAST 1-137  
BW DW | 60S ribosomal protein L24-A | RL24A_YEAST 1-155  
BX DX | 60S ribosomal protein L25 | RL25_YEAST 1-142  
BY DY | 60S ribosomal protein L26-A | RL26A_YEAST 1-127  
BZ DZ | 60S ribosomal protein L27-A | RL27A_YEAST 1-136  
Ba Da | 60S ribosomal protein L28 | RL28_YEAST 1-149  
Bb Db | 60S ribosomal protein L29 | RL29_YEAST 1-59  
Bc Dc | 60S ribosomal protein L30 | RL30_YEAST 1-105  
Bd Dd | 60S ribosomal protein L31-A | RL31A_YEAST 1-113  
Be De | 60S ribosomal protein L32 | RL32_YEAST 1-130  
Bf Df | 60S ribosomal protein L33-A | RL33A_YEAST 1-107  
Bg Dg | 60S ribosomal protein L34-A | RL34A_YEAST 1-121  
Bh Dh | 60S ribosomal protein L35-A | RL35A_YEAST 1-120  
Bi Di | 60S ribosomal protein L36-A | RL36A_YEAST 1-100  
Bj Dj | 60S ribosomal protein L37-A | RL37A_YEAST 1-88  
Bk Dk | 60S ribosomal protein L38 | RL38_YEAST 1-78  
Bl Dl | 60S ribosomal protein L39 | RL39_YEAST 1-51  
Bm Dm | 60S ribosomal protein L40 | RL401_YEAST 1-128  
Bn Dn | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
Bo Do | 60S ribosomal protein L42-A | RL44A_YEAST 1-106  
Bp Dp | 60S ribosomal protein L43-A | RL34A_YEAST 1-92, RL43A_YEAST 1-92  
Ch | Suppressor protein STM1 | RLA0_YEAST 1-273  
DK | Ribosomal protein L12 |  
Dq | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312  
Dr | Ribosomal protein P1 alpha |  
Ds | Ribosomal protein P2 beta |  
  
Non-standard residues in 4v88.cif #1  
---  
MG — magnesium ion  
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)  
ZN — zinc ion  
  
4v88.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show "Selection Inspector"

> show target m

> sym #1

4v88.cif mmCIF Assemblies  
---  
1| author_defined_assembly| 1 copy of chains A1-A4,AA-AZ,Aa-Ah,BA-BJ,BL-BZ,Ba-
Bp  
2| author_defined_assembly| 1 copy of chains A5-A8,CA-CZ,Ca-Ch,DA-DZ,Da-Ds  
  

> log metadata #1

Metadata for 4v88.cif #1  
---  
Title | The structure of the eukaryotic ribosome at 3.0 A resolution.  
Citation | Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L.,
Yusupova, G., Yusupov, M. (2011). The structure of the eukaryotic ribosome at
3.0 angstrom resolution. Science, 334, 1524-1529. PMID: 22096102  
Non-standard residues | MG — magnesium ion  
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)  
ZN — zinc ion  
Sources (natural) | Saccharomyces cerevisiae (baker's yeast)  
Saccharomyces cerevisiae  
Experimental method | X-ray diffraction  
Resolution | 3.0Å  
  
> log chains #1

Chain information for 4v88.cif #1  
---  
Chain | Description | UniProt  
A1 A5 | 25S rRNA |  
A2 | 18S RIBOSOMAL RNA |  
A3 A7 | 5S rRNA |  
A4 A8 | 5.8S rRNA |  
A6 | 18S rRNA |  
AA CA | 40S ribosomal protein S0-A | RSSA1_YEAST 1-252  
AB CB | 40S ribosomal protein S1-A | RS3A1_YEAST 1-255  
AC CC | 40S ribosomal protein S2 | RS2_YEAST 1-254  
AD CD | 40S ribosomal protein S3 | RS3_YEAST 1-240  
AE CE | 40S ribosomal protein S4-A | RS4A_YEAST 1-261  
AF CF | 40S ribosomal protein S5 | RS5_YEAST 1-225  
AG CG | 40S ribosomal protein S6-A | RS6A_YEAST 1-236  
AH CH | 40S ribosomal protein S7-A | RS7A_YEAST 1-190  
AI CI | 40S ribosomal protein S8-A | RS8A_YEAST 1-200  
AJ CJ | 40S ribosomal protein S9-A | RS9A_YEAST 1-197  
AK CK | 40S ribosomal protein S10-A | RS10A_YEAST 1-105  
AL CL | 40S ribosomal protein S11-A | RS11A_YEAST 1-156  
AM CM | 40S ribosomal protein S12 | RS12_YEAST 1-143  
AN CN | 40S ribosomal protein S13 | RS13_YEAST 1-151  
AO CO | 40S ribosomal protein S14-A | RS14A_YEAST 1-137  
AP CP | 40S ribosomal protein S15 | RS15_YEAST 1-142  
AQ CQ | 40S ribosomal protein S16-A | RS16A_YEAST 1-143  
AR CR | 40S ribosomal protein S17-A | RS17A_YEAST 1-136  
AS CS | 40S ribosomal protein S18-A | RS18A_YEAST 1-146  
AT CT | 40S ribosomal protein S19-A | RS19A_YEAST 1-144  
AU CU | 40S ribosomal protein S20 | RS20_YEAST 1-121  
AV CV | 40S ribosomal protein S21-A | RS21A_YEAST 1-87  
AW CW | 40S ribosomal protein S22-A | RS22A_YEAST 1-130  
AX CX | 40S ribosomal protein S23-A | RS23A_YEAST 1-145  
AY CY | 40S ribosomal protein S24-A | RS24A_YEAST 1-135  
AZ CZ | 40S ribosomal protein S25-A | RS25A_YEAST 1-108  
Aa Ca | 40S ribosomal protein S26-A | RS26A_YEAST 1-119  
Ab Cb | 40S ribosomal protein S27-A | RS27_YEAST 1-82  
Ac Cc | 40S ribosomal protein S28-A | RS28A_YEAST 1-67  
Ad Cd | 40S ribosomal protein S29-A | RS29A_YEAST 1-56  
Ae Ce | 40S ribosomal protein S30-A | RS30A_YEAST 1-63  
Af Cf | 40S ribosomal protein S31 | RS27A_YEAST 1-152  
Ag Cg | Guanine nucleotide-binding protein subunit beta-like protein (ASC1,
RACK1) | GBLP_YEAST 1-319  
Ah | Suppressor protein STM1 | STM1_YEAST 1-273  
BA DA | 60S ribosomal protein L2-A | RL2A_YEAST 1-254  
BB DB | 60S ribosomal protein L3 | RL3_YEAST 1-387  
BC DC | 60S ribosomal protein L4-A | RL4A_YEAST 1-362  
BD DD | 60S ribosomal protein L5 | RL5_YEAST 1-297  
BE DE | 60S ribosomal protein L6-A | RL6A_YEAST 1-176  
BF DF | 60S ribosomal protein L7-A | RL7A_YEAST 1-244  
BG DG | 60S ribosomal protein L8-A | RL8A_YEAST 1-256  
BH DH | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
BI DI | 60S ribosomal protein L10 | RL10_YEAST 1-221  
BJ DJ | 60S ribosomal protein L11-A | RL11A_YEAST 1-174  
BL DL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199  
BM DM | 60S ribosomal protein L14-A | RL14A_YEAST 1-138  
BN DN | 60S ribosomal protein L15-A | RL15A_YEAST 1-204  
BO DO | 60S ribosomal protein L16-A, 60S ribosomal protein L16-B | RL16A_YEAST
1-199  
BP DP | 60S ribosomal protein L17-A | RL17A_YEAST 1-184  
BQ DQ | 60S ribosomal protein L18-A | RL18A_YEAST 1-186  
BR DR | 60S ribosomal protein L19-A | RL19A_YEAST 1-189  
BS DS | 60S ribosomal protein L20-A | RL20A_YEAST 1-172  
BT DT | 60S ribosomal protein L21-A | RL21A_YEAST 1-160  
BU DU | 60S ribosomal protein L22-A | RL22A_YEAST 1-121  
BV DV | 60S ribosomal protein L23-A | RL23A_YEAST 1-137  
BW DW | 60S ribosomal protein L24-A | RL24A_YEAST 1-155  
BX DX | 60S ribosomal protein L25 | RL25_YEAST 1-142  
BY DY | 60S ribosomal protein L26-A | RL26A_YEAST 1-127  
BZ DZ | 60S ribosomal protein L27-A | RL27A_YEAST 1-136  
Ba Da | 60S ribosomal protein L28 | RL28_YEAST 1-149  
Bb Db | 60S ribosomal protein L29 | RL29_YEAST 1-59  
Bc Dc | 60S ribosomal protein L30 | RL30_YEAST 1-105  
Bd Dd | 60S ribosomal protein L31-A | RL31A_YEAST 1-113  
Be De | 60S ribosomal protein L32 | RL32_YEAST 1-130  
Bf Df | 60S ribosomal protein L33-A | RL33A_YEAST 1-107  
Bg Dg | 60S ribosomal protein L34-A | RL34A_YEAST 1-121  
Bh Dh | 60S ribosomal protein L35-A | RL35A_YEAST 1-120  
Bi Di | 60S ribosomal protein L36-A | RL36A_YEAST 1-100  
Bj Dj | 60S ribosomal protein L37-A | RL37A_YEAST 1-88  
Bk Dk | 60S ribosomal protein L38 | RL38_YEAST 1-78  
Bl Dl | 60S ribosomal protein L39 | RL39_YEAST 1-51  
Bm Dm | 60S ribosomal protein L40 | RL401_YEAST 1-128  
Bn Dn | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
Bo Do | 60S ribosomal protein L42-A | RL44A_YEAST 1-106  
Bp Dp | 60S ribosomal protein L43-A | RL34A_YEAST 1-92, RL43A_YEAST 1-92  
Ch | Suppressor protein STM1 | RLA0_YEAST 1-273  
DK | Ribosomal protein L12 |  
Dq | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312  
Dr | Ribosomal protein P1 alpha |  
Ds | Ribosomal protein P2 beta |  
  

> ui tool show "Selection Inspector"

> sequence chain #1/A1#1/A5

Alignment identifier is 1  

> sequence chain #1/A6

Alignment identifier is 1/A6  

> select /A6:1-2

42 atoms, 46 bonds, 2 residues, 1 model selected  

> select /A6:1-757

15877 atoms, 17746 bonds, 556 pseudobonds, 752 residues, 3 models selected  

> sequence chain #1/A1#1/A5

Alignment identifier is 2  

> select /A1,A5:3-3396

134731 atoms, 150808 bonds, 5706 pseudobonds, 6299 residues, 3 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /A1 /A5

Alignment identifier is 3  

> sequence chain /A2

Alignment identifier is 1/A2  

> sequence chain /A3 /A7

Alignment identifier is 4  

> sequence chain /A4 /A8

Alignment identifier is 5  

> sequence chain /A6

Destroying pre-existing alignment with identifier 1/A6  
Alignment identifier is 1/A6  

> sequence chain /AA /CA

Alignment identifier is 6  

> sequence chain /AB /CB

Alignment identifier is 7  

> sequence chain /AC /CC

Alignment identifier is 8  

> sequence chain /AD /CD

Alignment identifier is 9  

> sequence chain /AE /CE

Alignment identifier is 10  

> sequence chain /AF /CF

Alignment identifier is 11  

> sequence chain /AG /CG

Alignment identifier is 12  

> sequence chain /AH /CH

Alignment identifier is 13  

> sequence chain /AI /CI

Alignment identifier is 14  

> sequence chain /AJ /CJ

Alignment identifier is 15  

> sequence chain /AK /CK

Alignment identifier is 16  

> sequence chain /AL /CL

Alignment identifier is 17  

> sequence chain /AM /CM

Alignment identifier is 18  

> sequence chain /AN /CN

Alignment identifier is 19  

> sequence chain /AO /CO

Alignment identifier is 20  

> sequence chain /AP /CP

Alignment identifier is 21  

> sequence chain /AQ /CQ

Alignment identifier is 22  

> sequence chain /AR /CR

Alignment identifier is 23  

> sequence chain /AS /CS

Alignment identifier is 24  

> sequence chain /AT /CT

Alignment identifier is 25  

> sequence chain /AU /CU

Alignment identifier is 26  

> sequence chain /AV /CV

Alignment identifier is 27  

> sequence chain /AW /CW

Alignment identifier is 28  

> sequence chain /AX /CX

Alignment identifier is 29  

> sequence chain /AY /CY

Alignment identifier is 30  

> sequence chain /AZ /CZ

Alignment identifier is 31  

> sequence chain /Aa /Ca

Alignment identifier is 32  

> sequence chain /Ab /Cb

Alignment identifier is 33  

> sequence chain /Ac /Cc

Alignment identifier is 34  

> sequence chain /Ad /Cd

Alignment identifier is 35  

> sequence chain /Ae /Ce

Alignment identifier is 36  

> sequence chain /Af /Cf

Alignment identifier is 37  

> sequence chain /Ag /Cg

Alignment identifier is 38  

> sequence chain /Ah

Alignment identifier is 1/Ah  

> sequence chain /BA /DA

Alignment identifier is 39  

> sequence chain /BB /DB

Alignment identifier is 40  

> sequence chain /BC /DC

Alignment identifier is 41  

> sequence chain /BD /DD

Alignment identifier is 42  

> sequence chain /BE /DE

Alignment identifier is 43  

> sequence chain /BF /DF

Alignment identifier is 44  

> sequence chain /BG /DG

Alignment identifier is 45  

> sequence chain /BH /DH

Alignment identifier is 46  

> sequence chain /BI /DI

Alignment identifier is 47  

> sequence chain /BJ /DJ

Alignment identifier is 48  

> sequence chain /BL /DL

Alignment identifier is 49  

> sequence chain /BM /DM

Alignment identifier is 50  

> sequence chain /BN /DN

Alignment identifier is 51  

> sequence chain /BO /DO

Alignment identifier is 52  

> sequence chain /BP /DP

Alignment identifier is 53  

> sequence chain /BQ /DQ

Alignment identifier is 54  

> sequence chain /BR /DR

Alignment identifier is 55  

> sequence chain /BS /DS

Alignment identifier is 56  

> sequence chain /BT /DT

Alignment identifier is 57  

> sequence chain /BU /DU

Alignment identifier is 58  

> sequence chain /BV /DV

Alignment identifier is 59  

> sequence chain /BW /DW

Alignment identifier is 60  

> sequence chain /BX /DX

Alignment identifier is 61  

> sequence chain /BY /DY

Alignment identifier is 62  

> sequence chain /BZ /DZ

Alignment identifier is 63  

> sequence chain /Ba /Da

Alignment identifier is 64  

> sequence chain /Bb /Db

Alignment identifier is 65  

> sequence chain /Bc /Dc

Alignment identifier is 66  

> sequence chain /Bd /Dd

Alignment identifier is 67  

> sequence chain /Be /De

Alignment identifier is 68  

> sequence chain /Bf /Df

Alignment identifier is 69  

> sequence chain /Bg /Dg

Alignment identifier is 70  

> sequence chain /Bh /Dh

Alignment identifier is 71  

> sequence chain /Bi /Di

Alignment identifier is 72  

> sequence chain /Bj /Dj

Alignment identifier is 73  

> sequence chain /Bk /Dk

Alignment identifier is 74  

> sequence chain /Bl /Dl

Alignment identifier is 75  

> sequence chain /Bm /Dm

Alignment identifier is 76  

> sequence chain /Bn /Dn

Alignment identifier is 77  

> sequence chain /Bo /Do

Alignment identifier is 78  

> sequence chain /Bp /Dp

Alignment identifier is 79  

> sequence chain /Ch

Alignment identifier is 1/Ch  

> sequence chain /DK

Alignment identifier is 1/DK  

> sequence chain /Dq

Alignment identifier is 1/Dq  

> sequence chain /Dr

Alignment identifier is 1/Dr  

> sequence chain /Ds

Alignment identifier is 1/Ds  

> close


===== Log before crash end =====

Log:
Startup Messages  
---  
notes | 2023-03-20 10:31:13,869:INFO:OpenGL_accelerate module loaded  
2023-03-20 10:31:13,877:INFO:Using accelerated ArrayDatatype  
  
UCSF ChimeraX version: 1.6.dev202303162359 (2023-03-16)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z15T000A4SM/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 4 Tage, 1 Stunde und 33 Minuten

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          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
    ChimeraX-AddH: 2.2.3
    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.dev202303162359
    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: 1.3.3
    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: 1.3.6
    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
    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: 1.10.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    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: 1.28.3
    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: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.2
    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: 6.0.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.4
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.5
    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
    pandas: 1.5.3
    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: 3.1.1
    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: 6.4.2
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.1
    qtconsole: 5.4.0
    QtPy: 2.3.0
    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
    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: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.5
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 3 years ago

Cc:	Tom Goddard added
Component:	Unassigned → UI
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash in garbage collection

Crash was in _cleanup, which calls full garbage collection 100 milliseconds after a tool is deleted in order to break callback loops, particularly settings-change callback loops. The 'close' command was being executed and there was a large structure open which probably took more that .1 seconds to dispose of. I am inclined to removed the .1 second garbage collection call since there have been recent changes to settings-change handling which should render the formerly problematic callbacks harmless.

comment:2 by pett, 3 years ago

Resolution:	→ fixed
Status:	accepted → closed

Fix: https://github.com/RBVI/ChimeraX/commit/15455f21c6f200c5e63d9c9189eb7fbcae7e3b52

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