![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17364 closed defect (can't reproduce)
Crash closing dock widget
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | 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-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00000001fe49c840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 52)
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{
"uptime" : 14000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 3462,
"osVersion" : {
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"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-04-13 07:10:23.7525 +0530",
"codeSigningMonitor" : 1,
"incident" : "B29BA178-6251-4F5B-AD86-59DEBB5971E4",
"pid" : 6053,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-13 07:08:31.2062 +0530",
"procStartAbsTime" : 345231316517,
"procExitAbsTime" : 347931286136,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0B8C3D55-E7D9-FFA6-FF44-349177FD6221",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "811F8255-26A1-414B-B8D8-460CFBB1616B",
"wakeTime" : 5915,
"sleepWakeUUID" : "700E6451-C08C-477A-99DF-B25A8E596821",
"sip" : "enabled",
"vmRegionInfo" : "0x41722cad3928 is not in any region. Bytes after previous region: 71477595289897 Bytes before following region: 33594484639448\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000c1722cad3928","rawCodes":[1,212696119982376],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000c1722cad3928 -> 0x000041722cad3928 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":6053},
"vmregioninfo" : "0x41722cad3928 is not in any region. Bytes after previous region: 71477595289897 Bytes before following region: 33594484639448\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
"name" : "_nw.cpython-311-darwin.so"
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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"name" : "libsystem_c.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=2.2G written=1156K(0%) resident=1156K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 416K 22 \nColorSync 640K 32 \nCoreAnimation 992K 58 \nCoreGraphics 48K 3 \nCoreUI image data 4560K 33 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 1.7G 84 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 672K 42 \nStack 195.0M 43 \nStack Guard 56.0M 1 \nVM_ALLOCATE 166.1M 132 \nVM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)\n__AUTH 5216K 665 \n__AUTH_CONST 70.3M 912 \n__CTF 824 1 \n__DATA 32.9M 1050 \n__DATA_CONST 33.9M 1068 \n__DATA_DIRTY 2761K 339 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 636.8M 150 \n__OBJC_RW 2374K 1 \n__TEXT 1.2G 1088 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 2 \nmapped file 278.5M 62 \nowned unmapped memory 4848K 1 \npage table in kernel 1156K 1 \nshared memory 3168K 25 \n=========== ======= ======= \nTOTAL 4.5G 5849 \nTOTAL, minus reserved VM space 4.4G 5849 \n",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/abhishekdey/Downloads/fold_2025_04_03_09_58_model_4.cif
Chain information for fold_2025_04_03_09_58_model_4.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open "/Users/abhishekdey/Downloads/JEV simRNA 85.pdb"
Chain information for JEV simRNA 85.pdb #2
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #1 to #2/A pairing bs matrix Nucleic cutoffDistance 3.19
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 3.19
Matchmaker JEV simRNA 85.pdb, chain A (#2) with
fold_2025_04_03_09_58_model_4.cif, chain A (#1), sequence alignment score =
340
RMSD between 21 pruned atom pairs is 1.482 angstroms; (across all 85 pairs:
23.505)
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
Log from Fri Apr 11 06:08:41 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
Log from Fri Apr 11 05:44:17 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
Log from Thu Apr 10 17:10:03 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
Log from Thu Apr 10 16:52:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
Log from Thu Apr 10 06:59:20 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/abhishekdey/Downloads/7o7z.cif
Summary of feedback from opening /Users/abhishekdey/Downloads/7o7z.cif
---
warning | Unable to fetch template for 'SPD': will use incomplete information in mmCIF file
notes | Fetching CCD 1MA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/1MA/1MA.cif
Fetching CCD 2MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/2MG/2MG.cif
Fetching CCD 4AC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/4AC/4AC.cif
Fetching CCD 5MC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/5MC/5MC.cif
Fetching CCD 5MU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/5MU/5MU.cif
Fetching CCD 6MZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/6MZ/6MZ.cif
Fetching CCD A2M from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/A2M/A2M.cif
Fetching CCD AAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/AAC/AAC.cif
Fetching CCD AME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/AME/AME.cif
Fetching CCD AYA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/AYA/AYA.cif
Fetching CCD B8N from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/B8N/B8N.cif
Fetching CCD G7M from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/G7M/G7M.cif
Fetching CCD GTP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GTP/GTP.cif
Fetching CCD H2U from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/H2U/H2U.cif
Fetching CCD HIC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/HIC/HIC.cif
Fetching CCD HY3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/HY3/HY3.cif
Fetching CCD M2G from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/M2G/M2G.cif
Fetching CCD M3L from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/M3L/M3L.cif
Fetching CCD MA6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/MA6/MA6.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD MLZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/MLZ/MLZ.cif
Fetching CCD NMM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/NMM/NMM.cif
Fetching CCD OMC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/OMC/OMC.cif
Fetching CCD OMG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif
Fetching CCD OMU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/OMU/OMU.cif
Fetching CCD SAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/SAC/SAC.cif
Fetching CCD SPM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/SPM/SPM.cif
Fetching CCD UNX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/UNX/UNX.cif
Fetching CCD UR3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/UR3/UR3.cif
Fetching CCD UY1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/UY1/UY1.cif
Fetching CCD V5N from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/V5N/V5N.cif
Fetching CCD YYG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/YYG/YYG.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
7o7z.cif title:
Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a
pseudoknot (classified for pseudoknot) [more info...]
Chain information for 7o7z.cif #1
---
Chain | Description | UniProt
A2 | 18S rRNA |
AA | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
AB | Ribosomal protein S28 | G1TIB4_RABIT 1-69
AC | Ribosomal protein S27a | G1SK22_RABIT 1-156
AD | 40S ribosomal protein S30 | G1T8A2_RABIT 1-133
AE | Ribosomal protein eS26 |
AF | RACK1 | G1SJB4_RABIT 1-317
AG | uS14 | G1U7M4_RABIT 1-56
AH | mRNA containing SARS-CoV-2 sequence |
AI | E-site tRNA |
AT | P-site Phe-tRNA(Phe) |
AZ | 40S ribosomal protein SA | G1TLT8_RABIT 1-295
Aa | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
Ab | Ribosomal protein uS5 |
Ac | 40S ribosomal protein S3 | G1TNM3_RABIT -37-243
Ad | Ribosomal protein eS4 |
Ae | Ribosomal protein S5 | G1TFM5_RABIT 1-204
Af | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
Ag | 40S ribosomal protein S7 | G1SVB0_RABIT -237-194
Ah | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
Ai | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
Aj | eS10 | G1TPV3_RABIT 1-165
Ak | 40S ribosomal protein S11 | G1TRM4_RABIT 1-158
Al | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
Am | uS15 | G1SP51_RABIT 1-151
An | 40S ribosomal protein uS11 | G1T1F0_RABIT 1-151
Ao | 40S ribosomal protein uS19 | G1U0Q2_RABIT 1-145
Ap | uS9 | G1SGX4_RABIT -25-146
Aq | 40S ribosomal protein eS17 | G1TU13_RABIT 1-135
Ar | 40S ribosomal protein S18 | G1TPG3_RABIT 1-152
As | Ribosomal protein eS19 |
At | 40S ribosomal protein uS10 | G1SIZ2_RABIT 1-119
Au | Ribosomal protein eS21 |
Av | Ribosomal protein S15a | G1TG89_RABIT 1-130
Aw | 40S ribosomal protein S23 | G1SZ47_RABIT 1-143
Ax | 40S ribosomal protein S24 | G1T3D8_RABIT 1-130
Ay | 40S ribosomal protein S25 | G1TDB3_RABIT 2-125
Az | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
B5 | 28S rRNA |
B7 | 5S |
B8 | 5.8S rRNA |
BA | Ribosomal protein uL2 |
BB | Ribosomal protein L3 | G1TL06_RABIT 1-403
BC | 60S ribosomal protein L4 | G1SVW5_RABIT 1-413
BD | Ribosomal_L18_c domain-containing protein | G1SYJ6_RABIT 1-297
BE | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
BF | Ribosomal Protein uL30 |
BG | Ribosomal protein eL8 |
BH | 60S ribosomal protein L9 | G1SWI6_RABIT 1-192
BI | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
BJ | Ribosomal protein L11 | G1TUB8_RABIT 1-178
BK | Replicase polyprotein 1ab | R1AB_SARS2 4254-5324
BL | Ribosomal protein eL13 |
BM | Ribosomal protein L14 | G1SZ12_RABIT 1-218
BN | Ribosomal protein L15 | G1T0C1_RABIT 1-204
BO | Ribosomal protein uL13 |
BP | uL22 | G1TVT6_RABIT 1-184
BQ | Ribosomal Protein eL18 |
BR | 60S ribosomal protein L19 | RL19_BOVIN 1-196
BS | Ribosomal protein eL20 |
BT | eL21 | G1SHQ2_RABIT 1-160
BU | Ribosomal protein eL22 |
BV | Ribosomal protein L23 | G1T6D1_RABIT 1-140
BW | eL24 | G1SE28_RABIT 1-157
BX | uL23 | G1SE76_RABIT 1-156
BY | Ribosomal protein L26 | G1SQH0_RABIT 1-145
BZ | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
Ba | 60S ribosomal protein L27a | G1SNY0_RABIT 1-148
Bb | 60S ribosomal protein L29 | G1SGR6_RABIT 1-245
Bc | eL30 | G1TDL2_RABIT 1-115
Bd | eL31 | G1SHG0_RABIT 1-125
Be | eL32 | G1U437_RABIT 1-135
Bf | eL33 | G1SF08_RABIT 1-110
Bg | 60S ribosomal protein L34 | G1TXG5_RABIT 1-117
Bh | uL29 | G1SIT5_RABIT 1-123
Bi | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
Bj | Ribosomal protein L37 | U3KPD5_RABIT 1-97
Bk | eL38 | G1U001_RABIT 1-70
Bl | eL39 | G1TTN1_RABIT 1-51
Bm | 60S ribosomal protein L40 |
Bo | eL42 | G1U344_RABIT 1-106
Bp | eL43 | G1SY53_RABIT 1-92
Br | Ribosomal protein eL28 |
Bs | 60S acidic ribosomal protein P0 | G1SPK4_RABIT 1-318
Bt | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Bv | Ribosomal protein uL1 | G1SKZ8_RABIT 1-217
Non-standard residues in 7o7z.cif #1
---
AAC — acetylamino-acetic acid
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
GTP — guanosine-5'-triphosphate
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UNX — unknown atom or ion
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
> show target m
> select add #1
229742 atoms, 243775 bonds, 8384 pseudobonds, 21082 residues, 4 models
selected
> select subtract #1
Nothing selected
> hide #!1 models
> select add #1
229742 atoms, 243775 bonds, 8384 pseudobonds, 21082 residues, 4 models
selected
> show #!1 models
> select subtract #1
Nothing selected
> select add #1
229742 atoms, 243775 bonds, 8384 pseudobonds, 21082 residues, 4 models
selected
> ui tool show "Show Sequence Viewer"
> sequence chain /AH
Alignment identifier is 1/AH
> select clear
> select /AH:3451-3545
2018 atoms, 2253 bonds, 67 pseudobonds, 95 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /AH
Alignment identifier is 1/AH
> select clear
> select /AH
2028 atoms, 2253 bonds, 70 pseudobonds, 105 residues, 3 models selected
> cartoon (#!1 & sel)
> surface hidePatches (#!1 & sel)
> style (#!1 & sel) ball
Changed 2028 atom styles
> color (#!1 & sel) red
OpenType support missing for ".AppleSystemUIFont", script 11
> save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
——— End of log from Thu Apr 10 06:59:20 2025 ———
opened ChimeraX session
> open
> /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_0.cif
Chain information for fold_jevfse_115_2025_04_03_16_00_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> select add #1
229742 atoms, 243775 bonds, 8384 pseudobonds, 21082 residues, 4 models
selected
> hide #!1 models
> show #!1 models
> select subtract #1
Nothing selected
> ui tool show Matchmaker
> matchmaker #2 to #1/AH pairing bs
Using Nucleic matrix instead of BLOSUM-62 to match to 7o7z.cif #1/AH
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_0.cif, chain A (#2), sequence alignment
score = 124.6
RMSD between 3 pruned atom pairs is 1.176 angstroms; (across all 95 pairs:
45.421)
> open
> /Users/abhishekdey/Downloads/fold_hiv_115_2025_04_03_17_20/fold_hiv_115_2025_04_03_17_20_model_4.cif
Chain information for fold_hiv_115_2025_04_03_17_20_model_4.cif #3
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_4.cif
Chain information for fold_jevfse_115_2025_04_03_16_00_model_4.cif #4
---
Chain | Description
A | .
Computing secondary structure
> hide #2 models
> hide #3 models
> show #2 models
> open "/Users/abhishekdey/Downloads/JEV115-ad5deff5_sim_minE_TOTAL-000001_AA
> (2).pdb"
Chain information for JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb #5
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #5/A to #1/AH pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match
JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb #5/A to 7o7z.cif #1/AH
Computing secondary structure
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb, chain A (#5), sequence
alignment score = 124.6
RMSD between 7 pruned atom pairs is 1.083 angstroms; (across all 95 pairs:
43.163)
> ui tool show Matchmaker
> hide #2 models
> hide #4 models
> hide #5 models
> open /Users/abhishekdey/Downloads/fold_jev_5_100_model_4.cif format mmcif
Chain information for fold_jev_5_100_model_4.cif #6
---
Chain | Description
A | .
Computing secondary structure
> select add #6
2125 atoms, 2371 bonds, 100 residues, 1 model selected
> color sel forest green
> ui tool show Matchmaker
> matchmaker #6 to #1/AH pairing bs
Using Nucleic matrix instead of BLOSUM-62 to match to 7o7z.cif #1/AH
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with fold_jev_5_100_model_4.cif, chain A
(#6), sequence alignment score = 103.6
RMSD between 6 pruned atom pairs is 0.649 angstroms; (across all 88 pairs:
51.930)
> show #5 models
> hide #5 models
> show #4 models
> select add #4
4574 atoms, 5104 bonds, 215 residues, 2 models selected
> select subtract #4
2125 atoms, 2371 bonds, 100 residues, 1 model selected
> show #3 models
> hide #6 models
> hide #3 models
> show #3 models
> select add #3
4586 atoms, 5126 bonds, 215 residues, 2 models selected
> select add #4
7035 atoms, 7859 bonds, 330 residues, 3 models selected
> cartoon (#3-4 & sel)
> ui tool show Matchmaker
> matchmaker #6 to #1/AH pairing bs matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with fold_jev_5_100_model_4.cif, chain A
(#6), sequence alignment score = 103.6
RMSD between 6 pruned atom pairs is 0.649 angstroms; (across all 88 pairs:
51.930)
> ui tool show Matchmaker
> matchmaker #6 to #1/AH pairing bs matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with fold_jev_5_100_model_4.cif, chain A
(#6), sequence alignment score = 103.6
RMSD between 6 pruned atom pairs is 0.649 angstroms; (across all 88 pairs:
51.930)
> show #6 models
> ui tool show Matchmaker
> matchmaker #4 to #1/AH pairing bs matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment
score = 124.6
RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs:
46.532)
> matchmaker #4 to #1/AH pairing bs matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment
score = 124.6
RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs:
46.532)
> select subtract #6
4910 atoms, 5488 bonds, 230 residues, 2 models selected
> select subtract #3
2449 atoms, 2733 bonds, 115 residues, 1 model selected
> hide #3 models
> select subtract #4
Nothing selected
> hide #4 models
> show #4 models
> hide #6 models
> ui tool show Matchmaker
> matchmaker #4 to #1/AH pairing bs matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment
score = 124.6
RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs:
46.532)
> matchmaker #4 to #1/AH pairing bs matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment
score = 124.6
RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs:
46.532)
> matchmaker #4/A to #1/AH pairing ss matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment
score = 124.6
RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs:
46.532)
> hide #4 models
> show #3 models
> ui tool show Matchmaker
> matchmaker #3/A to #1/AH pairing ss matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_hiv_115_2025_04_03_17_20_model_4.cif, chain A (#3), sequence alignment
score = 121.4
RMSD between 6 pruned atom pairs is 1.123 angstroms; (across all 83 pairs:
65.777)
> hide #!1 models
> show #!1 models
OpenType support missing for ".AppleSystemUIFont", script 11
> save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
——— End of log from Thu Apr 10 16:52:14 2025 ———
opened ChimeraX session
> open
> /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_2.cif
> /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_3.cif
Chain information for fold_jevfse_115_2025_04_03_16_00_model_2.cif #7
---
Chain | Description
A | .
Chain information for fold_jevfse_115_2025_04_03_16_00_model_3.cif #8
---
Chain | Description
A | .
Computing secondary structure
[Repeated 1 time(s)]
> hide #3 models
> ui tool show Matchmaker
> matchmaker #7/A to #1/AH pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match
fold_jevfse_115_2025_04_03_16_00_model_2.cif #7/A to 7o7z.cif #1/AH
Computing secondary structure
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7), sequence alignment
score = 124.6
RMSD between 8 pruned atom pairs is 0.729 angstroms; (across all 95 pairs:
38.947)
> hide #7 models
> open
> /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_4.cif
Chain information for fold_jevfse_115_2025_04_03_16_00_model_4.cif #9
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #8/A to #1/AH pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match
fold_jevfse_115_2025_04_03_16_00_model_3.cif #8/A to 7o7z.cif #1/AH
Computing secondary structure
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_3.cif, chain A (#8), sequence alignment
score = 124.6
RMSD between 3 pruned atom pairs is 1.480 angstroms; (across all 95 pairs:
49.946)
> hide #!1 models
> show #!1 models
> hide #8 models
> show #7 models
> hide #7 models
> ui tool show Matchmaker
> matchmaker #9/A to #1/AH pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match
fold_jevfse_115_2025_04_03_16_00_model_4.cif #9/A to 7o7z.cif #1/AH
Computing secondary structure
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with
fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#9), sequence alignment
score = 124.6
RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs:
46.532)
> hide #9 models
> hide #!1 models
> show #9 models
> show #8 models
> show #7 models
> hide #8 models
> hide #9 models
> hide #7 models
> show #8 models
> show #9 models
> delete atoms #8-9
> delete bonds #8-9
> show #7 models
> show #!1 models
> hide #7 models
> show #5 models
> hide #!1 models
> show #!1 models
> hide #5 models
> hide #!1 models
> show #4 models
> delete atoms #4
> delete bonds #4
> show #2 models
> delete atoms #2
> delete bonds #2
> show #!1 models
> show #3 models
> hide #3 models
> hide #!1 models
> show #6 models
> delete atoms #6
> delete bonds #6
> show #7 models
> show #5 models
> show #3 models
> show #!1 models
OpenType support missing for ".AppleSystemUIFont", script 11
> save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
——— End of log from Thu Apr 10 17:10:03 2025 ———
opened ChimeraX session
> hide #7 models
> show #7 models
> hide #3 models
> hide #5 models
> hide #!1 models
> show #!1 models
> select add #7
2449 atoms, 2733 bonds, 115 residues, 1 model selected
> color sel forest green
> select subtract #7
Nothing selected
> show #5 models
> ui tool show Matchmaker
> matchmaker #5 to #7
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with
JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb, chain A (#5), sequence
alignment score = 460
RMSD between 8 pruned atom pairs is 1.279 angstroms; (across all 115 pairs:
29.570)
> matchmaker #5 to #7
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with
JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb, chain A (#5), sequence
alignment score = 460
RMSD between 8 pruned atom pairs is 1.279 angstroms; (across all 115 pairs:
29.570)
> hide #!1 models
> hide #7 models
> show #!1 models
> hide #5 models
> show #7 models
> color #3 #2020e1ff
> color #3 #111174ff
> color #3 #1b1dc7ff
> color #3 #0c0d58ff
> color #3 #101175ff
> show #3 models
OpenType support missing for ".AppleSystemUIFont", script 11
> save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
——— End of log from Fri Apr 11 05:44:17 2025 ———
opened ChimeraX session
> open /Users/abhishekdey/Downloads/fold_2025_04_03_09_58_model_4.cif
Chain information for fold_2025_04_03_09_58_model_4.cif #2
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #7
Using Nucleic matrix instead of BLOSUM-62 for matching
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with
fold_2025_04_03_09_58_model_4.cif, chain A (#2), sequence alignment score =
340
RMSD between 26 pruned atom pairs is 1.006 angstroms; (across all 85 pairs:
26.431)
> matchmaker #2 to #7
Using Nucleic matrix instead of BLOSUM-62 for matching
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with
fold_2025_04_03_09_58_model_4.cif, chain A (#2), sequence alignment score =
340
RMSD between 26 pruned atom pairs is 1.006 angstroms; (across all 85 pairs:
26.431)
> color #2 #eca185ff
> color #2 #ec901cff
> hide #!1 models
> hide #3 models
> hide #7 models
> show #7 models
> hide #2 models
> show #2 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #2 to #1/AH pairing bs
Using Nucleic matrix instead of BLOSUM-62 to match to 7o7z.cif #1/AH
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7o7z.cif, chain AH (#1) with fold_2025_04_03_09_58_model_4.cif,
chain A (#2), sequence alignment score = 97.4
RMSD between 4 pruned atom pairs is 1.256 angstroms; (across all 82 pairs:
46.803)
> ui tool show Matchmaker
> matchmaker #2 to #7/A pairing bs matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with
fold_2025_04_03_09_58_model_4.cif, chain A (#2), sequence alignment score =
340
RMSD between 26 pruned atom pairs is 1.006 angstroms; (across all 85 pairs:
26.431)
> hide #7 models
> hide #!1 models
> show #!1 models
OpenType support missing for ".AppleSystemUIFont", script 11
> save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs
——— End of log from Fri Apr 11 06:08:41 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYD92LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 35 seconds
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash closing dock widget |
comment:2 by , 7 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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