![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17230 closed defect (nonchimerax)
Graphics crash, macOS 14.4, Intel Iris Plus Graphics
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.4-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff84b303100 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 556 in swap_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 58)
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{
"uptime" : 88000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 8867,
"osVersion" : {
"train" : "macOS 14.4",
"build" : "23E214",
"releaseType" : "User"
},
"captureTime" : "2025-03-28 12:48:12.5660 -0700",
"codeSigningMonitor" : 0,
"incident" : "44C6053D-9802-4CCD-96CF-034C1AEB1CA2",
"pid" : 37245,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-28 12:45:42.3235 -0700",
"procStartAbsTime" : 88644726043598,
"procExitAbsTime" : 88794945044171,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8CEBA582-07F3-579A-96CC-7C82CB1C2547","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "08D9F78E-89A6-80DE-2F38-23E7E4549B72",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 5851,
"bridgeVersion" : {"build":"21P4222","train":"8.4"},
"sleepWakeUUID" : "EA722F72-6509-4182-9886-43F9B3A16A96",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":37245},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
"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,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/39models.cxs
Log from Wed Mar 12 11:29:24 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Sun Jan 26 22:23:23 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8ytu.cif
8ytu.cif title:
Mipa-PETase from Micromonospora pattaloongensis [more info...]
Chain information for 8ytu.cif #1
---
Chain | Description | UniProt
A B C | cutinase | A0A1H3QT72_9ACTN 39-294
Non-standard residues in 8ytu.cif #1
---
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
8ytu.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
36 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select :EDO
4 atoms, 3 bonds, 1 residue, 1 model selected
> select :GOL
6 atoms, 5 bonds, 1 residue, 1 model selected
> select :GOL
6 atoms, 5 bonds, 1 residue, 1 model selected
> select :GOL
6 atoms, 5 bonds, 1 residue, 1 model selected
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8ytu_validation_2fo-fc_map_coef.cif
Summary of feedback from opening
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Science-Fellows_Rheas-factory/Structures/8ytu_validation_2fo-fc_map_coef.cif
---
warning | No mmCIF models found.
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8ytu-sf.cif
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Science-Fellows_Rheas-factory/Structures/8ytu-sf.cif
---
warning | No mmCIF models found.
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8ytv.cif
8ytv.cif title:
The M19 variant of Mipa-Petase from Micromonospora pattaloongensis [more
info...]
Chain information for 8ytv.cif #2
---
Chain | Description | UniProt
A B | cutinase | A0A1H3QT72_9ACTN 39-294
8ytv.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
51 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #2
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8ytv-aligned.cif
Summary of feedback from opening
/Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
Science-Fellows_Rheas-factory/Structures/8ytv-aligned.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 558
Unknown polymer entity '1' on line 724
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 8ytv-aligned.cif #2
---
Chain | Description
A | No description available
B | No description available
51 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8ytw-aligned.cif
Summary of feedback from opening
/Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
Science-Fellows_Rheas-factory/Structures/8ytw-aligned.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 288
Unknown polymer entity '1' on line 428
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 8ytw-aligned.cif #3
---
Chain | Description
A | No description available
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8yty-aligned.cif
Summary of feedback from opening
/Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
Science-Fellows_Rheas-factory/Structures/8yty-aligned.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 288
Unknown polymer entity '1' on line 430
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 8yty-aligned.cif #4
---
Chain | Description
A | No description available
129 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8ytz-aligned.cif
Summary of feedback from opening
/Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
Science-Fellows_Rheas-factory/Structures/8ytz-aligned.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 288
Unknown polymer entity '1' on line 433
Missing or incomplete sequence information. Inferred polymer connectivity.
notes | Fetching CCD 1PE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/1PE/1PE.cif
Fetching CCD ACT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif
Chain information for 8ytz-aligned.cif #5
---
Chain | Description
A | No description available
> select #2/B:48-296
1852 atoms, 1903 bonds, 249 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /B:45-300
1909 atoms, 1965 bonds, 256 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /C:44-300
1914 atoms, 1970 bonds, 257 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/All-str-aligned.cxs
> set bgColor white
> ui mousemode right select
Drag select of 11 atoms, 5 bonds
> delete atoms sel
> delete bonds sel
> select :EDO
4 atoms, 3 bonds, 1 residue, 1 model selected
> select :EDO
4 atoms, 3 bonds, 1 residue, 1 model selected
> select :EDO
4 atoms, 3 bonds, 1 residue, 1 model selected
> select :EDO
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel
> color sel pink
> view sel
> color sel blue
> ui tool show "Side View"
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/5xjh-aligned.pdb
5xjh-aligned.pdb title:
Crystal structure of petase from ideonella sakaiensis [more info...]
Chain information for 5xjh-aligned.pdb #6
---
Chain | Description
A | petase
> select #6/A:106 #6/A:237 #6/A:206
29 atoms, 28 bonds, 3 residues, 1 model selected
> show sel
> color sel hotpink
> color sel magenta
> select #6/A:160 #6/A:237 #6/A:206
24 atoms, 22 bonds, 3 residues, 1 model selected
> color sel magenta
> show sel atoms
> color sel byhetero
> select add #6
2073 atoms, 1977 bonds, 405 residues, 1 model selected
> select subtract #6
Nothing selected
> save
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/All-str-aligned.cxs
——— End of log from Sun Jan 26 22:23:23 2025 ———
opened ChimeraX session
> hide #2 models
> hide #6 models
> hide #1 models
> show #4-5#!3 cartoons
> show #2 models
> show #1 models
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Rhea_134_148_Details/8qrj_LCC_ICCG_x.cif
8qrj_LCC_ICCG_x.cif title:
LCC-ICCG PETase mutant H218Y [more info...]
Chain information for 8qrj_LCC_ICCG_x.cif #7
---
Chain | Description | UniProt
A | Leaf-branch compost cutinase | PETH_UNKP 1-293
Non-standard residues in 8qrj_LCC_ICCG_x.cif #7
---
CA — calcium ion
EDO — 1,2-ethanediol (ethylene glycol)
P33 — 3,6,9,12,15,18-hexaoxaicosane-1,20-diol (heptaethylene glycol; PEG330)
25 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #7
> close
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/01Group01_8qrj_3pet_6A_m0_id_698.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/02Group01_8qrj_3pet_6A_m1_id_359.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/03Group01_8qrj_3pet_10A_m4_id_401.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/04Group01_8qrj_3pet_6A_m0_id_211.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/05Group01_8qrj_3pet_6A_m0_id_387.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/06Group01_8qrj_3pet_6A_m2_id_580.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/07Group01_8qrj_3pet_6A_m0_id_547.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/08Group01_8qrj_3pet_6A_m2_id_677.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/09Group01_8qrj_3pet_6A_m1_id_709.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/10Group01_8qrj_3pet_6A_m0_id_117.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/11Group01_8qrj_3pet_6A_m0_id_260.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/12Group01_8qrj_3pet_6A_m0_id_58.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/13Group02_8qrj_3pet_6A_m2_id_70.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/14Group02_8qrj_3pet_6A_m0_id_40.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/15Group02_8qrj_3pet_6A_m2_id_638.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/16Group02_8qrj_3pet_10A_m7_id_551.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/17Group02_8qrj_3pet_6A_m0_id_26.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/18Group03_8qrj_3pet_6A_m2_id_78.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/19Group03_8qrj_3pet_6A_m0_id_162.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/20Group03_8qrj_3pet_6A_m0_id_415.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/21Group03_8qrj_3pet_6A_m0_id_146.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/22Group03_8qrj_3pet_6A_m0_id_138.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/23Group03_8qrj_3pet_10A_m4_id_458.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/24Group03_8qrj_3pet_6A_m1_id_330.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/25Group04_8qrj_3pet_6A_m1_id_323.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/26Group04_8qrj_3pet_6A_m2_id_54.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/27Group05_8qrj_3pet_6A_m2_id_322.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/28Group05_8qrj_3pet_6A_m0_id_540.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/29Group05_8qrj_3pet_6A_m2_id_533.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/30Group05_8qrj_3pet_6A_m0_id_669.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/31Group05_8qrj_3pet_6A_m1_id_218.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/32Group05_8qrj_3pet_6A_m2_id_103.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/33Group05_8qrj_3pet_6A_m0_id_408.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/34Group05_8qrj_3pet_6A_m0_id_383.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/35Group06_8qrj_3pet_6A_m1_id_568.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/36Group06_8qrj_3pet_6A_m2_id_148.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/37Group06_8qrj_3pet_6A_m2_id_477.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/38Group07_8qrj_3pet_6A_m2_id_487.pdb
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/39Group07_8qrj_3pet_6A_m2_id_504.pdb
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Chain information for 01Group01_8qrj_3pet_6A_m0_id_698.pdb #1
---
Chain | Description
A | No description available
Chain information for 02Group01_8qrj_3pet_6A_m1_id_359.pdb #2
---
Chain | Description
A | No description available
Chain information for 03Group01_8qrj_3pet_10A_m4_id_401.pdb #3
---
Chain | Description
A | No description available
Chain information for 04Group01_8qrj_3pet_6A_m0_id_211.pdb #4
---
Chain | Description
A | No description available
Chain information for 05Group01_8qrj_3pet_6A_m0_id_387.pdb #5
---
Chain | Description
A | No description available
Chain information for 06Group01_8qrj_3pet_6A_m2_id_580.pdb #6
---
Chain | Description
A | No description available
Chain information for 07Group01_8qrj_3pet_6A_m0_id_547.pdb #7
---
Chain | Description
A | No description available
Chain information for 08Group01_8qrj_3pet_6A_m2_id_677.pdb #8
---
Chain | Description
A | No description available
Chain information for 09Group01_8qrj_3pet_6A_m1_id_709.pdb #9
---
Chain | Description
A | No description available
Chain information for 10Group01_8qrj_3pet_6A_m0_id_117.pdb #10
---
Chain | Description
A | No description available
Chain information for 11Group01_8qrj_3pet_6A_m0_id_260.pdb #11
---
Chain | Description
A | No description available
Chain information for 12Group01_8qrj_3pet_6A_m0_id_58.pdb #12
---
Chain | Description
A | No description available
Chain information for 13Group02_8qrj_3pet_6A_m2_id_70.pdb #13
---
Chain | Description
A | No description available
Chain information for 14Group02_8qrj_3pet_6A_m0_id_40.pdb #14
---
Chain | Description
A | No description available
Chain information for 15Group02_8qrj_3pet_6A_m2_id_638.pdb #15
---
Chain | Description
A | No description available
Chain information for 16Group02_8qrj_3pet_10A_m7_id_551.pdb #16
---
Chain | Description
A | No description available
Chain information for 17Group02_8qrj_3pet_6A_m0_id_26.pdb #17
---
Chain | Description
A | No description available
Chain information for 18Group03_8qrj_3pet_6A_m2_id_78.pdb #18
---
Chain | Description
A | No description available
Chain information for 19Group03_8qrj_3pet_6A_m0_id_162.pdb #19
---
Chain | Description
A | No description available
Chain information for 20Group03_8qrj_3pet_6A_m0_id_415.pdb #20
---
Chain | Description
A | No description available
Chain information for 21Group03_8qrj_3pet_6A_m0_id_146.pdb #21
---
Chain | Description
A | No description available
Chain information for 22Group03_8qrj_3pet_6A_m0_id_138.pdb #22
---
Chain | Description
A | No description available
Chain information for 23Group03_8qrj_3pet_10A_m4_id_458.pdb #23
---
Chain | Description
A | No description available
Chain information for 24Group03_8qrj_3pet_6A_m1_id_330.pdb #24
---
Chain | Description
A | No description available
Chain information for 25Group04_8qrj_3pet_6A_m1_id_323.pdb #25
---
Chain | Description
A | No description available
Chain information for 26Group04_8qrj_3pet_6A_m2_id_54.pdb #26
---
Chain | Description
A | No description available
Chain information for 27Group05_8qrj_3pet_6A_m2_id_322.pdb #27
---
Chain | Description
A | No description available
Chain information for 28Group05_8qrj_3pet_6A_m0_id_540.pdb #28
---
Chain | Description
A | No description available
Chain information for 29Group05_8qrj_3pet_6A_m2_id_533.pdb #29
---
Chain | Description
A | No description available
Chain information for 30Group05_8qrj_3pet_6A_m0_id_669.pdb #30
---
Chain | Description
A | No description available
Chain information for 31Group05_8qrj_3pet_6A_m1_id_218.pdb #31
---
Chain | Description
A | No description available
Chain information for 32Group05_8qrj_3pet_6A_m2_id_103.pdb #32
---
Chain | Description
A | No description available
Chain information for 33Group05_8qrj_3pet_6A_m0_id_408.pdb #33
---
Chain | Description
A | No description available
Chain information for 34Group05_8qrj_3pet_6A_m0_id_383.pdb #34
---
Chain | Description
A | No description available
Chain information for 35Group06_8qrj_3pet_6A_m1_id_568.pdb #35
---
Chain | Description
A | No description available
Chain information for 36Group06_8qrj_3pet_6A_m2_id_148.pdb #36
---
Chain | Description
A | No description available
Chain information for 37Group06_8qrj_3pet_6A_m2_id_477.pdb #37
---
Chain | Description
A | No description available
Chain information for 38Group07_8qrj_3pet_6A_m2_id_487.pdb #38
---
Chain | Description
A | No description available
Chain information for 39Group07_8qrj_3pet_6A_m2_id_504.pdb #39
---
Chain | Description
A | No description available
> align #2 toAtoms #1
Unequal number of atoms to pair, 1995 and 1989
> align #2 toAtoms #1
Unequal number of atoms to pair, 1995 and 1989
> align #2 toResidues #1
Expected a keyword
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
02Group01_8qrj_3pet_6A_m1_id_359.pdb, chain A (#2), sequence alignment score =
1241.3
RMSD between 258 pruned atom pairs is 0.280 angstroms; (across all 258 pairs:
0.280)
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
03Group01_8qrj_3pet_10A_m4_id_401.pdb, chain A (#3), sequence alignment score
= 1258.8
RMSD between 258 pruned atom pairs is 0.238 angstroms; (across all 258 pairs:
0.238)
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
04Group01_8qrj_3pet_6A_m0_id_211.pdb, chain A (#4), sequence alignment score =
1229.6
RMSD between 258 pruned atom pairs is 0.172 angstroms; (across all 258 pairs:
0.172)
> select down
Nothing selected
> matchmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
05Group01_8qrj_3pet_6A_m0_id_387.pdb, chain A (#5), sequence alignment score =
1276.6
RMSD between 258 pruned atom pairs is 0.192 angstroms; (across all 258 pairs:
0.192)
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
06Group01_8qrj_3pet_6A_m2_id_580.pdb, chain A (#6), sequence alignment score =
1215.5
RMSD between 258 pruned atom pairs is 0.220 angstroms; (across all 258 pairs:
0.220)
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
07Group01_8qrj_3pet_6A_m0_id_547.pdb, chain A (#7), sequence alignment score =
1247.7
RMSD between 258 pruned atom pairs is 0.235 angstroms; (across all 258 pairs:
0.235)
> matchmaker #8 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
08Group01_8qrj_3pet_6A_m2_id_677.pdb, chain A (#8), sequence alignment score =
1223
RMSD between 258 pruned atom pairs is 0.215 angstroms; (across all 258 pairs:
0.215)
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
09Group01_8qrj_3pet_6A_m1_id_709.pdb, chain A (#9), sequence alignment score =
1217.5
RMSD between 258 pruned atom pairs is 0.228 angstroms; (across all 258 pairs:
0.228)
> matchmaker #10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
10Group01_8qrj_3pet_6A_m0_id_117.pdb, chain A (#10), sequence alignment score
= 1268.9
RMSD between 258 pruned atom pairs is 0.194 angstroms; (across all 258 pairs:
0.194)
> matchmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
11Group01_8qrj_3pet_6A_m0_id_260.pdb, chain A (#11), sequence alignment score
= 1261
RMSD between 258 pruned atom pairs is 0.171 angstroms; (across all 258 pairs:
0.171)
> matchmaker #12 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
12Group01_8qrj_3pet_6A_m0_id_58.pdb, chain A (#12), sequence alignment score =
1218.1
RMSD between 258 pruned atom pairs is 0.293 angstroms; (across all 258 pairs:
0.293)
> matchmaker #13 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
13Group02_8qrj_3pet_6A_m2_id_70.pdb, chain A (#13), sequence alignment score =
1252.8
RMSD between 258 pruned atom pairs is 0.305 angstroms; (across all 258 pairs:
0.305)
> matchmaker #14 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
14Group02_8qrj_3pet_6A_m0_id_40.pdb, chain A (#14), sequence alignment score =
1231.1
RMSD between 258 pruned atom pairs is 0.239 angstroms; (across all 258 pairs:
0.239)
> matchmaker #15 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
15Group02_8qrj_3pet_6A_m2_id_638.pdb, chain A (#15), sequence alignment score
= 1239.5
RMSD between 258 pruned atom pairs is 0.282 angstroms; (across all 258 pairs:
0.282)
> matchmaker #16 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
16Group02_8qrj_3pet_10A_m7_id_551.pdb, chain A (#16), sequence alignment score
= 1220.3
RMSD between 258 pruned atom pairs is 0.232 angstroms; (across all 258 pairs:
0.232)
> matchmaker #17 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
17Group02_8qrj_3pet_6A_m0_id_26.pdb, chain A (#17), sequence alignment score =
1226.9
RMSD between 258 pruned atom pairs is 0.216 angstroms; (across all 258 pairs:
0.216)
> matchmaker #18 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
18Group03_8qrj_3pet_6A_m2_id_78.pdb, chain A (#18), sequence alignment score =
1224.1
RMSD between 258 pruned atom pairs is 0.248 angstroms; (across all 258 pairs:
0.248)
> matchmaker #19 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
19Group03_8qrj_3pet_6A_m0_id_162.pdb, chain A (#19), sequence alignment score
= 1248.2
RMSD between 258 pruned atom pairs is 0.218 angstroms; (across all 258 pairs:
0.218)
> matchmaker #20 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
20Group03_8qrj_3pet_6A_m0_id_415.pdb, chain A (#20), sequence alignment score
= 1237.7
RMSD between 258 pruned atom pairs is 0.227 angstroms; (across all 258 pairs:
0.227)
> matchmaker #21 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
21Group03_8qrj_3pet_6A_m0_id_146.pdb, chain A (#21), sequence alignment score
= 1263.3
RMSD between 258 pruned atom pairs is 0.268 angstroms; (across all 258 pairs:
0.268)
> matchmaker #22 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
22Group03_8qrj_3pet_6A_m0_id_138.pdb, chain A (#22), sequence alignment score
= 1261.9
RMSD between 258 pruned atom pairs is 0.162 angstroms; (across all 258 pairs:
0.162)
> matchmaker #23 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
23Group03_8qrj_3pet_10A_m4_id_458.pdb, chain A (#23), sequence alignment score
= 1248.3
RMSD between 258 pruned atom pairs is 0.214 angstroms; (across all 258 pairs:
0.214)
> matchmaker #24 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
24Group03_8qrj_3pet_6A_m1_id_330.pdb, chain A (#24), sequence alignment score
= 1248.6
RMSD between 253 pruned atom pairs is 0.219 angstroms; (across all 258 pairs:
0.484)
> matchmaker #25 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
25Group04_8qrj_3pet_6A_m1_id_323.pdb, chain A (#25), sequence alignment score
= 1252.5
RMSD between 258 pruned atom pairs is 0.261 angstroms; (across all 258 pairs:
0.261)
> matchmaker #26 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
26Group04_8qrj_3pet_6A_m2_id_54.pdb, chain A (#26), sequence alignment score =
1242.8
RMSD between 258 pruned atom pairs is 0.240 angstroms; (across all 258 pairs:
0.240)
> matchmaker #27 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
27Group05_8qrj_3pet_6A_m2_id_322.pdb, chain A (#27), sequence alignment score
= 1271
RMSD between 251 pruned atom pairs is 0.280 angstroms; (across all 258 pairs:
0.875)
> matchmaker #28 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
28Group05_8qrj_3pet_6A_m0_id_540.pdb, chain A (#28), sequence alignment score
= 1279.2
RMSD between 258 pruned atom pairs is 0.234 angstroms; (across all 258 pairs:
0.234)
> matchmaker #29 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
29Group05_8qrj_3pet_6A_m2_id_533.pdb, chain A (#29), sequence alignment score
= 1231.2
RMSD between 258 pruned atom pairs is 0.219 angstroms; (across all 258 pairs:
0.219)
> matchmaker #30 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
30Group05_8qrj_3pet_6A_m0_id_669.pdb, chain A (#30), sequence alignment score
= 1243.8
RMSD between 257 pruned atom pairs is 0.199 angstroms; (across all 258 pairs:
0.246)
> matchmaker #31 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
31Group05_8qrj_3pet_6A_m1_id_218.pdb, chain A (#31), sequence alignment score
= 1249
RMSD between 258 pruned atom pairs is 0.228 angstroms; (across all 258 pairs:
0.228)
> matchmaker #32 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
32Group05_8qrj_3pet_6A_m2_id_103.pdb, chain A (#32), sequence alignment score
= 1221.1
RMSD between 250 pruned atom pairs is 0.294 angstroms; (across all 258 pairs:
0.776)
> matchmaker #33 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
33Group05_8qrj_3pet_6A_m0_id_408.pdb, chain A (#33), sequence alignment score
= 1254.5
RMSD between 258 pruned atom pairs is 0.261 angstroms; (across all 258 pairs:
0.261)
> matchmaker #34 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
34Group05_8qrj_3pet_6A_m0_id_383.pdb, chain A (#34), sequence alignment score
= 1253.5
RMSD between 258 pruned atom pairs is 0.302 angstroms; (across all 258 pairs:
0.302)
> matchmaker #35 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
35Group06_8qrj_3pet_6A_m1_id_568.pdb, chain A (#35), sequence alignment score
= 1239.9
RMSD between 257 pruned atom pairs is 0.258 angstroms; (across all 258 pairs:
0.304)
> matchmaker #36 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
36Group06_8qrj_3pet_6A_m2_id_148.pdb, chain A (#36), sequence alignment score
= 1262.4
RMSD between 258 pruned atom pairs is 0.268 angstroms; (across all 258 pairs:
0.268)
> matchmaker #37 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
37Group06_8qrj_3pet_6A_m2_id_477.pdb, chain A (#37), sequence alignment score
= 1251
RMSD between 258 pruned atom pairs is 0.272 angstroms; (across all 258 pairs:
0.272)
> matchmaker #38 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
38Group07_8qrj_3pet_6A_m2_id_487.pdb, chain A (#38), sequence alignment score
= 1223.9
RMSD between 250 pruned atom pairs is 0.325 angstroms; (across all 258 pairs:
0.851)
> matchmaker #39 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with
39Group07_8qrj_3pet_6A_m2_id_504.pdb, chain A (#39), sequence alignment score
= 1218.6
RMSD between 258 pruned atom pairs is 0.220 angstroms; (across all 258 pairs:
0.220)
> style stick
Changed 77777 atom styles
> show atoms
[Repeated 1 time(s)]
> hide atoms
> undo
[Repeated 2 time(s)]
> save
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/Hit-
> structures/Final_39_PDBs_One_Fasta_File/39_aligned_structures.cxs
> color #17 #ff40ffff
> undo
> hide #1 models
> hide #2 models
> hide #3 models
> hide #5 models
> hide #4 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> hide #25 models
> hide #26 models
> hide #27 models
> hide #28 models
> hide #29 models
> hide #30 models
> hide #32 models
> hide #33 models
> hide #34 models
> hide #35 models
> hide #36 models
> hide #37 models
> hide #38 models
> hide #39 models
> color #17 #942192ff
> show #17,31 atoms
> show #16 models
> hide #16 models
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/readme.txt
Unrecognized file suffix '.txt'
> open
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8ytv-aligned.cif
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/8yty-aligned.cif
Summary of feedback from opening
/Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
Science-Fellows_Rheas-factory/Structures/8ytv-aligned.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 558
Unknown polymer entity '1' on line 724
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
Science-Fellows_Rheas-factory/Structures/8yty-aligned.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 288
Unknown polymer entity '1' on line 430
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 8ytv-aligned.cif #40
---
Chain | Description
A | No description available
B | No description available
51 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for 8yty-aligned.cif #41
---
Chain | Description
A | No description available
129 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #40 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 8ytv-
aligned.cif, chain A (#40), sequence alignment score = 728.4
RMSD between 232 pruned atom pairs is 0.760 angstroms; (across all 249 pairs:
1.216)
> matchmaker #41 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 8yty-
aligned.cif, chain A (#41), sequence alignment score = 678.5
RMSD between 230 pruned atom pairs is 0.851 angstroms; (across all 247 pairs:
1.310)
> matchmaker #40 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 8ytv-
aligned.cif, chain A (#40), sequence alignment score = 728.4
RMSD between 232 pruned atom pairs is 0.760 angstroms; (across all 249 pairs:
1.216)
> select #40/B:48-296
1852 atoms, 1903 bonds, 249 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> rename #40 _MipaP-M198ytv-aligned.cif
> rename #40 MipaP-M198ytv-aligned.cif
> rename #41 Kubu-P-M12+P185-8yty-aligned.cif
> hide #40 models
> hide #41 models
> show #40 models
> show #41 models
> show #17,31,40-41 atoms
> select :LIG
1560 atoms, 1638 bonds, 39 residues, 39 models selected
> color sel grey
> select clear
> select :LIG
1560 atoms, 1638 bonds, 39 residues, 39 models selected
> style sel & #17,31 sphere
Changed 80 atom styles
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select :LIG
1560 atoms, 1638 bonds, 39 residues, 39 models selected
> transparency 75 sel atoms
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 75 atoms sel
Expected ',' or a keyword
> transparency sel 75 atoms
> select clear
> select :HOH
550 atoms, 550 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> hide #40 models
> hide #41 models
> show #41 models
> hide #41 models
> show #41 models
> color #41 #00fa92ff
> color #41 #00fdffff
> color #41 #0096ffff
> color #40 #ff8ad8ff
> select :LIG
1560 atoms, 1638 bonds, 39 residues, 39 models selected
> transparency 50 atoms sel
Expected ',' or a keyword
> transparency sel 50 atoms
> select clear
> show #40 models
> hide #40 models
> show #40 models
> hide #41 models
> hide #40 models
> show #41 models
> show #40 models
> hide #40 models
> show #40 models
> hide #40 models
> show #40 models
> hide #40 models
> show #40 models
> hide #40 models
> show #40 models
> hide #40 models
> hide #41 models
> show #41 models
> show #40 models
> hide #17,31,40-41 atoms
> select :LIG
1560 atoms, 1638 bonds, 39 residues, 39 models selected
> show sel atoms
> select sel @ show sel atoms
> select clear
> select #17:LIG
40 atoms, 42 bonds, 1 residue, 1 model selected
> color sel grey blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel bluegrey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel blue
> select clear
> select #17:LIG
40 atoms, 42 bonds, 1 residue, 1 model selected
> color sel purple
> select cleaer
Expected an objects specifier or a keyword
> select clear
> hide #31 models
> hide #17 models
> show #31 models
> show #17 models
> show #39 models
> hide #39 models
> show #37 models
> hide #37 models
> show #36 models
> hide #36 models
> select #17:87
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> undo
> select clear
> select #17:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel
> hide sel
> select #17:87
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40:167
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> save
> /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley-
> Science-Fellows_Rheas-factory/Structures/39models.cxs
——— End of log from Wed Mar 12 11:29:24 2025 ———
opened ChimeraX session
> select :4 :5 :16 :18 :26 :45 :49 :50 :54 :56 :64 :65 :68 :71: 73 :98 :101
> :110 :114 :121 :125 :127 :138 :142 :143 :158 :164 :185 :189 :194 :212 :215
> :216 :218 :219 : 222 :225 :229 :231 :233 :236 :237 :241 :243 :246 :249 :254
14758 atoms, 13295 bonds, 1917 residues, 41 models selected
> show sel atoms
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.5.10
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 580~1678
Software:
System Software Overview:
System Version: macOS 14.4 (23E214)
Kernel Version: Darwin 23.4.0
Time since boot: 4 days, 1 hour, 20 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL S2421HN:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: FNJ2ZN3
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
ChimeraX-Clipper: 0.23.1
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 7 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 14.4, Intel Iris Plus Graphics |
This ChimeraX crash happened in the Mac Intel OpenGL graphics driver. Unfortunately Apple's Intel graphics drivers are rather unstable. There is nothing we can do to fix this. All newer Macs using Apple silicon GPUs have stable OpenGL graphics.
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Reported by Chandrima Majumdar