Opened 7 months ago

Closed 7 months ago

#17154 closed defect (duplicate)

Crash in garbage collection

Reported by: blz208813@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000043aa77000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030c08b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030b07f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030a073000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000309067000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030805b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030704f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000306043000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000305037000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030402b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030301f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000302013000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000208094840 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in 
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in 
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2828 in set_matrix
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 817 in set_projection_matrix
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 938 in _update_projection
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 239 in _draw_scene
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
  File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.segment._segment, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 60)


{"app_name":"ChimeraX","timestamp":"2025-03-21 12:40:56.00 +0530","app_version":"1.7.1","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"21A3578F-9E6F-42BB-820A-31DCDE7A2913"}
{
  "uptime" : 240000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,7",
  "coalitionID" : 1041,
  "osVersion" : {
    "train" : "macOS 15.3.1",
    "build" : "24D70",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-21 12:40:26.4165 +0530",
  "codeSigningMonitor" : 1,
  "incident" : "21A3578F-9E6F-42BB-820A-31DCDE7A2913",
  "pid" : 43650,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-11 10:48:43.0740 +0530",
  "procStartAbsTime" : 4167473456947,
  "procExitAbsTime" : 5995196794377,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"6057E19D-553A-51AC-ADD4-3339719C7BD4","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "1D0068F0-47FD-79A0-FA05-44EC197363DB",
  "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" : "98556F33-A2B3-421C-AFAA-B1A38C0540D4",
  "wakeTime" : 5671,
  "sleepWakeUUID" : "7B164327-B36C-4C9F-9FB5-7AAAF5355171",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 4344512343\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      102f40000-102f44000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43650},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 4344512343\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      102f40000-102f44000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5503941272},{"value":99},{"value":95},{"value":0},{"value":0},{"value":17644243533945957998},{"value":17644243525222377006},{"value":14757395258967641293},{"value":4294967286},{"value":5503941202},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8865538752},{"value":0},{"value":11},{"value":259},{"value":8724760864,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4364518960,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":4362646808,"symbolLocation":0,"symbol":"visit_decref"},{"value":6122358992},{"value":0},{"value":4365453896,"symbolLocation":59712,"symbol":"_PyRuntime"}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6953254768},"cpsr":{"value":1073745920},"fp":{"value":5503941344},"sp":{"value":5503941312},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J115_class_00_final_volume.mrc

Opened cryosparc_P2_J115_class_00_final_volume.mrc as #1, grid size
192,192,192, pixel 2.75, shown at level 0.455, step 1, values float32  

> open
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J115_class_01_final_volume.mrc

Opened cryosparc_P2_J115_class_01_final_volume.mrc as #2, grid size
192,192,192, pixel 2.75, shown at level 0.436, step 1, values float32  

> open
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J115_class_02_final_volume.mrc

Opened cryosparc_P2_J115_class_02_final_volume.mrc as #3, grid size
192,192,192, pixel 2.75, shown at level 0.435, step 1, values float32  

> volume #1 level 0.5143

> volume #2 level 0.481

> volume #3 level 0.4929

> volume #2 level 0.4635

> volume #3 level 0.4696

> ui tool show "Side View"

> volume #1 level 0.4984

> volume #1 level 0.4666

> open
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J120_006_volume_map_sharp.mrc
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J122_011_volume_map_sharp.mrc

Opened cryosparc_P2_J120_006_volume_map_sharp.mrc as #4.1, grid size
480,480,480, pixel 1.1, shown at level 0.178, step 2, values float32  
Opened cryosparc_P2_J122_011_volume_map_sharp.mrc as #4.2, grid size
480,480,480, pixel 1.1, shown at level 0.179, step 2, values float32  

> volume #4.1 step 1

> volume #4.2 step 1

> close

> open
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J127_007_volume_map_sharp.mrc
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J128_006_volume_map_sharp.mrc
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J129_007_volume_map_sharp.mrc
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J130_006_volume_map_sharp.mrc
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J131_007_volume_map_sharp.mrc

Opened cryosparc_P2_J127_007_volume_map_sharp.mrc as #1.1, grid size
480,480,480, pixel 1.1, shown at level 0.174, step 2, values float32  
Opened cryosparc_P2_J128_006_volume_map_sharp.mrc as #1.2, grid size
480,480,480, pixel 1.1, shown at level 0.177, step 2, values float32  
Opened cryosparc_P2_J129_007_volume_map_sharp.mrc as #1.3, grid size
480,480,480, pixel 1.1, shown at level 0.178, step 2, values float32  
Opened cryosparc_P2_J130_006_volume_map_sharp.mrc as #1.4, grid size
480,480,480, pixel 1.1, shown at level 0.162, step 2, values float32  
Opened cryosparc_P2_J131_007_volume_map_sharp.mrc as #1.5, grid size
480,480,480, pixel 1.1, shown at level 0.177, step 2, values float32  

> volume #1.1 step 1

> volume #1.2 step 1

> volume #1.3 step 1

> volume #1.4 step 1

> volume #1.5 step 1

> volume #1.1 level 0.181

> volume #1.1 level 0.169

> set bgColor white

> set bgColor #ffffff00

> set bgColor white

> set bgColor black

> set bgColor transparent

> volume #1.4 level 0.1602

> volume #1.5 level 0.1594

> volume #1.4 level 0.1315

> close session

> open /Users/kirti/Desktop/FHV/FHV_Peptide/fold_2025_02_18_14_53_model_0.cif
> /Users/kirti/Desktop/FHV/FHV_Peptide/model_angeloJ331.cif

Summary of feedback from opening
/Users/kirti/Desktop/FHV/FHV_Peptide/model_angeloJ331.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for fold_2025_02_18_14_53_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Chain information for model_angeloJ331.cif #2  
---  
Chain | Description  
A0 Aa7 Aag Aah Aat Aav Ad Adj Aec Aeh Aej Aek Afg Afr Ag Agl Ah5 Ahu Ai1 Ai2
Aiz Aj2 Ajf Ajh Ajn Ajo Ak0 Ak4 Ak5 Ak8 Akg Akr Alf Alh Alt Am2 Anh | No
description available  
A1 Aa5 | No description available  
A2 Ao | No description available  
A3 A4 A5 Aa Aad Aai Aak Abv Abw Ac1 Ac6 Ac8 Aco Ad5 Ad7 Add Adr Ads Adt Adu
Ae7 Ael Aep Af1 Af4 Af6 Af7 Afe Afm Afn Afy Ag3 Ag4 Ag5 Agf Agg Ags Agt Agu
Agx Ah0 Ahg Ahh Ahi Ahj Ahn Aih Air Aiu Aiw Aiy Ajl Ajr Ajs Ajv Ajx Akd Ald
Alo Am3 Amk Amq Anw Anz Aq As | No description available  
A6 Ab3 Ab4 Ab7 Abb Ae8 Afh Aft Afw Ag9 Aga Agc Agj Agy Ah1 Ah4 Aha Ahb Ai3 Aic
Aif Aij Ail Aj0 Aj5 Aku Al1 Alx Am4 Ani Aw | No description available  
A7 | No description available  
A8 Aau Abn Abp Acd Adb Adh Adv Adw Aef Aeg Aei Afb Ah Ahp Ahv Am5 Ame An0 | No
description available  
A9 | No description available  
Aa0 Aaj | No description available  
Aa1 | No description available  
Aa2 Aaf Abx Am Ax | No description available  
Aa3 Acj Ae9 Aeb Aed Aem Aen Af0 Af3 Afp Ag8 Agd Age Agw Ahc Ahd Ahs Ais Aiv
Aju Akb Akk Alg Ali Alj Alp Alr Amy Anm Ann Anp | No description available  
Aa4 Abs Abt Abu Acb Acc Ach Ack Acl Acp Aj Ajm | No description available  
Aa6 | No description available  
Aa8 | No description available  
Aa9 Agp Aii Aj4 Aja Ajt Amw | No description available  
Aaa Ajg All | No description available  
Aab Aby Af | No description available  
Aac Az | No description available  
Aae Aal Aay Aaz Ab0 Ab1 Ab6 Ab8 Abc Abd Abf Abg Ac3 Act Acv Acw Ad0 Ad1 Ad2
Adc Adl Adn Adp Ady Adz Ae6 Aee Aer Aet Aeu Aew Aex Af9 Afa Afi Afk Afu Afv
Agb Agi Agr Am7 | No description available  
Aam Ac4 Acq Adq Aeo Afz Ag0 Ag6 Ahz Aiq Ajy Amr Ant | No description available  
Aan Aap Aax Ab9 Aba Abe Acs Acu Acx Adk Afj Agk Ah3 Ahq Ai0 Ai6 Ai7 Ai9 Aib
Aj6 Aj8 Ajp Ak Ak6 Akf Aki Akt Akv Akw Al0 Al3 Al4 Al5 Ala Alc Ama Ank | No
description available  
Aao Abr Ac2 Ac7 Acg Acm Acn Acr Ad6 Ae3 Aea Aid Al2 Al8 Aln Am6 Amp Amz An4
An6 Anf Ang Anv At | No description available  
Aaq | No description available  
Aar Abm An | No description available  
Aas Abl Adf Ag1 Agn Ajk Ak2 Al Av | No description available  
Aaw Ae1 Ami Amj | No description available  
Ab | No description available  
Ab2 Abk Aes Aj7 Aka Akh Am1 | No description available  
Ab5 Abi Ado Adx Af8 Akz | No description available  
Abh Akx An2 | No description available  
Abj Agv Ahe Akq Am0 | No description available  
Abo Abq Ace Adg Adi Aez Ap | No description available  
Abz Ac5 | No description available  
Ac | No description available  
Ac0 Acz Ajw Anl | No description available  
Ac9 Aci | No description available  
Aca | No description available  
Acf Ad4 Ad8 Ada Af2 Af5 Afd Afo Afx | No description available  
Acy Ae5 Aey | No description available  
Ad3 Aev Afs Aig Ak3 Alu Amb Amg Amu An1 | No description available  
Ad9 Aix | No description available  
Ade Ahw | No description available  
Adm | No description available  
Ae Ag7 Ain Aje An5 Anx | No description available  
Ae0 | No description available  
Ae2 | No description available  
Ae4 Ai5 Ajd Ake Amv | No description available  
Aeq Aim Anb Ano | No description available  
Afc | No description available  
Aff | No description available  
Afl | No description available  
Afq | No description available  
Ag2 | No description available  
Agh | No description available  
Agm Ago Agz Ahm Aho Aio Ajb Ajc Aji Ajz Akc Akl Al7 Alb Alm Aml Amm Amt Amx
Anj Anq Anr Ans | No description available  
Agq | No description available  
Ah2 | No description available  
Ah6 | No description available  
Ah7 | No description available  
Ah8 Ah9 Ahk Aia Ajq Akm Anu | No description available  
Ahf | No description available  
Ahl | No description available  
Ahr | No description available  
Aht | No description available  
Ahx | No description available  
Ahy | No description available  
Ai | No description available  
Ai4 | No description available  
Ai8 Amn | No description available  
Aie | No description available  
Aik | No description available  
Aip | No description available  
Ait | No description available  
Aj1 | No description available  
Aj3 | No description available  
Aj9 | No description available  
Ajj | No description available  
Ak1 Al9 Ana Ane Any | No description available  
Ak7 Amf | No description available  
Ak9 | No description available  
Akj Alw | No description available  
Akn | No description available  
Ako | No description available  
Akp | No description available  
Aks Alk | No description available  
Aky | No description available  
Al6 | No description available  
Ale | No description available  
Alq | No description available  
Als | No description available  
Alv | No description available  
Aly | No description available  
Alz An3 | No description available  
Am8 Amd Amh And Au | No description available  
Am9 | No description available  
Amc | No description available  
Amo | No description available  
Ams | No description available  
Anc | No description available  
Ar | No description available  
Ay | No description available  
  

> hide #!2 models

> show #!2 models

> hide #1 models

> hide all

> show cartoons

> show #1 models

> color #1 #00fdffff

> color #2 #ff2600ff

> ui tool show Matchmaker

> matchmaker #1 to #2

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 model_angeloJ331.cif, chain A2 (#2) with
fold_2025_02_18_14_53_model_0.cif, chain A (#1), sequence alignment score =
62.7  
RMSD between 8 pruned atom pairs is 0.876 angstroms; (across all 11 pairs:
2.900)  
  

> open
> /Users/kirti/Desktop/FHV/FHV_Peptide/cryosparc_P6_J331_013_volume_map_sharp.mrc

MRC file is truncated. Failed reading 1 values, type int32  

> open
> /Users/kirti/Desktop/FHV/FHV_Peptide/cryosparc_P6_J331_013_volume_map_sharp.mrc

Failed opening file
/Users/kirti/Desktop/FHV/FHV_Peptide/cryosparc_P6_J331_013_volume_map_sharp.mrc:  
MRC file is truncated. Failed reading 1 values, type int32  

> open
> /Users/kirti/Desktop/FHV/FHV_Peptide/cryosparc_P6_J331_013_volume_map_sharp.mrc

Failed opening file
/Users/kirti/Desktop/FHV/FHV_Peptide/cryosparc_P6_J331_013_volume_map_sharp.mrc:  
MRC file is truncated. Failed reading 1 values, type int32  

> open /Users/kirti/Desktop/FHV/FHV_Peptide/J331_reducedmap.mrc

MRC file is truncated. Failed reading 1 values, type int32  

> ui tool show "Map Coordinates"

> close

> open
> /Users/kirti/Desktop/FHV/FHV_Peptide/cryosparc_P6_J331_013_volume_map_sharp.mrc

Opened cryosparc_P6_J331_013_volume_map_sharp.mrc as #1, grid size
576,576,576, pixel 0.978, shown at level 0.379, step 4, values float32  

> volume #1 step 1

> set bgColor white

> set bgColor #ffffff00

> transparency 30

> transparency 50

> color dim gray

> open /Users/kirti/Desktop/FHV/FHV_Peptide/fold_2025_02_18_14_53_model_0.cif
> /Users/kirti/Desktop/FHV/FHV_Peptide/model_angeloJ331.cif

Summary of feedback from opening
/Users/kirti/Desktop/FHV/FHV_Peptide/model_angeloJ331.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for fold_2025_02_18_14_53_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Chain information for model_angeloJ331.cif #3  
---  
Chain | Description  
A0 Aa7 Aag Aah Aat Aav Ad Adj Aec Aeh Aej Aek Afg Afr Ag Agl Ah5 Ahu Ai1 Ai2
Aiz Aj2 Ajf Ajh Ajn Ajo Ak0 Ak4 Ak5 Ak8 Akg Akr Alf Alh Alt Am2 Anh | No
description available  
A1 Aa5 | No description available  
A2 Ao | No description available  
A3 A4 A5 Aa Aad Aai Aak Abv Abw Ac1 Ac6 Ac8 Aco Ad5 Ad7 Add Adr Ads Adt Adu
Ae7 Ael Aep Af1 Af4 Af6 Af7 Afe Afm Afn Afy Ag3 Ag4 Ag5 Agf Agg Ags Agt Agu
Agx Ah0 Ahg Ahh Ahi Ahj Ahn Aih Air Aiu Aiw Aiy Ajl Ajr Ajs Ajv Ajx Akd Ald
Alo Am3 Amk Amq Anw Anz Aq As | No description available  
A6 Ab3 Ab4 Ab7 Abb Ae8 Afh Aft Afw Ag9 Aga Agc Agj Agy Ah1 Ah4 Aha Ahb Ai3 Aic
Aif Aij Ail Aj0 Aj5 Aku Al1 Alx Am4 Ani Aw | No description available  
A7 | No description available  
A8 Aau Abn Abp Acd Adb Adh Adv Adw Aef Aeg Aei Afb Ah Ahp Ahv Am5 Ame An0 | No
description available  
A9 | No description available  
Aa0 Aaj | No description available  
Aa1 | No description available  
Aa2 Aaf Abx Am Ax | No description available  
Aa3 Acj Ae9 Aeb Aed Aem Aen Af0 Af3 Afp Ag8 Agd Age Agw Ahc Ahd Ahs Ais Aiv
Aju Akb Akk Alg Ali Alj Alp Alr Amy Anm Ann Anp | No description available  
Aa4 Abs Abt Abu Acb Acc Ach Ack Acl Acp Aj Ajm | No description available  
Aa6 | No description available  
Aa8 | No description available  
Aa9 Agp Aii Aj4 Aja Ajt Amw | No description available  
Aaa Ajg All | No description available  
Aab Aby Af | No description available  
Aac Az | No description available  
Aae Aal Aay Aaz Ab0 Ab1 Ab6 Ab8 Abc Abd Abf Abg Ac3 Act Acv Acw Ad0 Ad1 Ad2
Adc Adl Adn Adp Ady Adz Ae6 Aee Aer Aet Aeu Aew Aex Af9 Afa Afi Afk Afu Afv
Agb Agi Agr Am7 | No description available  
Aam Ac4 Acq Adq Aeo Afz Ag0 Ag6 Ahz Aiq Ajy Amr Ant | No description available  
Aan Aap Aax Ab9 Aba Abe Acs Acu Acx Adk Afj Agk Ah3 Ahq Ai0 Ai6 Ai7 Ai9 Aib
Aj6 Aj8 Ajp Ak Ak6 Akf Aki Akt Akv Akw Al0 Al3 Al4 Al5 Ala Alc Ama Ank | No
description available  
Aao Abr Ac2 Ac7 Acg Acm Acn Acr Ad6 Ae3 Aea Aid Al2 Al8 Aln Am6 Amp Amz An4
An6 Anf Ang Anv At | No description available  
Aaq | No description available  
Aar Abm An | No description available  
Aas Abl Adf Ag1 Agn Ajk Ak2 Al Av | No description available  
Aaw Ae1 Ami Amj | No description available  
Ab | No description available  
Ab2 Abk Aes Aj7 Aka Akh Am1 | No description available  
Ab5 Abi Ado Adx Af8 Akz | No description available  
Abh Akx An2 | No description available  
Abj Agv Ahe Akq Am0 | No description available  
Abo Abq Ace Adg Adi Aez Ap | No description available  
Abz Ac5 | No description available  
Ac | No description available  
Ac0 Acz Ajw Anl | No description available  
Ac9 Aci | No description available  
Aca | No description available  
Acf Ad4 Ad8 Ada Af2 Af5 Afd Afo Afx | No description available  
Acy Ae5 Aey | No description available  
Ad3 Aev Afs Aig Ak3 Alu Amb Amg Amu An1 | No description available  
Ad9 Aix | No description available  
Ade Ahw | No description available  
Adm | No description available  
Ae Ag7 Ain Aje An5 Anx | No description available  
Ae0 | No description available  
Ae2 | No description available  
Ae4 Ai5 Ajd Ake Amv | No description available  
Aeq Aim Anb Ano | No description available  
Afc | No description available  
Aff | No description available  
Afl | No description available  
Afq | No description available  
Ag2 | No description available  
Agh | No description available  
Agm Ago Agz Ahm Aho Aio Ajb Ajc Aji Ajz Akc Akl Al7 Alb Alm Aml Amm Amt Amx
Anj Anq Anr Ans | No description available  
Agq | No description available  
Ah2 | No description available  
Ah6 | No description available  
Ah7 | No description available  
Ah8 Ah9 Ahk Aia Ajq Akm Anu | No description available  
Ahf | No description available  
Ahl | No description available  
Ahr | No description available  
Aht | No description available  
Ahx | No description available  
Ahy | No description available  
Ai | No description available  
Ai4 | No description available  
Ai8 Amn | No description available  
Aie | No description available  
Aik | No description available  
Aip | No description available  
Ait | No description available  
Aj1 | No description available  
Aj3 | No description available  
Aj9 | No description available  
Ajj | No description available  
Ak1 Al9 Ana Ane Any | No description available  
Ak7 Amf | No description available  
Ak9 | No description available  
Akj Alw | No description available  
Akn | No description available  
Ako | No description available  
Akp | No description available  
Aks Alk | No description available  
Aky | No description available  
Al6 | No description available  
Ale | No description available  
Alq | No description available  
Als | No description available  
Alv | No description available  
Aly | No description available  
Alz An3 | No description available  
Am8 Amd Amh And Au | No description available  
Am9 | No description available  
Amc | No description available  
Amo | No description available  
Ams | No description available  
Anc | No description available  
Ar | No description available  
Ay | No description available  
  

> hide #2 models

> hide #!1 models

> hide all

> show cartoons

> color #3 #ff2600ff

> ui tool show Matchmaker

> matchmaker #!3 to #2

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 fold_2025_02_18_14_53_model_0.cif, chain A (#2) with
model_angeloJ331.cif, chain A2 (#3), sequence alignment score = 62.7  
RMSD between 8 pruned atom pairs is 0.876 angstroms; (across all 11 pairs:
2.900)  
  

> close #3

> show #!1 models

> hide #!1 models

> open /Users/kirti/Desktop/FHV/FHV_Peptide/model_angeloJ331.cif

Summary of feedback from opening
/Users/kirti/Desktop/FHV/FHV_Peptide/model_angeloJ331.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for model_angeloJ331.cif #3  
---  
Chain | Description  
A0 Aa7 Aag Aah Aat Aav Ad Adj Aec Aeh Aej Aek Afg Afr Ag Agl Ah5 Ahu Ai1 Ai2
Aiz Aj2 Ajf Ajh Ajn Ajo Ak0 Ak4 Ak5 Ak8 Akg Akr Alf Alh Alt Am2 Anh | No
description available  
A1 Aa5 | No description available  
A2 Ao | No description available  
A3 A4 A5 Aa Aad Aai Aak Abv Abw Ac1 Ac6 Ac8 Aco Ad5 Ad7 Add Adr Ads Adt Adu
Ae7 Ael Aep Af1 Af4 Af6 Af7 Afe Afm Afn Afy Ag3 Ag4 Ag5 Agf Agg Ags Agt Agu
Agx Ah0 Ahg Ahh Ahi Ahj Ahn Aih Air Aiu Aiw Aiy Ajl Ajr Ajs Ajv Ajx Akd Ald
Alo Am3 Amk Amq Anw Anz Aq As | No description available  
A6 Ab3 Ab4 Ab7 Abb Ae8 Afh Aft Afw Ag9 Aga Agc Agj Agy Ah1 Ah4 Aha Ahb Ai3 Aic
Aif Aij Ail Aj0 Aj5 Aku Al1 Alx Am4 Ani Aw | No description available  
A7 | No description available  
A8 Aau Abn Abp Acd Adb Adh Adv Adw Aef Aeg Aei Afb Ah Ahp Ahv Am5 Ame An0 | No
description available  
A9 | No description available  
Aa0 Aaj | No description available  
Aa1 | No description available  
Aa2 Aaf Abx Am Ax | No description available  
Aa3 Acj Ae9 Aeb Aed Aem Aen Af0 Af3 Afp Ag8 Agd Age Agw Ahc Ahd Ahs Ais Aiv
Aju Akb Akk Alg Ali Alj Alp Alr Amy Anm Ann Anp | No description available  
Aa4 Abs Abt Abu Acb Acc Ach Ack Acl Acp Aj Ajm | No description available  
Aa6 | No description available  
Aa8 | No description available  
Aa9 Agp Aii Aj4 Aja Ajt Amw | No description available  
Aaa Ajg All | No description available  
Aab Aby Af | No description available  
Aac Az | No description available  
Aae Aal Aay Aaz Ab0 Ab1 Ab6 Ab8 Abc Abd Abf Abg Ac3 Act Acv Acw Ad0 Ad1 Ad2
Adc Adl Adn Adp Ady Adz Ae6 Aee Aer Aet Aeu Aew Aex Af9 Afa Afi Afk Afu Afv
Agb Agi Agr Am7 | No description available  
Aam Ac4 Acq Adq Aeo Afz Ag0 Ag6 Ahz Aiq Ajy Amr Ant | No description available  
Aan Aap Aax Ab9 Aba Abe Acs Acu Acx Adk Afj Agk Ah3 Ahq Ai0 Ai6 Ai7 Ai9 Aib
Aj6 Aj8 Ajp Ak Ak6 Akf Aki Akt Akv Akw Al0 Al3 Al4 Al5 Ala Alc Ama Ank | No
description available  
Aao Abr Ac2 Ac7 Acg Acm Acn Acr Ad6 Ae3 Aea Aid Al2 Al8 Aln Am6 Amp Amz An4
An6 Anf Ang Anv At | No description available  
Aaq | No description available  
Aar Abm An | No description available  
Aas Abl Adf Ag1 Agn Ajk Ak2 Al Av | No description available  
Aaw Ae1 Ami Amj | No description available  
Ab | No description available  
Ab2 Abk Aes Aj7 Aka Akh Am1 | No description available  
Ab5 Abi Ado Adx Af8 Akz | No description available  
Abh Akx An2 | No description available  
Abj Agv Ahe Akq Am0 | No description available  
Abo Abq Ace Adg Adi Aez Ap | No description available  
Abz Ac5 | No description available  
Ac | No description available  
Ac0 Acz Ajw Anl | No description available  
Ac9 Aci | No description available  
Aca | No description available  
Acf Ad4 Ad8 Ada Af2 Af5 Afd Afo Afx | No description available  
Acy Ae5 Aey | No description available  
Ad3 Aev Afs Aig Ak3 Alu Amb Amg Amu An1 | No description available  
Ad9 Aix | No description available  
Ade Ahw | No description available  
Adm | No description available  
Ae Ag7 Ain Aje An5 Anx | No description available  
Ae0 | No description available  
Ae2 | No description available  
Ae4 Ai5 Ajd Ake Amv | No description available  
Aeq Aim Anb Ano | No description available  
Afc | No description available  
Aff | No description available  
Afl | No description available  
Afq | No description available  
Ag2 | No description available  
Agh | No description available  
Agm Ago Agz Ahm Aho Aio Ajb Ajc Aji Ajz Akc Akl Al7 Alb Alm Aml Amm Amt Amx
Anj Anq Anr Ans | No description available  
Agq | No description available  
Ah2 | No description available  
Ah6 | No description available  
Ah7 | No description available  
Ah8 Ah9 Ahk Aia Ajq Akm Anu | No description available  
Ahf | No description available  
Ahl | No description available  
Ahr | No description available  
Aht | No description available  
Ahx | No description available  
Ahy | No description available  
Ai | No description available  
Ai4 | No description available  
Ai8 Amn | No description available  
Aie | No description available  
Aik | No description available  
Aip | No description available  
Ait | No description available  
Aj1 | No description available  
Aj3 | No description available  
Aj9 | No description available  
Ajj | No description available  
Ak1 Al9 Ana Ane Any | No description available  
Ak7 Amf | No description available  
Ak9 | No description available  
Akj Alw | No description available  
Akn | No description available  
Ako | No description available  
Akp | No description available  
Aks Alk | No description available  
Aky | No description available  
Al6 | No description available  
Ale | No description available  
Alq | No description available  
Als | No description available  
Alv | No description available  
Aly | No description available  
Alz An3 | No description available  
Am8 Amd Amh And Au | No description available  
Am9 | No description available  
Amc | No description available  
Amo | No description available  
Ams | No description available  
Anc | No description available  
Ar | No description available  
Ay | No description available  
  

> hide all

> show cartoons

> color #3 #ff2600ff

> ui tool show Matchmaker

> matchmaker #2 to #3

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 model_angeloJ331.cif, chain A2 (#3) with
fold_2025_02_18_14_53_model_0.cif, chain A (#2), sequence alignment score =
62.7  
RMSD between 8 pruned atom pairs is 0.876 angstroms; (across all 11 pairs:
2.900)  
  

> color #2 #0433ffff

> show #!1 models

> show #2 models

> hide #2 models

> hide #!3 models

> ui tool show "Segment Map"

Segmenting cryosparc_P6_J331_013_volume_map_sharp.mrc, density threshold
0.378563  
Only showing 60 of 2870 regions.  
Showing 60 of 2870 region surfaces  
60414 watershed regions, grouped to 2870 regions  
Showing cryosparc_P6_J331_013_volume_map_sharp.seg - 2870 regions, 60 surfaces  

> close #4

Segmenting cryosparc_P6_J331_013_volume_map_sharp.mrc, density threshold
0.378563  
Only showing 60 of 9687 regions.  
Showing 60 of 9687 region surfaces  
60414 watershed regions, grouped to 9687 regions  
Showing cryosparc_P6_J331_013_volume_map_sharp.seg - 9687 regions, 60 surfaces  

> close #4

Segmenting cryosparc_P6_J331_013_volume_map_sharp.mrc, density threshold
0.378563  
Only showing 60 of 2870 regions.  
Showing 60 of 2870 region surfaces  
60414 watershed regions, grouped to 2870 regions  
Showing cryosparc_P6_J331_013_volume_map_sharp.seg - 2870 regions, 60 surfaces  
Smoothing and grouping, standard deviation 5 voxels  
Only showing 60 of 1157 regions.  
Showing 60 of 1157 region surfaces  
Got 1157 regions after smoothing 5 voxels.  
Drag select of 88701, 1987 of 21900 triangles, 89983, 120 of 71500 triangles,
89910, 14969 of 59444 triangles, 1 cryosparc_P6_J331_013_volume_map_sharp.mrc  

> select clear

Drag select of 88701, 15865 of 21900 triangles, 89982, 5016 of 61924
triangles, 90019, 6627 of 52664 triangles, 1
cryosparc_P6_J331_013_volume_map_sharp.mrc  

> hide #!1 models

> show #!1 models

> select clear

Smoothing and grouping, standard deviation 6 voxels  
Only showing 60 of 611 regions.  
Showing 60 of 611 region surfaces  
Got 611 regions after smoothing 6 voxels.  
Smoothing and grouping, standard deviation 7 voxels  
Only showing 60 of 442 regions.  
Showing 60 of 442 region surfaces  
Got 442 regions after smoothing 7 voxels.  

> hide #!1 models

> close #4

> show #!1 models

> show #2 models

> show #!3 models

Drag select of 1 cryosparc_P6_J331_013_volume_map_sharp.mrc  

> select #1

2 models selected  

> set bgColor black

> set bgColor transparent

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> ui tool show "Side View"

> open /Users/kirti/Desktop/Chimera_fitting_fhv/J54/fit3_3asu_3fold.pdb

Chain information for fit3_3asu_3fold.pdb  
---  
Chain | Description  
4.1/A 4.1/B 4.1/C | No description available  
4.2/A 4.3/A 4.4/A 4.5/A 4.6/A | No description available  
4.2/B 4.3/B 4.4/B 4.5/B 4.6/B | No description available  
4.2/C 4.3/C 4.4/C 4.5/C 4.6/C | No description available  
4.1/D 4.1/E 4.1/F | No description available  
4.2/D 4.3/D 4.4/D 4.5/D 4.6/D | No description available  
4.2/E 4.3/E 4.4/E 4.5/E 4.6/E | No description available  
4.2/F 4.3/F 4.4/F 4.5/F 4.6/F | No description available  
4.1/R 4.2/R 4.3/R 4.4/R 4.5/R 4.6/R | No description available  
  

> open
> /Users/kirti/Desktop/Chimera_fitting_fhv/J54/ALLREMOVE_fit1_1asu_3fold.pdb

Summary of feedback from opening
/Users/kirti/Desktop/Chimera_fitting_fhv/J54/ALLREMOVE_fit1_1asu_3fold.pdb  
---  
warnings | Cannot find LINK/SSBOND residue CA (401 )  
Cannot find LINK/SSBOND residue CA (402 )  
Cannot find LINK/SSBOND residue CA (402 )  
Cannot find LINK/SSBOND residue CA (401 )  
Cannot find LINK/SSBOND residue CA (401 )  
5 messages similar to the above omitted  
  
Chain information for ALLREMOVE_fit1_1asu_3fold.pdb #5  
---  
Chain | Description  
A B C | No description available  
D E F | No description available  
  

> close #4

> close #5

> open /Users/kirti/Desktop/Chimera_fitting_fhv/J54/3fold_FHV_combined.pdb

Chain information for 3fold_FHV_combined.pdb #4  
---  
Chain | Description  
A G H I J K | No description available  
B L M N O P | No description available  
C Q S T U V | No description available  
D W X Y Z a | No description available  
E b c d e f | No description available  
F g h i j k | No description available  
R l m n o p | No description available  
  

> hide all

> show cartoons

> hide #2 models

> hide #!3 models

> select add #4

49926 atoms, 48372 bonds, 66 pseudobonds, 9012 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.99417,-0.10115,0.037474,24.455,0.09709,0.99047,0.097701,-31.597,-0.047,-0.093492,0.99451,37.05

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.99417,-0.10115,0.037474,35.812,0.09709,0.99047,0.097701,-31.557,-0.047,-0.093492,0.99451,49.5

> select subtract #4

Nothing selected  

> fitmap #4 inMap #1

Fit molecule 3fold_FHV_combined.pdb (#4) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 49926 atoms  
average map value = 0.2645, steps = 236  
shifted from previous position = 18.4  
rotated from previous position = 8.54 degrees  
atoms outside contour = 35436, contour level = 0.37856  
  
Position of 3fold_FHV_combined.pdb (#4) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99994724 0.00497949 0.00898495 14.17767688  
-0.00493396 0.99997491 -0.00508267 19.02319430  
-0.00901004 0.00503808 0.99994672 17.31822474  
Axis 0.44190538 0.78572060 -0.43285422  
Axis point 2586.28361930 0.00000000 -888.16400049  
Rotation angle (degrees) 0.65612344  
Shift along axis 13.71584070  
  

> rainbow #!4

> select add #4

49926 atoms, 48372 bonds, 66 pseudobonds, 9012 residues, 3 models selected  

> select subtract #4

Nothing selected  

> hide #!4 models

> show #!4 models

> coulombic #!4

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3fold_FHV_combined.pdb_A SES surface #4.3: minimum,
-17.39, mean -2.26, maximum 9.59  
Coulombic values for 3fold_FHV_combined.pdb_B SES surface #4.4: minimum,
-17.18, mean -2.16, maximum 9.50  
Coulombic values for 3fold_FHV_combined.pdb_C SES surface #4.5: minimum,
-21.82, mean -2.09, maximum 9.79  
Coulombic values for 3fold_FHV_combined.pdb_D SES surface #4.6: minimum,
-2.99, mean 2.68, maximum 11.82  
Coulombic values for 3fold_FHV_combined.pdb_E SES surface #4.7: minimum,
-4.97, mean 2.80, maximum 11.76  
Coulombic values for 3fold_FHV_combined.pdb_F SES surface #4.8: minimum,
-4.26, mean 2.80, maximum 14.17  
Coulombic values for 3fold_FHV_combined.pdb_G SES surface #4.9: minimum,
-17.54, mean -2.28, maximum 9.81  
Coulombic values for 3fold_FHV_combined.pdb_H SES surface #4.10: minimum,
-17.51, mean -2.28, maximum 9.39  
Coulombic values for 3fold_FHV_combined.pdb_I SES surface #4.11: minimum,
-17.53, mean -2.26, maximum 9.51  
Coulombic values for 3fold_FHV_combined.pdb_J SES surface #4.12: minimum,
-17.02, mean -2.28, maximum 9.59  
Coulombic values for 3fold_FHV_combined.pdb_K SES surface #4.13: minimum,
-17.63, mean -2.26, maximum 9.82  
Coulombic values for 3fold_FHV_combined.pdb_L SES surface #4.14: minimum,
-17.37, mean -2.17, maximum 9.42  
Coulombic values for 3fold_FHV_combined.pdb_M SES surface #4.15: minimum,
-17.61, mean -2.16, maximum 9.32  
Coulombic values for 3fold_FHV_combined.pdb_N SES surface #4.16: minimum,
-17.90, mean -2.17, maximum 9.46  
Coulombic values for 3fold_FHV_combined.pdb_O SES surface #4.17: minimum,
-17.47, mean -2.15, maximum 14.07  
Coulombic values for 3fold_FHV_combined.pdb_P SES surface #4.18: minimum,
-17.61, mean -2.12, maximum 9.40  
Coulombic values for 3fold_FHV_combined.pdb_Q SES surface #4.19: minimum,
-17.58, mean -2.12, maximum 9.91  
Coulombic values for 3fold_FHV_combined.pdb_R SES surface #4.20: minimum,
-20.64, mean -10.17, maximum -0.09  
Coulombic values for 3fold_FHV_combined.pdb_S SES surface #4.21: minimum,
-18.31, mean -2.10, maximum 9.97  
Coulombic values for 3fold_FHV_combined.pdb_T SES surface #4.22: minimum,
-17.82, mean -2.11, maximum 9.87  
Coulombic values for 3fold_FHV_combined.pdb_U SES surface #4.23: minimum,
-18.19, mean -2.10, maximum 9.68  
Coulombic values for 3fold_FHV_combined.pdb_V SES surface #4.24: minimum,
-18.25, mean -2.09, maximum 9.74  
Coulombic values for 3fold_FHV_combined.pdb_W SES surface #4.25: minimum,
-2.98, mean 2.69, maximum 11.29  
Coulombic values for 3fold_FHV_combined.pdb_X SES surface #4.26: minimum,
-2.97, mean 2.70, maximum 11.70  
Coulombic values for 3fold_FHV_combined.pdb_Y SES surface #4.27: minimum,
-2.98, mean 2.71, maximum 11.63  
Coulombic values for 3fold_FHV_combined.pdb_Z SES surface #4.28: minimum,
-3.05, mean 2.73, maximum 12.47  
Coulombic values for 3fold_FHV_combined.pdb_a SES surface #4.29: minimum,
-2.95, mean 2.70, maximum 11.84  
Coulombic values for 3fold_FHV_combined.pdb_b SES surface #4.30: minimum,
-4.85, mean 2.80, maximum 11.65  
Coulombic values for 3fold_FHV_combined.pdb_c SES surface #4.31: minimum,
-4.88, mean 2.79, maximum 11.73  
Coulombic values for 3fold_FHV_combined.pdb_d SES surface #4.32: minimum,
-5.02, mean 2.80, maximum 11.78  
Coulombic values for 3fold_FHV_combined.pdb_e SES surface #4.33: minimum,
-5.06, mean 2.85, maximum 11.52  
Coulombic values for 3fold_FHV_combined.pdb_f SES surface #4.34: minimum,
-4.94, mean 2.81, maximum 11.48  
Coulombic values for 3fold_FHV_combined.pdb_g SES surface #4.35: minimum,
-4.34, mean 2.80, maximum 13.58  
Coulombic values for 3fold_FHV_combined.pdb_h SES surface #4.36: minimum,
-4.40, mean 2.80, maximum 13.64  
Coulombic values for 3fold_FHV_combined.pdb_i SES surface #4.37: minimum,
-4.36, mean 2.77, maximum 13.80  
Coulombic values for 3fold_FHV_combined.pdb_j SES surface #4.38: minimum,
-4.34, mean 2.77, maximum 14.37  
Coulombic values for 3fold_FHV_combined.pdb_k SES surface #4.39: minimum,
-4.41, mean 2.81, maximum 13.85  
Coulombic values for 3fold_FHV_combined.pdb_l SES surface #4.40: minimum,
-20.63, mean -10.14, maximum -0.02  
Coulombic values for 3fold_FHV_combined.pdb_m SES surface #4.41: minimum,
-20.94, mean -10.17, maximum -0.10  
Coulombic values for 3fold_FHV_combined.pdb_n SES surface #4.42: minimum,
-20.71, mean -10.19, maximum -0.21  
Coulombic values for 3fold_FHV_combined.pdb_o SES surface #4.43: minimum,
-20.69, mean -10.18, maximum -0.14  
Coulombic values for 3fold_FHV_combined.pdb_p SES surface #4.44: minimum,
-20.56, mean -10.17, maximum -0.01  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color #1,4 cyan

> undo

> close #4

> open "/Users/kirti/Desktop/Chimera_fitting_fhv/J54/final_fit3_3asu_3fold
> copy.pdb"

Chain information for final_fit3_3asu_3fold copy.pdb  
---  
Chain | Description  
4.1/A 4.1/B 4.1/C | No description available  
4.2/A 4.3/A 4.4/A 4.5/A 4.6/A | No description available  
4.2/B 4.3/B 4.4/B 4.5/B 4.6/B | No description available  
4.2/C 4.3/C 4.4/C 4.5/C 4.6/C | No description available  
4.1/D 4.1/E 4.1/F | No description available  
4.2/D 4.3/D 4.4/D 4.5/D 4.6/D | No description available  
4.2/E 4.3/E 4.4/E 4.5/E 4.6/E | No description available  
4.2/F 4.3/F 4.4/F 4.5/F 4.6/F | No description available  
4.1/R 4.2/R 4.3/R 4.4/R 4.5/R 4.6/R | No description available  
  

> hide all

> show cartoons

> select add #4

49926 atoms, 48372 bonds, 66 pseudobonds, 9012 residues, 19 models selected  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> view matrix models #4,1,0,0,2.3468,0,1,0,17.65,0,0,1,1.5792

> view matrix models #4,1,0,0,0.22502,0,1,0,21.165,0,0,1,5.7679

> hide #!4 models

> show #!4 models

> select subtract #4

Nothing selected  

> select add #4

49926 atoms, 48372 bonds, 66 pseudobonds, 9012 residues, 19 models selected  

> view matrix models #4,1,0,0,11.87,0,1,0,9.9011,0,0,1,17.178

> view matrix models #4,1,0,0,10.585,0,1,0,11.039,0,0,1,18.549

> select subtract #4

Nothing selected  

> select add #4

49926 atoms, 48372 bonds, 66 pseudobonds, 9012 residues, 19 models selected  

> hide #!4 models

> show #!4 models

> view matrix models #4,1,0,0,14.806,0,1,0,17.725,0,0,1,14.881

> select subtract #4

Nothing selected  

> fitmap #4 inMap #1

Fit molecules final_fit3_3asu_3fold copy.pdb (#4.1), final_fit3_3asu_3fold
copy.pdb (#4.2), final_fit3_3asu_3fold copy.pdb (#4.3), final_fit3_3asu_3fold
copy.pdb (#4.4), final_fit3_3asu_3fold copy.pdb (#4.5), final_fit3_3asu_3fold
copy.pdb (#4.6) to map cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using
49926 atoms  
average map value = 0.2028, steps = 196  
shifted from previous position = 2.13  
rotated from previous position = 0.82 degrees  
atoms outside contour = 40020, contour level = 0.37856  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.1) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99991127 0.00926115 0.00957470 -6.49916289  
-0.00921073 0.99994355 -0.00529739 3.14184179  
-0.00962322 0.00520873 0.99994013 -0.40741334  
Axis 0.36685620 0.67035968 -0.64500731  
Axis point -47.57925485 0.00000000 677.75736340  
Rotation angle (degrees) 0.82045329  
Shift along axis -0.01530954  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.2) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99991127 0.00926115 0.00957470 -6.49916289  
-0.00921073 0.99994355 -0.00529739 3.14184179  
-0.00962322 0.00520873 0.99994013 -0.40741334  
Axis 0.36685620 0.67035968 -0.64500731  
Axis point -47.57925485 0.00000000 677.75736340  
Rotation angle (degrees) 0.82045329  
Shift along axis -0.01530954  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.3) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99991127 0.00926115 0.00957470 -6.49916289  
-0.00921073 0.99994355 -0.00529739 3.14184179  
-0.00962322 0.00520873 0.99994013 -0.40741334  
Axis 0.36685620 0.67035968 -0.64500731  
Axis point -47.57925485 0.00000000 677.75736340  
Rotation angle (degrees) 0.82045329  
Shift along axis -0.01530954  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.4) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99991127 0.00926115 0.00957470 -6.49916289  
-0.00921073 0.99994355 -0.00529739 3.14184179  
-0.00962322 0.00520873 0.99994013 -0.40741334  
Axis 0.36685620 0.67035968 -0.64500731  
Axis point -47.57925485 0.00000000 677.75736340  
Rotation angle (degrees) 0.82045329  
Shift along axis -0.01530954  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.5) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99991127 0.00926115 0.00957470 -6.49916289  
-0.00921073 0.99994355 -0.00529739 3.14184179  
-0.00962322 0.00520873 0.99994013 -0.40741334  
Axis 0.36685620 0.67035968 -0.64500731  
Axis point -47.57925485 0.00000000 677.75736340  
Rotation angle (degrees) 0.82045329  
Shift along axis -0.01530954  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.6) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99991127 0.00926115 0.00957470 -6.49916289  
-0.00921073 0.99994355 -0.00529739 3.14184179  
-0.00962322 0.00520873 0.99994013 -0.40741334  
Axis 0.36685620 0.67035968 -0.64500731  
Axis point -47.57925485 0.00000000 677.75736340  
Rotation angle (degrees) 0.82045329  
Shift along axis -0.01530954  
  

> hide #!1 models

> show #!1 models

> select add #4.1

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> select subtract #4.1

Nothing selected  

> select add #4.2

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> select subtract #4.2

Nothing selected  

> select add #4.1

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> select subtract #4.1

Nothing selected  

> select add #4.2

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4.2,0.98669,0.053915,0.15343,-37.418,-0.040041,0.99494,-0.092124,23.536,-0.15762,0.084754,0.98386,9.7239

> view matrix models
> #4.2,0.95022,-6.5173e-05,0.31159,-37.993,0.010816,0.9994,-0.032776,3.2416,-0.3114,0.034514,0.94965,60.14

> view matrix models
> #4.2,0.9827,0.090043,0.16183,-47.984,-0.066563,0.98718,-0.14508,38.869,-0.17281,0.13179,0.9761,0.73766

> select subtract #4.2

Nothing selected  

> select add #4.2

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> select subtract #4.2

Nothing selected  

> select add #4.2

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> view matrix models
> #4.2,0.99984,0.017932,0.00045942,-7.5851,-0.01792,0.99745,0.069055,-5.274,0.00078001,-0.069052,0.99761,18.676

> select subtract #4.2

Nothing selected  

> fitmap #4.2 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.2) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.3433, steps = 84  
shifted from previous position = 5.74  
rotated from previous position = 4.64 degrees  
atoms outside contour = 4757, contour level = 0.37856  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.2) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99991857 0.00162607 0.01265748 -1.27647086  
-0.00151082 0.99995737 -0.00910924 1.85985041  
-0.01267175 0.00908938 0.99987840 3.39283452  
Axis 0.58056406 0.80804149 -0.10007157  
Axis point 269.91214378 0.00000000 121.95051015  
Rotation angle (degrees) 0.89804617  
Shift along axis 0.42223692  
  

> select add #4.3

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> select subtract #4.3

Nothing selected  

> select add #4.4

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> select subtract #4.4

Nothing selected  

> select add #4.3

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> fitmap #4.3 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.3) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.1802, steps = 60  
shifted from previous position = 2.94  
rotated from previous position = 1.67 degrees  
atoms outside contour = 7012, contour level = 0.37856  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.3) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00294121 0.00846196 -1.54517221  
0.00276020 0.99976879 0.02132481 -1.52707353  
-0.00852272 -0.02130060 0.99973679 5.99306622  
Axis -0.92187869 0.36733512 0.12330693  
Axis point 0.00000000 270.81770902 102.15066895  
Rotation angle (degrees) 1.32472627  
Shift along axis 1.60250017  
  

> select subtract #4.3

Nothing selected  

> hide #!4.3 models

> show #!4.3 models

> hide #!4.3 models

> show #!4.3 models

> hide #!4.3 models

> show #!4.3 models

> hide #!4.3 models

> volume #1 level 0.3

> show #!4.3 models

> fitmap #4.3 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.3) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.1803, steps = 44  
shifted from previous position = 0.0209  
rotated from previous position = 0.016 degrees  
atoms outside contour = 6431, contour level = 0.3  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.3) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99995966 -0.00286774 0.00851172 -1.59131559  
0.00268342 0.99976334 0.02158841 -1.55941489  
-0.00857162 -0.02156470 0.99973071 6.07444147  
Axis -0.92321238 0.36547884 0.11876073  
Axis point 0.00000000 271.47774776 102.64557545  
Rotation angle (degrees) 1.33919165  
Shift along axis 1.62059422  
  

> fitmap #4.3 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.3) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.1802, steps = 44  
shifted from previous position = 0.0186  
rotated from previous position = 0.0118 degrees  
atoms outside contour = 6432, contour level = 0.3  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.3) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99996118 -0.00271810 0.00838143 -1.58635111  
0.00253618 0.99976261 0.02164006 -1.55850411  
-0.00843826 -0.02161796 0.99973069 6.07195910  
Axis -0.92611003 0.36009233 0.11248880  
Axis point 0.00000000 271.33303566 101.46956848  
Rotation angle (degrees) 1.33824683  
Shift along axis 1.59095767  
  

> select add #4.3

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> view matrix models
> #4.3,0.99595,-0.06174,0.0653,1.7648,0.056534,0.99529,0.078778,-20.17,-0.069856,-0.074767,0.99475,29.174

> hide #!4.3 models

> show #!4.3 models

> fitmap #4.3 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.3) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.342, steps = 108  
shifted from previous position = 5.3  
rotated from previous position = 7.1 degrees  
atoms outside contour = 3754, contour level = 0.3  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.3) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997667 0.00555162 0.00398028 1.20385251  
-0.00552234 0.99995789 -0.00732947 3.15411386  
-0.00402080 0.00730732 0.99996522 0.40073093  
Axis 0.73103068 0.39961240 -0.55308596  
Axis point 0.00000000 -198.51943421 326.85626488  
Rotation angle (degrees) 0.57360100  
Shift along axis 1.91883747  
  

> select subtract #4.3

Nothing selected  

> select add #4.4

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> select subtract #4.4

Nothing selected  

> select add #4.4

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> fitmap #4.4 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.4) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.3404, steps = 100  
shifted from previous position = 5.77  
rotated from previous position = 0.339 degrees  
atoms outside contour = 3795, contour level = 0.3  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.4) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99993726 0.00360887 0.01060432 -0.11464156  
-0.00353861 0.99997171 -0.00663688 1.65017405  
-0.01062797 0.00659894 0.99992175 2.20085964  
Axis 0.50866230 0.81597309 -0.27468269  
Axis point 224.41994565 0.00000000 44.93134268  
Rotation angle (degrees) 0.74546285  
Shift along axis 0.68364575  
  

> select subtract #4.4

Nothing selected  

> select add #4.5

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> fitmap #4.5 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.5) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.1867, steps = 192  
shifted from previous position = 2.24  
rotated from previous position = 5.98 degrees  
atoms outside contour = 6337, contour level = 0.3  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.5) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99502613 0.07871960 0.06104281 -39.00429736  
-0.08184285 0.99536645 0.05047162 4.70494963  
-0.05678686 -0.05521650 0.99685826 28.11476555  
Axis -0.46875786 0.52260918 -0.71214164  
Axis point 24.98704474 492.77097161 0.00000000  
Rotation angle (degrees) 6.47283364  
Shift along axis 0.72072572  
  

> select subtract #4.5

Nothing selected  

> hide #!4.5 models

> show #!4.5 models

> select add #4.5

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> view matrix models
> #4.5,0.99856,0.052214,0.012582,-19.822,-0.051639,0.99777,-0.042378,18.781,-0.014766,0.041667,0.99902,-13.547

> ui mousemode right "translate selected models"

> view matrix models
> #4.5,0.99856,0.052214,0.012582,-21.51,-0.051639,0.99777,-0.042378,16.206,-0.014766,0.041667,0.99902,-12.287

> ui mousemode right "rotate selected models"

> view matrix models
> #4.5,0.9993,0.03467,-0.014403,-9.6407,-0.035905,0.99465,-0.096877,26.399,0.010967,0.097326,0.99519,-35.396

> ui mousemode right "translate selected models"

> view matrix models
> #4.5,0.9993,0.03467,-0.014403,-9.0974,-0.035905,0.99465,-0.096877,27.381,0.010967,0.097326,0.99519,-35.169

> ui mousemode right "rotate selected models"

> view matrix models
> #4.5,0.96816,-0.051865,-0.24489,76.439,0.077655,0.99226,0.096855,-33.058,0.23797,-0.11279,0.9647,6.4482

> view matrix models
> #4.5,0.95536,-0.08025,-0.28433,97.119,0.12047,0.98457,0.12689,-44.16,0.26976,-0.15547,0.95029,19.125

> fitmap #4.5 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.5) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.3445, steps = 124  
shifted from previous position = 2.3  
rotated from previous position = 19.4 degrees  
atoms outside contour = 3730, contour level = 0.3  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.5) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997379 -0.00301102 0.00658408 2.18583371  
0.00302531 0.99999309 -0.00216040 -2.12528931  
-0.00657753 0.00218026 0.99997599 2.36337609  
Axis 0.28714839 0.87068213 0.39932246  
Axis point 377.50209397 0.00000000 -342.65482001  
Rotation angle (degrees) 0.43305810  
Shift along axis -0.27904364  
  

> select subtract #4.5

Nothing selected  

> select add #4.6

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> fitmap #4.6 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.6) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.1855, steps = 108  
shifted from previous position = 2.04  
rotated from previous position = 5.99 degrees  
atoms outside contour = 6362, contour level = 0.3  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.6) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99800730 0.03860326 0.04991214 -22.25225296  
-0.04277387 0.99542934 0.08538635 -2.85205151  
-0.04638781 -0.08735113 0.99509696 41.06121022  
Axis -0.80773007 0.45030393 -0.38052398  
Axis point 0.00000000 471.10353609 64.23470619  
Rotation angle (degrees) 6.13824243  
Shift along axis 1.06474889  
  

> hide #!4.6 models

> show #!4.6 models

> hide #!4.6 models

> show #!4.6 models

> select subtract #4.6

Nothing selected  

> select add #4.6

8321 atoms, 8062 bonds, 11 pseudobonds, 1502 residues, 3 models selected  

> view matrix models
> #4.6,0.98822,0.14642,-0.04443,-41.367,-0.14537,0.98904,0.025939,29.975,0.04774,-0.019175,0.99868,-1.8407

> view matrix models
> #4.6,0.97007,0.18122,-0.16162,-30.181,-0.15292,0.97297,0.17306,12.705,0.18861,-0.14316,0.97156,16.176

> view matrix models
> #4.6,0.99372,0.11039,-0.018394,-34.528,-0.11084,0.99351,-0.025452,29.916,0.015465,0.027331,0.99951,-11.236

> view matrix models
> #4.6,0.96422,0.22008,-0.14782,-44.484,-0.2327,0.96972,-0.074169,70.805,0.12702,0.10591,0.98623,-58.436

> view matrix models
> #4.6,0.96197,0.21029,-0.17435,-36.322,-0.21689,0.976,-0.019476,56.433,0.16607,0.056551,0.98449,-49.298

> view matrix models
> #4.6,0.99498,0.09433,-0.033491,-26.83,-0.095998,0.99401,-0.052279,31.156,0.028359,0.055231,0.99807,-23.107

> view matrix models
> #4.6,0.95507,0.16541,-0.24594,-7.8457,-0.17204,0.98507,-0.0055644,41.938,0.24135,0.047625,0.96927,-59.046

> view matrix models
> #4.6,0.99158,0.026974,-0.12664,12.133,-0.0064711,0.98716,0.1596,-19.659,0.12932,-0.15743,0.97903,31.846

> view matrix models
> #4.6,0.99816,0.057663,0.018997,-23.664,-0.055078,0.9917,-0.11621,34.174,-0.02554,0.11495,0.99304,-31.635

> fitmap #4.6 inMap #1

Fit molecule final_fit3_3asu_3fold copy.pdb (#4.6) to map
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) using 8321 atoms  
average map value = 0.3473, steps = 84  
shifted from previous position = 4.77  
rotated from previous position = 7.06 degrees  
atoms outside contour = 3713, contour level = 0.3  
  
Position of final_fit3_3asu_3fold copy.pdb (#4.6) relative to
cryosparc_P6_J331_013_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998336 0.00388605 0.00426372 0.49473003  
-0.00386041 0.99997452 -0.00600433 0.81241558  
-0.00428695 0.00598777 0.99997288 1.43539442  
Axis 0.72062399 0.51382294 -0.46549657  
Axis point 0.00000000 -247.36806265 127.30234578  
Rotation angle (degrees) 0.47674284  
Shift along axis 0.10578092  
  

> select subtract #4.6

Nothing selected  

> save /Users/kirti/Desktop/FHV/FHV_Peptide/fit1_3fold_j331.pdb models #4
> relModel #1

> save /Users/kirti/Desktop/FHV/FHV_Peptide/fit1_3fold_j331.mrc models #1

> hide #!1 models

> view clip false

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #4

49926 atoms, 48372 bonds, 66 pseudobonds, 9012 residues, 19 models selected  

> hide #!1 models

> color #4 silver models

> show #!1 models

> select subtract #4

Nothing selected  

> show #2 models

> show #!3 models

> ui tool show "Side View"

> volume #1 level 0.38

> volume #1 level 0.35

> hide #2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #2 models

> select sequence ser268

Nothing selected  

> sel268

Unknown command: sel268  

> sel:268

Unknown command: sel:268  

> sel: 268

Unknown command: sel: 268  

> select : 268

108 atoms, 90 bonds, 18 residues, 6 models selected  

> color sel blue

> select clear

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #2 models

> hide #!1 models

> hide #!3 models

> hide #!4 models

> hide #!4.1 models

> hide #!4.2 models

> hide #!4.3 models

> hide #!4.4 models

> hide #!4.5 models

> hide #!4.6 models

> open
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J138_006_volume_map_sharp.mrc

Opened cryosparc_P2_J138_006_volume_map_sharp.mrc as #5, grid size
480,480,480, pixel 1.1, shown at level 0.174, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.1736

> volume #5 level 0.158

> volume #5 style image region 0,0,239,479,479,239 step 1 showOutlineBox true

> volume #5 region 0,0,0,479,479,479 step 1

> volume #5 region 0,0,0,479,479,479 step 1 imageMode "tilted slab"
> tiltedSlabAxis -0.04185,0.0145,0.999 tiltedSlabOffset 203.2
> tiltedSlabSpacing 1.1 tiltedSlabPlaneCount 96

> volume #5 colorMode opaque8 orthoplanes xyz positionPlanes 239,239,239
> imageMode orthoplanes

> volume #5 imageMode "box faces"

> volume #5 style surface

> volume #5 style mesh

> volume #5 style image region 0,0,239,479,479,239 step 1 colorMode auto8
> imageMode "full region"

> set bgColor white

> set bgColor #ffffff00

> volume #5 color #00fdff color #ffffb3 color #ffffb3

> volume #5 color #ff2600 color #ffffb3 color #ffffb3

> volume #5 color #0096ff color #ffffb3 color #ffffb3

> volume #5 color #00fdff color #ffffb3 color #ffffb3

> volume #5 color #fffc79 color #ffffb3 color #ffffb3

> volume #5 color #fffb00 color #ffffb3 color #ffffb3

> volume #5 color #fffc79 color #ffffb3 color #ffffb3

> volume #5 color #ffd479 color #ffffb3 color #ffffb3

> volume #5 color #00fdff color #ffffb3 color #ffffb3

> volume #5 color #fffc79 color #ffffb3 color #ffffb3

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/kirti/Desktop/movie6.mp4

Movie saved to /Users/kirti/Desktop/movie6.mp4  
  

> volume #5 region 0,0,0,479,479,479 step 1

> volume #5 style surface region 0,0,0,479,479,479 step 1

> set bgColor black

> set bgColor transparent

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/kirti/Desktop/movie7.mp4

Movie saved to /Users/kirti/Desktop/movie7.mp4  
  

> volume #5 level 0.1825

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/kirti/Desktop/movie8.mp4

Movie saved to /Users/kirti/Desktop/movie8.mp4  
  

> close #5

> open
> /Users/kirti/Desktop/FHV/GENOME_WT_C1/CS/cryosparc_P2_J138_006_volume_map_sharp.mrc

Opened cryosparc_P2_J138_006_volume_map_sharp.mrc as #5, grid size
480,480,480, pixel 1.1, shown at level 0.174, step 2, values float32  

> volume #5 color #fffc79

> volume #5 color #fffc7905

> volume #5 color #fffc79d8

> volume #5 color #fffc79d6

> volume #5 color #d6d475

> volume #5 step 1

> volume #5 level 0.1826


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: MNEJ3HN/A
      Chip: Apple M2
      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 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 31 days, 23 hours, 28 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by pett, 7 months ago

Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by pett, 7 months ago

Resolution: → duplicate
Status: accepted → closed

Hi Kirti,

Thanks for reporting this problem. It has been fixed in more recent releases of ChimeraX, so if you upgrade your version you won't run into this problem anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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