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Opened 6 months ago
Closed 6 months ago
#17463 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x000000032930b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003282ff000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003272f3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003262e7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003252db000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003242cf000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003232c3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003222b7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003212ab000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032029f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031f293000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031e287000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d27b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002064c0840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw (total: 55)
{"app_name":"ChimeraX","timestamp":"2025-04-23 11:51:39.00 +0200","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3.2 (24D81)","roots_installed":0,"name":"ChimeraX","incident_id":"43F1B610-AD23-4214-931F-66A738E6F3F1"}
{
"uptime" : 1600000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,10",
"coalitionID" : 108507,
"osVersion" : {
"train" : "macOS 15.3.2",
"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-04-23 11:51:30.4395 +0200",
"codeSigningMonitor" : 2,
"incident" : "43F1B610-AD23-4214-931F-66A738E6F3F1",
"pid" : 90924,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-22 11:04:48.1015 +0200",
"procStartAbsTime" : 37116519207882,
"procExitAbsTime" : 39057523446455,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0C85A65A-8BEB-5896-AB7B-5BA22FAC5202","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "820E7200-C29B-4093-9420-1F4486D6A2A5",
"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" : "A9707307-4948-4C64-A65D-BAB9C1F7E5D1",
"wakeTime" : 66479,
"sleepWakeUUID" : "FB21CE56-5A2A-4CE1-88FA-29E37778D314",
"sip" : "enabled",
"vmRegionInfo" : "0x4a6f3d5e9c38 is not in any region. Bytes after previous region: 81360595098681 Bytes before following region: 23711484830664\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000ca6f3d5e9c38","rawCodes":[1,222579119791160],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000ca6f3d5e9c38 -> 0x00004a6f3d5e9c38 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":90924},
"vmregioninfo" : "0x4a6f3d5e9c38 is not in any region. Bytes after previous region: 81360595098681 Bytes before following region: 23711484830664\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"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":4966480536},{"value":99},{"value":109},{"value":6096993856},{"value":4957446458},{"value":16105234514351846370},{"value":16105234505723378594},{"value":14757395258967641293},{"value":4294967286},{"value":4966480466},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8836358848},{"value":0},{"value":11},{"value":259},{"value":8695580960,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4390323760,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8658571264,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":8658571264,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6924074864},"cpsr":{"value":1073741824},"fp":{"value":4966480608},"sp":{"value":4966480576},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kanwalkayastha/Downloads/cryosparc_P3_J795_005_volume_map.mrc
Opened cryosparc_P3_J795_005_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.1, shown at level 0.0845, step 1, values float32
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
> open
> /Users/kanwalkayastha/Downloads/cryosparc_P3_J795_005_volume_map_sharp.mrc
Opened cryosparc_P3_J795_005_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.1, shown at level 0.0832, step 1, values float32
> hide #!1 models
> hide #!2 models
> show #!1 models
> transparency #1.1 50
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Results/AF3/fold_l145w_cl_gitrimer_cl_scfv16_ccl19/fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif
> format mmcif
Chain information for fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> style stick
Changed 11969 atom styles
> show cartoons
Computing secondary structure
> hide atoms
> select /E:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2243 atoms, 2302 bonds, 297 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #3
9726 atoms, 9908 bonds, 1235 residues, 1 model selected
> view matrix models #3,1,0,0,131.83,0,1,0,104.85,0,0,1,82.879
> view matrix models #3,1,0,0,145.65,0,1,0,108.4,0,0,1,112.05
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.27639,0.9239,0.26462,142.15,0.36416,-0.3555,0.86082,113.84,0.88938,-0.14156,-0.4347,112.25
> view matrix models
> #3,0.26741,0.96269,-0.04158,144.47,0.4657,-0.09134,0.88021,108.31,0.84357,-0.25474,-0.47275,114.92
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.26741,0.96269,-0.04158,142.05,0.4657,-0.09134,0.88021,123.2,0.84357,-0.25474,-0.47275,130.99
> view matrix models
> #3,0.26741,0.96269,-0.04158,136.91,0.4657,-0.09134,0.88021,121.62,0.84357,-0.25474,-0.47275,134.01
> fitmap #3 inMap #1
Fit molecule fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#3) to map
cryosparc_P3_J795_005_volume_map.mrc (#1) using 9726 atoms
average map value = 0.1414, steps = 256
shifted from previous position = 6.05
rotated from previous position = 21 degrees
atoms outside contour = 3211, contour level = 0.084452
Position of fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#3) relative
to cryosparc_P3_J795_005_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32808294 0.86759543 -0.37368403 139.50801987
0.46531493 0.19583518 0.86320948 125.86015578
0.82209708 -0.45708506 -0.33945492 135.99629082
Axis -0.72298525 -0.65480245 -0.22028635
Axis point -0.00000000 39.68690321 52.91964641
Rotation angle (degrees) 114.06472585
Shift along axis -213.23390613
> select clear
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Results/AF3/fold_l145w_cl_gitrimer_cl_scfv16_ccl19/fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif
> format mmcif
Chain information for fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> style stick
Changed 21695 atom styles
> show cartoons
Computing secondary structure
> hide atoms
> select #4/E:61
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
57 atoms, 56 bonds, 8 residues, 1 model selected
> select up
2243 atoms, 2302 bonds, 297 residues, 1 model selected
> select ~sel & ##selected
9726 atoms, 9908 bonds, 1235 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4
2243 atoms, 2302 bonds, 297 residues, 1 model selected
> view matrix models #4,1,0,0,124.19,0,1,0,230.59,0,0,1,105.97
> view matrix models #4,1,0,0,110.61,0,1,0,242.99,0,0,1,128.27
> view matrix models #4,1,0,0,111.48,0,1,0,241.3,0,0,1,134.89
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.9588,-0.25037,0.13424,134.85,-0.15428,0.06211,-0.98607,179.3,0.23855,-0.96616,-0.098177,62.741
> view matrix models
> #4,-0.74404,0.58524,0.32234,162.34,-0.24888,0.20497,-0.9466,185.96,-0.62006,-0.78453,-0.0068525,82.245
> view matrix models
> #4,-0.5766,0.81513,0.055645,156.17,-0.25094,-0.11187,-0.96152,176.71,-0.77754,-0.56837,0.26905,100.89
> view matrix models
> #4,-0.42169,0.062209,0.9046,166.43,0.82533,-0.38683,0.41134,208.62,0.37551,0.92005,0.11178,120.91
> view matrix models
> #4,-0.28391,-0.13022,0.94997,161.14,0.93929,-0.23689,0.24824,204.96,0.19271,0.96277,0.18957,127.44
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.28391,-0.13022,0.94997,142.62,0.93929,-0.23689,0.24824,196.4,0.19271,0.96277,0.18957,147.37
> fitmap #4 inMap #1
Fit molecule fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#4) to map
cryosparc_P3_J795_005_volume_map.mrc (#1) using 2243 atoms
average map value = 0.1064, steps = 164
shifted from previous position = 4.11
rotated from previous position = 29.1 degrees
atoms outside contour = 1038, contour level = 0.084452
Position of fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#4) relative
to cryosparc_P3_J795_005_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.15035846 0.25651395 0.95477376 154.75125418
0.82134960 -0.50510670 0.26505104 185.62003692
0.55025191 0.82405571 -0.13474056 138.26208365
Axis 0.62688406 0.45364254 0.63342310
Axis point -2.86855852 40.74612527 0.00000000
Rotation angle (degrees) 153.52164522
Shift along axis 268.79463681
> select clear
> volume #1 level 0.1322
> ui mousemode right "rotate selected models"
> select add #4
2243 atoms, 2302 bonds, 297 residues, 1 model selected
> view matrix models
> #4,-0.77435,0.27069,-0.57193,103.93,0.43305,-0.43231,-0.79093,151.65,-0.46135,-0.86014,0.21754,118.61
> view matrix models
> #4,-0.66866,0.74343,0.014313,138.29,0.0036469,0.022528,-0.99974,161.53,-0.74356,-0.66843,-0.017775,118.36
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.66866,0.74343,0.014313,126.78,0.0036469,0.022528,-0.99974,150.58,-0.74356,-0.66843,-0.017775,86.276
> view matrix models
> #4,-0.66866,0.74343,0.014313,129.65,0.0036469,0.022528,-0.99974,146.88,-0.74356,-0.66843,-0.017775,86.767
> fitmap #4 inMap #1
Fit molecule fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#4) to map
cryosparc_P3_J795_005_volume_map.mrc (#1) using 2243 atoms
average map value = 0.1388, steps = 188
shifted from previous position = 2.33
rotated from previous position = 36.5 degrees
atoms outside contour = 1032, contour level = 0.13216
Position of fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#4) relative
to cryosparc_P3_J795_005_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.44677301 0.86473595 -0.22940275 129.05694150
-0.32353307 -0.39522849 -0.85972135 138.20697478
-0.83409846 -0.30988092 0.45634809 110.32756325
Axis 0.38124898 0.41928460 -0.82392332
Axis point 124.02001324 65.41528074 0.00000000
Rotation angle (degrees) 133.85428516
Shift along axis 16.24943156
> select clear
> select #3/F:19
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
616 atoms, 628 bonds, 77 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> transparency #2.1 50
> volume #2 level 0.1381
> hide #!2 models
> select #3/B:87
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> select clear
> hide #!2 models
> select #3/B:155
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #3/B:174
20 atoms, 19 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!2 models
> volume #2 level 0.1703
> fitmap #3 inMap #2
Fit molecule fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#3) to map
cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) using 9110 atoms
average map value = 0.1795, steps = 60
shifted from previous position = 0.0838
rotated from previous position = 0.262 degrees
atoms outside contour = 5360, contour level = 0.1703
Position of fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#3) relative
to cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.33138286 0.86612058 -0.37419319 139.56509332
0.46729909 0.19387235 0.86258048 125.90575591
0.81964441 -0.46070452 -0.34049138 136.09742703
Axis -0.72456955 -0.65369015 -0.21837617
Axis point 0.00000000 40.08501631 53.02797708
Rotation angle (degrees) 114.05529445
Shift along axis -213.14840468
> fitmap #3 inMap #2
Fit molecule fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#3) to map
cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) using 9110 atoms
average map value = 0.1795, steps = 44
shifted from previous position = 0.0175
rotated from previous position = 0.0146 degrees
atoms outside contour = 5358, contour level = 0.1703
Position of fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#3) relative
to cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.33125501 0.86621642 -0.37408453 139.55407732
0.46741829 0.19375005 0.86254336 125.92158481
0.81962812 -0.46057576 -0.34070472 136.09460454
Axis -0.72456084 -0.65369582 -0.21838812
Axis point -0.00000000 40.08325467 53.01952043
Rotation angle (degrees) 114.06983588
Shift along axis -213.15127756
> select add #3
9110 atoms, 9280 bonds, 1158 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #4 models
> fitmap #3 inMap #2
Fit molecule fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#3) to map
cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) using 9110 atoms
average map value = 0.1794, steps = 40
shifted from previous position = 0.0185
rotated from previous position = 0.00852 degrees
atoms outside contour = 5360, contour level = 0.1703
Position of fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#3) relative
to cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.33130218 0.86617039 -0.37414934 139.56053039
0.46733705 0.19384073 0.86256701 125.91062793
0.81965538 -0.46062418 -0.34057366 136.07949848
Axis -0.72455265 -0.65370325 -0.21839304
Axis point 0.00000000 40.07364371 53.01537515
Rotation angle (degrees) 114.06139906
Shift along axis -213.14595440
> hide #3 models
> show #4 models
> fitmap #4 inMap #2
Fit molecule fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#4) to map
cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) using 2243 atoms
average map value = 0.1738, steps = 44
shifted from previous position = 0.0127
rotated from previous position = 0.0686 degrees
atoms outside contour = 1154, contour level = 0.1703
Position of fold_l145w_cl_gitrimer_cl_scfv16_ccl19_model_0.cif (#4) relative
to cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.44695590 0.86441605 -0.23025054 129.02254933
-0.32248987 -0.39578340 -0.85985801 138.19431572
-0.83440440 -0.31006515 0.45566314 110.31288541
Axis 0.38157803 0.41930671 -0.82375973
Axis point 123.97722027 65.46533369 0.00000000
Rotation angle (degrees) 133.91083517
Shift along axis 16.30666167
> show #3 models
> hide #!2 models
> select #3/B:25
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/B:29
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!2 models
> hide #!2 models
> select #3/B:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> select clear
> hide #!2 models
> select #3/B:22
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> hide #!2 models
> select #3/B:147
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #3/B:148
21 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!2 models
> select #3/A:282
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
105 atoms, 107 bonds, 14 residues, 1 model selected
> select up
3089 atoms, 3155 bonds, 387 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> hide #4 models
> select #3/B:350
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
161 atoms, 162 bonds, 20 residues, 1 model selected
> select up
2835 atoms, 2883 bonds, 355 residues, 1 model selected
> save "/Users/kanwalkayastha/OneDrive - Universiteit
> Leiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gai_J795sharp.pdb" models #3
> selectedOnly true
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gai_J795sharp.pdb
Summary of feedback from opening
/Users/kanwalkayastha/Library/CloudStorage/OneDrive-
UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gai_J795sharp.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 6 LYS A 8 1 3
Start residue of secondary structure not found: HELIX 2 2 SER A 9 PHE A 19 1
11
Start residue of secondary structure not found: HELIX 3 3 TYR A 41 LEU A 43 1
3
Start residue of secondary structure not found: HELIX 4 4 LYS A 51 PHE A 86 1
36
Start residue of secondary structure not found: HELIX 5 5 MET A 92 PHE A 107 1
16
55 messages similar to the above omitted
Chain information for Gai_J795sharp.pdb #5
---
Chain | Description
B | No description available
> hide #3 models
> show #3 models
> select #3/C:7
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
197 atoms, 196 bonds, 25 residues, 1 model selected
> select up
2638 atoms, 2686 bonds, 345 residues, 1 model selected
> save "/Users/kanwalkayastha/OneDrive - Universiteit
> Leiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gb1_J795sharp.pdb" models #3
> selectedOnly true
> select #3/D:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
164 atoms, 163 bonds, 22 residues, 1 model selected
> select up
548 atoms, 556 bonds, 71 residues, 1 model selected
> save "/Users/kanwalkayastha/OneDrive - Universiteit
> Leiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gy2_J795sharp.pdb" models #3
> selectedOnly true
> hide #5 models
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gb1_J795sharp.pdb
Summary of feedback from opening
/Users/kanwalkayastha/Library/CloudStorage/OneDrive-
UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gb1_J795sharp.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 6 LYS A 8 1 3
Start residue of secondary structure not found: HELIX 2 2 SER A 9 PHE A 19 1
11
Start residue of secondary structure not found: HELIX 3 3 TYR A 41 LEU A 43 1
3
Start residue of secondary structure not found: HELIX 4 4 LYS A 51 PHE A 86 1
36
Start residue of secondary structure not found: HELIX 5 5 MET A 92 PHE A 107 1
16
54 messages similar to the above omitted
Chain information for Gb1_J795sharp.pdb #6
---
Chain | Description
C | No description available
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gy2_J795sharp.pdb
Summary of feedback from opening
/Users/kanwalkayastha/Library/CloudStorage/OneDrive-
UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gy2_J795sharp.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 6 LYS A 8 1 3
Start residue of secondary structure not found: HELIX 2 2 SER A 9 PHE A 19 1
11
Start residue of secondary structure not found: HELIX 3 3 TYR A 41 LEU A 43 1
3
Start residue of secondary structure not found: HELIX 4 4 LYS A 51 PHE A 86 1
36
Start residue of secondary structure not found: HELIX 5 5 MET A 92 PHE A 107 1
16
81 messages similar to the above omitted
Chain information for Gy2_J795sharp.pdb #7
---
Chain | Description
D | No description available
> hide #3 models
> hide #6 models
> show #6 models
> show #4 models
> save "/Users/kanwalkayastha/OneDrive - Universiteit
> Leiden/Projects/CCR7/L145W/Complex/Chimerax/C19/scFv16_J795sharp.pdb" models
> #4
> hide #4 models
> show #3 models
> select clear
> show #3,6-7 cartoons
> select #3/A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
141 atoms, 142 bonds, 18 residues, 1 model selected
> select up
3089 atoms, 3155 bonds, 387 residues, 1 model selected
> save "/Users/kanwalkayastha/OneDrive - Universiteit
> Leiden/Projects/CCR7/L145W/Complex/Chimerax/C19/CCR7_J795sharp.pdb" models
> #3 selectedOnly true
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/scFv16_J795sharp.pdb
Chain information for scFv16_J795sharp.pdb #8
---
Chain | Description
E | No description available
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/CCR7_J795sharp.pdb
Summary of feedback from opening
/Users/kanwalkayastha/Library/CloudStorage/OneDrive-
UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/CCR7_J795sharp.pdb
---
warnings | Start residue of secondary structure not found: HELIX 24 24 ALA B 8 LYS B 30 1 23
Start residue of secondary structure not found: HELIX 25 25 ALA B 31 ARG B 33
1 3
Start residue of secondary structure not found: HELIX 26 26 LYS B 47 HIS B 58
1 12
Start residue of secondary structure not found: HELIX 27 27 GLU B 64 CYS B 67
1 4
Start residue of secondary structure not found: HELIX 28 28 LYS B 68 TYR B 70
1 3
60 messages similar to the above omitted
Chain information for CCR7_J795sharp.pdb #9
---
Chain | Description
A | No description available
> hide #3 models
> select add #3
9110 atoms, 9280 bonds, 1158 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #6 models
> show #6 models
> hide #7 models
> show #7 models
> hide #8 models
> show #8 models
> hide #9 models
> show #9 models
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/Phenix/C19/RebuildModel_9/Gai_J795sharp_rebuilt.pdb
Chain information for Gai_J795sharp_rebuilt.pdb #10
---
Chain | Description
B | No description available
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/Phenix/C19/RebuildModel_10/Gb1_J795sharp_rebuilt.pdb
Chain information for Gb1_J795sharp_rebuilt.pdb #11
---
Chain | Description
C | No description available
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/Phenix/C19/RebuildModel_11/Gy2_J795sharp_rebuilt.pdb
Chain information for Gy2_J795sharp_rebuilt.pdb #12
---
Chain | Description
D | No description available
> hide #9 models
> hide #7 models
> hide #8 models
> hide #11 models
> hide #12 models
> hide #6 models
> show #5 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #!2 models
> select #5/B:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #10/B:193
18 atoms, 16 bonds, 2 residues, 2 models selected
> show sel atoms
> show #!2 models
> hide sel atoms
> select #10/B:192
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #5/B:192
22 atoms, 22 bonds, 2 residues, 2 models selected
> show sel atoms
> hide #5 models
> select clear
> show #10 atoms
> ui tool show "Side View"
Drag select of 2 cryosparc_P3_J795_005_volume_map_sharp.mrc , 1 atoms
> select clear
> hide #!2 models
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gai_J795sharp_rebuilt-
> coot-0.pdb
Chain information for Gai_J795sharp_rebuilt-coot-0.pdb #13
---
Chain | Description
B | No description available
> show #!2 models
> show #10,13 atoms
> hide #10 models
> open pubchem
'pubchem' has no suffix
> open pubchem 135398619
'pubchem' has no suffix
> open pubchem135398619
'pubchem135398619' has no suffix
> open pubchem:135398619
Fetching url
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/135398619/SDF?record_type=3d
failed:
HTTP Error 404: PUGREST.NotFound
> open /Users/kanwalkayastha/Downloads/GDP.cif
Summary of feedback from opening /Users/kanwalkayastha/Downloads/GDP.cif
---
warning | No mmCIF models found.
> open /Users/kanwalkayastha/Downloads/GDP_ideal.sdf
> hide #14 models
> show #14 models
> hide #14 models
> show #14 models
> view #14 clip false
> select add #14
43 atoms, 45 bonds, 1 residue, 1 model selected
> view matrix models #14,1,0,0,28.041,0,1,0,103.08,0,0,1,84.918
> view matrix models #14,1,0,0,92.824,0,1,0,88.407,0,0,1,108.54
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.87471,-0.15305,-0.45985,93.94,0.47303,-0.06306,-0.87879,89.047,0.1055,-0.9862,0.12756,109.31
> view matrix models
> #14,-0.90698,-0.41545,-0.069264,94.058,0.083161,-0.015427,-0.99642,89.23,0.41289,-0.90949,0.048541,109.12
> view matrix models
> #14,-0.71131,-0.63701,0.29707,94.04,-0.56369,0.26452,-0.78249,89.324,0.41987,-0.72405,-0.54723,109.11
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.71131,-0.63701,0.29707,107.23,-0.56369,0.26452,-0.78249,102.09,0.41987,-0.72405,-0.54723,108.79
> view matrix models
> #14,-0.71131,-0.63701,0.29707,115.38,-0.56369,0.26452,-0.78249,105.32,0.41987,-0.72405,-0.54723,118.32
> view matrix models
> #14,-0.71131,-0.63701,0.29707,99.018,-0.56369,0.26452,-0.78249,109.29,0.41987,-0.72405,-0.54723,115.25
> view matrix models
> #14,-0.71131,-0.63701,0.29707,122.74,-0.56369,0.26452,-0.78249,105.61,0.41987,-0.72405,-0.54723,113.01
> view matrix models
> #14,-0.71131,-0.63701,0.29707,121.92,-0.56369,0.26452,-0.78249,111.51,0.41987,-0.72405,-0.54723,116.66
> view matrix models
> #14,-0.71131,-0.63701,0.29707,123.63,-0.56369,0.26452,-0.78249,112.54,0.41987,-0.72405,-0.54723,114.16
> view matrix models
> #14,-0.71131,-0.63701,0.29707,123.89,-0.56369,0.26452,-0.78249,112.72,0.41987,-0.72405,-0.54723,114.79
> view matrix models
> #14,-0.71131,-0.63701,0.29707,123.46,-0.56369,0.26452,-0.78249,112.54,0.41987,-0.72405,-0.54723,114.28
> view matrix models
> #14,-0.71131,-0.63701,0.29707,123.2,-0.56369,0.26452,-0.78249,112.42,0.41987,-0.72405,-0.54723,114.64
> view matrix models
> #14,-0.71131,-0.63701,0.29707,123.65,-0.56369,0.26452,-0.78249,112.33,0.41987,-0.72405,-0.54723,115.24
> select clear
> save /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gai_J795sharp_rebuilt-
> coot-0+GDP.pdb models #13-14
> save /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gai_J795sharp_rebuilt-
> coot-0+GDP.pdb models #13-14 relModel #13
> save /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/Gai_J795sharp_rebuilt-
> coot-0+GDP.pdb models #14 relModel #13
> open
> /Users/kanwalkayastha/Downloads/cryosparc_P3_J767_006_volume_map_sharp.mrc
Opened cryosparc_P3_J767_006_volume_map_sharp.mrc as #15, grid size
256,256,256, pixel 1.1, shown at level 0.0734, step 1, values float32
> ui tool show Matchmaker
> select add #15
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.94335,0.2747,-0.18611,253.56,0.28682,0.9571,-0.04116,-26.338,0.16682,-0.09221,-0.98167,300.89
> view matrix models
> #15,0.52604,0.75503,-0.39142,19.526,0.78472,-0.60835,-0.11887,138.12,-0.32787,-0.24463,-0.9125,378.37
> volume #15 flipNormals
Missing "flipNormals" keyword's argument
> volume flip #15
Opened cryosparc_P3_J767_006_volume_map_sharp.mrc z flip as #16, grid size
256,256,256, pixel 1.1, shown at step 1, values float32
> close #15
> select add #16
2 models selected
> view matrix models
> #16,-0.63359,0.70427,0.32028,95.435,-0.77353,-0.56863,-0.27985,363.3,-0.01497,-0.42505,0.90504,136.33
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.63359,0.70427,0.32028,88.928,-0.77353,-0.56863,-0.27985,372.23,-0.01497,-0.42505,0.90504,88.231
> view matrix models
> #16,-0.63359,0.70427,0.32028,84.441,-0.77353,-0.56863,-0.27985,370.32,-0.01497,-0.42505,0.90504,87.456
> view matrix models
> #16,-0.63359,0.70427,0.32028,84.874,-0.77353,-0.56863,-0.27985,372.63,-0.01497,-0.42505,0.90504,86.597
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.66737,0.73784,-0.10099,136.89,-0.73716,-0.67377,-0.051274,354.17,-0.10588,0.040227,0.99357,22.655
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.66737,0.73784,-0.10099,139.17,-0.73716,-0.67377,-0.051274,355.51,-0.10588,0.040227,0.99357,11.938
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 2 maps.
> hide #14 models
> hide #13 models
> fitmap #16 inMap #2
Fit map cryosparc_P3_J767_006_volume_map_sharp.mrc z flip in map
cryosparc_P3_J795_005_volume_map_sharp.mrc using 167555 points
correlation = 0.8927, correlation about mean = 0.7043, overlap = 3940
steps = 224, shift = 10.6, angle = 22.4 degrees
Position of cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.85262301 0.50227604 0.14405825 174.28213786
-0.51065228 -0.85939522 -0.02596355 341.91862778
0.11076210 -0.09570079 0.98922855 -1.00250122
Axis -0.06864767 0.03277593 -0.99710242
Axis point 133.96130261 147.09247430 0.00000000
Rotation angle (degrees) 149.47355826
Shift along axis 0.24223455
> transparency sel 50
> select subtract #16
Nothing selected
> volume #16 level 0.1221
> hide #!16 models
> show #!16 models
> volume #16 level 0.1587
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #16
Fit map cryosparc_P3_J795_005_volume_map_sharp.mrc in map
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip using 40651 points
correlation = 0.927, correlation about mean = 0.6585, overlap = 2766
steps = 44, shift = 0.141, angle = 0.418 degrees
Position of cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) relative to
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) coordinates:
Matrix rotation and translation
-0.85118844 -0.51145378 0.11786968 322.50420712
0.50284658 -0.85901503 -0.09611705 206.13633165
0.15041125 -0.02254335 0.98836645 -16.55467265
Axis 0.07230931 -0.03198234 0.99686935
Axis point 133.58598685 147.02235497 0.00000000
Rotation angle (degrees) 149.41987026
Shift along axis 0.22448932
> hide #!2 models
> volume #16 level 0.1374
> volume #16 level 0.116
> show #9 models
> hide #9 models
> show #10 models
> show #11 models
> show #12 models
> hide #12 models
> hide #11 models
> fitmap #10 inMap #16
Fit molecule Gai_J795sharp_rebuilt.pdb (#10) to map
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) using 2834 atoms
average map value = 0.1685, steps = 60
shifted from previous position = 0.533
rotated from previous position = 1.25 degrees
atoms outside contour = 1001, contour level = 0.11605
Position of Gai_J795sharp_rebuilt.pdb (#10) relative to
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) coordinates:
Matrix rotation and translation
-0.85447177 -0.50270807 0.13100607 320.01235528
0.49397274 -0.86430425 -0.09470529 207.97648287
0.16083821 -0.01620957 0.98684766 -18.63297636
Axis 0.07847908 -0.02982582 0.99646950
Axis point 132.76940381 146.74171815 0.00000000
Rotation angle (degrees) 149.99298468
Shift along axis 0.34401270
> hide #10 models
> show #11 models
> fitmap #11 inMap #16
Fit molecule Gb1_J795sharp_rebuilt.pdb (#11) to map
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) using 2637 atoms
average map value = 0.2732, steps = 48
shifted from previous position = 0.469
rotated from previous position = 0.859 degrees
atoms outside contour = 417, contour level = 0.11605
Position of Gb1_J795sharp_rebuilt.pdb (#11) relative to
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) coordinates:
Matrix rotation and translation
-0.84618358 -0.51976159 0.11756371 323.36355585
0.51000074 -0.85384708 -0.10413644 205.20911341
0.15450755 -0.02816096 0.98759018 -16.18883974
Axis 0.07353258 -0.03575596 0.99665163
Axis point 133.62529366 147.46040503 0.00000000
Rotation angle (degrees) 148.89480441
Shift along axis 0.30567377
> hide #11 models
> show #12 models
> fitmap #12 inMap #16
Fit molecule Gy2_J795sharp_rebuilt.pdb (#12) to map
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) using 547 atoms
average map value = 0.1798, steps = 48
shifted from previous position = 0.991
rotated from previous position = 1.04 degrees
atoms outside contour = 178, contour level = 0.11605
Position of Gy2_J795sharp_rebuilt.pdb (#12) relative to
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) coordinates:
Matrix rotation and translation
-0.85943391 -0.49716885 0.11914902 322.50196030
0.48786698 -0.86721933 -0.09958131 209.89901794
0.15283706 -0.02745468 0.98786997 -15.91547804
Axis 0.07298439 -0.03408867 0.99675034
Axis point 134.00028465 147.43367751 0.00000000
Rotation angle (degrees) 150.38802056
Shift along axis 0.51867267
> hide #12 models
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/Phenix/C19/RebuildModel_13/scFv16_J795sharp_rebuilt.pdb
Chain information for scFv16_J795sharp_rebuilt.pdb #15
---
Chain | Description
E | No description available
> fitmap #15 inMap #16
Fit molecule scFv16_J795sharp_rebuilt.pdb (#15) to map
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) using 2242 atoms
average map value = 0.1754, steps = 76
shifted from previous position = 0.407
rotated from previous position = 0.556 degrees
atoms outside contour = 838, contour level = 0.11605
Position of scFv16_J795sharp_rebuilt.pdb (#15) relative to
cryosparc_P3_J767_006_volume_map_sharp.mrc z flip (#16) coordinates:
Matrix rotation and translation
-0.84753930 -0.51865205 0.11259302 323.68773144
0.51028355 -0.85465629 -0.09577744 204.14699239
0.14590350 -0.02372078 0.98901440 -15.99082693
Axis 0.06982280 -0.03227781 0.99703707
Axis point 133.95019535 146.92844542 0.00000000
Rotation angle (degrees) 148.93590357
Shift along axis 0.06791993
> hide #15 models
> show #14 models
> hide #14 models
> show #14 models
> fitmap #14 inMap #16
Fit molecule GDP (#14) to map cryosparc_P3_J767_006_volume_map_sharp.mrc z
flip (#16) using 43 atoms
average map value = 0.2764, steps = 72
shifted from previous position = 1.61
rotated from previous position = 16.1 degrees
atoms outside contour = 4, contour level = 0.11605
Position of GDP (#14) relative to cryosparc_P3_J767_006_volume_map_sharp.mrc z
flip (#16) coordinates:
Matrix rotation and translation
0.98706123 0.14284832 0.07283190 171.78575886
0.04044822 -0.66136066 0.74897664 161.32281526
0.15515821 -0.73633988 -0.65858143 113.70542016
Axis -0.99611028 -0.05521118 -0.06867344
Axis point 0.00000000 98.53884782 17.03154447
Rotation angle (degrees) 131.79292673
Shift along axis -187.83292580
> hide #14 models
> show #!2 models
> hide #!16 models
> show #14 models
> fitmap #14 inMap #2
Fit molecule GDP (#14) to map cryosparc_P3_J795_005_volume_map_sharp.mrc (#2)
using 43 atoms
average map value = 0.3251, steps = 52
shifted from previous position = 0.661
rotated from previous position = 4.8 degrees
atoms outside contour = 9, contour level = 0.1703
Position of GDP (#14) relative to cryosparc_P3_J795_005_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.76053641 -0.61609390 0.20496994 124.84284271
-0.55566725 0.45428221 -0.69632003 112.97343400
0.33588432 -0.64347182 -0.68784136 115.55032925
Axis 0.34413733 -0.85248914 0.39348667
Axis point 82.54862537 0.00000000 86.72439317
Rotation angle (degrees) 175.59628914
Shift along axis -7.87802940
> fitmap #14 inMap #2
Fit molecule GDP (#14) to map cryosparc_P3_J795_005_volume_map_sharp.mrc (#2)
using 43 atoms
average map value = 0.325, steps = 36
shifted from previous position = 0.0176
rotated from previous position = 0.226 degrees
atoms outside contour = 9, contour level = 0.1703
Position of GDP (#14) relative to cryosparc_P3_J795_005_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.76236392 -0.61427100 0.20364772 124.85482925
-0.55266716 0.45426503 -0.69871475 112.96117379
0.33669017 -0.64522433 -0.68580267 115.54143143
Axis 0.34274266 -0.85247631 0.39472979
Axis point 82.41619284 0.00000000 86.84702170
Rotation angle (degrees) 175.52449276
Shift along axis -7.89600346
> fitmap #14 inMap #2
Fit molecule GDP (#14) to map cryosparc_P3_J795_005_volume_map_sharp.mrc (#2)
using 43 atoms
average map value = 0.3252, steps = 28
shifted from previous position = 0.0248
rotated from previous position = 0.247 degrees
atoms outside contour = 9, contour level = 0.1703
Position of GDP (#14) relative to cryosparc_P3_J795_005_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.76067416 -0.61627459 0.20391286 124.83466739
-0.55536275 0.45521242 -0.69595537 112.97180939
0.33607594 -0.64264087 -0.68852427 115.55309715
Axis 0.34400195 -0.85275791 0.39302240
Axis point 82.50327783 0.00000000 86.71270021
Rotation angle (degrees) 175.55560519
Shift along axis -7.97927898
> fitmap #14 inMap #2
Fit molecule GDP (#14) to map cryosparc_P3_J795_005_volume_map_sharp.mrc (#2)
using 43 atoms
average map value = 0.3251, steps = 36
shifted from previous position = 0.0097
rotated from previous position = 0.113 degrees
atoms outside contour = 9, contour level = 0.1703
Position of GDP (#14) relative to cryosparc_P3_J795_005_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.76087193 -0.61562037 0.20514742 124.84269328
-0.55524188 0.45404300 -0.69681520 112.97723797
0.33582788 -0.64409356 -0.68728678 115.55239285
Axis 0.34389961 -0.85241970 0.39384479
Axis point 82.53982357 0.00000000 86.74729560
Rotation angle (degrees) 175.60381445
Shift along axis -7.86096085
> fitmap #14 inMap #2
Fit molecule GDP (#14) to map cryosparc_P3_J795_005_volume_map_sharp.mrc (#2)
using 43 atoms
average map value = 0.325, steps = 36
shifted from previous position = 0.0207
rotated from previous position = 0.158 degrees
atoms outside contour = 9, contour level = 0.1703
Position of GDP (#14) relative to cryosparc_P3_J795_005_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.76217979 -0.61455962 0.20346608 124.85302756
-0.55296357 0.45461280 -0.69825389 112.96040773
0.33662036 -0.64470433 -0.68632577 115.54165820
Axis 0.34287431 -0.85257810 0.39439548
Axis point 82.41925778 0.00000000 86.82370049
Rotation angle (degrees) 175.52125897
Shift along axis -7.92956619
> fitmap #14 inMap #2
Fit molecule GDP (#14) to map cryosparc_P3_J795_005_volume_map_sharp.mrc (#2)
using 43 atoms
average map value = 0.3252, steps = 28
shifted from previous position = 0.0233
rotated from previous position = 0.206 degrees
atoms outside contour = 9, contour level = 0.1703
Position of GDP (#14) relative to cryosparc_P3_J795_005_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.76073321 -0.61626422 0.20372382 124.83449833
-0.55524470 0.45533682 -0.69596818 112.97090249
0.33613733 -0.64256268 -0.68856728 115.55271929
Axis 0.34395180 -0.85279354 0.39298898
Axis point 82.49372352 0.00000000 86.71436830
Rotation angle (degrees) 175.54735287
Shift along axis -7.99285942
> fitmap #14 inMap #2
Fit molecule GDP (#14) to map cryosparc_P3_J795_005_volume_map_sharp.mrc (#2)
using 43 atoms
average map value = 0.3251, steps = 36
shifted from previous position = 0.0102
rotated from previous position = 0.123 degrees
atoms outside contour = 9, contour level = 0.1703
Position of GDP (#14) relative to cryosparc_P3_J795_005_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.76095640 -0.61554974 0.20504602 124.84275446
-0.55509621 0.45407409 -0.69691099 112.97685922
0.33587730 -0.64413914 -0.68721991 115.55217516
Axis 0.34383378 -0.85242829 0.39388368
Axis point 82.53210604 0.00000000 86.75270301
Rotation angle (degrees) 175.59877524
Shift along axis -7.86539884
> show #10 models
> show #!16 models
> volume #16 level 0.1465
> hide #!2 models
> volume #16 level 0.1374
> volume #16 level 0.1252
> hide #!16 models
> show #!2 models
> select #10/B:177@NH2
1 atom, 1 residue, 1 model selected
> select add #14/?:1@H15
2 atoms, 2 residues, 4 models selected
> select clear
> select #14/?:1@H15
1 atom, 1 residue, 1 model selected
> select add #10/B:177@NH2
2 atoms, 2 residues, 2 models selected
> ui mousemode right distance
> distance #14/?:1@H15 #10/B:177@NH2
Distance between GDP #14/? UNL 1 H15 and Gai_J795sharp_rebuilt.pdb #10/B ARG
177 NH2: 3.649Å
> distance #10/B:177@NH1 #14/?:1@H15
Distance between Gai_J795sharp_rebuilt.pdb #10/B ARG 177 NH1 and GDP #14/? UNL
1 H15: 2.613Å
> select clear
> hide #10 models
> show #13 models
> show #15 models
> hide #15 models
> show #15 models
> show #12 models
> show #11 models
> show #10 models
> hide #10 models
> show #9 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> fitmap #9 inMap #2
Fit molecule CCR7_J795sharp.pdb (#9) to map
cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) using 3089 atoms
average map value = 0.09722, steps = 204
shifted from previous position = 3.62
rotated from previous position = 16.4 degrees
atoms outside contour = 2756, contour level = 0.1703
Position of CCR7_J795sharp.pdb (#9) relative to
cryosparc_P3_J795_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.95890765 -0.11033558 0.26138511 -22.67429254
0.09509959 0.99298389 0.07027840 -26.11549665
-0.26730541 -0.04253288 0.96267272 54.20746294
Axis -0.19507026 0.91419753 0.35523299
Axis point 186.81671933 0.00000000 116.26193846
Rotation angle (degrees) 16.80740516
Shift along axis -0.19536329
> open /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Coot/CCR7_J795sharp_rebuilt-
> coot-0.pdb
Chain information for CCR7_J795sharp_rebuilt-coot-0.pdb #18
---
Chain | Description
A | No description available
> hide #9 models
> hide #!17 models
> hide #17.1 models
> molmap #18 20
Opened CCR7_J795sharp_rebuilt-coot-0.pdb map 20 as #19, grid size 28,29,35,
pixel 6.67, shown at level 0.0214, step 1, values float32
> volume #2 level 0.09506
> hide #!19 models
> volume #2 level 0.1757
> select #18/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
37 atoms, 36 bonds, 5 residues, 1 model selected
> select up
3088 atoms, 3155 bonds, 387 residues, 1 model selected
> select down
37 atoms, 36 bonds, 5 residues, 1 model selected
> select add #18/A:9
43 atoms, 41 bonds, 6 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #9/A #18/A
Alignment identifier is 1
> select #3/A:24 #9/A:24 #18/A:24
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #3/A:1-24 #9/A:1-24 #18/A:1-24
537 atoms, 540 bonds, 72 residues, 3 models selected
. [ID: 1] region 3 chains [1-24] RMSD: 4.462
> delete atoms (#18 & sel)
> delete bonds (#18 & sel)
> select #3/A:387 #9/A:387 #18/A:387
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #3/A:347-387 #9/A:347-387 #18/A:347-387
995 atoms, 1010 bonds, 123 residues, 3 models selected
. [ID: 1] region 3 chains [347-387] RMSD: 12.490
> select #3/A:387 #9/A:387 #18/A:387
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #3/A:387 #9/A:387 #18/A:387
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #3/A:346-387 #9/A:346-387 #18/A:346-387
1013 atoms, 1028 bonds, 126 residues, 3 models selected
. [ID: 1] region 3 chains [346-387] RMSD: 12.405
> select #3/A:345 #9/A:345 #18/A:345
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #3/A:345-387 #9/A:345-387 #18/A:345-387
1025 atoms, 1040 bonds, 129 residues, 3 models selected
. [ID: 1] region 3 chains [345-387] RMSD: 12.321
> delete atoms (#18 & sel)
> delete bonds (#18 & sel)
> select clear
> molmap #18 20
Opened CCR7_J795sharp_rebuilt-coot-0.pdb map 20 as #19, grid size 26,27,28,
pixel 6.67, shown at level 0.0287, step 1, values float32
> hide #18 models
> volume resample #19 onGrid #2
Opened CCR7_J795sharp_rebuilt-coot-0.pdb map 20 resampled as #20, grid size
256,256,256, pixel 1.1, shown at step 1, values float32
> save /Users/kanwalkayastha/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/Projects/CCR7/L145W/Complex/Chimerax/C19/CCR7_locref.mrc
> models #20
> transparency #2.1#20.1 0
> transparency #2.1#20.1 50
> show #18 models
> volume #2 level 0.1461
> open /Users/kanwalkayastha/Downloads/cryosparc_P3_J802_mask.mrc
Opened cryosparc_P3_J802_mask.mrc as #21, grid size 256,256,256, pixel 1.1,
shown at level 0.893, step 1, values float32
> volume #21 style mesh
> volume #21 level 1
> open
> /Users/kanwalkayastha/Downloads/cryosparc_P3_J798_005_volume_map_sharp.mrc
Opened cryosparc_P3_J798_005_volume_map_sharp.mrc as #22, grid size
256,256,256, pixel 1.1, shown at level 0.0859, step 1, values float32
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> show #!22 models
> volume #22 level 0.146
> transparency #2.1#22.1 0
> transparency #2.1#22.1 50
> volume #2 level 0.1649
> volume #22 level 0.165
===== Log before crash end =====
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Mac16,10
Model Number: MU9E3FN/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 32 days, 16 hours, 3 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG HDR 4K:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.0
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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