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Opened 19 months ago
Closed 19 months ago
#14898 closed defect (can't reproduce)
Crash deleting hydrogens
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Calculated structure H bonds
Deleted hydrogens
Fatal Python error: Segmentation fault
Thread 0x00000003730db000 (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 0x000000029e73f000 (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 0x000000029d733000 (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 0x000000029c727000 (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 0x000000029b71b000 (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 0x000000029a70f000 (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 0x0000000299703000 (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 0x00000002986f7000 (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 0x00000002976eb000 (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 0x00000002966df000 (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 0x00000002956d3000 (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 0x00000002946c7000 (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 0x000000028d793000 (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 0x000000028c787000 (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 0x00000001dbfd1000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 811 in delete
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/delete.py", line 50 in delete_atoms
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/delete.py", line 33 in delete
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
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, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 67)
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{
"uptime" : 1200000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 537,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-04-04 01:52:18.4467 -0400",
"codeSigningMonitor" : 1,
"incident" : "9CA20702-0DCB-4538-A868-093315978509",
"pid" : 62225,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-03 20:08:26.0474 -0400",
"procStartAbsTime" : 30936620527144,
"procExitAbsTime" : 31085753381199,
"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":"165C76E9-F318-5D41-8780-1155C9E39A80","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5D245DA2-71E6-C254-45C1-E0901EC3DAD5",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 515,
"sleepWakeUUID" : "663B6F64-08DD-42BD-9667-DA1BE65CE3D5",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4335157248\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102654000-102658000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":62225},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4335157248\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102654000-102658000 [ 16K] r-x\/r-x SM=COW ...acOS\/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":6131692568},{"value":104},{"value":103},{"value":101},{"value":0},{"value":5262313689581168102},{"value":5262313686287267302},{"value":14757395258967641293},{"value":4294967286},{"value":6131692498},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8137225024},{"value":0},{"value":11},{"value":7985762304,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":7985762528,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4358358576,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":17},{"value":6259373387},{"value":6131694136},{"value":105562142408400}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6534667456},"cpsr":{"value":1073745920},"fp":{"value":6131692640},"sp":{"value":6131692608},"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
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/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/fig4a_new_fignumber.cxs
Opened myo1c_adp_a_best.pdb map 20 as #2300.6, grid size 88,87,81, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_b_best.pdb map 20 as #2301.6, grid size 88,87,81, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_a_best.pdb map 20 as #2302.6, grid size 78,75,77, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_b_best.pdb map 20 as #2303.6, grid size 78,75,77, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_a_best.pdb map 20 as #2304.6, grid size 76,77,81, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_b_best.pdb map 20 as #2305.6, grid size 77,77,81, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_a_best.pdb map 20 as #2306.6, grid size 84,71,73, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_b_best.pdb map 20 as #2307.6, grid size 84,72,71, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_a_best.pdb map 20 as #2308.6, grid size 68,67,68, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_b_best.pdb map 20 as #2309.6, grid size 68,67,69, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_a_best.pdb map 20 as #2310.6, grid size 101,93,117, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_adp_b_best.pdb map 20 as #2311.6, grid size 101,93,118, pixel 2,
shown at level 0.01, step 1, values float32
opened ChimeraX session
> open
> /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/fig3f.cxs
Opened myo1c_rigor_best_win.mrc as #3, grid size 224,224,224, pixel 1.33,
shown at step 1, values float32
Opened copy of myo1c_adp_a_best.pdb map 10 as #24, grid size 45,39,54, pixel
3.33, shown at step 1, values float32
Opened myo1c_adp_a_best.mrc as #1, grid size 224,224,224, pixel 1.35, shown at
step 1, values float32
Opened myo1c_adp_b_best.mrc as #2, grid size 224,224,224, pixel 1.35, shown at
step 1, values float32
Opened myo1c_adp_a_best.pdb map 4 as #301, grid size 51,44,52, pixel 1.33,
shown at step 1, values float32
Opened myo1c_delntr_rigor_best.mrc as #4, grid size 224,224,224, pixel 1.34,
shown at step 1, values float32
opened ChimeraX session
> open
> /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/myo1c_subdomain_transforms_rigor_to_delntr_ploop.cxs
Opened myo1c_rigor_best.pdb map 20 as #2300.6, grid size 89,86,81, pixel 2,
shown at step 1, values float32
Opened myo1c_delntr_rigor_best.pdb map 20 as #2301.6, grid size 88,86,81,
pixel 2, shown at step 1, values float32
Opened myo1c_rigor_best.pdb map 20 as #2302.6, grid size 78,75,77, pixel 2,
shown at step 1, values float32
Opened myo1c_delntr_rigor_best.pdb map 20 as #2303.6, grid size 78,75,77,
pixel 2, shown at step 1, values float32
Opened myo1c_rigor_best.pdb map 20 as #2304.6, grid size 77,77,81, pixel 2,
shown at step 1, values float32
Opened myo1c_delntr_rigor_best.pdb map 20 as #2305.6, grid size 77,77,81,
pixel 2, shown at step 1, values float32
Opened myo1c_rigor_best.pdb map 20 as #2306.6, grid size 84,72,71, pixel 2,
shown at step 1, values float32
Opened myo1c_delntr_rigor_best.pdb map 20 as #2307.6, grid size 85,71,72,
pixel 2, shown at step 1, values float32
Opened myo1c_rigor_best.pdb map 20 as #2308.6, grid size 68,67,69, pixel 2,
shown at step 1, values float32
Opened myo1c_delntr_rigor_best.pdb map 20 as #2309.6, grid size 68,67,69,
pixel 2, shown at step 1, values float32
Opened myo1c_rigor_best.pdb map 20 as #2310.6, grid size 102,93,117, pixel 2,
shown at step 1, values float32
Opened myo1c_delntr_rigor_best.pdb map 20 as #2311.6, grid size 102,94,118,
pixel 2, shown at step 1, values float32
Opened myo1c_rigor_refine3.pdb map 20 as #2312.6, grid size 88,86,81, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2313.6, grid size 88,86,81,
pixel 2, shown at level 0.01, step 1, values float32
Opened myo1c_rigor_refine3.pdb map 20 as #2314.6, grid size 78,75,77, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2315.6, grid size 78,75,77,
pixel 2, shown at level 0.01, step 1, values float32
Opened myo1c_rigor_refine3.pdb map 20 as #2316.6, grid size 77,77,81, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2317.6, grid size 76,77,81,
pixel 2, shown at level 0.01, step 1, values float32
Opened myo1c_rigor_refine3.pdb map 20 as #2318.6, grid size 84,72,71, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2319.6, grid size 84,71,72,
pixel 2, shown at level 0.01, step 1, values float32
Opened myo1c_rigor_refine3.pdb map 20 as #2320.6, grid size 68,67,69, pixel 2,
shown at level 0.01, step 1, values float32
Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2321.6, grid size 68,67,69,
pixel 2, shown at level 0.01, step 1, values float32
Opened myo1c_rigor_refine3.pdb map 20 as #2322.6, grid size 101,93,117, pixel
2, shown at level 0.01, step 1, values float32
Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2323.6, grid size 102,94,117,
pixel 2, shown at level 0.01, step 1, values float32
opened ChimeraX session
> style sphere
Changed 156083 atom styles
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> show #!5 models
> hide #!1 models
> hide #!5 models
> select #3/P:158
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/P:157
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> hide #!3 models
> show #!3 models
> select #3/P:108@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> show #!1 models
> hide #!3 models
> style #!1 stick
Changed 31301 atom styles
> style #!1 sphere
Changed 31301 atom styles
> show #!3 models
> select #1/P:53,107-108,157
46 atoms, 43 bonds, 4 residues, 1 model selected
> hide sel atoms
> hide #!1 models
> open
> /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_vols/myo1c_adp_b_best.pdb
Chain information for myo1c_adp_b_best.pdb #7
---
Chain | Description
B C D | No description available
P | No description available
R | No description available
> select #7
31465 atoms, 31792 bonds, 1988 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> matchmaker #7 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_b_best.pdb, chain
P (#7), sequence alignment score = 548.4
RMSD between 106 pruned atom pairs is 0.333 angstroms; (across all 106 pairs:
0.333)
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> color #7 lightgray atoms
> color #7/P:143-387,529-566 gold atoms
> color #7/P:388-442,437-528,565-584 chocolate atoms
> color #7/P:627-900 pink atoms
> color #7/P:1-126,584-626 lightblue atoms
> color #7/P:127-142 50,100,50 atoms
> color #7/R pink atoms
> color #7/P:1-11 magenta atoms
> transparency #7 30 atoms
> color #7 lightgray ribbons
> color #1/P:MG 0,0,75 ribbons
> color #7/P:143-387,529-566 gold ribbons
> color #7/P:388-442,437-528,565-584 chocolate ribbons
> color #7/P:627-900 pink ribbons
> color #7/P:1-126,584-626 lightblue ribbons
> color #7/P:127-142 50,100,50 ribbons
> color #7/R pink ribbons
> color #7/P:1-11 magenta ribbons
> transparency #7 30 ribbons
> color #7 byhetero
> ribbon #7
> ribbon #7,1,3,2
> hide #!1 models
> select clear
> graphics silhouettes true width 1
> graphics silhouettes true width 2
> view name t23
> zoom 0.3
moved plane near -200.64222072851862 [-0.46188862 0.72357466 0.51293139]
moved plane far -200.64222072851862 [-0.46188862 0.72357466 0.51293139]
> color #7 lightgray atoms
> color #7/P:127-387,529-566 gold atoms
> color #7/P:388-442,437-528,565-584 chocolate atoms
> color #7/P:627-900 pink atoms
> color #7/P:1-126,584-626 lightblue atoms
> color #7/R pink atoms
> color #7/P:1-11 magenta atoms
> transparency #7 30 atoms
> color #7 lightgray ribbons
> color #1/P:MG 0,0,75 ribbons
> color #7/P:127-387,529-566 gold ribbons
> color #7/P:388-442,437-528,565-584 chocolate ribbons
> color #7/P:627-900 pink ribbons
> color #7/P:1-126,584-626 lightblue ribbons
> color #7/R pink ribbons
> color #7/P:1-11 magenta ribbons
> transparency #7 30 ribbons
> color #7 byhetero
> view t23
> select #7/P:53,107-108,157
46 atoms, 43 bonds, 4 residues, 1 model selected
> show sel atoms
> hide H
> graphics silhouettes true width 3
> ~ribbon se
> cartoon hide se
Expected an atoms specifier or a keyword
> ~ribbon sel
> style sel stick
Changed 46 atom styles
> style sel sphere
Changed 46 atom styles
> select clear
> ~show #1-10 m
> show #1 models
> select #1/P:53,107-108,157
46 atoms, 43 bonds, 4 residues, 1 model selected
> ~ribbon sel
> style sphere sel
Expected a keyword
> ~ribbon sel
> style sel sphere
Changed 46 atom styles
> show sel atoms
> ~ribbon sel
> style sel sphere
Changed 46 atom styles
> show sel atoms
> hide H
> show #!2 models
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #7 models
> transparency #7 30 ribbons
> transparency #7 30 atoms
> hide #!1 models
> show #!1 models
> transparency #1 0 atoms
> transparency #1 0 ribbons
> transparency #7 30 ribbons
> transparency #7 70 ribbons
> transparency #7 70 atoms
> transparency #7 100 atoms
> transparency #7 70 atoms
> transparency #7 90 atoms
> transparency #7 90 ribbons
> ~show #1-10 m
> show #1,7 models
> ~show #1-10 m
> show #3,7 models
> transparency #3 0 ribbons
> transparency #3 0 atoms
> ~show #1
> ~show #1-10 m
> show #1,3 models
> transparency #1 90 atoms
> transparency #1 90 ribbons
> transparency #1 0 atoms
> matchmaker #3 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_a_best.pdb, chain
P (#3), sequence alignment score = 543.6
RMSD between 106 pruned atom pairs is 0.472 angstroms; (across all 106 pairs:
0.472)
> matchmaker #7 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_b_best.pdb, chain
P (#7), sequence alignment score = 548.4
RMSD between 106 pruned atom pairs is 0.333 angstroms; (across all 106 pairs:
0.333)
> clip front off
> clip back off
> ribbon #1
> select #3/P:53,107-108,157
46 atoms, 43 bonds, 1 pseudobond, 4 residues, 2 models selected
> ~ribbon sel
> show sel
> hide H
> ~show #1-10 m
> show #1,7 models
> transparency #7 0 atoms
> transparency #7 0 ribbons
> ~show #1-10 m
> show #3,7 models
> ~show #3
> transparency #3 90 atoms
> transparency #3 90 ribbons
> ~show #1-10 m
> show #1,7 models
> ~show #1-10 m
> show #1,3 models
> ~show #1-10 m
> show #3 models
> combine #3
> ribbon #3
> ~show #1-10 m
> show #3 models
> ~show #1-10 m
> show #8 models
> transparency #8 0 ribbons
> select #8/P:53,107-108,157
46 atoms, 43 bonds, 4 residues, 1 model selected
> show sel&~H
> transparency #8 0 atoms
> style sel stick
Changed 46 atom styles
> clip near -1\
Invalid "near" argument: Expected 'off' or a number
> clip near -1
> select #8/P:109@N
1 atom, 1 residue, 1 model selected
> show sel
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 1 item
> style sel stick
Changed 1 atom style
> select #8/P:106@C
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 1 atom style
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 1 item
> hide sel atoms
> select #8/P:54@N
1 atom, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 1 item
> style sel stick
Changed 1 atom style
> clip near -1
> clip near 1
> select #8/P:110
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
50 atoms, 49 bonds, 5 residues, 1 model selected
> select up
52 atoms, 50 bonds, 6 residues, 1 model selected
> select up
64 atoms, 62 bonds, 6 residues, 1 model selected
> setattr sel r ribbon_hide_backbone true
Assigning ribbon_hide_backbone attribute to 6 items
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 6 items
> show sel cartoons
> select #8/P:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> setattr sel r ribbon_hide_backbone true
Assigning ribbon_hide_backbone attribute to 1 item
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 1 item
> hide sel cartoons
> select #8/P:108
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> view t23
> clip near -1
> clip near 1
> select clear
> view t23
> clip near -1
> select #8/P:243
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
160 atoms, 159 bonds, 11 residues, 1 model selected
> select up
11612 atoms, 11736 bonds, 711 residues, 1 model selected
> select down
160 atoms, 159 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select #8/P:245
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
238 atoms, 239 bonds, 14 residues, 1 model selected
> hide sel cartoons
> color #7 lightgray atoms
> color #7/P:127-387,529-566 gold atoms
> color #7/P:388-442,437-528,565-584 chocolate atoms
> color #7/P:627-900 pink atoms
> color #7/P:1-126,584-626 lightblue atoms
> color #7/R pink atoms
> color #7/P:1-11 magenta atoms
> transparency #7 30 atoms
> color #7 lightgray ribbons
> color #1/P:MG 0,0,75 ribbons
> color #7/P:127-387,529-566 gold ribbons
> color #7/P:388-442,437-528,565-584 chocolate ribbons
> color #7/P:627-900 pink ribbons
> color #7/P:1-126,584-626 lightblue ribbons
> color #7/R pink ribbons
> color #7/P:1-11 magenta ribbons
> transparency #7 30 ribbons
> color #7 byhetero
> color #8 lightgray atoms
> color #8/P:127-387,529-566 gold atoms
> color #8/P:388-442,437-528,565-584 chocolate atoms
> color #8/P:627-900 pink atoms
> color #8/P:1-126,584-626 lightblue atoms
> color #8/R pink atoms
> color #8/P:1-11 magenta atoms
> transparency #8 30 atoms
> color #8 lightgray ribbons
> color #1/P:MG 0,0,75 ribbons
> color #8/P:127-387,529-566 gold ribbons
> color #8/P:388-442,437-528,565-584 chocolate ribbons
> color #8/P:627-900 pink ribbons
> color #8/P:1-126,584-626 lightblue ribbons
> color #8/R pink ribbons
> color #8/P:1-11 magenta ribbons
> transparency #8 30 ribbons
> color #8 byhetero
> select #8/P:593
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #8/P:592
36 atoms, 35 bonds, 2 residues, 1 model selected
> select add #8/P:607
55 atoms, 53 bonds, 3 residues, 1 model selected
> select down
55 atoms, 53 bonds, 3 residues, 1 model selected
> select up
374 atoms, 378 bonds, 22 residues, 1 model selected
> hide sel cartoons
> select #8/P:43
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #8/P:37
38 atoms, 36 bonds, 2 residues, 1 model selected
> select up
134 atoms, 135 bonds, 7 residues, 1 model selected
> select up
11612 atoms, 11736 bonds, 711 residues, 1 model selected
> select down
134 atoms, 135 bonds, 7 residues, 1 model selected
> select add #8/P:33
158 atoms, 158 bonds, 8 residues, 1 model selected
> select up
328 atoms, 330 bonds, 18 residues, 1 model selected
> hide sel cartoons
Drag select of 5 residues
> select up
146 atoms, 144 bonds, 9 residues, 1 model selected
> hide sel cartoons
Drag select of 5 residues
> hide sel cartoons
> clip far -1
> clip far 1
> select #8/P:83
10 atoms, 9 bonds, 1 residue, 1 model selected
Drag select of 4 residues
> select add #8/P:76
98 atoms, 23 bonds, 6 residues, 1 model selected
Drag select of 2 residues
Drag select of 4 residues
> select up
775 atoms, 781 bonds, 47 residues, 1 model selected
> hide sel cartoons
> clip far 1
Drag select of 11 residues
> select up
221 atoms, 222 bonds, 15 residues, 1 model selected
> hide sel cartoons
Drag select of 6 residues
> select up
566 atoms, 573 bonds, 34 residues, 1 model selected
Drag select of 3 residues
Drag select of 8 residues
Drag select of 1 residues
Drag select of 2 residues
Drag select of 5 residues
> select up
535 atoms, 542 bonds, 32 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #8/P:400
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
358 atoms, 361 bonds, 21 residues, 1 model selected
> select add #8/P:397
369 atoms, 371 bonds, 22 residues, 1 model selected
> select add #8/P:396
383 atoms, 384 bonds, 23 residues, 1 model selected
> hide sel cartoons
Drag select of 7 residues
> select up
229 atoms, 232 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select #8/P:184
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #8/P:355
31 atoms, 30 bonds, 2 residues, 1 model selected
> select add #8/P:202
51 atoms, 50 bonds, 3 residues, 1 model selected
> select up
724 atoms, 731 bonds, 45 residues, 1 model selected
> select add #8/P:188
739 atoms, 745 bonds, 46 residues, 1 model selected
> select add #8/P:191
763 atoms, 768 bonds, 47 residues, 1 model selected
> select up
871 atoms, 880 bonds, 53 residues, 1 model selected
> hide sel cartoons
Drag select of 18 residues
> select up
876 atoms, 877 bonds, 53 residues, 1 model selected
> hide sel cartoons
> select #8/P:363
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
49 atoms, 48 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #8/P:65
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
135 atoms, 136 bonds, 7 residues, 1 model selected
> hide sel cartoons
Drag select of 4 residues
> select up
207 atoms, 208 bonds, 13 residues, 1 model selected
> hide sel cartoons
Drag select of 1 residues
> select up
65 atoms, 65 bonds, 4 residues, 1 model selected
> select add #8/P:366
84 atoms, 83 bonds, 5 residues, 1 model selected
> select up
279 atoms, 281 bonds, 18 residues, 1 model selected
> hide sel cartoons
> select #8/P:390
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
177 atoms, 180 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select #8/P:48,62,131-180,101-126,380-386,587-591
1375 atoms, 1379 bonds, 90 residues, 1 model selected
> select #8/P:48-62,131-180,101-126,380-386,587-591
1598 atoms, 1606 bonds, 103 residues, 1 model selected
> view t23
> clip far -1
> clip far 1
> ~ribbon #8
> ribbon sel
> clip far 1
> ~ribbon #1-10
> select #1-8/P:48-62,131-180,101-126,380-386,587-591
11186 atoms, 11242 bonds, 2 pseudobonds, 721 residues, 8 models selected
> ribbon sel
> ~show #1-10 m
> show #1,3 models
> transparency #1 0 ribbons
> select clear
> select #2-8/P:53,107-108,157
276 atoms, 258 bonds, 2 pseudobonds, 24 residues, 7 models selected
> show sel&~H
> transparency sel 0
> transparency sel 0 atoms
> ~ribbon sel
> ~show #1-10 m
> show #8 models
> ~show #1-10 m
> show #1,3 models
> ~show #1-10 m
> show #8 models
> ~show #1-10 m
> show #1,3 models
> color #1-8 lightgray atoms
> color #1-8/P:127-387,529-566 gold atoms
> color #1-8/P:388-442,437-528,565-584 chocolate atoms
> color #1-8/P:627-900 pink atoms
> color #1-8/P:1-126,584-626 lightblue atoms
> color #1-8/R pink atoms
> color #1-8/P:1-11 magenta atoms
> transparency #1-8 30 atoms
> color #1-8 lightgray ribbons
> color #1-8/P:127-387,529-566 gold ribbons
> color #1-8/P:388-442,437-528,565-584 chocolate ribbons
> color #1-8/P:627-900 pink ribbons
> color #1-8/P:1-126,584-626 lightblue ribbons
> color #1-8/R pink ribbons
> color #1-8/P:1-11 magenta ribbons
> transparency #1-8 30 ribbons
> color #1-8 byhetero
> transparency #1 90 ribbons
> hide #!3 models
> show #!3 models
> transparency #3 0 ribbons
> transparency #2-10 0
> transparency #2-10 0 atoms
> ~show #1-10 m
> show #8 models
> ~show #1-10 m
> show #1,3 models
> hide #!3 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!1 models
> show #!3 models
> show #!8 models
> matchmaker #7 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_b_best.pdb, chain
P (#7), sequence alignment score = 548.4
RMSD between 106 pruned atom pairs is 0.333 angstroms; (across all 106 pairs:
0.333)
> matchmaker #2 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with
myo1c_delntr_rigor_best.pdb, chain P (#2), sequence alignment score = 556.2
RMSD between 106 pruned atom pairs is 0.197 angstroms; (across all 106 pairs:
0.197)
> matchmaker #3 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_a_best.pdb, chain
P (#3), sequence alignment score = 543.6
RMSD between 106 pruned atom pairs is 0.472 angstroms; (across all 106 pairs:
0.472)
> matchmaker #4 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_rigor_best.pdb, chain
P (#4), sequence alignment score = 559.2
RMSD between 106 pruned atom pairs is 0.156 angstroms; (across all 106 pairs:
0.156)
> matchmaker #5 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with
myo1c_delntr_rigor_best.pdb, chain P (#5), sequence alignment score = 556.2
RMSD between 106 pruned atom pairs is 0.195 angstroms; (across all 106 pairs:
0.195)
> matchmaker #7 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_b_best.pdb, chain
P (#7), sequence alignment score = 548.4
RMSD between 106 pruned atom pairs is 0.333 angstroms; (across all 106 pairs:
0.333)
> matchmaker #8 to #1/P:388-409,442-525@ca,n,c,o
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 myo1c_rigor_best.pdb, chain P (#1) with copy of
myo1c_adp_a_best.pdb, chain P (#8), sequence alignment score = 543.6
RMSD between 106 pruned atom pairs is 0.472 angstroms; (across all 106 pairs:
0.472)
> ~show #1-10 m
> show #8 models
> ~show #1-10 m
> show #1,3 models
> style sphere
Changed 218715 atom styles
> select clear
> ~show #1-10 m
> show #8 models
> style sphere
Changed 218715 atom styles
> ~show #1-10 m
> show #1,3 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8
31167 atoms, 31490 bonds, 2 pseudobonds, 1968 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone true
Assigning ribbon_hide_backbone attribute to 1968 items
> transparency #1-10 0 atoms
> transparency #1-10 0 ribbons
> transparency #8 90 ribbons
> transparency #8 0 atoms
> ~show #1-10 m
> show #1,10 models
> ~show #1-10 m
> show #1,8 models
> ~show #8
> select #1-7/P:53,107-108,157
276 atoms, 258 bonds, 2 pseudobonds, 24 residues, 7 models selected
> show sel
> hide H
> ~ribbon sel
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #7,8 models
> select ~sel & ##selected
187200 atoms, 189160 bonds, 6 pseudobonds, 11822 residues, 11 models selected
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #1,8 models
> ~show #1-10 m
> show #3,8 models
> select clear
> ~show #1-10 m
> show #7,8 models
> style #7#!8 stick
Changed 62632 atom styles
> ~show #1-10 m
> show #3,8 models
> style #!3,8 stick
Changed 62334 atom styles
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> style #!5,8 sphere
Changed 62288 atom styles
> ~show #1-10 m
> show #3,8 models
> style #!3,8 sphere
Changed 62334 atom styles
> select #3/P:53@CG
1 atom, 1 residue, 1 model selected
> select add #3/P:157@OD1
2 atoms, 2 residues, 1 model selected
> select up
28 atoms, 26 bonds, 2 residues, 1 model selected
> style sel ball
Changed 28 atom styles
> select clear
> style #!3,8 ball
Changed 62334 atom styles
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #5,8 models
> style #!5,8 ball
Changed 62288 atom styles
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> hide #7 models
> show #7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select #7/P:592
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select up
188 atoms, 190 bonds, 12 residues, 1 model selected
> show sel cartoons
> select #7/P:604
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel cartoons
> select up
186 atoms, 187 bonds, 10 residues, 1 model selected
> show sel cartoons
> select #7/P:592-604
203 atoms, 205 bonds, 13 residues, 1 model selected
> select up
374 atoms, 378 bonds, 22 residues, 1 model selected
> hide sel cartoons
> save
> /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/fig3d_p_loop.cxs
> show #!1 models
> style sel stick
Changed 374 atom styles
> select clear
> style #7#!1 stick
Changed 62766 atom styles
> hide #!1 models
> select #7/P:53@CA
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel cartoons
> style sel sphere
Changed 14 atom styles
> style sel ball
Changed 14 atom styles
> select clear
> select #7/P:108@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #7/P:107@C
8 atoms, 6 bonds, 2 residues, 1 model selected
> select up
18 atoms, 17 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 18 atom styles
> select #7/P:157@CA
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel ball
Changed 14 atom styles
> show sel cartoons
> save
> /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/fig3d_p_loop.cxs
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> style stick
Changed 218715 atom styles
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #5,8 models
> ~show #1-10 m
> show #3,8 models
> ~show #1-10 m
> show #7,8 models
> select #8/P:48-62,131-180,101-126,380-386,587-591
1598 atoms, 1606 bonds, 103 residues, 1 model selected
> show sel cartoons
> select clear
> select #8/P:53,107-108,157
46 atoms, 43 bonds, 4 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> hide H
> transparency sel 90 a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency sel 90 atoms
> hide sel cartoons
> show sel atoms
> select up
438 atoms, 439 bonds, 29 residues, 1 model selected
> select down
46 atoms, 43 bonds, 4 residues, 1 model selected
> hide H
> select #8/P:53,107-108,157
46 atoms, 43 bonds, 4 residues, 1 model selected
> ~show #1-10 m
> show #3,8 models
> select clear
> ~show #1-10 m
> show #7,8 models
> ~show #1-10 m
> show #7,8 models
> select #8/P:53,107-108,157
46 atoms, 43 bonds, 4 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #7/P:53,107-108,157
46 atoms, 43 bonds, 4 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 4 items
> show sel cartoons
> ui tool show H-Bonds
> hbonds sel color #000000 radius 0.05 dashes 4 restrict both interModel false
> distSlop 0.6 angleSlop 40.0 select true reveal true
2 hydrogen bonds found
> delete H
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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 - 88
OpenGL renderer: Apple M1 Max
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: MacBookPro18,2
Model Number: Z14X000HSLL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 22 days, 16 hours, 20 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
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-Clipper: 0.22.4
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-ISOLDE: 1.7.1
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 , 19 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash deleting hydrogens |
comment:2 by , 19 months ago
| Cc: | added |
|---|---|
| Resolution: | → can't reproduce |
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Chuck's next ticket (#14899) seems more tractable to work with, so closing this one.