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Opened 7 hours ago
#19884 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x00000003110c7000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003100bb000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030f0af000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030e0a3000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030d097000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030c08b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030b07f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030a073000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000309067000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030805b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030704f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000306043000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000305037000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030402b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030301f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000302013000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000301007000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000207223080 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 143 in render
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.connect_structure._cs, chimerax.atom_search.ast, chimerax.chem_group._chem_group, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, PIL._imaging, kiwisolver._cext, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 122)
{"app_name":"ChimeraX","timestamp":"2026-02-23 15:11:40.00 +0200","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.3 (25D125)","roots_installed":0,"name":"ChimeraX","incident_id":"F907CAF8-FEDD-42A8-9A54-1DFB125F5DEB"}
{
"uptime" : 170000,
"procRole" : "Background",
"version" : 2,
"userID" : 1011626602,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 18554,
"osVersion" : {
"train" : "macOS 26.3",
"build" : "25D125",
"releaseType" : "User"
},
"captureTime" : "2026-02-23 15:09:51.7270 +0200",
"codeSigningMonitor" : 2,
"incident" : "F907CAF8-FEDD-42A8-9A54-1DFB125F5DEB",
"pid" : 16293,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-02-23 13:24:43.9350 +0200",
"procStartAbsTime" : 4044923528847,
"procExitAbsTime" : 4196310242713,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7153AE3B-C72D-5E6A-802F-76E7C91C4E5A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "31622414-D700-AB9C-C51E-CAAD8E597596",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "575EC0E3-5A59-4C85-82FE-D6A5E505DE42",
"wakeTime" : 19851,
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System Profile:
Network Service: Wi-Fi, AirPort, en0
Boot Volume File System Type: apfs
Memory Module: LPDDR5, Hynix
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Display: spdisplays_display, 1920 x 1080 (1080p FHD - Full High Definition), Main, MirrorOff, Online
Model: Mac16,8, BootROM 13822.81.10, proc 14:10:4 processors, 48 GB, SMC
Graphics: Apple M4 Pro, Apple M4 Pro, Built-In
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4388), wl0: Dec 6 2025 00:30:14 version 23.41.8.0.41.51.201 FWID 01-990604ea
IO80211_driverkit-1540.16 "IO80211_driverkit-1540.16" Jan 27 2026 21:04:24
AirPort:
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5
> alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr;
> sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001
> minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001;
> close sel; show $2
> alias centersel cofr sel; clip near 10 position cofr; clip far -10 position
> cofr; cofr centerOfView showpivot true; view sel
> alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine
> $1.* close true
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add reset_mouse_and_help command "mousemode alt right
> contour ; mousemode right clip ; mousemode alt left 'translate selected
> models' ; mousemode shift left 'rotate selected models' ; mousemode alt
> control left 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/avenka/Phenix/cryosparc_P1_J559_008_volume_map_zflip.mrc format
> mrc
Opened cryosparc_P1_J559_008_volume_map_zflip.mrc as #1, grid size
512,512,512, pixel 0.828, shown at level 0.0114, step 1, values float32
> open
> /Users/avenka/Phenix/RealSpaceRefine_27/cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif
Summary of feedback from opening
/Users/avenka/Phenix/RealSpaceRefine_27/cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 801
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "25" on line 159
Bad residue range for struct_conf "26" on line 160
Bad residue range for struct_conf "64" on line 198
Bad residue range for struct_conf "71" on line 205
Bad residue range for struct_conf "72" on line 206
Invalid sheet range for struct_sheet_range "12 1" on line 791
Invalid sheet range for struct_sheet_range "13 1" on line 792
Invalid sheet range for struct_sheet_range "14 1" on line 793
Invalid sheet range for struct_sheet_range "15 1" on line 794
Invalid sheet range for struct_sheet_range "16 1" on line 795
1 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for
cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> select ~sel & ##selected
Nothing selected
> phenix location /Applications/Phenix/phenix-1.21.2-5419
Using Phenix installation /Applications/Phenix/phenix-1.21.2-5419
> runscript /Users/avenka/Chimera/chimera_startup.py
> hide surfaces
> show cartoons
> hide atoms
> show atoms
> hide atoms
> style ball
Changed 25786 atom styles
> hide #!1 models
> show surfaces
> hide surfaces
> show #!1 models
> color #1 #d783ffff models
> color #1 #ff85ffff models
> color #1 #ff8ad8ff models
> color #1 #005493ff models
> color #1 #0096ffff models
> color #1 #00fdffff models
> color #1 #73fdffff models
> color #1 #73fcd6ff models
> color #1 #73fa79ff models
> color #1 #ff9300ff models
> color #1 #941100ff models
> color #1 #945200ff models
> color #1 #424242ff models
> color #1 #5e5e5eff models
> color #1 #797979ff models
> color #1 #919191ff models
> color #1 #9191919a models
> color #1 #91919180 models
> color #1 #d783ffff models
> color #1 #d783ff7d models
> color #1 #942193ff models
> color #1 #941751ff models
> color #1 #009193ff models
> color #1 #005493ff models
> color #1 #919191ff models
> color #1 #941100ff models
> color #1 #945200ff models
> color #1 #94520090 models
> color #1 #94520080 models
> volume #1 level 0.04573
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 68
shifted from previous position = 0.821
rotated from previous position = 1.17 degrees
atoms outside contour = 12796, contour level = 0.045734
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994527 -0.01021184 -0.00227366 1.96900846
0.01025000 0.99979510 0.01745561 -6.34297659
0.00209494 -0.01747796 0.99984505 3.58169120
Axis -0.85789511 -0.10728378 0.50249993
Axis point 0.00000000 178.98483963 360.61639686
Rotation angle (degrees) 1.16662538
Shift along axis 0.79109534
> volume #1 level 0.1012
> select add #2
25786 atoms, 26051 bonds, 509 pseudobonds, 1592 residues, 3 models selected
> select subtract #2
6 models selected
> select add #2
25786 atoms, 26051 bonds, 509 pseudobonds, 1592 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99995,-0.010212,-0.0022737,0.031366,0.01025,0.9998,0.017456,-8.2915,0.0020949,-0.017478,0.99985,8.724
> select subtract #2
6 models selected
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 88
shifted from previous position = 5.84
rotated from previous position = 0.011 degrees
atoms outside contour = 20045, contour level = 0.10123
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994638 -0.01012733 -0.00216334 1.92778569
0.01016384 0.99979366 0.01758815 -6.36017685
0.00198477 -0.01760920 0.99984298 3.62136214
Axis -0.86186460 -0.10157332 0.49686242
Axis point 0.00000000 180.33141256 359.20595398
Rotation angle (degrees) 1.17002116
Shift along axis 0.78385279
> surface dust #1 size 8.28
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 40
shifted from previous position = 0.00236
rotated from previous position = 0.00378 degrees
atoms outside contour = 20046, contour level = 0.10123
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994683 -0.01009279 -0.00211335 1.90807689
0.01012846 0.99979356 0.01761382 -6.36000891
0.00193514 -0.01763429 0.99984263 3.63628925
Axis -0.86312655 -0.09913591 0.49516122
Axis point 0.00000000 180.98546204 358.78838914
Rotation angle (degrees) 1.16999547
Shift along axis 0.78414287
> volume style mesh
> volume style image
> volume style surface
> ui mousemode right select
> lighting full
> lighting simple
> ui tool show "Selection Inspector"
> ui tool show "Side View"
> view
> color bfactor
25786 atoms, 1592 residues, 6 surfaces, atom bfactor range 57.2 to 422
> hbonds reveal true
777 hydrogen bonds found
> ~hbonds
> show atoms
> hide cartoons
> volume #1 change image level -0.003346,0 level 0.01135,0.8 level 0.5315,1
> volume #1 level 0.08508
> hide #!2 models
> volume #1 level 0.09226
> volume #1 level 0.112
> select clear
> ui mousemode right translate
> show #!2 models
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 98 residues in model #2 to IUPAC-IUB
standards.
Chain information for
cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif
---
Chain | Description
2.2/A | No description available
2.2/B | No description available
2.2/C | No description available
2.2/D | No description available
2.2/E | No description available
2.2/F | No description available
> clipper associate #1 toModel #2
Opened cryosparc_P1_J559_008_volume_map_zflip.mrc as #2.1.1.1, grid size
512,512,512, pixel 0.828, shown at step 1, values float32
> isolde sim start /A-F
ISOLDE: started sim
Average map value = 0.08309 for 25786 atoms, 20876 outside contour
> fitmap #2.2 inMap #2.1.1.1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif
(#2.2) to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#2.1.1.1) using
25786 atoms
average map value = 0.08347, steps = 28
shifted from previous position = 0.0454
rotated from previous position = 0.0658 degrees
atoms outside contour = 20827, contour level = 0.15353
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2.2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#2.1.1.1) coordinates:
Matrix rotation and translation
0.99999939 -0.00108136 0.00022404 0.14591462
0.00108129 0.99999937 0.00031622 -0.33515581
-0.00022439 -0.00031598 0.99999992 0.10594800
Axis -0.27518468 0.19519460 0.94136733
Axis point 308.98415648 133.27645773 0.00000000
Rotation angle (degrees) 0.06581413
Shift along axis -0.00583809
===== Log before crash end =====
Log:
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5
> alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr;
> sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001
> minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001;
> close sel; show $2
> alias centersel cofr sel; clip near 10 position cofr; clip far -10 position
> cofr; cofr centerOfView showpivot true; view sel
> alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine
> $1.* close true
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add reset_mouse_and_help command "mousemode alt right
> contour ; mousemode right clip ; mousemode alt left 'translate selected
> models' ; mousemode shift left 'rotate selected models' ; mousemode alt
> control left 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/avenka/Phenix/cryosparc_P1_J559_008_volume_map_zflip.mrc format
> mrc
Opened cryosparc_P1_J559_008_volume_map_zflip.mrc as #1, grid size
512,512,512, pixel 0.828, shown at level 0.0114, step 1, values float32
> open
> /Users/avenka/Phenix/RealSpaceRefine_27/cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb
> format pdb
Chain information for
cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> show cartoons
> hide atoms
> style ball
Changed 25786 atom styles
> style stick
Changed 25786 atom styles
> hide #!1 models
> show surfaces
> hide surfaces
> show atoms
> hide cartoons
> color bychain
> show #!1 models
> color #1 #d783ffff models
> color #1 #d783ff8b models
> color #1 #d783ff80 models
> volume #1 level 0.01648
> volume #1 level 0.02538
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 68
shifted from previous position = 0.821
rotated from previous position = 1.17 degrees
atoms outside contour = 8771, contour level = 0.025381
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994521 -0.01021839 -0.00227399 1.97042028
0.01025655 0.99979500 0.01745768 -6.34467796
0.00209514 -0.01748005 0.99984502 3.58202075
Axis -0.85778227 -0.10726970 0.50269553
Axis point 0.00000000 178.97302423 360.67277228
Rotation angle (degrees) 1.16691793
Shift along axis 0.79106592
> show cartoons
> hide atoms
> select add #2
25786 atoms, 26051 bonds, 2 pseudobonds, 1592 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99995,-0.010218,-0.002274,1.3303,0.010257,0.99979,0.017458,-8.9578,0.0020951,-0.01748,0.99985,10.246
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06156, steps = 72
shifted from previous position = 4.61
rotated from previous position = 1.93 degrees
atoms outside contour = 9283, contour level = 0.025381
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99984993 0.01620662 0.00612007 -7.59530758
-0.01619696 0.99986750 -0.00162492 -0.12875742
-0.00614559 0.00152554 0.99997995 3.81445331
Axis 0.09055572 0.35255976 -0.93139749
Axis point 81.69913135 445.46285237 0.00000000
Rotation angle (degrees) 0.99671863
Shift along axis -4.28596546
> hide sel cartoons
> show sel atoms
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06156, steps = 48
shifted from previous position = 0.00504
rotated from previous position = 0.0204 degrees
atoms outside contour = 9281, contour level = 0.025381
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99984740 0.01633957 0.00617993 -7.63691974
-0.01632781 0.99986479 -0.00194989 -0.02450475
-0.00621096 0.00184869 0.99997900 3.75754808
Axis 0.10808541 0.35257195 -0.92952168
Axis point 88.28911915 439.59092347 0.00000000
Rotation angle (degrees) 1.00686157
Shift along axis -4.32680169
> view matrix models
> #2,0.99985,0.01634,0.0061799,-8.4953,-0.016328,0.99986,-0.0019499,0.26563,-0.006211,0.0018487,0.99998,5.2844
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98843,-0.11248,0.10178,0.13568,0.099762,0.98745,0.12243,-48.371,-0.11427,-0.11086,0.98724,54.234
> view matrix models
> #2,0.63006,-0.76993,-0.10113,255.66,0.76942,0.60136,0.21531,-129.97,-0.10495,-0.21347,0.9713,76.94
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.63006,-0.76993,-0.10113,257.72,0.76942,0.60136,0.21531,-132.42,-0.10495,-0.21347,0.9713,71.456
> view matrix models
> #2,0.63006,-0.76993,-0.10113,264.48,0.76942,0.60136,0.21531,-128.34,-0.10495,-0.21347,0.9713,71.469
> volume #1 level 0.1091
> show sel cartoons
> hide sel atoms
> view matrix models
> #2,0.63006,-0.76993,-0.10113,250.76,0.76942,0.60136,0.21531,-123.77,-0.10495,-0.21347,0.9713,73.583
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97871,-0.19968,-0.047526,47.848,0.20018,0.87734,0.43611,-107.88,-0.045388,-0.43634,0.89864,122.61
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.97871,-0.19968,-0.047526,57.636,0.20018,0.87734,0.43611,-110.74,-0.045388,-0.43634,0.89864,124.98
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98872,-0.14471,0.038759,25.68,0.11074,0.88022,0.46146,-97.878,-0.10089,-0.45196,0.88631,142.57
> view matrix models
> #2,0.9695,-0.21272,-0.12171,78.164,0.22228,0.97239,0.07112,-56.85,0.10322,-0.096004,0.99001,3.714
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 136
shifted from previous position = 3.56
rotated from previous position = 14.2 degrees
atoms outside contour = 20515, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994652 -0.01011729 -0.00214235 1.91990026
0.01015348 0.99979335 0.01761124 -6.36409519
0.00196372 -0.01763205 0.99984261 3.63015046
Axis -0.86245665 -0.10048175 0.49605639
Axis point 0.00000000 180.61080679 359.00929382
Rotation angle (degrees) 1.17074434
Shift along axis 0.78440398
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99995,-0.010117,-0.0021423,-1.2187,0.010153,0.99979,0.017611,-6.0876,0.0019637,-0.017632,0.99984,7.8602
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.96448,0.12654,-0.23188,27.254,-0.12118,0.99193,0.037306,19.05,0.23473,-0.007883,0.97203,-37.347
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.96448,0.12654,-0.23188,30.279,-0.12118,0.99193,0.037306,11.811,0.23473,-0.007883,0.97203,-36.32
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.93584,-0.091789,-0.34027,104.65,0.01548,0.97526,-0.22051,41.628,0.3521,0.20109,0.91411,-91.867
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.93584,-0.091789,-0.34027,100.83,0.01548,0.97526,-0.22051,49.27,0.3521,0.20109,0.91411,-92.095
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.0537, steps = 104
shifted from previous position = 6.6
rotated from previous position = 6.34 degrees
atoms outside contour = 21452, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.96360151 -0.01430515 -0.26695972 68.80085531
-0.03886002 0.98046720 -0.19280551 52.65581295
0.26450336 0.19616174 0.94422378 -77.91044535
Axis 0.59019074 -0.80640359 -0.03725778
Axis point 338.53102992 0.00000000 209.24942069
Rotation angle (degrees) 19.24005259
Shift along axis 1.04656143
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99902,0.0012894,-0.044248,10.389,0.0012188,0.9984,0.056612,-12.943,0.04425,-0.05661,0.99742,9.4238
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 88
shifted from previous position = 6.3
rotated from previous position = 3.35 degrees
atoms outside contour = 20522, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994638 -0.01011859 -0.00220417 1.93224659
0.01015569 0.99979478 0.01752883 -6.34113208
0.00202635 -0.01755028 0.99984393 3.61412347
Axis -0.86111578 -0.10384993 0.49768946
Axis point 0.00000000 180.23797807 359.16430702
Rotation angle (degrees) 1.16710440
Shift along axis 0.79334922
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99995,-0.010119,-0.0022042,1.5273,0.010156,0.99979,0.017529,-5.1177,0.0020263,-0.01755,0.99984,7.492
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98704,-0.081136,-0.13842,48.104,0.070566,0.99432,-0.079638,4.0723,0.1441,0.068839,0.98717,-37.639
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98704,-0.081136,-0.13842,47.525,0.070566,0.99432,-0.079638,3.9883,0.1441,0.068839,0.98717,-36.599
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98739,-0.083732,-0.13436,47.118,0.07423,0.99447,-0.074245,2.0281,0.13983,0.063336,0.98815,-34.771
> view matrix models
> #2,0.9669,-0.097398,-0.23585,76.013,0.06576,0.98818,-0.13849,18.88,0.24655,0.11839,0.96187,-63.053
> open /Users/avenka/Downloads/cryosparc_P1_J559_008_volume_map.mrc format mrc
Opened cryosparc_P1_J559_008_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.828, shown at level 0.0114, step 1, values float32
> hide #!1 models
> volume #3 level 0.09771
> view matrix models
> #2,-0.57582,-0.78641,-0.22358,541.49,-0.62569,0.5999,-0.49863,322.25,0.52626,-0.14723,-0.83748,318.23
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.57582,-0.78641,-0.22358,590.46,-0.62569,0.5999,-0.49863,246.32,0.52626,-0.14723,-0.83748,326.76
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.2554,-0.87338,-0.41471,581.71,-0.87874,0.38858,-0.27717,295.97,0.40322,0.29364,-0.86671,267.93
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.2554,-0.87338,-0.41471,531.08,-0.87874,0.38858,-0.27717,369.97,0.40322,0.29364,-0.86671,245.53
> color #3 #ffffb280 models
> color #3 #945200ff models
> color #3 #94520084 models
> color #3 #94520080 models
> fitmap #2 inMap #3
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map.mrc (#3) using 25786 atoms
average map value = 0.05534, steps = 132
shifted from previous position = 4.61
rotated from previous position = 10.4 degrees
atoms outside contour = 21465, contour level = 0.097709
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.09187478 -0.86703126 -0.48970993 513.31700694
-0.89143621 0.29076595 -0.34755812 405.93202181
0.44373473 0.40461334 -0.79961712 201.83015587
Axis 0.62731587 -0.77849889 -0.02035389
Axis point 377.03500646 0.00000000 205.13923181
Rotation angle (degrees) 143.16477796
Shift along axis 1.88624623
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.083275,-0.84732,-0.52452,514.89,-0.86996,0.31853,-0.37644,401.85,0.48604,0.42496,-0.76366,180.99
> view matrix models
> #2,0.01237,-0.80206,-0.59712,500.89,-0.74479,0.39106,-0.5407,395.62,0.66718,0.45142,-0.59253,100.61
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.01237,-0.80206,-0.59712,513.64,-0.74479,0.39106,-0.5407,403.62,0.66718,0.45142,-0.59253,90.903
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.046374,-0.85805,-0.51146,499.67,-0.84064,0.24306,-0.484,442.29,0.53961,0.4524,-0.71004,142.81
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.046374,-0.85805,-0.51146,485.94,-0.84064,0.24306,-0.484,440.17,0.53961,0.4524,-0.71004,147.05
> view matrix models
> #2,0.046374,-0.85805,-0.51146,486.65,-0.84064,0.24306,-0.484,440.48,0.53961,0.4524,-0.71004,146.86
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.6008,-0.72474,-0.33733,304.73,-0.79821,-0.56685,-0.20379,538.81,-0.043515,0.3917,-0.91906,327.31
> view matrix models
> #2,-0.2162,-0.81429,-0.53869,538.89,-0.91399,0.36282,-0.18162,366.45,0.34334,0.45309,-0.8227,212.29
> view matrix models
> #2,0.11003,-0.8337,-0.54115,474.54,-0.88871,0.16127,-0.42916,455.78,0.44506,0.52814,-0.72318,153.99
> fitmap #2 inMap #3
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map.mrc (#3) using 25786 atoms
average map value = 0.05966, steps = 136
shifted from previous position = 3.37
rotated from previous position = 12.6 degrees
atoms outside contour = 20775, contour level = 0.097709
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.15285460 -0.84843563 -0.50674692 463.93388237
-0.76689194 0.22158013 -0.60231138 456.37223157
0.62330749 0.48068620 -0.61678890 101.06362099
Axis 0.69097788 -0.72100124 0.05202679
Axis point 416.71588201 0.00000000 223.26552193
Rotation angle (degrees) 128.40214273
Shift along axis -3.21887912
> hide #!3 models
> show #!1 models
> runscript /Users/avenka/Chimera/chimera_startup.py
[Repeated 1 time(s)]FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> runscript /Users/avenka/Chimera/chimera_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> phenix location /Applications/Phenix/phenix-1.21.2-5419
Using Phenix installation /Applications/Phenix/phenix-1.21.2-5419
> view matrix models
> #2,0.37912,0.89926,0.21819,-100.2,-0.84492,0.43256,-0.31465,367.64,-0.37733,-0.065065,0.92379,95.073
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.37912,0.89926,0.21819,-102.41,-0.84492,0.43256,-0.31465,364.1,-0.37733,-0.065065,0.92379,116.57
> view matrix models
> #2,0.37912,0.89926,0.21819,-97.95,-0.84492,0.43256,-0.31465,366.74,-0.37733,-0.065065,0.92379,119.27
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.86692,0.18176,0.46412,-105.41,-0.36181,0.86993,0.33514,35.161,-0.34284,-0.45846,0.81992,215.51
> view matrix models
> #2,0.95112,0.044574,0.3056,-60.893,-0.056164,0.99799,0.029234,9.6969,-0.30369,-0.044969,0.95171,93.586
> view matrix models
> #2,0.9994,-0.031829,-0.013831,13.127,0.030364,0.99495,-0.095663,18.811,0.016806,0.095186,0.99532,-12.387
> view matrix models
> #2,0.96779,0.040366,-0.24849,55.157,-0.076511,0.98753,-0.13757,51.888,0.23984,0.15215,0.95882,-63.432
> view matrix models
> #2,0.96724,-0.24698,0.058649,48.838,0.24958,0.96744,-0.042008,-33.291,-0.046365,0.05527,0.99739,8.7539
Average map value = 0.04623 for 25786 atoms, 22347 outside contour
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06195, steps = 128
shifted from previous position = 12.2
rotated from previous position = 9.75 degrees
atoms outside contour = 20858, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99208033 -0.12229480 -0.02864614 34.34093797
0.12308916 0.99200529 0.02783080 -33.67161185
0.02501356 -0.03113642 0.99920210 1.28512125
Axis -0.22854516 -0.20797427 0.95105931
Axis point 289.98274086 262.72939976 0.00000000
Rotation angle (degrees) 7.41213390
Shift along axis 0.37660010
> view matrix models
> #2,0.99843,-0.0027311,0.055991,-9.8315,0.010553,0.99011,-0.13989,26.414,-0.055055,0.14026,0.98858,-14.942
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99843,-0.0027311,0.055991,-10.925,0.010553,0.99011,-0.13989,29.952,-0.055055,0.14026,0.98858,-8.0729
> view matrix models
> #2,0.99843,-0.0027311,0.055991,-17.462,0.010553,0.99011,-0.13989,35.365,-0.055055,0.14026,0.98858,-8.3464
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98588,-0.077829,-0.14829,44.465,0.053032,0.98497,-0.16438,32.703,0.15885,0.1542,0.97519,-53.525
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98588,-0.077829,-0.14829,48.279,0.053032,0.98497,-0.16438,29.396,0.15885,0.1542,0.97519,-52.84
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98786,-0.13066,-0.083988,44.999,0.14392,0.97335,0.17855,-60.86,0.058421,-0.18847,0.98034,38.053
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98786,-0.13066,-0.083988,46.482,0.14392,0.97335,0.17855,-60.595,0.058421,-0.18847,0.98034,37.278
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.96337,-0.25119,-0.093886,78.674,0.26085,0.959,0.11082,-67.812,0.0622,-0.13125,0.9894,22.719
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.96337,-0.25119,-0.093886,80.549,0.26085,0.959,0.11082,-70.825,0.0622,-0.13125,0.9894,21.371
> ui mousemode right translate
> select subtract #2
6 models selected
> show atoms
> hide cartoons
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 152
shifted from previous position = 4.88
rotated from previous position = 16.1 degrees
atoms outside contour = 20515, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994659 -0.01010822 -0.00215449 1.92046438
0.01014460 0.99979352 0.01760702 -6.36320804
0.00197606 -0.01762793 0.99984266 3.62598808
Axis -0.86254020 -0.10111454 0.49578246
Axis point 0.00000000 180.42349393 359.01162573
Rotation angle (degrees) 1.17035379
Shift along axis 0.78463643
> volume #1 level 0.05067
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: Z1FF000KKKS/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 Performance and 4 Efficiency)
Memory: 48 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 7 days, 23 hours, 11 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
P27h-20:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
LEN P27h-10:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-ChopChopMF: 1.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-clix: 0.2.5
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-crai: 0.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
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: 2.5.1
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: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.4.12
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RMF: 0.16
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cripser: 0.0.22
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
DiffFit: 0.7.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
finufft: 2.4.1
fonttools: 4.58.4
fsspec: 2025.7.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
pandas: 2.3.3
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 26.0.1
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt5: 5.15.11
PyQt5-Qt5: 5.15.18
PyQt5_sip: 12.17.2
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.9.7
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
torch: 2.2.0
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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