id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19884	ChimeraX bug report submission	abhinandan.venkateshamurthy@…		"{{{
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,
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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
}}}
"	defect	new	normal		Unassigned