id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20076 Crash in event loop t.jenne@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.7.4-x86_64-i386-64bit 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: Segmentation fault Thread 0x000070001db13000 (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 0x000070001cb10000 (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 0x000070001bb0d000 (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 0x000070001ab0a000 (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 0x0000700019b07000 (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 0x0000700018b04000 (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 0x0000700017b01000 (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 0x0000700016afe000 (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 0x0000700015afb000 (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 0x0000700014af8000 (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 0x0000700013af5000 (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 0x00007ff8466fa100 (most recent call first): 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, kiwisolver._cext, cython.cimports.libc.math, scipy._lib._ccallback_c, 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._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.optimize._group_columns, scipy._lib.messagestream, 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.spatial._ckdtree, 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, scipy.optimize._direct, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.special.cython_special, scipy.stats._stats, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._ansari_swilk_statistics, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.stats._unuran.unuran_wrapper, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering (total: 186) {""app_name"":""ChimeraX"",""timestamp"":""2026-03-26 18:09:08.00 +0100"",""app_version"":""1.10.0"",""slice_uuid"":""f855cdda-9ed8-308a-81a6-2e57ba7af811"",""build_version"":""1.10.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.7.4 (24G517)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""E9D2AE20-CCF9-43A0-BCEC-BE5E6208800A""} { ""uptime"" : 570000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 505, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,2"", ""coalitionID"" : 17979, ""osVersion"" : { ""train"" : ""macOS 15.7.4"", ""build"" : ""24G517"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2026-03-26 18:08:23.2713 +0100"", ""codeSigningMonitor"" : 0, ""incident"" : ""E9D2AE20-CCF9-43A0-BCEC-BE5E6208800A"", ""pid"" : 57970, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2026-03-26 17:55:27.0837 +0100"", ""procStartAbsTime"" : 575987125306944, ""procExitAbsTime"" : 576763024933039, ""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"":""147FB74A-67FC-5DE3-BB3F-66C7D1767748"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""F807DD34-8580-A287-FFF1-122ABF3A1AB9"", ""appleIntelligenceStatus"" : {""reasons"":[""selectedSiriLanguageIneligible"",""deviceNotCapable""],""state"":""unavailable""}, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""bootSessionUUID"" : ""B39A1246-136D-486A-B7AF-0B341DED3C70"", ""wakeTime"" : 36601, ""bridgeVersion"" : {""build"":""23P3120"",""train"":""10.3""}, ""sleepWakeUUID"" : ""F502DAF4-1809-4214-A487-665AA702C04E"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x33fb34964b30 is not in any region. 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\n__LINKEDIT 206.5M 301 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2396K 2 \n__TEXT 1.5G 1264 \n__TEXT (graphics) 1072K 7 \n__TPRO_CONST 16 2 \ndyld private memory 14.5M 111 \nmapped file 562.1M 77 \nshared memory 3004K 29 \n=========== ======= ======= \nTOTAL 6.3G 5527 \nTOTAL, minus reserved VM space 6.1G 5527 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"" } }, ""logWritingSignature"" : ""48244c313a22f236d44269ae659f3c0030828824"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""670e9bd77a111748a97092a1"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""67d07fb744f1a3655d87002b"" }, ""deploymentId"" : 240000016 }, { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : { }, ""deploymentId"" : 240000044 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/Timo/Documents/PhD/PhD_THESIS/Figures_PhD/ClpG- > Plasticity/FigureB_ClpG-Thesis_Xl-MS_3D/ClpG-N1-N2-interaction_AF.cxs Log from Tue Mar 17 19:06:19 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/Timo/Documents/PhD/PhD_THESIS/Figures_PhD/ClpG- > Plasticity/Figure_ClpG-Thesis_N1-N2-interaction/Hydrophobic- > groove_LEALF_N2.cxs Log from Tue Jul 2 10:07:59 2024UCSF ChimeraX version: 1.7.dev202304302138 (2023-04-30) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/Timo/Documents/PhD/Structures/Hydrophobic-groove_N2.cxs Log from Thu May 4 11:54:44 2023UCSF ChimeraX version: 1.7.dev202304302138 (2023-04-30) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Timo/Documents/PhD/Structures/ClpG_AF.pdb Chain information for ClpG_AF.pdb #1 --- Chain | Description A B C D E F | No description available > select /A:1150-2098 7351 atoms, 7460 bonds, 949 residues, 1 model selected > select /B:1150-2098 7351 atoms, 7460 bonds, 949 residues, 1 model selected > select /C:1150-2098 7351 atoms, 7460 bonds, 949 residues, 1 model selected > select /D:1150-2098 7351 atoms, 7460 bonds, 949 residues, 1 model selected > select /E:1150-2098 7351 atoms, 7460 bonds, 949 residues, 1 model selected > select /F:1-949 7351 atoms, 7460 bonds, 949 residues, 1 model selected > renumber #1 4745 residues renumbered > renumber #2 No residues specified > renumber #1 0 residues renumbered > select clear > save /Users/Timo/Desktop/ClpG_AF.pdb relModel #1 > renumber #1 /A 1 Expected a keyword > renumber #1 /A 0 residues renumbered > renumber #1 /B 0 residues renumbered > renumber #1 /C 0 residues renumbered > renumber #1 /D 0 residues renumbered > renumber #1 /E 0 residues renumbered > renumber #1 /F 0 residues renumbered > view clip false > save /Users/Timo/Desktop/1.pdb relModel #1 > save /Users/Timo/Desktop/1.pdb displayedOnly true > mlp Map values for surface ""ClpG_AF.pdb_A SES surface"": minimum -31.13, mean -5.486, maximum 24.82 Map values for surface ""ClpG_AF.pdb_B SES surface"": minimum -31.1, mean -5.467, maximum 24.28 Map values for surface ""ClpG_AF.pdb_C SES surface"": minimum -29.78, mean -5.456, maximum 24.26 Map values for surface ""ClpG_AF.pdb_D SES surface"": minimum -30.01, mean -5.504, maximum 25.78 Map values for surface ""ClpG_AF.pdb_E SES surface"": minimum -31.47, mean -5.462, maximum 24.52 Map values for surface ""ClpG_AF.pdb_F SES surface"": minimum -30.77, mean -5.468, maximum 23.6 To also show corresponding color key, enter the above mlp command and add key true > select #1 /C,D,E,F 29404 atoms, 29840 bonds, 3796 residues, 1 model selected > hide sel cartoons > hide sel surfaces > hide sel atoms > select #1 /A,B 14702 atoms, 14920 bonds, 1898 residues, 1 model selected > hide sel atoms > select #1 /A,B :246-949 10950 atoms, 11110 bonds, 1408 residues, 1 model selected > hide sel surfaces > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > sequence chain /B Alignment identifier is 1/B > select /B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:49-53 41 atoms, 41 bonds, 5 residues, 1 model selected > select /B:54 4 atoms, 3 bonds, 1 residue, 1 model selected > select /B:54-58 31 atoms, 30 bonds, 5 residues, 1 model selected > select /B:53 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:49-53 41 atoms, 41 bonds, 5 residues, 1 model selected > select /B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:49-105 419 atoms, 427 bonds, 57 residues, 1 model selected > hide sel surfaces > hide sel cartoons > show sel cartoons > undo [Repeated 2 time(s)] > hide sel cartoons > hide sel surfaces > show sel surfaces > select #1 /A,B 1-245 Expected a keyword > select #1 /A,B :1-245 3752 atoms, 3808 bonds, 490 residues, 1 model selected > show sel cartoons > transparency (#!1 & sel) 60 > transparency (#!1 & sel) 40 > color #1 /A,B :1-245 grey > mlp sel Map values for surface ""ClpG_AF.pdb_A SES surface"": minimum -31.13, mean -5.486, maximum 24.82 Map values for surface ""ClpG_AF.pdb_B SES surface"": minimum -31.1, mean -5.467, maximum 24.28 To also show corresponding color key, enter the above mlp command and add key true > transparency (#!1 & sel) 40 > select /B:47 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:47-90 331 atoms, 338 bonds, 44 residues, 1 model selected > select /B:106 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:47-106 438 atoms, 447 bonds, 60 residues, 1 model selected > hide sel surfaces > select /B:63 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:63-64 19 atoms, 19 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 19 atom styles > select /B:64-65 12 atoms, 11 bonds, 2 residues, 1 model selected > select /B:64-65 12 atoms, 11 bonds, 2 residues, 1 model selected > select /B:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:64 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select /B:63 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:63-64 19 atoms, 19 bonds, 2 residues, 1 model selected > select /B:63 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:63 11 atoms, 11 bonds, 1 residue, 1 model selected > color #1 /B :63 orange > select /B:66 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:66 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:68 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:68-69 22 atoms, 23 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > select /B:197@CD1 1 atom, 1 residue, 1 model selected > select add /B:197@CD1 1 atom, 1 bond, 1 residue, 1 model selected > select clear > select /B:69 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:68-69 22 atoms, 23 bonds, 2 residues, 1 model selected > color #1 /B :68-69 orange > select #1 /B :1-245 1876 atoms, 1904 bonds, 245 residues, 1 model selected > hide sel atoms [Repeated 2 time(s)] > show sel atoms > hide sel atoms > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel surfaces > show sel surfaces > select #1 /B :63,68,69 33 atoms, 34 bonds, 3 residues, 1 model selected > hide sel atoms > show sel atoms > color (#!1 & sel) orange red > undo > hide sel surfaces > color (#!1 & sel) orange red > show sel surfaces > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting full > lighting soft > lighting flat > lighting simple > select /A:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:49-52 30 atoms, 29 bonds, 4 residues, 1 model selected > select /B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:53 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:53 11 atoms, 11 bonds, 1 residue, 1 model selected > select > /B:32-43,48-52,108-110,114-129,137-146,148-157,161-171,187-203,210-220,224-231,236-247,263-268,272-277,288-299,316-328,346-350,356-372,384-387,401-410,422-429,433-436,449-467,473-486,494-512,516-538,541-571,578-589,598-605,607-613,619-633,656-668,671-673,679-682,686-690,706-713,724-726,729-741,767-775,784-798,801-806,818-839,847-857,863-885 3878 atoms, 3880 bonds, 483 residues, 1 model selected > select /B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:52 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:52-53 19 atoms, 19 bonds, 2 residues, 1 model selected > select /B:49,52-53 27 atoms, 26 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 27 atom styles > color (#!1 & sel) orange > undo > select clear > open ""/Users/Timo/Documents/PhD/Structures/Alignment ClpG-N2 & ClpC- > NTD/ClpG-N2.cif"" Summary of feedback from opening /Users/Timo/Documents/PhD/Structures/Alignment ClpG-N2 & ClpC-NTD/ClpG-N2.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for ClpG-N2.cif #2 --- Chain | Description C | No description available Drag select of 2 residues > select clear > ui mousemode right ""translate selected models"" Drag select of 9 residues > view matrix models #2,1,0,0,-45.083,0,1,0,-33.357,0,0,1,-43.517 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.99207,0.11531,0.050112,-37.917,-0.11147,0.99104,-0.073564,-32.656,-0.058145,0.067394,0.99603,-38.728 > view matrix models > #2,0.82409,-0.46087,-0.32935,-71.395,0.54589,0.80139,0.2445,-51.675,0.15125,-0.38128,0.912,-68.616 > view matrix models > #2,0.98714,0.14723,0.06229,-35.902,-0.14101,0.98548,-0.094583,-32.666,-0.075311,0.084583,0.99357,-37.48 > select #2 1172 atoms, 1187 bonds, 154 residues, 1 model selected > color #2 grey > mlp sel Map values for surface ""ClpG-N2.cif_C SES surface"": minimum -24.4, mean -6.102, maximum 21.85 To also show corresponding color key, enter the above mlp command and add key true > hide sel cartoons > show sel cartoons > transparency (#!2 & sel) 40 > view matrix models > #2,0.98928,-0.13599,0.053177,-59.687,0.13268,0.98926,0.061372,-35.612,-0.060951,-0.053659,0.9967,-49.248 > view matrix models > #2,0.5747,0.80478,-0.14852,24.177,-0.75863,0.45583,-0.46552,-69.736,-0.30693,0.3802,0.87249,-9.9188 > view matrix models > #2,0.80662,-0.58723,-0.067281,-95.365,0.57691,0.7574,0.30581,-60.358,-0.12863,-0.28549,0.94971,-67.89 > view matrix models > #2,0.79727,-0.59919,-0.07304,-96.257,0.58888,0.74549,0.31219,-61.5,-0.13261,-0.29191,0.94721,-68.381 > view matrix models > #2,0.49447,-0.8312,-0.25418,-112.09,0.82594,0.35823,0.43531,-96.931,-0.27078,-0.42519,0.86365,-77.913 > view matrix models > #2,0.47797,0.85333,-0.20828,29.736,-0.80238,0.32769,-0.4988,-79.774,-0.35739,0.40553,0.84132,-7.0192 > ui mousemode right ""move picked models"" > view matrix models > #2,0.47797,0.85333,-0.20828,-3.6517,-0.80238,0.32769,-0.4988,-61.559,-0.35739,0.40553,0.84132,45.195 > select #1 /A 7351 atoms, 7460 bonds, 949 residues, 1 model selected > hide sel surfaces > hide sel atoms > hide sel cartoons > select #1 /B :1-106 807 atoms, 820 bonds, 106 residues, 1 model selected > hide sel surfaces > view matrix models #1,1,0,0,-11.922,0,1,0,-5.5371,0,0,1,-9.2183 > select #1/B:69 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:69 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:68 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:68 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:64 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color (#!1 & sel) orange red > select #1/B:69 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:69-70 22 atoms, 22 bonds, 2 residues, 1 model selected > select #1/B:68-69 22 atoms, 23 bonds, 2 residues, 1 model selected > select #1/B:68-69 22 atoms, 23 bonds, 2 residues, 1 model selected > select #1/B:68 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:68 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms > color (#!1 & sel) gray > select > #1/B:32-43,48-52,108-110,114-129,137-146,148-157,161-171,187-203,210-220,224-231,236-247,263-268,272-277,288-299,316-328,346-350,356-372,384-387,401-410,422-429,433-436,449-467,473-486,494-512,516-538,541-571,578-589,598-605,607-613,619-633,656-668,671-673,679-682,686-690,706-713,724-726,729-741,767-775,784-798,801-806,818-839,847-857,863-885 3878 atoms, 3880 bonds, 483 residues, 1 model selected > select #1/B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:49 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:52 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:52-53 19 atoms, 19 bonds, 2 residues, 1 model selected > select #1/B:49,52-53 27 atoms, 26 bonds, 3 residues, 1 model selected > color (#!1 & sel) yellow > select clear > select #1/B:49,52-53 27 atoms, 26 bonds, 3 residues, 1 model selected > color (#!1 & sel) orange > ui mousemode right ""move picked models"" > view matrix models > #2,0.47797,0.85333,-0.20828,3.3584,-0.80238,0.32769,-0.4988,-53.684,-0.35739,0.40553,0.84132,57.019 > select clear > save /Users/Timo/Documents/PhD/Structures/Hydrophobic-groove_N2.cxs > save /Users/Timo/Documents/PhD/Structures/Hydrophobic-groove_N2.png width > 1215 height 609 supersample 3 > save /Users/Timo/Documents/PhD/Structures/Hydrophobic-groove_N2.png width > 2000 height 1002 supersample 3 > save /Users/Timo/Documents/PhD/Structures/Hydrophobic-groove_N2.pdb > select #1/B:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:120 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > color (#!1 & sel) magenta > select #1/B:193 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:193 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > color (#!1 & sel) magenta > select #2 1172 atoms, 1187 bonds, 154 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/C Alignment identifier is 2/C > renumber #2 1 Expected a keyword > renumber #2 /C 1 Expected a keyword > renumber #2 /C start 1 154 residues renumbered > renumber #2 /C start 107 154 residues renumbered > select #2/C:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:120-121 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/C:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:120,193 16 atoms, 14 bonds, 2 residues, 1 model selected > select > #2/C:108-110,114-129,137-146,148-157,161-171,187-202,210-220,224-231,236-247 757 atoms, 757 bonds, 97 residues, 1 model selected > select #2/C:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:120-121 17 atoms, 16 bonds, 2 residues, 1 model selected > select > #2/C:108-110,114-129,137-146,148-157,161-171,187-202,210-220,224-231,236-247 757 atoms, 757 bonds, 97 residues, 1 model selected > select #2/C:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:120 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > color (#!2 & sel) orange red > select #2/C:193 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:193 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > color (#!2 & sel) blue > select #2/C:112 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:112 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > show sel atoms > color (#!2 & sel) orange > select #2/C:213 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:213 11 atoms, 11 bonds, 1 residue, 1 model selected > style sel stick Changed 11 atom styles > show sel atoms > color (#!2 & sel) orange > select clear > save /Users/Timo/Documents/PhD/Structures/Hydrophobic-groove_N2.cxs ——— End of log from Thu May 4 11:54:44 2023 ——— opened ChimeraX session > set bgColor white > lighting gentle > select 45278 atoms, 45947 bonds, 5848 residues, 2 models selected > color (#!1-2 & sel) light sea green > select 1:106 Expected an objects specifier or a keyword > select :1-106 4842 atoms, 4920 bonds, 636 residues, 1 model selected > color (#!1 & sel) cornflower blue > select clear > select :107-300 10112 atoms, 10235 bonds, 1318 residues, 2 models selected > mlp sel Map values for surface ""ClpG_AF.pdb_A SES surface"": minimum -31.13, mean -5.486, maximum 24.82 Map values for surface ""ClpG_AF.pdb_B SES surface"": minimum -31.1, mean -5.467, maximum 24.28 Map values for surface ""ClpG_AF.pdb_C SES surface"": minimum -29.78, mean -5.456, maximum 24.26 Map values for surface ""ClpG_AF.pdb_D SES surface"": minimum -30.01, mean -5.504, maximum 25.78 Map values for surface ""ClpG_AF.pdb_E SES surface"": minimum -31.47, mean -5.462, maximum 24.52 Map values for surface ""ClpG_AF.pdb_F SES surface"": minimum -30.77, mean -5.468, maximum 23.6 Map values for surface ""ClpG-N2.cif_C SES surface"": minimum -25.05, mean -6.111, maximum 22.19 To also show corresponding color key, enter the above mlp command and add key true > select #1 A Expected a keyword > select #1 /A 7351 atoms, 7460 bonds, 949 residues, 1 model selected > hide sel surfaces > select #1 /C-F 29404 atoms, 29840 bonds, 3796 residues, 1 model selected > hide sel surfaces > select #1 :260-300 1950 atoms, 1962 bonds, 246 residues, 1 model selected > hide sel surfaces > lighting soft [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting soft > lighting gentle > matchmaker #2 /C to #1 /B Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ClpG_AF.pdb, chain B (#1) with ClpG-N2.cif, chain C (#2), sequence alignment score = 773.4 RMSD between 154 pruned atom pairs is 0.001 angstroms; (across all 154 pairs: 0.001) > select #1 44106 atoms, 44760 bonds, 5694 residues, 1 model selected > hide sel surfaces > select clear > select 45278 atoms, 45947 bonds, 5848 residues, 2 models selected > hide sel atoms > select :49-53 246 atoms, 246 bonds, 30 residues, 1 model selected > color (#!1 & sel) orange red > select #1/B:49,52,53 27 atoms, 26 bonds, 3 residues, 1 model selected > show sel atoms > select clear > ui tool show ""Side View"" > select clear > select #1/B:62 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:62,67 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 16 atom styles > color (#!1 & sel) yellow > color (#!1 & sel) orange > select clear > select #1/B:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > color (#!1 & sel) yellow > select #1/B:122 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > color (#!1 & sel) yellow > select 45278 atoms, 45947 bonds, 5848 residues, 4 models selected > transparency 50 > select #2/C:117@OE1 1 atom, 1 residue, 1 model selected > select #2/C:117@OE1 1 atom, 1 residue, 1 model selected > select 45278 atoms, 45947 bonds, 5848 residues, 4 models selected > hide sel surfaces > select clear > select #1/B:117@OE2 1 atom, 1 residue, 1 model selected > select #1/B:117@OE1 1 atom, 1 residue, 1 model selected > select add #1/B:62@OD1 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #1/B:117@OE1 #1/B:62@OD1 Distance between ClpG_AF.pdb #1/B GLU 117 OE1 and ASP 62 OD1: 22.679Å > select add #1/B:67@OD1 3 atoms, 3 residues, 2 models selected > select subtract #1/B:62@OD1 2 atoms, 2 residues, 2 models selected > distance #1/B:117@OE1 #1/B:67@OD1 Distance between ClpG_AF.pdb #1/B GLU 117 OE1 and ASP 67 OD1: 27.664Å > select add #1/B:122@OE2 3 atoms, 3 residues, 2 models selected > select subtract #1/B:117@OE1 2 atoms, 2 residues, 2 models selected > distance #1/B:67@OD1 #1/B:122@OE2 Distance between ClpG_AF.pdb #1/B ASP 67 OD1 and GLU 122 OE2: 37.689Å > select add #1/B:62@OD1 3 atoms, 3 residues, 2 models selected > select subtract #1/B:67@OD1 2 atoms, 2 residues, 2 models selected > distance #1/B:122@OE2 #1/B:62@OD1 Distance between ClpG_AF.pdb #1/B GLU 122 OE2 and ASP 62 OD1: 32.165Å > ui tool show ""Side View"" > select clear > open > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_model_0.cif Chain information for fold_2024_07_01_16_56_model_0.cif #4 --- Chain | Description A | . > open > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_model_1.cif Chain information for fold_2024_07_01_16_56_model_1.cif #5 --- Chain | Description A | . > open > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_model_2.cif Chain information for fold_2024_07_01_16_56_model_2.cif #6 --- Chain | Description A | . > open > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_model_3.cif Chain information for fold_2024_07_01_16_56_model_3.cif #7 --- Chain | Description A | . > open > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_model_4.cif Chain information for fold_2024_07_01_16_56_model_4.cif #8 --- Chain | Description A | . > matchmaker #4 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ClpG-N2.cif, chain C (#2) with fold_2024_07_01_16_56_model_0.cif, chain A (#4), sequence alignment score = 697.7 RMSD between 140 pruned atom pairs is 0.376 angstroms; (across all 140 pairs: 0.376) > matchmaker #5 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ClpG-N2.cif, chain C (#2) with fold_2024_07_01_16_56_model_1.cif, chain A (#5), sequence alignment score = 700.7 RMSD between 140 pruned atom pairs is 0.353 angstroms; (across all 140 pairs: 0.353) > matchmaker #6 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ClpG-N2.cif, chain C (#2) with fold_2024_07_01_16_56_model_2.cif, chain A (#6), sequence alignment score = 700.7 RMSD between 140 pruned atom pairs is 0.388 angstroms; (across all 140 pairs: 0.388) > matchmaker #7 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ClpG-N2.cif, chain C (#2) with fold_2024_07_01_16_56_model_3.cif, chain A (#7), sequence alignment score = 700.7 RMSD between 140 pruned atom pairs is 0.351 angstroms; (across all 140 pairs: 0.351) > matchmaker #8 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ClpG-N2.cif, chain C (#2) with fold_2024_07_01_16_56_model_4.cif, chain A (#8), sequence alignment score = 700.7 RMSD between 139 pruned atom pairs is 0.360 angstroms; (across all 140 pairs: 0.420) > select #4-8 9420 atoms, 9560 bonds, 1230 residues, 5 models selected > color sel forest green > select #4-8 :62 40 atoms, 35 bonds, 5 residues, 5 models selected > show sel atoms > undo > select #4-8 :67 40 atoms, 35 bonds, 5 residues, 5 models selected > show sel atoms > select #4-8 :49-53 205 atoms, 205 bonds, 25 residues, 5 models selected > color sel yellow > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #4 models > show #5 models > show #4 models > hide #5 models > hide #4 models > show #5 models > show #6 models > hide #5 models > hide #6 models > show #7 models > hide #7 models > show #8 models > open > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_full_data_0.json fold_2024_07_01_16_56_full_data_0.json does not look like Mole Online json file, does not contain Channels. > open > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_summary_confidences_4.json fold_2024_07_01_16_56_summary_confidences_4.json does not look like Mole Online json file, does not contain Channels. > ui tool show ""AlphaFold Error Plot"" Must choose path to predicted aligned file > alphafold pae #8 file > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_full_data_4.json > ui tool show ""AlphaFold Error Plot"" > alphafold pae #7 file > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_full_data_3.json > ui tool show ""AlphaFold Error Plot"" > alphafold pae #4 file > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_full_data_0.json > ui tool show ""AlphaFold Error Plot"" > alphafold pae #5 file > /Users/Timo/Downloads/fold_2024_07_01_16_56/fold_2024_07_01_16_56_full_data_1.json > open > /Users/Timo/Downloads/ClpG-N1-N2_RoseTTAFold2_X1_24a8d/rf2_seed0_00_pred.pdb Chain information for rf2_seed0_00_pred.pdb #9 --- Chain | Description A | No description available > matchmaker #9 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ClpG-N2.cif, chain C (#2) with rf2_seed0_00_pred.pdb, chain A (#9), sequence alignment score = 676.7 RMSD between 132 pruned atom pairs is 0.492 angstroms; (across all 140 pairs: 1.494) > select #9 3746 atoms, 3772 bonds, 246 residues, 1 model selected > color sel magenta > hide #8 models > select #9 :49-53 83 atoms, 83 bonds, 5 residues, 1 model selected > color sel lime > select #9 :49,52,53 58 atoms, 57 bonds, 3 residues, 1 model selected > style sel ball Changed 58 atom styles > show sel atoms > hide #!1 models > hide #!2 models > hide #3.1 models > hide #9 models > hide #!3 models > open > /Users/Timo/Downloads/ClpG-N1-N2_RoseTTAFold2_X1_24a8d/rf2_seed0_00_pred.pdb Chain information for rf2_seed0_00_pred.pdb #10 --- Chain | Description A | No description available > open > /Users/Timo/Downloads/ClpG-N1-N2_RoseTTAFold2_X1_24a8d/rf2_seed1_00_pred.pdb Chain information for rf2_seed1_00_pred.pdb #11 --- Chain | Description A | No description available > open > /Users/Timo/Downloads/ClpG-N1-N2_RoseTTAFold2_X1_24a8d/rf2_seed2_00_pred.pdb Chain information for rf2_seed2_00_pred.pdb #12 --- Chain | Description A | No description available > open > /Users/Timo/Downloads/ClpG-N1-N2_RoseTTAFold2_X1_24a8d/rf2_seed3_00_pred.pdb Chain information for rf2_seed3_00_pred.pdb #13 --- Chain | Description A | No description available > open > /Users/Timo/Downloads/ClpG-N1-N2_RoseTTAFold2_X1_24a8d/rf2_seed4_00_pred.pdb Chain information for rf2_seed4_00_pred.pdb #14 --- Chain | Description A | No description available > matchmaker #10-14 to #9 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rf2_seed0_00_pred.pdb, chain A (#9) with rf2_seed0_00_pred.pdb, chain A (#10), sequence alignment score = 1236.5 RMSD between 246 pruned atom pairs is 0.000 angstroms; (across all 246 pairs: 0.000) Matchmaker rf2_seed0_00_pred.pdb, chain A (#9) with rf2_seed1_00_pred.pdb, chain A (#11), sequence alignment score = 1226.3 RMSD between 170 pruned atom pairs is 0.613 angstroms; (across all 246 pairs: 4.215) Matchmaker rf2_seed0_00_pred.pdb, chain A (#9) with rf2_seed2_00_pred.pdb, chain A (#12), sequence alignment score = 1201.1 RMSD between 140 pruned atom pairs is 0.528 angstroms; (across all 246 pairs: 9.917) Matchmaker rf2_seed0_00_pred.pdb, chain A (#9) with rf2_seed3_00_pred.pdb, chain A (#13), sequence alignment score = 1218.5 RMSD between 171 pruned atom pairs is 0.759 angstroms; (across all 246 pairs: 6.821) Matchmaker rf2_seed0_00_pred.pdb, chain A (#9) with rf2_seed4_00_pred.pdb, chain A (#14), sequence alignment score = 1223.3 RMSD between 145 pruned atom pairs is 0.494 angstroms; (across all 246 pairs: 9.066) > ui mousemode right zoom > ui mousemode right translate > select #9-14 :49-53 498 atoms, 498 bonds, 30 residues, 6 models selected > select #9-14 :49,52,53 348 atoms, 342 bonds, 18 residues, 6 models selected > show sel & #10-14 atoms > select #9-14 :106-250 13032 atoms, 13116 bonds, 846 residues, 6 models selected > mlp sel & #10-14 Map values for surface ""rf2_seed0_00_pred.pdb_A SES surface"": minimum -26.36, mean -4.604, maximum 24.88 Map values for surface ""rf2_seed4_00_pred.pdb_A SES surface"": minimum -29.29, mean -4.524, maximum 24.38 Map values for surface ""rf2_seed2_00_pred.pdb_A SES surface"": minimum -28.63, mean -4.523, maximum 24.05 Map values for surface ""rf2_seed1_00_pred.pdb_A SES surface"": minimum -26.11, mean -4.478, maximum 22.7 Map values for surface ""rf2_seed3_00_pred.pdb_A SES surface"": minimum -27.81, mean -4.586, maximum 25.29 To also show corresponding color key, enter the above mlp command and add key true > hide #!14 models > hide #!13 models > hide #!11 models > hide #!12 models > show #!11 models > hide #!10 models > select #11/A:86 16 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #11/A:85 16 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #11/A:83 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #11/A:190@O 1 atom, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > select #11/A:83 12 atoms, 11 bonds, 1 residue, 1 model selected > ui tool show Contacts > contacts sel resSeparation 12 intraRes true ignoreHiddenModels true select > true color #31a42b reveal true No contacts > contacts sel resSeparation 12 intraRes true ignoreHiddenModels true select > true color #31a42b reveal true No atoms match given atom specifier > select #11/A:83 12 atoms, 11 bonds, 1 residue, 1 model selected > ui tool show Contacts > select #11/A:84 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > ui tool show Contacts > contacts sel resSeparation 12 intraRes true ignoreHiddenModels true select > true color #31a42b reveal true No contacts > hide #!11 models > show #!12 models > select #12/A:86 16 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear [Repeated 1 time(s)] > select #12/A:85 16 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > hide #!12 models > show #!13 models > hide #!13 models > show #!14 models > open /Users/Timo/Downloads/ClpG-N1-N2_RoseTTAFold2_X1_24a8d/rf2_seed0_00.npz Unrecognized file suffix '.npz' > close #9,15#10-14 > show #4 models > show #5 models > close #4-8 > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select #2 1172 atoms, 1187 bonds, 154 residues, 1 model selected > mlp sel Map values for surface ""ClpG-N2.cif_C SES surface"": minimum -24.06, mean -6.101, maximum 22.36 To also show corresponding color key, enter the above mlp command and add key true > select clear > show #!3 models > show #3.1 models > hide #3.1 models > select #1/B:67@CA 1 atom, 1 residue, 1 model selected > select #1/B:62@CA 1 atom, 1 residue, 1 model selected > select add #1/B:67@CA 2 atoms, 2 residues, 2 models selected > color (#!1 & sel) black > select #2 :62,67 Nothing selected > select 12 :62,67 Expected an objects specifier or a keyword > select #1 :62,67 96 atoms, 84 bonds, 12 residues, 1 model selected > color (#!1 & sel) purple > color (#!1 & sel) black > color (#!1 & sel) yellow > show #3.1 models > show #!3 target m > pbond color black Unknown command: pbond color black > pbond color black Unknown command: pbond color black > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select add #3 96 atoms, 84 bonds, 4 pseudobonds, 12 residues, 9 models selected > color black > color (#!1 & sel) black > select clear > select add #3 4 pseudobonds, 2 models selected > dashes 8 Unknown command: dashes 8 > dashes 6 Unknown command: dashes 6 > pbond dashes 6 Unknown command: pbond dashes 6 > style dashes 6 Changed 1 pseudobond dash > style dashes 10 Changed 1 pseudobond dash > style dashes 12 Changed 1 pseudobond dash > style dashes 16 Changed 1 pseudobond dash > select clear > style radius 1 Expected a keyword > style size 1 Expected a keyword > radius 1 Unknown command: radius 1 > select add #3 4 pseudobonds, 2 models selected > radius 1 Unknown command: radius 1 > style radius 1 Expected a keyword > style radius 2 Expected a keyword > size radius 2 Expected a keyword > size pseudobondRadius 2 Changed 4 pseudobond radii > size pseudobondRadius 0.02 Changed 4 pseudobond radii > size pseudobondRadius 0.1 Changed 4 pseudobond radii > size pseudobondRadius 0.2 Changed 4 pseudobond radii > select clear > size pseudobondRadius 0.1 Changed 4 pseudobond radii > select add #3 4 pseudobonds, 2 models selected > color white No visible atoms, bonds, or surfaces selected > select clear > select add #3 4 pseudobonds, 2 models selected No visible atoms, bonds, or surfaces selected > select subtract #3.1 4 pseudobonds, 1 model selected No visible atoms, bonds, or surfaces selected > save /Users/Timo/Documents/PhD/Structures/Hydrophobic-groove_LEALF_N2.cxs ——— End of log from Tue Jul 2 10:07:59 2024 ——— > view name session-start opened ChimeraX session > open ""/Users/Timo/Documents/PhD/Structures/Alignment ClpG-N2 & ClpC- > NTD/ClpG-N2.cif"" Summary of feedback from opening /Users/Timo/Documents/PhD/Structures/Alignment ClpG-N2 & ClpC-NTD/ClpG-N2.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for ClpG-N2.cif #4 --- Chain | Description C | No description available Computing secondary structure > hide #!3 models > hide #3.1 models > close #4 > select :1-106 4842 atoms, 4920 bonds, 636 residues, 1 model selected > color sel light sea green > select clear > select :107-260 8204 atoms, 8309 bonds, 1078 residues, 2 models selected > color sel cornflower blue > select clear > ui tool show ""Side View"" > lighting simple > select :107-260 8204 atoms, 8309 bonds, 1078 residues, 2 models selected > mlp sel Map values for surface ""ClpG-N2.cif_C SES surface"": minimum -24.06, mean -6.101, maximum 22.36 Map values for surface ""ClpG_AF.pdb_A SES surface"": minimum -31.13, mean -5.486, maximum 24.82 Map values for surface ""ClpG_AF.pdb_B SES surface"": minimum -31.1, mean -5.467, maximum 24.28 Map values for surface ""ClpG_AF.pdb_C SES surface"": minimum -29.78, mean -5.456, maximum 24.26 Map values for surface ""ClpG_AF.pdb_D SES surface"": minimum -30.01, mean -5.504, maximum 25.78 Map values for surface ""ClpG_AF.pdb_E SES surface"": minimum -31.47, mean -5.462, maximum 24.52 Map values for surface ""ClpG_AF.pdb_F SES surface"": minimum -30.77, mean -5.468, maximum 23.6 > hide #1.1 models > hide #1.3 models > hide #1.2 models > show #1.2 models > hide #1.2 models > hide #1.5 models > hide #1.6 models > select #1/D 7351 atoms, 7460 bonds, 949 residues, 1 model selected > hide sel > hide sel surfaces > lighting full > lighting soft > hide #!2 models > show #!2 models > hide #!2 models > hide #2.1 models > show #2.1 models > hide #!2 models > show #!2 models > hide #1.4 models > show #1.4 models > hide #!2 models > hide #1.4 models > show #1.4 models > hide #!1 models > show #!1 models > select :49,52,53,63,63,112,120,193 396 atoms, 369 bonds, 45 residues, 2 models selected > hide atoms > show sel atoms > select #1:49,52,53,63,63,112,120,193 372 atoms, 348 bonds, 42 residues, 1 model selected > show sel atoms > select subtract #1.3 310 atoms, 290 bonds, 35 residues, 7 models selected > select add #1.3 7661 atoms, 290 bonds, 984 residues, 6 models selected > close #1.3 > show #1.2 models > hide #1.2 models > show #1.1 models > close #1.1 > close #1.5 > close #1.6 > hide atoms > select #1/B:49,52,53,63,63,112,120,193 62 atoms, 58 bonds, 7 residues, 1 model selected > show sel atoms > select #1/B:49,52,53,63,64,112,120,193 70 atoms, 66 bonds, 8 residues, 1 model selected > show sel atoms > style sel stick Changed 70 atom styles > style sel ball Changed 70 atom styles > style sel stick Changed 70 atom styles > select #1/B:112,120,193 24 atoms, 21 bonds, 3 residues, 1 model selected > ui tool show ""Color Actions"" > color sel orange red target apf > select #1/B:49,52,53,63,64 46 atoms, 45 bonds, 5 residues, 1 model selected > ui tool show ""Color Actions"" > color sel yellow target apf > lighting soft [Repeated 1 time(s)] > color (#!1 & sel) #feff00ff target apf > select clear > select #1/B:49,52,53,63,64 46 atoms, 45 bonds, 5 residues, 1 model selected > color (#!1 & sel) orange red > undo > color sel orange red target apf > select #1/B:112,120,193 24 atoms, 21 bonds, 3 residues, 1 model selected > color sel yellow target apf > undo [Repeated 2 time(s)] > select clear > show #1/B:107-260 surfaces > hide #1/B:107-260 surfaces > show #!2 models > hide #!2 models > show #!2 models > hide #!2.1 models > save /Users/Timo/Documents/PhD/PhD_THESIS/Figures_PhD/ClpG- > Plasticity/Figure_ClpG- > Thesis_N1-N2-interaction/ClpG-N1-N2-interaction_AF.cxs ——— End of log from Tue Mar 17 19:06:19 2026 ——— > view name session-start opened ChimeraX session > hide atoms > ui tool show ""Side View"" > ui tool show XMAS > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models /Users/Timo/Library/Application Support/ChimeraX/1.10/lib/python/site- packages/openpyxl/worksheet/_reader.py:313: UserWarning: Failed to load a conditional formatting rule. It will be discarded. Cause: expected warn(msg) Peptide pair mapping of XlinkX evidence file: /Users/Timo/Documents/PhD/Data/Mass- spectrometry/Analysis/final_replicates_WT_Y541A/DHSO- DSSO_merged/XMAS_new/DHSO-DSSO_XMAS_WT_N1-N2-specific_crosslink_both.xlsx Unique peptide pairs: 2 out of 2 Unique peptide pairs with pseudobonds: 2 /Users/Timo/Library/Application Support/ChimeraX/1.10/lib/python/site- packages/chimerax/XMAS/info_file.py:46: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. self.df = pd.concat([self.df, df_add], ignore_index=True) Pseudobonds are stored in /Users/Timo/Documents/PhD/Data/Mass- spectrometry/Analysis/final_replicates_WT_Y541A/DHSO- DSSO_merged/XMAS_new/DHSO-DSSO_XMAS_WT_N1-N2-specific_crosslink_both_1.pb Mapping information is stored in /Users/Timo/Documents/PhD/Data/Mass- spectrometry/Analysis/final_replicates_WT_Y541A/DHSO- DSSO_merged/XMAS_new/DHSO-DSSO_XMAS_WT_N1-N2-specific_crosslink_both_1.tsv > select :62,117,122 174 atoms, 154 bonds, 74 pseudobonds, 20 residues, 4 models selected > style sel ball Changed 174 atom styles > show sel atoms > select clear > select subtract #4 Nothing selected > select add #4 72 pseudobonds, 1 model selected > hide #4 models > undo > select #1/B:62,117,122 26 atoms, 23 bonds, 4 pseudobonds, 3 residues, 3 models selected > style sel ball Changed 26 atom styles > show sel atoms > select clear > close #2 Please select pseudobonds > select clear > select /B:62@OD2 1 atom, 1 residue, 1 model selected > select /B:122@OE2 1 atom, 1 residue, 1 model selected > select add /B:62@OD2 2 atoms, 2 residues, 2 models selected > distance /B:122@OE2 /B:62@OD2 Distance between /B GLU 122 OE2 and ASP 62 OD2: 31.777Å > show #!3 models > show #3.1 models > hide #3.1 models > hide #4 models > show #4 models > hide #4 models > hide #!3 models > show #!3 models > show #3.1 models > hide #3.1 models > hide #!3 models > show #!3 models > show #4 models > hide #!3 models > show #!3 models > hide #4 models > hide sel ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-23.7.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. 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: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2,4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2094.80.5.0.0 (iBridge: 23.16.13120.0.0,0) OS Loader Version: 583~2317 Software: System Software Overview: System Version: macOS 15.7.4 (24G517) Kernel Version: Darwin 24.6.0 Time since boot: 11 Tage, 7 Stunden und 23 Minuten Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal U28E590: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: HTPJ206301 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 14,15 BK550Y: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 906NTBK9X965 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 2,60 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 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-Clashes: 2.3 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-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-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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 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-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 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-XMAS: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 et_xmlfile: 2.0.0 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 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 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 openpyxl: 3.1.5 openvr: 1.26.701 packaging: 24.2 pandas: 2.3.1 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: 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 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 QtRangeSlider: 0.1.5 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 seaborn: 0.13.2 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 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 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 closed normal Core can't reproduce Tom Goddard all ChimeraX