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Opened 4 hours ago
#20076 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-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. Bytes after previous region: 57147592981297 Bytes before following region: 48399104193744\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 1735de000-17e9b9000 [179.9M] r--\/rwx SM=COW Object_id=45408de4\n---> GAP OF 0x5ffe81647000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000033fb34964b30","rawCodes":[1,57154012072752],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000033fb34964b30"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":57970},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x33fb34964b30 is not in any region. Bytes after previous region: 57147592981297 Bytes before following region: 48399104193744\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 1735de000-17e9b9000 [179.9M] r--\/rwx SM=COW Object_id=45408de4\n---> GAP OF 0x5ffe81647000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
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"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
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"base" : 140703271288832,
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 22350868,
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"name" : "dyld"
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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===== 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
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