Opened 9 hours ago

Closed 6 hours ago

#19197 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: nirakar.basnet@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-15.7.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000034440b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003433ff000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003423f3000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003413e7000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003403db000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033f3cf000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033e3c3000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033d3b7000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033c3ab000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033b39f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033a393000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000339387000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033837b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033736f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000336363000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000002057ca140 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mlp._mlp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, PIL._webp (total: 124)


{"app_name":"ChimeraX","timestamp":"2025-10-17 16:24:51.00 -0400","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.7.1 (24G231)","roots_installed":0,"name":"ChimeraX","incident_id":"5F7F2539-7567-4D37-809C-733B5793660A"}
{
  "uptime" : 280000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac15,7",
  "coalitionID" : 59400,
  "osVersion" : {
    "train" : "macOS 15.7.1",
    "build" : "24G231",
    "releaseType" : "User"
  },
  "captureTime" : "2025-10-17 16:22:45.2054 -0400",
  "codeSigningMonitor" : 1,
  "incident" : "5F7F2539-7567-4D37-809C-733B5793660A",
  "pid" : 47842,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-10-16 10:24:19.1847 -0400",
  "procStartAbsTime" : 5782518730032,
  "procExitAbsTime" : 6895705619157,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"8E152946-D05D-51FB-A160-513C9C526A96","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "BD1308D5-7C1C-C889-AD39-6908BB6F1170",
  "appleIntelligenceStatus" : {"state":"available"},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "28265B25-C5A1-4A52-A818-A721073E7D91",
  "wakeTime" : 23120,
  "sleepWakeUUID" : "2433B658-3394-4719-A33A-7828552F4AB8",
  "sip" : "enabled",
  "vmRegionInfo" : "0x24b00000169 is not in any region.  Bytes after previous region: 2040109465962  Bytes before following region: 103031970463383\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x0001024b00000169","rawCodes":[1,283996122513769],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0001024b00000169 -> 0x0000024b00000169 (possible pointer authentication failure)"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":47842},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0x24b00000169 is not in any region.  Bytes after previous region: 2040109465962  Bytes before following region: 103031970463383\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 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},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6100810840},{"value":80},{"value":115},{"value":1153027057755449088},{"value":1027},{"value":16860872871700459653},{"value":16860872863195156933},{"value":14757395258967641293},{"value":4294967286},{"value":6100810769},{"value":0},{"value":49},{"value":4294967280},{"value":328},{"value":8699123016},{"value":0},{"value":11},{"value":259},{"value":8681988640,"symbolLocation":224,"symbol":"_main_thread"},{"value":316},{"value":1},{"value":4387489328,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8643170304,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8643170304,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6837172296},"cpsr":{"value":1073745920},"fp":{"value":6100810912},"sp":{"value":6100810880},"esr":{"value":1442840704,"description":" 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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3AFC

3afc title:  
Mouse Semaphorin 6A extracellular domain [more info...]  
  
Chain information for 3afc #1  
---  
Chain | Description | UniProt  
A B | Semaphorin-6A | SEM6A_MOUSE 19-570  
  
Non-standard residues in 3afc #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> close session

> open 3OKY

3oky title:  
Plexin A2 in complex with Semaphorin 6A [more info...]  
  
Chain information for 3oky #1  
---  
Chain | Description | UniProt  
A | Plexin-A2 | PLXA2_MOUSE 35-703  
B | Putative uncharacterized protein | Q8BUT0_MOUSE 19-571  
  
Non-standard residues in 3oky #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
3oky mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sequence chain #1/B

Alignment identifier is 1/B  

> select /B:20-568

4302 atoms, 4411 bonds, 3 pseudobonds, 540 residues, 2 models selected  

> select /A:37-657

4767 atoms, 4889 bonds, 2 pseudobonds, 609 residues, 2 models selected  

> close session

> open 7Y4Q

Summary of feedback from opening 7Y4Q fetched from pdb  
---  
note | Fetching compressed mmCIF 7y4q from http://files.rcsb.org/download/7y4q.cif  
  
7y4q title:  
Semaphorin 6D in complex with Plexin A1 [more info...]  
  
Chain information for 7y4q #1  
---  
Chain | Description | UniProt  
A B | Plexin-A1 | PLXA1_HUMAN 27-708  
C D | Semaphorin 6D | A0A0G2JZC4_RAT 22-570  
  
Non-standard residues in 7y4q #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> sequence chain #1/A#1/B

Alignment identifier is 1  

> select /A:39-708

5235 atoms, 5371 bonds, 670 residues, 1 model selected  

> select /B:39-708

5235 atoms, 5371 bonds, 670 residues, 1 model selected  

> select /B:39-708

5235 atoms, 5371 bonds, 670 residues, 1 model selected  

> select /A:39-708

5235 atoms, 5371 bonds, 670 residues, 1 model selected  

> select /B:39-708

5235 atoms, 5371 bonds, 670 residues, 1 model selected  

> select /C:23-569

4196 atoms, 4306 bonds, 3 pseudobonds, 525 residues, 2 models selected  

> select /A:39-708

5235 atoms, 5371 bonds, 670 residues, 1 model selected  

> select /B:39-708

5235 atoms, 5371 bonds, 670 residues, 1 model selected  

> close session

> open 3NVQ

3nvq title:  
Molecular mechanism of guidance cue recognition [more info...]  
  
Chain information for 3nvq #1  
---  
Chain | Description | UniProt  
A E | Semaphorin-7A | SEM7A_HUMAN 45-634  
B F | Plexin-C1 | PLXC1_HUMAN 35-507  
  
Non-standard residues in 3nvq #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose  
  

> select /A:46-633

4706 atoms, 4848 bonds, 588 residues, 1 model selected  

> select /E:46-633

4706 atoms, 4848 bonds, 588 residues, 1 model selected  

> close session

> open 3OKY

3oky title:  
Plexin A2 in complex with Semaphorin 6A [more info...]  
  
Chain information for 3oky #1  
---  
Chain | Description | UniProt  
A | Plexin-A2 | PLXA2_MOUSE 35-703  
B | Putative uncharacterized protein | Q8BUT0_MOUSE 19-571  
  
Non-standard residues in 3oky #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
3oky mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> select /A

5025 atoms, 4964 bonds, 2 pseudobonds, 800 residues, 2 models selected  

> hide target m

> show target m

> hide (#!1 & sel) target a

> cartoon hide (#!1 & sel)

> hide sel atoms

> show sel atoms

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> select clear

> hide atoms

> mlp

Map values for surface "3oky_A SES surface": minimum -31.67, mean -5.644,
maximum 22.68  
Map values for surface "3oky_B SES surface": minimum -27.95, mean -5.548,
maximum 24.2  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp

Map values for surface "3oky_A SES surface": minimum -31.67, mean -5.644,
maximum 22.68  
Map values for surface "3oky_B SES surface": minimum -27.95, mean -5.548,
maximum 24.2  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide surfaces

> open 10LZ

Fetching url http://files.rcsb.org/download/10lz.cif failed:  
HTTP Error 404: Not Found  

> open 1oLZ

Summary of feedback from opening 1oLZ fetched from pdb  
---  
note | Fetching compressed mmCIF 1olz from http://files.rcsb.org/download/1olz.cif  
  
1olz title:  
The ligand-binding face of the semaphorins revealed by the high resolution
crystal structure of SEMA4D [more info...]  
  
Chain information for 1olz #2  
---  
Chain | Description | UniProt  
A B | SEMAPHORIN 4D | SM4D_HUMAN 1-656  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Computing secondary structure  
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 3oky, chain B (#1) with 1olz, chain B (#2), sequence alignment
score = 1014.8  
RMSD between 357 pruned atom pairs is 0.943 angstroms; (across all 490 pairs:
4.945)  
  

> hide #!1 models

> select add #1

9600 atoms, 9445 bonds, 5 pseudobonds, 1551 residues, 3 models selected  

> select #2/A:3-628

4914 atoms, 5042 bonds, 1 pseudobond, 622 residues, 2 models selected  

> hide sel cartoons

> show #!1 models

> hide #!1 models

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
1olz #2/A VAL 628 CB  
1olz #2/A VAL 628 O  
1olz #2/A VAL 628 CA  
1olz #2/A VAL 628 CG2  
1olz #2/A VAL 628 C  
1olz #2/A VAL 628 CG1  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 1olz_A SES surface #2.2: minimum, -16.94, mean -0.02,
maximum 17.23  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select clear

> select add #2.2

4914 atoms, 622 residues, 1 model selected  

> select subtract #2.2

1 model selected  

> select add #2.2

4914 atoms, 622 residues, 1 model selected  

> close #2.2

> select add #1.3

9216 atoms, 1162 residues, 2 models selected  

> select subtract #1.3

4914 atoms, 622 residues, 2 models selected  

> show #!1 models

> hide #!1 models

> close #1.3

> close #1.2

> select add #2

10669 atoms, 10084 bonds, 2 pseudobonds, 2085 residues, 3 models selected  

> color sel bychain

> mlp sel

Map values for surface "1olz_A SES surface": minimum -28.99, mean -5.13,
maximum 25.01  
Map values for surface "1olz_B SES surface": minimum -29.33, mean -5.23,
maximum 23.49  
To also show corresponding color key, enter the above mlp command and add key
true  

> select subtract #2.3

5755 atoms, 5042 bonds, 1 pseudobond, 1463 residues, 5 models selected  

> select add #2.3

10669 atoms, 5042 bonds, 1 pseudobond, 2085 residues, 4 models selected  

> select subtract #2.2

5755 atoms, 1463 residues, 4 models selected  

> select add #2.2

10669 atoms, 2085 residues, 3 models selected  

> hide sel surfaces

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
1olz #2/B VAL 628 CB  
1olz #2/B VAL 628 O  
1olz #2/B VAL 628 CA  
1olz #2/B VAL 628 CG2  
1olz #2/B VAL 628 C  
1olz #2/B VAL 628 CG1  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 1olz_A SES surface #2.2: minimum, -16.94, mean -0.02,
maximum 17.23  
Coulombic values for 1olz_B SES surface #2.3: minimum, -20.03, mean -0.11,
maximum 12.49  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close #2.2

> close #2.3

> select clear

Cell requested for row 2 is out of bounds for table with 4 rows! Resizing
table model.  

> open Q92854 fromDatabase uniprot associate #2/A,B

Summary of feedback from opening Q92854 fetched from uniprot  
---  
notes | Fetching compressed Q92854 UniProt info from https://www.uniprot.org/uniprot/Q92854.xml  
Alignment identifier is Q92854  
Associated 1olz chain A to Q92854 with 7 mismatches  
Associated 1olz chain B to Q92854 with 7 mismatches  
  
Opened UniProt Q92854  

> select clear

> select #2/A-B:144-194

802 atoms, 826 bonds, 102 residues, 1 model selected  

> select #2/A-B:144-296

2408 atoms, 2472 bonds, 2 pseudobonds, 298 residues, 2 models selected  

> select #2/A-B:44

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select #2/A-B:44-146

1604 atoms, 1642 bonds, 206 residues, 1 model selected  

> select clear

> set bgColor white

> set bgColor black

> select #2/A

5312 atoms, 5042 bonds, 1 pseudobond, 1020 residues, 2 models selected  

> select #2/B

5357 atoms, 5042 bonds, 1 pseudobond, 1065 residues, 2 models selected  

> cartoon style (#!2 & sel) modeHelix tube sides 20

> select clear

> set bgColor black

> set bgColor white

> style #2 sphere

Changed 10669 atom styles  

> select add #2

10669 atoms, 10084 bonds, 2 pseudobonds, 2085 residues, 3 models selected  

> style sel sphere

Changed 10669 atom styles  

> style sel ball

Changed 10669 atom styles  

> style sel stick

Changed 10669 atom styles  

> close #2.1

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting flat

> set bgColor gray

> select clear

> select add #2

10669 atoms, 10084 bonds, 2085 residues, 1 model selected  

> cartoon style (sel & coil) xsection oval

> cartoon style sel xsection barbell modeHelix default

> select sideonly

9331 atoms, 7460 bonds, 2244 residues, 2 models selected  

> close #1

> cartoon style sel xsection rectangle modeHelix default

> cartoon style sel xsection oval modeHelix default

> cartoon style sel modeHelix tube sides 20

> select clear

> lighting full

> lighting soft

> lighting full

> lighting simple

Alignment identifier is 1  

> select /A-B:3

22 atoms, 22 bonds, 2 residues, 1 model selected  

> select /A-B:3-87

1396 atoms, 1432 bonds, 170 residues, 1 model selected  

> select clear

> select /A-B:3

22 atoms, 22 bonds, 2 residues, 1 model selected  

> select /A-B:3-80

1286 atoms, 1320 bonds, 156 residues, 1 model selected  

> select /A-B:5

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A-B:5-53

818 atoms, 842 bonds, 98 residues, 1 model selected  

> select /A-B:47

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A-B:47-56

146 atoms, 146 bonds, 20 residues, 1 model selected  

> select /A-B:238

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select /A-B:238-243

74 atoms, 72 bonds, 12 residues, 1 model selected  

> select clear

> select
> /A-B:9-11,19-21,31-34,40-44,48-53,56-65,91-98,101-106,113-118,123-124,129-130,143-148,151-157,165-170,176-177,189-196,209-217,228-236,254-258,261-262,267-268,271-278,287-293,301-308,322-325,333-336,378-383,392-395,399-408,414-422,426-432,437-444,454-457,465-469,474-478,499-502,507-510,539-546,551-553,563-568,571-572,580-583,587-590,599-608,613-626

4212 atoms, 4224 bonds, 518 residues, 1 model selected  

> select clear

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Sema4d_1olz.cxs

> close session

> open 3OKY format mmcif fromDatabase pdb

3oky title:  
Plexin A2 in complex with Semaphorin 6A [more info...]  
  
Chain information for 3oky #1  
---  
Chain | Description | UniProt  
A | Plexin-A2 | PLXA2_MOUSE 35-703  
B | Putative uncharacterized protein | Q8BUT0_MOUSE 19-571  
  
Non-standard residues in 3oky #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
3oky mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/B

Alignment identifier is 1/B  

> select /A:37-657

4767 atoms, 4889 bonds, 2 pseudobonds, 609 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> hide atoms

> close #1.1

> sequence chain #1/B

Alignment identifier is 1/B  

> select clear

> select /B:20-36

135 atoms, 139 bonds, 17 residues, 1 model selected  

> select /B:41

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /B:41-52

79 atoms, 80 bonds, 10 residues, 1 model selected  

> open 1got

Summary of feedback from opening 1got fetched from pdb  
---  
notes | Fetching compressed mmCIF 1got from http://files.rcsb.org/download/1got.cif  
Fetching CCD GDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif  
  
1got title:  
Heterotrimeric complex of A GT-α/gi-α chimera and the GT-β-γ subunits [more
info...]  
  
Chain information for 1got #2  
---  
Chain | Description | UniProt  
A | GT-ALPHA/GI-ALPHA CHIMERA | GBT1_BOVIN 2-350  
B | GT-BETA | GBB1_BOVIN 1-340  
G | GT-GAMMA | GBG1_BOVIN 2-66  
  
Non-standard residues in 1got #2  
---  
GDP — guanosine-5'-diphosphate  
  

> hide #1 models

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:6-343

2722 atoms, 2766 bonds, 338 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/G:9-66

474 atoms, 479 bonds, 58 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #2 atoms

> select clear

> select #1/B:20-73

428 atoms, 438 bonds, 52 residues, 1 model selected  

> select clear

> delete atoms #2/B:2-47

> ui tool show Matchmaker

> matchmaker #2 to #1

Computing secondary structure  
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 3oky, chain B (#1) with 1got, chain B (#2), sequence alignment
score = 81.5  
RMSD between 34 pruned atom pairs is 1.216 angstroms; (across all 202 pairs:
16.414)  
  

> select add #1

9600 atoms, 9445 bonds, 1551 residues, 1 model selected  

> show #1 models

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

Drag select of 3 residues  

> delete atoms sel

> delete bonds sel

> select clear

> select #1/B:20-73

428 atoms, 438 bonds, 52 residues, 1 model selected  

> select clear

> hide (#1 & (protein|nucleic)) target a

> cartoon hide #1

> show (#1 & backbone) target ab

> hide #1 atoms

> show #1 cartoons

> select #1/A

5025 atoms, 4964 bonds, 800 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide (#1 & (protein|nucleic)) target a

> cartoon hide #1

> show (#1 & backbone) target ab

> show #1 cartoons

> select #1/B:20-73

428 atoms, 438 bonds, 52 residues, 1 model selected  

> select clear

> select
> #1/B:28-30,40-41,60-64,67-71,75-80,88-89,93-96,121-128,131-136,143-148,159-160,174-178,181-187,195-200,207-208,221-228,231-239,250-258,277-280,284-285,291-292,295-299,303-305,308-316,325-331,344-346,353-355,411-413,420-429,435-442,446-452,464-470,489-493,498-502,507-511,533-536,541-544,553-554

1568 atoms, 1569 bonds, 193 residues, 1 model selected  

> select
> #1/B:31-36,82-84,100-110,241-244,332-339,357-361,380-395,404-408,473-478,494-496,515-519,521-528

637 atoms, 636 bonds, 80 residues, 1 model selected  

> select
> #1/B:28-30,40-41,60-64,67-71,75-80,88-89,93-96,121-128,131-136,143-148,159-160,174-178,181-187,195-200,207-208,221-228,231-239,250-258,277-280,284-285,291-292,295-299,303-305,308-316,325-331,344-346,353-355,411-413,420-429,435-442,446-452,464-470,489-493,498-502,507-511,533-536,541-544,553-554

1568 atoms, 1569 bonds, 193 residues, 1 model selected  

> select clear

> select #1/B:74

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:74-76

26 atoms, 26 bonds, 3 residues, 1 model selected  

> select #1/B:27

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:27-30

28 atoms, 27 bonds, 4 residues, 1 model selected  

> select clear

> select #1/B:39

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:39-41

25 atoms, 26 bonds, 3 residues, 1 model selected  

> select clear

> select #1/B:59-60

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/B:59-81

191 atoms, 193 bonds, 23 residues, 1 model selected  

> select #1/B:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:58-96

320 atoms, 324 bonds, 39 residues, 1 model selected  

> color sel red

> select #1/B:120-121

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #1/B:120-208

695 atoms, 710 bonds, 89 residues, 1 model selected  

> select #1/B:120

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/B:120-171

416 atoms, 426 bonds, 52 residues, 1 model selected  

> select #1/B:120

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/B:120-163

348 atoms, 355 bonds, 44 residues, 1 model selected  

> color sel orange red

> color sel orange

> select clear

> select #1/B:173-174

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/B:173-214

321 atoms, 326 bonds, 42 residues, 1 model selected  

> color sel yellow

> select #1/B:221

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #1/B:221-280

502 atoms, 515 bonds, 60 residues, 1 model selected  

> color sel lime

> select clear

> select #1/B:284

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/B:284-317

265 atoms, 270 bonds, 34 residues, 1 model selected  

> select #1/B:284-317

265 atoms, 270 bonds, 34 residues, 1 model selected  

> select #1/B:284

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/B:284-341

440 atoms, 450 bonds, 58 residues, 1 model selected  

> color sel cyan

> select #1/B:420

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:420-432

93 atoms, 94 bonds, 13 residues, 1 model selected  

> select #1/B:411

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/B:411-470

441 atoms, 447 bonds, 55 residues, 1 model selected  

> color sel purple

> select #1/B:489

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/B:489-563

576 atoms, 588 bonds, 75 residues, 1 model selected  

> select #1/B:487-488

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/B:487-488

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/B:435-436

17 atoms, 17 bonds, 2 residues, 1 model selected  

> select #1/B:435-440

50 atoms, 51 bonds, 6 residues, 1 model selected  

> select #1/B:488

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:510

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/B:510-511

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/B:488-489

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #1/B:488-511

177 atoms, 179 bonds, 24 residues, 1 model selected  

> select #1/B:488

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:488-537

385 atoms, 393 bonds, 50 residues, 1 model selected  

> select #1/B:488

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:488-528

305 atoms, 308 bonds, 41 residues, 1 model selected  

> select #1/B:487

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:487

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:488

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:488-514

200 atoms, 202 bonds, 27 residues, 1 model selected  

> color sel hot pink

> select #1/B:532-533

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #1/B:532-563

253 atoms, 258 bonds, 32 residues, 1 model selected  

> select #1/B:520-521

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/B:520-563

344 atoms, 351 bonds, 44 residues, 1 model selected  

> select #1/B:490

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:490-494

44 atoms, 43 bonds, 5 residues, 1 model selected  

> select #1/B:533

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/B:533-538

51 atoms, 52 bonds, 6 residues, 1 model selected  

> select #1/B:521

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/B:521-563

335 atoms, 342 bonds, 43 residues, 1 model selected  

> select #1/B:516

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/B:516-563

378 atoms, 386 bonds, 48 residues, 1 model selected  

> color sel blue

> select
> #1/B:31-36,82-84,100-110,241-244,332-339,357-361,380-395,404-408,473-478,494-496,515-519,521-528

637 atoms, 636 bonds, 80 residues, 1 model selected  

> cartoon style sel modeHelix tube sides 20

> cartoon style #2/B modeHelix tube sides 10

> cartoon style #1/B modeHelix tube sides 10

> cartoon style #1/B modeHelix tube sides 5

Invalid "sides" argument: Expected an even integer  

> cartoon style #1/B modeHelix tube sides 5

Invalid "sides" argument: Expected an even integer  

> cartoon style #1/B modeHelix tube sides 8

> cartoon style #1/B modeHelix tube sides 4

> cartoon style #1/B modeHelix tube sides 2

Invalid "sides" argument: Must be greater than or equal to 3  

> cartoon style #1/B modeHelix tube sides 3

Invalid "sides" argument: Expected an even integer  

> cartoon style #1/B modeHelix tube sides 4

> cartoon style #1/B modeHelix tube sides 6

> select clear

> select helix

637 atoms, 636 bonds, 80 residues, 1 model selected  

> color sel white

> color sel dim gray

> color sel cornflower blue

> color sel light sea green

> select clear

> select coil

3077 atoms, 3073 bonds, 397 residues, 2 models selected  

> color (#1 & sel) forest green

> select clear

> select coil

3077 atoms, 3073 bonds, 397 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light gray

> color sel gray

> color sel slate gray

> select clear

> select coil

3077 atoms, 3073 bonds, 397 residues, 2 models selected  

> color sel peru

> color sel cadet blue

> color sel green yellow

> select clear

> lighting full

> lighting flat

> lighting simple

> lighting soft

> graphics silhouettes false

> set bgColor gray

> set bgColor black

> set bgColor white

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> lighting full

> lighting flat

> select coil

3077 atoms, 3073 bonds, 397 residues, 2 models selected  

> color sel snow

> color sel lemon chiffon

> select clear

> cartoon style #1/B modeHelix tube sides 6 width 1.5 thickness 0.3

> undo

> cartoon style #1/B Helix width 1.5 thick 0.3

Expected a keyword  

> cartoon style #1/B helix width 1.5 thick 0.3

Expected a keyword  

> cartoon style helix width 1.5 thickness 0.3

> cartoon style helix width 1.5 thickness 0

Invalid "thickness" argument: Must be greater than 0  

> cartoon style helix width 1.5 thickness 1

> cartoon style helix width 1 thickness 1

> lighting shadows true intensity 0.5

> lighting full

> cartoon style coil width 0.1 thickness 0.5

> cartoon style coil width 0.1 thickness 0.1

> cartoon style coil width 0.1 thickness 0.2

> cartoon style coil width 0.1 thickness 0.3

> cartoon style coil width 0.1 thickness 0.2

> cartoon style tubes width 0.1 thick 0.2

Expected an atoms specifier or a keyword  

> cartoon style helix width 0.1 thickness 0.3

> cartoon style #1/B modeHelix tube radius 4

> cartoon style #1/B modeHelix tube radius 1

> cartoon style strand width 0.1 thickness 0.3

> undo

> cartoon style strand width 1 thickness 1

> cartoon style strand width 2 thickness 1

> cartoon style strand width 4 thickness 1

> cartoon style strand width 3 thickness 1

> cartoon style strand width 3 thickness 2

> cartoon style strand width 2 thickness 2

> cartoon style strand width 2 thickness 0.5

> cartoon style strand width 3 thickness 0.5

> cartoon style strand width 2.5 thickness 0.5

Drag select of 557 residues  
Drag select of 541 residues  
Drag select of 563 residues  

> view sel

> select clear

> lighting flat

> select helix

637 atoms, 636 bonds, 80 residues, 1 model selected  

> color sel gray

> select clear

Drag select of 4 residues  

> set bgColor gray

> set bgColor black

> set bgColor white

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting soft

> graphics silhouettes false

> ui tool show "Side View"

> nucleotides sel tube/slab shape ellipsoid

> save /Users/nirakar.basnet/Desktop/image5.png supersample 3

> save /Users/nirakar.basnet/Desktop/image6.png supersample 3

> show #2 models

> hide #1 models

Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> select add #2

2923 atoms, 2320 bonds, 914 residues, 2 models selected  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  
Alignment identifier is 2/B  

> select clear

> select #2/B:48

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:48-51

37 atoms, 36 bonds, 4 residues, 1 model selected  

> select #2/B:48

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:48

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:48

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:48-84

300 atoms, 306 bonds, 37 residues, 1 model selected  

> select clear

> select #2/B:48

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:48-50

29 atoms, 28 bonds, 3 residues, 1 model selected  

> select clear

Drag select of 293 residues  

> rainbow sel

> select clear

> show #1 models

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Sema6A_3ok.cxs

> hide #2 models

Drag select of 563 residues  

> rainbow sel

> undo

> select strand

2814 atoms, 2816 bonds, 353 residues, 2 models selected  

> rainbow sel & #1

> select clear

> undo

> close session

> open
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Sema6A_3ok.cxs
> format session

opened ChimeraX session  

> hide #2 models

> hide #1 models

> show #2 models

> select add #2

2888 atoms, 2320 bonds, 910 residues, 1 model selected  

> select add #1

7445 atoms, 6783 bonds, 1658 residues, 2 models selected  

> show #1 models

> hide #1 models

> select clear

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> select add #1

4557 atoms, 4463 bonds, 748 residues, 1 model selected  

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> select clear

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Sema6A.tif
> width 1140 height 792 supersample 3 transparentBackground true

> hide #1 models

> show #2 models

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Beta_prop.tif
> width 1140 height 792 supersample 3

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Beta_prop.tif
> width 1140 height 792 supersample 3 transparentBackground true

> close session

> open
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Sema6A_3ok.cxs
> format session

opened ChimeraX session  

> hide #1 models

> select add #2

2888 atoms, 2320 bonds, 910 residues, 1 model selected  

> save /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/beta-
> prop.pdb models #2 selectedOnly true relModel #2

> hide #2 models

> show #1 models

> undo

> select add #1

7445 atoms, 6783 bonds, 1658 residues, 2 models selected  

> show #1 models

> select subtract #1

2888 atoms, 2320 bonds, 910 residues, 1 model selected  

> select add #1

7445 atoms, 6783 bonds, 1658 residues, 2 models selected  

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Sema6A.pdb
> models #1 displayedOnly true selectedOnly true relModel #1

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> select clear

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Sema6a.png
> width 1140 height 792 supersample 1 transparentBackground true

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/Sema6a_2.png
> width 1140 height 792 supersample 3 transparentBackground true

> hide #1 models

> show #2 models

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/beta_prop_2.png
> width 1328 height 781 supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> open 30ky

Fetching url http://files.rcsb.org/download/30ky.cif failed:  
HTTP Error 404: Not Found  

> open 3oky

3oky title:  
Plexin A2 in complex with Semaphorin 6A [more info...]  
  
Chain information for 3oky #3  
---  
Chain | Description | UniProt  
A | Plexin-A2 | PLXA2_MOUSE 35-703  
B | Putative uncharacterized protein | Q8BUT0_MOUSE 19-571  
  
Non-standard residues in 3oky #3  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
3oky mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> select #3/B

4547 atoms, 4451 bonds, 3 pseudobonds, 749 residues, 2 models selected  

> hide #1 models

> delete atoms (#!3 & sel)

> delete bonds (#!3 & sel)

> lighting full

> close #3.1

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> view

> hide #3 atoms

> select add #3

5053 atoms, 4993 bonds, 802 residues, 1 model selected  
Alignment identifier is 3/A  

> select clear

> set bgColor gray

> select strand

4728 atoms, 4738 bonds, 589 residues, 3 models selected  

> rainbow sel & #3

> select clear

> show #1 models

> hide #3 models

> show #3 models

> hide #1 models

> ui tool show Matchmaker

> matchmaker #1-2 to #3

Computing secondary structure  
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 3oky, chain A (#3) with 3oky, chain B (#1), sequence alignment
score = 368.6  
RMSD between 188 pruned atom pairs is 1.145 angstroms; (across all 428 pairs:
10.480)  
  
Matchmaker 3oky, chain A (#3) with 1got, chain B (#2), sequence alignment
score = 69.8  
RMSD between 10 pruned atom pairs is 1.315 angstroms; (across all 183 pairs:
20.510)  
  

> show #2 models

> show #1 models

> hide #1 models

> hide #2 models

> show #2 models

> hide #3 models

> hide #2 models

> show #1 models

> show #3 models

> hide #1 models

> cartoon style #3 modeHelix tube sides 20

> cartoon style #3 modeHelix tube radius 2

> cartoon style #3 modeHelix tube radius 1

> select coil

5377 atoms, 5378 bonds, 701 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel wheat

> select clear

> cartoon style coil width 1.5 thickness 0.3

> cartoon style coil width 1 thickness 0.3

> cartoon style coil width 1 thickness 0.2

> cartoon style strand width 2 thickness 2

> cartoon style strand width 2 thickness 1

> cartoon style strand width 2 thick0.5

Expected a keyword  

> cartoon style strand width 2 thickness 0.5

> cartoon style strand width 2 thickness 0.1

> cartoon style strand width 2.5 thickness 0.1

> cartoon style #3 modeHelix tube radius 1

> select coil

5377 atoms, 5378 bonds, 701 residues, 3 models selected  

> select coil

5377 atoms, 5378 bonds, 701 residues, 3 models selected  

> select helix

1190 atoms, 1190 bonds, 149 residues, 2 models selected  

> color sel gainsboro

> color sel gray

> color sel dim gray

> select clear

> color gray

> undo

> select coil

5377 atoms, 5378 bonds, 701 residues, 3 models selected  

> select helix

1190 atoms, 1190 bonds, 149 residues, 2 models selected  

> color sel light gray

> color sel silver

> color sel dark gray

> select clear

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/plexinA1.png
> width 1143 height 792 supersample 3 transparentBackground true

> lighting soft

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/plexinA1.png
> width 1143 height 792 supersample 3

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/plexinA1.png
> width 1143 height 792 supersample 3 transparentBackground true

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_and_plexin.cxs
> includeMaps true

> close session

> open 3AFC format mmcif fromDatabase pdb

3afc title:  
Mouse Semaphorin 6A extracellular domain [more info...]  
  
Chain information for 3afc #1  
---  
Chain | Description | UniProt  
A B | Semaphorin-6A | SEM6A_MOUSE 19-570  
  
Non-standard residues in 3afc #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close #1.1

> hide atoms

> select strand

3068 atoms, 3070 bonds, 378 residues, 1 model selected  

> rainbow sel

> color sel bychain

> undo

> select clear

> color bychain

> cartoon style modeHelix tube sides 20

> cartoon style #3 modeHelix tube radius 1

> cartoon style modeHelix tube radius 1

> select /A

4345 atoms, 4363 bonds, 627 residues, 1 model selected  

> select /B

4059 atoms, 4054 bonds, 602 residues, 1 model selected  

> color sel pale turquoise

> select clear

> select /A/B

8404 atoms, 8417 bonds, 1229 residues, 1 model selected  

> select /B

4059 atoms, 4054 bonds, 602 residues, 1 model selected  

> color sel medium turquoise

> color sel turquoise

> select clear

> select strand

3068 atoms, 3070 bonds, 378 residues, 1 model selected  

> rainbow sel

> select clear

> color bychain

> undo

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_dimer.cxs
> includeMaps true

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_dimer.png
> width 1143 height 792 supersample 3 transparentBackground true

> show surfaces

> color #1.1 #00fa92ff

> undo

> volume style surface

No volumes specified  

> volume style image

No volumes specified  

> volume style mesh

No volumes specified  

> surface splitbycolor

Missing or invalid "surfaces" argument: empty atom specifier  

> surface #1.1 splitbycolor

Expected a keyword  

> surface #1.1 splitbycolor 7

Expected a keyword  

> volume hide

No volumes specified  

> select add #1.1

4239 atoms, 534 residues, 1 model selected  

> transparency (#!1 & sel) 20

> surface style #1.1 mesh

> surface style #1.1 solid

> surface style #1.1 dot

> select clear

> select add #1.1

4239 atoms, 534 residues, 1 model selected  

> surface style #1.1 solid

> transparency (#!1 & sel) 80

> transparency (#!1 & sel) 60

> select clear

> transparency 50

> transparency 40

> transparency 90

> transparency 70

> transparency 0

> surface smooth

Missing or invalid "surfaces" argument: empty atom specifier  

> surface smooth 1

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> surface smooth f 1

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> rainbow

> undo

> surface

> surface sharpBoundaries false

> surface sharpBoundaries false transparency 50

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> select add #1.1

4239 atoms, 534 residues, 2 models selected  

> select subtract #1.1

Nothing selected  

> select add #1.2

3943 atoms, 499 residues, 2 models selected  

> color sel lavender

> color sel turquoise

> color sel medium spring green

> color sel medium turquoise

> surface sharpBoundaries false transparency 50

> select clear

> hide #1.1 models

> hide #1.2 models

> select /B

4059 atoms, 4054 bonds, 602 residues, 1 model selected  

> rainbow sel

Surface #1.2 does not have atom patches, cannot color by atom  

> select clear

> show #1.1 models

> show #1.2 models

> surface dust

Missing or invalid "surfaces" argument: empty atom specifier  

> surface dust 5

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> surface dust #1 5

Expected a keyword  

> transparency 0

> color #1.2 mediumturquoise

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_dimer_surf.png
> width 1143 height 792 supersample 3 transparentBackground true

> transparency 40

> transparency 60

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_dimer_surf2.png
> width 1143 height 792 supersample 3 transparentBackground true

> transparency 40

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_dimer_surf3.png
> width 1143 height 792 supersample 3

> set bgColor white

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_dimer_surf3.png
> width 1143 height 792 supersample 3 transparentBackground true

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_dimer_2.cxs
> includeMaps true

> close session

> open 3oky format mmcif fromDatabase pdb

3oky title:  
Plexin A2 in complex with Semaphorin 6A [more info...]  
  
Chain information for 3oky #1  
---  
Chain | Description | UniProt  
A | Plexin-A2 | PLXA2_MOUSE 35-703  
B | Putative uncharacterized protein | Q8BUT0_MOUSE 19-571  
  
Non-standard residues in 3oky #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
3oky mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> color bychain

> close session

> open 3oky

3oky title:  
Plexin A2 in complex with Semaphorin 6A [more info...]  
  
Chain information for 3oky #1  
---  
Chain | Description | UniProt  
A | Plexin-A2 | PLXA2_MOUSE 35-703  
B | Putative uncharacterized protein | Q8BUT0_MOUSE 19-571  
  
Non-standard residues in 3oky #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
3oky mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> close session

> open 2AL8

Fetching url http://files.rcsb.org/download/2al8.cif failed:  
HTTP Error 404: Not Found  

> open 3AL8

Summary of feedback from opening 3AL8 fetched from pdb  
---  
note | Fetching compressed mmCIF 3al8 from http://files.rcsb.org/download/3al8.cif  
  
3al8 title:  
Plexin A2 / Semaphorin 6A complex [more info...]  
  
Chain information for 3al8 #1  
---  
Chain | Description | UniProt  
A | Semaphorin-6A | SEM6A_MOUSE 19-570  
B | Plexin-A2 | PLXA2_MOUSE 31-561  
  
Non-standard residues in 3al8 #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3al8 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  

> close session

> open /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/3OKY.cif

3OKY.cif title:  
Plexin A2 in complex with Semaphorin 6A [more info...]  
  
Chain information for 3OKY.cif #1  
---  
Chain | Description | UniProt  
A | Plexin-A2 | PLXA2_MOUSE 35-703  
B | Putative uncharacterized protein | Q8BUT0_MOUSE 19-571  
  
Non-standard residues in 3OKY.cif #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3OKY.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> close #1.1

> hide cartoons

> show cartoons

> hide atoms

> show surfaces

> select /B

4547 atoms, 4451 bonds, 749 residues, 1 model selected  

> color sel bychain

> hide #1.2 models

> close #1.2

> close #1.1

> select clear

> open 3Afc

3afc title:  
Mouse Semaphorin 6A extracellular domain [more info...]  
  
Chain information for 3afc #2  
---  
Chain | Description | UniProt  
A B | Semaphorin-6A | SEM6A_MOUSE 19-570  
  
Non-standard residues in 3afc #2  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #2/A to #1/B pairing ss

Computing secondary structure  
Parameters  
---  
Chain pairing | ss  
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 3OKY.cif, chain B (#1) with 3afc, chain A (#2), sequence alignment
score = 2790.7  
RMSD between 512 pruned atom pairs is 0.516 angstroms; (across all 531 pairs:
0.764)  
  

> open 3oky

3oky title:  
Plexin A2 in complex with Semaphorin 6A [more info...]  
  
Chain information for 3oky #3  
---  
Chain | Description | UniProt  
A | Plexin-A2 | PLXA2_MOUSE 35-703  
B | Putative uncharacterized protein | Q8BUT0_MOUSE 19-571  
  
Non-standard residues in 3oky #3  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
3oky mmCIF Assemblies  
---  
1| author_defined_assembly  
  

Cell requested for row 0 is out of bounds for table with 4 rows! Resizing
table model.  

> hide #1 models

> show #1 models

> matchmaker #2/B to #3/B pairing ss

Computing secondary structure  
Parameters  
---  
Chain pairing | ss  
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 3oky, chain B (#3) with 3afc, chain B (#2), sequence alignment
score = 2674.3  
RMSD between 481 pruned atom pairs is 0.628 angstroms; (across all 493 pairs:
0.831)  
  

> hide #1 models

> show #1 models

> matchmaker #2/A to #3/B pairing ss

Computing secondary structure  
Parameters  
---  
Chain pairing | ss  
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 3oky, chain B (#3) with 3afc, chain A (#2), sequence alignment
score = 2790.7  
RMSD between 512 pruned atom pairs is 0.516 angstroms; (across all 531 pairs:
0.764)  
  

> hide #1 models

> hide #!3 models

> show #!3 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!3 models

> show #!3 models

> matchmaker #3/B to #2/B pairing ss

Computing secondary structure  
Parameters  
---  
Chain pairing | ss  
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 3afc, chain B (#2) with 3oky, chain B (#3), sequence alignment
score = 2674.3  
RMSD between 481 pruned atom pairs is 0.628 angstroms; (across all 493 pairs:
0.831)  
  

> set bgColor white

> set bgColor black

> set bgColor gray

> show atoms

> hide atoms

> close #3.1

> close #2.1

> color bychain

> show surfaces

> hide #2.1 models

> transparency 40\

Missing or invalid "percent" argument: Expected a number  

> transparency 40

> transparency 60

> select #2/A#2/B

8404 atoms, 8417 bonds, 1229 residues, 1 model selected  

> color sel bychain

Drag select of 3afc_B SES surface, 231 of 420994 triangles  

> select #2/A

4345 atoms, 4363 bonds, 627 residues, 1 model selected  

> color sel dark turquoise

> undo

> select clear

> show #2.1 models

> select add #2.1

4239 atoms, 534 residues, 1 model selected  

> color sel medium spring green

> color sel turquoise

> select subtract #2.1

1 model selected  

> select add #2.2

3943 atoms, 499 residues, 1 model selected  

> color sel blue

> color sel medium purple

> select clear

> hide #3.1 models

> show #3.1 models

> hide #3.2 models

> select add #3.1

4767 atoms, 609 residues, 1 model selected  

> color sel pale green

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> hide #2.2 models

> show #2.2 models

> show #3.2 models

> hide #3.2 models

> select add #1.1

9534 atoms, 1218 residues, 3 models selected  

> color sel magenta

> undo

> select subtract #3.1

4767 atoms, 609 residues, 3 models selected  

> color sel pale violet red

> color sel pink

> select subtract #1.1

1 model selected  

> select add #3.2

4302 atoms, 540 residues, 1 model selected  

> select subtract #3.2

1 model selected  

> select add #3.1

4767 atoms, 609 residues, 1 model selected  

> color sel light green

> color sel lemon chiffon

> select clear

> ui tool show "Side View"

> transparency 60

> transparency 50

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_plexin.cxs

> save
> /Users/nirakar.basnet/Documents/Presentation/2025/techdev_2025/sema_and_plexin.png
> width 1143 height 792 supersample 3 transparentBackground true

> cartoon style #2#1.1#3.1#!1,3 modeHelix tube sides 20


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,7
      Model Number: Z1AK0014ELL/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 performance and 6 efficiency)
      Memory: 36 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.1 (24G231)
      Kernel Version: Darwin 24.6.0
      Time since boot: 14 days, 3 hours, 7 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 18
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL S2721HS:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        LG Ultra HD:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    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: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by pett, 7 hours ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

Reported by Nirakar Basnet

comment:2 by Tom Goddard, 6 hours ago

Resolution: → duplicate
Status: assigned → closed

The ChimeraX bug report panel said what we know about this crash:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here ​https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."

Current ChimeraX daily builds use a newer Qt 6.9.2 that does not seem to have this crash, but the newer Qt introduces other Mac crashes that are about equally common. Still you might try the ChimeraX daily build if this multi-display Mac crash is causing you to lose ChimeraX sessions.

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