Opened 4 days ago

Last modified 3 days ago

#19197 closed defect

Crash on Mac waking from sleep — at Version 1

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 Eric Pettersen) 

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 (1)

comment:1 by Eric Pettersen, 4 days 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

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