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Opened 3 days ago
Last modified 3 days ago
#19197 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
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