id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19197 ChimeraX bug report submission nirakar.basnet@… "{{{ 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 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{""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"" : 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""com.apple.Foundation"", ""size"" : 14587296, ""uuid"" : ""186c53da-a25e-3835-a8bb-409faf53e4e7"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3603"" } ], ""sharedCache"" : { ""base"" : 6832504832, ""size"" : 5039341568, ""uuid"" : ""e93019e7-f1c3-3ee2-9cac-6c6940bee5d1"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.8G resident=0K(0%) swapped_out_or_unallocated=1.8G(100%)\nWritable regions: Total=106.4G written=291.6M(0%) resident=53.8M(0%) swapped_out=237.8M(0%) unallocated=106.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 2080K 80 \nCG raster data 432K 9 \nColorSync 624K 33 \nCoreAnimation 3488K 191 \nCoreGraphics 112K 7 \nCoreGraphics (reserved) 16K 1 reserved VM address space (unallocated)\nCoreImage 48K 3 \nCoreServices 624K 2 \nCoreUI image data 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""0710076d2e067b1f29262f5341236b7b7deb5348"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""654439cdafbf5b61207873a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000012 } ] } } ===== 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 }}} " defect new normal Unassigned