id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16730 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Thread 0x000000044a18f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003470af000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003460a3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000345097000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034408b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034307f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000342073000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000341067000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034005b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033f04f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033e043000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033d037000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033c02b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033b01f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033a013000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000339007000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001f9ce4240 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.dssp._dssp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, psutil._psutil_osx, psutil._psutil_posix, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, 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.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, cftime._cftime, netCDF4._netCDF4, lxml._elementpath, lxml.etree (total: 132) {""app_name"":""ChimeraX"",""timestamp"":""2025-01-29 18:59:57.00 +0100"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.2 (24C101)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""DE1FE111-C4BF-4321-A0BC-76BC80C57B21""} { ""uptime"" : 390000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,6"", ""coalitionID"" : 82156, ""osVersion"" : { ""train"" : ""macOS 15.2"", ""build"" : ""24C101"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-01-29 18:59:52.5630 +0100"", ""codeSigningMonitor"" : 1, ""incident"" : ""DE1FE111-C4BF-4321-A0BC-76BC80C57B21"", ""pid"" : 44603, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-01-28 12:15:22.0840 +0100"", ""procStartAbsTime"" : 8667286744054, ""procExitAbsTime"" : 9559693911542, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""0B854952-B91C-511E-9D40-67EBCC719858"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""4AAB6390-76F2-0A24-A7A7-7A75AB52E181"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""EE6025EA-9EDC-4E50-8EED-322C1E5B3419"", ""wakeTime"" : 28921, ""sleepWakeUUID"" : ""397551EE-487D-43B4-B06A-7E39CE6734AB"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x727272727272 is not in any region. Bytes after previous region: 20274058293875 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [102.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END"", ""exception"" : {""codes"":""0x0000000000000101, 0x7272727272727272"",""rawCodes"":[257,8246779703540740722],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGBUS"",""subtype"":""UNKNOWN_0x101 at 0x7272727272727272 -> 0x0000727272727272 (possible pointer authentication failure)""}, ""termination"" : {""flags"":0,""code"":10,""namespace"":""SIGNAL"",""indicator"":""Bus error: 10"",""byProc"":""ChimeraX"",""byPid"":44603}, ""vmregioninfo"" : ""0x727272727272 is not in any region. Bytes after previous region: 20274058293875 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [102.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END"", ""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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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/ctn700/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT > model building/SERT-IBL-NA-CL-cholesterols-waters_final_model_- > _prepared.mae"" Chain information for SERT-IBL-NA-CL-cholesterols-waters_final_model_- _prepared.mae #1 --- Chain | Description A | No description available Opened SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae containing 1 structures (8650 atoms, 8779 bonds) > set bgColor white > lighting soft > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > graphics silhouettes false > graphics silhouettes true > rainbow > color byhetero > combine #1/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 > select #1:IBL 36 atoms, 38 bonds, 1 residue, 1 model selected > view sel > select clear > select #1/A:701@C08 1 atom, 1 residue, 1 model selected > select up 36 atoms, 38 bonds, 1 residue, 1 model selected > ui tool show H-Bonds The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hbonds sel color #fffb00 showDist true interModel false distSlop 1.0 > angleSlop 40.0 twoColors true slopColor #fffb00 intraMol false select true > reveal true 1 hydrogen bonds found 0 strict hydrogen bonds found > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 36 atoms, 38 bonds, 1 residue, 1 model selected > ui tool show H-Bonds The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show Contacts The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > contacts sel overlapCutoff -0.3 interModel false intraMol false > ignoreHiddenModels true select true color #00fdff reveal true log true Allowed overlap: -0.3 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: False 38 contacts atom1 atom2 overlap distance SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 HN07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CD1 0.392 2.308 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 HN07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CG 0.176 2.524 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 N07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CD1 0.118 3.207 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C03 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 HA3 0.067 2.633 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H013 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 169 O -0.062 2.542 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H141 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 335 O -0.063 2.543 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C12 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A SER 336 O -0.072 3.252 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 HN07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CE1 -0.091 2.791 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C17 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 CG2 -0.092 3.492 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C03 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 CG2 -0.110 3.510 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C01 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 173 HB2 -0.113 2.813 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C04 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 CA -0.122 3.522 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C08 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 HE1 -0.128 2.828 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C12 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 O -0.130 3.310 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C04 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 HA3 -0.145 2.845 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H151 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 OH -0.160 2.660 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 N07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CE1 -0.164 3.489 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H121 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A SER 336 O -0.173 2.653 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C17 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 HG21 -0.175 2.875 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H152 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CE2 -0.181 2.881 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H123 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 O -0.188 2.668 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H102 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A SER 438 HB3 -0.197 2.197 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H123 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 96 O -0.199 2.679 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H012 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 C -0.208 2.908 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 N07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CG -0.210 3.535 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H151 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 CZ -0.211 2.911 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C03 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 CA -0.212 3.612 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C16 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 HG21 -0.226 2.926 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H152 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CZ -0.237 2.937 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C12 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 96 O -0.241 3.421 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C01 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A LEU 443 HD23 -0.246 2.946 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C15 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 OH -0.256 3.456 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C03 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 HG22 -0.256 2.956 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C08 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 CE1 -0.259 3.659 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 HC04 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 169 CB -0.264 2.964 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C01 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A LEU 443 HG -0.265 2.965 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H151 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 CE1 -0.276 2.976 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H013 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 173 HB2 -0.283 2.283 38 contacts > ~display HC > select clear > select #1/A:701@C08 1 atom, 1 residue, 1 model selected > select up 36 atoms, 38 bonds, 1 residue, 1 model selected > color sel cyan > color sel byhetero > color sel cyan > hide #!1 models > hide #2 models > show #!1 models > show #2 models > hide #2 models > show #2 models > hide #!1 models > select #2/A:701@C09 1 atom, 1 residue, 1 model selected > select up 36 atoms, 38 bonds, 1 residue, 1 model selected > color sel cyan > color sel byhetero > show #!1 models > select clear > transparency #1 90 cartoons The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #2 models > select #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 214 atoms, 207 bonds, 14 residues, 1 model selected > show #2 models > hide #!1 models > hide #2 cartoons > show #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 cartoons > rainbow sel > color sel byhetero > show #!1 models > hide #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 cartoons > hide #!1 models > select add #2 8650 atoms, 8779 bonds, 549 residues, 1 model selected > rainbow sel > undo > show sel atoms > undo > show sel cartoons > rainbow sel > color sel byhetero > hide #2 cartoons > show #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 cartoons > show #!1 models > label #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 height 0.5 > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > hide label Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #2.1 models > show #2.1 models > close #2.1 > label #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 height 0.5 > show :NA,CL,HOH > select clear > select add #1/B:1@CL 1 atom, 1 residue, 1 model selected > select add #1/C:1@NA 2 atoms, 2 residues, 1 model selected > select add #1/C:2@NA 3 atoms, 3 residues, 1 model selected > label sel height 0.5 > select clear > select add #2.1 1 model selected > hide #!1 models > hide #!1.1 models > hide #1.2 models > hide #1.3 models > hide #!2 models > show #!2 models > select add #2 8650 atoms, 8779 bonds, 549 residues, 2 models selected > select subtract #2 Nothing selected > select add #2.1 1 model selected No visible residues selected > select add #2 8650 atoms, 8779 bonds, 549 residues, 2 models selected > label (#!2 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > show #1.3 models > hide #1.3 models > close #2.1 > label #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 height 0.5 > select add #1/B:1@CL 1 atom, 1 residue, 1 model selected > select add #1/C:1@NA 2 atoms, 2 residues, 1 model selected > select add #1/C:2@NA 3 atoms, 3 residues, 1 model selected > label sel height 0.5 > select clear > select add #1/B:1@CL 1 atom, 1 residue, 1 model selected > select add #1/C:1@NA 2 atoms, 2 residues, 1 model selected > select add #1/C:2@NA 3 atoms, 3 residues, 1 model selected > label sel height 0.5 > hide #!2 models > label sel height 0.5 > ui mousemode right label > label #1/B:1 > select clear > show #!2 models > show #1.3 models > hide #1.3 models > show #1.3 models > label sel height 0.5 > label height 0.5 > select clear > show #!1.1 models > show #1.2 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 36 atoms, 38 bonds, 1 residue, 1 model selected > view sel > movie record > turn y 2 180 > wait 180 > movie encode /Users/ctn700/Desktop/movie1.mp4 Movie saved to /Users/ctn700/Desktop/movie1.mp4 > ui tool show ""Side View"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > graphics silhouettes false > graphics silhouettes true > save IBL_BS.png supersample 4 height 2000 width 2000 > save IBL_BS.png supersample 4 > select clear > save IBL_BS.png supersample 4 > hide label Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide labels Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > ~label #1-2 residues > save IBL_BS.png supersample 4 > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/AtCAT4_Arg_MD_model.pdb"" AtCAT4_Arg_MD_model.pdb title: Alphafold monomer V2.0 prediction for cationic amino acid transporter 4, vacuolar (Q8W4K3) [more info...] Chain information for AtCAT4_Arg_MD_model.pdb #3 --- Chain | Description A | No description available Non-standard residues in AtCAT4_Arg_MD_model.pdb #3 --- CLR — (CLR) The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!1 models > hide #!1.1 models > hide #1.2 models > hide #2 models > view > rainbow #!3 > color #!3 byhetero > label #3/A:108 > select clear > select #3:ZR Nothing selected > select #3:602 27 atoms, 26 bonds, 1 residue, 1 model selected > show sel atoms > close #3 > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/AtCAT4_Arg_MD_model.pdb"" AtCAT4_Arg_MD_model.pdb title: Alphafold monomer V2.0 prediction for cationic amino acid transporter 4, vacuolar (Q8W4K3) [more info...] Chain information for AtCAT4_Arg_MD_model.pdb #3 --- Chain | Description A | No description available Non-standard residues in AtCAT4_Arg_MD_model.pdb #3 --- ARG — (ARG) CLR — (CLR) > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 27 atoms, 26 bonds, 1 residue, 1 model selected > view sel > select clear > dssp > rainbow #3 > color #3 byhetero > select clear > select #3:21-56 393 atoms, 393 bonds, 28 residues, 1 model selected > select #4:21-56 Nothing selected > select #3:21-56 393 atoms, 393 bonds, 28 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > ~display HC > select #3:21-56 393 atoms, 393 bonds, 28 residues, 1 model selected > hide sel cartoons > select clear > label #3:21-56 height 0.5 > ui tool show ""Side View"" > label delete residues > ui tool show H-Bonds The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 27 atoms, 26 bonds, 1 residue, 1 model selected > hbonds sel color #fffb00 showDist true interModel false distSlop 1.0 > angleSlop 40.0 twoColors true slopColor #fffb00 intraMol false select true > reveal true 14 hydrogen bonds found 4 strict hydrogen bonds found > hbonds sel color #fffb00 showDist true interModel false distSlop 1.0 > angleSlop 40.0 twoColors true slopColor #ff9300 intraMol false select true > reveal true 15 hydrogen bonds found 4 strict hydrogen bonds found > select #3/A:602@CA 1 atom, 1 residue, 1 model selected > select up 27 atoms, 26 bonds, 1 residue, 1 model selected > select up 8379 atoms, 8472 bonds, 554 residues, 1 model selected > select down 27 atoms, 26 bonds, 1 residue, 1 model selected > view sel > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb"" Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #4 --- Chain | Description A | No description available B | No description available > ματψημακερ #4 το #3 Unknown command: ματψημακερ #4 το #3 > matchmaker #4 to #3 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 AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb, chain A (#4), sequence alignment score = 2438 RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs: 1.231) > dssp > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/phenix-folder-leicester- > dataset/eLBOW_7/elbow.ORN.8xj5_C_ORN_sdf.001.cif"" Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive- Nexus365/Dimitris - Newstead Lab/Postdoc/phenix-folder-leicester- dataset/eLBOW_7/elbow.ORN.8xj5_C_ORN_sdf.001.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 19 No mmCIF models found. > select clear > select #4/A:603@C07 1 atom, 1 residue, 1 model selected > select up 22 atoms, 20 bonds, 1 residue, 1 model selected > select clear > rainbow #!3-4 > color #!3-4 byhetero > dssp > tile 2 models tiled > tile off > matchmaker #4 to #3 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 AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb, chain A (#4), sequence alignment score = 2438 RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs: 1.231) > tile columns 2 spacingFactor 0.7 2 models tiled > hide #!3 models > tile off > matchmaker #4 to #3 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 AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb, chain A (#4), sequence alignment score = 2438 RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs: 1.231) > show #!3 models > ui tool show ""Side View"" > view > hide #!3 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb"" Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #5 --- Chain | Description A | No description available B | No description available > matchmaker #5 to #3 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 AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb, chain A (#5), sequence alignment score = 2438 RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs: 1.231) > rainbow #!4-5 > color #!4-5 byhetero > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 22 atoms, 20 bonds, 1 residue, 1 model selected > view sel > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb"" Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #6 --- Chain | Description A | No description available B | No description available > matchmaker #6 to #3 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 AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb, chain A (#6), sequence alignment score = 2438 RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs: 1.231) > hide #!5 models > addh #6 Summary of feedback from adding hydrogens to AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6 --- notes | No usable SEQRES records for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb (#6) chain A; guessing termini instead Termini for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb (#6) chain B determined from SEQRES records Chain-initial residues that are actual N termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A PRO 21, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/B GLN 1, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A PRO 21, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A TYR 456 Chain-initial residues that are not actual N termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A TYR 456 Chain-final residues that are actual C termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/B SER 114, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A GLY 410, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A ASN 582 Chain-final residues that are not actual C termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A ASN 582, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A GLY 410 Missing OXT added to C-terminal residue AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A GLY 410 Missing OXT added to C-terminal residue AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #6/A ASN 582 507 hydrogen bonds Adding 'H' to AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #6/A TYR 456 4865 hydrogens added > select #6/A:603@H07 1 atom, 1 residue, 1 model selected > select up 24 atoms, 22 bonds, 1 residue, 1 model selected > select clear > addcharges Unknown command: addcharges > ui tool show ""Add Charges"" Closest equivalent command: addcharge #6 standardizeResidues 5BU,CSL,MSE,UMS Using Amber 20 recommended default charges and atom types for standard residues Populating font family aliases took 64 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. Assigning partial charges to residue CLR (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpfzgctahe/ante.in.mol2 -fi mol2 -o /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpfzgctahe/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (CLR) `` (CLR) `Welcome to antechamber 20.0: molecular input file processor.` (CLR) `` (CLR) `Info: Finished reading file (/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpfzgctahe/ante.in.mol2); atoms read (74), bonds read (77).` (CLR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (CLR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (CLR) `` (CLR) `` (CLR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (CLR) `Info: Total number of electrons: 216; net charge: 0` (CLR) `` (CLR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (CLR) `` (CLR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (CLR) `` (CLR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (CLR) `` Charges for residue CLR determined Assigning partial charges to residue AV0 (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpf621mhux/ante.in.mol2 -fi mol2 -o /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpf621mhux/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (AV0) `` (AV0) `Welcome to antechamber 20.0: molecular input file processor.` (AV0) `` (AV0) `Info: Finished reading file (/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpf621mhux/ante.in.mol2); atoms read (157), bonds read (160).` (AV0) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (AV0) `` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (AV0) `Info: Total number of electrons: 546; net charge: 0` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (AV0) `` Charges for residue AV0 determined Assigning partial charges to residue ORN (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuktuqyo_/ante.in.mol2 -fi mol2 -o /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuktuqyo_/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (ORN) `` (ORN) `Welcome to antechamber 20.0: molecular input file processor.` (ORN) `` (ORN) `Info: Finished reading file (/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuktuqyo_/ante.in.mol2); atoms read (24), bonds read (22).` (ORN) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (ORN) `` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (ORN) `Info: Total number of electrons: 74; net charge: 1` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (ORN) `` Charges for residue ORN determined > select #6/A:603@C02 1 atom, 1 residue, 1 model selected > select up 24 atoms, 22 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #fffb00 showDist true interModel false distSlop 1.0 > angleSlop 40.0 twoColors true slopColor #ff9300 intraMol false select true > reveal true 1 hydrogen bonds found 0 strict hydrogen bonds found > dssp > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/cryosparc_P60_J191_006_volume_map_sharp.mrc"" Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #7, grid size 288,288,288, pixel 0.835, shown at level 0.0608, step 2, values float32 > label #6/A:402 > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb"" Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #8 --- Chain | Description A | No description available B | No description available > hide #!6 models > select add #6 9795 atoms, 9911 bonds, 2 pseudobonds, 635 residues, 5 models selected > select subtract #6 Nothing selected > select add #7 4 models selected > show #!7 target m > view #7 clip false > volume #7 step 1 > volume #7 level 0.055 > volume #7 level 0.55 > volume #7 level 0.055 > volume #7 level 0.065 > volume #7 level 0.075 > volume #7 level 0.085 > volume #7 level 0.105 > volume #7 level 0.45 > volume #7 level 0.155 > select #7:ORN Nothing selected > view > select #8:ORN 22 atoms, 20 bonds, 1 residue, 1 model selected > view sel > transparency 50 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 26 residues in model #8 to IUPAC-IUB standards. Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb --- Chain | Description 8.2/A | No description available 8.2/B | No description available > isolde tutorial > clipper associate #7 toModel #8 Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #8.1.1.1, grid size 288,288,288, pixel 0.835, shown at step 1, values float32 > volume #8.1.1.1 level 0.155 > addh #8.2 Summary of feedback from adding hydrogens to AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2 --- notes | No usable SEQRES records for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb (#8.2) chain A; guessing termini instead Termini for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb (#8.2) chain B determined from SEQRES records Chain-initial residues that are actual N termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A PRO 21, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/B GLN 1, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A PRO 21, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A TYR 456 Chain-initial residues that are not actual N termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A TYR 456 Chain-final residues that are actual C termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/B SER 114, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A GLY 410, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A ASN 582 Chain-final residues that are not actual C termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A ASN 582, AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A GLY 410 Missing OXT added to C-terminal residue AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A GLY 410 Missing OXT added to C-terminal residue AtCAT4_final- coot-9_saved_ongrid_J185-ORN.pdb #8.2/A ASN 582 507 hydrogen bonds Adding 'H' to AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #8.2/A TYR 456 4865 hydrogens added Loading residue template for CLR from internal database > isolde parameterise sel override false Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmplkns969s/ante.in.mol2 -fi mol2 -o /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmplkns969s/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (ORN) `` (ORN) `Welcome to antechamber 20.0: molecular input file processor.` (ORN) `` (ORN) `Info: Finished reading file (/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmplkns969s/ante.in.mol2); atoms read (24), bonds read (22).` (ORN) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (ORN) `` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (ORN) `Info: Total number of electrons: 74; net charge: 1` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (ORN) `` Charges for residue ORN determined OpenMM ffXML file ORN written to the current working directory. New template added to forcefield as USER_ORN. This ligand should now work in all remaining simulations for this session. To use in future sessions, load the ffXML file with ISOLDE's Load Residue MD Definition(s) button. > isolde parameterise sel override false Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsafcl9ai/ante.in.mol2 -fi mol2 -o /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsafcl9ai/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (AV0) `` (AV0) `Welcome to antechamber 20.0: molecular input file processor.` (AV0) `` (AV0) `Info: Finished reading file (/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsafcl9ai/ante.in.mol2); atoms read (157), bonds read (160).` (AV0) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (AV0) `` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (AV0) `Info: Total number of electrons: 546; net charge: 0` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (AV0) `` Charges for residue AV0 determined OpenMM ffXML file AV0 written to the current working directory. New template added to forcefield as USER_AV0. This ligand should now work in all remaining simulations for this session. To use in future sessions, load the ffXML file with ISOLDE's Load Residue MD Definition(s) button. > select #8:ORN 24 atoms, 22 bonds, 1 residue, 1 model selected > label delete residues > view sel > isolde sim start #8.2/A:603 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro- > fix.pdb"" AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb title: AtCAT4_final-coot-9_saved_ongrid_J185-ORN [more info...] Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro- fix.pdb #7 --- Chain | Description A | No description available B | No description available Non-standard residues in AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro- fix.pdb #7 --- AV0 — (AV0) CLR — (CLR) ORN — (ORN) > hide #!8 models > close #8 > close #6 > close #5 > close #4 > matchmaker #3 to #7 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 AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb, chain A (#7) with AtCAT4_Arg_MD_model.pdb, chain A (#3), sequence alignment score = 2438 RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs: 1.231) > show #!3 models > hide #!3.1 models > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/cryosparc_P60_J191_006_volume_map_sharp.mrc"" Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #4, grid size 288,288,288, pixel 0.835, shown at level 0.0608, step 2, values float32 > hide #!3 models > clipper associate #4 toModel #7 Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #4.1.1.1, grid size 288,288,288, pixel 0.835, shown at level 0.233, step 1, values float32 AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb title: AtCAT4_final-coot-9_saved_ongrid_J185-ORN [more info...] Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro- fix.pdb --- Chain | Description 4.2/A | No description available 4.2/B | No description available Non-standard residues in AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro- fix.pdb #4.2 --- AV0 — (AV0) CLR — (CLR) ORN — (ORN) > addh #4 Summary of feedback from adding hydrogens to AtCAT4_final- coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2 --- notes | No usable SEQRES records for AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb (#4.2) chain A; guessing termini instead No usable SEQRES records for AtCAT4_final- coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb (#4.2) chain B; guessing termini instead Chain-initial residues that are actual N termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A PRO 21, AtCAT4_final- coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/B GLN 1 Chain-initial residues that are not actual N termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A TYR 456 Chain-final residues that are actual C termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/B SER 114 Chain-final residues that are not actual C termini: AtCAT4_final- coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A ASN 582, AtCAT4_final- coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A GLY 410 507 hydrogen bonds Adding 'H' to AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A TYR 456 AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A ASN 582 is not terminus, removing H atom from 'C' 4863 hydrogens added > select clear > hide #!4.1 models > show #!4.1 models > isolde start > start isolde Unknown command: start isolde > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 26 residues in model #4.2 to IUPAC-IUB standards. Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 Loading residue template for CLR from internal database > isolde parameterise sel override false Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpa8rasspx/ante.in.mol2 -fi mol2 -o /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpa8rasspx/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (AV0) `` (AV0) `Welcome to antechamber 20.0: molecular input file processor.` (AV0) `` (AV0) `Info: Finished reading file (/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpa8rasspx/ante.in.mol2); atoms read (157), bonds read (160).` (AV0) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (AV0) `` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (AV0) `Info: Total number of electrons: 546; net charge: 0` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (AV0) `` (AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (AV0) `` Charges for residue AV0 determined OpenMM ffXML file AV0 written to the current working directory. New template added to forcefield as USER_AV0. This ligand should now work in all remaining simulations for this session. To use in future sessions, load the ffXML file with ISOLDE's Load Residue MD Definition(s) button. > isolde parameterise sel override false Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuzxihuxn/ante.in.mol2 -fi mol2 -o /var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuzxihuxn/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (ORN) `` (ORN) `Welcome to antechamber 20.0: molecular input file processor.` (ORN) `` (ORN) `Info: Finished reading file (/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuzxihuxn/ante.in.mol2); atoms read (22), bonds read (21).` (ORN) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (ORN) `` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (ORN) `Info: Total number of electrons: 72; net charge: 1` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (ORN) `` (ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (ORN) `` Charges for residue ORN determined OpenMM ffXML file ORN written to the current working directory. New template added to forcefield as USER_ORN. This ligand should now work in all remaining simulations for this session. To use in future sessions, load the ffXML file with ISOLDE's Load Residue MD Definition(s) button. > isolde sim start #4.2/A:603 ISOLDE: started sim > view sel > volume #4.1.1.1 level 0.1873 > rainbow sel > select clear > volume #4.1.1.1 level 0.1553 > volume #4.1.1.1 level 0.1793 > select up 22 atoms, 21 bonds, 1 residue, 1 model selected > view sel > show #!3 models > hide #!3 models > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #4.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select up 8063 atoms, 8158 bonds, 520 residues, 1 model selected > select up 9791 atoms, 9908 bonds, 635 residues, 2 models selected > select down 8063 atoms, 8158 bonds, 520 residues, 2 models selected > select up 9791 atoms, 9908 bonds, 635 residues, 2 models selected > isolde sim start #4.2/B,A,C ISOLDE: started sim > select clear > rainbow #!4.2 > color #!4.2 bychain > show #!4.2 cartoons > rainbow #!4.2 > color #!4.2 bychain > color #!4.2 byhetero > ui tool show ""Ramachandran Plot"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > isolde pepflip #4.2/A:54 > isolde pepflip #4.2/A:134 > volume #4.1.1.1 level 0.07538 > volume #4.1.1.1 level 0.142 > isolde pepflip #4.2/A:134 > ui tool show ""Build Structure"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. You must select exactly one atom to modify. > ui tool show ""Build Structure"" > build start atom #4.2 res HOH > build modify #4.2/het:1@He O 2 geometry trigonal name O1 resName UNL > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 17 residues in model #4.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > select up 9794 atoms, 9910 bonds, 636 residues, 1 model selected > select up 9794 atoms, 9910 bonds, 636 residues, 3 models selected > select down 9794 atoms, 9910 bonds, 636 residues, 2 models selected > select down 3 atoms, 2 bonds, 1 residue, 2 models selected > select up 9794 atoms, 9910 bonds, 636 residues, 1 model selected > isolde sim start #4.2/B,A,C-het ISOLDE: started sim > select clear > volume #4.1.1.1 level 0.155 > select up 40 atoms, 38 bonds, 2 residues, 1 model selected > select down 2 atoms, 2 residues, 2 models selected > select clear > select up 95 atoms, 96 bonds, 7 residues, 2 models selected > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 6 residues in model #4.2 to IUPAC-IUB standards. ISOLDE: stopped sim > combine #4 > hide #!4 models > hide #!4.1 models > hide #4.3 models > hide #!5 models > hide #!4.2 models > show #!5 models > hide #!5 atoms > dssp > select #5:ORN 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #5:ORN 22 atoms, 21 bonds, 1 residue, 1 model selected > ui tool show ""Side View"" > view sel > select clear > select #5:ORN 22 atoms, 21 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #fffb00 showDist true interModel false distSlop 1.0 > angleSlop 40.0 twoColors true slopColor #ff9300 intraMol false select true > reveal true 7 hydrogen bonds found 4 strict hydrogen bonds found > ui tool show H-Bonds > hbonds sel color #fffb00 showDist true interModel false distSlop 1.5 > angleSlop 40.0 twoColors true slopColor #ff9300 intraMol false select true > reveal true 14 hydrogen bonds found 7 strict hydrogen bonds found > ui tool show H-Bonds > hbonds sel color #fffb00 interModel false distSlop 1.5 angleSlop 40.0 > intraMol false select true reveal true 15 hydrogen bonds found > select clear > select #5:116,117 33 atoms, 33 bonds, 2 residues, 1 model selected > show sel atoms > select clear > ~display HC > select clear > select #5:237 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > ~display HC > select clear > select #5:116,117,237,274,HOH,ORN,389,323,45 155 atoms, 149 bonds, 6 pseudobonds, 10 residues, 2 models selected > select #5:116,117,237,274,HOH,ORN,389,323,45,240 174 atoms, 167 bonds, 7 pseudobonds, 11 residues, 2 models selected > select #5:116,117,237,274,HOH,ORN,389,323,45,240,243 186 atoms, 178 bonds, 9 pseudobonds, 12 residues, 2 models selected > select #5:116,117,237,274,HOH,ORN,389,323,45,240,243,UNL 189 atoms, 180 bonds, 12 pseudobonds, 13 residues, 2 models selected > select #5:116,117,237,274,HOH,ORN,389,323,45,240,243,UNL,40,41 241 atoms, 231 bonds, 14 pseudobonds, 17 residues, 2 models selected > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/cryosparc_P60_J191_006_volume_map_sharp.mrc"" Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #6, grid size 288,288,288, pixel 0.835, shown at level 0.0608, step 2, values float32 > volume #6 step 1 > mask #6 near sel range 3 Unknown command: mask #6 near sel range 3 > volume zone #6 nearAtoms sel range 3 > transparency #6.1 50 > volume #6 level 0.1389 > select clear > hide #!5 cartoons > show #!5 cartoons > transparency #6 cartoon 50 Missing or invalid ""percent"" argument: Expected a number > transparency #6 50 cartoons > transparency #5 50 cartoons > transparency #5 85 cartoons > select clear > select #5:116,117,237,274,HOH,ORN,389,323,45,240,243,UNL,40,41 241 atoms, 231 bonds, 14 pseudobonds, 17 residues, 2 models selected > view sel > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/ctn700/Desktop/movie2.mp4 Movie saved to /Users/ctn700/Desktop/movie2.mp4 > select #5:21-56 1097 atoms, 1111 bonds, 72 residues, 1 model selected > transparency #5 0 sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #5:sel 0 cartoons > select clear > transparency #5:21-56 0 cartoons > dssp > volume zone #6 nearAtoms sel range 3 inPlace True Expected a keyword > volume zone #6 nearAtoms sel range 3.5 inPlace True Expected a keyword > select #5:116,117,237,274,HOH,ORN,389,323,45,240,243,UNL,40,41 241 atoms, 231 bonds, 14 pseudobonds, 17 residues, 2 models selected > volume zone #6 nearAtoms sel range 3.5 > select clear > lighting soft > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting full > lighting shadows false > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting full > lighting shadows false > hide #!6 models > select clear > select #5:ORN 22 atoms, 21 bonds, 1 residue, 1 model selected > view sel > select #5:ORN 22 atoms, 21 bonds, 1 residue, 1 model selected > show #!6 models > select clear > volume zone #6 nearAtoms sel range 3.5 no atoms specified for zone > select #5:ORN 22 atoms, 21 bonds, 1 residue, 1 model selected > volume zone #6 nearAtoms sel range 3.5 > volume #6 style mesh > volume #6 color black > volume #6 color #929292 > volume #6 color #00f900 > volume #6 color #0433ff > volume #6 color #7a81ff > volume #6 color #0433ff > volume zone #6 nearAtoms sel range 4 > select clear > select #5:ORN 22 atoms, 21 bonds, 1 residue, 1 model selected > view sel > select clear ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,6 Model Number: MNWA3DK/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.61.3 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 9 days, 4 hours, 25 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: HP P34hc G4: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 ChimeraX-Clipper: 0.23.1 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect new normal Unassigned