id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14986 Crash in garbage collection ywyin@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.5-arm64-arm-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003bff53000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029f06b000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029e05f000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002933d3000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002923c7000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002913bb000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002903af000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028f3a3000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028e397000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028d38b000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028c37f000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028b373000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001dc406080 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 1014 in to_h36 File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 1084 in _h_name File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 949 in new_hydrogen File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 910 in add_altloc_hyds File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 909 in _attach_hydrogens File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 225 in add_hydrogens File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 184 in hbond_add_hydrogens File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 77 in cmd_addh File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 95 in assign_charges File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 525 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 582 in run_expanded_command File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 72 in func_plus_tip File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 339 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 420 in run_shortcut File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 402 in try_shortcut File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1376 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 66 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py"", line 205 in callback File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, 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.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, 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.__nnls, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 122) {""app_name"":""ChimeraX"",""timestamp"":""2024-04-20 12:34:10.00 -0500"",""app_version"":""1.7.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.7.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.5 (22G74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""41E54B49-1453-48AC-B1B3-833B19684E87""} { ""uptime"" : 1100000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,2"", ""coalitionID"" : 26000, ""osVersion"" : { ""train"" : ""macOS 13.5"", ""build"" : ""22G74"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-04-20 12:33:56.2699 -0500"", ""incident"" : ""41E54B49-1453-48AC-B1B3-833B19684E87"", ""pid"" : 195, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-02-23 13:18:41.3318 -0600"", ""procStartAbsTime"" : 5492455492347, ""procExitAbsTime"" : 27557874772456, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.0"",""CFBundleVersion"":""1.7.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""214F2311-E1E7-53FA-949D-A6D5511FF473"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""045D10A6-ECFD-536B-1ED8-A9486C2FD00B"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 2213, ""sleepWakeUUID"" : ""670F2591-543C-4F0F-B451-4CACEEF74DBE"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. Bytes before following region: 105562108854103\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600218000000-600220000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":195}, ""vmregioninfo"" : ""0xa9 is not in any region. Bytes before following region: 105562108854103\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600218000000-600220000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""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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""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""cf4ed35e2fedda631c9b192db5c275730b17ab42"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""63508beab3714d3622fc7808"" }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1cez Summary of feedback from opening 1cez fetched from pdb --- note | Fetching compressed mmCIF 1cez from http://files.rcsb.org/download/1cez.cif 1cez title: Crystal structure of A T7 RNA polymerase-T7 promoter complex [more info...] Chain information for 1cez #1 --- Chain | Description | UniProt A | PROTEIN (BACTERIOPHAGE T7 RNA POLYMERASE) | RPOL_BPT7 1-883 N | DNA (5'-D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3') | T | DNA (5'-D(P*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3') | > cartoon style modeHelix tube sides 20 > open 8q63 Summary of feedback from opening 8q63 fetched from pdb --- note | Fetching compressed mmCIF 8q63 from http://files.rcsb.org/download/8q63.cif 8q63 title: Cryo-EM structure of IC8', a second state of yeast mitochondrial RNA polymerase transcription initiation complex with 8-mer RNA, pppGpGpUpApApApUpG [more info...] Chain information for 8q63 #2 --- Chain | Description | UniProt A | DNA-directed RNA polymerase, mitochondrial | RPOM_YEAST 100-1351 B | Mitochondrial transcription factor 1 | MTF1_YEAST 2-341 C | RNA (pppGpGpUpApApApUpG) | N | Non-template DNA (37-mer) | T | Template DNA (37-MER) | Non-standard residues in 8q63 #2 --- GTP — guanosine-5'-triphosphate > show cartoons > hide atoms > select #2/B 2698 atoms, 2773 bonds, 329 residues, 1 model selected > hide sel cartoons > ui tool show Matchmaker > mmaker #2 to #1 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 1cez, chain A (#1) with 8q63, chain A (#2), sequence alignment score = 1283.6 RMSD between 316 pruned atom pairs is 1.028 angstroms; (across all 751 pairs: 14.861) > cartoon style sel modeHelix tube sides 20 > color sel orange > select #2/A 7200 atoms, 7360 bonds, 4 pseudobonds, 915 residues, 2 models selected > color (#!2 & sel) forest green > color (#!2 & sel) light sea green > select #2/N 642 atoms, 722 bonds, 31 residues, 1 model selected > hide sel cartoons > select #2/T 630 atoms, 705 bonds, 31 residues, 1 model selected > hide sel cartoons > select #2/C 176 atoms, 197 bonds, 8 residues, 1 model selected > hide sel cartoons > select #1/N 322 atoms, 340 bonds, 33 residues, 1 model selected > hide sel cartoons > select #1/T 366 atoms, 394 bonds, 31 residues, 1 model selected > hide sel cartoons > mmaker #2/A:200-600 to #1/A/1-266 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 1cez, chain A (#1) with 8q63, chain A (#2), sequence alignment score = 133.3 RMSD between 47 pruned atom pairs is 1.084 angstroms; (across all 142 pairs: 11.360) > select #1/A/1-266 7078 atoms, 6791 bonds, 1 pseudobond, 1301 residues, 2 models selected > hide #!2 models > select #1/A:1-266 1900 atoms, 1933 bonds, 1 pseudobond, 245 residues, 2 models selected > color (#!1 & sel) purple > mmaker #2/A:200-600 to #1/A:1-266 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 1cez, chain A (#1) with 8q63, chain A (#2), sequence alignment score = 128.7 RMSD between 47 pruned atom pairs is 1.084 angstroms; (across all 142 pairs: 11.425) > show #!2 models > select #1/A:267-882 4734 atoms, 4852 bonds, 616 residues, 1 model selected > hide sel cartoons > select #2/A:392-1356 7145 atoms, 7303 bonds, 4 pseudobonds, 909 residues, 2 models selected > select #2/A:500-1356 6259 atoms, 6399 bonds, 4 pseudobonds, 801 residues, 2 models selected > select #2/A:550-1355 5904 atoms, 6043 bonds, 3 pseudobonds, 754 residues, 2 models selected > select #2/A:650-1355 5413 atoms, 5542 bonds, 2 pseudobonds, 689 residues, 2 models selected > select #2/A:669-1355 5266 atoms, 5394 bonds, 2 pseudobonds, 670 residues, 2 models selected > hide sel cartoons > select #1/T 366 atoms, 394 bonds, 31 residues, 1 model selected > show sel cartoons > select #1/N 322 atoms, 340 bonds, 33 residues, 1 model selected > show sel cartoons > select clear > save ""/Users/whitneyyin/Dropbox/Whitney_misc/Fire lab/NTD266_T7_Rpo41.gif"" > width 626 height 647 supersample 4 > open 7a8p Summary of feedback from opening 7a8p fetched from pdb --- notes | Fetching compressed mmCIF 7a8p from http://files.rcsb.org/download/7a8p.cif Fetching CCD R4Q from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/R4Q/R4Q.cif 7a8p title: Structure of human mitochondrial RNA polymerase in complex with IMT inhibitor. [more info...] Chain information for 7a8p #3 --- Chain | Description | UniProt A | DNA-directed RNA polymerase, mitochondrial | RPOM_HUMAN 105-1230 Non-standard residues in 7a8p #3 --- R4Q — (3~{R})-1-[(2~{R})-2-[4-(2-chloranyl-4-fluoranyl- phenyl)-2-oxidanylidene-chromen-7-yl]oxypropanoyl]piperidine-3-carboxylic acid > mmaker #3 to #2 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 8q63, chain A (#2) with 7a8p, chain A (#3), sequence alignment score = 1496.6 RMSD between 363 pruned atom pairs is 1.029 angstroms; (across all 707 pairs: 16.727) > cartoon style modeHelix tube sides 20 > open 3spa Summary of feedback from opening 3spa fetched from pdb --- notes | Fetching compressed mmCIF 3spa from http://files.rcsb.org/download/3spa.cif Fetching CCD CL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif 3spa title: Crystal Structure of Human Mitochondrial RNA Polymerase [more info...] Chain information for 3spa #4 --- Chain | Description | UniProt A | DNA-directed RNA polymerase, mitochondrial | RPOM_HUMAN 105-1230 B | Nonamer peptide | Non-standard residues in 3spa #4 --- CL — chloride ion GOL — glycerol (glycerin; propane-1,2,3-triol) SO4 — sulfate ion > mmaker #4 to#2 > matchmaker #4 to#2 Expected a keyword > mmaker #4 to #2 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 8q63, chain A (#2) with 3spa, chain A (#4), sequence alignment score = 1547.4 RMSD between 355 pruned atom pairs is 0.996 angstroms; (across all 731 pairs: 16.714) > cartoon style modeHelix tube sides 20 > hide #!3 models > mmaker #4/A:1-660 to #1/A:1-266 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 1cez, chain A (#1) with 3spa, chain A (#4), sequence alignment score = 158.1 RMSD between 65 pruned atom pairs is 1.143 angstroms; (across all 217 pairs: 12.763) > select #4/A:700-1250 3821 atoms, 3897 bonds, 2 pseudobonds, 494 residues, 2 models selected > hide sel cartoons > hide sel atoms > hide #!2 models > view t7_POLRMT_NTD Expected an objects specifier or a view name or a keyword > view name t7_POLRMT_NTD > hide sel atoms > show #!2 models > save ""/Users/whitneyyin/Dropbox/Whitney_misc/Fire lab/T7_mtRNAPs.cxs"" > ui tool show ""Side View"" > select clear > select #1/A:883 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel cartoons > select #4/A:1@O1 1 atom, 1 residue, 1 model selected Drag select of 10 atoms, 9 bonds > hide sel atoms Drag select of 3 atoms > hide sel atoms > select #1/T,N 688 atoms, 734 bonds, 31 pseudobonds, 64 residues, 2 models selected > nucleotides sel tube/slab shape box > nucleotides sel atoms > style nucleic & sel stick Changed 656 atom styles > show sel atoms > select clear > select #1/T,N:HOH 32 atoms, 32 residues, 1 model selected > hide sel atoms > save ""/Users/whitneyyin/Dropbox/Whitney_misc/Fire lab/T7_mtRNAPs.cxs"" > hide #!2 models > hide #!4 models > show #!3 models > show #!2 models > hide #!3 models > hide #!2 models > show #!4 models > open ""/Users/whitneyyin/Dropbox/Manuscripts/Noe > Baruch/NAR_AtPols/AtPolls.cxs"" opened ChimeraX session > show #1 models > hide #2 models > hide #!3 models > show #!3 models > show #!4 models > log metadata #4 No models had metadata > log chains #4 Chain information for 2kfz #4 --- Chain | Description | UniProt A | KLENOW FRAGMENT OF DNA POLYMERASE I | DPO1_ECOLI 324-928 B | 5'-D(*GP*CP*TP*TP*AP*(US1)P*G)-3' | > log metadata #3 No models had metadata > log chains #3 Chain information for 4n5s #3 --- Chain | Description | UniProt A | DNA polymerase I, thermostable | DPO1_THEAQ 281-832 B | 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3' | C | 5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' | > select add #3 5394 atoms, 5003 bonds, 70 pseudobonds, 1114 residues, 3 models selected > hide #!4 models > select #1/A:576-621 377 atoms, 386 bonds, 46 residues, 1 model selected > color sel lime > select #1/A:648-712 467 atoms, 472 bonds, 65 residues, 1 model selected > show #!4 models > hide #!4 models > show #!4 models > color sel magenta > select #1/A 8123 atoms, 8282 bonds, 1034 residues, 1 model selected > color sel dark gray > select #1/A:648-712 467 atoms, 472 bonds, 65 residues, 1 model selected > color sel magenta > select #1/A:576-621 377 atoms, 386 bonds, 46 residues, 1 model selected > color sel cyan > hide #!4 models > hide #!3 models > show #!3 models > show #!4 models > hide #!3 models > select #1/A:844-869 205 atoms, 209 bonds, 26 residues, 1 model selected > color sel red > show #!3 models > hide #!4 models > select #1/A:512 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!4 models > cartoon style sel modeHelix tube sides 20 > hide #!4 models > show #!4 models > cartoon style sel modeHelix tube sides 20 > select add #4 5142 atoms, 4916 bonds, 13 pseudobonds, 924 residues, 4 models selected > cartoon style (#1#!4 & sel) modeHelix tube sides 20 > select clear > save ""/Users/whitneyyin/Dropbox/Whitney_misc/Fire lab/AtPolB_KF.png"" width > 846 height 647 supersample 3 > save ""/Users/whitneyyin/Dropbox/Manuscripts/Noe > Baruch/NAR_AtPols/AtPolB_KF.png"" width 846 height 647 supersample 3 > hide #1 models > open /Users/whitneyyin/Dropbox/mtReplisome/Figs/twinkles_gp4_v5.cxs opened ChimeraX session > select #11/A:359, 369 11 atoms, 9 bonds, 2 residues, 1 model selected > show sel atoms > select #11/A:359, 369,357 22 atoms, 19 bonds, 3 residues, 1 model selected > show sel atoms > show #!13 models > hide #!11 models > show #!12 models > hide #!12 models > show #!12 models > hide #!13 models > select #12/A-F:354-374 1080 atoms, 1104 bonds, 126 residues, 6 models selected > show #!11 models > hide #!12 models > show #!13 models > hide #!11 models > select add #13 30406 atoms, 31131 bonds, 3752 residues, 22 models selected > color sel & #13.7-8#!13.1-6,9 bychain > select #13/A-F:354-374 1080 atoms, 1104 bonds, 126 residues, 6 models selected > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!10 models > hide #!10 models > show #9 models > hide #9 models > show #!10 models > show #9 models > hide #!10 models > hide #9 models > show #!6 models > hide #!6 models > show #7 models > hide #7 models > show #7 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!13 models > hide #!11 models > show #!11 models > show #!13 models > hide #7 models > mmaker #11 to #13 Specify a single 'to' model only > mmaker #11:A to #13:A No 'to' model specified > mmaker #11/A to #13/A 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 hTWN_hex_spiral_ATP6_ssDNA.pdb, chain A (#13.1) with hTWN_hexamer_ssDNA.pdb, chain A (#11), sequence alignment score = 3437.9 RMSD between 600 pruned atom pairs is 0.000 angstroms; (across all 600 pairs: 0.000) > show #7 models > hide #!11 models > show #!11 models > hide #!11 models > mmaker #11/C to #13/C Specify a single 'to' model only > show #!11 models > hide #7 models > mmaker #11/C:400-600 to #13/C:400-600 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 hTWN_hex_spiral_ATP6_ssDNA.pdb, chain C (#13.3) with hTWN_hexamer_ssDNA.pdb, chain C (#11), sequence alignment score = 1055.2 RMSD between 201 pruned atom pairs is 0.000 angstroms; (across all 201 pairs: 0.000) > hide #!13 models > hide #!11 models > show #!13 models > select #13/A-F:357-389 1560 atoms, 1584 bonds, 198 residues, 6 models selected > color (#!13.1-6 & sel) yellow > show #!11 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!11 models > show #!11 models > hide #!11 models > show #7 models > hide #!13 models > show #!13 models > show #!8 models > hide #7 models > mmaker #8 to #13/C:1-300 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 hTWN_hex_spiral_ATP6_ssDNA.pdb, chain C (#13.3) with 5ikn_chainH_NTD.pdb, chain H (#8), sequence alignment score = 80.1 RMSD between 70 pruned atom pairs is 1.062 angstroms; (across all 122 pairs: 7.400) > select add #13 29326 atoms, 30027 bonds, 3626 residues, 22 models selected > color sel bychain > select #13/A-F:357-368 582 atoms, 600 bonds, 72 residues, 6 models selected > select #13/A-F:368-382 738 atoms, 738 bonds, 90 residues, 6 models selected > select #13/A-F:368-389 1020 atoms, 1020 bonds, 132 residues, 6 models selected > color (#!13.1-6 & sel) yellow > hide #!8 models > show #7 models > hide #7 models > select #13/C:315,319,359,369,374 45 atoms, 42 bonds, 5 residues, 1 model selected > show sel atoms > color (#!13.3 & sel) red > color sel byhetero > select #13/C:315,319,359,369,374,381 53 atoms, 49 bonds, 6 residues, 1 model selected > select #13/C:315,319,359,369,374,381, 368, 367 68 atoms, 64 bonds, 8 residues, 1 model selected > show sel atoms > color (#!13.3 & sel) red > color sel byhetero > select #13/D:475 5 atoms, 4 bonds, 1 residue, 1 model selected > select #13/D:475,474 19 atoms, 20 bonds, 2 residues, 1 model selected > select #13/D:475,481 13 atoms, 11 bonds, 2 residues, 1 model selected > select #13/D:475,481,474, Expected an objects specifier or a keyword > select #13/D:475,481,474,485 38 atoms, 38 bonds, 4 residues, 1 model selected > select #13/D:475,481,474,485,609 49 atoms, 48 bonds, 5 residues, 1 model selected > select #13.3/C:374@CD 1 atom, 1 residue, 1 model selected > select #13/D:475,481,474,485 38 atoms, 38 bonds, 4 residues, 1 model selected > show sel atoms > color sel byhetero > select #13/D:475,481,474,485,460 43 atoms, 42 bonds, 5 residues, 1 model selected > select #13/D:475,481,474,485,463 49 atoms, 48 bonds, 5 residues, 1 model selected > select #13/D:475,481,474,485,463 49 atoms, 48 bonds, 5 residues, 1 model selected > select #13/C:475,481,474,485,463 49 atoms, 48 bonds, 5 residues, 1 model selected > select #13/D:475,481,474,485,463 49 atoms, 48 bonds, 5 residues, 1 model selected > select clear > show #!28 models > mmaker #28/C to #13/C Specify a single 'to' model only > hide #!13 models > show #!13 models > hide #!28 models > show #!28 models > mmaker #28/C:400-600 to #13/C:400-600 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 hTWN_hex_spiral_ATP6_ssDNA.pdb, chain C (#13.3) with twn_W315L_7mer, chain C (#28), sequence alignment score = 862 RMSD between 164 pruned atom pairs is 0.749 angstroms; (across all 174 pairs: 1.408) > hide #!28 models > show #!28 models > select #13/A-F:445 54 atoms, 48 bonds, 6 residues, 6 models selected > style sel sphere Changed 54 atom styles > show sel atoms > select #13/A-F:445,609 120 atoms, 108 bonds, 12 residues, 6 models selected > show sel atoms > style sel sphere Changed 120 atom styles > color sel byhetero > hide #!28 models > select #13.4/D:468 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > ui tool show Distances > select #13.3/C:381@CD2 1 atom, 1 residue, 1 model selected > select #13.4/D:445@CB 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select #13.3/C:381@CG 1 atom, 1 residue, 1 model selected > select #13.3/C:381@CB 1 atom, 1 residue, 1 model selected > select #13.3/C:609@CG 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select add #13.4/D:445@CB 1 atom, 1 bond, 1 residue, 2 models selected Exactly two atoms must be selected! No distances to delete! > select clear > select #13.4/D:445@CB 1 atom, 1 residue, 1 model selected > select add #13.3/C:381@CD2 2 atoms, 2 residues, 3 models selected > distance #13.4/D:445@CB #13.3/C:381@CD2 Distance between hTWN_hex_spiral_ATP6_ssDNA.pdb #13.4/D GLU 445 CB and hTWN_hex_spiral_ATP6_ssDNA.pdb #13.3/C LEU 381 CD2: 21.309Å > select #13.3/C:381@CD2 1 atom, 1 residue, 1 model selected > select add #13.3/C:609@CG 2 atoms, 2 residues, 2 models selected > distance #13.3/C:381@CD2 #13.3/C:609@CG Distance between hTWN_hex_spiral_ATP6_ssDNA.pdb #13.3/C LEU 381 CD2 and ARG 609 CG: 16.203Å > select #13/D:441,457,458 30 atoms, 30 bonds, 3 residues, 1 model selected > select #13/D:4457,458 9 atoms, 8 bonds, 1 residue, 1 model selected > select #13/D:457,458 16 atoms, 15 bonds, 2 residues, 1 model selected > select #13/C:391 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #13.4/D:468@CG 1 atom, 1 residue, 1 model selected > color (#!13.4 & sel) red > color sel byhetero > select #13.4/D:475@CA 1 atom, 1 residue, 1 model selected > color (#!13.4 & sel) red > color sel byhetero > select #13.4/D:485@CE2 1 atom, 1 residue, 1 model selected > color (#!13.4 & sel) red > color sel byhetero > select #13.4/D:485@CA 1 atom, 1 residue, 1 model selected > select clear > select #13.4/D:485@CE2 1 atom, 1 residue, 1 model selected > color (#!13.4 & sel) red > select #13.4/D:485@CB 1 atom, 1 residue, 1 model selected > select #13.4/D:485@CD2 1 atom, 1 residue, 1 model selected > select #13/D:485,475,468 24 atoms, 22 bonds, 3 residues, 1 model selected > color (#!13.4 & sel) red > color sel byhetero > select clear > save /Users/whitneyyin/Dropbox/mtReplisome/Figs/disease_muts_interface4.png > width 704 height 647 supersample 4 > hide #!14 models > hide #14.1 models > save > /Users/whitneyyin/Dropbox/mtReplisome/Figs/disease_muts_interface_overview4.png > width 704 height 647 supersample 3 > show #7 models > show #!11 models > hide #!11 models > show #!11 models > hide #!13 models > hide #!11 models > show #!11 models > hide #!11 models > show #!13 models > show #!11 models > hide #!13 models > hide #7 models > select #11/D:485,475,468 24 atoms, 22 bonds, 3 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select #11/D:485,475,468 24 atoms, 22 bonds, 3 residues, 1 model selected > color sel byhetero > color sel red > select #11/C:475,481,474,485,463 49 atoms, 48 bonds, 5 residues, 1 model selected > select #11/C:475,481,474,485,463 49 atoms, 48 bonds, 5 residues, 1 model selected > show sel atoms > select #11/C:315 14 atoms, 15 bonds, 1 residue, 1 model selected > select #11/C:315,359,369 25 atoms, 24 bonds, 3 residues, 1 model selected > select #11/C:315,359,369,374 36 atoms, 34 bonds, 4 residues, 1 model selected > select #11/C:315,359,369,374,375,381 53 atoms, 50 bonds, 6 residues, 1 model selected > select #11/C:315,359,369,374,370,375,381 64 atoms, 62 bonds, 7 residues, 1 model selected > show sel atoms > color sel red > color sel byhetero > select #11/C:382-385 30 atoms, 29 bonds, 4 residues, 1 model selected > color sel yellow > select #11/C:384 7 atoms, 6 bonds, 1 residue, 1 model selected > select #11/C:385 9 atoms, 8 bonds, 1 residue, 1 model selected > select #11/C:385 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel cornflower blue > select #11/C:543 11 atoms, 10 bonds, 1 residue, 1 model selected > select #11/D:478 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #11/D:436 4 atoms, 3 bonds, 1 residue, 1 model selected > select #11/C:333-339 55 atoms, 55 bonds, 7 residues, 1 model selected > hide sel cartoons > select #11/D:43-56 105 atoms, 106 bonds, 14 residues, 1 model selected > select #11/D:43-56 105 atoms, 106 bonds, 14 residues, 1 model selected > hide sel cartoons > save /Users/whitneyyin/Dropbox/mtReplisome/Figs/disease_muts_interface5.png > width 704 height 647 supersample 3 > show #!6 models > hide #!11 models > select #6:84 77 atoms, 70 bonds, 7 residues, 1 model selected > show sel atoms > color (#!6 & sel) red > select #6:84,111 161 atoms, 154 bonds, 14 residues, 1 model selected > show sel atoms > color sel byhetero > show #!8 models > hide #!6 models > select #8:84,111 23 atoms, 22 bonds, 2 residues, 1 model selected > hide #!8 models > show #!8 models > show sel atoms > show #!11 models > hide #!11 models > show #!11 models > show #!13 models > hide #!13 models > select #11:152-153 108 atoms, 102 bonds, 12 residues, 1 model selected > hide #!8 models > show sel atoms > color sel byhetero > select #11/C:150 8 atoms, 7 bonds, 1 residue, 1 model selected > select #11:149-150,152-153 210 atoms, 198 bonds, 24 residues, 1 model selected > show sel atoms > color sel byhetero > select #11:149-150,152-153,147 264 atoms, 246 bonds, 30 residues, 1 model selected > show sel atoms > color sel byhetero > show #!8 models > hide #!11 models > show #!11 models > select up 1356 atoms, 1380 bonds, 162 residues, 1 model selected > select up 32652 atoms, 33414 bonds, 4104 residues, 1 model selected > select up 32972 atoms, 33765 bonds, 4120 residues, 1 model selected > select #8:84,111,130 34 atoms, 33 bonds, 3 residues, 1 model selected > show sel atoms > select clear > select #11/C:235 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #11/C:234 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #11/C:235@CB 1 atom, 1 residue, 1 model selected > select #11/C:235@OE1 1 atom, 1 residue, 1 model selected > color sel byhetero > select #11/C:235@OE2 1 atom, 1 residue, 1 model selected > color sel byhetero > save /Users/whitneyyin/Dropbox/mtReplisome/Figs/twinkles_gp4_v3.cxs > hide #!8 models > select #11:43 54 atoms, 48 bonds, 6 residues, 1 model selected > show sel atoms > style sel sphere Changed 54 atom styles > select #11:41-43 174 atoms, 168 bonds, 18 residues, 1 model selected > show sel cartoons > select #11:41-45 264 atoms, 258 bonds, 30 residues, 1 model selected > show sel cartoons > select #11:41-450 19464 atoms, 19926 bonds, 2460 residues, 1 model selected > show sel cartoons > show #!8 models > hide #!11 models > show #!11 models > hide #!8 models > select #11/C:633-685 385 atoms, 389 bonds, 52 residues, 1 model selected > show sel atoms > show #7 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!6 models > hide #7 models > select #6/H to #7 Expected a keyword > show #7 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #7 models > select #6/H to #7/H Expected a keyword > mmaker #6/H 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 5ikn_chainH.pdb, chain H (#7) with 5ikn, chain H (#6), sequence alignment score = 2495.5 RMSD between 486 pruned atom pairs is 0.000 angstroms; (across all 486 pairs: 0.000) > show #!11 models > hide #!11 models > coulombic #!6 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 5ikn_D SES surface #6.2: minimum, -19.04, mean -1.92, maximum 13.75 Coulombic values for 5ikn_E SES surface #6.3: minimum, -20.03, mean -2.00, maximum 14.54 Coulombic values for 5ikn_F SES surface #6.4: minimum, -19.52, mean -2.10, maximum 21.12 Coulombic values for 5ikn_G SES surface #6.5: minimum, -20.01, mean -2.04, maximum 13.03 Coulombic values for 5ikn_H SES surface #6.6: minimum, -21.34, mean -1.96, maximum 13.57 Coulombic values for 5ikn_I SES surface #6.7: minimum, -18.18, mean -1.59, maximum 14.59 Coulombic values for 5ikn_J SES surface #6.8: minimum, -28.56, mean -2.07, maximum 13.98 To also show corresponding color key, enter the above coulombic command and add key true > hide #!6 surfaces > coulombic #!6 Coulombic values for 5ikn_D SES surface #6.2: minimum, -19.04, mean -1.92, maximum 13.75 Coulombic values for 5ikn_E SES surface #6.3: minimum, -20.03, mean -2.00, maximum 14.54 Coulombic values for 5ikn_F SES surface #6.4: minimum, -19.52, mean -2.10, maximum 21.12 Coulombic values for 5ikn_G SES surface #6.5: minimum, -20.01, mean -2.04, maximum 13.03 Coulombic values for 5ikn_H SES surface #6.6: minimum, -21.34, mean -1.96, maximum 13.57 Coulombic values for 5ikn_I SES surface #6.7: minimum, -18.18, mean -1.59, maximum 14.59 Coulombic values for 5ikn_J SES surface #6.8: minimum, -28.56, mean -2.07, maximum 13.98 To also show corresponding color key, enter the above coulombic command and add key true > show #!11 models > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for hTWN_hexamer_ssDNA.pdb_C SES surface #11.2: minimum, -26.56, mean -0.42, maximum 13.81 To also show corresponding color key, enter the above coulombic command and add key true > select add #11 32972 atoms, 33765 bonds, 4120 residues, 3 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for hTWN_hexamer_ssDNA.pdb_A SES surface #11.3: minimum, -19.53, mean -0.41, maximum 14.15 Coulombic values for hTWN_hexamer_ssDNA.pdb_B SES surface #11.4: minimum, -18.37, mean -0.41, maximum 14.57 Coulombic values for hTWN_hexamer_ssDNA.pdb_C SES surface #11.2: minimum, -26.56, mean -0.42, maximum 13.81 Coulombic values for hTWN_hexamer_ssDNA.pdb_D SES surface #11.5: minimum, -18.42, mean -0.42, maximum 13.92 Coulombic values for hTWN_hexamer_ssDNA.pdb_E SES surface #11.6: minimum, -20.41, mean -0.41, maximum 14.42 Coulombic values for hTWN_hexamer_ssDNA.pdb_F SES surface #11.7: minimum, -18.41, mean -0.41, maximum 14.39 Coulombic values for hTWN_hexamer_ssDNA.pdb_T SES surface #11.8: minimum, -17.59, mean -9.20, maximum 0.08 To also show corresponding color key, enter the above coulombic command and add key true > hide #!6 models > hide sel surfaces > show sel surfaces > select #11/T 320 atoms, 351 bonds, 16 residues, 1 model selected > hide sel surfaces > hide #!11 models > show #!6 models > hide #!6 models > show #!4 models > hide #!4 models > show #!5 models > coulombic #!5 The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: gp4_ssDNA_6n7v #5/D LYS 440 gp4_ssDNA_6n7v #5/E LYS 440 gp4_ssDNA_6n7v #5/F LYS 440 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for gp4_ssDNA_6n7v_A SES surface #5.3: minimum, -17.09, mean -0.53, maximum 11.41 Coulombic values for gp4_ssDNA_6n7v_B SES surface #5.4: minimum, -15.70, mean -0.72, maximum 15.40 Coulombic values for gp4_ssDNA_6n7v_C SES surface #5.5: minimum, -16.00, mean -1.04, maximum 12.16 Coulombic values for gp4_ssDNA_6n7v_D SES surface #5.6: minimum, -17.95, mean -0.49, maximum 12.66 Coulombic values for gp4_ssDNA_6n7v_E SES surface #5.7: minimum, -16.51, mean -0.13, maximum 12.66 Coulombic values for gp4_ssDNA_6n7v_F SES surface #5.8: minimum, -16.88, mean -0.02, maximum 12.73 Coulombic values for gp4_ssDNA_6n7v_T SES surface #5.9: minimum, -17.70, mean -9.31, maximum -0.57 To also show corresponding color key, enter the above coulombic command and add key true > select #5/T 320 atoms, 351 bonds, 16 residues, 1 model selected > hide sel surfaces > select add #5 12861 atoms, 13037 bonds, 41 pseudobonds, 1632 residues, 10 models selected > hide sel surfaces > mmaker #5 to #11 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 hTWN_hexamer_ssDNA.pdb, chain A (#11) with gp4_ssDNA_6n7v, chain C (#5), sequence alignment score = 303.4 RMSD between 153 pruned atom pairs is 1.187 angstroms; (across all 256 pairs: 3.350) > show #!11 models > hide sel surfaces > select add #11 45833 atoms, 46802 bonds, 41 pseudobonds, 5752 residues, 21 models selected > hide sel surfaces > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!5 models > ui tool show Distances > select #11/D:94 7 atoms, 6 bonds, 1 residue, 1 model selected > select #11/D:94 7 atoms, 6 bonds, 1 residue, 1 model selected > select #11/A:596 7 atoms, 6 bonds, 1 residue, 1 model selected Exactly two atoms must be selected! > select #11/A:94 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #11/A:596 14 atoms, 12 bonds, 2 residues, 2 models selected Exactly two atoms must be selected! > select #11/A:94 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #11/A:598 14 atoms, 13 bonds, 2 residues, 2 models selected Exactly two atoms must be selected! > select clear > select #11/A:598 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #11/A:94 14 atoms, 13 bonds, 2 residues, 2 models selected Exactly two atoms must be selected! > select #11/A:93 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #11/A:598 16 atoms, 15 bonds, 2 residues, 2 models selected > select clear > select add #11/A:94 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #11/A:90 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #11/F:654 14 atoms, 12 bonds, 2 residues, 2 models selected Exactly two atoms must be selected! > select clear > select #11/A:92 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #11/A:598 11 atoms, 10 bonds, 2 residues, 2 models selected Exactly two atoms must be selected! > show sel atoms > select clear > select #11/A:94 7 atoms, 6 bonds, 1 residue, 1 model selected Exactly two atoms must be selected! > select #11/A:93 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #11/A:595 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #11/A:595@CG1 1 atom, 1 residue, 1 model selected > select add #11/A:93@NE2 2 atoms, 2 residues, 2 models selected > distance #11/A:595@CG1 #11/A:93@NE2 Distance between hTWN_hexamer_ssDNA.pdb #11/A VAL 595 CG1 and GLN 93 NE2: 93.888Å > show #!6 models > hide sel surfaces > select clear > hide #!6,11 surfaces > hide #!6 models > open t7p1 't7p1' has no suffix > open 1t7p Summary of feedback from opening 1t7p fetched from pdb --- notes | Fetching compressed mmCIF 1t7p from http://files.rcsb.org/download/1t7p.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 1t7p title: T7 DNA polymerase complexed to DNA primer/template,A nucleoside triphosphate, and its processivity factor thioredoxin [more info...] Chain information for 1t7p #22 --- Chain | Description | UniProt A | DNA-directed DNA polymerase | DPOL_BPT7 1-704 B | Thioredoxin 1 | THIO_ECO57 1-108 P | DNA (5'-D(P*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*2DA)-3') | T | DNA (5'-D(P*CP*CP*TP*TP*GP*GP*CP*AP*CP*TP*GP*GP*C)-3') | Non-standard residues in 1t7p #22 --- 2DA — 2',3'-dideoxyadenosine-5'-monophosphate DG3 — 2'-3'-dideoxyguanosine-5'-triphosphate MG — magnesium ion > open 1tk0 Summary of feedback from opening 1tk0 fetched from pdb --- note | Fetching compressed mmCIF 1tk0 from http://files.rcsb.org/download/1tk0.cif 1tk0 title: T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site [more info...] Chain information for 1tk0 #31 --- Chain | Description | UniProt A | DNA polymerase | DPOL_BPT7 1-704 B | Thioredoxin 1 | THIO_ECOLI 1-108 P | 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*A*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DDG))-3' | T | 5'-D(*CP*CP*CP*(8OG)P*CP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3' | Non-standard residues in 1tk0 #31 --- 1PE — pentaethylene glycol (PEG400) 8OG — 8-oxo-2'-deoxy-guanosine-5'-monophosphate (8-oxo-7,8-dihydro-2'-deoxy- guanosine-5'-monophosphate) DCT — 2',3'-dideoxycytidine 5'-triphosphate DDG — 2',3'-dideoxy-guanosine-5'-monophosphate MES — 2-(N-morpholino)-ethanesulfonic acid MG — magnesium ion SO4 — sulfate ion > view #31 clip false > color #!11,22,31 bychain > select clear > select #22/A:242 8 atoms, 7 bonds, 1 residue, 1 model selected > select #22/A:242 8 atoms, 7 bonds, 1 residue, 1 model selected > select #22/A:240 9 atoms, 8 bonds, 1 residue, 1 model selected > select #22/A:242 8 atoms, 7 bonds, 1 residue, 1 model selected > select #22/A:246 8 atoms, 7 bonds, 1 residue, 1 model selected > select #31/A 5973 atoms, 5640 bonds, 19 pseudobonds, 1155 residues, 3 models selected > select #31/B 829 atoms, 817 bonds, 132 residues, 1 model selected > select #31/C Nothing selected > select #31/D Nothing selected > select #31/A 5973 atoms, 5640 bonds, 19 pseudobonds, 1155 residues, 3 models selected > select #31/B 829 atoms, 817 bonds, 132 residues, 1 model selected > hide sel cartoons > select #31/A 5973 atoms, 5640 bonds, 19 pseudobonds, 1155 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #31/T 346 atoms, 356 bonds, 43 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #31/P 280 atoms, 294 bonds, 31 residues, 1 model selected > hide sel cartoons > hide sel atoms > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue DDG (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmpnuiterw0/ante.in.mol2 -fi mol2 -o /var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmpnuiterw0/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (DDG) `` (DDG) `Welcome to antechamber 20.0: molecular input file processor.` (DDG) `` (DDG) `Info: Finished reading file (/var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmpnuiterw0/ante.in.mol2); atoms read (38), bonds read (40).` (DDG) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (DDG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (DDG) `` (DDG) `` (DDG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (DDG) `Info: Total number of electrons: 180; net charge: -1` (DDG) `` (DDG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (DDG) `` (DDG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (DDG) `` (DDG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (DDG) `` Charges for residue DDG determined Coulombic values for 1tk0_P SES surface #31.4: minimum, -17.89, mean -9.17, maximum -1.02 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > select #22/A:558 8 atoms, 7 bonds, 1 residue, 1 model selected > select #22/A:558 8 atoms, 7 bonds, 1 residue, 1 model selected > select #22/A:557 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > coulombic #!11,22,31 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue 8OG (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmp3dv184hs/ante.in.mol2 -fi mol2 -o /var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmp3dv184hs/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (8OG) `` (8OG) `Welcome to antechamber 20.0: molecular input file processor.` (8OG) `` (8OG) `Info: Finished reading file (/var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmp3dv184hs/ante.in.mol2); atoms read (46), bonds read (48).` (8OG) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (8OG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (8OG) `` (8OG) `` (8OG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (8OG) `Info: Total number of electrons: 236; net charge: -2` (8OG) `` (8OG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (8OG) `` (8OG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (8OG) `` (8OG) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (8OG) `` Charges for residue 8OG determined Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue 2DA (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmpyu4ttyc8/ante.in.mol2 -fi mol2 -o /var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmpyu4ttyc8/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (2DA) `` (2DA) `Welcome to antechamber 20.0: molecular input file processor.` (2DA) `` (2DA) `Info: Finished reading file (/var/folders/6v/30r6wz6546z91nmf8vnqjfmm0000gp/T/tmpyu4ttyc8/ante.in.mol2); atoms read (37), bonds read (39).` (2DA) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (2DA) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (2DA) `` (2DA) `` (2DA) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (2DA) `Info: Total number of electrons: 172; net charge: -1` (2DA) `` (2DA) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (2DA) `` (2DA) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (2DA) `` (2DA) `Running: /Applications/ChimeraX-1.7.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (2DA) `` Charges for residue 2DA determined Coulombic values for hTWN_hexamer_ssDNA.pdb_A SES surface #11.3: minimum, -19.53, mean -0.41, maximum 14.15 Coulombic values for hTWN_hexamer_ssDNA.pdb_B SES surface #11.4: minimum, -18.37, mean -0.41, maximum 14.57 Coulombic values for hTWN_hexamer_ssDNA.pdb_C SES surface #11.2: minimum, -26.56, mean -0.42, maximum 13.81 Coulombic values for hTWN_hexamer_ssDNA.pdb_D SES surface #11.5: minimum, -18.42, mean -0.42, maximum 13.92 Coulombic values for hTWN_hexamer_ssDNA.pdb_E SES surface #11.6: minimum, -20.41, mean -0.41, maximum 14.42 Coulombic values for hTWN_hexamer_ssDNA.pdb_F SES surface #11.7: minimum, -18.41, mean -0.41, maximum 14.39 Coulombic values for hTWN_hexamer_ssDNA.pdb_T SES surface #11.8: minimum, -17.59, mean -9.20, maximum 0.08 Coulombic values for 1t7p_A SES surface #22.4: minimum, -27.81, mean -1.81, maximum 15.71 Coulombic values for 1t7p_B SES surface #22.5: minimum, -12.34, mean -2.71, maximum 7.75 Coulombic values for 1t7p_P SES surface #22.6: minimum, -17.31, mean -9.14, maximum -1.65 Coulombic values for 1t7p_T SES surface #22.7: minimum, -33.02, mean -9.27, maximum -1.32 Coulombic values for 1tk0_A SES surface #31.5: minimum, -26.09, mean -1.82, maximum 14.84 Coulombic values for 1tk0_B SES surface #31.6: minimum, -12.66, mean -2.62, maximum 7.13 Coulombic values for 1tk0_P SES surface #31.4: minimum, -17.89, mean -9.17, maximum -1.02 Coulombic values for 1tk0_T SES surface #31.7: minimum, -18.48, mean -9.87, maximum -1.95 To also show corresponding color key, enter the above coulombic command and add key true > hide #!11,22,31 surfaces > close #31 > view #22 clip false > select add #22 7092 atoms, 6790 bonds, 44 pseudobonds, 1298 residues, 4 models selected > color sel bychain > select clear > select #22/A,B 6529 atoms, 6213 bonds, 13 pseudobonds, 1228 residues, 3 models selected > coulombic sel Coulombic values for 1t7p_A SES surface #22.4: minimum, -27.81, mean -1.81, maximum 15.71 Coulombic values for 1t7p_B SES surface #22.5: minimum, -12.34, mean -2.71, maximum 7.75 To also show corresponding color key, enter the above coulombic command and add key true > hide #!11 models > select clear > show #!18 models > mmaker #22/A to #18/A 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 PolgA_Rter.pdb, chain A (#18) with 1t7p, chain A (#22), sequence alignment score = 371.1 RMSD between 101 pruned atom pairs is 1.234 angstroms; (across all 600 pairs: 20.981) > view #18 clip false > hide #!18,22 surfaces > show #!18,22 surfaces > hide #!18 models > hide #!22 models > show #!18 models > coulombic #!18 The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: PolgA_Rter.pdb #18/A ARG 627 PolgA_Rter.pdb #18/A GLU 895 PolgA_Rter.pdb #18/A LYS 990 PolgA_Rter.pdb #18/A SER 1235 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z1610005LLL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 8422.141.2 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.5 (22G74) Kernel Version: Darwin 22.6.0 Time since boot: 78 days, 14 hours, 23 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX