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Opened 18 months ago
Closed 18 months ago
#14986 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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},
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"name" : "_serialize.cpython-311-darwin.so"
},
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"arch" : "arm64",
"base" : 5837864960,
"size" : 98304,
"uuid" : "82fc2b2c-7e2c-373e-a0e2-f985faf1abe3",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
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"arch" : "arm64",
"base" : 5065916416,
"size" : 1507328,
"uuid" : "de01d584-3ef2-3c2e-8fb9-af751bf6d741",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5065015296,
"size" : 131072,
"uuid" : "74626364-51fd-3790-856c-82aa8d3a0019",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5827805184,
"size" : 49152,
"uuid" : "d20cbda7-2087-35fe-a1fb-cea7b1957a0a",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atom_search\/ast.cpython-311-darwin.so",
"name" : "ast.cpython-311-darwin.so"
},
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"arch" : "arm64",
"base" : 5068210176,
"size" : 65536,
"uuid" : "64a3b1e1-2a83-3940-9124-9d768a4cf697",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/chem_group\/_chem_group.cpython-311-darwin.so",
"name" : "_chem_group.cpython-311-darwin.so"
},
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"arch" : "arm64",
"base" : 5829853184,
"size" : 16384,
"uuid" : "ce45423d-d98f-391f-81c6-dc292e2b4348",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/coulombic\/_esp.cpython-311-darwin.so",
"name" : "_esp.cpython-311-darwin.so"
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"arch" : "arm64e",
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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===== 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
Change History (2)
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Whitney,
--Eric