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Opened 15 months ago
Last modified 15 months ago
#15728 closed defect
Crash in python_instances_of_class — at Version 1
| 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 (last modified by )
The following bug report has been submitted:
Platform: macOS-14.6-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000036805b000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000036704f000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000366043000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000365037000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000036402b000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000036301f000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000362013000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000361007000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035754f000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000356543000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000355537000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035452b000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035351f000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000352513000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000351507000 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f4bc8f40 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 52 in
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61 in
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61 in python_instances_of_class
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Users/rafaelrocha/Library/CloudStorage/OneDrive-Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py", line 155 in
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 72 in _exec_python
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 95 in open_python_script
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py", line 49 in runscript
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, chimerax.graphics._graphics, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.mmcif.mmcif_write, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 132)
{"app_name":"ChimeraX","timestamp":"2024-08-05 14:54:48.00 +0200","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6 (23G80)","roots_installed":0,"name":"ChimeraX","incident_id":"892C26EB-B210-4641-B986-EB7A2B15D036"}
{
"uptime" : 99000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 24110,
"osVersion" : {
"train" : "macOS 14.6",
"build" : "23G80",
"releaseType" : "User"
},
"captureTime" : "2024-08-05 14:54:32.4364 +0200",
"codeSigningMonitor" : 1,
"incident" : "892C26EB-B210-4641-B986-EB7A2B15D036",
"pid" : 21511,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-05 11:31:01.3737 +0200",
"procStartAbsTime" : 2084095277621,
"procExitAbsTime" : 2377157706534,
"procName" : "ChimeraX",
"procPath" : "\/Users\/USER\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A6907575-19A7-5D31-A01D-81182354117A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "55B4CC08-BA3F-AB23-EB21-A242E290EFF8",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 15906,
"sleepWakeUUID" : "229A4B2C-A2FE-4DD8-A9F5-19B1EFC8AD21",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
> set selectionWidth 4
Done loading forcefield
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/complexIIIdimer/cryosparc_P31_J245_map_sharp_Zflipped_NOSEQ/manualAnnotation.cxs"
Opened cryosparc_P31_J245_map_sharp_Zflipped.mrc as #1.1.1.1, grid size
290,290,290, pixel 1.16, shown at level 0.337, step 1, values float32
opened ChimeraX session
> runscript /Users/rafaelrocha/Library/CloudStorage/OneDrive-
> Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> #1 alignmentsMod1Mod.txt
Traceback (most recent call last):
File "/Users/rafaelrocha/Library/CloudStorage/OneDrive-
Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py",
line 16, in
inpAligns = open(sys.argv[2],'r').readlines()
^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory:
'alignmentsMod1Mod.txt'
Error opening python file /Users/rafaelrocha/Library/CloudStorage/OneDrive-
Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> cd /Users/rafaelrocha/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ
Current working directory is:
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ
> runscript /Users/rafaelrocha/Library/CloudStorage/OneDrive-
> Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> #1 alignmentsMod1Mod.txt
Traceback (most recent call last):
File "/Users/rafaelrocha/Library/CloudStorage/OneDrive-
Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py",
line 16, in
inpAligns = open(sys.argv[2],'r').readlines()
^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory:
'alignmentsMod1Mod.txt'
Error opening python file /Users/rafaelrocha/Library/CloudStorage/OneDrive-
Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> cd /Users/rafaelrocha/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ
Current working directory is:
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ
> cd
> /Users/rafaelrocha/supercomplex/complexIIIdimer/cryosparc_P31_J245_map_sharp_Zflipped_NOSEQ
Current working directory is:
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/complexIIIdimer/cryosparc_P31_J245_map_sharp_Zflipped_NOSEQ
> runscript /Users/rafaelrocha/Library/CloudStorage/OneDrive-
> Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> #1 alignmentsMod1Mod.txt
['1', '8']
['1', '8']
['11']
['1', '1']
['11']
['1', '1']
['1', '3']
['1', '3']
['11']
['1', '1']
['1', '4']
['1', '4']
['1', '15']
['1', '15']
['11']
['1', '1']
['1', '9']
['1', '9']
['1', '4']
['1', '4']
['1', '28']
['1', '28']
['1', '15']
['1', '15']
['7', '15']
['7', '15']
['2', '44']
['2', '44']
['1', '7']
['1', '7']
['1', '8']
['1', '8']
['1', '13']
['1', '13']
['11']
['1', '1']
['1', '31']
['1', '31']
['12']
['1', '2']
['6', '22']
['6', '22']
['5', '21']
['5', '21']
['3', '140']
['3', '140']
['1', '3']
['1', '3']
['1', '8']
['1', '8']
['2', '18']
['2', '18']
['1', '7']
['1', '7']
['7', '12']
['7', '12']
['1', '10']
['1', '10']
['12']
['1', '2']
['1', '10']
['1', '10']
['4', '63']
['4', '63']
['9', '11']
['9', '11']
['11']
['1', '1']
['1', '5']
['1', '5']
['5', '33']
['5', '33']
['1', '4']
['1', '4']
['1', '74']
['1', '74']
['3', '18']
['3', '18']
['2', '22']
['2', '22']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['2', '81']
['2', '81']
['1', '8']
['1', '8']
['1', '5']
['1', '5']
['14', '47']
['14', '47']
['1', '5']
['1', '5']
['1', '3']
['1', '3']
['11']
['1', '1']
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['1', '5']
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['1', '4']
['1', '7']
['1', '7']
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['1', '14']
['1', '25']
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['1', '20']
['1', '8']
['1', '8']
['11']
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['1', '2']
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['1', '18']
['1', '70']
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['1', '7']
['1', '7']
['1', '32']
['1', '32']
['11']
['1', '1']
['12']
['1', '2']
['9', '18']
['9', '18']
['11']
['1', '1']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '10']
['1', '10']
['1', '5']
['1', '5']
['12']
['1', '2']
['1', '20']
['1', '20']
['1', '7']
['1', '7']
['11']
['1', '1']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['12']
['1', '2']
['1', '3']
['1', '3']
['11', '32']
['11', '32']
['1', '12']
['1', '12']
['1', '3']
['1', '3']
['2', '15']
['2', '15']
['11']
['1', '1']
['11']
['1', '1']
['1', '153']
['1', '153']
['11']
['1', '1']
['1', '39']
['1', '39']
['1', '27']
['1', '27']
['1', '37']
['1', '37']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['1', '56']
['1', '56']
['1', '9']
['1', '9']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '3']
['1', '3']
['12']
['1', '2']
['11']
['1', '1']
['1', '10']
['1', '10']
['1', '4']
['1', '4']
['11']
['1', '1']
['12']
['1', '2']
['1', '30']
['1', '30']
['3', '45']
['3', '45']
['1', '9']
['1', '9']
['2', '4']
['2', '4']
['12']
['1', '2']
['1', '59']
['1', '59']
['1', '13']
['1', '13']
['1', '34']
['1', '34']
['1', '5']
['1', '5']
['3', '25']
['3', '25']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['6', '20']
['6', '20']
['1', '11']
['1', '11']
['3', '39']
['3', '39']
['1', '27']
['1', '27']
['1', '21']
['1', '21']
['11']
['1', '1']
['1', '4']
['1', '4']
['2', '33']
['2', '33']
['11']
['1', '1']
['11']
['1', '1']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['1', '8']
['1', '8']
LtaP35.1590.mRNA_A
LtaP35.1450.mRNA_A
LtaP07.0060.mRNA_A
LtaP32.3800.mRNA_A
LtaP13.0770.mRNA_A
sp|P14548.2|CYB_LEITA_A
LtaP35.0210.mRNA_A
GET91263.1_A
LtaP35.0250.mRNA_A
GET89654.1_A
> combine #1 close false name renamedAndRenumberedModel
Renumering chain LtaP35.1590.mRNA_A
['1', '8']
> select #15/GC
66 atoms, 66 bonds, 8 residues, 1 model selected
0
17
>17
> renumber #15/GC start 17
8 residues renumbered
['1', '1']
> select #15/Bd
4 atoms, 3 bonds, 1 residue, 1 model selected
24
25
>1
> renumber #15/Bd start 25
1 residues renumbered
> changechains #15/Bd GC
Chain IDs of 1 residues changed
['1', '1']
> select #15/Ca
4 atoms, 3 bonds, 1 residue, 1 model selected
25
26
>1
> renumber #15/Ca start 26
1 residues renumbered
> changechains #15/Ca GC
Chain IDs of 1 residues changed
['1', '3']
> select #15/AP
19 atoms, 19 bonds, 3 residues, 1 model selected
26
27
>1
> renumber #15/AP start 27
3 residues renumbered
> changechains #15/AP GC
Chain IDs of 3 residues changed
['1', '1']
> select #15/BN
6 atoms, 5 bonds, 1 residue, 1 model selected
29
30
>1
> renumber #15/BN start 30
1 residues renumbered
> changechains #15/BN GC
Chain IDs of 1 residues changed
['1', '4']
> select #15/FF
32 atoms, 32 bonds, 4 residues, 1 model selected
30
31
>1
> renumber #15/FF start 31
4 residues renumbered
> changechains #15/FF GC
Chain IDs of 4 residues changed
['1', '15']
> select #15/Fo
103 atoms, 106 bonds, 15 residues, 1 model selected
34
35
>1
> renumber #15/Fo start 35
0 residues renumbered
> changechains #15/Fo GC
Chain IDs of 15 residues changed
['1', '1']
> select #15/Cy
8 atoms, 7 bonds, 1 residue, 1 model selected
49
50
>1
> renumber #15/Cy start 50
1 residues renumbered
> changechains #15/Cy GC
Chain IDs of 1 residues changed
['1', '9']
> select #15/EY
66 atoms, 67 bonds, 9 residues, 1 model selected
50
51
>1
> renumber #15/EY start 51
0 residues renumbered
> changechains #15/EY GC
Chain IDs of 9 residues changed
['1', '4']
> select #15/FV
24 atoms, 23 bonds, 4 residues, 1 model selected
59
60
>1
> renumber #15/FV start 60
4 residues renumbered
> changechains #15/FV GC
Chain IDs of 4 residues changed
['1', '28']
> select #15/Ey
210 atoms, 213 bonds, 28 residues, 1 model selected
63
64
>1
> renumber #15/Ey start 64
0 residues renumbered
> changechains #15/Ey GC
Chain IDs of 28 residues changed
['1', '15']
> select #15/K
102 atoms, 102 bonds, 15 residues, 1 model selected
91
92
>1
> renumber #15/K start 92
0 residues renumbered
> changechains #15/K GC
Chain IDs of 15 residues changed
['7', '15']
> select #15/L
184 atoms, 187 bonds, 22 residues, 1 model selected
106
107
>1
> renumber #15/L start 107
0 residues renumbered
> changechains #15/L GC
Chain IDs of 22 residues changed
['2', '44']
> select #15/Ee
355 atoms, 363 bonds, 44 residues, 1 model selected
128
129
>1
> renumber #15/Ee start 129
0 residues renumbered
> changechains #15/Ee GC
Chain IDs of 44 residues changed
Renumering chain LtaP35.1450.mRNA_A
['1', '7']
> select #15/Gc
52 atoms, 52 bonds, 7 residues, 1 model selected
0
2
>2
> renumber #15/Gc start 2
7 residues renumbered
['1', '8']
> select #15/Ex
55 atoms, 56 bonds, 8 residues, 1 model selected
8
10
>2
> renumber #15/Ex start 10
8 residues renumbered
> changechains #15/Ex Gc
Chain IDs of 8 residues changed
['1', '13']
> select #15/E6
98 atoms, 100 bonds, 13 residues, 1 model selected
17
18
>1
> renumber #15/E6 start 18
13 residues renumbered
> changechains #15/E6 Gc
Chain IDs of 13 residues changed
['1', '1']
> select #15/Ai
11 atoms, 10 bonds, 1 residue, 1 model selected
30
31
>1
> renumber #15/Ai start 31
1 residues renumbered
> changechains #15/Ai Gc
Chain IDs of 1 residues changed
['1', '31']
> select #15/0
233 atoms, 235 bonds, 31 residues, 1 model selected
31
32
>1
> renumber #15/0 start 32
0 residues renumbered
> changechains #15/0 Gc
Chain IDs of 31 residues changed
['1', '2']
> select #15/U
11 atoms, 10 bonds, 2 residues, 1 model selected
62
63
>1
> renumber #15/U start 63
2 residues renumbered
> changechains #15/U Gc
Chain IDs of 2 residues changed
['6', '22']
> select #15/d
176 atoms, 182 bonds, 22 residues, 1 model selected
64
65
>1
> renumber #15/d start 65
0 residues renumbered
> changechains #15/d Gc
Chain IDs of 22 residues changed
['5', '21']
> select #15/EV
161 atoms, 160 bonds, 21 residues, 1 model selected
86
87
>1
> renumber #15/EV start 87
0 residues renumbered
> changechains #15/EV Gc
Chain IDs of 21 residues changed
> delete #15/Ew:132
> renumber #15/Ew:133-9999999 start 132
118 residues renumbered
['3', '139']
> select #15/Ew
1064 atoms, 1076 bonds, 1 pseudobond, 142 residues, 2 models selected
107
108
>1
> renumber #15/Ew start 108
0 residues renumbered
> changechains #15/Ew Gc
Chain IDs of 142 residues changed
['1', '3']
> select #15/GO
18 atoms, 18 bonds, 3 residues, 1 model selected
249
250
>1
> renumber #15/GO start 250
3 residues renumbered
> changechains #15/GO Gc
Chain IDs of 3 residues changed
['1', '8']
> select #15/Z
69 atoms, 71 bonds, 8 residues, 1 model selected
252
253
>1
> renumber #15/Z start 253
8 residues renumbered
> changechains #15/Z Gc
Chain IDs of 8 residues changed
['2', '18']
> select #15/ES
163 atoms, 164 bonds, 18 residues, 1 model selected
260
262
>2
> renumber #15/ES start 262
0 residues renumbered
> changechains #15/ES Gc
Chain IDs of 18 residues changed
['1', '7']
> select #15/Fc
40 atoms, 41 bonds, 7 residues, 1 model selected
279
282
>3
> renumber #15/Fc start 282
0 residues renumbered
> changechains #15/Fc Gc
Chain IDs of 7 residues changed
['7', '12']
> select #15/Fa
177 atoms, 179 bonds, 24 residues, 1 model selected
288
289
>1
> renumber #15/Fa start 289
0 residues renumbered
> changechains #15/Fa Gc
Chain IDs of 24 residues changed
['1', '10']
> select #15/2
81 atoms, 83 bonds, 10 residues, 1 model selected
312
314
>2
> renumber #15/2 start 314
10 residues renumbered
> changechains #15/2 Gc
Chain IDs of 10 residues changed
['1', '2']
> select #15/E
16 atoms, 16 bonds, 2 residues, 1 model selected
323
326
>3
> renumber #15/E start 326
2 residues renumbered
> changechains #15/E Gc
Chain IDs of 2 residues changed
['1', '10']
> select #15/Ff
75 atoms, 76 bonds, 10 residues, 1 model selected
327
328
>1
> renumber #15/Ff start 328
0 residues renumbered
> changechains #15/Ff Gc
Chain IDs of 10 residues changed
['4', '63']
> select #15/E2
1095 atoms, 1118 bonds, 132 residues, 1 model selected
337
338
>1
> renumber #15/E2 start 338
0 residues renumbered
> changechains #15/E2 Gc
Chain IDs of 132 residues changed
['9', '11']
> select #15/W
182 atoms, 189 bonds, 20 residues, 1 model selected
469
470
>1
> renumber #15/W start 470
0 residues renumbered
> changechains #15/W Gc
Chain IDs of 20 residues changed
['1', '1']
> select #15/BM
7 atoms, 6 bonds, 1 residue, 1 model selected
489
490
>1
> renumber #15/BM start 490
1 residues renumbered
> changechains #15/BM Gc
Chain IDs of 1 residues changed
Renumering chain LtaP07.0060.mRNA_A
['1', '5']
> select #15/A
32 atoms, 33 bonds, 5 residues, 1 model selected
0
5
>5
> renumber #15/A start 5
5 residues renumbered
['5', '33']
> select #15/Fd
314 atoms, 324 bonds, 36 residues, 1 model selected
9
10
>1
> renumber #15/Fd start 10
0 residues renumbered
> changechains #15/Fd A
Chain IDs of 36 residues changed
['1', '4']
> select #15/Ef
24 atoms, 23 bonds, 4 residues, 1 model selected
45
46
>1
> renumber #15/Ef start 46
4 residues renumbered
> changechains #15/Ef A
Chain IDs of 4 residues changed
['1', '74']
> select #15/Eg
577 atoms, 589 bonds, 74 residues, 1 model selected
49
50
>1
> renumber #15/Eg start 50
0 residues renumbered
> changechains #15/Eg A
Chain IDs of 74 residues changed
['3', '18']
> select #15/j
160 atoms, 162 bonds, 22 residues, 1 model selected
123
124
>1
> renumber #15/j start 124
0 residues renumbered
> changechains #15/j A
Chain IDs of 22 residues changed
> renumber #15/Ei:7-9999999 start 8
25 residues renumbered
> ~bond #15/Ei:6@C #15/Ei:8@N
['2', '21']
> select #15/Ei
187 atoms, 196 bonds, 25 residues, 1 model selected
145
145
>0
> delete #15/Ei:1
> renumber #15/Ei start 146
25 residues renumbered
> changechains #15/Ei A
Chain IDs of 25 residues changed
['1', '4']
> select #15/Bi
23 atoms, 22 bonds, 4 residues, 1 model selected
170
168
>-2
> delete #15/Bi:3
> delete #15/Bi:2
> delete #15/Bi:1
> renumber #15/Bi start 171
1 residues renumbered
> changechains #15/Bi A
Chain IDs of 1 residues changed
['1', '3']
> select #15/GM
21 atoms, 20 bonds, 3 residues, 1 model selected
171
171
>0
> delete #15/GM:1
> renumber #15/GM start 172
2 residues renumbered
> changechains #15/GM A
Chain IDs of 2 residues changed
['2', '81']
> select #15/E8
695 atoms, 717 bonds, 86 residues, 1 model selected
173
174
>1
> renumber #15/E8 start 174
0 residues renumbered
> changechains #15/E8 A
Chain IDs of 86 residues changed
Renumering chain LtaP32.3800.mRNA_A
['1', '8']
> select #15/N
66 atoms, 69 bonds, 8 residues, 1 model selected
0
34
>34
> renumber #15/N start 34
0 residues renumbered
['1', '5']
> select #15/GZ
35 atoms, 34 bonds, 5 residues, 1 model selected
41
42
>1
> renumber #15/GZ start 42
5 residues renumbered
> changechains #15/GZ N
Chain IDs of 5 residues changed
['14', '47']
> select #15/FT
810 atoms, 833 bonds, 101 residues, 1 model selected
46
47
>1
> renumber #15/FT start 47
0 residues renumbered
> changechains #15/FT N
Chain IDs of 101 residues changed
Renumering chain LtaP13.0770.mRNA_A
['1', '5']
> select #15/4
50 atoms, 51 bonds, 5 residues, 1 model selected
0
25
>25
> renumber #15/4 start 25
5 residues renumbered
['1', '3']
> select #15/D
20 atoms, 20 bonds, 3 residues, 1 model selected
29
30
>1
> renumber #15/D start 30
3 residues renumbered
> changechains #15/D 4
Chain IDs of 3 residues changed
['1', '1']
> select #15/CN
6 atoms, 5 bonds, 1 residue, 1 model selected
32
33
>1
> renumber #15/CN start 33
1 residues renumbered
> changechains #15/CN 4
Chain IDs of 1 residues changed
['1', '7']
> select #15/FG
48 atoms, 48 bonds, 7 residues, 1 model selected
33
34
>1
> renumber #15/FG start 34
7 residues renumbered
> changechains #15/FG 4
Chain IDs of 7 residues changed
['1', '14']
> select #15/GH
92 atoms, 92 bonds, 14 residues, 1 model selected
40
57
>17
> renumber #15/GH start 57
0 residues renumbered
> changechains #15/GH 4
Chain IDs of 14 residues changed
['1', '5']
> select #15/GW
46 atoms, 46 bonds, 5 residues, 1 model selected
70
71
>1
> renumber #15/GW start 71
5 residues renumbered
> changechains #15/GW 4
Chain IDs of 5 residues changed
['1', '4']
> select #15/Fj
24 atoms, 23 bonds, 4 residues, 1 model selected
75
76
>1
> renumber #15/Fj start 76
4 residues renumbered
> changechains #15/Fj 4
Chain IDs of 4 residues changed
['1', '7']
> select #15/E4
48 atoms, 48 bonds, 7 residues, 1 model selected
79
80
>1
> renumber #15/E4 start 80
7 residues renumbered
> changechains #15/E4 4
Chain IDs of 7 residues changed
['1', '14']
> select #15/Er
99 atoms, 102 bonds, 14 residues, 1 model selected
86
87
>1
> renumber #15/Er start 87
0 residues renumbered
> changechains #15/Er 4
Chain IDs of 14 residues changed
['1', '25']
> select #15/ER
208 atoms, 211 bonds, 25 residues, 1 model selected
100
101
>1
> renumber #15/ER start 101
25 residues renumbered
> changechains #15/ER 4
Chain IDs of 25 residues changed
['1', '20']
> select #15/Fz
146 atoms, 147 bonds, 20 residues, 1 model selected
125
124
>-1
> delete #15/Fz:2
> delete #15/Fz:1
> renumber #15/Fz start 126
20 residues renumbered
> changechains #15/Fz 4
Chain IDs of 20 residues changed
['1', '8']
> select #15/p
62 atoms, 62 bonds, 8 residues, 1 model selected
143
144
>1
> renumber #15/p start 144
8 residues renumbered
> changechains #15/p 4
Traceback (most recent call last):
File "/Users/rafaelrocha/Library/CloudStorage/OneDrive-
Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py",
line 190, in
run(session, f'changechains {outModel}/{hC} {firstChain}')
File
"/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/change_chains/cmd.py", line 91, in cmd_change_chains
raise UserError("Proposed chainID change conflicts with existing residue %s" %
r)
chimerax.core.errors.UserError: Proposed chainID change conflicts with
existing residue renamedAndRenumberedModel #15/4 LEU 144
Error opening python file /Users/rafaelrocha/Library/CloudStorage/OneDrive-
Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> close session
> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/complexIIIdimer/cryosparc_P31_J245_map_sharp_Zflipped_NOSEQ/cryosparc_P31_J245_map_sharp_Zflipped_NOSEQ.cif"
Summary of feedback from opening
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/complexIIIdimer/cryosparc_P31_J245_map_sharp_Zflipped_NOSEQ/cryosparc_P31_J245_map_sharp_Zflipped_NOSEQ.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for cryosparc_P31_J245_map_sharp_Zflipped_NOSEQ.cif #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
A | No description available
A3 | No description available
A7 | No description available
A8 | No description available
AA | No description available
AB | No description available
AD | No description available
AE | No description available
AF | No description available
AH Ck Du | No description available
AK DC | No description available
AL | No description available
AN | No description available
AP | No description available
AQ BE CD DN Df Dl Dn Gj | No description available
AU | No description available
AY | No description available
AZ | No description available
Ab | No description available
Ad | No description available
Ae S | No description available
Af | No description available
Ah | No description available
Aj | No description available
Al | No description available
Am | No description available
Aq C5 Ct Cv DV | No description available
As E | No description available
Av | No description available
Aw | No description available
Ay B3 | No description available
Az | No description available
B | No description available
B1 | No description available
BB | No description available
BD | No description available
BK | No description available
BL | No description available
BO | No description available
BS | No description available
BU | No description available
BW | No description available
Bi | No description available
Bk | No description available
Br U | No description available
Bu | No description available
Bx | No description available
Bz | No description available
C | No description available
C2 | No description available
CC | No description available
CE | No description available
CG | No description available
CT | No description available
CW | No description available
CY | No description available
Cd | No description available
Ch | No description available
Cl | No description available
D | No description available
D9 | No description available
DB | No description available
DF | No description available
DS | No description available
DY | No description available
E0 | No description available
E1 | No description available
E2 | No description available
E3 | No description available
E4 | No description available
E5 | No description available
E6 | No description available
E7 | No description available
E8 | No description available
E9 | No description available
EJ | No description available
EK | No description available
EL | No description available
EM | No description available
EN | No description available
EO | No description available
EP | No description available
EQ | No description available
ER | No description available
ES | No description available
ET | No description available
EU | No description available
EV | No description available
EW | No description available
EX | No description available
EY | No description available
EZ | No description available
Ea | No description available
Eb | No description available
Ec | No description available
Ed | No description available
Ee | No description available
Ef | No description available
Eg | No description available
Eh | No description available
Ei | No description available
Ej | No description available
Ek | No description available
El | No description available
Em | No description available
En | No description available
Eo | No description available
Ep | No description available
Eq | No description available
Er | No description available
Es | No description available
Et | No description available
Eu | No description available
Ev | No description available
Ew | No description available
Ex | No description available
Ey | No description available
Ez | No description available
F | No description available
F0 | No description available
F1 | No description available
F2 | No description available
F3 | No description available
F4 | No description available
F5 | No description available
F6 | No description available
F7 | No description available
F8 | No description available
F9 | No description available
FA | No description available
FB | No description available
FC | No description available
FD | No description available
FE | No description available
FF | No description available
FG | No description available
FH | No description available
FI | No description available
FJ | No description available
FK | No description available
FL | No description available
FM | No description available
FN | No description available
FO | No description available
FP | No description available
FQ | No description available
FR | No description available
FS | No description available
FT | No description available
FU | No description available
FV | No description available
FW | No description available
FX | No description available
FY | No description available
FZ | No description available
Fa | No description available
Fb | No description available
Fc | No description available
Fd | No description available
Fe | No description available
Ff | No description available
Fg | No description available
Fh | No description available
Fi | No description available
Fj | No description available
Fk | No description available
Fl | No description available
Fm | No description available
Fn | No description available
Fo | No description available
Fp | No description available
Fq | No description available
Fr | No description available
Fs | No description available
Ft | No description available
Fu | No description available
Fv | No description available
Fw | No description available
Fx | No description available
Fy | No description available
Fz | No description available
G | No description available
GA | No description available
GB | No description available
GC | No description available
GD | No description available
GE | No description available
GF | No description available
GG | No description available
GH | No description available
GI | No description available
GJ | No description available
GK | No description available
GL | No description available
GM | No description available
GN | No description available
GO | No description available
GP | No description available
GQ | No description available
GR | No description available
GS | No description available
GT | No description available
GU | No description available
GV | No description available
GW | No description available
GX | No description available
GY | No description available
GZ | No description available
Ga | No description available
Gb | No description available
Gc | No description available
Gd | No description available
Ge | No description available
Gf | No description available
Gg | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> hide atoms
> show cartoons
> select #1/p
62 atoms, 62 bonds, 8 residues, 1 model selected
> select #1/4, D, CN, FG, GH, GW, Fj, E4, Er, ER, Fz, p, Dk, Bz, Br, F6, q,
> Aw, X, Y, 9, c, Ge, Du, Ad, t, FU, By, AH, GV, Dq, GT, DS, Fp, 7, 8, FJ, Fu,
> FN, D6, Dl, Dk, Dt, C2, GR, FK, Gb
3488 atoms, 3515 bonds, 459 residues, 1 model selected
> color #1 gray
> color #1/4, D, CN, FG, GH, GW, Fj, E4, Er, ER, Fz, p, Dk, Bz, Br, F6, q, Aw,
> X, Y, 9, c, Ge, Du, Ad, t, FU, By, AH, GV, Dq, GT, DS, Fp, 7, 8, FJ, Fu, FN,
> D6, Dl, Dk, Dt, C2, GR, FK, Gb magenta
> select clear
> select #1/p
62 atoms, 62 bonds, 8 residues, 1 model selected
> runscript /Users/rafaelrocha/Library/CloudStorage/OneDrive-
> Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> #1 alignmentsMod1Mod.txt
['1', '8']
['1', '8']
['11']
['1', '1']
['11']
['1', '1']
['1', '3']
['1', '3']
['11']
['1', '1']
['1', '4']
['1', '4']
['1', '15']
['1', '15']
['11']
['1', '1']
['1', '9']
['1', '9']
['1', '4']
['1', '4']
['1', '28']
['1', '28']
['1', '15']
['1', '15']
['7', '15']
['7', '15']
['2', '44']
['2', '44']
['1', '7']
['1', '7']
['1', '8']
['1', '8']
['1', '13']
['1', '13']
['11']
['1', '1']
['1', '31']
['1', '31']
['12']
['1', '2']
['6', '22']
['6', '22']
['5', '21']
['5', '21']
['3', '140']
['3', '140']
['1', '3']
['1', '3']
['1', '8']
['1', '8']
['2', '18']
['2', '18']
['1', '7']
['1', '7']
['7', '12']
['7', '12']
['1', '10']
['1', '10']
['12']
['1', '2']
['1', '10']
['1', '10']
['4', '63']
['4', '63']
['9', '11']
['9', '11']
['11']
['1', '1']
['1', '5']
['1', '5']
['5', '33']
['5', '33']
['1', '4']
['1', '4']
['1', '74']
['1', '74']
['3', '18']
['3', '18']
['2', '22']
['2', '22']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['2', '81']
['2', '81']
['1', '8']
['1', '8']
['1', '5']
['1', '5']
['14', '47']
['14', '47']
['1', '5']
['1', '5']
['1', '3']
['1', '3']
['11']
['1', '1']
['1', '7']
['1', '7']
['1', '14']
['1', '14']
['1', '5']
['1', '5']
['1', '4']
['1', '4']
['1', '7']
['1', '7']
['1', '14']
['1', '14']
['1', '25']
['1', '25']
['1', '20']
['1', '20']
['1', '8']
['1', '8']
['11']
['1', '1']
['12']
['1', '2']
['12']
['1', '2']
['1', '18']
['1', '18']
['1', '70']
['1', '70']
['12']
['1', '2']
['12']
['1', '2']
['1', '12']
['1', '12']
['1', '5']
['1', '5']
['1', '14']
['1', '14']
['1', '3']
['1', '3']
['12']
['1', '2']
['1', '3']
['1', '3']
['1', '7']
['1', '7']
['1', '32']
['1', '32']
['11']
['1', '1']
['12']
['1', '2']
['9', '18']
['9', '18']
['11']
['1', '1']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '10']
['1', '10']
['1', '5']
['1', '5']
['12']
['1', '2']
['1', '20']
['1', '20']
['1', '7']
['1', '7']
['11']
['1', '1']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['12']
['1', '2']
['1', '3']
['1', '3']
['11', '32']
['11', '32']
['1', '12']
['1', '12']
['1', '3']
['1', '3']
['2', '15']
['2', '15']
['11']
['1', '1']
['11']
['1', '1']
['1', '153']
['1', '153']
['11']
['1', '1']
['1', '39']
['1', '39']
['1', '27']
['1', '27']
['1', '37']
['1', '37']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['1', '56']
['1', '56']
['1', '9']
['1', '9']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '3']
['1', '3']
['12']
['1', '2']
['11']
['1', '1']
['1', '10']
['1', '10']
['1', '4']
['1', '4']
['11']
['1', '1']
['12']
['1', '2']
['1', '30']
['1', '30']
['3', '45']
['3', '45']
['1', '9']
['1', '9']
['2', '4']
['2', '4']
['12']
['1', '2']
['1', '59']
['1', '59']
['1', '13']
['1', '13']
['1', '34']
['1', '34']
['1', '5']
['1', '5']
['3', '25']
['3', '25']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['6', '20']
['6', '20']
['1', '11']
['1', '11']
['3', '39']
['3', '39']
['1', '27']
['1', '27']
['1', '21']
['1', '21']
['11']
['1', '1']
['1', '4']
['1', '4']
['2', '33']
['2', '33']
['11']
['1', '1']
['11']
['1', '1']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['1', '8']
['1', '8']
LtaP35.1590.mRNA_A
LtaP35.1450.mRNA_A
LtaP07.0060.mRNA_A
LtaP32.3800.mRNA_A
LtaP13.0770.mRNA_A
sp|P14548.2|CYB_LEITA_A
LtaP35.0210.mRNA_A
GET91263.1_A
LtaP35.0250.mRNA_A
GET89654.1_A
> combine #1 close false name renamedAndRenumberedModel
Renumering chain LtaP35.1590.mRNA_A
['1', '8']
> select #2/GC
66 atoms, 66 bonds, 8 residues, 1 model selected
0
17
>17
> renumber #2/GC start 17
8 residues renumbered
['1', '1']
> select #2/Bd
4 atoms, 3 bonds, 1 residue, 1 model selected
24
25
>1
> renumber #2/Bd start 25
1 residues renumbered
> changechains #2/Bd GC
Chain IDs of 1 residues changed
['1', '1']
> select #2/Ca
4 atoms, 3 bonds, 1 residue, 1 model selected
25
26
>1
> renumber #2/Ca start 26
1 residues renumbered
> changechains #2/Ca GC
Chain IDs of 1 residues changed
['1', '3']
> select #2/AP
19 atoms, 19 bonds, 3 residues, 1 model selected
26
27
>1
> renumber #2/AP start 27
3 residues renumbered
> changechains #2/AP GC
Chain IDs of 3 residues changed
['1', '1']
> select #2/BN
6 atoms, 5 bonds, 1 residue, 1 model selected
29
30
>1
> renumber #2/BN start 30
1 residues renumbered
> changechains #2/BN GC
Chain IDs of 1 residues changed
['1', '4']
> select #2/FF
32 atoms, 32 bonds, 4 residues, 1 model selected
30
31
>1
> renumber #2/FF start 31
4 residues renumbered
> changechains #2/FF GC
Chain IDs of 4 residues changed
['1', '15']
> select #2/Fo
103 atoms, 106 bonds, 15 residues, 1 model selected
34
35
>1
> renumber #2/Fo start 35
15 residues renumbered
> changechains #2/Fo GC
Chain IDs of 15 residues changed
['1', '1']
> select #2/Cy
8 atoms, 7 bonds, 1 residue, 1 model selected
49
50
>1
> renumber #2/Cy start 50
1 residues renumbered
> changechains #2/Cy GC
Chain IDs of 1 residues changed
['1', '9']
> select #2/EY
66 atoms, 67 bonds, 9 residues, 1 model selected
50
51
>1
> renumber #2/EY start 51
9 residues renumbered
> changechains #2/EY GC
Chain IDs of 9 residues changed
['1', '4']
> select #2/FV
24 atoms, 23 bonds, 4 residues, 1 model selected
59
60
>1
> renumber #2/FV start 60
4 residues renumbered
> changechains #2/FV GC
Chain IDs of 4 residues changed
['1', '28']
> select #2/Ey
210 atoms, 213 bonds, 28 residues, 1 model selected
63
64
>1
> renumber #2/Ey start 64
28 residues renumbered
> changechains #2/Ey GC
Chain IDs of 28 residues changed
['1', '15']
> select #2/K
102 atoms, 102 bonds, 15 residues, 1 model selected
91
92
>1
> renumber #2/K start 92
15 residues renumbered
> changechains #2/K GC
Chain IDs of 15 residues changed
['7', '15']
> select #2/L
184 atoms, 187 bonds, 22 residues, 1 model selected
106
107
>1
> renumber #2/L start 107
22 residues renumbered
> changechains #2/L GC
Chain IDs of 22 residues changed
['2', '44']
> select #2/Ee
355 atoms, 363 bonds, 44 residues, 1 model selected
128
129
>1
> renumber #2/Ee start 129
44 residues renumbered
> changechains #2/Ee GC
Chain IDs of 44 residues changed
Renumering chain LtaP35.1450.mRNA_A
['1', '7']
> select #2/Gc
52 atoms, 52 bonds, 7 residues, 1 model selected
0
2
>2
> renumber #2/Gc start 2
7 residues renumbered
['1', '8']
> select #2/Ex
55 atoms, 56 bonds, 8 residues, 1 model selected
8
10
>2
> renumber #2/Ex start 10
8 residues renumbered
> changechains #2/Ex Gc
Chain IDs of 8 residues changed
['1', '13']
> select #2/E6
98 atoms, 100 bonds, 13 residues, 1 model selected
17
18
>1
> renumber #2/E6 start 18
13 residues renumbered
> changechains #2/E6 Gc
Chain IDs of 13 residues changed
['1', '1']
> select #2/Ai
11 atoms, 10 bonds, 1 residue, 1 model selected
30
31
>1
> renumber #2/Ai start 31
1 residues renumbered
> changechains #2/Ai Gc
Chain IDs of 1 residues changed
['1', '31']
> select #2/0
233 atoms, 235 bonds, 31 residues, 1 model selected
31
32
>1
> renumber #2/0 start 32
31 residues renumbered
> changechains #2/0 Gc
Chain IDs of 31 residues changed
['1', '2']
> select #2/U
11 atoms, 10 bonds, 2 residues, 1 model selected
62
63
>1
> renumber #2/U start 63
2 residues renumbered
> changechains #2/U Gc
Chain IDs of 2 residues changed
['6', '22']
> select #2/d
176 atoms, 182 bonds, 22 residues, 1 model selected
64
65
>1
> renumber #2/d start 65
22 residues renumbered
> changechains #2/d Gc
Chain IDs of 22 residues changed
['5', '21']
> select #2/EV
161 atoms, 160 bonds, 21 residues, 1 model selected
86
87
>1
> renumber #2/EV start 87
21 residues renumbered
> changechains #2/EV Gc
Chain IDs of 21 residues changed
[deleted to fit within ticket limits]
> swapaa #3/FL:32 LEU
Using Dunbrack library
mutadedModel #3/FL PHE 32: phi -60.1, psi -35.6 trans
Applying LEU rotamer (chi angles: -69.2 172.7) to mutadedModel #3/FL LEU 32
> color #3/FL:32 yellow
> swapaa #3/FL:36 LYS
Using Dunbrack library
mutadedModel #3/FL SER 36: phi -97.7, psi -28.8 trans
Applying LYS rotamer (chi angles: -67.6 -178.3 175.0 65.8) to mutadedModel
#3/FL LYS 36
> color #3/FL:36 yellow
> swapaa #3/FL:37 THR
Using Dunbrack library
mutadedModel #3/FL ASN 37: phi -87.3, psi none trans
Applying THR rotamer (chi angles: 61.1) to mutadedModel #3/FL THR 37
> color #3/FL:37 yellow
> swapaa #3/FL:41 GLU
Using Dunbrack library
mutadedModel #3/FL ALA 41: phi -66.4, psi -35.3 trans
Applying GLU rotamer (chi angles: -66.4 80.3 9.3) to mutadedModel #3/FL GLU 41
> color #3/FL:41 yellow
> swapaa #3/FL:42 LYS
Using Dunbrack library
mutadedModel #3/FL ALA 42: phi -60.9, psi 27.0 trans
Applying LYS rotamer (chi angles: -81.0 76.8 69.7 -179.2) to mutadedModel
#3/FL LYS 42
> color #3/FL:42 yellow
> swapaa #3/FL:43 GLU
Using Dunbrack library
mutadedModel #3/FL ASN 43: phi 40.0, psi none trans
Applying GLU rotamer (chi angles: -166.0 -80.1 -49.5) to mutadedModel #3/FL
GLU 43
> color #3/FL:43 yellow
> swapaa #3/FL:45 HIS
Using Dunbrack library
mutadedModel #3/FL LYS 45: phi none, psi 143.3 trans
Applying HIS rotamer (chi angles: 63.0 85.6) to mutadedModel #3/FL HIS 45
> color #3/FL:45 yellow
> swapaa #3/FL:46 CYS
Using Dunbrack library
mutadedModel #3/FL VAL 46: phi -81.7, psi 38.8 trans
Applying CYS rotamer (chi angles: -177.5) to mutadedModel #3/FL CYS 46
> color #3/FL:46 yellow
> swapaa #3/FL:51 PHE
Using Dunbrack library
mutadedModel #3/FL HIS 51: phi -68.3, psi -28.5 trans
Applying PHE rotamer (chi angles: 72.6 33.9) to mutadedModel #3/FL PHE 51
> color #3/FL:51 yellow
> swapaa #3/FL:53 ILE
Using Dunbrack library
mutadedModel #3/FL GLN 53: phi -62.8, psi -38.1 trans
Applying ILE rotamer (chi angles: -68.1 168.5) to mutadedModel #3/FL ILE 53
> color #3/FL:53 yellow
> swapaa #3/FL:54 VAL
Using Dunbrack library
mutadedModel #3/FL CYS 54: phi -68.2, psi -36.2 trans
Applying VAL rotamer (chi angles: 173.1) to mutadedModel #3/FL VAL 54
> color #3/FL:54 yellow
> swapaa #3/FL:55 HIS
Using Dunbrack library
mutadedModel #3/FL ARG 55: phi -71.9, psi -51.0 trans
Applying HIS rotamer (chi angles: -178.1 -106.2) to mutadedModel #3/FL HIS 55
> color #3/FL:55 yellow
> swapaa #3/FL:56 CYS
Using Dunbrack library
mutadedModel #3/FL SER 56: phi -57.5, psi -29.8 trans
Applying CYS rotamer (chi angles: 64.7) to mutadedModel #3/FL CYS 56
> color #3/FL:56 yellow
> swapaa #3/FL:58 ASP
Using Dunbrack library
mutadedModel #3/FL ALA 58: phi -67.1, psi -37.9 trans
Applying ASP rotamer (chi angles: -71.0 -16.3) to mutadedModel #3/FL ASP 58
> color #3/FL:58 yellow
> swapaa #3/FL:59 VAL
Using Dunbrack library
mutadedModel #3/FL GLU 59: phi -69.9, psi -29.7 trans
Applying VAL rotamer (chi angles: 173.2) to mutadedModel #3/FL VAL 59
> color #3/FL:59 yellow
> swapaa #3/FL:60 CYS
Using Dunbrack library
mutadedModel #3/FL GLU 60: phi -76.7, psi -28.4 trans
Applying CYS rotamer (chi angles: -68.1) to mutadedModel #3/FL CYS 60
> color #3/FL:60 yellow
> swapaa #3/FL:62 ASP
Using Dunbrack library
mutadedModel #3/FL GLU 62: phi -65.6, psi -28.6 trans
Applying ASP rotamer (chi angles: -71.2 -15.9) to mutadedModel #3/FL ASP 62
> color #3/FL:62 yellow
> swapaa #3/FL:64 LYS
Using Dunbrack library
mutadedModel #3/FL GLU 64: phi -86.4, psi -26.0 trans
Applying LYS rotamer (chi angles: -66.2 -173.9 -72.7 -66.8) to mutadedModel
#3/FL LYS 64
> color #3/FL:64 yellow
> swapaa #3/FL:69 LEU
Using Dunbrack library
mutadedModel #3/FL ARG 69: phi -116.4, psi 144.3 trans
Applying LEU rotamer (chi angles: -60.1 174.9) to mutadedModel #3/FL LEU 69
> color #3/FL:69 yellow
> swapaa #3/FL:70 LYS
Using Dunbrack library
mutadedModel #3/FL VAL 70: phi -55.2, psi none trans
Applying LYS rotamer (chi angles: -179.1 68.7 81.0 -81.3) to mutadedModel
#3/FL LYS 70
> color #3/FL:70 yellow
> select #3/GA
898 atoms, 919 bonds, 108 residues, 1 model selected
> bond #3/GA:17@C #3/GA:18@N reasonable false
Created 0 bonds
> bond #3/GA:18@C #3/GA:19@N reasonable false
Created 0 bonds
> bond #3/GA:19@C #3/GA:20@N reasonable false
Created 1 bond
> bond #3/GA:57@C #3/GA:58@N reasonable false
Created 0 bonds
> bond #3/GA:58@C #3/GA:59@N reasonable false
Created 0 bonds
> bond #3/GA:59@C #3/GA:60@N reasonable false
Created 0 bonds
> bond #3/GA:60@C #3/GA:61@N reasonable false
Created 0 bonds
> bond #3/GA:61@C #3/GA:62@N reasonable false
Created 0 bonds
> bond #3/GA:62@C #3/GA:63@N reasonable false
Created 0 bonds
> bond #3/GA:63@C #3/GA:64@N reasonable false
Created 0 bonds
> bond #3/GA:64@C #3/GA:65@N reasonable false
Created 0 bonds
> bond #3/GA:65@C #3/GA:66@N reasonable false
Created 0 bonds
> bond #3/GA:66@C #3/GA:67@N reasonable false
Created 0 bonds
> bond #3/GA:67@C #3/GA:68@N reasonable false
Created 0 bonds
> bond #3/GA:68@C #3/GA:69@N reasonable false
Created 0 bonds
> bond #3/GA:69@C #3/GA:70@N reasonable false
Created 0 bonds
> bond #3/GA:70@C #3/GA:71@N reasonable false
Created 0 bonds
> bond #3/GA:71@C #3/GA:72@N reasonable false
Created 0 bonds
> bond #3/GA:72@C #3/GA:73@N reasonable false
Created 0 bonds
> bond #3/GA:73@C #3/GA:74@N reasonable false
Created 0 bonds
> bond #3/GA:74@C #3/GA:75@N reasonable false
Created 0 bonds
> bond #3/GA:75@C #3/GA:76@N reasonable false
Created 0 bonds
> bond #3/GA:76@C #3/GA:77@N reasonable false
Created 0 bonds
> bond #3/GA:77@C #3/GA:78@N reasonable false
Created 0 bonds
> bond #3/GA:78@C #3/GA:79@N reasonable false
Created 0 bonds
> bond #3/GA:79@C #3/GA:80@N reasonable false
Created 0 bonds
> bond #3/GA:80@C #3/GA:81@N reasonable false
Created 0 bonds
> bond #3/GA:81@C #3/GA:82@N reasonable false
Created 0 bonds
> bond #3/GA:82@C #3/GA:83@N reasonable false
Created 0 bonds
> bond #3/GA:83@C #3/GA:84@N reasonable false
Created 0 bonds
> bond #3/GA:84@C #3/GA:85@N reasonable false
Created 0 bonds
> bond #3/GA:85@C #3/GA:86@N reasonable false
Created 0 bonds
> bond #3/GA:86@C #3/GA:87@N reasonable false
Created 0 bonds
> bond #3/GA:87@C #3/GA:88@N reasonable false
Created 0 bonds
> bond #3/GA:88@C #3/GA:89@N reasonable false
Created 0 bonds
> bond #3/GA:89@C #3/GA:90@N reasonable false
Created 0 bonds
> bond #3/GA:90@C #3/GA:91@N reasonable false
Created 0 bonds
> bond #3/GA:91@C #3/GA:92@N reasonable false
Created 0 bonds
> bond #3/GA:92@C #3/GA:93@N reasonable false
Created 0 bonds
> bond #3/GA:93@C #3/GA:94@N reasonable false
Created 0 bonds
> bond #3/GA:94@C #3/GA:95@N reasonable false
Created 0 bonds
> bond #3/GA:95@C #3/GA:96@N reasonable false
Created 1 bond
> bond #3/GA:20@C #3/GA:21@N reasonable false
Created 0 bonds
> bond #3/GA:21@C #3/GA:22@N reasonable false
Created 0 bonds
> bond #3/GA:22@C #3/GA:23@N reasonable false
Created 0 bonds
> bond #3/GA:23@C #3/GA:24@N reasonable false
Created 0 bonds
> bond #3/GA:24@C #3/GA:25@N reasonable false
Created 0 bonds
> bond #3/GA:25@C #3/GA:26@N reasonable false
Created 0 bonds
> bond #3/GA:26@C #3/GA:27@N reasonable false
Created 0 bonds
> bond #3/GA:27@C #3/GA:28@N reasonable false
Created 0 bonds
> bond #3/GA:28@C #3/GA:29@N reasonable false
Created 0 bonds
> bond #3/GA:29@C #3/GA:30@N reasonable false
Created 0 bonds
> bond #3/GA:30@C #3/GA:31@N reasonable false
Created 0 bonds
> bond #3/GA:31@C #3/GA:32@N reasonable false
Created 0 bonds
> bond #3/GA:32@C #3/GA:33@N reasonable false
Created 0 bonds
> bond #3/GA:33@C #3/GA:34@N reasonable false
Created 0 bonds
> bond #3/GA:34@C #3/GA:35@N reasonable false
Created 0 bonds
> bond #3/GA:35@C #3/GA:36@N reasonable false
Created 0 bonds
> bond #3/GA:36@C #3/GA:37@N reasonable false
Created 0 bonds
> bond #3/GA:37@C #3/GA:38@N reasonable false
Created 0 bonds
> bond #3/GA:38@C #3/GA:39@N reasonable false
Created 0 bonds
> bond #3/GA:39@C #3/GA:40@N reasonable false
Created 0 bonds
> bond #3/GA:40@C #3/GA:41@N reasonable false
Created 0 bonds
> bond #3/GA:41@C #3/GA:42@N reasonable false
Created 0 bonds
> bond #3/GA:42@C #3/GA:43@N reasonable false
Created 0 bonds
> bond #3/GA:45@C #3/GA:46@N reasonable false
Created 0 bonds
> bond #3/GA:46@C #3/GA:47@N reasonable false
Created 0 bonds
> bond #3/GA:47@C #3/GA:48@N reasonable false
Created 0 bonds
> bond #3/GA:48@C #3/GA:49@N reasonable false
Created 0 bonds
> bond #3/GA:49@C #3/GA:50@N reasonable false
Created 0 bonds
> bond #3/GA:50@C #3/GA:51@N reasonable false
Created 0 bonds
> bond #3/GA:51@C #3/GA:52@N reasonable false
Created 0 bonds
> bond #3/GA:52@C #3/GA:53@N reasonable false
Created 0 bonds
> bond #3/GA:53@C #3/GA:54@N reasonable false
Created 0 bonds
> bond #3/GA:54@C #3/GA:55@N reasonable false
Created 0 bonds
> bond #3/GA:96@C #3/GA:97@N reasonable false
Created 0 bonds
> bond #3/GA:97@C #3/GA:98@N reasonable false
Created 0 bonds
> bond #3/GA:98@C #3/GA:99@N reasonable false
Created 0 bonds
> bond #3/GA:99@C #3/GA:100@N reasonable false
Created 0 bonds
> bond #3/GA:100@C #3/GA:101@N reasonable false
Created 0 bonds
> bond #3/GA:101@C #3/GA:102@N reasonable false
Created 0 bonds
> bond #3/GA:102@C #3/GA:103@N reasonable false
Created 0 bonds
> bond #3/GA:103@C #3/GA:104@N reasonable false
Created 0 bonds
> bond #3/GA:104@C #3/GA:105@N reasonable false
Created 0 bonds
> bond #3/GA:105@C #3/GA:106@N reasonable false
Created 0 bonds
> bond #3/GA:106@C #3/GA:107@N reasonable false
Created 0 bonds
> bond #3/GA:107@C #3/GA:108@N reasonable false
Created 0 bonds
> bond #3/GA:108@C #3/GA:109@N reasonable false
Created 0 bonds
> bond #3/GA:109@C #3/GA:110@N reasonable false
Created 0 bonds
> bond #3/GA:110@C #3/GA:111@N reasonable false
Created 0 bonds
> bond #3/GA:111@C #3/GA:112@N reasonable false
Created 0 bonds
> bond #3/GA:112@C #3/GA:113@N reasonable false
Created 0 bonds
> bond #3/GA:113@C #3/GA:114@N reasonable false
Created 0 bonds
> bond #3/GA:114@C #3/GA:115@N reasonable false
Created 0 bonds
> bond #3/GA:115@C #3/GA:116@N reasonable false
Created 0 bonds
> bond #3/GA:116@C #3/GA:117@N reasonable false
Created 0 bonds
> bond #3/GA:117@C #3/GA:118@N reasonable false
Created 0 bonds
> bond #3/GA:118@C #3/GA:119@N reasonable false
Created 0 bonds
> bond #3/GA:119@C #3/GA:120@N reasonable false
Created 0 bonds
> bond #3/GA:120@C #3/GA:121@N reasonable false
Created 0 bonds
> bond #3/GA:121@C #3/GA:122@N reasonable false
Created 0 bonds
> bond #3/GA:13@C #3/GA:14@N reasonable false
Created 0 bonds
> bond #3/GA:14@C #3/GA:15@N reasonable false
Created 0 bonds
> bond #3/GA:15@C #3/GA:16@N reasonable false
Created 0 bonds
> bond #3/GA:16@C #3/GA:17@N reasonable false
Created 1 bond
> swapaa #3/GA:13 ARG
Using Dunbrack library
mutadedModel #3/GA ALA 13: phi none, psi 168.3 trans
Applying ARG rotamer (chi angles: -66.2 179.5 66.1 84.3) to mutadedModel #3/GA
ARG 13
> color #3/GA:13 yellow
> swapaa #3/GA:14 ALA
Using Dunbrack library
Swapping mutadedModel #3/GA PRO 14 to ALA
> color #3/GA:14 yellow
> swapaa #3/GA:16 ALA
Using Dunbrack library
Swapping mutadedModel #3/GA VAL 16 to ALA
> color #3/GA:16 yellow
> swapaa #3/GA:17 ARG
Using Dunbrack library
mutadedModel #3/GA LYS 17: phi 169.1, psi 144.1 trans
Applying ARG rotamer (chi angles: -178.8 66.8 177.6 173.0) to mutadedModel
#3/GA ARG 17
> color #3/GA:17 yellow
> swapaa #3/GA:18 PRO
Using Dunbrack library
mutadedModel #3/GA SER 18: phi -84.6, psi 76.8 trans
Applying PRO rotamer (chi angles: 31.0 -35.4) to mutadedModel #3/GA PRO 18
> color #3/GA:18 yellow
> swapaa #3/GA:20 PRO
Using Dunbrack library
mutadedModel #3/GA SER 20: phi 71.5, psi 107.7 cis
Applying PRO rotamer (chi angles: 27.3 -34.5) to mutadedModel #3/GA PRO 20
> color #3/GA:20 yellow
> swapaa #3/GA:21 THR
Using Dunbrack library
mutadedModel #3/GA LEU 21: phi -57.2, psi 126.1 trans
Applying THR rotamer (chi angles: -58.5) to mutadedModel #3/GA THR 21
> color #3/GA:21 yellow
> swapaa #3/GA:23 TYR
Using Dunbrack library
mutadedModel #3/GA ARG 23: phi -87.1, psi 157.5 trans
Applying TYR rotamer (chi angles: -68.2 93.4) to mutadedModel #3/GA TYR 23
> color #3/GA:23 yellow
> swapaa #3/GA:24 GLY
Using Dunbrack library
Swapping mutadedModel #3/GA ALA 24 to GLY
> color #3/GA:24 yellow
> swapaa #3/GA:25 TRP
Using Dunbrack library
mutadedModel #3/GA TYR 25: phi -99.9, psi 150.6 trans
Applying TRP rotamer (chi angles: 58.7 138.2) to mutadedModel #3/GA TRP 25
> color #3/GA:25 yellow
> swapaa #3/GA:28 THR
Using Dunbrack library
mutadedModel #3/GA VAL 28: phi -79.9, psi 141.8 trans
Applying THR rotamer (chi angles: -61.0) to mutadedModel #3/GA THR 28
> color #3/GA:28 yellow
> swapaa #3/GA:29 GLU
Using Dunbrack library
mutadedModel #3/GA SER 29: phi -88.8, psi 170.2 trans
Applying GLU rotamer (chi angles: 73.7 -79.6 8.8) to mutadedModel #3/GA GLU 29
> color #3/GA:29 yellow
> swapaa #3/GA:30 GLN
Using Dunbrack library
mutadedModel #3/GA GLU 30: phi -64.0, psi 127.0 trans
Applying GLN rotamer (chi angles: -66.9 -179.0 150.8) to mutadedModel #3/GA
GLN 30
> color #3/GA:30 yellow
> swapaa #3/GA:31 LYS
Using Dunbrack library
mutadedModel #3/GA THR 31: phi -102.7, psi -14.2 trans
Applying LYS rotamer (chi angles: -63.9 -175.4 -70.7 -66.8) to mutadedModel
#3/GA LYS 31
> color #3/GA:31 yellow
> swapaa #3/GA:35 GLU
Using Dunbrack library
mutadedModel #3/GA ILE 35: phi -43.9, psi -61.0 trans
Applying GLU rotamer (chi angles: -67.2 81.7 -1.2) to mutadedModel #3/GA GLU
35
> color #3/GA:35 yellow
> swapaa #3/GA:36 TYR
Using Dunbrack library
mutadedModel #3/GA PHE 36: phi -39.8, psi -35.6 trans
Applying TYR rotamer (chi angles: -72.8 109.9) to mutadedModel #3/GA TYR 36
> color #3/GA:36 yellow
> swapaa #3/GA:37 GLU
Using Dunbrack library
mutadedModel #3/GA SER 37: phi -102.3, psi 162.0 trans
Applying GLU rotamer (chi angles: -64.0 -179.4 -7.3) to mutadedModel #3/GA GLU
37
> color #3/GA:37 yellow
> swapaa #3/GA:40 GLU
Using Dunbrack library
mutadedModel #3/GA SER 40: phi -98.8, psi 160.7 trans
Applying GLU rotamer (chi angles: -61.2 -67.2 -53.2) to mutadedModel #3/GA GLU
40
> color #3/GA:40 yellow
> swapaa #3/GA:41 SER
Using Dunbrack library
mutadedModel #3/GA THR 41: phi -91.8, psi 173.9 trans
Applying SER rotamer (chi angles: 67.3) to mutadedModel #3/GA SER 41
> color #3/GA:41 yellow
> swapaa #3/GA:42 LYS
Using Dunbrack library
mutadedModel #3/GA PRO 42: phi -73.1, psi -17.7 trans
Applying LYS rotamer (chi angles: -64.2 -64.1 -70.5 -68.2) to mutadedModel
#3/GA LYS 42
> color #3/GA:42 yellow
> swapaa #3/GA:43 TYR
Using Dunbrack library
mutadedModel #3/GA ARG 43: phi -83.7, psi none trans
Applying TYR rotamer (chi angles: 63.6 90.2) to mutadedModel #3/GA TYR 43
> color #3/GA:43 yellow
> swapaa #3/GA:45 LYS
Using Dunbrack library
mutadedModel #3/GA ARG 45: phi none, psi 140.5 trans
Applying LYS rotamer (chi angles: -177.2 177.1 179.5 179.9) to mutadedModel
#3/GA LYS 45
> color #3/GA:45 yellow
> swapaa #3/GA:47 ASP
Using Dunbrack library
mutadedModel #3/GA SER 47: phi -117.2, psi 166.1 trans
Applying ASP rotamer (chi angles: 64.4 15.7) to mutadedModel #3/GA ASP 47
> color #3/GA:47 yellow
> swapaa #3/GA:50 LYS
Using Dunbrack library
mutadedModel #3/GA SER 50: phi -108.9, psi 168.3 trans
Applying LYS rotamer (chi angles: 66.0 -176.8 -70.4 -66.4) to mutadedModel
#3/GA LYS 50
> color #3/GA:50 yellow
> swapaa #3/GA:53 ASP
Using Dunbrack library
mutadedModel #3/GA VAL 53: phi -80.7, psi 116.8 trans
Applying ASP rotamer (chi angles: -176.0 -13.8) to mutadedModel #3/GA ASP 53
> color #3/GA:53 yellow
> swapaa #3/GA:54 VAL
Using Dunbrack library
mutadedModel #3/GA SER 54: phi -140.7, psi 75.9 trans
Applying VAL rotamer (chi angles: -68.9) to mutadedModel #3/GA VAL 54
> color #3/GA:54 yellow
> swapaa #3/GA:55 ALA
Using Dunbrack library
Swapping mutadedModel #3/GA GLY 55 to ALA
> color #3/GA:55 yellow
> swapaa #3/GA:57 VAL
Using Dunbrack library
mutadedModel #3/GA ASN 57: phi none, psi 101.3 trans
Applying VAL rotamer (chi angles: 175.9) to mutadedModel #3/GA VAL 57
> color #3/GA:57 yellow
> swapaa #3/GA:58 GLU
Using Dunbrack library
mutadedModel #3/GA VAL 58: phi -62.5, psi 126.9 trans
Applying GLU rotamer (chi angles: -67.8 -178.3 -1.3) to mutadedModel #3/GA GLU
58
> color #3/GA:58 yellow
> swapaa #3/GA:61 TYR
Using Dunbrack library
mutadedModel #3/GA PHE 61: phi -135.3, psi 157.9 trans
Applying TYR rotamer (chi angles: -60.7 89.5) to mutadedModel #3/GA TYR 61
> color #3/GA:61 yellow
> swapaa #3/GA:62 SER
Using Dunbrack library
mutadedModel #3/GA ALA 62: phi -121.6, psi 171.5 trans
Applying SER rotamer (chi angles: 66.6) to mutadedModel #3/GA SER 62
> color #3/GA:62 yellow
> swapaa #3/GA:63 ASP
Using Dunbrack library
mutadedModel #3/GA SER 63: phi -79.9, psi -177.0 trans
Applying ASP rotamer (chi angles: 68.3 72.8) to mutadedModel #3/GA ASP 63
> color #3/GA:63 yellow
> swapaa #3/GA:64 PHE
Using Dunbrack library
mutadedModel #3/GA TYR 64: phi -116.9, psi -18.9 trans
Applying PHE rotamer (chi angles: 65.4 87.2) to mutadedModel #3/GA PHE 64
> color #3/GA:64 yellow
> swapaa #3/GA:65 MET
Using Dunbrack library
mutadedModel #3/GA GLN 65: phi -70.1, psi -23.2 trans
Applying MET rotamer (chi angles: -68.3 -57.9 -66.4) to mutadedModel #3/GA MET
65
> color #3/GA:65 yellow
> swapaa #3/GA:66 GLN
Using Dunbrack library
mutadedModel #3/GA LEU 66: phi -103.5, psi -15.0 trans
Applying GLN rotamer (chi angles: -64.8 178.6 65.4) to mutadedModel #3/GA GLN
66
> color #3/GA:66 yellow
> swapaa #3/GA:67 VAL
Using Dunbrack library
mutadedModel #3/GA THR 67: phi -93.7, psi 156.6 trans
Applying VAL rotamer (chi angles: -60.8) to mutadedModel #3/GA VAL 67
> color #3/GA:67 yellow
> swapaa #3/GA:70 TYR
Using Dunbrack library
mutadedModel #3/GA HIS 70: phi -118.9, psi 60.7 trans
Applying TYR rotamer (chi angles: 61.3 88.8) to mutadedModel #3/GA TYR 70
> color #3/GA:70 yellow
> swapaa #3/GA:71 PHE
Using Dunbrack library
mutadedModel #3/GA TYR 71: phi -72.0, psi 141.0 trans
Applying PHE rotamer (chi angles: -176.2 76.3) to mutadedModel #3/GA PHE 71
> color #3/GA:71 yellow
> swapaa #3/GA:73 ILE
Using Dunbrack library
mutadedModel #3/GA ASP 73: phi -78.6, psi -28.8 trans
Applying ILE rotamer (chi angles: 65.7 171.7) to mutadedModel #3/GA ILE 73
> color #3/GA:73 yellow
> swapaa #3/GA:75 SER
Using Dunbrack library
mutadedModel #3/GA GLU 75: phi -87.1, psi -37.3 trans
Applying SER rotamer (chi angles: 64.4) to mutadedModel #3/GA SER 75
> color #3/GA:75 yellow
> swapaa #3/GA:79 THR
Using Dunbrack library
mutadedModel #3/GA LEU 79: phi -71.7, psi -32.4 trans
Applying THR rotamer (chi angles: 59.6) to mutadedModel #3/GA THR 79
> color #3/GA:79 yellow
> swapaa #3/GA:81 LEU
Using Dunbrack library
mutadedModel #3/GA GLU 81: phi -71.3, psi -27.3 trans
Applying LEU rotamer (chi angles: -174.3 58.9) to mutadedModel #3/GA LEU 81
> color #3/GA:81 yellow
> swapaa #3/GA:82 TYR
Using Dunbrack library
mutadedModel #3/GA PHE 82: phi -74.0, psi -44.1 trans
Applying TYR rotamer (chi angles: -175.9 75.8) to mutadedModel #3/GA TYR 82
> color #3/GA:82 yellow
> swapaa #3/GA:84 MET
Using Dunbrack library
mutadedModel #3/GA LEU 84: phi -69.8, psi -42.8 trans
Applying MET rotamer (chi angles: -68.8 -59.1 -67.3) to mutadedModel #3/GA MET
84
> color #3/GA:84 yellow
> swapaa #3/GA:85 ILE
Using Dunbrack library
mutadedModel #3/GA ASN 85: phi -74.3, psi -36.8 trans
Applying ILE rotamer (chi angles: -67.0 169.0) to mutadedModel #3/GA ILE 85
> color #3/GA:85 yellow
> swapaa #3/GA:86 GLN
Using Dunbrack library
mutadedModel #3/GA ARG 86: phi -62.1, psi -37.6 trans
Applying GLN rotamer (chi angles: -67.8 -63.9 -49.3) to mutadedModel #3/GA GLN
86
> color #3/GA:86 yellow
> swapaa #3/GA:90 LEU
Using Dunbrack library
mutadedModel #3/GA GLU 90: phi -80.2, psi -37.0 trans
Applying LEU rotamer (chi angles: -66.5 174.5) to mutadedModel #3/GA LEU 90
> color #3/GA:90 yellow
> swapaa #3/GA:91 SER
Using Dunbrack library
mutadedModel #3/GA ALA 91: phi -102.1, psi -34.7 trans
Applying SER rotamer (chi angles: 64.1) to mutadedModel #3/GA SER 91
> color #3/GA:91 yellow
> swapaa #3/GA:92 MET
Using Dunbrack library
mutadedModel #3/GA GLN 92: phi -109.1, psi -18.5 trans
Applying MET rotamer (chi angles: -64.1 178.1 69.9) to mutadedModel #3/GA MET
92
> color #3/GA:92 yellow
> swapaa #3/GA:96 PHE
Using Dunbrack library
mutadedModel #3/GA TYR 96: phi -35.7, psi -33.5 trans
Applying PHE rotamer (chi angles: -73.7 48.5) to mutadedModel #3/GA PHE 96
> color #3/GA:96 yellow
> swapaa #3/GA:98 PHE
Using Dunbrack library
mutadedModel #3/GA TRP 98: phi -72.2, psi -43.9 trans
Applying PHE rotamer (chi angles: -175.1 75.2) to mutadedModel #3/GA PHE 98
> color #3/GA:98 yellow
> swapaa #3/GA:99 MET
Using Dunbrack library
mutadedModel #3/GA ARG 99: phi -68.2, psi -72.7 trans
Applying MET rotamer (chi angles: -68.9 -60.6 -67.8) to mutadedModel #3/GA MET
99
> color #3/GA:99 yellow
> swapaa #3/GA:100 HIS
Using Dunbrack library
mutadedModel #3/GA GLN 100: phi -43.8, psi -34.9 trans
Applying HIS rotamer (chi angles: 67.0 -78.4) to mutadedModel #3/GA HIS 100
> color #3/GA:100 yellow
> swapaa #3/GA:103 HIS
Using Dunbrack library
mutadedModel #3/GA PHE 103: phi -65.4, psi -48.6 trans
Applying HIS rotamer (chi angles: -70.7 171.6) to mutadedModel #3/GA HIS 103
> color #3/GA:103 yellow
> swapaa #3/GA:104 LYS
Using Dunbrack library
mutadedModel #3/GA GLU 104: phi -65.0, psi -32.9 trans
Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to mutadedModel
#3/GA LYS 104
> color #3/GA:104 yellow
> swapaa #3/GA:105 SER
Using Dunbrack library
mutadedModel #3/GA ALA 105: phi -67.1, psi -47.8 trans
Applying SER rotamer (chi angles: 63.0) to mutadedModel #3/GA SER 105
> color #3/GA:105 yellow
> swapaa #3/GA:106 ILE
Using Dunbrack library
mutadedModel #3/GA GLU 106: phi -60.4, psi -42.3 trans
Applying ILE rotamer (chi angles: 63.6 171.5) to mutadedModel #3/GA ILE 106
> color #3/GA:106 yellow
> swapaa #3/GA:107 GLU
Using Dunbrack library
mutadedModel #3/GA LEU 107: phi -60.1, psi -43.3 trans
Applying GLU rotamer (chi angles: -177.3 177.0 -1.2) to mutadedModel #3/GA GLU
107
> color #3/GA:107 yellow
> swapaa #3/GA:110 ASP
Using Dunbrack library
mutadedModel #3/GA LEU 110: phi -51.6, psi -38.9 trans
Applying ASP rotamer (chi angles: -174.3 64.3) to mutadedModel #3/GA ASP 110
> color #3/GA:110 yellow
> swapaa #3/GA:111 ASP
Using Dunbrack library
mutadedModel #3/GA GLU 111: phi -85.4, psi -24.8 trans
Applying ASP rotamer (chi angles: -65.3 -30.9) to mutadedModel #3/GA ASP 111
> color #3/GA:111 yellow
> swapaa #3/GA:112 SER
Using Dunbrack library
mutadedModel #3/GA ALA 112: phi -73.5, psi -29.7 trans
Applying SER rotamer (chi angles: 65.8) to mutadedModel #3/GA SER 112
> color #3/GA:112 yellow
> swapaa #3/GA:113 ILE
Using Dunbrack library
mutadedModel #3/GA LEU 113: phi -66.1, psi -48.9 trans
Applying ILE rotamer (chi angles: -66.5 168.5) to mutadedModel #3/GA ILE 113
> color #3/GA:113 yellow
> swapaa #3/GA:114 ARG
Using Dunbrack library
mutadedModel #3/GA PHE 114: phi -53.7, psi -28.4 trans
Applying ARG rotamer (chi angles: 68.1 177.4 65.8 -106.4) to mutadedModel
#3/GA ARG 114
> color #3/GA:114 yellow
> swapaa #3/GA:115 LYS
Using Dunbrack library
mutadedModel #3/GA VAL 115: phi -81.2, psi -60.4 trans
Applying LYS rotamer (chi angles: -70.3 -176.8 174.9 65.8) to mutadedModel
#3/GA LYS 115
> color #3/GA:115 yellow
> swapaa #3/GA:117 ALA
Using Dunbrack library
Swapping mutadedModel #3/GA GLU 117 to ALA
> color #3/GA:117 yellow
> swapaa #3/GA:118 TRP
Using Dunbrack library
mutadedModel #3/GA ALA 118: phi -72.7, psi 4.7 trans
Applying TRP rotamer (chi angles: -178.6 25.7) to mutadedModel #3/GA TRP 118
> color #3/GA:118 yellow
> swapaa #3/GA:119 TRP
Using Dunbrack library
mutadedModel #3/GA ARG 119: phi -87.0, psi 163.7 trans
Applying TRP rotamer (chi angles: 58.2 63.0) to mutadedModel #3/GA TRP 119
> color #3/GA:119 yellow
> color #3/GA:120 cyan
> color #3/GA:121 cyan
> color #3/GA:122 cyan
> select #3/GQ
540 atoms, 542 bonds, 73 residues, 1 model selected
> bond #3/GQ:35@C #3/GQ:36@N reasonable false
Created 0 bonds
> bond #3/GQ:36@C #3/GQ:37@N reasonable false
Created 0 bonds
> bond #3/GQ:37@C #3/GQ:38@N reasonable false
Created 0 bonds
> bond #3/GQ:38@C #3/GQ:39@N reasonable false
Created 1 bond
> bond #3/GQ:74@C #3/GQ:75@N reasonable false
Created 0 bonds
> bond #3/GQ:75@C #3/GQ:76@N reasonable false
Created 1 bond
> bond #3/GQ:73@C #3/GQ:74@N reasonable false
Created 1 bond
> bond #3/GQ:76@C #3/GQ:77@N reasonable false
Created 1 bond
> bond #3/GQ:34@C #3/GQ:35@N reasonable false
Created 1 bond
> bond #3/GQ:72@C #3/GQ:73@N reasonable false
Created 1 bond
> bond #3/GQ:77@C #3/GQ:78@N reasonable false
Created 1 bond
> bond #3/GQ:39@C #3/GQ:40@N reasonable false
Created 0 bonds
> bond #3/GQ:40@C #3/GQ:41@N reasonable false
Created 0 bonds
> bond #3/GQ:41@C #3/GQ:42@N reasonable false
Created 0 bonds
> bond #3/GQ:42@C #3/GQ:43@N reasonable false
Created 0 bonds
> bond #3/GQ:43@C #3/GQ:44@N reasonable false
Created 0 bonds
> bond #3/GQ:44@C #3/GQ:45@N reasonable false
Created 0 bonds
> bond #3/GQ:45@C #3/GQ:46@N reasonable false
Created 0 bonds
> bond #3/GQ:46@C #3/GQ:47@N reasonable false
Created 0 bonds
> bond #3/GQ:47@C #3/GQ:48@N reasonable false
Created 0 bonds
> bond #3/GQ:48@C #3/GQ:49@N reasonable false
Created 0 bonds
> bond #3/GQ:49@C #3/GQ:50@N reasonable false
Created 0 bonds
> bond #3/GQ:50@C #3/GQ:51@N reasonable false
Created 0 bonds
> bond #3/GQ:51@C #3/GQ:52@N reasonable false
Created 0 bonds
> bond #3/GQ:52@C #3/GQ:53@N reasonable false
Created 0 bonds
> bond #3/GQ:53@C #3/GQ:54@N reasonable false
Created 0 bonds
> bond #3/GQ:54@C #3/GQ:55@N reasonable false
Created 0 bonds
> bond #3/GQ:55@C #3/GQ:56@N reasonable false
Created 0 bonds
> bond #3/GQ:56@C #3/GQ:57@N reasonable false
Created 0 bonds
> bond #3/GQ:57@C #3/GQ:58@N reasonable false
Created 0 bonds
> bond #3/GQ:58@C #3/GQ:59@N reasonable false
Created 0 bonds
> bond #3/GQ:59@C #3/GQ:60@N reasonable false
Created 0 bonds
> bond #3/GQ:60@C #3/GQ:61@N reasonable false
Created 0 bonds
> bond #3/GQ:61@C #3/GQ:62@N reasonable false
Created 0 bonds
> bond #3/GQ:62@C #3/GQ:63@N reasonable false
Created 0 bonds
> bond #3/GQ:63@C #3/GQ:64@N reasonable false
Created 0 bonds
> bond #3/GQ:64@C #3/GQ:65@N reasonable false
Created 0 bonds
> bond #3/GQ:65@C #3/GQ:66@N reasonable false
Created 0 bonds
> bond #3/GQ:66@C #3/GQ:67@N reasonable false
Created 0 bonds
> bond #3/GQ:67@C #3/GQ:68@N reasonable false
Created 0 bonds
> bond #3/GQ:68@C #3/GQ:69@N reasonable false
Created 0 bonds
> bond #3/GQ:69@C #3/GQ:70@N reasonable false
Created 0 bonds
> bond #3/GQ:70@C #3/GQ:71@N reasonable false
Created 0 bonds
> bond #3/GQ:71@C #3/GQ:72@N reasonable false
Created 1 bond
> bond #3/GQ:78@C #3/GQ:79@N reasonable false
Created 0 bonds
> bond #3/GQ:79@C #3/GQ:80@N reasonable false
Created 0 bonds
> bond #3/GQ:80@C #3/GQ:81@N reasonable false
Created 0 bonds
> bond #3/GQ:81@C #3/GQ:82@N reasonable false
Created 0 bonds
> bond #3/GQ:82@C #3/GQ:83@N reasonable false
Created 0 bonds
> bond #3/GQ:83@C #3/GQ:84@N reasonable false
Created 0 bonds
> bond #3/GQ:84@C #3/GQ:85@N reasonable false
Created 0 bonds
> bond #3/GQ:13@C #3/GQ:14@N reasonable false
Created 0 bonds
> bond #3/GQ:14@C #3/GQ:15@N reasonable false
Created 0 bonds
> bond #3/GQ:15@C #3/GQ:16@N reasonable false
Created 0 bonds
> bond #3/GQ:16@C #3/GQ:17@N reasonable false
Created 0 bonds
> bond #3/GQ:17@C #3/GQ:18@N reasonable false
Created 0 bonds
> bond #3/GQ:18@C #3/GQ:19@N reasonable false
Created 0 bonds
> bond #3/GQ:19@C #3/GQ:20@N reasonable false
Created 0 bonds
> bond #3/GQ:20@C #3/GQ:21@N reasonable false
Created 0 bonds
> bond #3/GQ:21@C #3/GQ:22@N reasonable false
Created 0 bonds
> bond #3/GQ:22@C #3/GQ:23@N reasonable false
Created 0 bonds
> bond #3/GQ:23@C #3/GQ:24@N reasonable false
Created 0 bonds
> bond #3/GQ:24@C #3/GQ:25@N reasonable false
Created 0 bonds
> bond #3/GQ:25@C #3/GQ:26@N reasonable false
Created 0 bonds
> bond #3/GQ:26@C #3/GQ:27@N reasonable false
Created 0 bonds
> bond #3/GQ:27@C #3/GQ:28@N reasonable false
Created 0 bonds
> bond #3/GQ:28@C #3/GQ:29@N reasonable false
Created 0 bonds
> bond #3/GQ:29@C #3/GQ:30@N reasonable false
Created 0 bonds
> bond #3/GQ:30@C #3/GQ:31@N reasonable false
Created 0 bonds
> bond #3/GQ:31@C #3/GQ:32@N reasonable false
Created 0 bonds
> bond #3/GQ:32@C #3/GQ:33@N reasonable false
Created 0 bonds
> bond #3/GQ:33@C #3/GQ:34@N reasonable false
Created 1 bond
> swapaa #3/GQ:13 MET
Using Dunbrack library
mutadedModel #3/GQ GLY 13: phi none, psi 144.5 trans
Applying MET rotamer (chi angles: -78.6 67.3 73.0) to mutadedModel #3/GQ MET
13
> color #3/GQ:13 yellow
> swapaa #3/GQ:14 THR
Using Dunbrack library
mutadedModel #3/GQ ILE 14: phi 156.8, psi 46.1 trans
Applying THR rotamer (chi angles: -173.3) to mutadedModel #3/GQ THR 14
> color #3/GQ:14 yellow
> swapaa #3/GQ:19 LYS
Using Dunbrack library
mutadedModel #3/GQ THR 19: phi -106.1, psi 134.5 trans
Applying LYS rotamer (chi angles: -163.8 -88.4 117.5 177.3) to mutadedModel
#3/GQ LYS 19
> color #3/GQ:19 yellow
> swapaa #3/GQ:20 GLY
Using Dunbrack library
Swapping mutadedModel #3/GQ SER 20 to GLY
> color #3/GQ:20 yellow
> swapaa #3/GQ:22 VAL
Using Dunbrack library
mutadedModel #3/GQ ASN 22: phi -68.5, psi 112.0 trans
Applying VAL rotamer (chi angles: 177.0) to mutadedModel #3/GQ VAL 22
> color #3/GQ:22 yellow
> swapaa #3/GQ:25 MET
Using Dunbrack library
mutadedModel #3/GQ ASN 25: phi -65.8, psi 70.9 trans
Applying MET rotamer (chi angles: -177.5 179.3 71.4) to mutadedModel #3/GQ MET
25
> color #3/GQ:25 yellow
> swapaa #3/GQ:26 LYS
Using Dunbrack library
mutadedModel #3/GQ THR 26: phi -117.6, psi 165.5 trans
Applying LYS rotamer (chi angles: 65.4 -176.8 -70.4 -66.0) to mutadedModel
#3/GQ LYS 26
> color #3/GQ:26 yellow
> swapaa #3/GQ:27 PHE
Using Dunbrack library
mutadedModel #3/GQ TYR 27: phi -120.8, psi 33.2 trans
Applying PHE rotamer (chi angles: 56.2 88.2) to mutadedModel #3/GQ PHE 27
> color #3/GQ:27 yellow
> swapaa #3/GQ:28 ASP
Using Dunbrack library
mutadedModel #3/GQ THR 28: phi -126.2, psi 120.0 trans
Applying ASP rotamer (chi angles: -175.9 -11.3) to mutadedModel #3/GQ ASP 28
> color #3/GQ:28 yellow
> swapaa #3/GQ:29 SER
Using Dunbrack library
mutadedModel #3/GQ VAL 29: phi -136.5, psi 157.5 trans
Applying SER rotamer (chi angles: 64.6) to mutadedModel #3/GQ SER 29
> color #3/GQ:29 yellow
> swapaa #3/GQ:30 LEU
Using Dunbrack library
mutadedModel #3/GQ THR 30: phi -80.2, psi 111.4 trans
Applying LEU rotamer (chi angles: -179.4 62.6) to mutadedModel #3/GQ LEU 30
> color #3/GQ:30 yellow
> swapaa #3/GQ:31 LYS
Using Dunbrack library
mutadedModel #3/GQ PHE 31: phi -81.4, psi 130.6 trans
Applying LYS rotamer (chi angles: -65.5 -177.3 -176.9 -64.6) to mutadedModel
#3/GQ LYS 31
> color #3/GQ:31 yellow
> swapaa #3/GQ:33 ALA
Using Dunbrack library
Swapping mutadedModel #3/GQ SER 33 to ALA
> color #3/GQ:33 yellow
> swapaa #3/GQ:34 TYR
Using Dunbrack library
mutadedModel #3/GQ PHE 34: phi 30.6, psi 35.4 trans
Applying TYR rotamer (chi angles: -59.7 79.1) to mutadedModel #3/GQ TYR 34
> color #3/GQ:34 yellow
> swapaa #3/GQ:35 VAL
Using Dunbrack library
mutadedModel #3/GQ ASN 35: phi -135.9, psi 104.6 trans
Applying VAL rotamer (chi angles: -179.8) to mutadedModel #3/GQ VAL 35
> color #3/GQ:35 yellow
> swapaa #3/GQ:37 LYS
Using Dunbrack library
mutadedModel #3/GQ ARG 37: phi -79.6, psi 136.8 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to mutadedModel
#3/GQ LYS 37
> color #3/GQ:37 yellow
> swapaa #3/GQ:39 PHE
Using Dunbrack library
mutadedModel #3/GQ ASN 39: phi -60.1, psi -20.0 trans
Applying PHE rotamer (chi angles: 72.0 88.6) to mutadedModel #3/GQ PHE 39
> color #3/GQ:39 yellow
> swapaa #3/GQ:41 THR
Using Dunbrack library
mutadedModel #3/GQ ILE 41: phi -79.5, psi -50.2 trans
Applying THR rotamer (chi angles: 58.9) to mutadedModel #3/GQ THR 41
> color #3/GQ:41 yellow
> swapaa #3/GQ:42 GLN
Using Dunbrack library
mutadedModel #3/GQ LYS 42: phi -51.2, psi -61.0 trans
Applying GLN rotamer (chi angles: -70.1 176.3 35.5) to mutadedModel #3/GQ GLN
42
> color #3/GQ:42 yellow
> swapaa #3/GQ:43 PHE
Using Dunbrack library
mutadedModel #3/GQ SER 43: phi -6.0, psi -75.0 trans
Applying PHE rotamer (chi angles: -178.6 77.3) to mutadedModel #3/GQ PHE 43
> color #3/GQ:43 yellow
> swapaa #3/GQ:44 PHE
Using Dunbrack library
mutadedModel #3/GQ ARG 44: phi -68.3, psi -31.5 trans
Applying PHE rotamer (chi angles: -73.1 104.8) to mutadedModel #3/GQ PHE 44
> color #3/GQ:44 yellow
> swapaa #3/GQ:45 VAL
Using Dunbrack library
mutadedModel #3/GQ THR 45: phi -89.0, psi -41.9 trans
Applying VAL rotamer (chi angles: 174.9) to mutadedModel #3/GQ VAL 45
> color #3/GQ:45 yellow
> swapaa #3/GQ:47 GLY
Using Dunbrack library
Swapping mutadedModel #3/GQ ALA 47 to GLY
> color #3/GQ:47 yellow
> swapaa #3/GQ:49 TRP
Using Dunbrack library
mutadedModel #3/GQ ARG 49: phi -76.6, psi -36.0 trans
Applying TRP rotamer (chi angles: -178.2 -121.6) to mutadedModel #3/GQ TRP 49
> color #3/GQ:49 yellow
> swapaa #3/GQ:52 SER
Using Dunbrack library
mutadedModel #3/GQ GLU 52: phi -71.4, psi -18.4 trans
Applying SER rotamer (chi angles: 68.0) to mutadedModel #3/GQ SER 52
> color #3/GQ:52 yellow
> swapaa #3/GQ:53 ASN
Using Dunbrack library
mutadedModel #3/GQ ASP 53: phi -80.3, psi -30.4 trans
Applying ASN rotamer (chi angles: -71.8 -0.4) to mutadedModel #3/GQ ASN 53
> color #3/GQ:53 yellow
> swapaa #3/GQ:54 MET
Using Dunbrack library
mutadedModel #3/GQ PHE 54: phi -106.5, psi -12.5 trans
Applying MET rotamer (chi angles: -64.0 -61.6 -69.6) to mutadedModel #3/GQ MET
54
> color #3/GQ:54 yellow
> swapaa #3/GQ:56 THR
Using Dunbrack library
mutadedModel #3/GQ LEU 56: phi -63.8, psi -29.7 trans
Applying THR rotamer (chi angles: 59.1) to mutadedModel #3/GQ THR 56
> color #3/GQ:56 yellow
> swapaa #3/GQ:57 ASN
Using Dunbrack library
mutadedModel #3/GQ ILE 57: phi -76.7, psi -34.9 trans
Applying ASN rotamer (chi angles: -171.3 -2.9) to mutadedModel #3/GQ ASN 57
> color #3/GQ:57 yellow
> swapaa #3/GQ:58 PHE
Using Dunbrack library
mutadedModel #3/GQ TYR 58: phi -75.2, psi -28.7 trans
Applying PHE rotamer (chi angles: -71.7 130.8) to mutadedModel #3/GQ PHE 58
> color #3/GQ:58 yellow
> swapaa #3/GQ:59 VAL
Using Dunbrack library
mutadedModel #3/GQ ILE 59: phi -72.7, psi -37.5 trans
Applying VAL rotamer (chi angles: 173.1) to mutadedModel #3/GQ VAL 59
> color #3/GQ:59 yellow
> swapaa #3/GQ:60 ILE
Using Dunbrack library
mutadedModel #3/GQ LEU 60: phi -52.1, psi -52.8 trans
Applying ILE rotamer (chi angles: -64.9 -62.5) to mutadedModel #3/GQ ILE 60
> color #3/GQ:60 yellow
> swapaa #3/GQ:61 GLY
Using Dunbrack library
Swapping mutadedModel #3/GQ ALA 61 to GLY
> color #3/GQ:61 yellow
> swapaa #3/GQ:63 LEU
Using Dunbrack library
mutadedModel #3/GQ THR 63: phi -59.7, psi -24.3 trans
Applying LEU rotamer (chi angles: -67.7 173.8) to mutadedModel #3/GQ LEU 63
> color #3/GQ:63 yellow
> swapaa #3/GQ:64 ILE
Using Dunbrack library
mutadedModel #3/GQ ARG 64: phi -79.4, psi -30.3 trans
Applying ILE rotamer (chi angles: -66.7 169.1) to mutadedModel #3/GQ ILE 64
> color #3/GQ:64 yellow
> swapaa #3/GQ:68 ALA
Using Dunbrack library
Swapping mutadedModel #3/GQ GLY 68 to ALA
> color #3/GQ:68 yellow
> swapaa #3/GQ:69 ASN
Using Dunbrack library
mutadedModel #3/GQ ILE 69: phi -114.4, psi -7.4 trans
Applying ASN rotamer (chi angles: -66.1 -72.6) to mutadedModel #3/GQ ASN 69
> color #3/GQ:69 yellow
> swapaa #3/GQ:71 GLY
Using Dunbrack library
Swapping mutadedModel #3/GQ ALA 71 to GLY
> color #3/GQ:71 yellow
> swapaa #3/GQ:72 LEU
Using Dunbrack library
mutadedModel #3/GQ ASP 72: phi -23.0, psi 2.6 trans
Applying LEU rotamer (chi angles: -64.8 174.3) to mutadedModel #3/GQ LEU 72
> color #3/GQ:72 yellow
> swapaa #3/GQ:73 SER
Using Dunbrack library
mutadedModel #3/GQ GLY 73: phi -28.8, psi 74.9 trans
Applying SER rotamer (chi angles: 179.0) to mutadedModel #3/GQ SER 73
> color #3/GQ:73 yellow
> swapaa #3/GQ:74 GLY
Using Dunbrack library
Swapping mutadedModel #3/GQ PHE 74 to GLY
> color #3/GQ:74 yellow
> swapaa #3/GQ:75 ALA
Using Dunbrack library
Swapping mutadedModel #3/GQ GLY 75 to ALA
> color #3/GQ:75 yellow
> swapaa #3/GQ:76 TRP
Using Dunbrack library
mutadedModel #3/GQ GLY 76: phi 71.9, psi -26.0 cis
Applying TRP rotamer (chi angles: -63.9 106.5) to mutadedModel #3/GQ TRP 76
> color #3/GQ:76 yellow
> swapaa #3/GQ:77 PRO
Using Dunbrack library
mutadedModel #3/GQ ALA 77: phi -11.6, psi 8.8 trans
Applying PRO rotamer (chi angles: 27.3 -34.5) to mutadedModel #3/GQ PRO 77
> color #3/GQ:77 yellow
> swapaa #3/GQ:78 PRO
Using Dunbrack library
mutadedModel #3/GQ GLY 78: phi -102.3, psi 121.7 trans
Applying PRO rotamer (chi angles: -23.4 35.4) to mutadedModel #3/GQ PRO 78
> color #3/GQ:78 yellow
> swapaa #3/GQ:80 PRO
Using Dunbrack library
mutadedModel #3/GQ LYS 80: phi -29.8, psi -25.7 trans
Applying PRO rotamer (chi angles: -26.4 37.1) to mutadedModel #3/GQ PRO 80
> color #3/GQ:80 yellow
> swapaa #3/GQ:81 HIS
Using Dunbrack library
mutadedModel #3/GQ GLU 81: phi -68.3, psi -23.7 trans
Applying HIS rotamer (chi angles: -172.8 -25.8) to mutadedModel #3/GQ HIS 81
> color #3/GQ:81 yellow
> swapaa #3/GQ:82 SER
Using Dunbrack library
mutadedModel #3/GQ LEU 82: phi -86.2, psi -47.3 trans
Applying SER rotamer (chi angles: -65.4) to mutadedModel #3/GQ SER 82
> color #3/GQ:82 yellow
> swapaa #3/GQ:83 LEU
Using Dunbrack library
mutadedModel #3/GQ PHE 83: phi -111.3, psi -20.9 trans
Applying LEU rotamer (chi angles: -60.7 176.5) to mutadedModel #3/GQ LEU 83
> color #3/GQ:83 yellow
> swapaa #3/GQ:84 HIS
Using Dunbrack library
mutadedModel #3/GQ ALA 84: phi -64.0, psi 2.6 trans
Applying HIS rotamer (chi angles: -176.8 -22.7) to mutadedModel #3/GQ HIS 84
> color #3/GQ:84 yellow
> swapaa #3/GQ:85 PRO
Using Dunbrack library
mutadedModel #3/GQ GLY 85: phi -83.8, psi none trans
Applying PRO rotamer (chi angles: 27.0 -34.6) to mutadedModel #3/GQ PRO 85
> color #3/GQ:85 yellow
> close #3
> close #2
> runscript /Users/rafaelrocha/Library/CloudStorage/OneDrive-
> Personal/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> #1 alignmentsMod1Mod.txt
['1', '8']
['1', '8']
['11']
['1', '1']
['11']
['1', '1']
['1', '3']
['1', '3']
['11']
['1', '1']
['1', '4']
['1', '4']
['1', '15']
['1', '15']
['11']
['1', '1']
['1', '9']
['1', '9']
['1', '4']
['1', '4']
['1', '28']
['1', '28']
['1', '15']
['1', '15']
['7', '15']
['7', '15']
['2', '44']
['2', '44']
['1', '7']
['1', '7']
['1', '8']
['1', '8']
['1', '13']
['1', '13']
['11']
['1', '1']
['1', '31']
['1', '31']
['12']
['1', '2']
['6', '22']
['6', '22']
['5', '21']
['5', '21']
['3', '140']
['3', '140']
['1', '3']
['1', '3']
['1', '8']
['1', '8']
['2', '18']
['2', '18']
['1', '7']
['1', '7']
['7', '12']
['7', '12']
['1', '10']
['1', '10']
['12']
['1', '2']
['1', '10']
['1', '10']
['4', '63']
['4', '63']
['9', '11']
['9', '11']
['11']
['1', '1']
['1', '5']
['1', '5']
['5', '33']
['5', '33']
['1', '4']
['1', '4']
['1', '74']
['1', '74']
['3', '18']
['3', '18']
['2', '22']
['2', '22']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['2', '81']
['2', '81']
['1', '8']
['1', '8']
['1', '5']
['1', '5']
['14', '47']
['14', '47']
['1', '5']
['1', '5']
['1', '3']
['1', '3']
['11']
['1', '1']
['1', '7']
['1', '7']
['1', '14']
['1', '14']
['1', '5']
['1', '5']
['1', '4']
['1', '4']
['1', '7']
['1', '7']
['1', '14']
['1', '14']
['1', '25']
['1', '25']
['1', '20']
['1', '20']
['1', '8']
['1', '8']
['11']
['1', '1']
['12']
['1', '2']
['12']
['1', '2']
['1', '18']
['1', '18']
['1', '70']
['1', '70']
['12']
['1', '2']
['12']
['1', '2']
['1', '12']
['1', '12']
['1', '5']
['1', '5']
['1', '14']
['1', '14']
['1', '3']
['1', '3']
['12']
['1', '2']
['1', '3']
['1', '3']
['1', '7']
['1', '7']
['1', '32']
['1', '32']
['11']
['1', '1']
['12']
['1', '2']
['9', '18']
['9', '18']
['11']
['1', '1']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '10']
['1', '10']
['1', '5']
['1', '5']
['12']
['1', '2']
['1', '20']
['1', '20']
['1', '7']
['1', '7']
['11']
['1', '1']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['12']
['1', '2']
['1', '3']
['1', '3']
['1', '12']
['1', '12']
['1', '3']
['1', '3']
['2', '15']
['2', '15']
['11']
['1', '1']
['11']
['1', '1']
['1', '153']
['1', '153']
['11']
['1', '1']
['1', '39']
['1', '39']
['1', '27']
['1', '27']
['1', '37']
['1', '37']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['1', '56']
['1', '56']
['1', '9']
['1', '9']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '3']
['1', '3']
['12']
['1', '2']
['1', '10']
['1', '10']
['1', '4']
['1', '4']
['11']
['1', '1']
['12']
['1', '2']
['1', '30']
['1', '30']
['3', '45']
['3', '45']
['1', '9']
['1', '9']
['12']
['1', '2']
['1', '59']
['1', '59']
['1', '13']
['1', '13']
['1', '34']
['1', '34']
['1', '5']
['1', '5']
['3', '25']
['3', '25']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['6', '20']
['6', '20']
['1', '11']
['1', '11']
['3', '39']
['3', '39']
['1', '27']
['1', '27']
['1', '21']
['1', '21']
['11']
['1', '1']
['1', '4']
['1', '4']
['2', '33']
['2', '33']
['11']
['1', '1']
['11']
['1', '1']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['1', '8']
['1', '8']
LtaP35.1590.mRNA_A
LtaP35.1450.mRNA_A
LtaP07.0060.mRNA_A
LtaP32.3800.mRNA_A
LtaP13.0770.mRNA_A
sp|P14548.2|CYB_LEITA_A
LtaP35.0210.mRNA_A
GET91263.1_A
LtaP35.0250.mRNA_A
GET89654.1_A
> combine #1 close false name renamedAndRenumberedModel
===== Log before crash end =====
Log:
> set selectionWidth 4
Done loading forcefield
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AX002ENFN/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6 (23G80)
Kernel Version: Darwin 23.6.0
Time since boot: 4 days, 2 hours, 21 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U3223QE:
Resolution: 6720 x 3780
UI Looks like: 3360 x 1890 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
ASUS VG278HE:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (1)
comment:1 by , 15 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
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