id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17745 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x000000031d533000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031c527000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031b51b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a50f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000319503000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003184f7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003174eb000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003164df000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003154d3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003144c7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003134bb000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001f02a0c80 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, psutil._psutil_osx, psutil._psutil_posix, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw 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""_distance_pybind.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13594492928, ""size"" : 638976, ""uuid"" : ""1054ddef-4190-3041-95be-e16119344536"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/transform\/_rotation.cpython-311-darwin.so"", ""name"" : ""_rotation.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13380730880, ""size"" : 32768, ""uuid"" : ""d08bc19e-a473-3d91-9401-19d68cabbac8"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_direct.cpython-311-darwin.so"", ""name"" : ""_direct.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13108396032, ""size"" : 16384, ""uuid"" : ""644b1794-90c5-3838-9ffa-b772683aeb37"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so"", ""name"" : ""_sw.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13108477952, ""size"" : 16384, ""uuid"" : ""02f24514-9c56-3aa2-806f-b6eae4e7cf23"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib"", ""name"" : ""libalign_algs.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13108559872, ""size"" : 16384, ""uuid"" : ""4e700338-6839-3c7c-9f41-a201e7f185e5"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so"", ""name"" : ""_dssp.cpython-311-darwin.so"" }, { ""source"" : ""P"", 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""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""656d6f547ef77657a87e2c88ad7e4901310b8afd"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000187 }, { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { ""VISUAL_INTELLIGENCE_VICTORIA"" : ""66d8b2f77cd4b62688efd2cf"" }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ { ""treatmentId"" : ""ccf01f2d-382e-4ccc-a332-b3f688bc9bbf"", ""experimentId"" : ""67f46b1a73932228c9baf274"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250515_ACP-DH-ER-comparison.cxs"" Log from Thu May 15 15:40:08 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Sequences and Structures/hFASN_NADPH_DH- > ACP_Model.pdb"" Chain information for hFASN_NADPH_DH-ACP_Model.pdb #1 --- Chain | Description A | No description available B | No description available > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Sequences and Structures/hFASN_NADPH_ER- > ACP_Model.pdb"" Chain information for hFASN_NADPH_ER-ACP_Model.pdb #2 --- Chain | Description A | No description available B | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > color gray #1 ; Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1/A:1-406 #2a3890 > color #1/B:1-406 #2a3890 > color #1/A:491-815 #8cc63f > color #1/B:491-815 #8cc63f > color #1/A:859-1101 #f26521 > color #1/B:859-1101 #f26521 > color #1/A:1115-1404 #ff0000 > color #1/B:1115-1404 #ff0000 > color #1/A:1413-1518 #228B22 > color #1/B:1413-1518 #228B22 > color #1/A:1525-1855 #ffde17 > color #1/B:1525-1855 #ffde17 > color #1/A:1886-2108 #006838 > color #1/B:1886-2108 #006838 > color #1/A:2127-2192 #ee2b7b > color #1/B:2127-2192 #ee2b7b > color gray #2 ; Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #2/A:1-406 #2a3890 > color #2/B:1-406 #2a3890 > color #2/A:491-815 #8cc63f > color #2/B:491-815 #8cc63f > color #2/A:859-1101 #f26521 > color #2/B:859-1101 #f26521 > color #2/A:1115-1404 #ff0000 > color #2/B:1115-1404 #ff0000 > color #2/A:1413-1518 #228B22 > color #2/B:1413-1518 #228B22 > color #2/A:1525-1855 #ffde17 > color #2/B:1525-1855 #ffde17 > color #2/A:1886-2108 #006838 > color #2/B:1886-2108 #006838 > color #2/A:2127-2192 #ee2b7b > color #2/B:2127-2192 #ee2b7b > color gray #1 ; Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color gray #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color grey #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color grey #1/A Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color gray All > color #1/A:1-406 #2a3890 > color #1/B:1-406 #2a3890 > color #1/A:491-815 #8cc63f > color #1/B:491-815 #8cc63f > color #1/A:859-1101 #f26521 > color #1/B:859-1101 #f26521 > color #1/A:1115-1404 #ff0000 > color #1/B:1115-1404 #ff0000 > color #1/A:1413-1518 #228B22 > color #1/B:1413-1518 #228B22 > color #1/A:1525-1855 #ffde17 > color #1/B:1525-1855 #ffde17 > color #1/A:1886-2108 #006838 > color #1/B:1886-2108 #006838 > color #1/A:2127-2192 #ee2b7b > color #1/B:2127-2192 #ee2b7b > color #2/A:1-406 #2a3890 > color #2/B:1-406 #2a3890 > color #2/A:491-815 #8cc63f > color #2/B:491-815 #8cc63f > color #2/A:859-1101 #f26521 > color #2/B:859-1101 #f26521 > color #2/A:1115-1404 #ff0000 > color #2/B:1115-1404 #ff0000 > color #2/A:1413-1518 #228B22 > color #2/B:1413-1518 #228B22 > color #2/A:1525-1855 #ffde17 > color #2/B:1525-1855 #ffde17 > color #2/A:1886-2108 #006838 > color #2/B:1886-2108 #006838 > color #2/A:2127-2192 #ee2b7b > color #2/B:2127-2192 #ee2b7b > ui tool show ""Model Panel"" > combine #1 > combine #2 > rename #3 DH-ACP > rename #4 ER-ACP > rename #1 hFAS > hide #!2 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > show #!4 models > show #!3 models > show #!2 models > hide #!3 models > hide #!4 models > hide #!1 models > color #2/A:2127-2192 #ee2b7b > color #2/B:2127-2192 #ee2b7b > color #4/A:2127-2192 #ee2b7b > color #4/B:2127-2192 #ee2b7b > hide #!2 models > show #!4 models > select #4/B:1203 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 46 atoms, 45 bonds, 3 residues, 1 model selected > select up 13661 atoms, 13808 bonds, 894 residues, 1 model selected > select up 13781 atoms, 13927 bonds, 902 residues, 1 model selected > select up 18751 atoms, 18957 bonds, 1219 residues, 1 model selected > select up 18787 atoms, 18992 bonds, 1221 residues, 1 model selected > select up 19891 atoms, 20097 bonds, 1289 residues, 1 model selected > select down 18787 atoms, 18992 bonds, 1221 residues, 1 model selected > select down 18751 atoms, 18957 bonds, 1219 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4/A:1079 16 atoms, 15 bonds, 1 residue, 1 model selected > select up 97 atoms, 96 bonds, 7 residues, 1 model selected > select up 4548 atoms, 4603 bonds, 290 residues, 1 model selected > select up 4607 atoms, 4662 bonds, 294 residues, 1 model selected > select up 18208 atoms, 18410 bonds, 1184 residues, 1 model selected > select up 18314 atoms, 18516 bonds, 1191 residues, 1 model selected > select up 18703 atoms, 18909 bonds, 1216 residues, 1 model selected > select up 18851 atoms, 19065 bonds, 1218 residues, 1 model selected > select up 20139 atoms, 20361 bonds, 1290 residues, 1 model selected > select down 18851 atoms, 19065 bonds, 1218 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 55 atoms, 59 bonds > delete atoms sel > delete bonds sel > hide #!4 models > show #!3 models > select #3/A:1899 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 157 atoms, 159 bonds, 10 residues, 1 model selected > select up 13661 atoms, 13808 bonds, 894 residues, 1 model selected > select up 13813 atoms, 13959 bonds, 904 residues, 1 model selected > select up 18704 atoms, 18910 bonds, 1216 residues, 1 model selected > select up 18852 atoms, 19066 bonds, 1218 residues, 1 model selected > select up 38891 atoms, 39319 bonds, 2509 residues, 1 model selected > select down 18852 atoms, 19066 bonds, 1218 residues, 1 model selected > delete atoms sel > delete bonds sel > undo Undo failed, probably because structures have been modified. > select #3/B:1840 20 atoms, 20 bonds, 1 residue, 1 model selected > select up 162 atoms, 163 bonds, 10 residues, 1 model selected > select up 13661 atoms, 13808 bonds, 894 residues, 1 model selected > select up 13781 atoms, 13927 bonds, 902 residues, 1 model selected > select up 18751 atoms, 18957 bonds, 1219 residues, 1 model selected > select down 13781 atoms, 13927 bonds, 902 residues, 1 model selected > select up 18751 atoms, 18957 bonds, 1219 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 55 atoms, 59 bonds [Repeated 1 time(s)] > delete atoms sel > delete bonds sel Drag select of 55 atoms, 59 bonds > delete atoms sel > delete bonds sel > hide #!3 models > show #!4 models > select #4/B:2512@O1A 1 atom, 1 residue, 1 model selected > select up 74 atoms, 78 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > show #!3 models > hide #!3 models > hide #!4 models > show #!1 models > select #1/B:2185 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 157 atoms, 156 bonds, 9 residues, 1 model selected > select up 1140 atoms, 1140 bonds, 70 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/250515_ACP-DH-ER-comparison.cxs"" > show #!3 models > show #!4 models > hide #!3 models > hide #!4 models > surface #1 > transparency #1 80 > transparency #1 50 > ui tool show ""Surface Color"" > color single #1.2 > ui tool show ""Color Actions"" > color light gray target s > transparency #1 50 > transparency #1 30 > color surfacemap Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color surfacemap fromcartoon Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color fromribbons #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color surface fromribbons #1 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color surface fromcartoons #1 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color romcartoons surface #1 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color fromcartoons surfaces #1 Expected ',' or a keyword > color fromcartoons surfaces > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!4 models > show #!3 models > hide #!4 models > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/250515_ACP-DH-ER-comparison.cxs"" > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Sequences and > Structures/hFASN_NADPH_State1_Model.pdb"" Chain information for hFASN_NADPH_State1_Model.pdb #5 --- Chain | Description A | No description available B | No description available > hide #!1 models > hide #!3 models > color #5 gray > hide #!5 models > show #!4 models > hide #!4 models > show #!5 models > color #5/A:1-406 #2a3890 > color #5/B:1-406 #2a3890 > color #5/A:491-815 #8cc63f > color #5/B:491-815 #8cc63f > color #5/A:859-1101 #f26521 > color #5/B:859-1101 #f26521 > color #5/A:1115-1404 #ff0000 > color #5/B:1115-1404 #ff0000 > color #5/A:1413-1518 #228B22 > color #5/B:1413-1518 #228B22 > color #5/A:1525-1855 #ffde17 > color #5/B:1525-1855 #ffde17 > color #5/A:1886-2108 #006838 > color #5/B:1886-2108 #006838 > color #5/A:2127-2192 #ee2b7b > color #5/B:2127-2192 #ee2b7b > color #5 fromcartoons surfaces > surface #5 > color #5 fromcartoons surfaces > show #!1 models > hide #!1 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!3 models > show #!3 models > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/250515_ACP-DH-ER-comparison.cxs"" ——— End of log from Thu May 15 15:40:08 2025 ——— opened ChimeraX session > select #3/B:2186 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 157 atoms, 156 bonds, 9 residues, 1 model selected > select up 1140 atoms, 1140 bonds, 70 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #8f71ff intraModel false distSlop 1.5 intraMol false > intraRes false reveal true 75 hydrogen bonds found > show #!1 models > hide #6 models > hide #!5 models > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > show #!4 models > show #!3 models > hide #!4 models > hbonds sel color #8f71ff intraModel false distSlop 1.5 intraMol false > intraRes false reveal true 75 hydrogen bonds found > ui tool show ""Side View"" > hide #!1 models > hide #!3 models > show #!2 models > select #2/B:2162 16 atoms, 15 bonds, 1 residue, 1 model selected > select up 222 atoms, 221 bonds, 13 residues, 1 model selected > select up 1140 atoms, 1140 bonds, 70 residues, 1 model selected > hbonds sel color #8f71ff interModel false distSlop 1.5 intraMol false > intraRes false reveal true 3 hydrogen bonds found > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Nature_ACP 241123/ACP engaged with MAT.cxs"" Opened ACP-MAT_class6.mrc as #1, grid size 360,360,360, pixel 0.835, shown at level 0.0042, step 1, values float32 opened ChimeraX session > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Nature_ACP 241123/ACP in transition.cxs"" Opened ACP_in_transition_class9.mrc as #1, grid size 360,360,360, pixel 0.835, shown at level 0.00322, step 1, values float32 opened ChimeraX session > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Nature_ACP 241123/ACP engaged with MAT.cxs"" Opened ACP-MAT_class6.mrc as #1, grid size 360,360,360, pixel 0.835, shown at level 0.0042, step 1, values float32 opened ChimeraX session > hide #!1 models > color #2/A:1-406 #2a3890 > color #2/B:1-406 #2a3890 > color #2/A:491-815 #8cc63f > color #2/B:491-815 #8cc63f > color #2/A:859-1101 #f26521 > color #2/B:859-1101 #f26521 > color #3/A:1-406 #2a3890 > color #3/B:1-406 #2a3890 > color #3/A:491-815 #8cc63f > color #3/B:491-815 #8cc63f > color #3/A:859-1101 #f26521 > color #3/B:859-1101 #f26521 > color #2:2127-2192 #ee2b7b > color #2/A:2127-2192 #ee2b7b > color #2 #ee2b7b > surface #2-3 > transparency #2-3 80 > select #2/A:38@N 1 atom, 1 residue, 1 model selected > show sel atoms > select clear > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > lighting flat > lighting full > lighting shadows false > lighting shadows true > lighting simple > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT.cxs"" > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT.png"" width 1344 height 850 supersample 3 > transparentBackground true > view view1 Expected an objects specifier or a view name or a keyword > view name view1 > view list Named views: view1 > view view1 > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/ACP-highlight_structures/250205_KR- > studies.cxs"" opened ChimeraX session > view list Named views: view2, view3, view4 > view view2 > view view3 > view view4 > view view2 > hide #!2 models > select #4/A:111 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 103 atoms, 105 bonds, 12 residues, 1 model selected > select up 1777 atoms, 1799 bonds, 235 residues, 1 model selected > ui tool show ""Color Actions"" > color sel cornflower blue > select #4/B:117 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 112 atoms, 112 bonds, 15 residues, 1 model selected > select up 1379 atoms, 1396 bonds, 183 residues, 1 model selected > color sel cyan > select up 1688 atoms, 1708 bonds, 224 residues, 1 model selected > select down 1379 atoms, 1396 bonds, 183 residues, 1 model selected > select up 1688 atoms, 1708 bonds, 224 residues, 1 model selected > color sel cyan > select #4/G:44 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 91 atoms, 90 bonds, 12 residues, 1 model selected > select up 538 atoms, 542 bonds, 70 residues, 1 model selected > color sel purple > select clear > select #4/G:44 8 atoms, 7 bonds, 1 residue, 1 model selected > select ~sel & ##selected 4032 atoms, 4077 bonds, 75 pseudobonds, 530 residues, 4 models selected > select up 4034 atoms, 4077 bonds, 75 pseudobonds, 531 residues, 4 models selected > hide sel atoms > select clear > select #4/G:36 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select ::name=""4HH"" 33 atoms, 31 bonds, 2 residues, 2 models selected > show #!4 atoms > undo > select ::name=""4HH""::name=""HOH""::name=""NAP""::name=""UHC"" 236 atoms, 193 bonds, 6 pseudobonds, 53 residues, 5 models selected > show sel & #!4 atoms > select clear > show #!1 models > hide #!1 models > select #4/B:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 112 atoms, 112 bonds, 15 residues, 1 model selected > select up 1379 atoms, 1396 bonds, 183 residues, 1 model selected > select up 1688 atoms, 1708 bonds, 224 residues, 1 model selected > color sel #6d96fbff > color sel #6d94fbff > color sel #6d89fbff > color sel #6d72fbff > color sel #6d67fbff > color sel #6d5efbff > color sel #6d51fbff > color sel #6d4efbff > color sel #6d4afbff > color sel #6d49fbff > color sel #6d4afbff > color sel #6d49fbff > color sel #6d45fbff > color sel #6d36fbff > color sel #6d28fbff > color sel #6d24fbff > color sel #6d22fbff > color sel #6d23fbff > color sel #6d24fbff > color sel #6d25fbff > color sel #6d24fbff > color sel #6d23fbff > color sel #6d22fbff > color sel #6d21fbff > color sel #6d20fbff > color sel #6d1ffbff > color sel #6d1efbff > color sel #6d1dfbff > color sel #6d1afbff > color sel #6d16fbff > color sel #6d13fbff > color sel #6d0ffbff > color sel #6d10fbff > color sel #6d0ffbff > color sel #6d0efbff > color sel #6d0dfbff > color sel #6d0cfbff > color sel #6d0afbff > color sel #6d09fbff > color sel #6d07fbff > color sel #6d06fbff > color sel #6d05fbff > color sel #6d04fbff > color sel #6d03fbff > color sel #6d05fbff > select clear > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR.cxs"" > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR_1.png"" width 1344 height 850 supersample 4 > transparentBackground true > show #!1 models > select #1/A:1423 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 109 atoms, 111 bonds, 6 residues, 1 model selected > select up 1638 atoms, 1655 bonds, 106 residues, 1 model selected > select up 4833 atoms, 4876 bonds, 315 residues, 1 model selected > select down 1638 atoms, 1655 bonds, 106 residues, 1 model selected > color sel #008744ff > color sel #048744ff > color sel #0b8744ff > color sel #228744ff > color sel #288744ff > color sel #338744ff > color sel #3d8744ff > color sel #468744ff > color sel #4a8744ff > color sel #548744ff > color sel #598744ff > color sel #628744ff > color sel #6a8744ff > color sel #6f8744ff > color sel #718744ff > color sel #748744ff > color sel #778744ff > color sel #788744ff > color sel #798744ff > color sel #7d8744ff > color sel #808744ff > color sel #898744ff > color sel #908744ff > color sel #918744ff > color sel #918944ff > color sel #919644ff > color sel #919d44ff > color sel #919f44ff > color sel #91a044ff > color sel #91a144ff > color sel #91a344ff > color sel #91a844ff > color sel #91aa44ff > color sel #91ab44ff > color sel #91aa44ff > color sel #91a944ff > color sel #91a844ff > color sel #91a744ff > color sel #91a444ff > color sel #91a244ff > color sel #919e44ff > color sel #919d44ff > color sel #919c44ff > color sel #919a44ff > color sel #919944ff > color sel #919844ff > color sel #919744ff > color sel #919644ff > color sel #919444ff > color sel #919244ff > color sel #919044ff > color sel #918d44ff > color sel #918c44ff > color sel #918d44ff > color sel #918e44ff > color sel #918f44ff > color sel #919044ff > color sel #918f44ff > color sel #918b44ff > color sel #916d44ff > color sel #915f44ff > color sel #915a44ff > color sel #915944ff > color sel #915844ff > color sel #915244ff > color sel #914844ff > color sel #913d44ff > color sel #913544ff > color sel #913244ff > color sel #913344ff > color sel #913444ff > color sel #913544ff > color sel #913844ff > color sel #913c44ff > color sel #914044ff > color sel #914344ff > color sel #914a44ff > color sel #914f44ff > color sel #915d44ff > color sel #916b44ff > color sel #917144ff > color sel #917944ff > color sel #917c44ff > color sel #917e44ff > color sel #918044ff > color sel #918844ff > color sel #918843ff > color sel #918841ff > color sel #91883eff > color sel #91883bff > color sel #918839ff > color sel #918837ff > color sel #918835ff > color sel #918834ff > color sel #918832ff > color sel #918830ff > color sel #91882fff > color sel #91882eff > color sel #91882dff > color sel #91882aff > color sel #918827ff > color sel #918826ff > color sel #918827ff > color sel #918828ff > color sel #918827ff > color sel #918825ff > color sel #918821ff > select clear > show #!2 models > select #4/B:117 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 112 atoms, 112 bonds, 15 residues, 1 model selected > select up 1379 atoms, 1396 bonds, 183 residues, 1 model selected > select up 1688 atoms, 1708 bonds, 224 residues, 1 model selected > color sel #5e00c5ff > color sel #5e00caff > color sel #5e00cdff > color sel #5e00d2ff > color sel #5e00d6ff > color sel #5e00daff > color sel #5e00e1ff > color sel #5e00e4ff > color sel #5e00e5ff > color sel #5e00e6ff > color sel #5e00ebff > color sel #5e00eeff > color sel #5e00f0ff > color sel #5e00f1ff > color sel #5e00f6ff > color sel #5e00fdff > color sel #5e00ffff > color sel #5e01ffff > color sel #5e16ffff > color sel #5e1effff > color sel #5e2affff > color sel #5e2effff > color sel #5e2fffff > color sel #5e31ffff > color sel #5e39ffff > color sel #5e41ffff > color sel #5e4effff > color sel #5e4fffff > color sel #5e50ffff > color sel #5e4fffff > color sel #5e4effff > color sel #5e4dffff > color sel #5e48ffff > color sel #5e44ffff > color sel #5e3cffff > color sel #5e37ffff > color sel #5e36ffff > color sel #5e34ffff > color sel #5e32ffff > color sel #5e2dffff > color sel #5e2bffff > color sel #5e2affff > color sel #5e29ffff > color sel #5e2affff > color sel #5e2bffff > color sel #5e2cffff > color sel #5e2dffff > color sel #5e2effff > color sel #5e2fffff > color sel #5e30ffff > color sel #5e32ffff > color sel #5e33ffff > color sel #5e34ffff > color sel #5e35ffff > color sel #5e36ffff > color sel #5e37ffff > color sel #5e36ffff > color sel #5e35ffff > color sel #5e34ffff > color sel #5e33ffff > color sel #5c33ffff > color sel #5833ffff > color sel #5533ffff > color sel #5433ffff > color sel #5333ffff > color sel #5233ffff > color sel #5133ffff > color sel #4f33ffff > color sel #4e33ffff > color sel #4d33ffff > select clear > select #1/A:1423 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 109 atoms, 111 bonds, 6 residues, 1 model selected > select up 1638 atoms, 1655 bonds, 106 residues, 1 model selected > color sel #4d33ffff > color sel #228b22ff > select clear > select #1/A:1423 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 109 atoms, 111 bonds, 6 residues, 1 model selected > select up 1638 atoms, 1655 bonds, 106 residues, 1 model selected > color sel #228b22ff > color sel #238b22ff > color sel #248b22ff > color sel #258b22ff > color sel #278b22ff > color sel #288b22ff > color sel #2a8b22ff > color sel #2b8b22ff > color sel #2c8b22ff > color sel #2d8b22ff > color sel #2e8b22ff > color sel #2f8b22ff > color sel #318b22ff > color sel #328b22ff > color sel #348b22ff > color sel #388b22ff > color sel #3a8b22ff > color sel #3b8b22ff > color sel #3c8b22ff > color sel #3d8b22ff > color sel #418b22ff > color sel #468b22ff > color sel #488b22ff > color sel #4b8b22ff > color sel #4c8b22ff > color sel #4d8b22ff > color sel #4e8b22ff > color sel #4f8b22ff > color sel #508b22ff > color sel #518b22ff > color sel #528b22ff > color sel #538b22ff > color sel #548b22ff > color sel #558b22ff > color sel #568b22ff > color sel #578b22ff > color sel #588b22ff > color sel #598b22ff > color sel #5a8b22ff > color sel #5b8b22ff > color sel #5c8b22ff > color sel #5d8b22ff > color sel #5e8b22ff > color sel #5f8b22ff > color sel #5e8b22ff > color sel #5d8b22ff > color sel #5c8b22ff > color sel #5b8b22ff > color sel #5a8b22ff > color sel #598b22ff > color sel #588b22ff > color sel #598b22ff > color sel #5a8b22ff > color sel #5b8b22ff > color sel #5a8b22ff > color sel #5b8b22ff > color sel #5c8b22ff > color sel #5d8b22ff > color sel #5e8b22ff > color sel #608b22ff > color sel #638b22ff > color sel #658b22ff > color sel #668b22ff > color sel #698b22ff > color sel #6a8b22ff > color sel #6d8b22ff > color sel #6f8b22ff > color sel #708b22ff > color sel #718b22ff > color sel #738b22ff > color sel #748b22ff > color sel #768b22ff > color sel #778b22ff > color sel #788b22ff > color sel #798b22ff > color sel #7a8b22ff > color sel #7b8b22ff > color sel #7c8b22ff > color sel #7d8b22ff > color sel #7e8b22ff > color sel #7d8b22ff > color sel #7c8b22ff > color sel #7b8b22ff > color sel #758b22ff > color sel #708b22ff > color sel #628b22ff > color sel #618b22ff > color sel #608b22ff > color sel #5f8b22ff > color sel #5e8b22ff > color sel #5d8b22ff > color sel #5c8b22ff > color sel #5b8b22ff > color sel #5a8b22ff > color sel #598b22ff > color sel #588b22ff > color sel #568b22ff > color sel #558b22ff > color sel #548b22ff > color sel #528b22ff > color sel #518b22ff > color sel #508b22ff > color sel #4f8b22ff > color sel #4e8b22ff > color sel #4d8b22ff > color sel #4c8b22ff > color sel #4d8b22ff > color sel #4e8b22ff > color sel #4f8b22ff > color sel #508b22ff > color sel #518b22ff > color sel #528b22ff > color sel #518b22ff > color sel #538b22ff > color sel #548b22ff > color sel #588b22ff > color sel #598b22ff > color sel #5a8b22ff > color sel #5b8b22ff > color sel #5c8b22ff > color sel #5d8b22ff > color sel #5e8b22ff > color sel #5f8b22ff > color sel #618b22ff > color sel #628b22ff > color sel #638b22ff > color sel #648b22ff > color sel #668b22ff > color sel #678b22ff > color sel #688b22ff > color sel #698b22ff > color sel #6a8b22ff > color sel #698b22ff > select clear > hide #!1-2,4 atoms > select ::name=""4HH""::name=""HOH""::name=""NAP""::name=""UHC"" 236 atoms, 193 bonds, 6 pseudobonds, 53 residues, 5 models selected > show sel & #!2,4 atoms > undo > show sel & #!2,4 atoms > select clear > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR_2.png"" width 1344 height 850 supersample 4 > transparentBackground true > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #6 models > hide #6 models > view list Named views: view2, view3, view4 > view view3 > view view4 > view view3 > view view4 > hide #!1 models > show #!1 models > hide #!1 models > hide #!4 models > show #!4 models > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > select #4/G:38 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 91 atoms, 90 bonds, 12 residues, 1 model selected > select up 538 atoms, 542 bonds, 70 residues, 1 model selected > ui tool show Contacts > contacts sel interModel false intraMol false ignoreHiddenModels true reveal > true 43 contacts > view view2 > select clear > select add #4/B:176@CZ 1 atom, 1 bond, 1 residue, 1 model selected > select add #4/G:37@CG 2 atoms, 1 bond, 2 residues, 1 model selected > select add #4/G:40@CB 3 atoms, 1 bond, 3 residues, 1 model selected > select add #4/G:56@CG 4 atoms, 2 bonds, 4 residues, 1 model selected > select add #4/G:36@CB 5 atoms, 2 bonds, 5 residues, 1 model selected > select up 19 atoms, 7 bonds, 12 residues, 1 model selected > select up 99 atoms, 92 bonds, 12 residues, 1 model selected > color sel byhetero > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR_.png"" width 1344 height 850 supersample 3 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR_3.png"" width 1344 height 850 supersample 4 > transparentBackground true > view name view5 > show #!1 models > show #!2 models > hide #!4 models > select #2/B:2164 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 247 atoms, 246 bonds, 15 residues, 1 model selected > select up 1051 atoms, 1051 bonds, 66 residues, 1 model selected > contacts sel intraModel false intraMol false ignoreHiddenModels true reveal > true 103 contacts > select H 3498 atoms, 19 pseudobonds, 445 residues, 4 models selected > hide sel & #!1-2 atoms > select clear > select #2/B:2160@CG2 1 atom, 1 residue, 1 model selected > select add #2/B:2157@CB 1 atom, 3 bonds, 1 residue, 2 models selected > select add #2/B:2156@CB 2 atoms, 3 bonds, 2 residues, 2 models selected > select up 8 atoms, 3 bonds, 5 residues, 2 models selected > select up 70 atoms, 67 bonds, 5 residues, 2 models selected > color sel byhetero > select clear > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR_4.png"" width 1344 height 850 supersample 4 > transparentBackground true > hide #!1 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > show #!2 models > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR.cxs"" > graphics silhouettes true > set bgColor white > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting full > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting shadows false > view list Named views: view2, view3, view4, view5 > view view5 > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > view view2 > hide #!2,4 atoms > select ::name=""4HH""::name=""HOH""::name=""NAP""::name=""UHC"" 236 atoms, 193 bonds, 6 pseudobonds, 53 residues, 5 models selected > show sel & #!2,4 atoms > select clear > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR_5.png"" width 1344 height 850 supersample 4 > transparentBackground true > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR_5.png"" width 5500 height 3478 supersample 4 > transparentBackground true > show #!1 models > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KR_6.png"" width 5500 height 3478 supersample 4 > transparentBackground true > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Nature_ACP 241123/ACP engaged with MAT.cxs"" Opened ACP-MAT_class6.mrc as #1, grid size 360,360,360, pixel 0.835, shown at level 0.0042, step 1, values float32 opened ChimeraX session > hide #2 models > hide #3 models > show #3 models > color #1 #b2b2b26f models > color #1 #b2b2b275 models > color #1 #b2b2b274 models > show #2 models > hide #2 models > show #2 models > hide #2 models > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/ACP- > highlight_structures/hFASN_NADPH_State1_Model.pdb"" Chain information for hFASN_NADPH_State1_Model.pdb #4 --- Chain | Description A | No description available B | No description available > hide #3 models > hide #!4 models > show #3 models > open ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250516_DH-ER-ACP-comparison.cxs"" opened ChimeraX session > show #!1 models > hide #!1 models > show #!5 models > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting full > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT_2.cxs"" > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Nature_ACP 241123/ACP engaged with MAT.cxs"" Opened ACP-MAT_class6.mrc as #1, grid size 360,360,360, pixel 0.835, shown at level 0.0042, step 1, values float32 opened ChimeraX session > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/ACP- > highlight_structures/hFASN_NADPH_State1_Model.pdb"" Chain information for hFASN_NADPH_State1_Model.pdb #4 --- Chain | Description A | No description available B | No description available > combine #4 > hide #!4 models > color #5 gray > color #5/A:1-406 #2a3890 > color #5/B:1-406 #2a3890 > color #5/A:491-815 #8cc63f > color #5/B:491-815 #8cc63f > color #5/A:859-1101 #f26521 > color #5/B:859-1101 #f26521 > color #5/A:1115-1404 #ff0000 > color #5/B:1115-1404 #ff0000 > color #5/A:1413-1518 #228B22 > color #5/B:1413-1518 #228B22 > color #5/A:1525-1855 #ffde17 > color #5/B:1525-1855 #ffde17 > color #5/A:1886-2108 #006838 > color #5/B:1886-2108 #006838 > color #5/A:2127-2192 #ee2b7b > color #5/B:2127-2192 #ee2b7b > matchmaker #3 to #5 bring #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker copy of hFASN_NADPH_State1_Model.pdb, chain A (#5) with condensing_monomer.pdb, chain B (#3), sequence alignment score = 4212 RMSD between 826 pruned atom pairs is 0.671 angstroms; (across all 854 pairs: 1.106) > hide #2 models > show #2 models > undo > redo > color #1 #21b2b2ff models > color #1 #21b2b237 models > color #1 #21b2b238 models > color #1 #21b2b237 models > hide #2 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > color #3/A:1-406 #2a3890 > color #3/B:1-406 #2a3890 > color #3/A:491-815 #8cc63f > color #3/B:491-815 #8cc63f > color #3/A:859-1101 #f26521 > color #3/B:859-1101 #f26521 > show #3 models > hide #!5 models > show #!5 models > hide #!1 models > hide #3 models > view name view1 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT_2.cxs"" > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT_2.png"" width 5500 height 3478 supersample 4 > transparentBackground true > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > hide #!5 models > show #3 models > show #!1 models > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT_3.png"" width 5500 height 3478 supersample 4 > transparentBackground true > turn x 25 > turn x -25 > view name view2 > view list Named views: view1, view2 > view view2 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT_4.png"" width 5500 height 3478 supersample 4 > transparentBackground true > view view1 > hide #3 models > hide #!1 models > show #!4 models > hide #!4 models > show #!5 models > color #5/A:1413-1518 #698B22 > color #5/B:1413-1518 #698B22 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT_5.png"" width 5500 height 3478 supersample 4 > transparentBackground true > show #!4 models > hide #!5 models > hide #!4 models > show #3 models > show #!1 models > view list Named views: view1, view2 > view view2 > color #1 #21b2b280 models > color #1 #21b2b266 models > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-MAT_6.png"" width 5500 height 3478 supersample 4 > transparentBackground true > show #2 models > select ::name=""NDP"" 592 atoms, 624 bonds, 8 residues, 2 models selected > show #2-3 atoms > undo > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Sequences and Structures/250203_acp- > highlight_structures.cxs"" Opened ACP-KS_position2_class1.mrc as #1, grid size 360,360,360, pixel 0.835, shown at level 0.00388, step 1, values float32 Opened ACP-KS_position1_class5.mrc as #2, grid size 360,360,360, pixel 0.835, shown at level 0.0043, step 1, values float32 opened ChimeraX session > show #!2 models > hide #!2 models > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Nature_ACP 241123/ACP engaged with KS.cxs"" Opened ACP-KS_position2_class1.mrc as #1, grid size 360,360,360, pixel 0.835, shown at level 0.00388, step 1, values float32 Opened ACP-KS_position1_class5.mrc as #2, grid size 360,360,360, pixel 0.835, shown at level 0.0043, step 1, values float32 opened ChimeraX session > ui tool show ""Side View"" > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #3 models > hide #4 models > show #4 models > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/ACP- > highlight_structures/hFASN_NADPH_State1_Model.pdb"" Chain information for hFASN_NADPH_State1_Model.pdb #5 --- Chain | Description A | No description available B | No description available > matchmaker #4 to #5 bring #1,#2,#3 Invalid ""bring"" argument: only initial part ""#1"" of atom specifier valid > matchmaker #4 to #5 bring #1#2#3 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hFASN_NADPH_State1_Model.pdb, chain A (#5) with condensing_domain.pdb, chain A (#4), sequence alignment score = 4209 RMSD between 826 pruned atom pairs is 0.671 angstroms; (across all 854 pairs: 1.106) > open ""/Volumes/grininger_shared/RUNNER/Chris/Reports: > Paper/2024:2_paper_ACP-highlight/Sequences and Structures/KS-ACP-model.pdb"" Chain information for KS-ACP-model.pdb #6 --- Chain | Description B | No description available C D | No description available > matchmaker #6 to #5 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hFASN_NADPH_State1_Model.pdb, chain B (#5) with KS-ACP-model.pdb, chain B (#6), sequence alignment score = 4420.5 Fewer than 3 residues aligned; cannot match hFASN_NADPH_State1_Model.pdb, chain B with KS-ACP-model.pdb, chain B > ui tool show ""Show Sequence Viewer"" > sequence chain #6/B Alignment identifier is 6/B > ui tool show ""Show Sequence Viewer"" > sequence chain #6/C Alignment identifier is 6/C > matchmaker #6/C to #5/A Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hFASN_NADPH_State1_Model.pdb, chain A (#5) with KS-ACP-model.pdb, chain C (#6), sequence alignment score = 4209 RMSD between 826 pruned atom pairs is 0.671 angstroms; (across all 854 pairs: 1.106) > hide #!2 models > show #!2 models > hide #!5 models > color gray #5#6 ; Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color gray #5#6 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color gray #5 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #5 gray > color #6 gray > color #6/A:1-406 #2a3890 > color #6/B:1-406 #2a3890 > color #6/A:491-815 #8cc63f > color #6/B:491-815 #8cc63f > color #6/A:859-1101 #f26521 > color #6/B:859-1101 #f26521 > color #6/A:1115-1404 #ff0000 > color #6/B:1115-1404 #ff0000 > color #6:1-406 #2a3890 > color #6:491-815 #8cc63f > color #6:859-1101 #f26521 > color #6:1115-1404 #ff0000 > color #2 #da8072ff models > color #2 #da80e5ff models > color #2 #dac9e5ff models > color #2 #48c9e5ff models > color #2 #48c9e566 models > hide #4 models > select clear > color #6:2127-2192 #ee2b7b > lighting full > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS.cxs"" > view name view1 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS.png"" width 5500 height 3478 supersample 4 > transparentBackground true > view name view2 > view name view1 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS.png"" width 5500 height 3478 supersample 3 > transparentBackground true > turn z 180 > turn y 180 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS_2.png"" width 1344 height 850 supersample 3 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS_2.png"" width 5500 height 3478 supersample 3 > transparentBackground true > turn y 180 > turn x 25 > turn x -25 > turn x 25 > view name view2 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS_3.png"" width 5500 height 3478 supersample 3 > transparentBackground true > hide #!2 models > show #6 surfaces > transparency #6 30 > transparency #6 50 > transparency #6 60 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS_4.png"" width 5500 height 3478 supersample 3 > transparentBackground true > turn x -25 > view name view3 > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS_5.png"" width 5500 height 3478 supersample 3 > transparentBackground true > save ""/Users/Chris/Local-backup/Reports: Paper/2024:2_paper_ACP- > highlight/Figures/250519_ACP-KS.cxs"" > select #6/B:2186@HB2 1 atom, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 1 residue, 2 models selected > select up 157 atoms, 156 bonds, 9 residues, 2 models selected > select up 1140 atoms, 1140 bonds, 70 residues, 2 models selected > hide sel surfaces > ui tool show Contacts > contacts sel intraModel false intraMol false ignoreHiddenModels true reveal > true No contacts > contacts sel interModel false intraMol false ignoreHiddenModels true reveal > true 102 contacts > hide #7 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Chris/Downloads/8vm0.cif Summary of feedback from opening /Users/Chris/Downloads/8vm0.cif --- note | Fetching CCD NDP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NDP/NDP.cif 8vm0.cif title: Composite structure of human FASN with NADPH in State 4 [more info...] Chain information for 8vm0.cif #1 --- Chain | Description | UniProt A B | Fatty acid synthase | FAS_HUMAN 2-2511 Non-standard residues in 8vm0.cif #1 --- NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYDA2D/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 13 Tage, 23 Stunden und 52 Minuten Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal G276HL: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX