id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16555 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.0-x86_64-i386-64bit 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 0x000070001f8b2000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001e8af000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001d8ac000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001c8a9000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001b8a6000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001a8a3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007000198a0000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001889d000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001789a000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700016897000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700015894000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700014891000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001388e000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001288b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700011888000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700010885000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070000f882000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070000e87f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070000d87c000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff84dee2680 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, 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._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.special._ufuncs_cxx, scipy.special._cdflib, 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 (total: 119) {""app_name"":""ChimeraX"",""timestamp"":""2025-01-06 10:38:22.00 +0800"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.0 (24A335)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""B7C335C4-FEE9-4F9C-B608-2A4EC9A9DF4F""} { ""uptime"" : 1000000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 560, ""osVersion"" : { ""train"" : ""macOS 15.0"", ""build"" : ""24A335"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-01-06 10:38:17.3221 +0800"", ""codeSigningMonitor"" : 0, ""incident"" : ""B7C335C4-FEE9-4F9C-B608-2A4EC9A9DF4F"", ""pid"" : 94678, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-01-03 21:14:17.1226 +0800"", ""procStartAbsTime"" : 1017775318471682, ""procExitAbsTime"" : 1087518888369563, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""AF0E444E-37B4-593A-957D-B5CF6828D46F"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""F7A40BD4-636A-5D03-BCEB-C22CD08BD04B"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""bootSessionUUID"" : ""7271DF61-C54B-4F26-A09D-192078EDC1F5"", ""wakeTime"" : 49, ""bridgeVersion"" : {""build"":""22P353"",""train"":""9.0""}, ""sleepWakeUUID"" : ""824D7BBD-B0F4-4798-BD61-D73322623494"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.932, shown at level 0.00588, step 2, values float32 > volume #1 level 0.003655 > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/local_c1_job195_new_2/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00613, step 2, values float32 > volume #2 level 0.004065 > close > open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 95 messages similar to the above omitted Chain information for c6_job26_Q2-coot-44.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available V | No description available W | 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 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 z | No description available > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00588, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/local_c6_job26_2/relion_locres_filtered.mrc No such file/path: /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/local_c6_job26_2/relion_locres_filtered.mrc > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc No such file/path: /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc No such file/path: /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc > volume #2-10 step 1 level 0.0045 > volume #4 step 1 level 0.0075 No volumes specified > volume #5 step 1 level 0.003 No volumes specified > volume #4 step 1 level 0.0055 No volumes specified > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 dark khaki > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/C deep pink > color #1/V steel blue > color #1/CV yellow green > color #1/8 red > hide #1 target a > show #1/B /D /Cc /2 /6:1-90 target r > hide #1/CM target r > show #1/2 /6:1-90 target a > nucleotides #1/2 /6:1-90 ladder > cartoon style protein xsection oval width 2.4 thickness 0.6 > volume zone #2 nearAtoms #1/B /D /Cc /2 /6 range 6 newMap true Opened run_class001.mrc zone as #3, grid size 480,480,480, pixel 0.932, shown at step 1, values float32 > volume #6 step 1 level 0.013 No volumes specified > surface dust #1-15 size 5 > color #6 silver > transparency #6 50 > surface dust #1-15 size 5 > volume #3 level 0.004806 > volume #3 step 1 level 0.013 > surface dust #1-15 size 5 > color #3 silver > transparency #3 50 > volume #3 level 0.0013 > volume #3 level 0.005 > close > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb --- warnings | Duplicate atom serial number found: 6524 Duplicate atom serial number found: 6525 Duplicate atom serial number found: 6526 Duplicate atom serial number found: 6527 Duplicate atom serial number found: 6528 542 messages similar to the above omitted Chain information for c6_job26_Q2-coot-56.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ck | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available V | No description available W | No description available Y | No description available Z | No description available j | No description available k | No description available l | No description available m | 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 z | No description available > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00588, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/local_c6_job26_2/relion_locres_filtered.mrc No such file/path: /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/local_c6_job26_2/relion_locres_filtered.mrc > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc No such file/path: /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc No such file/path: /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc > volume #2-10 step 1 level 0.0045 > volume #4 step 1 level 0.0075 No volumes specified > volume #5 step 1 level 0.003 No volumes specified > volume #4 step 1 level 0.0055 No volumes specified > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 dark khaki > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/C deep pink > color #1/V steel blue > color #1/CV yellow green > color #1/8 red > hide #1 target a > show #1/B /D /Cc /2 /6:1-90 target r > hide #1/CM target r > show #1/2 /6:1-90 target a > nucleotides #1/2 /6:1-90 ladder > cartoon style protein xsection oval width 2.4 thickness 0.6 > volume zone #2 nearAtoms #1/B /D /Cc /2 /6 range 6 newMap true Opened run_class001.mrc zone as #3, grid size 480,480,480, pixel 0.932, shown at step 1, values float32 > volume #3 step 1 level 0.013 > surface dust #1-15 size 5 > color #3 silver > transparency #3 50 > volume #3 step 1 level 0.0045 > view matrix camera > 0.4381,0.51596,0.73611,323.91,-0.87515,0.43191,0.21811,271.48,-0.20539,-0.73976,0.64076,242.62 > show #1/B /D /Cc /2 /6:1-100 target r > show #1/2 /6:1-100 target a > nucleotides #1/2 /6:1-100 ladder > nucleotides stubs > graphics silhouettes true > volume #3 level 0.005 > view matrix camera > 0.4381,0.51596,0.73611,323.91,-0.87515,0.43191,0.21811,271.48,-0.20539,-0.73976,0.64076,242.62 > save > /Users/lijuanyin/project/prp43/figure_new/figure4/q2_focus_dhx15_u6_view1.jpg > close > open /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/run_class001.mrc Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.932, shown at level 0.00668, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00588, step 2, values float32 > volume #2 level 0.005 > volume #2 level 0.01 > volume #2 level 0.008 > volume #2 level 0.009 > volume #2 level 0.006 > volume #2 level 0.005 > close > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb --- warnings | Duplicate atom serial number found: 6524 Duplicate atom serial number found: 6525 Duplicate atom serial number found: 6526 Duplicate atom serial number found: 6527 Duplicate atom serial number found: 6528 542 messages similar to the above omitted Chain information for c6_job26_Q2-coot-56.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ck | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available V | No description available W | No description available Y | No description available Z | No description available j | No description available k | No description available l | No description available m | 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 z | No description available > open /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00668, step 2, values float32 > volume #2-10 step 1 level 0.005 > volume #4 step 1 level 0.0075 No volumes specified > volume #5 step 1 level 0.003 No volumes specified > volume #4 step 1 level 0.0055 No volumes specified > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 green yellow > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/C deep pink > color #1/V steel blue > color #1/CV magenta > color #1/8:0-300 red > color zone #2-10 near #1 distance 6 > close > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb --- warnings | Duplicate atom serial number found: 6524 Duplicate atom serial number found: 6525 Duplicate atom serial number found: 6526 Duplicate atom serial number found: 6527 Duplicate atom serial number found: 6528 542 messages similar to the above omitted Chain information for c6_job26_Q2-coot-56.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ck | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available V | No description available W | No description available Y | No description available Z | No description available j | No description available k | No description available l | No description available m | 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 z | No description available > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00588, step 2, values float32 > volume #2-10 step 1 level 0.005 > volume #4 step 1 level 0.0075 No volumes specified > volume #5 step 1 level 0.003 No volumes specified > volume #4 step 1 level 0.0055 No volumes specified > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 green yellow > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/C deep pink > color #1/V steel blue > color #1/CV magenta > color #1/8:0-300 red > color #1 #3-10 silver > color #1/Cc orange > color #1/z tomato > color #1/1 forest green > color zone #2-10 near #1 distance 6 > hide #!1 models > close #2 > open > /Users/lijuanyin/project/prp43/deposit/for_reviewer_2/state_BstarQ2_focusing_on_DHX15/run_class001_dc3.mrc Opened run_class001_dc3.mrc as #2, grid size 160,160,160, pixel 2.8, shown at level 0.045, step 1, values float32 > volume #2 level 0.005 > volume #2 level 0.05 > volume #2 level 0.04295 > volume #2 level 0.04 > open > /Users/lijuanyin/project/prp43/deposit/for_reviewer_2/state_BstarQ2_focusing_on_DHX15/run_class001_focusing_refine.mrc Opened run_class001_focusing_refine.mrc as #3, grid size 480,480,480, pixel 0.932, shown at level 0.00588, step 2, values float32 > volume #3 step 1 > volume #3 step 2 > close #3 > close #2 > open > /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00588, step 2, values float32 > color zone #2-10 near #1 distance 6 > view matrix camera > 0.52209,0.083337,-0.84881,-259.14,0.81484,0.24518,0.52528,513.87,0.25189,-0.96589,0.060097,250.86 > volume #2 level 0.005 > surface dust #1-15 size 20 > save > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_1.jpg > close > open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 95 messages similar to the above omitted Chain information for c6_job26_Q2-coot-44.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available V | No description available W | 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 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 z | No description available > open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-35.pdb Chain information for c34_job27_ILS-coot-35.pdb #2 --- Chain | Description 0 | No description available 2 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available U | No description available W | No description available Y | 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 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 > open /Users/lijuanyin/project/prp43/deposit/published/5y88-ILS.cif- > coot-0.pdb Chain information for 5y88-ILS.cif-coot-0.pdb #3 --- Chain | Description 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 a | No description available b i | No description available c j | No description available d k | No description available e l | No description available f m | No description available g | No description available h | 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 x | No description available > volume #2-10 step 1 level 0.0045 No volumes specified > surface dust #1-15 size 20 No surfaces specified > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U lime > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 dark khaki > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1-10 silver > color #1-2/z tomato > color #1-2/1 forest green > color #1-2/5 /A:1898-3000 hot pink > color #1-2/2 lime > color #1-2/6 blue > color #1-2/8 red > color #2/U cyan > color #2/X green > color #2/x cyan > color #1-2/Cb dodger blue > color #1-2/CY dark red > hide #1-2 target a > show #1-2 target r > hide #1/CM target r > show #1-2/2-8 target a > nucleotides #1-2/2-8 ladder > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > view matrix camera > 0.10947,0.0052583,0.99397,808.15,-0.64091,0.76472,0.066542,251.91,-0.75977,-0.64433,0.087084,260.79 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #1-3 target a > show #1-3 target r > hide #!1 models > hide #!2 models > show #!2 models > hide #!3 models > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U lime > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 dark khaki > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1-10 silver > color #1-2/z tomato > color #1-2/1 forest green > color #1-2/5 /A:1898-3000 #3/B /A:1840-2100 hot pink > color #1-2/2 #3/F lime > color #1-2/6 #3/D blue > color #1-2/8 red > color #2/U cyan > color #2/X green > color #2/x cyan > color #1-2/Cb #3/U dodger blue > color #1-2/CY 33/V dark red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > hide #1-3 target a > show #1-3 target r > hide #1/CM target r > show #1-2/2-8 #3/B /D /F target a > nucleotides #1-2/2-8 #3/B /D /F ladder > color #1-2/CY #3/V dark red > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > view matrix camera > 0.10947,0.0052583,0.99397,808.15,-0.64091,0.76472,0.066542,251.91,-0.75977,-0.64433,0.087084,260.79 > hide #1.1 models > hide #2.1 models > hide #3.1 models > hide #!3 models > show #!3 models > hide #!1 models > save /Users/lijuanyin/project/prp43/figure_new/figure_s4/5y88_view1.jpg > close > open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-43.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-43.pdb --- warnings | Duplicate atom serial number found: 74678 Duplicate atom serial number found: 74679 Duplicate atom serial number found: 74680 Duplicate atom serial number found: 74681 Duplicate atom serial number found: 74682 2401 messages similar to the above omitted Chain information for c6_job26_Q2-coot-43.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available V | No description available W | No description available Y | No description available Z | No description available a | No 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similar to the above omitted Chain information for c34_job27_ILS-coot-34.pdb #2 --- Chain | Description 0 | No description available 2 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available U | No description available W | No description available Y | No description available a | No description available b | No description available c | No description available d | No description 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save /Users/lijuanyin/project/prp43/figure_new/figure_s4/ils_ntr_view2.jpg > close > open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 95 messages similar to the above omitted Chain information for c6_job26_Q2-coot-44.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available D | No description available E | No description available F | No 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#!3 models > close > open > /Users/lijuanyin/project/prp43/deposit/q1_tfip11/c34_job28_Q1-coot-48.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q1_tfip11/c34_job28_Q1-coot-48.pdb --- warnings | Duplicate atom serial number found: 4205 Duplicate atom serial number found: 4206 Duplicate atom serial number found: 4207 Duplicate atom serial number found: 4208 Duplicate atom serial number found: 4209 993 messages similar to the above omitted Chain information for c34_job28_Q1-coot-48.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CV | No description available CY | No description available Cb | No description available Ck | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available V | No description available W | No description available Y | No description available Z | No description available j | No description available k | No description available l | No description available m | 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 z | No description available > open /Users/lijuanyin/project/prp43/deposit/q1_tfip11/run_class001.mrc Opened run_class001.mrc as #2, grid size 160,160,160, pixel 2.8, shown at level 0.041, step 1, values float32 > volume #2-10 step 1 level 0.005 > surface dust #1-15 size 20 > set 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newMap true > volume zone #2 nearAtoms #1/Cb /Ck /CY range 6 newMap true Opened run_class001.mrc zone as #3, grid size 160,160,160, pixel 2.8, shown at step 1, values float32 > close #3 > volume zone #2 nearAtoms #1/Cb /Ck range 6 newMap true Opened run_class001.mrc zone as #3, grid size 160,160,160, pixel 2.8, shown at step 1, values float32 > volume #3 level 0.02527 > hide #!1 models > show #!1 models > surface dust #1-15 size 10 > color #3 silver > hide #1 target a > show #1/Cb target r > transparency #3 50 > show #1/Cb /Ck target r > color #1/CY /Ck dark red > hide cartoons > show #1/Cb target r > volume #3 level 0.03158 > volume #3 level 0.03103 > volume #3 level 0.03 > view matrix view matrix camera 0.51743,-0.042028,-0.8547,-2.7971,0.46455,-0.82501,0.3218,384.43,-0.71866,-0.56356,-0.40736,169.94 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0 > graphics silhouettes false > graphics silhouettes true > save /Users/lijuanyin/project/prp43/figure/figure_s3/TFIP11_local_view1.jpg > save > /Users/lijuanyin/project/prp43/figure_new/figure_s3/TFIP11_local_view1.jpg > close > open /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-38.pdb No such file/path: /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-38.pdb > open /Users/lijuanyin/project/prp43/deposit/q1/run_class001.mrc Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.932, shown at level 0.00702, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q1/multi/multi_ctf_c34_job28_dhx_high.mrc Opened multi_ctf_c34_job28_dhx_high.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00169, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_dhx_2/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #3, grid size 480,480,480, pixel 0.932, shown at level 0.00258, step 2, values float32 > volume #2-10 step 1 level 0.005 > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc /R pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U lime > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 dark khaki > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > volume zone #3 nearAtoms #1/CY:344-367 range 2 newMap true no atoms specified for zone > hide #1 target r > show #1/CY:344-367 target r > show #1/CY:344-367 target a > surface dust #1-15 size 10 > color #5 silver > transparency #5 50 > color #1 byhetero > close > open /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-39.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-39.pdb --- warnings | Duplicate atom serial number found: 4205 Duplicate atom serial number found: 4206 Duplicate atom serial number found: 4207 Duplicate atom serial number found: 4208 Duplicate atom serial number found: 4209 556 messages similar to the above omitted Chain information for c34_job28_Q1-coot-39.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available V | No description available W | No description available Y | No description available Z | No description available j | No description available k | No description available l | No description available m | 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 z | No description available > open /Users/lijuanyin/project/prp43/deposit/q1/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00702, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q1/multi/multi_ctf_c34_job28_dhx_high.mrc Opened multi_ctf_c34_job28_dhx_high.mrc as #3, grid size 480,480,480, pixel 0.932, shown at level 0.00169, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_dhx_2/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #4, grid size 480,480,480, pixel 0.932, shown at level 0.00258, step 2, values float32 > volume #2-10 step 1 level 0.005 > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc /R pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U lime > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 dark khaki > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > volume zone #3 nearAtoms #1/CY:344-367 range 2 newMap true Opened multi_ctf_c34_job28_dhx_high.mrc zone as #5, grid size 480,480,480, pixel 0.932, shown at step 1, values float32 > hide #1 target r > show #1/CY:344-367 target r > show #1/CY:344-367 target a > surface dust #1-15 size 10 > color #5 silver > transparency #5 50 > color #1 byhetero > hide #1 target a > show #1/CY:344-367 target r > show #1/CY:344-367 target a > style stick Changed 86901 atom styles > close #5 > volume zone #4 nearAtoms #1/CY:344-367 range 2 newMap true Opened relion_locres_filtered.mrc zone as #5, grid size 480,480,480, pixel 0.932, shown at step 1, values float32 > hide #1 target a > show #1/CY:344-367 target r > show #1/CY:344-367 target a > surface dust #1-15 size 10 > color #5 silver > transparency #5 50 > color #1 byhetero > surface dust #1-15 size 10 > view matrix view matrix camera 0.11237,0.97632,-0.18486,185.03,0.47491,-0.21618,-0.85307,243.39,-0.87283,0.008072,-0.48795,215.23 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > 0.11237,0.97632,-0.18486,185.03,0.47491,-0.21618,-0.85307,243.39,-0.87283,0.008072,-0.48795,215.23 > save > /Users/lijuanyin/project/prp43/figure_new/figure_s3/gcfc2_detail_view1.jpg > show cartoons > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_0.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_0.cif #6 --- Chain | Description A | . B | . C | . > close > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_0.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_0.cif #1 --- Chain | Description A | . B | . C | . > close > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_0.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_0.cif #1 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_1.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_1.cif #2 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_2.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_2.cif #3 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_3.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_3.cif #4 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_4.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_4.cif #5 --- Chain | Description A | . B | . C | . > mmaker #2-6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_1.cif, chain A (#2), sequence alignment score = 4374.2 RMSD between 352 pruned atom pairs is 1.195 angstroms; (across all 837 pairs: 28.901) Matchmaker fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#3), sequence alignment score = 4365.2 RMSD between 256 pruned atom pairs is 0.946 angstroms; (across all 837 pairs: 37.057) Matchmaker fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_3.cif, chain A (#4), sequence alignment score = 4380.8 RMSD between 378 pruned atom pairs is 0.778 angstroms; (across all 837 pairs: 25.335) Matchmaker fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_4.cif, chain A (#5), sequence alignment score = 4350.2 RMSD between 419 pruned atom pairs is 0.966 angstroms; (across all 837 pairs: 22.010) > hide #1 models > hide #2 models > hide #4 models > hide #5 models > close > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_0.cif Chain information for fold_yeast_ntr1_ntr2_prp45_model_0.cif #1 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_1.cif Chain information for fold_yeast_ntr1_ntr2_prp45_model_1.cif #2 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_2.cif Chain information for fold_yeast_ntr1_ntr2_prp45_model_2.cif #3 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_3.cif Chain information for fold_yeast_ntr1_ntr2_prp45_model_3.cif #4 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_4.cif Chain information for fold_yeast_ntr1_ntr2_prp45_model_4.cif #5 --- Chain | Description A | . B | . C | . > mmaker #2-6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_yeast_ntr1_ntr2_prp45_model_0.cif, chain A (#1) with fold_yeast_ntr1_ntr2_prp45_model_1.cif, chain A (#2), sequence alignment score = 3569.7 RMSD between 325 pruned atom pairs is 0.726 angstroms; (across all 708 pairs: 17.705) Matchmaker fold_yeast_ntr1_ntr2_prp45_model_0.cif, chain A (#1) with fold_yeast_ntr1_ntr2_prp45_model_2.cif, chain A (#3), sequence alignment score = 3633.9 RMSD between 393 pruned atom pairs is 0.821 angstroms; (across all 708 pairs: 23.511) Matchmaker fold_yeast_ntr1_ntr2_prp45_model_0.cif, chain A (#1) with fold_yeast_ntr1_ntr2_prp45_model_3.cif, chain A (#4), sequence alignment score = 3543.3 RMSD between 320 pruned atom pairs is 0.989 angstroms; (across all 708 pairs: 28.396) Matchmaker fold_yeast_ntr1_ntr2_prp45_model_0.cif, chain A (#1) with fold_yeast_ntr1_ntr2_prp45_model_4.cif, chain A (#5), sequence alignment score = 3553.5 RMSD between 346 pruned atom pairs is 0.881 angstroms; (across all 708 pairs: 39.832) > hide #1 models > hide #2 models > show #2 models > hide #2 models > hide #4 models > hide #5 models > show #2 models > hide #3 models > close > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_0.cif Chain information for fold_tfip11_gcfc2_snw1_3_model_0.cif #1 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_1.cif Chain information for fold_tfip11_gcfc2_snw1_3_model_1.cif #2 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_2.cif Chain information for fold_tfip11_gcfc2_snw1_3_model_2.cif #3 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_3.cif Chain information for fold_tfip11_gcfc2_snw1_3_model_3.cif #4 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_4.cif Chain information for fold_tfip11_gcfc2_snw1_3_model_4.cif #5 --- Chain | Description A | . B | . C | . > mmaker #2-6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_tfip11_gcfc2_snw1_3_model_1.cif, chain A (#2), sequence alignment score = 4939.4 RMSD between 455 pruned atom pairs is 0.909 angstroms; (across all 975 pairs: 45.021) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_tfip11_gcfc2_snw1_3_model_2.cif, chain A (#3), sequence alignment score = 4890.2 RMSD between 402 pruned atom pairs is 0.781 angstroms; (across all 975 pairs: 41.499) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_tfip11_gcfc2_snw1_3_model_3.cif, chain A (#4), sequence alignment score = 4577.6 RMSD between 232 pruned atom pairs is 0.736 angstroms; (across all 975 pairs: 37.629) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_tfip11_gcfc2_snw1_3_model_4.cif, chain A (#5), sequence alignment score = 4380.8 RMSD between 364 pruned atom pairs is 0.992 angstroms; (across all 975 pairs: 37.404) > hide #2 models > hide #3 models > hide #4 models > hide #5 models > close > open > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_tfip11_gcfc2_snw1_3_model_0.cif Chain information for fold_tfip11_gcfc2_snw1_3_model_0.cif #1 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_yeast_ntr1_ntr2_prp45_model_1.cif Chain information for fold_yeast_ntr1_ntr2_prp45_model_1.cif #2 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_human_ntr1_gcfc2_snw1_model_2.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_2.cif #3 --- Chain | Description A | . B | . C | . > surface dust #1-15 size 20 No surfaces specified > set bgColor white > windowsize 800 800 > color #1-3/B dark red > color #1-3/A dodger blue > color #1-3/C dark violet > mmaker #2-3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_yeast_ntr1_ntr2_prp45_model_1.cif, chain A (#2), sequence alignment score = 570.3 RMSD between 80 pruned atom pairs is 1.337 angstroms; (across all 639 pairs: 40.062) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#3), sequence alignment score = 1102.1 RMSD between 104 pruned atom pairs is 1.313 angstroms; (across all 779 pairs: 50.129) > mmaker #2-3/A to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_yeast_ntr1_ntr2_prp45_model_1.cif, chain A (#2), sequence alignment score = 570.3 RMSD between 80 pruned atom pairs is 1.337 angstroms; (across all 639 pairs: 40.062) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#3), sequence alignment score = 1102.1 RMSD between 104 pruned atom pairs is 1.313 angstroms; (across all 779 pairs: 50.129) > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_0.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_0.cif #4 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_1.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_1.cif #5 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_2.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_2.cif #6 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_3.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_3.cif #7 --- Chain | Description A | . B | . C | . > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_4.cif Chain information for fold_human_ntr1_gcfc2_snw1_model_4.cif #8 --- Chain | Description A | . B | . C | . > mmaker #2-10/A to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_yeast_ntr1_ntr2_prp45_model_1.cif, chain A (#2), sequence alignment score = 570.3 RMSD between 80 pruned atom pairs is 1.337 angstroms; (across all 639 pairs: 40.062) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#3), sequence alignment score = 1102.1 RMSD between 104 pruned atom pairs is 1.313 angstroms; (across all 779 pairs: 50.129) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#4), sequence alignment score = 1106.6 RMSD between 105 pruned atom pairs is 1.289 angstroms; (across all 789 pairs: 44.972) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_1.cif, chain A (#5), sequence alignment score = 1126.2 RMSD between 87 pruned atom pairs is 1.087 angstroms; (across all 789 pairs: 40.149) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#6), sequence alignment score = 1102.1 RMSD between 104 pruned atom pairs is 1.313 angstroms; (across all 779 pairs: 50.129) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_3.cif, chain A (#7), sequence alignment score = 1109.6 RMSD between 98 pruned atom pairs is 1.385 angstroms; (across all 791 pairs: 41.636) Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with fold_human_ntr1_gcfc2_snw1_model_4.cif, chain A (#8), sequence alignment score = 1149.2 RMSD between 96 pruned atom pairs is 1.200 angstroms; (across all 784 pairs: 43.119) > hide #2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #8 models > hide #7 models > hide #4 models > hide #5 models > hide #6 models > close #6-8 > close #4 > close #5 > show #2 models > hide #3 models > hide #2 models > show #2 models > hide #1 models > hide #2 models > show #3 models > hide #1-3 target r > show #1/A:418-860 /B /C #2/A:184-573 /B:236-321 /C:199-252 #3/A:319-725 > /B:254-340 /C:282-343 target r > show #1 models > show #2 models > hide #2 models > hide #3 models > show #2 models > hide #1 models > show #1 models > show #3 models > hide #3 models > hide #2 models > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > show #2 models > hide #1 models > show #3 models > hide #2 models > show #2 models > hide #3 models > show #1 models > hide #2 models > view matrix view matrix camera 0.22966,-0.85104,0.47222,50.764,-0.52782,-0.51655,-0.67423,-142.75,0.81772,-0.094403,-0.56783,-85.002 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.28808,0.21208,0.93383,-7.595,-0.93243,-0.28427,-0.22309,8.1887,0.21815,-0.93499,0.27964,10.063,#3,0.14178,0.89982,-0.41257,27.396,-0.32177,0.43604,0.84044,6.8166,0.93614,0.013594,0.35136,-30.218 > save > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/ct.jpg > show #2 models > hide #1 models > save > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/yeast.jpg > show #3 models > hide #2 models > save > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/human.jpg > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_2024_12_13_14_46/fold_2024_12_13_14_46_model_0.cif Chain information for fold_2024_12_13_14_46_model_0.cif #4 --- Chain | Description A | . B | . C | . D | . E | . > hide #3 models > show #4 cartoons > hide #4 atoms > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_0.cif Chain information for fold_syf1_2_ccdc12_model_0.cif #5 --- Chain | Description A | . B | . C | . > hide #4 models > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_1.cif Chain information for fold_syf1_2_ccdc12_model_1.cif #6 --- Chain | Description A | . B | . C | . > hide #5 models > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_2.cif Chain information for fold_syf1_2_ccdc12_model_2.cif #7 --- Chain | Description A | . B | . C | . > hide #6 models > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_3.cif Chain information for fold_syf1_2_ccdc12_model_3.cif #8 --- Chain | Description A | . B | . C | . > hide #7 models > open > /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_4.cif Chain information for fold_syf1_2_ccdc12_model_4.cif #9 --- Chain | Description A | . B | . C | . > hide #8 models > close > open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 95 messages similar to the above omitted Chain information for c34_job27_ILS-coot-41.pdb #1 --- Chain | Description 0 | No description available 2 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ci | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available U | No description available W | No description available Y | 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 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 > open /Users/lijuanyin/project/prp43/deposit/ils/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00799, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_body_high.mrc Opened multi_ctf_c34_job27_body_high.mrc as #3, grid size 480,480,480, pixel 0.932, shown at level 0.0045, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_bottom_high.mrc Opened multi_ctf_c34_job27_bottom_high.mrc as #4, grid size 480,480,480, pixel 0.932, shown at level 0.000984, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_ntr_high.mrc Opened multi_ctf_c34_job27_ntr_high.mrc as #5, grid size 480,480,480, pixel 0.932, shown at level 0.000544, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_prp43_high.mrc Opened multi_ctf_c34_job27_prp43_high.mrc as #6, grid size 480,480,480, pixel 0.932, shown at level 0.00086, step 2, values float32 > volume #3 step 1 level 0.01 > volume #4 step 1 level 0.01 > volume #5 step 1 level 0.01 > volume #6 step 1 level 0.01 > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM deep pink > color #1/6 /CB blue > color #1/A hot pink > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 green yellow > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/Ci dark blue > color zone #2-10 near #1 distance 6 > hide #!1 models > show #!1 models > show cartoons > hide atoms > view > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > hide #!1 models > hide #1 target a > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > show #1/B /D /F /R target r > volume zone #2 nearAtoms #1/Cj range 3 newMap true no atoms specified for zone > close > open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-53.pdb Chain information for c34_job27_ILS-coot-53.pdb #1 --- Chain | Description 0 | No description available 2 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ci | No description available Cj | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available U | No description available W | No description available Y | 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 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 > open /Users/lijuanyin/project/prp43/deposit/ils/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00799, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_body_high.mrc Opened multi_ctf_c34_job27_body_high.mrc as #3, grid size 480,480,480, pixel 0.932, shown at level 0.0045, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_bottom_high.mrc Opened multi_ctf_c34_job27_bottom_high.mrc as #4, grid size 480,480,480, pixel 0.932, shown at level 0.000984, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_ntr_high.mrc Opened multi_ctf_c34_job27_ntr_high.mrc as #5, grid size 480,480,480, pixel 0.932, shown at level 0.000544, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_prp43_high.mrc Opened multi_ctf_c34_job27_prp43_high.mrc as #6, grid size 480,480,480, pixel 0.932, shown at level 0.00086, step 2, values float32 > volume #3 step 1 level 0.01 > volume #4 step 1 level 0.01 > volume #5 step 1 level 0.01 > volume #6 step 1 level 0.01 > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM deep pink > color #1/6 /CB blue > color #1/A hot pink > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 green yellow > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/Ci dark blue > color zone #2-10 near #1 distance 6 > hide #1 target a > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > show #1/B /D /F /R target r > volume zone #2 nearAtoms #1/Cj range 3 newMap true Opened run_class001.mrc zone as #7, grid size 480,480,480, pixel 0.932, shown at step 1, values float32 > show #1/B /D /F /R /I target r > volume #7 level 0.005292 > volume #7 level 0.005 > volume #7 step 1 > volume #7 level 0.005606 > surface dust #1-15 size 20 > color #7 silver > color #7 blue > open > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_syf1_2_ccdc12_model_2.cif No such file/path: /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_syf1_2_ccdc12_model_2.cif > mmaker #8/A to #1/I No molecules/chains to match specified > open > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_4/fold_syf1_2_ccdc12_model_2.cif Chain information for fold_syf1_2_ccdc12_model_2.cif #8 --- Chain | Description A | . B | . C | . > mmaker #8/A to #1/I 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 c34_job27_ILS-coot-53.pdb, chain I (#1) with fold_syf1_2_ccdc12_model_2.cif, chain A (#8), sequence alignment score = 167.7 RMSD between 6 pruned atom pairs is 1.389 angstroms; (across all 208 pairs: 22.859) > mmaker #8/C to #1/I 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 c34_job27_ILS-coot-53.pdb, chain I (#1) with fold_syf1_2_ccdc12_model_2.cif, chain C (#8), sequence alignment score = 3787.8 RMSD between 322 pruned atom pairs is 1.005 angstroms; (across all 738 pairs: 8.963) > color #8/C light green > color #8/A deep sky blue > color #8/B plum > hide cartoons > show #1/B /F /R /I target r > show #8 target r > color #8/C light green > color #8/A deep sky blue > color #8/B plum > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > ui tool show ""Side View"" > view matrix view matrix camera 0.87577,-0.47201,0.10115,188.83,-0.0021702,0.2057,0.97861,296.73,-0.48273,-0.85726,0.17912,178.61 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.81114,0.20413,0.54807,191.94,0.54382,0.081561,-0.83523,210.08,-0.2152,0.97554,-0.044853,157.4 > lighting full > view matrix view matrix camera 0.87577,-0.47201,0.10115,188.83,-0.0021702,0.2057,0.97861,296.73,-0.48273,-0.85726,0.17912,178.61 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.81114,0.20413,0.54807,191.94,0.54382,0.081561,-0.83523,210.08,-0.2152,0.97554,-0.044853,157.4 > hide #8 models > save > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_4/unknown_ils.jpg > show #8 models > hide #!7 models > hide #!1 models > save > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_4/ccdc12_ils.jpg > show #!1 models > open > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_5/cryosparc_P1_J375_004_volume_map.mrc Opened cryosparc_P1_J375_004_volume_map.mrc as #9, grid size 480,480,480, pixel 0.932, shown at level 0.121, step 2, values float32 > close > open > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_5/cryosparc_P1_J375_004_volume_map.mrc Opened cryosparc_P1_J375_004_volume_map.mrc as #1, grid size 480,480,480, pixel 0.932, shown at level 0.121, step 2, values float32 > volume #1 step 1 > volume #1 level 0.1 > open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-53.pdb Chain information for c34_job27_ILS-coot-53.pdb #2 --- Chain | Description 0 | No description available 2 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ci | No description available Cj | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available U | No description available W | No description available Y | 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 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 > hide #!1 models > show #!1 models > close > open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-53.pdb Chain information for c34_job27_ILS-coot-53.pdb #1 --- Chain | Description 0 | No description available 2 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ci | No description available Cj | No description available D | No description available E | No description available F | 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 P | No description available R | No description available S | No description available T | No description available U | No description available W | No description available Y | 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 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 > open > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_5/cryosparc_P1_J375_004_volume_map.mrc Opened cryosparc_P1_J375_004_volume_map.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.121, step 2, values float32 > color #1 #3-10 silver > color #1/I /Y /CV light green > volume #2 level 0.1 > volume #2 step 1 > hide #!1 models > color zone #2-10 near #1 distance 6 > color zone #2-10 near #1 distance 12 > surface dust #1-15 size 20 > save > /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_5/cryoSPARC.jpg ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class001.mrc Opened run_it200_class001.mrc as #1, grid size 160,160,160, pixel 2.8, shown at level 6.84e-07, step 1, values float32 > open > /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class002.mrc Opened run_it200_class002.mrc as #2, grid size 160,160,160, pixel 2.8, shown at level 1.3e-05, step 1, values float32 > open > /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class003.mrc Opened run_it200_class003.mrc as #3, grid size 160,160,160, pixel 2.8, shown at level 1.06e-05, step 1, values float32 > open > /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class004.mrc Opened run_it200_class004.mrc as #4, grid size 160,160,160, pixel 2.8, shown at level 7.99e-06, step 1, values float32 > open > /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class005.mrc Opened run_it200_class005.mrc as #5, grid size 160,160,160, pixel 2.8, shown at level 1.83e-06, step 1, values float32 > open > /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class006.mrc Opened run_it200_class006.mrc as #6, grid size 160,160,160, pixel 2.8, shown at level 1.47e-05, step 1, values float32 OpenGL version: 4.1 ATI-6.1.13 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2,3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 64 GB System Firmware Version: 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0) OS Loader Version: 582~1023 Software: System Software Overview: System Version: macOS 15.0 (24A335) Kernel Version: Darwin 24.0.0 Time since boot: 17天5小时17分钟 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-020 Option ROM Version: 113-D32206U1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: C34H89x: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 50.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: H1AK500000 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: Apple USB-C Digital AV Adapter Adapter Firmware Version: 2,35 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-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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect new normal Unassigned