id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20464 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000302013000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000301007000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017f63b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 948 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017e62f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017d623000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017c617000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017b60b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017a5ff000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000001795f3000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000001785e7000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000001775db000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00000001ed7a7100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, PIL._imaging, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, 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, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, kiwisolver._cext, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 121) {""app_name"":""ChimeraX"",""timestamp"":""2026-06-05 09:49:21.00 +0200"",""app_version"":""1.11.1"",""slice_uuid"":""c20e09a8-923e-3fb3-856b-3e765bcb267b"",""build_version"":""1.11.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 26.3.1 (25D2128)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""773F4277-A842-4A88-8C3A-DB26D23541F0""} { ""uptime"" : 1500000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,2"", ""coalitionID"" : 516682, 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Bytes after previous region: 7871042113 Bytes before following region: 704638400 REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL Stack 32a594000-32ad98000 [ 8208K] rw-\/rwx SM=PRV thread 49 ---> GAP OF 0x1ff268000 BYTES MALLOC_SMALL 52a000000-52a400000 [ 4096K] rw-\/rwx SM=PRV "", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000500001240"",""rawCodes"":[1,21474841152],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000500001240""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":56719}, ""vmregioninfo"" : ""0x500001240 is not in any region. 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[ ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/pz/Downloads/cryosparc_P151_J169_014_volume_map_sharp.mrc Opened cryosparc_P151_J169_014_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.68, shown at level 0.032, step 2, values float32 > volume #1 step 1 > ui tool show Toolbar > lighting soft > surface dust #1 size 6.8 > volume #1 level 0.06324 > volume #1 level 0.05789 > volume #1 level 0.07305 > volume #1 level 0.057 > volume #1 level 0.06652 > volume #1 level 0.06133 > close #1 > open ""/Users/pz/Documents/structures/model building/MsbA R497A van > open/MsbA-R497A-van-open-2.78A_J1407.mrc"" Opened MsbA-R497A-van-open-2.78A_J1407.mrc as #1, grid size 400,400,400, pixel 0.68, shown at level 0.0141, step 2, values float32 > open ""/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA > R497A van open 27.04 A404.pdb"" Chain information for MsbA R497A van open 27.04 A404.pdb #2 --- Chain | Description A B | No description available > fitmap #2 inMap #1 Fit molecule MsbA R497A van open 27.04 A404.pdb (#2) to map MsbA-R497A-van- open-2.78A_J1407.mrc (#1) using 18118 atoms average map value = 0.06259, steps = 44 shifted from previous position = 0.0281 rotated from previous position = 0.0196 degrees atoms outside contour = 4275, contour level = 0.014051 Position of MsbA R497A van open 27.04 A404.pdb (#2) relative to MsbA-R497A-van-open-2.78A_J1407.mrc (#1) coordinates: Matrix rotation and translation 0.99999995 -0.00028328 0.00015275 0.02138794 0.00028326 0.99999995 0.00011788 -0.04615004 -0.00015279 -0.00011784 0.99999998 0.00954088 Axis -0.34386366 0.44572376 0.82649145 Axis point 131.39825309 51.15161870 0.00000000 Rotation angle (degrees) 0.01963769 Shift along axis -0.02003925 > surface dust #1 size 6.8 > volume #1 step 1 > volume #1 level 0.04068 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for MsbA R497A van open 27.04 A404.pdb #2.2 --- Chain | Description A B | No description available > clipper associate #1 toModel #2 Opened MsbA-R497A-van-open-2.78A_J1407.mrc as #2.1.1.1, grid size 400,400,400, pixel 0.68, shown at step 1, values float32 > select clear > select A:404 Expected an objects specifier or a keyword > select A?:404 Expected an objects specifier or a keyword > select A/:404 Expected an objects specifier or a keyword > select /A:404 7 atoms, 6 bonds, 1 residue, 1 model selected > view sel > isolde stepto /A:404 > isolde stepto next > volume #2.1.1.1 level 0.07958 > isolde stepto next > volume #2.1.1.1 level 0.08056 > volume #2.1.1.1 level 0.06596 > volume #2.1.1.1 level 0.05526 > isolde stepto next > isolde stepto prev > isolde sim stop No simulation is currently running! > isolde sim start /A:403 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start #!2.2/A:417 ISOLDE: started sim > select clear > volume #2.1.1.1 level 0.05644 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.0483 > volume #2.1.1.1 level 0.032 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto /A:442 > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02679 > isolde stepto next > volume #2.1.1.1 level 0.0372 > isolde stepto next > volume #2.1.1.1 level 0.02011 > volume #2.1.1.1 level 0.0417 > isolde stepto next > isolde stepto prev > isolde sim start /A:457 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start /A:465 ISOLDE: started sim > volume #2.1.1.1 level 0.02389 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > isolde stepto next > volume #2.1.1.1 level 0.04643 > isolde stepto next > volume #2.1.1.1 level 0.03405 > isolde sim start /A:467 ISOLDE: started sim > volume #2.1.1.1 level 0.03048 > volume #2.1.1.1 level 0.04592 > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.06017 > isolde stepto next > volume #2.1.1.1 level 0.06104 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.03428 > volume #2.1.1.1 level 0.05609 > isolde stepto next > volume #2.1.1.1 level 0.03685 > volume #2.1.1.1 level 0.05074 > isolde stepto next > volume #2.1.1.1 level 0.03477 > isolde stepto next > isolde stepto prev > isolde sim start /A:517 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > isolde sim start /A:529 ISOLDE: started sim > volume #2.1.1.1 level 0.01476 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #2.1.1.1 level 0.03214 > isolde stepto next > volume #2.1.1.1 level 0.0415 > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02462 > volume #2.1.1.1 level 0.03447 > isolde stepto next > volume #2.1.1.1 level 0.02166 > volume #2.1.1.1 level 0.03447 > isolde stepto next > volume #2.1.1.1 level 0.01901 > isolde sim start #!2.2/A:553 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde sim start /A:553 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > volume #2.1.1.1 level 0.04278 > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.04024 > isolde stepto next > volume #2.1.1.1 level 0.0246 > isolde sim start #!2.2/A:567 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.02969 > isolde stepto next > volume #2.1.1.1 level 0.02053 > volume #2.1.1.1 level 0.02786 > isolde stepto next > volume #2.1.1.1 level 0.01259 > volume #2.1.1.1 level 0.02932 > isolde stepto next > volume #2.1.1.1 level 0.01631 > isolde sim start /B:5 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #2.1.1.1 level 0.03365 > isolde stepto next > volume #2.1.1.1 level 0.03043 > volume #2.1.1.1 level 0.03607 > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02665 > isolde sim start /B:24 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #2.1.1.1 level 0.04653 > isolde stepto next > isolde sim start /B:41 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.03802 > isolde stepto next > volume #2.1.1.1 level 0.02146 > volume #2.1.1.1 level 0.0392 > isolde stepto next > volume #2.1.1.1 level 0.018 > volume #2.1.1.1 level 0.03284 > isolde stepto next > volume #2.1.1.1 level 0.03186 > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.01809 > volume #2.1.1.1 level 0.02547 > isolde stepto next > isolde sim start #!2.2/B:60 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02173 > volume #2.1.1.1 level 0.0292 > isolde stepto next > volume #2.1.1.1 level 0.02327 > isolde stepto next > volume #2.1.1.1 level 0.03082 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start /B:118 ISOLDE: started sim > volume #2.1.1.1 level 0.01993 > volume #2.1.1.1 level 0.02114 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.04014 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start #!2.2/B:131 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.0258 > volume #2.1.1.1 level 0.00941 > volume #2.1.1.1 level 0.03297 > isolde stepto next > isolde sim start /B:140 ISOLDE: started sim > isolde pepflip #!2.2/B:140 > isolde stepto next > isolde pepflip /B:141 > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /A:140 11 atoms, 10 bonds, 1 residue, 1 model selected > view sel > select clear > select /B:140 11 atoms, 10 bonds, 1 residue, 1 model selected > view sel > isolde sim start #!2.2/B:140 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:140 ISOLDE: started sim > isolde stepto prev > isolde pepflip /B:139 > isolde stepto next > isolde pepflip /B:140 > isolde stepto next > isolde pepflip /B:141 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde sim start /B:140 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:140 ISOLDE: started sim > select clear > isolde stepto next > isolde pepflip /B:141 > isolde stepto next > isolde pepflip /B:142 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde sim start #!2.2/B:140 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start #!2.2/B:147 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > volume #2.1.1.1 level 0.03799 > isolde stepto next > volume #2.1.1.1 level 0.02989 > volume #2.1.1.1 level 0.04314 > isolde stepto next > isolde stepto prev > volume #2.1.1.1 level 0.02557 > volume #2.1.1.1 level 0.01717 > volume #2.1.1.1 level 0.04009 > isolde stepto next > volume #2.1.1.1 level 0.02389 > isolde stepto next > volume #2.1.1.1 level 0.03525 > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.03643 > isolde stepto next > volume #2.1.1.1 level 0.02829 > volume #2.1.1.1 level 0.03469 > isolde stepto next > volume #2.1.1.1 level 0.02694 > isolde stepto next > volume #2.1.1.1 level 0.03451 > isolde stepto next > volume #2.1.1.1 level 0.02818 > isolde stepto next > volume #2.1.1.1 level 0.0336 > isolde sim start /B:164 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start #!2.2/B:168 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.03407 > isolde sim start #!2.2/B:169 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save ""/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA > R497A van open 1.06 B169.pdb"" relModel #2.1.1.1 > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02581 > volume #2.1.1.1 level 0.03252 > isolde stepto next > isolde sim start #!2.2/B:180 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.03336 > isolde sim start #!2.2/B:183 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #2.1.1.1 level 0.04343 > isolde stepto next > volume #2.1.1.1 level 0.03129 > volume #2.1.1.1 level 0.01915 > isolde sim start /B:187 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.03028 > isolde stepto next > volume #2.1.1.1 level 0.02453 > isolde stepto next > isolde stepto prev > isolde sim start /B:279 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.01878 > volume #2.1.1.1 level 0.02289 > isolde stepto next > volume #2.1.1.1 level 0.0203 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start /B:299 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.003304 > volume #2.1.1.1 level 0.01059 > volume #2.1.1.1 level 0.02759 > isolde stepto next > volume #2.1.1.1 level 0.03304 > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.04049 > isolde stepto next > volume #2.1.1.1 level 0.01465 > volume #2.1.1.1 level 0.03016 > isolde stepto next > isolde stepto /B:340 > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.0199 > volume #2.1.1.1 level 0.03669 > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02422 > volume #2.1.1.1 level 0.03573 > isolde stepto next > volume #2.1.1.1 level 0.02623 > volume #2.1.1.1 level 0.03454 > isolde stepto next > volume #2.1.1.1 level 0.03335 > isolde sim start #!2.2/B:378 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start /B:403 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start #!2.2/B:424 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.03573 > isolde stepto prev > save ""/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA > R497A van open 1.06 B422.pdb"" relModel #2.1.1.1 > isolde stepto prev > isolde stepto next > isolde sim start #!2.2/B:423 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.02472 > isolde sim start /B:425 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.0345 > isolde stepto prev > isolde stepto next > isolde sim start #!2.2/B:424 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.03259 > isolde stepto next > isolde sim start #!2.2/B:442 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02399 > volume #2.1.1.1 level 0.03641 > isolde stepto next > volume #2.1.1.1 level 0.01984 > volume #2.1.1.1 level 0.01302 > isolde sim start /B:448 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto prev > volume #2.1.1.1 level 0.03205 > isolde stepto next > volume #2.1.1.1 level 0.0223 > isolde sim start /B:448 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start /B:452 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:449-455 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02964 > isolde stepto next > volume #2.1.1.1 level 0.02457 > volume #2.1.1.1 level 0.03471 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > volume #2.1.1.1 level 0.04695 > isolde stepto next > volume #2.1.1.1 level 0.02345 > isolde stepto next > volume #2.1.1.1 level 0.03438 > isolde stepto next > isolde stepto prev > isolde sim start /B:506 ISOLDE: started sim > isolde sim pause > isolde sim resume > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start /B:504 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start /B:514 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > volume #2.1.1.1 level 0.02395 > isolde stepto next > isolde stepto prev > isolde sim start /B:525 ISOLDE: started sim > isolde stepto next > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.01788 > volume #2.1.1.1 level 0.03522 > isolde stepto next > volume #2.1.1.1 level 0.01988 > isolde sim start #!2.2/B:544 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start /B:553 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:553 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde sim start /B:551 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde stepto next > isolde sim start /B:551 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.02482 > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde stepto next > volume #2.1.1.1 level 0.03325 > isolde stepto next > isolde stepto prev > save ""/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA > R497A van open checked.pdb"" relModel #2.1.1.1 > isolde sim start #!2.2/A:477 ISOLDE: started sim > isolde cisflip /A:477 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:477 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:477 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > ui tool show ""Ramachandran Plot"" > isolde sim start /B:337 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto /B:337 > volume #2.1.1.1 level 0.01816 > volume #2.1.1.1 level 0.03148 > isolde sim start /B:337 ISOLDE: started sim > isolde pepflip /B:337 > isolde stepto next > isolde pepflip /B:338 > isolde stepto prev > isolde pepflip /B:337 > isolde stepto prev > isolde pepflip /B:336 > isolde stepto next > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:337 ISOLDE: started sim > select clear > isolde stepto prev > volume #2.1.1.1 level 0.01558 > isolde stepto next > volume #2.1.1.1 level 0.03392 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:354 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:354 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:441 ISOLDE: started sim > isolde stepto next > isolde pepflip /A:442 > isolde stepto prev > isolde pepflip /A:441 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde pepflip /A:440 > isolde stepto prev > isolde stepto next > isolde pepflip /A:441 > isolde stepto prev > isolde pepflip /A:440 > isolde stepto prev > isolde pepflip /A:439 > isolde stepto prev > isolde pepflip /A:438 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde pepflip /A:439 > isolde stepto next > isolde pepflip /A:440 > isolde stepto next > isolde cisflip /A:441 > isolde pepflip /A:441 > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde pepflip /A:438 > isolde stepto prev > isolde pepflip /A:436 > isolde stepto next > isolde pepflip /A:437 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:437 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:514 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:140 ISOLDE: started sim > isolde pepflip /B:140 > isolde stepto prev > isolde stepto next > isolde pepflip /B:141 > isolde stepto prev > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:240 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:551 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:551 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/B:224 ISOLDE: started sim > volume #2.1.1.1 level 0.02058 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:424 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:424 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:424 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/A:501 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:501 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto /A:441 > isolde sim start /A:441 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:441 ISOLDE: started sim > isolde stepto #!2.2/A:441 > isolde pepflip #!2.2/A:441 > isolde stepto next > isolde stepto prev > isolde pepflip /A:439 > isolde stepto next > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select B/:441 Expected an objects specifier or a keyword > select /B:441 24 atoms, 23 bonds, 1 residue, 1 model selected > select view Expected an objects specifier or a keyword > select view Expected an objects specifier or a keyword > view sel > select clear > isolde sim start #!2.2/A:441 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /B:439 21 atoms, 21 bonds, 1 residue, 1 model selected > view sel > isolde sim start /A:542 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:542 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/B:542 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim Multiple residues selected! Going to the first... > isolde sim start /A:442 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:452 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde sim start #!2.2/A:544 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:74 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/A:77 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:535 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:544 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:224 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:443 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:542 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #2.1.1.1 level 0.02634 > isolde sim start /B:164 ISOLDE: started sim > isolde pepflip /B:164 > isolde stepto next > isolde pepflip /B:165 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto prev > select ~sel & ##selected 18107 atoms, 18240 bonds, 1151 residues, 1 model selected > save ""/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA > R497A van open 4.06.pdb"" relModel #2.1.1.1 > volume #2.1.1.1 level 0.02953 > isolde sim start /B:164 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:140 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:140 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B Alignment identifier is 1 Could not find virtual screen for QCocoaScreen(0xc3014c6c0, ""PA278CV (1)"", QRect(-2560,-566 2560x1440), dpr=1, displayId=184, ) with displayId 184 > select > /A-B:9-54,56-58,61-110,113-118,121-123,125-145,147-161,165-212,214-219,223-270,273-278,281-322,382-389,407-409,412-418,433-437,447-456,460-465,469-471,483-496,513-526,539-542,562-568,571-577 12204 atoms, 12244 bonds, 764 residues, 1 model selected > select /A-B:342-345,371-376,399-402,419-422,501-505,531-535,547-552,555-560 1298 atoms, 1284 bonds, 80 residues, 1 model selected > select /A-B:5 48 atoms, 46 bonds, 2 residues, 1 model selected > select /A-B 18118 atoms, 18250 bonds, 1152 residues, 1 model selected > select /A-B:580 42 atoms, 42 bonds, 2 residues, 1 model selected > select /A-B 18118 atoms, 18250 bonds, 1152 residues, 1 model selected > select /A-B:580 42 atoms, 42 bonds, 2 residues, 1 model selected > select /A-B 18118 atoms, 18250 bonds, 1152 residues, 1 model selected > select clear > select /A-B:580 42 atoms, 42 bonds, 2 residues, 1 model selected > select /A-B 18118 atoms, 18250 bonds, 1152 residues, 1 model selected > save ""/Users/pz/Downloads/msba sequence"" format fasta alignment 1 > select /A-B:5 48 atoms, 46 bonds, 2 residues, 1 model selected > select /A-B:5-49 1456 atoms, 1472 bonds, 90 residues, 1 model selected > isolde sim start /A:12 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/A:512 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:512,515 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save ""/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA > R497A van open 4.06.pdb"" relModel #2.1.1.1 > isolde sim start /A:509-518 ISOLDE: started sim > hbonds 1253 hydrogen bonds found > hide hbonds > display H > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:390 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:382 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:382 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/B:382 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:551 ISOLDE: started sim > select clear > volume #2.1.1.1 level 0.04054 > isolde pepflip /B:551 > isolde stepto next > isolde pepflip /B:552 > isolde stepto prev > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:542 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:219 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:390 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/B:535 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:501 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > isolde sim start /B:382 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:535 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/B:390 ISOLDE: started sim > isolde sim pause > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:421 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:219 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:479,481 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde stepto /A:337 > isolde stepto next > isolde stepto /A:338 > isolde stepto /A:480 > isolde pepflip /A:480 > isolde stepto next > isolde stepto prev > isolde pepflip #!2.2/A:479 > isolde stepto next > isolde pepflip #!2.2/A:480 > isolde stepto next > isolde pepflip /A:481 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:480 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:480 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:480 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:506 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:480 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > ui tool show ""Side View"" > isolde sim start /A:480 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:432 ISOLDE: started sim > hbonds 1253 hydrogen bonds found > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > ~display hbond > hide hbond Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide hbonds > isolde sim start /B:439,441 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:382 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:379-385 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/B:520 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:516 ISOLDE: started sim Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:516 ISOLDE: started sim Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:382 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:93 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:541 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save ""/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA > R497A van open 4.06.pdb"" relModel #2.1.1.1 > close session > open ""/Users/pz/Documents/structures/not mine/LMNG-closed.pdb"" Chain information for LMNG-closed.pdb #1 --- Chain | Description A B | No description available > open ""/Users/pz/Documents/structures/model building/MsbA R497A van > closed/MsbA-R497A-van-closed-2.79A_J1408.mrc"" Opened MsbA-R497A-van-closed-2.79A_J1408.mrc as #2, grid size 400,400,400, pixel 0.68, shown at level 0.0137, step 2, values float32 > volume #2 step 1 > surface dust #2 size 6.8 > lighting simple > lighting soft > volume #2 level 0.02632 > select add #1 9020 atoms, 9142 bonds, 19 pseudobonds, 1158 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.55027,0.83497,-0.0039043,-51.737,-0.82209,0.54095,-0.17757,187.56,-0.14615,0.10092,0.9841,15.922 > view matrix models > #1,0.51729,0.84619,0.12794,-60.648,-0.85576,0.50978,0.088352,172.13,0.0095418,-0.15519,0.98784,27.8 > view matrix models > #1,0.90797,0.41817,0.027123,-43.01,-0.41626,0.89259,0.17322,54.941,0.048224,-0.16857,0.98451,24.948 > view matrix models > #1,0.90215,0.42068,-0.095662,-28.956,-0.41659,0.9071,0.060236,65.913,0.11211,-0.01449,0.99359,-0.88221 > view matrix models > #1,0.44133,0.89083,-0.1079,-29.475,-0.88527,0.4519,0.10997,180.21,0.14673,0.046989,0.98806,-12.751 > select subtract #1 Nothing selected > hide #!1 models > volume #2 level 0.0339 > vop flip #2 Opened MsbA-R497A-van-closed-2.79A_J1408.mrc z flip as #3, grid size 400,400,400, pixel 0.68, shown at step 1, values float32 > close #2 > surface dust #3 size 6.8 > show #!1 models > select add #1 9020 atoms, 9142 bonds, 19 pseudobonds, 1158 residues, 2 models selected > view matrix models > #1,0.087609,0.98419,-0.15392,9.5708,0.99443,-0.095492,-0.044576,27.32,-0.058569,-0.14916,-0.98708,276.49 > view matrix models > #1,0.17437,0.97251,-0.1543,-0.076924,0.98402,-0.17783,-0.0088091,35.163,-0.036008,-0.1503,-0.98798,273.83 > view matrix models > #1,0.17546,0.97547,-0.13291,3.5096,0.98384,-0.17863,-0.012216,34.411,-0.035658,-0.12862,-0.99105,285.84 > view matrix models > #1,0.17546,0.97547,-0.13291,1.5688,0.98384,-0.17863,-0.012216,34.756,-0.035658,-0.12862,-0.99105,283.67 > view matrix models > #1,0.17985,0.98272,-0.043812,-10.639,0.98311,-0.1811,-0.026481,36.886,-0.033958,-0.038309,-0.99869,272.53 > view matrix models > #1,0.33235,0.94261,-0.032125,-25.721,0.943,-0.33272,-0.0066497,57.089,-0.016957,-0.028084,-0.99946,269.39 > fitmap #1 inMap #3 Fit molecule LMNG-closed.pdb (#1) to map MsbA-R497A-van-closed-2.79A_J1408.mrc z flip (#3) using 9020 atoms average map value = 0.1008, steps = 104 shifted from previous position = 3.09 rotated from previous position = 9.57 degrees atoms outside contour = 1737, contour level = 0.033898 Position of LMNG-closed.pdb (#1) relative to MsbA-R497A-van- closed-2.79A_J1408.mrc z flip (#3) coordinates: Matrix rotation and translation 0.18356215 0.98298161 0.00721784 -17.78647697 0.98137254 -0.18282840 -0.05900612 38.55300354 -0.05668231 0.01791467 -0.99823153 265.85391199 Axis 0.76910697 0.63891754 -0.01608859 Axis point 0.00000000 22.33851026 133.29861512 Rotation angle (degrees) 177.13363952 Shift along axis 6.67527321 > select subtract #1 Nothing selected > volume #3 level 0.05158 > hide #!3 models > select ::name=""AOV""::name=""MG"" 66 atoms, 58 bonds, 14 pseudobonds, 4 residues, 2 models selected > delete sel > select add #1 8954 atoms, 9084 bonds, 1154 residues, 1 model selected > hide sel atoms > select clear > show #!3 models ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 87 residues in model #1 to IUPAC-IUB standards. Chain information for LMNG-closed.pdb #1.2 --- Chain | Description A B | No description available > clipper associate #3 toModel #1 Opened MsbA-R497A-van-closed-2.79A_J1408.mrc z flip as #1.1.1.1, grid size 400,400,400, pixel 0.68, shown at step 1, values float32 > isolde stepto /A:3 3 models selected > isolde stepto next > isolde stepto prev > volume #1.1.1.1 level 0.03554 > isolde stepto next > isolde sim start /A:4 Sim termination reason: None ISOLDE: stopped sim > addh #1.2 Summary of feedback from adding hydrogens to LMNG-closed.pdb #1.2 --- notes | Termini for LMNG-closed.pdb (#1.2) chain A determined from SEQRES records Termini for LMNG-closed.pdb (#1.2) chain B determined from SEQRES records Chain-initial residues that are actual N termini: /A ASN 3, /B ASN 3 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A GLN 579, /B GLN 579 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A GLN 579 Missing OXT added to C-terminal residue /B GLN 579 1105 hydrogen bonds 9202 hydrogens added > isolde sim start /A:3-7 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:12 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:18 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:22 ISOLDE: started sim > isolde stepto next > volume #1.1.1.1 level 0.0296 > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:28 ISOLDE: started sim > select clear > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:34 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:39 ISOLDE: started sim > isolde stepto next > volume #1.1.1.1 level 0.02237 > isolde stepto next > isolde stepto prev > volume #1.1.1.1 level 0.03592 > isolde stepto next > isolde stepto prev > isolde pepflip /A:43 Unable to flip peptide bond after 50 rounds. Giving up. > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:44 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:49 ISOLDE: started sim > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:53 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > close session > open emdb:27545 Summary of feedback from opening 27545 fetched from emdb --- notes | Fetching compressed map 27545 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-27545/map/emd_27545.map.gz Fetching map header 27545 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-27545/header/emd-27545.xml Opened emdb 27545 as #1, grid size 280,280,280, pixel 1.07, shown at level 0.17, step 2, values float32, fit PDB 8dmo > open emdb:27544 Opened emdb 27544 as #2, grid size 200,200,200, pixel 1.07, shown at level 0.14, step 1, values float32, fit PDB 8dmm > close #1 > lighting soft > surface dust #2 size 10.7 > open emdb:44445 Opened emdb 44445 as #1, grid size 270,270,270, pixel 0.832, shown at level 0.04, step 2, values float32, fit PDB 9bd7 > hide #!1 models > show #!1 models > hide #!2 models > open emdb:44444 Opened emdb 44444 as #3, grid size 270,270,270, pixel 0.832, shown at level 0.04, step 2, values float32, fit PDB 9bd6 > hide #!1 models > volume #1 step 1 > volume #3 step 1 > surface dust #3 size 8.32 > volume #3 level 0.03369 > volume #3 level 0.0298 > volume #3 level 0.03175 > show #!1 models > hide #!3 models > surface dust #1 size 8.32 > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/pz/Downloads/cryosparc_P77_J1566_013_volume_map_sharp (1).mrc"" Opened cryosparc_P77_J1566_013_volume_map_sharp (1).mrc as #1, grid size 400,400,400, pixel 0.68, shown at level 0.0333, step 2, values float32 OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z15S000JKD/A Chip: Apple M2 Total Number of Cores: 8 (4 Performance and 4 Efficiency) Memory: 8 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (25D2128) Kernel Version: Darwin 25.3.0 Time since boot: 90 days, 9 hours Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.26.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ISOLDE: 1.11.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect new normal Unassigned