id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15986 The X11 connection broke chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-5.15.0-113-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007efdcc258740 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, 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._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.linalg._flinalg, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 123) ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/alphafold/Downloads/194_fit.pdb Chain information for 194_fit.pdb #1 --- Chain | Description B | No description available > open > /home/net/shared/scripts/processing_server/uploads/processing/wss205/240904_1716_run_class001_emready/run_class001_emready.mrc Opened run_class001_emready.mrc as #2, grid size 448,448,448, pixel 1.21, shown at level 0.388, step 2, values float32 > open /alphafold- > libs/otter/shared/jumbo_phage/baseplate/J1716/model_angelo/model_angelo.cif Summary of feedback from opening /alphafold- libs/otter/shared/jumbo_phage/baseplate/J1716/model_angelo/model_angelo.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for model_angelo.cif #3 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 9 | No description available A0 | No description available A1 | No description available A3 AN | No description available A5 AM An | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AK | No description available AL | No description available AQ | No description available AR BS | No description available AV | No description available AW | No description available AY | No description available Ac | No description available Ad | No description available Ae | No description available Ah | No description available Al | No description available Am | No description available Ap | No description available Aq | No description available Ar | No description available As | No description available At | No description available Ax | No description available Ay | No description available Az | No description available B | No description available B0 | No description available B5 | No description available B7 | No description available BE | No description available BG | No description available BJ | No description available BQ | No description available BR | No description available BT | No description available BU | No description available BV | No description available Bd | No description available Bg | No description available Bi | No description available Bn | No description available Bp CX | No description available Bs | No description available Bv | No descriAn error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 272, in _draw_scene draw_highlight_outline(r, highlight_drawings, color = self._highlight_color, File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1625, in draw_highlight_outline r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1927, in finish_rendering_outline r.pop_framebuffer() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 764, in pop_framebuffer fb.activate() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 2313, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) The X11 connection broke (error 1). Did the X11 server die? le C9 Ca DR | No description available CC | No description available CD | No description available CF | No description available CM | No description available CN | No description available CO | No description available CP Cs | No description available CT | No description available Cc Co | No description available Cn | No description available Cp | No description available Ct | No description available D | No description available D0 | No description available D1 | No description available D2 | No description available D3 | No description available D4 | No description available D5 | No description available D6 | No description available D7 | No description available D8 | No description available D9 | No description available DE | No description available DX | No description available Da | No description available Db | No description available Dc | No description available Dd | No description available De | No description available Df | No description available Dg | No description available Dh | No description available Di | No description available Dj | No description available Dk | No description available Dl | No description available Dm | No description available Dn | No description available Do | No description available Dp | No description available Dq | No description available Dr | No description available Ds | No description available Dt | No description available Du | No description available Dv | No description available Dw | No description available Dx | No description available Dy | No description available Dz | No description available E | No description available EA | No description available EB | No description available EC | No description available ED | No description available EE | No description available EF | No description available EG | No description available EH | No description available EI | No description available EJ | No description available EK | No description available EL | No description available EM | No description available EN | No description available EO | No description available EP | No description available EQ | No description available ER | No description available ES | No description available ET | No description available EU | No description available EV | No description available EW | No description available EX | No description available EY | No description available EZ | No description available Ea | No description available Eb | No description available Ec | No description available Ed | No description available Ee | No description available Ef | No description available Eg | No description available Eh | No description available Ei | No description available Ej | No description available Ek | No description available El | No description available Em | No description available En | No description available Eo | No description available Ep | No description available Eq | No description available Er | No description available Es | No description available Et | No description available Eu | No description available Ev | No description available I | No description available J | No description available K | No description available N | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available 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 u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > hide #3 models > show #3 models > ui mousemode right ""translate selected models"" > select #2 2 models selected > select clear > select add #3 21751 atoms, 21935 bonds, 2750 residues, 1 model selected > view matrix models #3,1,0,0,117.72,0,1,0,165.49,0,0,1,180.34 > view matrix models #3,1,0,0,170.79,0,1,0,177.03,0,0,1,176.62 > view matrix models #3,1,0,0,172.93,0,1,0,180.94,0,0,1,177.31 > fitmap sel inMap #2 Fit molecule model_angelo.cif (#3) to map run_class001_emready.mrc (#2) using 21751 atoms average map value = 6.627, steps = 80 shifted from previous position = 7.81 rotated from previous position = 0.0291 degrees atoms outside contour = 85, contour level = 0.3881 Position of model_angelo.cif (#3) relative to run_class001_emready.mrc (#2) coordinates: Matrix rotation and translation 0.99999996 -0.00020506 -0.00019871 180.20542513 0.00020514 0.99999989 0.00042043 180.10928148 0.00019862 -0.00042047 0.99999989 180.20410645 Axis -0.82725970 -0.39088368 0.40354843 Axis point 0.00000000 569497.86960935 -291798.36669057 Rotation angle (degrees) 0.02912054 Shift along axis -146.75737908 > mmaker #1 to #3/Ef 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 model_angelo.cif, chain Ef (#3) with 194_fit.pdb, chain B (#1), sequence alignment score = 93.1 RMSD between 12 pruned atom pairs is 0.931 angstroms; (across all 54 pairs: 26.522) > hide #3 models > volume #2 step 1 > volume #2 level 4.45 > volume #2 color #ffffb233 > fitmap #1 inMap #2 Fit molecule 194_fit.pdb (#1) to map run_class001_emready.mrc (#2) using 2284 atoms average map value = 3.401, steps = 176 shifted from previous position = 2.23 rotated from previous position = 10.2 degrees atoms outside contour = 1531, contour level = 4.4501 Position of 194_fit.pdb (#1) relative to run_class001_emready.mrc (#2) coordinates: Matrix rotation and translation 0.99996287 0.00574574 -0.00642282 71.04367735 -0.00574121 0.99998326 0.00072290 205.97723342 0.00642687 -0.00068600 0.99997911 113.82964563 Axis -0.08147242 -0.74305538 -0.66425217 Axis point 6546.55547341 0.00000000 8049.29374242 Rotation angle (degrees) 0.49541553 Shift along axis -234.45218106 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for 194_fit.pdb --- Chain | Description 1.2/B | No description available > isolde set simFidelityMode Lowest/Fastest ISOLDE: setting sim fidelity mode to Lowest/Fastest nonbonded_cutoff_distance = 0.900000 use_gbsa = False > isolde set simFidelityMode Lowest/Fastest ISOLDE: setting sim fidelity mode to Lowest/Fastest nonbonded_cutoff_distance = 0.900000 use_gbsa = False > addh #1 Summary of feedback from adding hydrogens to 194_fit.pdb #1.2 --- notes | Termini for 194_fit.pdb (#1.2) chain B determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: 194_fit.pdb #1.2/B ALA 3 Chain-final residues that are actual C termini: 194_fit.pdb #1.2/B PRO 147 Chain-final residues that are not actual C termini: 122 hydrogen bonds 0 hydrogens added > isolde sim start #1.2/B > clipper associate #2 toModel #1 Opened run_class001_emready.mrc as #1.1.1.1, grid size 448,448,448, pixel 1.21, shown at step 1, values float32 > isolde sim start #1.2/B ISOLDE: started sim > hide sel atoms > show sel cartoons > ui mousemode right ""isolde tug residue"" > show #3 models > select add #3 24035 atoms, 24248 bonds, 2895 residues, 3 models selected > show sel atoms > hide sel atoms > show sel cartoons > hide #3 models > show #3 models > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start #3/A,B,C,D,E,F-z,0-9,AA-Az,A0-A9,BA-Bz,B0-B9,CA- > Cz,C0-C9,DA-Dz,D0-D9,EA-Ev #1.2/B ISOLDE: started sim > hide sel atoms > show sel cartoons > ui mousemode right ""isolde tug residue"" > 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 > hide sel atoms > show sel cartoons > show sel atoms > style sel stick Changed 24035 atom styles > isolde sim start #3/A,B,C,D,E,F-z,0-9,AA-Az,A0-A9,BA-Bz,B0-B9,CA- > Cz,C0-C9,DA-Dz,D0-D9,EA-Ev #1.2/B ISOLDE: started sim > select clear > select H 1139 atoms, 145 residues, 1 model selected > hide sel atoms > ui mousemode right ""isolde tug residue"" > hide sel atoms > select clear > hide atoms > show cartoons > select #3/ET 372 atoms, 378 bonds, 48 residues, 1 model selected > show sel atoms > select #1/B 2284 atoms, 2313 bonds, 145 residues, 1 model selected > show sel atoms > select H 1139 atoms, 145 residues, 1 model selected > hide sel atoms > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1/B:1-120 1865 atoms, 1886 bonds, 118 residues, 1 model selected > select H 1139 atoms, 145 residues, 1 model selected > hide sel atoms > isolde sim start #1.2/B ISOLDE: started sim > hide sel atoms > hide sel cartoons > show sel cartoons > ui mousemode right ""isolde tug residue"" > show sel atoms > select H 1139 atoms, 145 residues, 1 model selected > hide sel atoms > select add #3 22890 atoms, 21935 bonds, 2895 residues, 2 models selected > show sel atoms > select clear > select #1/B:1-110 1701 atoms, 1720 bonds, 108 residues, 1 model selected > select #1/B:110-200 603 atoms, 613 bonds, 38 residues, 1 model selected > hide sel atoms > show sel cartoons > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select clear > select #1 2284 atoms, 2313 bonds, 145 residues, 21 models selected > isolde sim start #1.2/B 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 4 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start #1.2/B 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 #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start #1.2/B:36 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 #1.2/B:33-39 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 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start #1.2/B:129 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 #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1 2284 atoms, 2313 bonds, 145 residues, 21 models selected > isolde sim start #1.2/B 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 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > hide sel atoms > show sel cartoons > isolde sim start #1.2/B ISOLDE: started sim > show sel cartoons > ui mousemode right ""isolde tug residue"" > show sel atoms > select #1 2284 atoms, 2313 bonds, 145 residues, 21 models selected > select H 1139 atoms, 145 residues, 1 model selected > hide sel atoms > ui mousemode right ""isolde tug 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 #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > hide #3 models > isolde sim start #1.2/B ISOLDE: started sim > show sel cartoons > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > isolde sim start #1.2/B ISOLDE: started sim > show sel atoms > show #3 models > hide sel atoms > select clear > hide atoms > show cartoons > ui mousemode right ""isolde tug residue"" > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > hide atoms > show atoms > hide #!1 models > show #!1 models > select #1 2284 atoms, 2313 bonds, 145 residues, 21 models selected > isolde sim start #1.2/B 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 #1.2/B ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /home/alphafold/Downloads/194_fit.pdb models #1 An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 272, in _draw_scene draw_highlight_outline(r, highlight_drawings, color = self._highlight_color, File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1625, in draw_highlight_outline r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1927, in finish_rendering_outline r.pop_framebuffer() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 764, in pop_framebuffer fb.activate() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 2313, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) The X11 connection broke (error 1). Did the X11 server die? ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 NVIDIA 535.183.01 OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_GB.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: To Be Filled By O.E.M. Model: To Be Filled By O.E.M. OS: Ubuntu 20.04 Focal Fossa Architecture: 64bit ELF Virtual Machine: none CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 125Gi 3.3Gi 119Gi 25Mi 3.1Gi 121Gi Swap: 15Gi 145Mi 15Gi Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2231] (rev a1) Subsystem: NVIDIA Corporation Device [10de:147e] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.3 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.2 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 pprintpp: 0.4.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Platform limitation Tom Goddard Zach Pearson all ChimeraX