id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7583 glTexImage3D: out of memory eddy731@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.15.0-46-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description open the tomogram in ChimeraX by ArtiaX Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /media/clark/Tomo2/tet/Agro/25/25_rec.mrc Opened 25_rec.mrc as #1, grid size 1023,1440,600, pixel 13.6,13.6,13.6, shown at step 1, values float32 > volume #1 region 0,0,0,1022,1439,599 step 4 [Repeated 1 time(s)] > volume #1 change image level 138.5,0 level 177,0.8 level 442.7,1 > volume #1 style mesh > volume #1 style image > volume #1 region 0,0,296,1022,1439,296 step 1 showOutlineBox true > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 13.6 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis 0.1308,0.3775,0.9167 tiltedSlabOffset 4831 > volume #1 tiltedSlabAxis -0.2602,0.2336,0.9369 tiltedSlabOffset -1168 > volume #1 tiltedSlabAxis -0.3643,0.422,0.8302 tiltedSlabOffset -1105 > volume #1 tiltedSlabAxis -0.3751,0.07138,0.9242 tiltedSlabOffset -4817 > volume scale #1 factor -1 Opened 25_rec.mrc scaled as #2, grid size 1023,1440,600, pixel 13.6,13.6,13.6, shown at step 1, values float32 > volume #2 tiltedSlabAxis -0.5679,0.04529,0.8219 tiltedSlabOffset -6583 > volume #2 tiltedSlabAxis -0.3416,-0.09773,0.9348 tiltedSlabOffset -5755 > set bgColor white > show #!1 models > hide #!2 models > volume #1 tiltedSlabAxis -0.2671,-0.1462,0.9525 tiltedSlabOffset -5906 > volume #1 tiltedSlabAxis -0.7231,-0.0757,0.6866 tiltedSlabOffset -9575 > volume #2 level -164.4,0 level -126.1,0.8 level 748.4,1 > volume #2 level -235.1,0.3906 level -126.1,0.8 level 748.4,1 > volume #2 level -235.1,0.3906 level -117.3,0.7375 level 748.4,1 > hide #!2 models > volume #1 level 74.43,0.2188 level 177,0.8 level 442.7,1 > volume #1 tiltedSlabAxis -0.4834,-0.4985,0.7196 tiltedSlabOffset -1.026e+04 > toolshed show Downloading bundle ChimeraX_ArtiaX-0.1-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/1.4/site-packages sysconfig: /home/clark/.local/lib/python3.9/site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/1.4/site-packages sysconfig: /home/clark/.local/lib/python3.9/site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/include/python3.9/typing- extensions sysconfig: /home/clark/.local/include/python3.9/typing-extensions WARNING: Value for scheme.scripts does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/bin sysconfig: /home/clark/.local/bin WARNING: Value for scheme.data does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX sysconfig: /home/clark/.local WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/include/python3.9/pandas sysconfig: /home/clark/.local/include/python3.9/pandas WARNING: Value for scheme.headers does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/include/python3.9/superqt sysconfig: /home/clark/.local/include/python3.9/superqt WARNING: Value for scheme.headers does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/include/python3.9/starfile sysconfig: /home/clark/.local/include/python3.9/starfile WARNING: Value for scheme.headers does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/include/python3.9/ChimeraX-ArtiaX sysconfig: /home/clark/.local/include/python3.9/ChimeraX-ArtiaX WARNING: Value for scheme.headers does not match. Please report this to distutils: /home/clark/.local/share/ChimeraX/include/python3.9/UNKNOWN sysconfig: /home/clark/.local/include/python3.9/UNKNOWN WARNING: You are using pip version 21.3.1; however, version 22.2.2 is available. You should consider upgrading via the '/usr/bin/chimerax -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing ./Downloads/ChimeraX_ArtiaX-0.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core>=1.3 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.4) Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (2.0) Requirement already satisfied: ChimeraX-UI>=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.18.3) Requirement already satisfied: ChimeraX-Log>=1.1.4 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.1.5) Requirement already satisfied: ChimeraX-BILD~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.0) Collecting superqt Downloading superqt-0.3.5-py3-none-any.whl (59 kB) Requirement already satisfied: ChimeraX-Markers~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.0) Requirement already satisfied: ChimeraX-Graphics~=1.1 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.1) Requirement already satisfied: ChimeraX-Geometry>=1.1 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.2) Requirement already satisfied: ChimeraX-IMOD~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.0) Requirement already satisfied: ChimeraX-SaveCommand>=1.5 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.5.1) Collecting starfile Using cached starfile-0.4.11-py3-none-any.whl (27 kB) Requirement already satisfied: ChimeraX-ModelPanel>=1.2.1 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.3.2) Requirement already satisfied: ChimeraX-OpenCommand>=1.7 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.9) Requirement already satisfied: ChimeraX-MouseModes~=1.1 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.1) Requirement already satisfied: ChimeraX-Atomic>=1.1 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.39.1) Requirement already satisfied: ChimeraX-Map~=1.1 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.1) Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX- ArtiaX==0.1) (2.6.6) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX- ArtiaX==0.1) (1.0) Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX- ArtiaX==0.1) (7.0) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX- Atomic>=1.1->ChimeraX-ArtiaX==0.1) (2.0.1) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX- ArtiaX==0.1) (2.0.2) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX- ArtiaX==0.1) (2.7) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX- ArtiaX==0.1) (1.0.2) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-BILD~=1.0->ChimeraX- ArtiaX==0.1) (1.2.2) Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-BILD~=1.0->ChimeraX- ArtiaX==0.1) (1.0) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.1->ChimeraX- ArtiaX==0.1) (2.0) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.1->ChimeraX- ArtiaX==0.1) (2.1) Requirement already satisfied: ChimeraX-StdCommands>=1.3.1,~=1.3 in /usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX- ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.1) (1.8) Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX- OpenCommand>=1.7->ChimeraX-ArtiaX==0.1) (1.0.1) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-UI>=1.0->ChimeraX- ArtiaX==0.1) (1.0) Collecting pandas Downloading pandas-1.4.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB) Collecting typing-extensions Downloading typing_extensions-4.3.0-py3-none-any.whl (25 kB) Requirement already satisfied: qtpy>=1.1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from superqt->ChimeraX-ArtiaX==0.1) (2.1.0) Requirement already satisfied: pygments>=2.4.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from superqt->ChimeraX-ArtiaX==0.1) (2.11.2) Requirement already satisfied: packaging in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from superqt->ChimeraX-ArtiaX==0.1) (21.3) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX-MapSeries~=2.0->ChimeraX- Map~=1.1->ChimeraX-ArtiaX==0.1) (2.0) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX- SelInspector~=1.0->ChimeraX-UI>=1.0->ChimeraX-ArtiaX==0.1) (1.0) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from ChimeraX- StdCommands>=1.3.1,~=1.3->ChimeraX-ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.1) (2.0) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from packaging->superqt->ChimeraX- ArtiaX==0.1) (3.0.9) Requirement already satisfied: numpy>=1.18.5 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from pandas->starfile->ChimeraX- ArtiaX==0.1) (1.22.1) Requirement already satisfied: python-dateutil>=2.8.1 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from pandas->starfile->ChimeraX- ArtiaX==0.1) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from pandas->starfile->ChimeraX- ArtiaX==0.1) (2022.1) Requirement already satisfied: six>=1.5 in /usr/lib/ucsf- chimerax/lib/python3.9/site-packages (from python- dateutil>=2.8.1->pandas->starfile->ChimeraX-ArtiaX==0.1) (1.16.0) Installing collected packages: typing-extensions, pandas, superqt, starfile, ChimeraX-ArtiaX Successfully installed ChimeraX-ArtiaX-0.1 pandas-1.4.4 starfile-0.4.11 superqt-0.3.5 typing-extensions-4.3.0 \--- Successfully installed ChimeraX-ArtiaX-0.1 pandas-1.4.4 starfile-0.4.11 superqt-0.3.5 typing-extensions-4.3.0 Installed ChimeraX-ArtiaX (0.1) Downloading bundle ChimeraX_ArtiaX-0.1-py3-none-any.whl Bundle installation canceled > volume #1 tiltedSlabAxis -0.4427,-0.2399,0.864 tiltedSlabOffset -6704 > ui tool show Toolbar > ui tool show ArtiaX Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho > volume #1 tiltedSlabAxis -0.3586,-0.28,0.8905 tiltedSlabOffset -6226 > volume #1 tiltedSlabAxis -0.2321,0.1462,0.9616 tiltedSlabOffset -718.2 > artiax add tomo #1 Opened 25_rec.mrc as #3.1.1, grid size 1023,1440,600, pixel 13.6,13.6,13.6, shown at level 176, step 1, values float32 > artiax tomo #3.1.1 sliceDirection 0,0,1 > artiax view xy 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 = 1285, description = b'out of memory', baseOperation = glTexImage3D, pyArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1023, 1440, 600, 0, GL_RED, GL_FLOAT, array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235, 149.99055], [155.93594, 160.395..., ), cArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1023, 1440, 600, 0, GL_RED, GL_FLOAT, array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235, 149.99055], [155.93594, 160.395..., ), cArguments = ( GL_TEXTURE_3D, 0, GL_R32F, 1023, 1440, 600, 0, GL_RED, GL_FLOAT, array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235, 149.99055], [155.93594, 160.395..., ) ) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/view.py"", line 165, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/view.py"", line 242, in _draw_scene draw_transparent(r, transparent_drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1531, in draw_transparent r.draw_transparent( File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 1242, in draw_transparent draw() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1533, in lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1539, in _draw_multiple d.draw(renderer, draw_pass) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/map/image3d.py"", line 783, in draw pd = self._update_planes(renderer) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/map/image3d.py"", line 548, in _update_planes pd = self._update_3d_texture_planes(view_dir) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/map/image3d.py"", line 600, in _update_3d_texture_planes pd = self._texture_3d_planes() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/map/image3d.py"", line 610, in _texture_3d_planes pd = Texture3dPlanes(self) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/map/image3d.py"", line 1147, in __init__ self._fill_textures() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/map/image3d.py"", line 1243, in _fill_textures t.reload_texture(td, now = True) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 3058, in reload_texture self.fill_opengl_texture() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 3068, in fill_opengl_texture self.initialize_texture(size, format, iformat, tdtype, ncomp, data) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 2961, in initialize_texture GL.glTexImage3D(gl_target, 0, iformat, size[0], size[1], size[2], File ""src/latebind.pyx"", line 39, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src/wrapper.pyx"", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/wrapper.pyx"", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage3D, pyArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1023, 1440, 600, 0, GL_RED, GL_FLOAT, array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235, 149.99055], [155.93594, 160.395..., ), cArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1023, 1440, 600, 0, GL_RED, GL_FLOAT, array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235, 149.99055], [155.93594, 160.395..., ), cArguments = ( GL_TEXTURE_3D, 0, GL_R32F, 1023, 1440, 600, 0, GL_RED, GL_FLOAT, array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235, 149.99055], [155.93594, 160.395..., ) ) Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1189, in __del__ self.delete() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1209, in delete raise RuntimeError(""Don't have opengl context needed to delete texture from drawing '%s' because drawing was never drawn"" % self.name) RuntimeError: Don't have opengl context needed to delete texture from drawing 'Image3D 3d texture planes' because drawing was never drawn Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 3019, in __del__ raise OpenGLError('OpenGL texture was not deleted before graphics.Texture destroyed') chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before graphics.Texture destroyed > artiax add tomo #2 Opened 25_rec.mrc scaled as #3.1.2, grid size 1023,1440,600, pixel 13.6,13.6,13.6, shown at level -126, step 1, values float32 > artiax tomo #3.1.2 sliceDirection 0,0,1 > artiax view xy OpenGL version: 4.5 (Core Profile) Mesa 21.2.6 OpenGL renderer: llvmpipe (LLVM 12.0.0, 256 bits) OpenGL vendor: Mesa/X.org Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:0 Manufacturer: Supermicro Model: SYS-7049GP-TRT OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virtual Machine: none CPU: 96 Intel(R) Xeon(R) Gold 6240R CPU @ 2.40GHz Cache Size: 36608 KB Memory: total used free shared buff/cache available Mem: 251Gi 12Gi 167Gi 93Mi 71Gi 236Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) DeviceName: ASPEED Video AST2500 Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:096d] Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2022.5.18.1 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-ArtiaX: 0.1 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 distro: 1.6.0 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.3 pandas: 1.4.4 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 starfile: 0.4.11 suds-community: 1.0.0 superqt: 0.3.5 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 typing-extensions: 4.3.0 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Graphics nonchimerax Utz Ermel all ChimeraX