id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5607 volume step 2: out of graphics memory chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.14.6-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd W1362_G1_montage_chimera Current working directory is: /Users/dparrell/Desktop/W1362_G1_montage_chimera > cd W1362_G1_montage_chimera Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > cd ./W1362_G1_montage_chimera Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > cd /Desktop/W1362_G1_montage_chimera Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > cd /Desktop/ Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > cd ../ Current working directory is: /Users/dparrell/Desktop > cd W1362_G1_montage_chimera Current working directory is: /Users/dparrell/Desktop/W1362_G1_montage_chimera > open > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__ER_seg.hdf > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__ERMem_seg.hdf > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__lipid_drops_seg.hdf > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__mitos_seg.hdf > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__NPC_seg.hdf > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__nucleus_seg.hdf > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec.mrc > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin4_rec_trim_preproc__golgi_seg.hdf > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin4_rec_trim_preproc__ribosomes_seg.hdf Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__ER_seg.hdf as #1, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32 Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__ERMem_seg.hdf as #2, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32 Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__lipid_drops_seg.hdf as #3, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32 Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__mitos_seg.hdf as #4, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32 Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__NPC_seg.hdf as #5, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32 Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__nucleus_seg.hdf as #6, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32 Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec.mrc as #7, grid size 1860,2496,326, pixel 27.6,27.6,27.6, shown at step 1, values float32 Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin4_rec_trim_preproc__golgi_seg.hdf as #8, grid size 2800,3750,288, pixel 18.4, shown at step 1, values float32 Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin4_rec_trim_preproc__ribosomes_seg.hdf as #9, grid size 2800,3750,288, pixel 18.4, shown at step 1, values float32 > volume #1 level 0.001684,0 level 0.1244,0.8 level 2.405,1 > volume #2 level 0.0008498,0 level 0.1642,0.8 level 2.124,1 > ui tool show ""Map Coordinates"" > volume #9 level 0.0673,0 level 0.1073,0.8 level 0.1566,1 > save /Users/dparrell/Desktop/W1362_G1_montage_chimera/W1362_G1_Montage.cxs > volume #7 level -0.8056,0 level 1.664,0.8 level 3.976,1 > volume #7 level -0.8056,0 level 1.664,0.8 level 3.976,1 > volume #7 color black color white color white > volume #7 color black color white color white > volume #7 level -3.905,0 level 1.664,0.8 level 3.976,1 > volume #7 level -3.905,0 level -0.4981,1 level 3.976,1 > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!9 models > hide #!8 models > hide #!7 models > show #!7 models > volume #7 level -4.036,0 level -0.4981,1 level 3.976,1 > volume #7 level -4.036,0 level 1.769,1 level 3.976,1 > volume #7 level -4.036,0 level 1.769,1 level 0.2873,0.5735 > volume #7 level -0.9976,0.04412 level 1.769,1 level 0.2873,0.5735 > volume #7 level -0.9976,0.04412 level 1.769,1 level 0.0757,1 > volume #7 level -0.6046,0 level 1.769,1 level 0.0757,1 > volume #7 level -0.6046,0 level 0.4156,1 level 0.0757,1 > volume #7 level -0.6046,0 level 4.757,1 level 0.0757,1 > volume #7 level -0.6046,0 level 4.757,1 level -0.15,1 > volume #7 level -2.458,0 level 4.757,1 level -0.15,1 > volume #7 level -2.458,0 level 4.757,1 level 0.3658,0.8824 > volume #7 level -2.168,0.01471 level 4.757,1 level 0.3658,0.8824 > volume #7 level -2.168,0.01471 level 1.726,1 level 0.3658,0.8824 > volume #8 level 0,0 level 0.3252,0.8 level 5.113,1 > volume #8 region 0,0,0,2799,3749,287 step 8 > volume #8 region 0,0,0,2799,3749,287 step 8 > volume #8 step 4 > volume #8 color #996600 > ui tool show ""Hide Dust"" > surface dust #7 size 165.71 No surfaces specified > volume #8 color #003399 > surface dust #8 size 359.75 > surface dust #8 size 731.31 > volume #9 color #cc6600 color white color white > volume #9 region 0,0,0,2799,3749,287 step 8 > volume #9 region 0,0,0,2799,3749,287 step 8 > volume #9 color #996600 > volume #9 step 4 > volume #9 level 0.09678 > surface dust #9 size 530.03 > surface dust #9 size 40 > surface dust #9 size 400 > volume #1 region 0,0,0,1859,2495,325 step 8 > volume #1 region 0,0,0,1859,2495,325 step 8 > volume #1 step 4 > volume #1 color #339933 > volume #1 step 2 > surface dust #1 size 350 > volume #3 level 0,0 level 0.731,0.8 level 9.668,1 > volume #3 color #ff00cc color white color white > volume #3 color #990099 color white color white > volume #3 region 0,0,0,1859,2495,325 step 8 > volume #3 region 0,0,0,1859,2495,325 step 8 > volume #3 color #990099 > volume #3 step 2 > volume #3 level 0.8893 > volume #3 level 0.5651 > surface dust #3 size 255.38 > surface dust #3 size 259.83 > surface dust #3 size 498.76 > surface dust #3 size 490.56 > surface dust #3 size 312.24 > surface undust #3 > surface dust #3 size 312.24 > volume #2 region 0,0,0,1859,2495,325 step 8 > volume #2 region 0,0,0,1859,2495,325 step 8 > volume #2 step 4 > volume #2 color #006600 > surface dust #2 size 89.87 > surface dust #2 size 128.7 > surface undust #2 > surface dust #2 size 531.85 > volume #4 level 0.004534,0 level 0.4042,0.8 level 2.061,1 > volume #4 region 0,0,0,1859,2495,325 step 8 > volume #4 region 0,0,0,1859,2495,325 step 8 > volume #2 color #ffff33 > volume #2 color #666600 > volume #2 color #33cc66 > volume #4 color #ffff33 > volume #4 step 2 > surface dust #4 size 165.71 > surface undust #4 > surface dust #4 size 440.75 > surface dust #4 size 60 > surface dust #4 size 600 > surface dust #4 size 600 > cd W1362_G1_montage_chimera Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > surface dust #4 size 80 > surface dust #4 size 800 > surface dust #4 size 800 > surface undust #4 > surface dust #4 size 2745.3 > surface undust #4 > surface dust #4 size 2000 > volume #5 level 0,0 level 0.5777,0.8 level 2.881,1 > volume #5 region 0,0,0,1859,2495,325 step 8 > volume #5 region 0,0,0,1859,2495,325 step 8 > volume #5 step 4 > surface dust #5 size 165.71 > surface undust #5 > surface dust #5 size 800 > volume #6 level 0,0 level 0.07658,0.8 level 1.612,1 > volume #6 color #cc3300 color white color white > volume #6 region 0,0,0,1859,2495,325 step 8 > volume #6 region 0,0,0,1859,2495,325 step 8 > volume #6 color #cc0000 > volume #6 step 2 > surface dust #6 size 984.22 > open > /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_lp8.mrc Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_lp8.mrc as #10, grid size 1860,2496,326, pixel 27.6,27.6,27.6, shown at step 1, values float32 > volume #10 level -0.2795,0 level 0.6702,0.8 level 1.786,1 > volume #10 level -1.638,0 level 0.6702,0.8 level 1.786,1 > volume #10 color black color #ffffb3 color #ffffb3 > volume #10 level -1.638,0 level 0.6702,0.8 level 1.786,1 > volume #10 level -1.638,0 level 0.06799,1 level 1.786,1 > volume #10 color black color white color #ffffb3 > volume #10 level -0.7891,0 level 0.06799,1 level 1.786,1 > volume #10 level -0.7891,0 level 0.4618,1 level 1.786,1 > volume #10 level -1.793,0 level 0.4618,1 level 1.786,1 > volume #10 level -1.793,0 level 0.2996,1 level 1.786,1 > volume #10 level -1.793,0 level 0.4436,1 level 1.786,1 > volume #10 level -1.649,0 level 0.4436,1 level 1.786,1 > volume #10 level -2.296,0 level 0.4436,1 level 1.786,1 > volume #10 level -2.296,0 level 0.2036,1 level 1.786,1 > volume #10 level -2.296,0 level 0.2036,1 level 1.786,1 > volume #10 color black color white color black > volume #10 level -2.296,0 level 0.2036,1 level 1.795,1 > volume #10 color black color white color white > volume #10 color black color white color #999999 > volume #10 color black color white color #666666 > volume #10 color black color white color white > volume #10 color black color #666666 color white > volume #10 level -2.296,0 level 0.2036,1 level 1.795,1 > volume #10 level -2.296,0 level -0.1874,1 level 1.795,1 > volume #10 level -2.296,0 level -0.1874,1 level 0.4349,1 > volume #10 color black color white color white > volume #10 color black color #333333 color white > volume #10 color black color #cccccc color white > volume #10 color black color #999999 color white > volume #10 color black color #999999 color white > volume #10 color black color #999999 color white > volume #10 level -2.296,0 level -0.02745,1 level 0.4349,1 > volume #10 level -2.296,0 level -0.02745,1 level 0.4349,1 > volume #10 level -2.296,0 level -0.02745,1 level 2.142,1 > volume #10 level -2.296,0 level -0.02745,1 level 0.3194,1 > volume #10 level -2.296,0 level -0.4008,1 level 0.3194,1 > volume #10 level -2.296,0 level -0.4008,1 level 0.7371,1 > volume #10 level -2.296,0 level -0.2408,1 level 0.7371,1 > volume #10 level -2.296,0 level -0.2408,1 level 0.7371,1 > volume #10 level -2.296,0 level -0.2408,1 level 0.4794,0.9853 > volume #10 level -2.296,0 level -1.361,0.3088 level 0.4794,0.9853 > volume #10 level -2.296,0 level -1.361,0.3088 level 1.742,1 > volume #10 level -2.296,0 level -0.143,1 level 1.742,1 > volume #10 level -2.296,0 level -0.143,1 level 0.4794,1 > volume #10 level -2.296,0 level -0.08079,1 level 0.4794,1 > volume #9 step 2 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. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 165, in draw self._draw_scene(camera, drawings) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 233, in _draw_scene draw_opaque(r, opaque_drawings) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 1498, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 1511, in _draw_multiple d.draw(renderer, draw_pass) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 751, in draw self.draw_self(renderer, draw_pass) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 758, in draw_self self._draw_geometry(renderer, opaque_only = any_transp) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 785, in _draw_geometry ds.activate_bindings(renderer) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 1858, in activate_bindings self.update_buffers() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 1846, in update_buffers b.update_buffer_data(data) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 2662, in update_buffer_data GL.glBufferData(btype, size, d, GL.GL_STATIC_DRAW) File ""src/latebind.pyx"", line 51, in OpenGL_accelerate.latebind.Curry.__call__ File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/OpenGL/GL/VERSION/GL_1_5.py"", line 89, in glBufferData return baseOperation( target, size, data, usage ) 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 = glBufferData, pyArgs = ( 34963, 6935638752, array([[ 1, 2, 2625002], [ 2625001, 1, 2625002], [ 2625000, 0, 2..., GL_STATIC_DRAW, ), cArgs = ( 34963, 6935638752, array([[ 1, 2, 2625002], [ 2625001, 1, 2625002], [ 2625000, 0, 2..., GL_STATIC_DRAW, ), cArguments = ( 34963, 6935638752, array([[ 1, 2, 2625002], [ 2625001, 1, 2625002], [ 2625000, 0, 2..., GL_STATIC_DRAW, ) ) > volume #9 level 0.04339 > close #9 > graphics reset Expected a keyword > graphics restart > ui mousemode right ""map eraser"" > volume erase #3 center -7789,-509.37,-1415.7 radius 34467 outside true Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__lipid_drops_seg.hdf copy as #11, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32 > volume erase #11 center 21132,2852.5,-5239.7 radius 15480 > volume erase #11 center -34913,18658,16.618 radius 15480 > volume erase #11 center -37616,-29297,850.9 radius 15480 > volume erase #11 center -39648,-9397.8,1294.3 radius 15480 > volume erase #11 center -31759,-4966.8,-247.23 radius 9306.2 > volume erase #11 center -30740,2985.9,6991.5 radius 9306.2 > volume erase #11 center -30400,-17661,7080 radius 9306.2 > volume erase #11 center -22433,-12279,8883.7 radius 9306.2 > surface dust #3 size 307.11 > surface dust #3 size 223.51 > surface dust #3 size 223.51 > graphics restart > surface dust #3 size 200 > surface dust #3 size 200 > graphics restart > graphics restart > surface dust #11 size 150 > volume erase #11 center -24935,7637.6,-3199.1 radius 3240 > volume erase #11 center -26311,2283.5,-5603 radius 3240 > volume erase #11 center -21785,-5301.1,-1777.9 radius 4446.3 > volume erase #11 center 4962.6,12813,-499.6 radius 16854 > volume erase #11 center 13277,-19909,-413.01 radius 11133 > volume erase #11 center -35306,-13571,-6981.1 radius 11133 > volume erase #11 center -33852,-25056,-2045.7 radius 11133 > volume erase #11 center -17764,41261,-2231.5 radius 12546 > volume erase #11 center -5494.8,11384,-1589.1 radius 12546 > volume erase #11 center -12243,-27373,-385.04 radius 2171.4 > volume erase #11 center -12230,-27677,-304.13 radius 2171.4 > volume erase #11 center -23427,-30536,-2959.7 radius 4308.4 > volume erase #11 center -25114,8951.4,1239.8 radius 4308.4 > volume erase #11 center -13684,-13144,-1186.5 radius 4170.5 > orient Unknown command: orient > view orient > surface dust #11 size 144.94 > surface dust #11 size 212.81 > surface dust #11 size 250 > save lipid_droplets_clean.mrc #11 > save /Users/dparrell/Desktop/W1362_G1_montage_chimera/W1362_G1_Montage.cxs OpenGL version: 4.1 ATI-2.11.26 OpenGL renderer: AMD Radeon Pro Vega 64X OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: iMac Pro Model Identifier: iMacPro1,1 Processor Name: Intel Xeon W Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 18 L2 Cache (per Core): 1 MB L3 Cache: 24.8 MB Hyper-Threading Technology: Enabled Memory: 256 GB Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0) Software: System Software Overview: System Version: macOS 10.14.6 (18G9323) Kernel Version: Darwin 18.7.0 Time since boot: 2:01 Graphics/Displays: Radeon Pro Vega 64X: Chipset Model: Radeon Pro Vega 64X Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 16 GB Vendor: AMD (0x1002) Device ID: 0x686b Revision ID: 0x0000 ROM Revision: 113-D0500D-114 VBIOS Version: 113-D05001A1XX-021 Option ROM Version: 113-D05001A1XX-021 EFI Driver Version: 01.01.114 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: iMac: Display Type: Built-In Retina LCD Resolution: 5120 x 2880 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Volume Data limitation all ChimeraX