Opened 2 years ago
Closed 2 years ago
#9826 closed defect (nonchimerax)
Crash recording movie
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-6.2.0-33-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x00007f32f37fe640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f32f3fff640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3310ff9640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/selectors.py", line 416 in select File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/connection.py", line 936 in wait File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f33117fa640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3311ffb640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f33127fc640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3312ffd640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f33137fe640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3313fff640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3330ff9640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f33317fa640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3331ffb640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f33327fc640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3332ffd640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f33337fe640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3333fff640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3378ff9640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f33797fa640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007f3379ffb640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Current thread 0x00007f33de69dc40 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/OpenGL/GL/images.py", line 369 in glReadPixels File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1275 in frame_buffer_image File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/view.py", line 492 in image_rgba File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/movie/movie.py", line 168 in capture_image File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 138 in invoke File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 237 in _activate File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 206 in activate File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 89 in draw_new_frame File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/std_commands/wait.py", line 43 in draw_frame File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/std_commands/wait.py", line 32 in wait File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 173 in _run_commands File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 160 in open_command_script File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 37 in open File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 447 in collated_open File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Thu Sep 21 21:26:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Thu Sep 21 18:27:05 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Sun Sep 17 10:41:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ad5wt_re3d_ctfref.mrc Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > open ad5wt_deltaIX_re3d_ctfref.mrc Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > ui tool show "Map Coordinates" > view orient > view initial > volume #1 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 style image region 0,0,396,799,799,396 step 1 showOutlineBox true > volume #1 style image region 0,0,396,799,799,396 step 1 showOutlineBox true > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > volume #1 region 0,0,0,799,799,799 step 4 > volume #1 style surface region 0,0,0,799,799,799 step 4 > volume #2 region 0,0,0,799,799,799 step 4 > volume #2 style surface region 0,0,0,799,799,799 step 4 > volume #1 showOutlineBox false > volume #2 showOutlineBox false > volume #2 level 0.02 > volume #2 change image level -0.0009087,0 level 0.02434,0.8 level 0.03987,1 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.01 > hide #!2 models > show #!1 models > volume #1 level 0.015 > volume #1 change image level -0.0008747,0 level 0.01593,0.8 level 0.02483,1 > volume #1 level 0.01 > hide #!1 models > show #!2 models > vop resample #2 onGrid #1 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > vop subtract #1 #3 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > volume #4 level 0.005 > shape icosahedron radius 450 divisions 1 color yellow > marker fromMesh #5 edgeRadius 6.0 color yellow > color radial #4 center 0,0,0 palette ^puor range 300,500 > volume #4 level 0.007 > volume #4 level 0.006 > color radial #4 center 0,0,0 palette ^rdgy range 300,500 > view initial > view orient > set bgColor white Fetching url http://www.colourlovers.com/api/palettes?keywords=BlGy&format=json&numResults=100 failed: HTTP Error 500: Internal Server Error > palette list No custom palettes. 315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > color radial #4 center 0,0,0 palette rdbu range 300,500 > color radial #4 center 0,0,0 palette ^rdbu range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-3 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-4 range 300,500 > select clear > color radial #4 center 0,0,0 palette ^rdbu-5 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-6 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-4 range 300,500 > ui tool show "Side View" > lighting soft > lighting full > lighting soft > hide #!5 models > show #5 models > lighting full > save ad5wt_ad5wtdeltaIX.tiff supersample 3 > lighting soft > lighting full > lighting soft > view name view1 > save /export0/people/vsreddy/data/Ad5_DeltaIX/ad5_deltaIX.cxs > lighting simple > view view1 > lighting full > volume #4 level 0.01 > view view1 > lighting full > lighting soft > lighting full > save ad5wt_ad5wtdeltaIX_highcont.tiff supersample 3 > save /export0/people/vsreddy/data/Ad5_DeltaIX/ad5_deltaIX.cxs ——— End of log from Sun Sep 17 10:41:16 2023 ——— opened ChimeraX session > lighting soft > lighting full > volume #4 level 0.02 > volume #4 level 0.01 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > view list Named views: view1 > view view1 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > hide #5.1 models > hide #5.2 models > hide #6 models > hide #!5 models > hide #!4 models > show #5 models > show #6 models > hide #6 models > hide #!5 models > show #!4 models > volume #4 style image region 0,0,399,799,799,399 step 1 originIndex > 399.5,399.5,399.5 showOutlineBox false > set bgColor black > volume #2 style image region 0,0,399,799,799,399 step 1 originIndex > 399.5,399.5,399.5 showOutlineBox false > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #4 red > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #4 #e01b24ff models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > open phenix_p9.pdb Chain information for phenix_p9.pdb #7 --- Chain | Description Q | No description available R | No description available S | No description available T | No description available > sym #7 I,222 Made 60 graphical clones for phenix_p9.pdb symmetry I,222 > ui tool show "Side View" > hide #!2 models > color #7 cyan > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > save diffmap_only_crossec.tiff supersample 3 > show #!7 models > save diffmap_p9model_crossec.tiff supersample 3 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > hide #!7 models > hide #!4 models > show #!4 models > view list Named views: view1 > view name view2 > view view2 > view view1 > color radial #4 center 0,0,0 palette ^puor range 300,500 > color radial #4 center 0,0,0 palette ^rdgy range 300,500 > color radial #4 center 0,0,0 palette rdgy range 300,500 > palette list No custom palettes. 315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > color radial #4 center 0,0,0 palette ylorrd range 300,500 > show #5 models > hide #5.1 models > show #6 models > set bgColor white > color radial #4 center 0,0,0 palette ylorrd-3 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-4 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-5 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-6 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-7 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-8 range 300,500 Fetching url http://www.colourlovers.com/api/palettes?keywords=YlOrRd-9&format=json&numResults=100 failed: HTTP Error 500: Internal Server Error > color radial #4 center 0,0,0 palette ylorrd-7 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-8 range 300,500 > color radial #4 center 0,0,0 palette ylorrd range 300,500 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.001 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > hide #!5 models > show #!7 models > hide #!7 models > hide #6 models > view view2 > color #4 red > set bgColor black > save diffmap_only_crossec_surf.tiff supersample 3 > show #!2 models > save diffmap_n_hexon_crossec_surf.tiff supersample 3 > hkcage 5 0 radius 450 color black > hide #!2 models > set bgColor white > view view1 > show #5 models > hide #5.1 models > color radial #4 center 0,0,0 palette ylorrd range 300,500 > show #6 models > show #5.1 models > hode #8 models Unknown command: hode #8 models > hide #8 models > show #8 models > open movie_diffmap_rock.cxc > view view1 > hide #8 models > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 120 > wait 120 > view view1 > wait 2 > show #8 models > rock y -30 120 > wait 120 > view view1 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y 30 120 > wait 120 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs ——— End of log from Thu Sep 21 18:27:05 2023 ——— opened ChimeraX session > hide #8 models > hide #6 models > hide #!5 models > hide #!4 models > show #!1 models > volume #1 level 0.007 > volume #1 level 0.006 > color radial #1 center 0,0,0 palette ^puor range 300,500 > volume #1 level 0.005 > volume #1 step 1 > volume #1 level 0.006 > volume #1 level 0.007 > open cmass_ad5_60_renum.pdb No such file/path: cmass_ad5_60_renum.pdb > open cmass_ad5_60_renum.pdb Chain information for cmass_ad5_60_renum.pdb #9 --- Chain | Description X | No description available > hide #!1 models > select #9 420 atoms, 419 pseudobonds, 420 residues, 2 models selected > style sel sphere Changed 420 atom styles > color (#!9 & sel) red > set #9 radius=2 Expected a keyword > setattr #9 radius=2 Missing or invalid "attrName" argument: Expected a text string > setattr #9 atom radius=2 Missing or invalid "attrValue" argument: Expected a text string > setattr #9 Atom radius=2 Missing or invalid "attrValue" argument: Expected a text string > setattr #9 atom radius 2 Assigning radius attribute to 420 items > setattr #9 atom radius 10 Assigning radius attribute to 420 items > show sel atoms > setattr #9 atom radius 10 color red Expected a keyword > select clear > setattr #9 atom radius=10 Missing or invalid "attrValue" argument: Expected a text string > close #9 > open tmp.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 50 Assigning radius attribute to 420 items > setattr #9 atom radius 20 Assigning radius attribute to 420 items > close #9 > open cmass_ad5_60.pdb Summary of feedback from opening cmass_ad5_60.pdb --- warnings | Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 54 messages similar to the above omitted > close #9 > open cmass60_tmp1.pdb > show #9 atoms > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > close #9 > open cmass60_tmp1.pdb > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > close #9 > open cmass60_tmp1.pdb > show #9 atoms > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > style #9 sphere Changed 420 atom styles > close #9 > open cmass60_tmp1.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 20 Assigning radius attribute to 420 items > setattr #9:HX1 color red Missing or invalid "attrValue" argument: Expected a text string > color #9:HX1 red > close #9 > open cmass_ad5_60_renum.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 20 Assigning radius attribute to 420 items > color #9:HX1 cornflowerblue > color #9:HX2 red > color #9:HX3 limegreen > color #9:HX4 gold > color #9:P3A forestgreen > color #9:HX3 lightbgreen Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #9:HX3 lightgreen > color #9:p8A yellow > color #9:p8B orange > color #9:HX4 khaki > show #!1 models > hide #!1 models > view view1 > ui tool show "Side View" > show #!1 models > hide #!1 models > show #!1 models > lighting soft > lighting simple > lighting soft > open movie_rock2.cxc > view view2 > movie record > rock y 30 180 > wait 180 > view view2 > wait 2 > hide #1 models > rock y -30 180 > wait 180 > view view2 > wait 2 > movie encode movie_ad5wt_markers.mp4 Movie saved to movie_ad5wt_markers.mp4 executed movie_rock2.cxc > view list Named views: view1, view2 > view view1 > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs ——— End of log from Thu Sep 21 21:26:56 2023 ——— opened ChimeraX session > show #1 models > lighting full > open movie_rock2.cxc > view view1 > hide #9 models > movie record > rock y 30 180 > wait 180 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Thu Sep 21 21:26:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Thu Sep 21 18:27:05 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Sun Sep 17 10:41:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ad5wt_re3d_ctfref.mrc Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > open ad5wt_deltaIX_re3d_ctfref.mrc Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > ui tool show "Map Coordinates" > view orient > view initial > volume #1 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 style image region 0,0,396,799,799,396 step 1 showOutlineBox true > volume #1 style image region 0,0,396,799,799,396 step 1 showOutlineBox true > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > volume #1 region 0,0,0,799,799,799 step 4 > volume #1 style surface region 0,0,0,799,799,799 step 4 > volume #2 region 0,0,0,799,799,799 step 4 > volume #2 style surface region 0,0,0,799,799,799 step 4 > volume #1 showOutlineBox false > volume #2 showOutlineBox false > volume #2 level 0.02 > volume #2 change image level -0.0009087,0 level 0.02434,0.8 level 0.03987,1 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.01 > hide #!2 models > show #!1 models > volume #1 level 0.015 > volume #1 change image level -0.0008747,0 level 0.01593,0.8 level 0.02483,1 > volume #1 level 0.01 > hide #!1 models > show #!2 models > vop resample #2 onGrid #1 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > vop subtract #1 #3 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > volume #4 level 0.005 > shape icosahedron radius 450 divisions 1 color yellow > marker fromMesh #5 edgeRadius 6.0 color yellow > color radial #4 center 0,0,0 palette ^puor range 300,500 > volume #4 level 0.007 > volume #4 level 0.006 > color radial #4 center 0,0,0 palette ^rdgy range 300,500 > view initial > view orient > set bgColor white Fetching url http://www.colourlovers.com/api/palettes?keywords=BlGy&format=json&numResults=100 failed: HTTP Error 500: Internal Server Error > palette list No custom palettes. 315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > color radial #4 center 0,0,0 palette rdbu range 300,500 > color radial #4 center 0,0,0 palette ^rdbu range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-3 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-4 range 300,500 > select clear > color radial #4 center 0,0,0 palette ^rdbu-5 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-6 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-4 range 300,500 > ui tool show "Side View" > lighting soft > lighting full > lighting soft > hide #!5 models > show #5 models > lighting full > save ad5wt_ad5wtdeltaIX.tiff supersample 3 > lighting soft > lighting full > lighting soft > view name view1 > save /export0/people/vsreddy/data/Ad5_DeltaIX/ad5_deltaIX.cxs > lighting simple > view view1 > lighting full > volume #4 level 0.01 > view view1 > lighting full > lighting soft > lighting full > save ad5wt_ad5wtdeltaIX_highcont.tiff supersample 3 > save /export0/people/vsreddy/data/Ad5_DeltaIX/ad5_deltaIX.cxs ——— End of log from Sun Sep 17 10:41:16 2023 ——— opened ChimeraX session > lighting soft > lighting full > volume #4 level 0.02 > volume #4 level 0.01 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > view list Named views: view1 > view view1 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > hide #5.1 models > hide #5.2 models > hide #6 models > hide #!5 models > hide #!4 models > show #5 models > show #6 models > hide #6 models > hide #!5 models > show #!4 models > volume #4 style image region 0,0,399,799,799,399 step 1 originIndex > 399.5,399.5,399.5 showOutlineBox false > set bgColor black > volume #2 style image region 0,0,399,799,799,399 step 1 originIndex > 399.5,399.5,399.5 showOutlineBox false > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #4 red > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #4 #e01b24ff models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > open phenix_p9.pdb Chain information for phenix_p9.pdb #7 --- Chain | Description Q | No description available R | No description available S | No description available T | No description available > sym #7 I,222 Made 60 graphical clones for phenix_p9.pdb symmetry I,222 > ui tool show "Side View" > hide #!2 models > color #7 cyan > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > save diffmap_only_crossec.tiff supersample 3 > show #!7 models > save diffmap_p9model_crossec.tiff supersample 3 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > hide #!7 models > hide #!4 models > show #!4 models > view list Named views: view1 > view name view2 > view view2 > view view1 > color radial #4 center 0,0,0 palette ^puor range 300,500 > color radial #4 center 0,0,0 palette ^rdgy range 300,500 > color radial #4 center 0,0,0 palette rdgy range 300,500 > palette list No custom palettes. 315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > color radial #4 center 0,0,0 palette ylorrd range 300,500 > show #5 models > hide #5.1 models > show #6 models > set bgColor white > color radial #4 center 0,0,0 palette ylorrd-3 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-4 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-5 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-6 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-7 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-8 range 300,500 Fetching url http://www.colourlovers.com/api/palettes?keywords=YlOrRd-9&format=json&numResults=100 failed: HTTP Error 500: Internal Server Error > color radial #4 center 0,0,0 palette ylorrd-7 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-8 range 300,500 > color radial #4 center 0,0,0 palette ylorrd range 300,500 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.001 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > hide #!5 models > show #!7 models > hide #!7 models > hide #6 models > view view2 > color #4 red > set bgColor black > save diffmap_only_crossec_surf.tiff supersample 3 > show #!2 models > save diffmap_n_hexon_crossec_surf.tiff supersample 3 > hkcage 5 0 radius 450 color black > hide #!2 models > set bgColor white > view view1 > show #5 models > hide #5.1 models > color radial #4 center 0,0,0 palette ylorrd range 300,500 > show #6 models > show #5.1 models > hode #8 models Unknown command: hode #8 models > hide #8 models > show #8 models > open movie_diffmap_rock.cxc > view view1 > hide #8 models > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 120 > wait 120 > view view1 > wait 2 > show #8 models > rock y -30 120 > wait 120 > view view1 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y 30 120 > wait 120 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs ——— End of log from Thu Sep 21 18:27:05 2023 ——— opened ChimeraX session > hide #8 models > hide #6 models > hide #!5 models > hide #!4 models > show #!1 models > volume #1 level 0.007 > volume #1 level 0.006 > color radial #1 center 0,0,0 palette ^puor range 300,500 > volume #1 level 0.005 > volume #1 step 1 > volume #1 level 0.006 > volume #1 level 0.007 > open cmass_ad5_60_renum.pdb No such file/path: cmass_ad5_60_renum.pdb > open cmass_ad5_60_renum.pdb Chain information for cmass_ad5_60_renum.pdb #9 --- Chain | Description X | No description available > hide #!1 models > select #9 420 atoms, 419 pseudobonds, 420 residues, 2 models selected > style sel sphere Changed 420 atom styles > color (#!9 & sel) red > set #9 radius=2 Expected a keyword > setattr #9 radius=2 Missing or invalid "attrName" argument: Expected a text string > setattr #9 atom radius=2 Missing or invalid "attrValue" argument: Expected a text string > setattr #9 Atom radius=2 Missing or invalid "attrValue" argument: Expected a text string > setattr #9 atom radius 2 Assigning radius attribute to 420 items > setattr #9 atom radius 10 Assigning radius attribute to 420 items > show sel atoms > setattr #9 atom radius 10 color red Expected a keyword > select clear > setattr #9 atom radius=10 Missing or invalid "attrValue" argument: Expected a text string > close #9 > open tmp.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 50 Assigning radius attribute to 420 items > setattr #9 atom radius 20 Assigning radius attribute to 420 items > close #9 > open cmass_ad5_60.pdb Summary of feedback from opening cmass_ad5_60.pdb --- warnings | Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 54 messages similar to the above omitted > close #9 > open cmass60_tmp1.pdb > show #9 atoms > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > close #9 > open cmass60_tmp1.pdb > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > close #9 > open cmass60_tmp1.pdb > show #9 atoms > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > style #9 sphere Changed 420 atom styles > close #9 > open cmass60_tmp1.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 20 Assigning radius attribute to 420 items > setattr #9:HX1 color red Missing or invalid "attrValue" argument: Expected a text string > color #9:HX1 red > close #9 > open cmass_ad5_60_renum.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 20 Assigning radius attribute to 420 items > color #9:HX1 cornflowerblue > color #9:HX2 red > color #9:HX3 limegreen > color #9:HX4 gold > color #9:P3A forestgreen > color #9:HX3 lightbgreen Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #9:HX3 lightgreen > color #9:p8A yellow > color #9:p8B orange > color #9:HX4 khaki > show #!1 models > hide #!1 models > view view1 > ui tool show "Side View" > show #!1 models > hide #!1 models > show #!1 models > lighting soft > lighting simple > lighting soft > open movie_rock2.cxc > view view2 > movie record > rock y 30 180 > wait 180 > view view2 > wait 2 > hide #1 models > rock y -30 180 > wait 180 > view view2 > wait 2 > movie encode movie_ad5wt_markers.mp4 Movie saved to movie_ad5wt_markers.mp4 executed movie_rock2.cxc > view list Named views: view1, view2 > view view1 > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs ——— End of log from Thu Sep 21 21:26:56 2023 ——— opened ChimeraX session OpenGL version: 3.3.0 NVIDIA 535.104.05 OpenGL renderer: NVIDIA T400 4GB/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: Dell Inc. Model: Precision 5860 Tower OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 16 Intel(R) Xeon(R) w3-2435 Cache Size: 23040 KB Memory: total used free shared buff/cache available Mem: 125Gi 5.2Gi 115Gi 5.0Mi 4.6Gi 118Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 55:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 5000] [10de:1eb0] (rev a1) Subsystem: Dell TU104GL [Quadro RTX 5000] [1028:129f] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
Component: | Unassigned → Input/Output |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Crash recording movie |
comment:2 by , 2 years ago
Resolution: | → nonchimerax |
---|---|
Status: | assigned → closed |
ChimeraX crashed in your graphics driver while trying to create an image for a movie.
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/OpenGL/GL/images.py", line 369 in glReadPixels
Strangely the bug report says your driver is for Nvidia T400 graphics with 4 GB of memory, while the operating system claims you have a Quadro RTX 5000 (usually with 16 GB of memory) (Subsystem: Dell TU104GL [Quadro RTX 5000] [1028:129f]). Maybe your machine has two graphics cards. At any rate, 4 GB of memory is not very much, and running out of graphics memory is a common reason for graphics drivers to crash.
Your graphics driver is recent. (August 2023)
If your machine has two graphics cards it would help if ChimeraX was running with the Quadro RTX 5000 with 16 Gbytes of memory, especially if you are looking at large maps. The log suggests you had 800 x 800 x 800 maps open which take a good bit of memory.
Reported by Vijay Reddy