Opened 2 years ago

Closed 2 years ago

#9826 closed defect (nonchimerax)

Crash recording movie

Reported by: vsreddy@… 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 Eric Pettersen, 2 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash recording movie

Reported by Vijay Reddy

comment:2 by Tom Goddard, 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.

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