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Opened 3 weeks ago
Closed 3 weeks ago
#19324 closed defect (duplicate)
ffmpeg: Permission denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
After Gromacs modeling of a protein (~230aa) in water for 1 nanosecond (1001 frames), cannot save the animation as a movie. Can you help, please?
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jleung/Downloads/GROMACS AF_NATA2 300k-iosmu/md/md.gro"
Summary of feedback from opening /Users/jleung/Downloads/GROMACS AF_NATA2
300k-iosmu/md/md.gro
---
note | Singleton residues assigned chain ID B
Chain information for Protein in water #1
---
Chain | Description
A | No description available
> open "/Users/jleung/Downloads/GROMACS AF_NATA2 300k-iosmu/md/traj.xtc"
Replaced existing frames of Protein in water #1 with 1001 new frames
> set bgColor white
> select ::name="SOL"
351102 atoms, 234068 bonds, 117034 residues, 1 model selected
> color sel #efffefff
[Repeated 1 time(s)]
> color sel #edfff0ff
> color sel #e6fff3ff
[Repeated 1 time(s)]
> color sel #e8fff2ff
> color sel #e9fff2ff
> color sel #eafff4ff
> color sel #f1fff4ff
> color sel #fafffeff
> color sel #fbfeffff
> color sel #f4f2ffff
> color sel light gray
> select protein
3712 atoms, 3774 bonds, 236 residues, 1 model selected
> color sel #f7fffdff
[Repeated 1 time(s)]
> color sel #fafffeff
> color sel #fcfbffff
> color sel #fdf6ffff
> color sel #ffeeffff
> color sel #ffe9ffff
> color sel #fee4ffff
> color sel #fee1ffff
> color sel #fedaffff
> color sel #fed4ffff
> color sel #feccffff
> color sel #fbc1ffff
> color sel #f8b7ffff
> color sel #f7b3ffff
> color sel #f6afffff
> color sel #f6adffff
> color sel #f5aaffff
> color sel #f5a9ffff
> color sel #f5a7ffff
> color sel #f5a5ffff
> color sel #f4a3ffff
> color sel #f39fffff
> color sel #f39bffff
> color sel #f294ffff
> color sel #f18dffff
> color sel #f18cffff
[Repeated 1 time(s)]
> color sel #ee8afcff
> color sel #e686f4ff
> color sel #dd81eaff
> color sel #d67ce2ff
> color sel #d27adeff
> color sel #cd77d9ff
> color sel #c975d5ff
> color sel #c572d0ff
> color sel #c070cbff
> color sel #bb6dc6ff
> color sel #b96bc3ff
> color sel #b66ac0ff
> color sel #b468beff
> color sel #b167bcff
> color sel #b066baff
> color sel #ae65b8ff
> color sel #ab64b5ff
> color sel #a962b2ff
> color sel #a761b1ff
> color sel #a661b0ff
> color sel #a660afff
> color sel #a560aeff
> color sel #a35facff
> color sel #a05daaff
> color sel #9d5ba6ff
> color sel #9b5aa4ff
> color sel #96579fff
> color sel #92559aff
> color sel #8f5397ff
> color sel #8c5194ff
> color sel #8a5092ff
> color sel #894f91ff
> color sel #884f90ff
> color sel #864e8eff
> color sel #854d8dff
> color sel #834c8bff
> color sel #824b89ff
> color sel #7e4986ff
> color sel #7c4883ff
[Repeated 1 time(s)]
> color sel #7b4882ff
> color sel #794780ff
> color sel #794680ff
> color sel #724278ff
> color sel #613967ff
> color sel #512f56ff
> color sel #482a4cff
> color sel #3e2442ff
> color sel #362039ff
> color sel #321d35ff
> color sel #2d1a2fff
> color sel #271629ff
> color sel #221424ff
> color sel #1d111eff
> color sel #180e1aff
> color sel #150c16ff
> color sel #120a13ff
> color sel #0f080fff
> color sel #0c070dff
> color sel #09050aff
> color sel #050305ff
> color sel #020102ff
> color sel #000000ff
> select clear
> color #000000ff
> color #2a182cff
> color #4a2b4fff
> color #693d6fff
> color #7e4985ff
> color #9d5ba6ff
> color #a45faeff
> color #ab63b5ff
> color #ac64b6ff
[Repeated 3 time(s)]
> color #ad64b7ff
> color #b368bdff
> color #bd6ec8ff
> color #bf6fcaff
> color #c170ccff
> color #c271ceff
[Repeated 1 time(s)]
> color #bd6ec8ff
> color #b368beff
> color #af66b9ff
> color #a761b0ff
> color #a45faeff
> color #a45fadff
> color #a962b3ff
> color #ad65b7ff
> color #b569bfff
> color #bb6dc6ff
> color #ca75d6ff
> color #cc76d8ff
> color #cd77d9ff
> color #d079dcff
> color #d37bdfff
[Repeated 1 time(s)]
> color #d179ddff
> color #d079dcff
> select ::name="SOL"
351102 atoms, 234068 bonds, 117034 residues, 1 model selected
> color sel #d382dcff
> color sel #dcd2dcff
> color sel #d8dcdaff
> select clear
> color #d8dddaff
> color #e2e6e4ff
> color #e8edeaff
> color #ecf1efff
> color #f0f5f2ff
> color #f1f6f3ff
> color #f6fbf8ff
> color #f8fdfbff
> color #f9fefbff
> color #f3f8f5ff
> color #e9eeecff
> color #dfe4e2ff
> color #dadedcff
> color #d7dbd9ff
> color #cfd3d1ff
> color #c6cac8ff
> color #c4c8c6ff
> color #bec2c0ff
> color #b6b9b8ff
> color #b9bdbbff
> color #d9dedbff
> color #e7ece9ff
> color #f2f7f5ff
> color #f9fefbff
> color #fafffcff
> select protein
3712 atoms, 3774 bonds, 236 residues, 1 model selected
> color sel #effff4ff
[Repeated 1 time(s)]
> color sel #f2fff4ff
> color sel #fffdf7ff
> color sel #fff1efff
> color sel #ffe5e7ff
> color sel #ffdbe2ff
> color sel #ffd9e1ff
> color sel #ffd7e0ff
> color sel #ffd2dfff
> color sel #ffcee0ff
> color sel #ffc3e3ff
> color sel #ffb6e6ff
> color sel #ffafe6ff
> color sel #ffa8e1ff
> color sel #ff9ad1ff
> color sel #ff90c6ff
> color sel #ff7fb5ff
> color sel #ff72aaff
> color sel #ff609cff
> color sel #ff3d80ff
> color sel #ff296eff
> color sel #ff1b61ff
> color sel #ff185dff
> color sel #ff114dff
> color sel #ff0c42ff
> color sel #ff0635ff
> color sel #ff032dff
> color sel #ff0126ff
> color sel #ff0125ff
> color sel #ff0124ff
> color sel #ff0324ff
> color sel #ff0524ff
> color sel #ff0924ff
> color sel #ff0a25ff
> color sel #ff0b25ff
> color sel #ff0c25ff
> color sel #ff0d26ff
> color sel #ff0e27ff
> style sel stick
Changed 3712 atom styles
> select clear
> color #ff0e27ff
> color #f10d25ff
> color #de0c22ff
> color #cd0b20ff
> color #c80b1fff
> color #c70b1fff
[Repeated 1 time(s)]
> color #c90b1fff
> color #dc0c22ff
> color #f20d25ff
> color #ff0e27ff
> color #ff0e1dff
> color #ff0f1eff
> color #ff617aff
> color #ffbeecff
> color #d1c8ffff
> color #d3deffff
> color #def7ffff
> color #ddf8ffff
> color #a4f2ffff
> color #35ecffff
> color #26eaffff
> color #16ecffff
> color #00faffff
> color #00fcffff
> color #00faffff
> color #adfffeff
> color #edfffdff
> color #ecf7ffff
> color #c9ceffff
> color #6265ffff
> color #4958ffff
> color #4156ffff
> color #4a5dffff
> color #8c89ffff
> color #ad9effff
> color #bfa9ffff
> color #ceb4ffff
> color #d0b7ffff
> color #dcceffff
> color #e8e7ffff
> color #edefffff
> color #eef1ffff
> color #f3fbffff
> color #f7fffcff
> color #f9fff6ff
> color #f9ffebff
> color #fcffe9ff
> color #fffce8ff
> color #fffbe7ff
> color #fffae9ff
> color #fff8eaff
> color #fff6eaff
[Repeated 1 time(s)]
> color #fff3edff
> color #fff0efff
> color #fff4faff
> color #fff6ffff
> color #fef5ffff
> color #fdf6ffff
> color #fffcfdff
> color #fffdfaff
[Repeated 1 time(s)]
> color #fffffcff
> color #f6fffeff
[Repeated 1 time(s)]
> color #f6ffffff
> color sel light gray
> select ribbon
Expected an objects specifier or a keyword
> select /A
3712 atoms, 3774 bonds, 236 residues, 1 model selected
> color sel red
> select clear
> select sol
Expected an objects specifier or a keyword
> hide atoms
> show atoms
> select ::name="CL"
327 atoms, 327 residues, 1 model selected
> hide sel atoms
> select ::name="NA"
331 atoms, 331 residues, 1 model selected
> hide sel atoms
> select /A
3712 atoms, 3774 bonds, 236 residues, 1 model selected
> color sel red
> style sel sphere
Changed 3712 atom styles
> select clear
> select ::name="SOL"
351102 atoms, 234068 bonds, 117034 residues, 1 model selected
> hide sel atoms
> color sel #f6ffffff
> color sel #dde5e6ff
> color sel #c4cbcbff
> color sel #bec5c5ff
> color sel #bdc4c4ff
> color sel #bfc6c6ff
> color sel #c1c8c8ff
> color sel #f5fdfeff
> color sel #f6ffffff
> style sel stick
Changed 351102 atom styles
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 3712 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select ::name="CL"
327 atoms, 327 residues, 1 model selected
> show sel atoms
> select ::name="NA"
331 atoms, 331 residues, 1 model selected
> show sel atoms
> select solvent
351760 atoms, 234068 bonds, 117692 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select solvent
351760 atoms, 234068 bonds, 117692 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select ions
Nothing selected
> show atoms
> hide atoms
> select solvent
351760 atoms, 234068 bonds, 117692 residues, 1 model selected
> show sel atoms
> color sel #f6ffffff
> color sel #e4ececff
> color sel #d1d9d9ff
> color sel #9ca2a2ff
> color sel #717575ff
> color sel #656868ff
[Repeated 1 time(s)]
> color sel #666a6aff
> color sel #c6cdcdff
> color sel #f6ffffff
[Repeated 1 time(s)]
> color sel #f6fffffd
> color sel #f6ffffa8
> color sel #f6ffff83
> color sel #f6ffff82
> color sel #f6ffff65
> color sel #f6ffff4d
> color sel #f6ffff3c
> color sel #f6ffff1b
> color sel #f6ffff00
> select clear
> select solvent
351760 atoms, 234068 bonds, 117692 residues, 1 model selected
> save "/Users/jleung/Desktop/GROMACS_AF2_NATA2 monomer_water.tif" width 878
> height 648 supersample 3
> color sel #f6ffff00
> color sel #dee7e700
> color sel #c9d0d000
> color sel #afb5b500
> color sel #a5abab00
> select clear
> color #a4aaaa00
> color #80858500
> color #696d6d00
> color #5f626200
[Repeated 1 time(s)]
> color #61656500
> color #70747400
> color #91969700
> color #979c9c00
> color #9da2a200
> color #9da3a300
> color #a4aaaa00
> color #a8afaf00
> color #bac1c100
> color #e1e9e900
> color #f6ffff00
[Repeated 1 time(s)]
> color #f6ffff24
> color #f6ffff72
> color #f6ffff93
> color #f6ffffaa
> color #f6ffffb1
> color #f6ffffb3
> color #f6ffffc0
> color #f6ffffc7
[Repeated 1 time(s)]
> color #f6ffffc8
> color #f6ffffcd
> color #f6ffffdc
> color #f6ffffde
[Repeated 1 time(s)]
> color #f6ffffdd
> color #f6ffffd9
> color #f6ffffc0
> color #f6ffffbc
[Repeated 1 time(s)]
> color #f6ffffbe
> color #f5fefebe
> color #838888be
> color #393b3bbe
> color #151515be
> color #0b0c0cbe
[Repeated 1 time(s)]
> color #1b1c1cbe
> color #414444be
> color #a1a7a7be
> color #c6cecebe
> color #c7cecebe
> color #c9d1d1be
> color #cad1d1be
> color #cad2d2be
> select protein
3712 atoms, 3774 bonds, 236 residues, 1 model selected
> color sel red
> select clear
> color #cad2d2bd
> color #cad2d298
> color #cad2d27e
> color #cad2d26e
> color #cad2d26d
> color #cad2d280
> color #cad2d2ad
> color #cad2d2cd
> color #cad2d2d7
> color #cad2d2de
> color #cad2d2dd
> color #cad2d2db
[Repeated 1 time(s)]
> color #cad2d2d6
> color #cad2d2c9
> color #cad2d2b5
> color #cad2d2a1
> color #cad2d296
> color #cad2d295
[Repeated 1 time(s)]
> color #d5dcdc95
> color #f6ffff95
> color #f3fcfc95
> color #d5dddd95
> color #c3cbcb95
> color #b7bebe95
> color #b3baba95
> color #a7adad95
> color #a4aaaa95
[Repeated 2 time(s)]
> color #a5abab95
> color #a7adad95
> color #a7aeae95
> color #a8aeae95
> color #aab0b095
> color #bac1c195
> color #c1c8c895
> color #c3caca95
[Repeated 1 time(s)]
> color #bbc2c295
> color #b3b9b995
> color #b93e5595
> color #b9405195
> color #b94b5c95
> color #b0aab995
> color #a6acb995
> color #a3b3b995
> color #a6b9af95
> color #a7b9ae95
> color #abb9ae95
> color #adb9af95
> color #afb9b195
> color #b0b9b195
[Repeated 1 time(s)]
> color #b0b9b167
> color #b0b9b100
> color #b0b9b10a
> color #b0b9b11f
> color #b0b9b12a
> color #b0b9b135
> color #b0b9b13a
> color #b0b9b142
[Repeated 1 time(s)]
> color #b0b9b147
> color #b0b9b14a
[Repeated 1 time(s)]
> color #b0b9b14f
> color #b0b9b156
> color #b0b9b159
> select protein
3712 atoms, 3774 bonds, 236 residues, 1 model selected
> color sel red
> select clear
> color #b0b9b158
> color #b0b9b153
> color #b0b9b14e
[Repeated 1 time(s)]
> color #b0b9b150
> color #b0b9b155
> color #b0b9b15b
> color #b0b9b160
> color #b0b9b166
> color #b0b9b16e
> color #b0b9b175
> color #b0b9b177
[Repeated 1 time(s)]
> color #b0b9b180
> color #b0b9b189
> color #b0b9b190
> color #b0b9b197
> color #b0b9b19d
> color #b0b9b1a3
> color #b0b9b1a4
> select /A
3712 atoms, 3774 bonds, 236 residues, 1 model selected
> color sel red
> select clear
> select /A
3712 atoms, 3774 bonds, 236 residues, 1 model selected
> select ::name="SOL"
351102 atoms, 234068 bonds, 117034 residues, 1 model selected
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:73-116
699 atoms, 713 bonds, 44 residues, 1 model selected
> select /A:116-133
270 atoms, 274 bonds, 18 residues, 1 model selected
> select /A:168
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:168-171
77 atoms, 76 bonds, 4 residues, 1 model selected
> select /A:116-126
163 atoms, 165 bonds, 11 residues, 1 model selected
> select /A:116-135
298 atoms, 302 bonds, 20 residues, 1 model selected
> movie record
> movie encode /Users/jleung/Desktop/movie1.mp4 framerate 25.0
Traceback (most recent call last):
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 211, in record_cb
run(ses, f'movie encode %s framerate %.1f'
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode
encode_op(session, output[-1], format, quality, qscale, bitrate,
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding
self.encoder.run(Status_Reporter())
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied:
'/Applications/Chimera/ChimeraX-1.10.app/Contents/bin/ffmpeg'
PermissionError: [Errno 13] Permission denied:
'/Applications/Chimera/ChimeraX-1.10.app/Contents/bin/ffmpeg'
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15Y000YKFN/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 5 hours, 15 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 2.1.2
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 2.2.6
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.0.1
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.8.1
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tomlkit: 0.13.2
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 3 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Build System |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: Permission denied |
comment:2 by , 3 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Jeffrey,
--Eric