id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10218 ffmpeg failure david.chalmers@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-5.14.21-150500.53-default-x86_64-with-glibc2.35 ChimeraX Version: 1.7.dev202308212127 (2023-08-21 21:27:52 UTC) Description Installed the flatpak version of chimerax on opensuse 15.5 The installed version seems to run OK, but the 'spin movie' function fails. It does not seem to write the image frames to /usr/tmp Thanks David Log: Startup Messages --- warning | QCoreApplication::postEvent: Unexpected null receiver note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7.dev202308212127 (2023-08-21) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /vcp1/people/david/step2_orient_contacts_1.pdb Summary of feedback from opening /vcp1/people/david/step2_orient_contacts_1.pdb --- warning | Duplicate atom serial number found: 2869 Chain information for step2_orient_contacts_1.pdb #1 --- Chain | Description ? | No description available > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > movie record > turn y 2 180 > wait 180 > movie encode /vcp1/people/david/Desktop/movie1.mp4 /usr/bin/ffmpeg -r 25 -i /tmp/chimovie_Jjjo-%05d.ppm -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt yuv420p -crf 20 /vcp1/people/david/Desktop/movie1.mp4 stdout: stderr: ffmpeg version 5.0.3 Copyright (c) 2000-2022 the FFmpeg developers built with gcc 12.2.0 (GCC) configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu --optflags='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous- unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer ' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-needed ' --disable-stripping --disable-doc --disable-static --enable-shared --disable-everything --enable- ffplay --enable-ffprobe --enable-gnutls --enable-libaom --enable-libdav1d --enable-libfdk-aac --enable-libmp3lame --enable-libfontconfig --enable- libfreetype --enable-libopus --enable-libpulse --enable-libspeex --enable- libtheora --enable-libvorbis --enable-libvpx --enable-libwebp --enable-openal --enable-opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2 --enable-libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable- encoder='ac3,alac,flac,libfdk_aac,g723_1,mp2,libmp3lame,libopus,libspeex,pcm_alaw,pcm_mulaw,pcm_f32le,pcm_s16be,pcm_s24be,pcm_s16le,pcm_s24le,pcm_s32le,pcm_u8,tta,libvorbis,wavpack,' --enable- encoder='ass,ffv1,libaom_av1,libvpx_vp8,libvpx_vp9,mjpeg_vaapi,rawvideo,theora,vp8_vaapi,libopenh264' --enable- decoder='adpcm_g722,alac,flac,g723_1,g729,libfdk_aac,libopus,libspeex,mp2,mp3,m4a,pcm_alaw,pcm_mulaw,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_s16be,pcm_s16be_planar,pcm_s24be,pcm_s16le,pcm_s16le_planar,pcm_s24le,pcm_s24le_planar,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_u8,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,tta,vorbis,wavpack,' --enable- decoder='ass,ffv1,mjpeg,mjpegb,libaom_av1,libdav1d,libvpx_vp8,libvpx_vp9,rawvideo,theora,vp8,vp9,libopenh264' --enable-encoder='bmp,gif,jpegls,png,tiff,webp,' --enable- decoder='bmp,gif,jpegls,png,tiff,webp,' --enable- hwaccel='vp8_vaapi,mjpeg_vaapi,' --enable- parser='aac,ac3,flac,mjpeg,mpegaudio,mpeg4video,opus,vp3,vp8,vp9,vorbis,' --enable- muxer='ac3,ass,flac,g722,gif,matroska,mp3,mpegvideo,rtp,ogg,opus,pcm_s16be,pcm_s16le,wav,webm,' --enable- demuxer='aac,ac3,ass,flac,g722,gif,image_jpeg_pipe,image_png_pipe,image_webp_pipe,matroska,mjpeg,mov,mp3,mpegvideo,ogg,pcm_mulaw,pcm_alaw,pcm_s16be,pcm_s16le,rtp,wav,' --enable- filter='atempo,crop,scale,overlay,amix,amerge,aresample,format,aformat,fps,transpose,pad,' --enable-indev='v4l2,xcbgrab,' --enable- protocol='crypto,file,pipe,rtp,srtp,rtsp,tcp,udp,unix,' --arch=x86_64 --enable-libopenh264 libavutil 57. 17.100 / 57. 17.100 libavcodec 59. 18.100 / 59. 18.100 libavformat 59. 16.100 / 59. 16.100 libavdevice 59. 4.100 / 59. 4.100 libavfilter 8. 24.100 / 8. 24.100 libswscale 6. 4.100 / 6. 4.100 libswresample 4. 3.100 / 4. 3.100 /tmp/chimovie_Jjjo-%05d.ppm: No such file or directory An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: \----------------------------- Exit value: 1 Error message: stdout: stderr: ffmpeg version 5.0.3 Copyright (c) 2000-2022 the FFmpeg developers built with gcc 12.2.0 (GCC) configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu --optflags='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous- unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer ' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-needed ' --disable-stripping --disable-doc --disable-static --enable-shared --disable-everything --enable- ffplay --enable-ffprobe --enable-gnutls --enable-libaom --enable-libdav1d --enable-libfdk-aac --enable-libmp3lame --enable-libfontconfig --enable- libfreetype --enable-libopus --enable-libpulse --enable-libspeex --enable- libtheora --enable-libvorbis --enable-libvpx --enable-libwebp --enable-openal --enable-opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2 --enable-libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable- encoder='ac3,alac,flac,libfdk_aac,g723_1,mp2,libmp3lame,libopus,libspeex,pcm_alaw,pcm_mulaw,pcm_f32le,pcm_s16be,pcm_s24be,pcm_s16le,pcm_s24le,pcm_s32le,pcm_u8,tta,libvorbis,wavpack,' --enable- encoder='ass,ffv1,libaom_av1,libvpx_vp8,libvpx_vp9,mjpeg_vaapi,rawvideo,theora,vp8_vaapi,libopenh264' --enable- decoder='adpcm_g722,alac,flac,g723_1,g729,libfdk_aac,libopus,libspeex,mp2,mp3,m4a,pcm_alaw,pcm_mulaw,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_s16be,pcm_s16be_planar,pcm_s24be,pcm_s16le,pcm_s16le_planar,pcm_s24le,pcm_s24le_planar,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_u8,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,tta,vorbis,wavpack,' --enable- decoder='ass,ffv1,mjpeg,mjpegb,libaom_av1,libdav1d,libvpx_vp8,libvpx_vp9,rawvideo,theora,vp8,vp9,libopenh264' --enable-encoder='bmp,gif,jpegls,png,tiff,webp,' --enable- decoder='bmp,gif,jpegls,png,tiff,webp,' --enable- hwaccel='vp8_vaapi,mjpeg_vaapi,' --enable- parser='aac,ac3,flac,mjpeg,mpegaudio,mpeg4video,opus,vp3,vp8,vp9,vorbis,' --enable- muxer='ac3,ass,flac,g722,gif,matroska,mp3,mpegvideo,rtp,ogg,opus,pcm_s16be,pcm_s16le,wav,webm,' --enable- demuxer='aac,ac3,ass,flac,g722,gif,image_jpeg_pipe,image_png_pipe,image_webp_pipe,matroska,mjpeg,mov,mp3,mpegvideo,ogg,pcm_mulaw,pcm_alaw,pcm_s16be,pcm_s16le,rtp,wav,' --enable- filter='atempo,crop,scale,overlay,amix,amerge,aresample,format,aformat,fps,transpose,pad,' --enable-indev='v4l2,xcbgrab,' --enable- protocol='crypto,file,pipe,rtp,srtp,rtsp,tcp,udp,unix,' --arch=x86_64 --enable-libopenh264 libavutil 57. 17.100 / 57. 17.100 libavcodec 59. 18.100 / 59. 18.100 libavformat 59. 16.100 / 59. 16.100 libavdevice 59. 4.100 / 59. 4.100 libavfilter 8. 24.100 / 8. 24.100 libswscale 6. 4.100 / 6. 4.100 libswresample 4. 3.100 / 4. 3.100 /tmp/chimovie_Jjjo-%05d.ppm: No such file or directory \----------------------------- > save /vcp1/people/david/Desktop/image1.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /vcp1/people/david/Desktop/movie1.mp4 /usr/bin/ffmpeg -r 25 -i /tmp/chimovie_Jjjo-%05d.ppm -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt yuv420p -crf 20 /vcp1/people/david/Desktop/movie1.mp4 stdout: stderr: ffmpeg version 5.0.3 Copyright (c) 2000-2022 the FFmpeg developers built with gcc 12.2.0 (GCC) configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu --optflags='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous- unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer ' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-needed ' --disable-stripping --disable-doc --disable-static --enable-shared --disable-everything --enable- ffplay --enable-ffprobe --enable-gnutls --enable-libaom --enable-libdav1d --enable-libfdk-aac --enable-libmp3lame --enable-libfontconfig --enable- libfreetype --enable-libopus --enable-libpulse --enable-libspeex --enable- libtheora --enable-libvorbis --enable-libvpx --enable-libwebp --enable-openal --enable-opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2 --enable-libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable- encoder='ac3,alac,flac,libfdk_aac,g723_1,mp2,libmp3lame,libopus,libspeex,pcm_alaw,pcm_mulaw,pcm_f32le,pcm_s16be,pcm_s24be,pcm_s16le,pcm_s24le,pcm_s32le,pcm_u8,tta,libvorbis,wavpack,' --enable- encoder='ass,ffv1,libaom_av1,libvpx_vp8,libvpx_vp9,mjpeg_vaapi,rawvideo,theora,vp8_vaapi,libopenh264' --enable- decoder='adpcm_g722,alac,flac,g723_1,g729,libfdk_aac,libopus,libspeex,mp2,mp3,m4a,pcm_alaw,pcm_mulaw,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_s16be,pcm_s16be_planar,pcm_s24be,pcm_s16le,pcm_s16le_planar,pcm_s24le,pcm_s24le_planar,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_u8,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,tta,vorbis,wavpack,' --enable- decoder='ass,ffv1,mjpeg,mjpegb,libaom_av1,libdav1d,libvpx_vp8,libvpx_vp9,rawvideo,theora,vp8,vp9,libopenh264' --enable-encoder='bmp,gif,jpegls,png,tiff,webp,' --enable- decoder='bmp,gif,jpegls,png,tiff,webp,' --enable- hwaccel='vp8_vaapi,mjpeg_vaapi,' --enable- parser='aac,ac3,flac,mjpeg,mpegaudio,mpeg4video,opus,vp3,vp8,vp9,vorbis,' --enable- muxer='ac3,ass,flac,g722,gif,matroska,mp3,mpegvideo,rtp,ogg,opus,pcm_s16be,pcm_s16le,wav,webm,' --enable- demuxer='aac,ac3,ass,flac,g722,gif,image_jpeg_pipe,image_png_pipe,image_webp_pipe,matroska,mjpeg,mov,mp3,mpegvideo,ogg,pcm_mulaw,pcm_alaw,pcm_s16be,pcm_s16le,rtp,wav,' --enable- filter='atempo,crop,scale,overlay,amix,amerge,aresample,format,aformat,fps,transpose,pad,' --enable-indev='v4l2,xcbgrab,' --enable- protocol='crypto,file,pipe,rtp,srtp,rtsp,tcp,udp,unix,' --arch=x86_64 --enable-libopenh264 libavutil 57. 17.100 / 57. 17.100 libavcodec 59. 18.100 / 59. 18.100 libavformat 59. 16.100 / 59. 16.100 libavdevice 59. 4.100 / 59. 4.100 libavfilter 8. 24.100 / 8. 24.100 libswscale 6. 4.100 / 6. 4.100 libswresample 4. 3.100 / 4. 3.100 /tmp/chimovie_Jjjo-%05d.ppm: No such file or directory An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: \----------------------------- Exit value: 1 Error message: stdout: stderr: ffmpeg version 5.0.3 Copyright (c) 2000-2022 the FFmpeg developers built with gcc 12.2.0 (GCC) configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu --optflags='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous- unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer ' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-needed ' --disable-stripping --disable-doc --disable-static --enable-shared --disable-everything --enable- ffplay --enable-ffprobe --enable-gnutls --enable-libaom --enable-libdav1d --enable-libfdk-aac --enable-libmp3lame --enable-libfontconfig --enable- libfreetype --enable-libopus --enable-libpulse --enable-libspeex --enable- libtheora --enable-libvorbis --enable-libvpx --enable-libwebp --enable-openal --enable-opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2 --enable-libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable- encoder='ac3,alac,flac,libfdk_aac,g723_1,mp2,libmp3lame,libopus,libspeex,pcm_alaw,pcm_mulaw,pcm_f32le,pcm_s16be,pcm_s24be,pcm_s16le,pcm_s24le,pcm_s32le,pcm_u8,tta,libvorbis,wavpack,' --enable- encoder='ass,ffv1,libaom_av1,libvpx_vp8,libvpx_vp9,mjpeg_vaapi,rawvideo,theora,vp8_vaapi,libopenh264' --enable- decoder='adpcm_g722,alac,flac,g723_1,g729,libfdk_aac,libopus,libspeex,mp2,mp3,m4a,pcm_alaw,pcm_mulaw,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_s16be,pcm_s16be_planar,pcm_s24be,pcm_s16le,pcm_s16le_planar,pcm_s24le,pcm_s24le_planar,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_u8,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,tta,vorbis,wavpack,' --enable- decoder='ass,ffv1,mjpeg,mjpegb,libaom_av1,libdav1d,libvpx_vp8,libvpx_vp9,rawvideo,theora,vp8,vp9,libopenh264' --enable-encoder='bmp,gif,jpegls,png,tiff,webp,' --enable- decoder='bmp,gif,jpegls,png,tiff,webp,' --enable- hwaccel='vp8_vaapi,mjpeg_vaapi,' --enable- parser='aac,ac3,flac,mjpeg,mpegaudio,mpeg4video,opus,vp3,vp8,vp9,vorbis,' --enable- muxer='ac3,ass,flac,g722,gif,matroska,mp3,mpegvideo,rtp,ogg,opus,pcm_s16be,pcm_s16le,wav,webm,' --enable- demuxer='aac,ac3,ass,flac,g722,gif,image_jpeg_pipe,image_png_pipe,image_webp_pipe,matroska,mjpeg,mov,mp3,mpegvideo,ogg,pcm_mulaw,pcm_alaw,pcm_s16be,pcm_s16le,rtp,wav,' --enable- filter='atempo,crop,scale,overlay,amix,amerge,aresample,format,aformat,fps,transpose,pad,' --enable-indev='v4l2,xcbgrab,' --enable- protocol='crypto,file,pipe,rtp,srtp,rtsp,tcp,udp,unix,' --arch=x86_64 --enable-libopenh264 libavutil 57. 17.100 / 57. 17.100 libavcodec 59. 18.100 / 59. 18.100 libavformat 59. 16.100 / 59. 16.100 libavdevice 59. 4.100 / 59. 4.100 libavfilter 8. 24.100 / 8. 24.100 libswscale 6. 4.100 / 6. 4.100 libswresample 4. 3.100 / 4. 3.100 /tmp/chimovie_Jjjo-%05d.ppm: No such file or directory \----------------------------- OpenGL version: 3.3.0 NVIDIA 520.61.05 OpenGL renderer: NVIDIA GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=/usr/share/xsessions/plasma5 XDG_SESSION_DESKTOP=KDE XDG_CURRENT_DESKTOP=KDE DISPLAY=:1 Manufacturer: Micro-Star International Co., Ltd. Model: MS-7B09 OS: Freedesktop SDK 22.08 Flatpak runtime Architecture: 64bit ELF Virtual Machine: detection failed CPU: 32 AMD Ryzen Threadripper 1950X 16-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 31Gi 6.9Gi 362Mi 903Mi 23Gi 22Gi Swap: 2.0Gi 878Mi 1.1Gi Graphics: 0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1) Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:3362] 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 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.7.22 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.47.1 ChimeraX-AtomicLibrary: 10.0.8 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.4 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: 1.7.dev202308212127 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: 1.1.2 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: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2 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: 2.1.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.10 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.2 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.9 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: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.1 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: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.31.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.2 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: 0.1.4 contourpy: 1.1.0 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7.post1 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.42.1 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.0 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.8 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.7 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.5 numpy: 1.25.1 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: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.2 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.7.1 tzdata: 2023.3 urllib3: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.8 }}} " defect closed normal 1.7 Input/Output fixed Tom Goddard all ChimeraX