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Opened 8 hours ago
#19917 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Linux-6.18.13-200.fc43.x86_64-x86_64-with-glibc2.40
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Making movies doesn't work with a flatpak installation.
The session leading to this bug report is a minimal way to replicate the bug. Here is what I did / how to replicate:
1. start the Flatpak ChimeraX from the desktop's app launcher
2. open any PDB entry
3. click the "Spin movie" button
Expected result: the movie is generated and saved in the ~/Desktop folder.
Actual result: "Error opening output files: Encoder not found"
(see full Log attached)
FFmpeg 7.1.2 (built with gcc 15) is installed system-wide and in PATH at /usr/bin/ffmpeg, but the ChimeraX Log shows it is trying to use ffmpeg 7.0.3 (built with gcc 14.3.0). This one is probably provided by the flatpak org.freedesktop.Platform.ffmpeg-full (24.08) installed on this system.
Log:
Startup Messages
---
note | CubeNTube: sphere eraser undo support enabled
> open /var/home/guillaume/codeberg/chimerax-config/init.cxc
> open commands/alphafold.cxc
> alias afresults mmaker ~$1 to $1; hide ~$1 models; view $1; mseries slider
> all; preset custom 'alphafold results'
> alias afcolor color bfactor $1 palette alphafold
executed alphafold.cxc
> open commands/backbonetrace.cxc
> alias bbsidechains hide $1 cartoons; hide $1 surfaces; hide $1; show
> $1@CA&protein; show $1@P&nucleic; style $1 stick; show $1&sidechain; show
> $1&~backbone&nucleic; size stickradius 0.1; size pseudobondradius 0.1
> alias bbtrace hide $1 cartoons; hide $1 surfaces; hide $1; show
> $1@CA&protein; show $1@P&nucleic; style $1 stick; size stickradius 0.1; size
> pseudobondradius 0.1
executed backbonetrace.cxc
> open commands/servalcat.cxc
> alias servalcatresults open refined.mmcif; open diffmap_normalized_fo.mrc;
> open diffmap_normalized_fofc.mrc; isolde start; clipper associate #2 toModel
> #1; clipper associate #3 toModel #1
executed servalcat.cxc
> open ui/defaults.cxc
> preset custom "guillaume default mol display"
Using preset: Custom / Guillaume Default Mol Display
Preset expands to these ChimeraX commands:
# My usual display mode
graphics silhouettes true
lighting soft
set bgcolor white
executed defaults.cxc
> open ui/aliases.cxc
> alias cofron cofr centerofview showPivot 3,0.1
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias mapsphere surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance $1; close #10000
> alias mapunsphere surface unzone ##~num_residues
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
executed aliases.cxc
> open ui/buttons.cxc
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add Models command "tool show 'Model Panel'"
> buttonpanel Shortcuts add Volumes command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add "Coot mode" command "preset custom 'oli coot mode
> mesh'"
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add "Clip 10" command "symclip 10"
> buttonpanel Shortcuts add "Show maps" command showmaps
> buttonpanel Shortcuts add "Map sphere 15" command "mapsphere 15"
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add "Clip off" command "clip off"
> buttonpanel Shortcuts add "Hide maps" command hidemaps
> buttonpanel Shortcuts add "Map unsphere" command mapunsphere
executed buttons.cxc
executed init.cxc
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1aoi
1aoi title:
Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 BP long DNA
fragment [more info...]
Chain information for 1aoi #1
---
Chain | Description | UniProt
A E | HISTONE H3 | H32_XENLA 20-135
B F | HISTONE H4 | H4_XENLA 16-102
C G | HISTONE H2A | H2A1_XENLA 4-119
D H | HISTONE H2B | H2B1_XENLA 24-122
I J | PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA |
Non-standard residues in 1aoi #1
---
MN — manganese (II) ion
> movie record
> turn y 2 180
> wait 180
> movie encode /var/home/guillaume/Desktop/movie1.mp4
/usr/bin/ffmpeg -r 25 -i /tmp/chimovie_Angk-%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 /var/home/guillaume/Desktop/movie1.mp4
stdout:
stderr:
ffmpeg version 7.0.3 Copyright (c) 2000-2025 the FFmpeg developers
built with gcc 14.3.0 (GCC)
configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu
--optflags='-O2 -pipe -g -Wp,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS
-fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-
unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer
-mno-omit-leaf-frame-pointer ' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-
needed ' --disable-stripping --disable-doc --disable-static --disable-encoders
--disable-decoders --enable-shared --enable-gnutls --enable-gcrypt --enable-
ladspa --enable-lcms2 --enable-libaom --enable-libdav1d --enable-libmp3lame
--enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-
libjxl --enable-libopus --enable-libpulse --enable-libspeex --enable-libtheora
--enable-libvorbis --enable-libvpx --enable-librsvg --enable-libwebp --enable-
libxml2 --enable-libopenjpeg --enable-libsvtav1 --enable-openal --enable-
opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2 --enable-
libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable-libopenh264
--arch=x86_64 --enable-libfdk-aac --enable-
encoder='a64multi,a64multi5,aac,libfdk_aac,ac3,adpcm_adx,adpcm_argo,adpcm_g722,adpcm_g726,adpcm_g726le,adpcm_ima_alp,adpcm_ima_amv,adpcm_ima_apm,adpcm_ima_qt,adpcm_ima_ssi,adpcm_ima_wav,adpcm_ima_ws,adpcm_ms,adpcm_swf,adpcm_yamaha,alac,alias_pix,amv,anull,apng,ass,asv1,asv2,av1_amf,av1_nvenc,av1_qsv,av1_vaapi,bitpacked,bmp,cinepak,cljr,dca,dfpwm,dnxhd,dpx,dvbsub,dvdsub,dvvideo,exr,ffv1,ffvhuff,flac,flashsv,flashsv2,flv,g723_1,gif,h261,h263,h263_v4l2m2m,h263p,h264_amf,h264_nvenc,h264_qsv,h264_v4l2m2m,h264_vaapi,hap,hdr,hevc_amf,hevc_nvenc,hevc_qsv,hevc_v4l2m2m,hevc_vaapi,huffyuv,ilbc,jpeg2000,jpegls,libaom,libaom_av1,libcodec2,libgsm,libgsm_ms,libilbc,libjxl,libmp3lame,libopencore_amrnb,libopenh264,libopenjpeg,libopus,librav1e,libspeex,libsvtav1,libtheora,libtwolame,libvo_amrwbenc,libvorbis,libvpx_vp8,libvpx_vp9,libwebp,libwebp_anim,libxvid,mjpeg,mjpeg_qsv,mjpeg_vaapi,mlp,mp2,mp2fixed,mpeg1video,mpeg2_qsv,mpeg2_vaapi,mpeg2video,mpeg4,mpeg4_v4l2m2m,msmpeg4v2,msmpeg4v3,msvideo1,nellymoser,opus,pam,pbm,pcm_alaw,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_mulaw,pcm_s16be,pcm_s16be_planar,pcm_s16le,pcm_s16le_planar,pcm_s24be,pcm_s24le,pcm_s24le_planar,pcm_s32be,pcm_s32le,pcm_s32le_planar,pcm_s8,pcm_s8_planar,pcm_u16be,pcm_u16le,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,pcm_u8,pcx,pgm,pgmyuv,phm,png,ppm,qoi,qtrle,r10k,r210,ra_144,rawvideo,roq,roq_dpcm,rpza,rv10,rv20,s302m,sbc,sgi,smc,snow,sonic,sonic_ls,speedhq,srt,ssa,subrip,sunrast,svq1,targa,text,tiff,truehd,tta,ttml,utvideo,v210,v308,v408,v410,vc1_qsv,vc1_v4l2m2m,vc2,vnull,vorbis,vp8_qsv,vp8_v4l2m2m,vp8_vaapi,vp9_qsv,vp9_vaapi,wavpack,wbmp,webvtt,wmav1,wmav2,wmv1,wmv2,wrapped_avframe,xbm,xface,xsub,xwd,y41p,yuv4,zlib,zmbv,'
--enable-
decoder='aasc,libfdk_aac,ac3,acelp_kelvin,adpcm_4xm,adpcm_adx,adpcm_afc,adpcm_agm,adpcm_aica,adpcm_argo,adpcm_ct,adpcm_dtk,adpcm_ea,adpcm_ea_maxis_xa,adpcm_ea_r1,adpcm_ea_r2,adpcm_ea_r3,adpcm_ea_xas,adpcm_g722,adpcm_g726,adpcm_g726le,adpcm_ima_acorn,adpcm_ima_alp,adpcm_ima_amv,adpcm_ima_apc,adpcm_ima_apm,adpcm_ima_cunning,adpcm_ima_dat4,adpcm_ima_dk3,adpcm_ima_dk4,adpcm_ima_ea_eacs,adpcm_ima_ea_sead,adpcm_ima_iss,adpcm_ima_moflex,adpcm_ima_mtf,adpcm_ima_oki,adpcm_ima_qt,adpcm_ima_qt_at,adpcm_ima_rad,adpcm_ima_smjpeg,adpcm_ima_ssi,adpcm_ima_wav,adpcm_ima_ws,adpcm_ms,adpcm_mtaf,adpcm_psx,adpcm_sbpro_2,adpcm_sbpro_3,adpcm_sbpro_4,adpcm_swf,adpcm_thp,adpcm_thp_le,adpcm_vima,adpcm_xa,adpcm_xmd,adpcm_yamaha,adpcm_zork,alac,alias_pix,amrnb,amrwb,amv,anm,ansi,anull,apac,ape,apng,arbc,argo,ass,asv1,asv2,atrac1,atrac3,atrac3al,atrac3p,atrac3pal,aura,aura2,av1,av1_qsv,bethsoftvid,bfi,bink,binkaudio_dct,binkaudio_rdft,bintext,bitpacked,bmp,bmv_audio,bmv_video,bonk,brender_pix,c93,cbd2_dpcm,ccaption,cdgraphics,cdtoons,cdxl,cinepak,clearvideo,cljr,cook,cpia,cscd,cyuv,dca,dds,derf_dpcm,dfa,dfpwm,dirac,dnxhd,dolby_e,dpx,dsd_lsbf,dsd_msbf,dsicinaudio,dsicinvideo,dss_sp,dvaudio,dvbsub,dvdsub,dvvideo,dxa,dxtory,eacmv,eamad,eatgq,eatgv,eatqi,eightbps,eightsvx_exp,eightsvx_fib,escape124,escape130,evrc,exr,ffv1,ffvhuff,ffwavesynth,fits,flac,flashsv,flashsv2,flic,flv,fmvc,fourxm,ftr,g723_1,g729,gdv,gem,gif,gremlin_dpcm,gsm,gsm_ms,gsm_ms_at,h261,h263,h263_v4l2m2m,h263i,h263p,hap,hca,hcom,hdr,hnm4_video,hq_hqa,hqx,huffyuv,hymt,iac,idcin,idf,iff_ilbm,ilbc,imc,indeo2,indeo3,indeo4,indeo5,interplay_acm,interplay_dpcm,interplay_video,ipu,jacosub,jpeg2000,jpegls,jv,kgv1,kmvc,lagarith,libaom,libaom_av1,libcodec2,libdav1d,libgsm,libgsm_ms,libilbc,libjxl,libopencore_amrnb,libopencore_amrwb,libopenh264,libopenjpeg,libopus,librsvg,libschroedinger,libspeex,libvorbis,libvpx_vp8,libvpx_vp9,libzvbi_teletext,loco,lscr,m101,mace3,mace6,mdec,media100,metasound,microdvd,mimic,misc4,mjpeg,mjpeg_qsv,mjpegb,mlp,mmvideo,motionpixels,mp1,mp1float,mp2,mp2float,mp3,mp3adu,mp3adufloat,mp3float,mp3on4,mp3on4float,mpc7,mpc8,mpeg1_v4l2m2m,mpeg1video,mpeg2_qsv,mpeg2_v4l2m2m,mpeg2video,mpeg4,mpeg4_v4l2m2m,mpegvideo,mpl2,msa1,mscc,msmpeg4v1,msmpeg4v2,msmpeg4v3,msnsiren,msp2,msrle,mss1,mss2,msvideo1,mszh,mts2,mv30,mvc1,mvc2,mvdv,mvha,mwsc,mxpeg,nellymoser,nuv,on2avc,opus,paf_audio,paf_video,pam,pbm,pcm_alaw,pcm_bluray,pcm_dvd,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_lxf,pcm_mulaw,pcm_s16be,pcm_s16be_planar,pcm_s16le,pcm_s16le_planar,pcm_s24be,pcm_s24daud,pcm_s24le,pcm_s24le_planar,pcm_s32be,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_sga,pcm_u16be,pcm_u16le,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,pcm_u8,pcm_vidc,pcx,pfm,pgm,pgmyuv,pgssub,pgx,phm,photocd,pictor,pjs,png,ppm,prosumer,psd,ptx,qcelp,qdm2,qdmc,qdraw,qoa,qoi,qpeg,qtrle,r10k,r210,ra_144,ra_288,rasc,rawvideo,realtext,rka,rl2,roq,roq_dpcm,rpza,rscc,rv10,rv20,s302m,sami,sanm,sbc,screenpresso,sdx2_dpcm,sgi,sgirle,shorten,simbiosis_imx,sipr,siren,smackaud,smacker,smc,smvjpeg,snow,sol_dpcm,sonic,sp5x,speedhq,speex,srgc,srt,ssa,stl,subrip,subviewer,subviewer1,sunrast,svq1,svq3,tak,targa,targa_y216,tdsc,text,theora,thp,tiertexseqvideo,tiff,tmv,truehd,truemotion1,truemotion2,truemotion2rt,truespeech,tscc,tscc2,tta,twinvq,txd,ulti,utvideo,v210,v210x,v308,v408,v410,vb,vble,vcr1,vmdaudio,vmdvideo,vmnc,vnull,vorbis,vp3,vp4,vp5,vp6,vp6a,vp6f,vp7,vp8,vp8_qsv,vp8_v4l2m2m,vp9,vp9_qsv,vp9_v4l2m2m,vplayer,vqa,vqc,wady_dpcm,wavarc,wavpack,wbmp,wcmv,webp,webvtt,wmav1,wmav2,wmavoice,wmv1,wmv2,wnv1,wrapped_avframe,ws_snd1,xan_dpcm,xan_wc3,xan_wc4,xbin,xbm,xface,xl,xpm,xsub,xwd,y41p,ylc,yop,yuv4,zero12v,zerocodec,zlib,zmbv,'
--disable-decoder='h264,hevc,vc1,vvc'
libavutil 59. 8.100 / 59. 8.100
libavcodec 61. 3.100 / 61. 3.100
libavformat 61. 1.100 / 61. 1.100
libavdevice 61. 1.100 / 61. 1.100
libavfilter 10. 1.100 / 10. 1.100
libswscale 8. 1.100 / 8. 1.100
libswresample 5. 1.100 / 5. 1.100
Input #0, image2, from '/tmp/chimovie_Angk-%05d.ppm':
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 2362x1845, 25 fps, 25 tbr, 25 tbn
[vost#0:0 @ 0x559c21437a80] Unknown encoder 'libx264'
[vost#0:0 @ 0x559c21437a80] Error selecting an encoder
Error opening output file /var/home/guillaume/Desktop/movie1.mp4.
Error opening output files: Encoder not found
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 8
Error message:
stdout:
stderr:
ffmpeg version 7.0.3 Copyright (c) 2000-2025 the FFmpeg developers
built with gcc 14.3.0 (GCC)
configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu
--optflags='-O2 -pipe -g -Wp,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS
-fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-
unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer
-mno-omit-leaf-frame-pointer ' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-
needed ' --disable-stripping --disable-doc --disable-static --disable-encoders
--disable-decoders --enable-shared --enable-gnutls --enable-gcrypt --enable-
ladspa --enable-lcms2 --enable-libaom --enable-libdav1d --enable-libmp3lame
--enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-
libjxl --enable-libopus --enable-libpulse --enable-libspeex --enable-libtheora
--enable-libvorbis --enable-libvpx --enable-librsvg --enable-libwebp --enable-
libxml2 --enable-libopenjpeg --enable-libsvtav1 --enable-openal --enable-
opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2 --enable-
libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable-libopenh264
--arch=x86_64 --enable-libfdk-aac --enable-
encoder='a64multi,a64multi5,aac,libfdk_aac,ac3,adpcm_adx,adpcm_argo,adpcm_g722,adpcm_g726,adpcm_g726le,adpcm_ima_alp,adpcm_ima_amv,adpcm_ima_apm,adpcm_ima_qt,adpcm_ima_ssi,adpcm_ima_wav,adpcm_ima_ws,adpcm_ms,adpcm_swf,adpcm_yamaha,alac,alias_pix,amv,anull,apng,ass,asv1,asv2,av1_amf,av1_nvenc,av1_qsv,av1_vaapi,bitpacked,bmp,cinepak,cljr,dca,dfpwm,dnxhd,dpx,dvbsub,dvdsub,dvvideo,exr,ffv1,ffvhuff,flac,flashsv,flashsv2,flv,g723_1,gif,h261,h263,h263_v4l2m2m,h263p,h264_amf,h264_nvenc,h264_qsv,h264_v4l2m2m,h264_vaapi,hap,hdr,hevc_amf,hevc_nvenc,hevc_qsv,hevc_v4l2m2m,hevc_vaapi,huffyuv,ilbc,jpeg2000,jpegls,libaom,libaom_av1,libcodec2,libgsm,libgsm_ms,libilbc,libjxl,libmp3lame,libopencore_amrnb,libopenh264,libopenjpeg,libopus,librav1e,libspeex,libsvtav1,libtheora,libtwolame,libvo_amrwbenc,libvorbis,libvpx_vp8,libvpx_vp9,libwebp,libwebp_anim,libxvid,mjpeg,mjpeg_qsv,mjpeg_vaapi,mlp,mp2,mp2fixed,mpeg1video,mpeg2_qsv,mpeg2_vaapi,mpeg2video,mpeg4,mpeg4_v4l2m2m,msmpeg4v2,msmpeg4v3,msvideo1,nellymoser,opus,pam,pbm,pcm_alaw,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_mulaw,pcm_s16be,pcm_s16be_planar,pcm_s16le,pcm_s16le_planar,pcm_s24be,pcm_s24le,pcm_s24le_planar,pcm_s32be,pcm_s32le,pcm_s32le_planar,pcm_s8,pcm_s8_planar,pcm_u16be,pcm_u16le,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,pcm_u8,pcx,pgm,pgmyuv,phm,png,ppm,qoi,qtrle,r10k,r210,ra_144,rawvideo,roq,roq_dpcm,rpza,rv10,rv20,s302m,sbc,sgi,smc,snow,sonic,sonic_ls,speedhq,srt,ssa,subrip,sunrast,svq1,targa,text,tiff,truehd,tta,ttml,utvideo,v210,v308,v408,v410,vc1_qsv,vc1_v4l2m2m,vc2,vnull,vorbis,vp8_qsv,vp8_v4l2m2m,vp8_vaapi,vp9_qsv,vp9_vaapi,wavpack,wbmp,webvtt,wmav1,wmav2,wmv1,wmv2,wrapped_avframe,xbm,xface,xsub,xwd,y41p,yuv4,zlib,zmbv,'
--enable-
decoder='aasc,libfdk_aac,ac3,acelp_kelvin,adpcm_4xm,adpcm_adx,adpcm_afc,adpcm_agm,adpcm_aica,adpcm_argo,adpcm_ct,adpcm_dtk,adpcm_ea,adpcm_ea_maxis_xa,adpcm_ea_r1,adpcm_ea_r2,adpcm_ea_r3,adpcm_ea_xas,adpcm_g722,adpcm_g726,adpcm_g726le,adpcm_ima_acorn,adpcm_ima_alp,adpcm_ima_amv,adpcm_ima_apc,adpcm_ima_apm,adpcm_ima_cunning,adpcm_ima_dat4,adpcm_ima_dk3,adpcm_ima_dk4,adpcm_ima_ea_eacs,adpcm_ima_ea_sead,adpcm_ima_iss,adpcm_ima_moflex,adpcm_ima_mtf,adpcm_ima_oki,adpcm_ima_qt,adpcm_ima_qt_at,adpcm_ima_rad,adpcm_ima_smjpeg,adpcm_ima_ssi,adpcm_ima_wav,adpcm_ima_ws,adpcm_ms,adpcm_mtaf,adpcm_psx,adpcm_sbpro_2,adpcm_sbpro_3,adpcm_sbpro_4,adpcm_swf,adpcm_thp,adpcm_thp_le,adpcm_vima,adpcm_xa,adpcm_xmd,adpcm_yamaha,adpcm_zork,alac,alias_pix,amrnb,amrwb,amv,anm,ansi,anull,apac,ape,apng,arbc,argo,ass,asv1,asv2,atrac1,atrac3,atrac3al,atrac3p,atrac3pal,aura,aura2,av1,av1_qsv,bethsoftvid,bfi,bink,binkaudio_dct,binkaudio_rdft,bintext,bitpacked,bmp,bmv_audio,bmv_video,bonk,brender_pix,c93,cbd2_dpcm,ccaption,cdgraphics,cdtoons,cdxl,cinepak,clearvideo,cljr,cook,cpia,cscd,cyuv,dca,dds,derf_dpcm,dfa,dfpwm,dirac,dnxhd,dolby_e,dpx,dsd_lsbf,dsd_msbf,dsicinaudio,dsicinvideo,dss_sp,dvaudio,dvbsub,dvdsub,dvvideo,dxa,dxtory,eacmv,eamad,eatgq,eatgv,eatqi,eightbps,eightsvx_exp,eightsvx_fib,escape124,escape130,evrc,exr,ffv1,ffvhuff,ffwavesynth,fits,flac,flashsv,flashsv2,flic,flv,fmvc,fourxm,ftr,g723_1,g729,gdv,gem,gif,gremlin_dpcm,gsm,gsm_ms,gsm_ms_at,h261,h263,h263_v4l2m2m,h263i,h263p,hap,hca,hcom,hdr,hnm4_video,hq_hqa,hqx,huffyuv,hymt,iac,idcin,idf,iff_ilbm,ilbc,imc,indeo2,indeo3,indeo4,indeo5,interplay_acm,interplay_dpcm,interplay_video,ipu,jacosub,jpeg2000,jpegls,jv,kgv1,kmvc,lagarith,libaom,libaom_av1,libcodec2,libdav1d,libgsm,libgsm_ms,libilbc,libjxl,libopencore_amrnb,libopencore_amrwb,libopenh264,libopenjpeg,libopus,librsvg,libschroedinger,libspeex,libvorbis,libvpx_vp8,libvpx_vp9,libzvbi_teletext,loco,lscr,m101,mace3,mace6,mdec,media100,metasound,microdvd,mimic,misc4,mjpeg,mjpeg_qsv,mjpegb,mlp,mmvideo,motionpixels,mp1,mp1float,mp2,mp2float,mp3,mp3adu,mp3adufloat,mp3float,mp3on4,mp3on4float,mpc7,mpc8,mpeg1_v4l2m2m,mpeg1video,mpeg2_qsv,mpeg2_v4l2m2m,mpeg2video,mpeg4,mpeg4_v4l2m2m,mpegvideo,mpl2,msa1,mscc,msmpeg4v1,msmpeg4v2,msmpeg4v3,msnsiren,msp2,msrle,mss1,mss2,msvideo1,mszh,mts2,mv30,mvc1,mvc2,mvdv,mvha,mwsc,mxpeg,nellymoser,nuv,on2avc,opus,paf_audio,paf_video,pam,pbm,pcm_alaw,pcm_bluray,pcm_dvd,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_lxf,pcm_mulaw,pcm_s16be,pcm_s16be_planar,pcm_s16le,pcm_s16le_planar,pcm_s24be,pcm_s24daud,pcm_s24le,pcm_s24le_planar,pcm_s32be,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_sga,pcm_u16be,pcm_u16le,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,pcm_u8,pcm_vidc,pcx,pfm,pgm,pgmyuv,pgssub,pgx,phm,photocd,pictor,pjs,png,ppm,prosumer,psd,ptx,qcelp,qdm2,qdmc,qdraw,qoa,qoi,qpeg,qtrle,r10k,r210,ra_144,ra_288,rasc,rawvideo,realtext,rka,rl2,roq,roq_dpcm,rpza,rscc,rv10,rv20,s302m,sami,sanm,sbc,screenpresso,sdx2_dpcm,sgi,sgirle,shorten,simbiosis_imx,sipr,siren,smackaud,smacker,smc,smvjpeg,snow,sol_dpcm,sonic,sp5x,speedhq,speex,srgc,srt,ssa,stl,subrip,subviewer,subviewer1,sunrast,svq1,svq3,tak,targa,targa_y216,tdsc,text,theora,thp,tiertexseqvideo,tiff,tmv,truehd,truemotion1,truemotion2,truemotion2rt,truespeech,tscc,tscc2,tta,twinvq,txd,ulti,utvideo,v210,v210x,v308,v408,v410,vb,vble,vcr1,vmdaudio,vmdvideo,vmnc,vnull,vorbis,vp3,vp4,vp5,vp6,vp6a,vp6f,vp7,vp8,vp8_qsv,vp8_v4l2m2m,vp9,vp9_qsv,vp9_v4l2m2m,vplayer,vqa,vqc,wady_dpcm,wavarc,wavpack,wbmp,wcmv,webp,webvtt,wmav1,wmav2,wmavoice,wmv1,wmv2,wnv1,wrapped_avframe,ws_snd1,xan_dpcm,xan_wc3,xan_wc4,xbin,xbm,xface,xl,xpm,xsub,xwd,y41p,ylc,yop,yuv4,zero12v,zerocodec,zlib,zmbv,'
--disable-decoder='h264,hevc,vc1,vvc'
libavutil 59. 8.100 / 59. 8.100
libavcodec 61. 3.100 / 61. 3.100
libavformat 61. 1.100 / 61. 1.100
libavdevice 61. 1.100 / 61. 1.100
libavfilter 10. 1.100 / 10. 1.100
libswscale 8. 1.100 / 8. 1.100
libswresample 5. 1.100 / 5. 1.100
Input #0, image2, from '/tmp/chimovie_Angk-%05d.ppm':
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 2362x1845, 25 fps, 25 tbr, 25 tbn
[vost#0:0 @ 0x559c21437a80] Unknown encoder 'libx264'
[vost#0:0 @ 0x559c21437a80] Error selecting an encoder
Error opening output file /var/home/guillaume/Desktop/movie1.mp4.
Error opening output files: Encoder not found
\-----------------------------
OpenGL version: 4.6 (Core Profile) Mesa 25.3.3 (git-a9c6420d8c)
OpenGL renderer: AMD Radeon 890M Graphics (radeonsi, gfx1150, LLVM 19.1.7, DRM 3.64, 6.18.13-200.fc43.x86_64)
OpenGL vendor: AMD
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:0
GNOME_SETUP_DISPLAY=:1
WAYLAND_DISPLAY=wayland-0
Manufacturer: Framework
Model: Laptop 13 (AMD Ryzen AI 300 Series)
OS: Freedesktop SDK 24.08
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 24 AMD Ryzen AI 9 HX 370 w/ Radeon 890M
Cache Size: 1024 KB
Memory:
total used free shared buff/cache available
Mem: 23Gi 7.4Gi 4.5Gi 2.5Gi 14Gi 15Gi
Swap: 8.0Gi 0B 8.0Gi
Graphics:
unknown
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2026.1.4
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-CubeNTube: 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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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