core.history.ObjectHistory: 'utf-8' codec can't encode characters: surrogates not allowed

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.14.6-109.bazzite.fc42.x86_64-x86_64-with-glibc2.40
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/home/osk/Documents/UNI/4. Semester/Grne Biotechnologie/Seminar mit
> Exkursion/SNAP.cxs"

Traceback (most recent call last):  
File "/app/lib/python3.11/site-packages/chimerax/core/triggerset.py", line
149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 351,
in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/app/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 460,
in add  
self._history.enqueue((item, typed))  
File "/app/lib/python3.11/site-packages/chimerax/core/history.py", line 182,
in enqueue  
self.save()  
File "/app/lib/python3.11/site-packages/chimerax/core/history.py", line 212,
in save  
self._history.save(self._queue)  
File "/app/lib/python3.11/site-packages/chimerax/core/history.py", line 120,
in save  
json.dump(obj, f, ensure_ascii=False)  
File "/app/lib/python3.11/json/__init__.py", line 180, in dump  
fp.write(chunk)  
UnicodeEncodeError: 'utf-8' codec can't encode characters in position 47-48:
surrogates not allowed  
  
Error processing trigger "command started":  
UnicodeEncodeError: 'utf-8' codec can't encode characters in position 47-48:
surrogates not allowed  
  
File "/app/lib/python3.11/json/__init__.py", line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Log from Tue Jul 1 11:16:47 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1XTG format mmcif fromDatabase pdb

1xtg title:  
Crystal structure of NEUROTOXIN BONT/A complexed with Synaptosomal-associated
protein 25 [more info...]  
  
Chain information for 1xtg #1  
---  
Chain | Description | UniProt  
A | NEUROTOXIN BONT/A |   
B | Synaptosomal-associated protein 25 | SN25_HUMAN 146-204  
  
Non-standard residues in 1xtg #1  
---  
CL — chloride ion  
ZN — zinc ion  
  

> select /A

3755 atoms, 3514 bonds, 3 pseudobonds, 748 residues, 2 models selected  

> color (#!1 & sel) orange red

> color (#!1 & sel) red

> lighting full

> show sel surfaces

> hide sel cartoons

> select /B

516 atoms, 466 bonds, 109 residues, 1 model selected  

> color sel cyan

> select add #1

4271 atoms, 3980 bonds, 4 pseudobonds, 857 residues, 2 models selected  

> select subtract #1

1 model selected  

> select /B

516 atoms, 466 bonds, 109 residues, 1 model selected  

> show sel surfaces

> select add #1

4271 atoms, 3980 bonds, 4 pseudobonds, 857 residues, 3 models selected  

> select subtract #1

2 models selected  

> encode movie quality higher format avi

Unknown command: encode movie quality higher format avi  

> movie record

> turn y 2 180

> wait 180

> movie encode /home/osk/Desktop/movie1.mp4

/usr/bin/ffmpeg -r 25 -i /tmp/chimovie_dTvd-%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 /home/osk/Desktop/movie1.mp4  
stdout:  
  
stderr:  
ffmpeg version 7.0.2 Copyright (c) 2000-2024 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_dTvd-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1833x1162, 25 fps, 25 tbr, 25 tbn  
[vost#0:0 @ 0x5611e9143c40] Unknown encoder 'libx264'  
[vost#0:0 @ 0x5611e9143c40] Error selecting an encoder  
Error opening output file /home/osk/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 7.0.2 Copyright (c) 2000-2024 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_dTvd-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1833x1162, 25 fps, 25 tbr, 25 tbn  
[vost#0:0 @ 0x5611e9143c40] Unknown encoder 'libx264'  
[vost#0:0 @ 0x5611e9143c40] Error selecting an encoder  
Error opening output file /home/osk/Desktop/movie1.mp4.  
Error opening output files: Encoder not found  
  
\-----------------------------  
  

> movie encode quality higher format avi

Movie saved to /home/osk/Desktop/movie.avi  
  

> movie encode quality higher format avi

No frames have been recorded  

> show atoms

> hide atoms

> undo

[Repeated 1 time(s)]

> movie encode quality higher format avi

No frames have been recorded  

> movie encode quality higher format avi

No frames have been recorded  

> save "/var/home/osk/Documents/UNI/4. Semester/Grüne Biotechnologie/Seminar
> mit Exkursion/SNAP.cxs"

——— End of log from Tue Jul 1 11:16:47 2025 ———

> view name session-start

Traceback (most recent call last):  
File "/app/lib/python3.11/site-packages/chimerax/core/triggerset.py", line
149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 351,
in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/app/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 460,
in add  
self._history.enqueue((item, typed))  
File "/app/lib/python3.11/site-packages/chimerax/core/history.py", line 182,
in enqueue  
self.save()  
File "/app/lib/python3.11/site-packages/chimerax/core/history.py", line 212,
in save  
self._history.save(self._queue)  
File "/app/lib/python3.11/site-packages/chimerax/core/history.py", line 120,
in save  
json.dump(obj, f, ensure_ascii=False)  
File "/app/lib/python3.11/json/__init__.py", line 180, in dump  
fp.write(chunk)  
UnicodeEncodeError: 'utf-8' codec can't encode characters in position 47-48:
surrogates not allowed  
  
Error processing trigger "command started":  
UnicodeEncodeError: 'utf-8' codec can't encode characters in position 47-48:
surrogates not allowed  
  
File "/app/lib/python3.11/json/__init__.py", line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
opened ChimeraX session  
Traceback (most recent call last):  
File "/app/lib/python3.11/site-packages/chimerax/core/triggerset.py", line
149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/ui/file_history.py", line 95,
in file_history_changed_cb  
self.update_html()  
File "/app/lib/python3.11/site-packages/chimerax/ui/file_history.py", line 88,
in update_html  
html= f'<html><style>{self.session.ui.dark_css()}</style><body>' +
self.history_html() + '</body></html>'  
^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/ui/file_history.py", line 60,
in history_html  
cmd = parse.quote(f.open_command())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/urllib/parse.py", line 887, in quote  
string = string.encode(encoding, errors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
UnicodeEncodeError: 'utf-8' codec can't encode characters in position 44-45:
surrogates not allowed  
  
Error processing trigger "file history changed":  
UnicodeEncodeError: 'utf-8' codec can't encode characters in position 44-45:
surrogates not allowed  
  
File "/app/lib/python3.11/urllib/parse.py", line 887, in quote  
string = string.encode(encoding, errors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 575.64
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=plasma
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:0
WAYLAND_DISPLAY=wayland-0
Manufacturer: HP
Model: OMEN Laptop 15-en0xxx
OS: Freedesktop SDK 24.08
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 12 AMD Ryzen 5 4600H with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            14Gi        10Gi       1.7Gi       473Mi       3.9Gi       4.2Gi
	Swap:          4.0Gi       3.6Gi       388Mi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU116M [GeForce GTX 1660 Ti Mobile] [10de:2191] (rev a1)	
	DeviceName: NVIDIA Graphics Device	
	Subsystem: Hewlett-Packard Company Device [103c:8786]

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    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: 2025.6.15
    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-LinuxSupport: 1.0.1
    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
    distro: 1.9.0
    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
    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: 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
    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
    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: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine: 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
    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