id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5679 Unknown crash after MatchMaker completion chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19043 ChimeraX Version: 1.3rc202111110135 (2021-11-11 01:35:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x000025b8 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000018dc (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\pool.py"", line 576 in _handle_results File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00003584 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\pool.py"", line 528 in _handle_tasks File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002c3c (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\connection.py"", line 816 in _exhaustive_wait File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\connection.py"", line 884 in wait File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\pool.py"", line 499 in _wait_for_updates File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\pool.py"", line 519 in _handle_workers File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000038a8 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000043f8 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00001830 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000042ec (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\threading.py"", line 930 in _bootstrap Current thread 0x00002f40 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== UCSF ChimeraX version: 1.3rc202111110135 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\Users\vero1\Documents\HFU\6. Semester\Structural Biology\CAP.cxs"" > format session opened ChimeraX session > close session > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural > Biology/CAPsterncGMP.pdb"" CAPsterncGMP.pdb title: A structural model of cap mutant (T127L and S128I) In CGMP- bound state [more info...] Chain information for CAPsterncGMP.pdb --- Chain | Description | UniProt 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | camp receptor protein | CRP_ECOLI > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural > Biology/CAPstern.pdb"" CAPstern.pdb title: A structural model of cap mutant (T127L and S128I) In the apo state [more info...] Chain information for CAPstern.pdb --- Chain | Description | UniProt 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | camp-activated global transcriptional regulator CRP | CRP_ECOLI > select > #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A 63640 atoms, 64160 bonds, 4180 residues, 20 models selected > cartoon hide sel > select #1.1/A 3182 atoms, 3208 bonds, 209 residues, 1 model selected > cartoon sel > select > #2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A#2.9/A#2.10/A#2.11/A#2.12/A#2.13/A#2.14/A#2.15/A#2.16/A#2.17/A#2.18/A#2.19/A#2.20/A 67300 atoms, 67820 bonds, 4180 residues, 20 models selected > cartoon hide sel > select #2.1/A 3365 atoms, 3391 bonds, 209 residues, 1 model selected > cartoon sel Alignment identifier is 2.1/A > select clear Drag select of 5 residues > select clear > ui tool show Matchmaker > matchmaker #1.2 to #1.1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker CAPsterncGMP.pdb, chain A (#1.1) with CAPsterncGMP.pdb, chain A (#1.2), sequence alignment score = 998.3 RMSD between 190 pruned atom pairs is 1.083 angstroms; (across all 209 pairs: 1.762) > ui tool show Matchmaker > matchmaker #2.1 to #1.1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker CAPsterncGMP.pdb, chain A (#1.1) with CAPstern.pdb, chain A (#2.1), sequence alignment score = 968.3 RMSD between 79 pruned atom pairs is 1.158 angstroms; (across all 209 pairs: 6.222) > ui tool show AlphaFold > close session > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/3kcc.pdb"" 3kcc.pdb title: Crystal structure of D138L mutant of catabolite gene activator protein [more info...] Chain information for 3kcc.pdb #1 --- Chain | Description | UniProt A | catabolite gene activator | CRP_ECOLI B | catabolite gene activator | CRP_ECOLI Non-standard residues in 3kcc.pdb #1 --- CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp) > close session > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/5ciz.pdb"" Non-standard residues in 5ciz.pdb #1 --- CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp) Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/D Alignment identifier is 1/E > select /A:127 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:127-128 13 atoms, 12 bonds, 2 residues, 1 model selected > color sel red > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/CAP.pdb"" Summary of feedback from opening C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/CAP.pdb --- warning | Ignored bad PDB record found on line 135735 MASTER 1455 0 0 16 24 0 0 6134080 40 0 34 CAP.pdb title: NMR structure of catabolite activator protein In the unliganded state [more info...] Chain information for CAP.pdb --- Chain | Description | UniProt 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A 2.1/B 2.2/B 2.3/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B 2.11/B 2.12/B 2.13/B 2.14/B 2.15/B 2.16/B 2.17/B 2.18/B 2.19/B 2.20/B | catabolite gene activator | CRP_ECO57 > select > #2.1/A#2.1/B#2.2/A#2.2/B#2.3/A#2.3/B#2.4/A#2.4/B#2.5/A#2.5/B#2.6/A#2.6/B#2.7/A#2.7/B#2.8/A#2.8/B#2.9/A#2.9/B#2.10/A#2.10/B#2.11/A#2.11/B#2.12/A#2.12/B#2.13/A#2.13/B#2.14/A#2.14/B#2.15/A#2.15/B#2.16/A#2.16/B#2.17/A#2.17/B#2.18/A#2.18/B#2.19/A#2.19/B#2.20/A#2.20/B 134080 atoms, 135120 bonds, 8360 residues, 20 models selected > cartoon hide sel > select #2.1/A 3352 atoms, 3378 bonds, 209 residues, 1 model selected > cartoon sel > ui tool show Matchmaker > matchmaker #2.1 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5ciz.pdb, chain A (#1) with CAP.pdb, chain A (#2.1), sequence alignment score = 844.7 RMSD between 102 pruned atom pairs is 1.181 angstroms; (across all 203 pairs: 4.899) > select clear > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural > Biology/CAPstern.pdb"" CAPstern.pdb title: A structural model of cap mutant (T127L and S128I) In the apo state [more info...] Chain information for CAPstern.pdb --- Chain | Description | UniProt 3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A | camp-activated global transcriptional regulator CRP | CRP_ECOLI > select > #1/A#3.1/A#3.2/A#3.3/A#3.4/A#3.5/A#3.6/A#3.7/A#3.8/A#3.9/A#3.10/A#3.11/A#3.12/A#3.13/A#3.14/A#3.15/A#3.16/A#3.17/A#3.18/A#3.19/A#3.20/A 68920 atoms, 69468 bonds, 4384 residues, 21 models selected > select clear > select #3.1/A 3365 atoms, 3391 bonds, 209 residues, 1 model selected > select > #1/A#3.1/A#3.2/A#3.3/A#3.4/A#3.5/A#3.6/A#3.7/A#3.8/A#3.9/A#3.10/A#3.11/A#3.12/A#3.13/A#3.14/A#3.15/A#3.16/A#3.17/A#3.18/A#3.19/A#3.20/A 68920 atoms, 69468 bonds, 4384 residues, 21 models selected > cartoon hide sel > select #1/A 1620 atoms, 1648 bonds, 204 residues, 1 model selected > cartoon sel > select #3.1/A 3365 atoms, 3391 bonds, 209 residues, 1 model selected > cartoon sel > ui tool show Matchmaker > matchmaker #3.1 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5ciz.pdb, chain A (#1) with CAPstern.pdb, chain A (#3.1), sequence alignment score = 929.9 RMSD between 92 pruned atom pairs is 1.059 angstroms; (across all 203 pairs: 5.839) Alignment identifier is 3.1/A > select #3.1/A:127 19 atoms, 18 bonds, 1 residue, 1 model selected > select #3.1/A:127-128 38 atoms, 37 bonds, 2 residues, 1 model selected > color sel orange red > show sel atoms Drag select of 92 atoms, 736 residues, 84 bonds, 132 shapes > select clear > select #3.1/A:127 19 atoms, 18 bonds, 1 residue, 1 model selected > select #3.1/A:127-129 53 atoms, 52 bonds, 3 residues, 1 model selected > select #3.1/A:127 19 atoms, 18 bonds, 1 residue, 1 model selected > select #3.1/A:127-128 38 atoms, 37 bonds, 2 residues, 1 model selected > color sel lime > hide sel atoms > save ""C:/Users/vero1/Documents/HFU/6. Semester/Structural > Biology/Capaktiv_Capinaktiv_CAP*inaktiv.x3d"" Cannot save 'C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/Capaktiv_Capinaktiv_CAP*inaktiv.x3d': [Errno 22] Invalid argument: 'C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/Capaktiv_Capinaktiv_CAP*inaktiv.x3d' > close session > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/5ciz.pdb"" Non-standard residues in 5ciz.pdb #1 --- CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp) > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural > Biology/CAPstern.pdb"" CAPstern.pdb title: A structural model of cap mutant (T127L and S128I) In the apo state [more info...] Chain information for CAPstern.pdb --- Chain | Description | UniProt 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | camp-activated global transcriptional regulator CRP | CRP_ECOLI > select #1/B 583 atoms, 591 bonds, 74 residues, 1 model selected > select #1/B 583 atoms, 591 bonds, 74 residues, 1 model selected > select #1/D 405 atoms, 452 bonds, 20 residues, 1 model selected > cartoon hide sel > hide sel target a > select #1/E 491 atoms, 552 bonds, 24 residues, 1 model selected > cartoon hide sel > hide sel target a > undo > select > #1/A#2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A#2.9/A#2.10/A#2.11/A#2.12/A#2.13/A#2.14/A#2.15/A#2.16/A#2.17/A#2.18/A#2.19/A#2.20/A 68920 atoms, 69468 bonds, 4384 residues, 21 models selected > cartoon hide sel > select #1/A 1620 atoms, 1648 bonds, 204 residues, 1 model selected > cartoon sel > select #2.1/A 3365 atoms, 3391 bonds, 209 residues, 1 model selected > cartoon sel > ui tool show Matchmaker > undo > cartoon sel > ui tool show Matchmaker > matchmaker #2.1 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5ciz.pdb, chain A (#1) with CAPstern.pdb, chain A (#2.1), sequence alignment score = 929.9 RMSD between 92 pruned atom pairs is 1.059 angstroms; (across all 203 pairs: 5.839) Alignment identifier is 2.1/A > select #2.1/A:127 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2.1/A:127-128 38 atoms, 37 bonds, 2 residues, 1 model selected > color sel magenta > select clear Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/D Alignment identifier is 1/E Alignment identifier is 1 > select #1/A:127 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:127-128 13 atoms, 12 bonds, 2 residues, 1 model selected > color sel cyan > color sel orange > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\vero1\Desktop\movie6.mp4 C:\Program Files\ChimeraX 1.3rc202111110135\bin\ffmpeg.exe -r 25 -i C:\Users\vero1\AppData\Local\Temp\chimovie_hnuT-%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 C:\Users\vero1\Desktop\movie6.mp4 stdout: stderr: ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers built with gcc 6.3.0 (GCC) configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2 --enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable- fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable- libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable- libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable- libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable- libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable- lzma --enable-zlib libavutil 55. 34.101 / 55. 34.101 libavcodec 57. 64.101 / 57. 64.101 libavformat 57. 56.101 / 57. 56.101 libavdevice 57. 1.100 / 57. 1.100 libavfilter 6. 65.100 / 6. 65.100 libswscale 4. 2.100 / 4. 2.100 libswresample 2. 3.100 / 2. 3.100 libpostproc 54. 1.100 / 54. 1.100 Input #0, image2, from 'C:\Users\vero1\AppData\Local\Temp\chimovie_hnuT-%05d.ppm': Duration: 00:00:07.20, start: 0.000000, bitrate: N/A Stream #0:0: Video: ppm, rgb24, 1760x974, 25 tbr, 25 tbn, 25 tbc [libx264 @ 0000000000615700] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX FMA3 AVX2 LZCNT BMI2 [libx264 @ 0000000000615700] profile High, level 4.0 [libx264 @ 0000000000615700] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00 Output #0, mp4, to 'C:\Users\vero1\Desktop\movie6.mp4': Metadata: encoder : Lavf57.56.101 Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 1760x974, q=-1--1, 25 fps, 12800 tbn, 25 tbc Metadata: encoder : Lavc57.64.101 libx264 Side data: cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1 Stream mapping: Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264)) Press [q] to stop, [?] for help frame= 31 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x frame= 47 fps= 44 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x frame= 57 fps= 29 q=25.0 size= 288kB time=00:00:00.16 bitrate=14749.1kbits/s speed=0.0824x frame= 69 fps= 28 q=25.0 size= 674kB time=00:00:00.64 bitrate=8622.0kbits/s speed=0.258x frame= 83 fps= 28 q=25.0 size= 1099kB time=00:00:01.20 bitrate=7505.2kbits/s speed=0.402x frame= 97 fps= 26 q=25.0 size= 1569kB time=00:00:01.76 bitrate=7303.5kbits/s speed=0.474x frame= 109 fps= 25 q=25.0 size= 1968kB time=00:00:02.24 bitrate=7196.5kbits/s speed=0.522x frame= 123 fps= 25 q=25.0 size= 2417kB time=00:00:02.80 bitrate=7071.7kbits/s speed=0.576x frame= 136 fps= 25 q=25.0 size= 2873kB time=00:00:03.32 bitrate=7089.4kbits/s speed=0.618x frame= 144 fps= 18 q=-1.0 Lsize= 4741kB time=00:00:05.64 bitrate=6885.5kbits/s speed=0.691x video:4738kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.054002% [libx264 @ 0000000000615700] frame I:1 Avg QP:12.92 size: 71964 [libx264 @ 0000000000615700] frame P:36 Avg QP:23.41 size: 52613 [libx264 @ 0000000000615700] frame B:107 Avg QP:28.22 size: 26962 [libx264 @ 0000000000615700] consecutive B-frames: 0.7% 0.0% 2.1% 97.2% [libx264 @ 0000000000615700] mb I I16..4: 59.6% 23.3% 17.1% [libx264 @ 0000000000615700] mb P I16..4: 0.9% 1.0% 6.2% P16..4: 2.9% 4.4% 5.0% 0.0% 0.0% skip:79.7% [libx264 @ 0000000000615700] mb B I16..4: 0.1% 0.2% 0.8% B16..8: 5.0% 6.1% 6.5% direct: 1.0% skip:80.5% L0:40.0% L1:40.1% BI:19.9% [libx264 @ 0000000000615700] 8x8 transform intra:15.3% inter:12.8% [libx264 @ 0000000000615700] coded y,uvDC,uvAC intra: 57.0% 68.8% 65.3% inter: 7.1% 5.7% 4.3% [libx264 @ 0000000000615700] i16 v,h,dc,p: 80% 11% 8% 1% [libx264 @ 0000000000615700] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 23% 6% 64% 1% 1% 1% 1% 1% 1% [libx264 @ 0000000000615700] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 19% 14% 18% 8% 8% 10% 8% 9% 7% [libx264 @ 0000000000615700] i8c dc,h,v,p: 60% 15% 17% 8% [libx264 @ 0000000000615700] Weighted P-Frames: Y:19.4% UV:16.7% [libx264 @ 0000000000615700] ref P L0: 55.5% 17.0% 17.5% 8.5% 1.5% [libx264 @ 0000000000615700] ref B L0: 89.8% 8.4% 1.8% [libx264 @ 0000000000615700] ref B L1: 96.2% 3.8% [libx264 @ 0000000000615700] kb/s:6737.53 Exiting normally, received signal 15. An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: \----------------------------- Exit value: 3221225786 Error message: stdout: stderr: ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers built with gcc 6.3.0 (GCC) configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2 --enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable- fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable- libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable- libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable- libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable- libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable- lzma --enable-zlib libavutil 55. 34.101 / 55. 34.101 libavcodec 57. 64.101 / 57. 64.101 libavformat 57. 56.101 / 57. 56.101 libavdevice 57. 1.100 / 57. 1.100 libavfilter 6. 65.100 / 6. 65.100 libswscale 4. 2.100 / 4. 2.100 libswresample 2. 3.100 / 2. 3.100 libpostproc 54. 1.100 / 54. 1.100 Input #0, image2, from 'C:\Users\vero1\AppData\Local\Temp\chimovie_hnuT-%05d.ppm': Duration: 00:00:07.20, start: 0.000000, bitrate: N/A Stream #0:0: Video: ppm, rgb24, 1760x974, 25 tbr, 25 tbn, 25 tbc [libx264 @ 0000000000615700] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX FMA3 AVX2 LZCNT BMI2 [libx264 @ 0000000000615700] profile High, level 4.0 [libx264 @ 0000000000615700] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00 Output #0, mp4, to 'C:\Users\vero1\Desktop\movie6.mp4': Metadata: encoder : Lavf57.56.101 Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 1760x974, q=-1--1, 25 fps, 12800 tbn, 25 tbc Metadata: encoder : Lavc57.64.101 libx264 Side data: cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1 Stream mapping: Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264)) Press [q] to stop, [?] for help frame= 31 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x frame= 47 fps= 44 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x frame= 57 fps= 29 q=25.0 size= 288kB time=00:00:00.16 bitrate=14749.1kbits/s speed=0.0824x frame= 69 fps= 28 q=25.0 size= 674kB time=00:00:00.64 bitrate=8622.0kbits/s speed=0.258x frame= 83 fps= 28 q=25.0 size= 1099kB time=00:00:01.20 bitrate=7505.2kbits/s speed=0.402x frame= 97 fps= 26 q=25.0 size= 1569kB time=00:00:01.76 bitrate=7303.5kbits/s speed=0.474x frame= 109 fps= 25 q=25.0 size= 1968kB time=00:00:02.24 bitrate=7196.5kbits/s speed=0.522x frame= 123 fps= 25 q=25.0 size= 2417kB time=00:00:02.80 bitrate=7071.7kbits/s speed=0.576x frame= 136 fps= 25 q=25.0 size= 2873kB time=00:00:03.32 bitrate=7089.4kbits/s speed=0.618x frame= 144 fps= 18 q=-1.0 Lsize= 4741kB time=00:00:05.64 bitrate=6885.5kbits/s speed=0.691x video:4738kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.054002% [libx264 @ 0000000000615700] frame I:1 Avg QP:12.92 size: 71964 [libx264 @ 0000000000615700] frame P:36 Avg QP:23.41 size: 52613 [libx264 @ 0000000000615700] frame B:107 Avg QP:28.22 size: 26962 [libx264 @ 0000000000615700] consecutive B-frames: 0.7% 0.0% 2.1% 97.2% [libx264 @ 0000000000615700] mb I I16..4: 59.6% 23.3% 17.1% [libx264 @ 0000000000615700] mb P I16..4: 0.9% 1.0% 6.2% P16..4: 2.9% 4.4% 5.0% 0.0% 0.0% skip:79.7% [libx264 @ 0000000000615700] mb B I16..4: 0.1% 0.2% 0.8% B16..8: 5.0% 6.1% 6.5% direct: 1.0% skip:80.5% L0:40.0% L1:40.1% BI:19.9% [libx264 @ 0000000000615700] 8x8 transform intra:15.3% inter:12.8% [libx264 @ 0000000000615700] coded y,uvDC,uvAC intra: 57.0% 68.8% 65.3% inter: 7.1% 5.7% 4.3% [libx264 @ 0000000000615700] i16 v,h,dc,p: 80% 11% 8% 1% [libx264 @ 0000000000615700] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 23% 6% 64% 1% 1% 1% 1% 1% 1% [libx264 @ 0000000000615700] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 19% 14% 18% 8% 8% 10% 8% 9% 7% [libx264 @ 0000000000615700] i8c dc,h,v,p: 60% 15% 17% 8% [libx264 @ 0000000000615700] Weighted P-Frames: Y:19.4% UV:16.7% [libx264 @ 0000000000615700] ref P L0: 55.5% 17.0% 17.5% 8.5% 1.5% [libx264 @ 0000000000615700] ref B L0: 89.8% 8.4% 1.8% [libx264 @ 0000000000615700] ref B L1: 96.2% 3.8% [libx264 @ 0000000000615700] kb/s:6737.53 Exiting normally, received signal 15. \----------------------------- > ui tool show ""Selection Inspector"" > save ""C:/Users/vero1/Documents/HFU/6. Semester/Structural > Biology/Capaktiv_mit_capstern.cxs"" > close session > open ""C:\Users\vero1\Documents\HFU\6. Semester\Structural > Biology\Capaktiv_mit_capstern.cxs"" format session opened ChimeraX session > close session > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/5ciz.pdb"" Non-standard residues in 5ciz.pdb #1 --- CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp) > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/CAP.cxs"" opened ChimeraX session > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/5ciz.pdb"" Non-standard residues in 5ciz.pdb #2 --- CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp) > ui tool show Matchmaker > matchmaker #2 to #1.1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker CAP.pdb, chain A (#1.1) with 5ciz.pdb, chain A (#2), sequence alignment score = 844.7 RMSD between 102 pruned atom pairs is 1.181 angstroms; (across all 203 pairs: 4.899) > select #1.1/A 3352 atoms, 3378 bonds, 209 residues, 1 model selected > select #1.20/B 3352 atoms, 3378 bonds, 209 residues, 1 model selected > select #1.20/A 3352 atoms, 3378 bonds, 209 residues, 1 model selected > cartoon sel > select #1.20/B 3352 atoms, 3378 bonds, 209 residues, 1 model selected > cartoon hide sel > select #1.20/A 3352 atoms, 3378 bonds, 209 residues, 1 model selected > color sel cyan > select #2/E 491 atoms, 552 bonds, 24 residues, 1 model selected > select #2/B 583 atoms, 591 bonds, 74 residues, 1 model selected > color sel orange > select #2/A 1620 atoms, 1648 bonds, 204 residues, 1 model selected > color sel orange > select #2/B 583 atoms, 591 bonds, 74 residues, 1 model selected > cartoon hide sel > save ""C:/Users/vero1/Documents/HFU/6. Semester/Structural > Biology/CapaktiviertundCapinaktiviert.cxs"" > close session > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/CAP.cxs"" opened ChimeraX session > select #1.20/A 3352 atoms, 3378 bonds, 209 residues, 1 model selected > cartoon sel > select #1.20/B 3352 atoms, 3378 bonds, 209 residues, 1 model selected > cartoon hide sel > rainbow sel > color sel cyan Drag select of 209 residues > color sel cyan > select clear > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural Biology/5ciz.pdb"" Non-standard residues in 5ciz.pdb #2 --- CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp) > ui tool show Matchmaker > matchmaker #2 to #1.20 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker CAP.pdb, chain A (#1.20) with 5ciz.pdb, chain A (#2), sequence alignment score = 826.1 RMSD between 101 pruned atom pairs is 1.204 angstroms; (across all 203 pairs: 4.873) > select #2/B 583 atoms, 591 bonds, 74 residues, 1 model selected > hide sel target a > cartoon hide sel > select #2/A 1620 atoms, 1648 bonds, 204 residues, 1 model selected > color sel orange > open ""C:/Users/vero1/Documents/HFU/6. Semester/Structural > Biology/CAPstern.pdb"" CAPstern.pdb title: A structural model of cap mutant (T127L and S128I) In the apo state [more info...] Chain information for CAPstern.pdb --- Chain | Description | UniProt 3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A | camp-activated global transcriptional regulator CRP | CRP_ECOLI > select #3.1/A 3365 atoms, 3391 bonds, 209 residues, 1 model selected > select > #2/A#3.1/A#3.2/A#3.3/A#3.4/A#3.5/A#3.6/A#3.7/A#3.8/A#3.9/A#3.10/A#3.11/A#3.12/A#3.13/A#3.14/A#3.15/A#3.16/A#3.17/A#3.18/A#3.19/A#3.20/A 68920 atoms, 69468 bonds, 4384 residues, 21 models selected > cartoon hide sel > select #2/A 1620 atoms, 1648 bonds, 204 residues, 1 model selected > cartoon sel > select #3.1/A 3365 atoms, 3391 bonds, 209 residues, 1 model selected > color sel hot pink > cartoon sel > ui tool show Matchmaker > matchmaker #2 to #3.1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker CAPstern.pdb, chain A (#3.1) with 5ciz.pdb, chain A (#2), sequence alignment score = 929.9 RMSD between 92 pruned atom pairs is 1.059 angstroms; (across all 203 pairs: 5.839) > select clear > ui tool show Matchmaker > matchmaker #2 to #1.20 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker CAP.pdb, chain A (#1.20) with 5ciz.pdb, chain A (#2), sequence alignment score = 826.1 RMSD between 101 pruned atom pairs is 1.204 angstroms; (across all 203 pairs: 4.873) > ui tool show Matchmaker > matchmaker #3.1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5ciz.pdb, chain A (#2) with CAPstern.pdb, chain A (#3.1), sequence alignment score = 929.9 RMSD between 92 pruned atom pairs is 1.059 angstroms; (across all 203 pairs: 5.839) ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3rc202111110135 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 - Build 20.19.15.4380 OpenGL renderer: Intel(R) HD Graphics 515 OpenGL vendor: Intel Manufacturer: LENOVO Model: 80ML OS: Microsoft Windows 10 Home (Build 19043) Memory: 8,498,610,176 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) m7-6Y75 CPU @ 1.20GHz OSLanguage: de-DE Locale: ('de_DE', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.7 ChimeraX-AddCharge: 1.1.5 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.2 ChimeraX-AtomicLibrary: 4.1.5 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202111110135 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.5.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.2 ParmEd: 3.2.0 parso: 0.8.2 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.22 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Core can't reproduce Eric Pettersen all ChimeraX