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#5679 closed defect (can't reproduce)
Unknown crash after MatchMaker completion
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Change History (6)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unknown crash after MatchMaker completion |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
comment:3 by , 4 years ago
Does matchmaker use the python multiprocessing module? I wonder what those 8 worker threads are doing? Maybe it is the molecular surface code making those threads, although I don't see any surface command, but maybe opening a session computed a surface. At any rate the thread that crashed was in the Qt event loop. That makes it seem that the last matchmaker command completed without crashing, and the log output looks like it completed.
Seems like we would need C++ stack traces on Windows to see where these Qt event loop crashes are happening.
comment:4 by , 4 years ago
No matchmaker does not use the multiprocessing module. I imagine it's QWebEngine using it. No ChimeraX code imports multiprocessing except for Segger and core, and both those uses are only to get a CPU count.
comment:5 by , 4 years ago
I don't see how it could be QWebEngine because I don't think it uses Python threads.
I tried running a molecular surface calculation and then sending an abort signal and the Python stack trace showed the threads including functions that were running the surface calculation, #5682. Also tried aborting after surface calc finished to see if it left idle worker threads, and it did not. So it does not appear to be surface calculation that makes the 8 threads we see in this report.
comment:6 by , 4 years ago
ISOLDE makes extensive use of multiprocessing, but I don't see it in the list of installed packages here.
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Also, 'move encode' received SIGTERM somehow.