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Opened 4 years ago
Closed 4 years ago
#6152 closed defect (can't reproduce)
Crash after running MatchMaker
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Thread 0x000044d8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Current thread 0x00002c08 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open "C:\Users\huash\Desktop\igm-var2CSA data\sturcture photo\TM
> overall.cxs" format session
Opened gobal map -TM 3.6A.mrc as #2, grid size 400,400,400, pixel 0.85, shown
at level 0.115, step 2, values float32
Opened gobal map -TM 3.6A.mrc 0 as #3.1, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 1 as #3.2, grid size 400,400,400, pixel 0.85,
shown at level 0.171, step 1, values float32
Opened gobal map -TM 3.6A.mrc 2 as #3.3, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 3 as #3.4, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 4 as #3.5, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 5 as #3.6, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 6 as #3.7, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 7 as #3.8, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 8 as #3.9, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 9 as #3.10, grid size 400,400,400, pixel 0.85,
shown at level 0.177, step 1, values float32
opened ChimeraX session
> color medium slate blue
> color slate blue
> color medium purple
> close session
> open "C:\Users\huash\Desktop\igm-var2CSA data\sturcture photo\var2CSA
> overall2 .cxs" format session
Opened var2CSA-IgMtotalmap3.56.mrc as #2, grid size 320,320,320, pixel 1.07,
shown at level 0.0941, step 2, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 0 as #3.1, grid size 320,320,320, pixel
1.07, shown at level 0.0941, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 as #3.2, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 2 as #3.3, grid size 320,320,320, pixel
1.07, shown at level 0.147, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 3 as #3.4, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 4 as #3.5, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 5 as #3.6, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 6 as #3.7, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 7 as #3.8, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 8 as #3.9, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 9 as #3.10, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 10 as #3.11, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 0 as #4.1, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 1 as #4.2, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 2 as #4.3, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 3 as #4.4, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 4 as #4.5, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 5 as #4.6, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 6 as #4.7, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 7 as #4.8, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 8 as #4.9, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 9 as #4.10, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 10 as #4.11, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 0 as #5.1, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 1 as #5.2, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 2 as #5.3, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 3 as #5.4, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 4 as #5.5, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 5 as #5.6, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 6 as #5.7, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 7 as #5.8, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 8 as #5.9, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 10 as #5.11, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 1 as #6.2, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
opened ChimeraX session
> hide #!5.6 models
> show #!5.6 models
> hide #!5.6 models
> show #!5.6 models
> hide #!5.6 models
> show #!5.6 models
> hide #!1 models
> show #!1 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5.1 models
> hide #!5.5 models
> show #!5.5 models
> hide #!5.6 models
> show #!5.6 models
> hide #!5.9 models
> show #!5.9 models
> hide #!5.11 models
> show #!5.11 models
> hide #!5.7 models
> show #!5.7 models
> hide #!5.6 models
> show #!5.6 models
> ui tool show "Color Actions"
> color medium purple
> undo
> color medium slate blue
> color slate blue
> color medium slate blue
> color medium purple
> undo
> volume #3.3 color #9f9fef4c
> volume #3.3 color #a3a3f54c
> ui tool show "Color Actions"
> color medium purple
> color slate blue
> color medium slate blue
> color dark slate blue
> color medium slate blue
> color medium purple
> color slate blue
> color medium slate blue
> color indigo
> color royal blue
> undo
> close session
> open "D:\igm-var2CSA data\sturcture photo\var2CSA overall2 .cxs" format
> session
No such file/path: D:\igm-var2CSA data\sturcture photo\var2CSA overall2 .cxs
> open "C:\Users\huash\Desktop\igm-var2CSA data\sturcture photo\var2CSA
> overall2 .cxs" format session
Opened var2CSA-IgMtotalmap3.56.mrc as #2, grid size 320,320,320, pixel 1.07,
shown at level 0.0941, step 2, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 0 as #3.1, grid size 320,320,320, pixel
1.07, shown at level 0.0941, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 as #3.2, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 2 as #3.3, grid size 320,320,320, pixel
1.07, shown at level 0.147, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 3 as #3.4, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 4 as #3.5, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 5 as #3.6, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 6 as #3.7, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 7 as #3.8, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 8 as #3.9, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 9 as #3.10, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 10 as #3.11, grid size 320,320,320, pixel
1.07, shown at level 0.13, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 0 as #4.1, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 1 as #4.2, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 2 as #4.3, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 3 as #4.4, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 4 as #4.5, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 5 as #4.6, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 6 as #4.7, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 7 as #4.8, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 8 as #4.9, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 9 as #4.10, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 10 as #4.11, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 0 as #5.1, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 1 as #5.2, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 2 as #5.3, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 3 as #5.4, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 4 as #5.5, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 5 as #5.6, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 6 as #5.7, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 7 as #5.8, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 8 as #5.9, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 10 as #5.11, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
Opened var2CSA-IgMtotalmap3.56.mrc 1 1 as #6.2, grid size 320,320,320, pixel
1.07, shown at level 0.08, step 1, values float32
opened ChimeraX session
> volume #3.3 color #00aaff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #aa55ff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #6060904c
> volume #3.3 color #9494de4c
> volume #3.3 color #1822de4c
> volume #3.3 color #cabcde4c
> volume #3.3 color #3234de4c
> volume #3.3 color #6f7ade4c
> volume #3.3 color #4949de4c
> volume #3.3 color #7adede4c
> volume #3.3 color #6e8cde4c
> volume #3.3 color #7875de4c
> volume #3.3 color #aa00ff4c
> volume #3.3 color #aaaaff4c
> ui tool show "Color Actions"
> color medium purple
> color slate blue
> color medium slate blue
> color light steel blue
> color pale turquoise
> color light sky blue
> color sky blue
> color aquamarine
> color medium purple
> color purple
> color dark magenta
> color dark orchid
> color medium violet red
> color medium orchid
> color blue violet
> color slate blue
> color medium slate blue
> color medium purple
> volume #3.3 color #aaaaff4c
> volume #3.3 color #00aaff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #aa00ff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #aa00ff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #0055ff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #aa00ff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #aa007f4c
> volume #3.3 color #aa00ff4c
> volume #3.3 color #0000ff4c
> volume #3.3 color #aa00ff4c
> volume #3.3 color #0000ff4c
> volume #3.3 color #aa00ff4c
> volume #3.3 color #0000ff4c
> volume #3.3 color #00ffff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #aaffff4c
> volume #3.3 color #aaaaff4c
> volume #3.3 color #00aaff4c
> volume #3.3 color #aa55ff4c
> volume #3.3 color #0055ff4c
> volume #3.3 color #aa00ff4c
> ui tool show "Color Actions"
> close session
> open "D:/igm-var2CSA data/sturcture photo/TM overall.cxs"
Opened gobal map -TM 3.6A.mrc as #2, grid size 400,400,400, pixel 0.85, shown
at level 0.115, step 2, values float32
Opened gobal map -TM 3.6A.mrc 0 as #3.1, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 1 as #3.2, grid size 400,400,400, pixel 0.85,
shown at level 0.171, step 1, values float32
Opened gobal map -TM 3.6A.mrc 2 as #3.3, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 3 as #3.4, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 4 as #3.5, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 5 as #3.6, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 6 as #3.7, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 7 as #3.8, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 8 as #3.9, grid size 400,400,400, pixel 0.85,
shown at level 0.115, step 1, values float32
Opened gobal map -TM 3.6A.mrc 9 as #3.10, grid size 400,400,400, pixel 0.85,
shown at level 0.177, step 1, values float32
opened ChimeraX session
> lighting shadows true
> lighting flat
> lighting soft
> ui tool show "Show Sequence Viewer"
> sequence chain /M
Alignment identifier is 1/M
> select /M:1615
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /M:1615-1622
69 atoms, 71 bonds, 8 residues, 1 model selected
> close session
> open "D:/桌面/figure/local pdb.pdb"
Chain information for local pdb.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
> open "C:/Users/huash/Desktop/local truncation pdb-coot-0.pdb"
Summary of feedback from opening C:/Users/huash/Desktop/local truncation pdb-
coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 354
ILE A 357 1 4
Start residue of secondary structure not found: HELIX 2 2 GLU A 415 SER A 420
1 6
Start residue of secondary structure not found: HELIX 5 5 PHE B 354 THR B 360
1 7
Start residue of secondary structure not found: HELIX 6 6 ASP B 416 ASN B 419
1 4
Start residue of secondary structure not found: HELIX 9 9 PHE C 354 ILE C 357
1 4
68 messages similar to the above omitted
Chain information for local truncation pdb-coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K L | No description available
M | No description available
> hide atoms
> show cartoons
> set bgColor black
> set bgColor white
> ui tool show "Build Structure"
> ui tool show "Model Panel"
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1
20963 atoms, 21483 bonds, 12 pseudobonds, 2658 residues, 2 models selected
> select #2
14211 atoms, 14567 bonds, 17 pseudobonds, 1788 residues, 2 models selected
> view #1 clip false
> show #!1 target m
> ui tool show "Selection Inspector"
> ui tool show Matchmaker
> matchmaker #!2 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 local pdb.pdb, chain A (#1) with local truncation pdb-coot-0.pdb,
chain A (#2), sequence alignment score = 632.6
RMSD between 125 pruned atom pairs is 0.913 angstroms; (across all 129 pairs:
0.991)
> select clear
> open "D:/igm-var2CSA data/sturcture
> photo/DBLMSP+IgM+J300-coot-7_real_space_refined_003.pdb"
Chain information for DBLMSP+IgM+J300-coot-7_real_space_refined_003.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E G | No description available
F | No description available
H | No description available
J | No description available
K | No description available
L | No description available
R | No description available
> ui tool show Matchmaker
> matchmaker #!2 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 local pdb.pdb, chain A (#1) with local truncation pdb-coot-0.pdb,
chain A (#2), sequence alignment score = 632.6
RMSD between 125 pruned atom pairs is 0.913 angstroms; (across all 129 pairs:
0.991)
> hide atoms
> show cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!2 to #3
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 DBLMSP+IgM+J300-coot-7_real_space_refined_003.pdb, chain L (#3)
with local truncation pdb-coot-0.pdb, chain K (#2), sequence alignment score =
620.9
RMSD between 100 pruned atom pairs is 0.855 angstroms; (across all 128 pairs:
11.866)
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!2-3 to #1/A pairing bs
Parameters
---
Chain pairing | bs
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 local pdb.pdb, chain A (#1) with local truncation pdb-coot-0.pdb,
chain A (#2), sequence alignment score = 632.6
RMSD between 125 pruned atom pairs is 0.913 angstroms; (across all 129 pairs:
0.991)
Matchmaker local pdb.pdb, chain A (#1) with
DBLMSP+IgM+J300-coot-7_real_space_refined_003.pdb, chain A (#3), sequence
alignment score = 1068.2
RMSD between 176 pruned atom pairs is 0.965 angstroms; (across all 231 pairs:
1.740)
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
OpenGL version: 3.3.0 NVIDIA 496.49
OpenGL renderer: NVIDIA GeForce RTX 2060 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Zephyrus G14 GA401IV_GA401IV
OS: Microsoft Windows 10 家庭中文版 (Build 19043)
Memory: 16,556,564,480
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 4800HS with Radeon Graphics
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
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: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
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: 1.31
ChimeraX-AtomicLibrary: 4.2
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: 2.6.1
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: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
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: 1.0.1
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: 1.6.1
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: 3.6.0
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: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
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: 3.0.6
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: 1.11.3
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: 2.2.0
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 (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Analysis |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash after running MatchMaker |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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