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Opened 7 weeks ago
Closed 7 weeks ago
#18679 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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-10-10.0.19045
ChimeraX Version: 1.11.dev202508300055 (2025-08-30 00:55:12 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Thread 0x000007f4 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00001fcc (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x000021f4 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\connection.py", line 828 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\connection.py", line 896 in wait
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00003948 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x000011b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00001910 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x0000010c (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00001d10 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00000f48 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00000914 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00002f7c (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00000ce4 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x000013e0 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x000021d8 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Thread 0x00003088 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 982 in run
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Current thread 0x000033e0 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.11.dev202508300055 (2025-08-30)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> open "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4 First test AF3/FL
> TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat/fold_fl_chicktrpv4_sdpiiirat_model_0.cif"
> "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4 First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat/fold_fl_chicktrpv4_sdpiiirat_model_1.cif"
> "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4 First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat/fold_fl_chicktrpv4_sdpiiirat_model_2.cif"
> "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4 First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat/fold_fl_chicktrpv4_sdpiiirat_model_3.cif"
> "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4 First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat/fold_fl_chicktrpv4_sdpiiirat_model_4.cif"
Chain information for fold_fl_chicktrpv4_sdpiiirat_model_0.cif #1
---
Chain | Description
A | .
B | .
Chain information for fold_fl_chicktrpv4_sdpiiirat_model_1.cif #2
---
Chain | Description
A | .
B | .
Chain information for fold_fl_chicktrpv4_sdpiiirat_model_2.cif #3
---
Chain | Description
A | .
B | .
Chain information for fold_fl_chicktrpv4_sdpiiirat_model_3.cif #4
---
Chain | Description
A | .
B | .
Chain information for fold_fl_chicktrpv4_sdpiiirat_model_4.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
> ui tool show Matchmaker
> select sequence PPPILKV
265 atoms, 275 bonds, 35 residues, 5 models selected
> matchmaker #2-5 & sel to #1/B & sel 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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.562 angstroms; (across all 7 pairs:
0.562)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.580 angstroms; (across all 7 pairs:
0.580)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.464 angstroms; (across all 7 pairs:
0.464)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.727 angstroms; (across all 7 pairs:
0.727)
> ui dockable false Matchmaker
> ui dockable true Matchmaker
> alphafold pae #1 file "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4
> First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat\\\fold_fl_chicktrpv4_sdpiiirat_full_data_0.json"
> color bfactor #1 palette alphafold
10211 atoms, 1276 residues, atom bfactor range 16.7 to 95.6
> color bfactor #1 palette alphafold
10211 atoms, 1276 residues, atom bfactor range 16.7 to 95.6
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #1 models
> show #2 models
> alphafold pae #1 file "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4
> First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat\\\fold_fl_chicktrpv4_sdpiiirat_full_data_0.json"
> color bfactor #1 palette alphafold
10211 atoms, 1276 residues, atom bfactor range 16.7 to 95.6
> color #1/B:39-822 lime
> color bfactor #1 palette alphafold
10211 atoms, 1276 residues, atom bfactor range 16.7 to 95.6
> alphafold pae #2 file "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4
> First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat\\\fold_fl_chicktrpv4_sdpiiirat_full_data_1.json"
> color bfactor #2 palette alphafold
10211 atoms, 1276 residues, atom bfactor range 16.6 to 95.4
> open "I:/Chimera/AF Presentation/TRPV4 AF3/TRPV4 pdb data/6F55-assembly1
> SdpIIISH3 TRPV4PRD.cif/6f55-assembly1.cif"
6f55-assembly1.cif title:
Complex structure of PACSIN SH3 domain and TRPV4 proline rich region [more
info...]
Chain information for 6f55-assembly1.cif #6
---
Chain | Description
A | PACSIN 3
B | PRR
> matchmaker #2-6 & sel to #1 & sel
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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.562 angstroms; (across all 7 pairs:
0.562)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.580 angstroms; (across all 7 pairs:
0.580)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.464 angstroms; (across all 7 pairs:
0.464)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.727 angstroms; (across all 7 pairs:
0.727)
> show #1 models
> show #3 models
> show #5 models
> show #4 models
> matchmaker #2-6 & sel to #1/B & sel 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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.562 angstroms; (across all 7 pairs:
0.562)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.580 angstroms; (across all 7 pairs:
0.580)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.464 angstroms; (across all 7 pairs:
0.464)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.727 angstroms; (across all 7 pairs:
0.727)
> matchmaker #6/B & sel to #4/A & sel pairing ss
No 'to' chains specified
> matchmaker #6/B & sel to #4/B & sel pairing ss
No molecules/chains to match specified
> select sequence PPPILKV
383 atoms, 395 bonds, 42 residues, 6 models selected
> matchmaker #6/B & sel to #4/B & sel pairing ss
Parameters
---
Chain pairing | ss
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 fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 5 pruned atom pairs is 1.511 angstroms; (across all 7 pairs:
3.105)
> matchmaker #6/B & sel to #4/B & sel pairing ss
Parameters
---
Chain pairing | ss
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 fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 5 pruned atom pairs is 1.511 angstroms; (across all 7 pairs:
3.105)
> matchmaker #6/B#6/B#6/B & sel to #4/B#5/B#3/B & sel pairing ss
Different number of reference/match chains (3 ref, 1 match)
> matchmaker #6/B#6/B#6/B#6/B#6/B & sel to #4/B#5/B#3/B#2/B#1/B & sel pairing
> ss
Different number of reference/match chains (5 ref, 1 match)
> matchmaker #6/B#6/B#6/B#6/B#6/B & sel to #4/B#5/B#3/B#2/B#1/B & sel pairing
> ss
Different number of reference/match chains (5 ref, 1 match)
> matchmaker #6/B & sel to #1/B & sel pairing ss
Parameters
---
Chain pairing | ss
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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
> matchmaker #6/B & sel to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
> matchmaker #6/B & sel to #2/B pairing ss
Parameters
---
Chain pairing | ss
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 fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 5 pruned atom pairs is 1.282 angstroms; (across all 7 pairs:
3.621)
> matchmaker #6/B & sel to #3/B pairing ss
Parameters
---
Chain pairing | ss
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 fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 4 pruned atom pairs is 0.805 angstroms; (across all 7 pairs:
3.165)
> select sequence PPPILKV
383 atoms, 395 bonds, 42 residues, 6 models selected
> matchmaker #2-6 & sel to #1/B 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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.562 angstroms; (across all 7 pairs:
0.562)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.580 angstroms; (across all 7 pairs:
0.580)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.464 angstroms; (across all 7 pairs:
0.464)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.727 angstroms; (across all 7 pairs:
0.727)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
> morph
Missing or invalid "structures" argument: empty atom specifier
> morph #1-5 frames 80 wrap true
Computed 401 frame morph #7
> coordset #7 1,401
> hide #7 models
> show #7 models
> select clear
> hide #6 models
> show #6 models
> hide #6 models
> select sequence PPPILKV
436 atoms, 450 bonds, 49 residues, 7 models selected
> select add #6
1583 atoms, 1610 bonds, 124 residues, 7 models selected
> select subtract #6
318 atoms, 330 bonds, 42 residues, 6 models selected
> morph #1-5 frames 80 wrap true
Computed 401 frame morph #8
> coordset #8 1,401
> matchmaker #2-5 & sel 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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.562 angstroms; (across all 7 pairs:
0.562)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.580 angstroms; (across all 7 pairs:
0.580)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.464 angstroms; (across all 7 pairs:
0.464)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.727 angstroms; (across all 7 pairs:
0.727)
> show #1 models
> show #2 models
> show #3 models
> show #5 models
> show #4 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #7 models
> hide #8 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> select sequence PPPILKV
489 atoms, 505 bonds, 56 residues, 8 models selected
> select sequence PPPILKV
489 atoms, 505 bonds, 56 residues, 8 models selected
> matchmaker #2-6 & sel to #1/B & sel 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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.562 angstroms; (across all 7 pairs:
0.562)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.580 angstroms; (across all 7 pairs:
0.580)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.464 angstroms; (across all 7 pairs:
0.464)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.727 angstroms; (across all 7 pairs:
0.727)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
> show #7 models
> show #8 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #1 models
> hide #2 models
> hide #7 models
> show #7 models
> hide #8 models
> show #8 models
> hide #7 models
> show #7 models
> hide #7 models
> show #5 models
> show #6 models
> hide #5 models
> select add #6
1636 atoms, 1665 bonds, 131 residues, 8 models selected
> select subtract #6
371 atoms, 385 bonds, 49 residues, 7 models selected
> select add #5
10529 atoms, 10788 bonds, 1318 residues, 7 models selected
> select add #4
20687 atoms, 21191 bonds, 2587 residues, 7 models selected
> select add #3
30845 atoms, 31594 bonds, 3856 residues, 7 models selected
> select add #1
41003 atoms, 41997 bonds, 5125 residues, 7 models selected
> select add #2
51161 atoms, 52400 bonds, 6394 residues, 7 models selected
> select subtract #1
40950 atoms, 41942 bonds, 5118 residues, 6 models selected
> select subtract #2
30739 atoms, 31484 bonds, 3842 residues, 5 models selected
> select subtract #3
20528 atoms, 21026 bonds, 2566 residues, 4 models selected
> select subtract #4
10317 atoms, 10568 bonds, 1290 residues, 3 models selected
> select add #6
11582 atoms, 11848 bonds, 1372 residues, 4 models selected
> select subtract #6
10317 atoms, 10568 bonds, 1290 residues, 3 models selected
> select subtract #5
106 atoms, 110 bonds, 14 residues, 2 models selected
> select add #7
10264 atoms, 10513 bonds, 1283 residues, 2 models selected
> select add #8
20422 atoms, 20916 bonds, 2552 residues, 2 models selected
> select subtract #7
10211 atoms, 10458 bonds, 1276 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #6
1265 atoms, 1280 bonds, 82 residues, 1 model selected
> select sequence PPPILKV
489 atoms, 505 bonds, 56 residues, 8 models selected
> select add #7
10647 atoms, 10908 bonds, 1325 residues, 8 models selected
> select subtract #7
436 atoms, 450 bonds, 49 residues, 7 models selected
> select add #6
1583 atoms, 1610 bonds, 124 residues, 7 models selected
> select subtract #6
318 atoms, 330 bonds, 42 residues, 6 models selected
> select add #5
10476 atoms, 10733 bonds, 1311 residues, 6 models selected
> select subtract #5
265 atoms, 275 bonds, 35 residues, 5 models selected
> select add #5
10476 atoms, 10733 bonds, 1311 residues, 6 models selected
> select add #4
20634 atoms, 21136 bonds, 2580 residues, 6 models selected
> select subtract #4
10423 atoms, 10678 bonds, 1304 residues, 5 models selected
> select subtract #5
212 atoms, 220 bonds, 28 residues, 4 models selected
> select add #5
10423 atoms, 10678 bonds, 1304 residues, 5 models selected
> select subtract #5
212 atoms, 220 bonds, 28 residues, 4 models selected
> select add #3
10370 atoms, 10623 bonds, 1297 residues, 4 models selected
> select subtract #3
159 atoms, 165 bonds, 21 residues, 3 models selected
> select add #2
10317 atoms, 10568 bonds, 1290 residues, 3 models selected
> select subtract #2
106 atoms, 110 bonds, 14 residues, 2 models selected
> select add #1
10264 atoms, 10513 bonds, 1283 residues, 2 models selected
> select subtract #1
53 atoms, 55 bonds, 7 residues, 1 model selected
> matchmaker #6 & sel to #8/B & sel pairing bs
No molecules/chains to match specified
> matchmaker #6 & sel to #8/A & sel pairing bs
No 'to' chains specified
> matchmaker #1-5 & sel to #6/B & sel pairing bs
No 'to' chains specified
> select add #8
10211 atoms, 10458 bonds, 1276 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #6
1265 atoms, 1280 bonds, 82 residues, 1 model selected
> color #6 #d307c9ff
> select clear
> show #7 models
> hide #7 models
> select sequence PPPILKV
489 atoms, 505 bonds, 56 residues, 8 models selected
> hide #6 models
> show #6 models
> show #7 models
> hide #8 models
> show #8 models
> open "I:/Chimera/AF Presentation/TRPV4 AF3/TRPV4 pdb
> data/AF-Q9HBA0-F1-model_v4.pdb"
AF-Q9HBA0-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for transient receptor potential cation
channel subfamily V member 4 (Q9HBA0) [more info...]
Chain information for AF-Q9HBA0-F1-model_v4.pdb #9
---
Chain | Description | UniProt
A | transient receptor potential cation channel subfamily V member 4 | TRPV4_HUMAN 1-871
Computing secondary structure
> select add #9
7416 atoms, 7605 bonds, 927 residues, 9 models selected
> hide #8 models
> hide #7 models
> hide #6 models
> show #6 models
> show #7 models
> show #8 models
> matchmaker #1-5,9 & sel to #6/B & sel 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 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.282 angstroms; (across all 7 pairs:
3.621)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.805 angstroms; (across all 7 pairs:
3.165)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.511 angstroms; (across all 7 pairs:
3.105)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.239 angstroms; (across all 7 pairs:
3.569)
Matchmaker 6f55-assembly1.cif, chain B (#6) with AF-Q9HBA0-F1-model_v4.pdb,
chain A (#9), sequence alignment score = 35
RMSD between 5 pruned atom pairs is 1.159 angstroms; (across all 7 pairs:
3.712)
> hide #8 models
> hide #7 models
> hide #6 models
> show #6 models
> select sequence PPPILKV
542 atoms, 560 bonds, 63 residues, 9 models selected
> matchmaker #1-5,9 & sel to #6/B & sel 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 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.282 angstroms; (across all 7 pairs:
3.621)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.805 angstroms; (across all 7 pairs:
3.165)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.511 angstroms; (across all 7 pairs:
3.105)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.239 angstroms; (across all 7 pairs:
3.569)
Matchmaker 6f55-assembly1.cif, chain B (#6) with AF-Q9HBA0-F1-model_v4.pdb,
chain A (#9), sequence alignment score = 35
RMSD between 5 pruned atom pairs is 1.159 angstroms; (across all 7 pairs:
3.712)
> matchmaker #1-5,7-9 & sel to #6/B & sel 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 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.282 angstroms; (across all 7 pairs:
3.621)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.805 angstroms; (across all 7 pairs:
3.165)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.511 angstroms; (across all 7 pairs:
3.105)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.239 angstroms; (across all 7 pairs:
3.569)
Matchmaker 6f55-assembly1.cif, chain B (#6) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#7), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.583 angstroms; (across all 7 pairs:
3.061)
Matchmaker 6f55-assembly1.cif, chain B (#6) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#8), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.889 angstroms; (across all 7 pairs:
3.193)
Matchmaker 6f55-assembly1.cif, chain B (#6) with AF-Q9HBA0-F1-model_v4.pdb,
chain A (#9), sequence alignment score = 35
RMSD between 5 pruned atom pairs is 1.159 angstroms; (across all 7 pairs:
3.712)
> show #1 models
> hide #1 models
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #7 models
> matchmaker #1-5,7-9 & sel to #6/B & sel 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 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.282 angstroms; (across all 7 pairs:
3.621)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.805 angstroms; (across all 7 pairs:
3.165)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.511 angstroms; (across all 7 pairs:
3.105)
Matchmaker 6f55-assembly1.cif, chain B (#6) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.239 angstroms; (across all 7 pairs:
3.569)
Matchmaker 6f55-assembly1.cif, chain B (#6) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#7), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.583 angstroms; (across all 7 pairs:
3.061)
Matchmaker 6f55-assembly1.cif, chain B (#6) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#8), sequence alignment
score = 35
RMSD between 4 pruned atom pairs is 0.889 angstroms; (across all 7 pairs:
3.193)
Matchmaker 6f55-assembly1.cif, chain B (#6) with AF-Q9HBA0-F1-model_v4.pdb,
chain A (#9), sequence alignment score = 35
RMSD between 5 pruned atom pairs is 1.159 angstroms; (across all 7 pairs:
3.712)
> show #8 models
> hide #8 models
> show #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #8 models
> show #8 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #9 models
> show #9 models
No sequence chosen for AlphaFold match
> alphafold match
> MSSEDDAGGEAPEGSFWEAGNYRRTVKRVDDGYRLCNDLISCFQERAKIEKNYAQQLTEWSRKWRTNVEKGPQYGTLEKAWHAFLTAADKLSEIHLVVRNHLAGEDSDKIKAWQKEAYHKQIIGGFKETKEAEDGFRKAQKPWVKKMKDVETSKKNYHAARKEEKTAHTRENHAKADSSVSQEQLRKLQERVEKCTQEAEKCKDQYEKMLEELNRYNPRYMEDMEQVFEGCQEAERKRLCFFKEMFLNLHQHLNLSTSESFQALYRDLYQVIMAADNQEDLKWWRNTHGPGMAMNWPQFEEWSLETQRPITKKEKSGKVADDVTLTSILPTRDGVVSQTPLQTRQGSFYQEEQNSLYDSLRAPTFVRKEDISEWSDEDTPKKYLDANGHEEDIKVPGVRVRALYDYTGQEADELSFKAGEELMKISEEDEQGWCKGRLLTGHVGLYPANYVEKVGL
Unable to reach AlphaFold sequence search web service
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py
No AlphaFold model with similar sequence for 1 sequences
Opened 0 AlphaFold model
> alphafold search
> MSSEDDAGGEAPEGSFWEAGNYRRTVKRVDDGYRLCNDLISCFQERAKIEKNYAQQLTEWSRKWRTNVEKGPQYGTLEKAWHAFLTAADKLSEIHLVVRNHLAGEDSDKIKAWQKEAYHKQIIGGFKETKEAEDGFRKAQKPWVKKMKDVETSKKNYHAARKEEKTAHTRENHAKADSSVSQEQLRKLQERVEKCTQEAEKCKDQYEKMLEELNRYNPRYMEDMEQVFEGCQEAERKRLCFFKEMFLNLHQHLNLSTSESFQALYRDLYQVIMAADNQEDLKWWRNTHGPGMAMNWPQFEEWSLETQRPITKKEKSGKVADDVTLTSILPTRDGVVSQTPLQTRQGSFYQEEQNSLYDSLRAPTFVRKEDISEWSDEDTPKKYLDANGHEEDIKVPGVRVRALYDYTGQEADELSFKAGEELMKISEEDEQGWCKGRLLTGHVGLYPANYVEKVGL
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
> alphafold predict
> MSSEDDAGGEAPEGSFWEAGNYRRTVKRVDDGYRLCNDLISCFQERAKIEKNYAQQLTEWSRKWRTNVEKGPQYGTLEKAWHAFLTAADKLSEIHLVVRNHLAGEDSDKIKAWQKEAYHKQIIGGFKETKEAEDGFRKAQKPWVKKMKDVETSKKNYHAARKEEKTAHTRENHAKADSSVSQEQLRKLQERVEKCTQEAEKCKDQYEKMLEELNRYNPRYMEDMEQVFEGCQEAERKRLCFFKEMFLNLHQHLNLSTSESFQALYRDLYQVIMAADNQEDLKWWRNTHGPGMAMNWPQFEEWSLETQRPITKKEKSGKVADDVTLTSILPTRDGVVSQTPLQTRQGSFYQEEQNSLYDSLRAPTFVRKEDISEWSDEDTPKKYLDANGHEEDIKVPGVRVRALYDYTGQEADELSFKAGEELMKISEEDEQGWCKGRLLTGHVGLYPANYVEKVGL
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> morph #1-5 frames 80 wrap true
Computed 401 frame morph #10
> coordset #10 1,401
> hide #8 models
> hide #9 models
> movie record
> movie encode C:\Users\RyanRechnen\Desktop\movie1.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> morph #1-5 frames 80 wrap true
Computed 401 frame morph #11
> coordset #11 1,401
> hide #10 models
> show #10 models
> alphafold predict
> MSSEDDAGGEAPEGSFWEAGNYRRTVKRVDDGYRLCNDLISCFQERAKIEKNYAQQLTEWSRKWRTNVEKGPQYGTLEKAWHAFLTAADKLSEIHLVVRNHLAGEDSDKIKAWQKEAYHKQIIGGFKETKEAEDGFRKAQKPWVKKMKDVETSKKNYHAARKEEKTAHTRENHAKADSSVSQEQLRKLQERVEKCTQEAEKCKDQYEKMLEELNRYNPRYMEDMEQVFEGCQEAERKRLCFFKEMFLNLHQHLNLSTSESFQALYRDLYQVIMAADNQEDLKWWRNTHGPGMAMNWPQFEEWSLETQRPITKKEKSGKVADDVTLTSILPTRDGVVSQTPLQTRQGSFYQEEQNSLYDSLRAPTFVRKEDISEWSDEDTPKKYLDANGHEEDIKVPGVRVRALYDYTGQEADELSFKAGEELMKISEEDEQGWCKGRLLTGHVGLYPANYVEKVGL
Running AlphaFold prediction
Alphafold prediction send sequence to Google Colab returned: None
> morph #1-5 frames 80 wrap true
Computed 401 frame morph #12
> coordset #12 1,401
Running AlphaFold prediction
> alphafold predict
> MSSEDDAGGEAPEGSFWEAGNYRRTVKRVDDGYRLCNDLISCFQERAKIEKNYAQQLTEWSRKWRTNVEKGPQYGTLEKAWHAFLTAADKLSEIHLVVRNHLAGEDSDKIKAWQKEAYHKQIIGGFKETKEAEDGFRKAQKPWVKKMKDVETSKKNYHAARKEEKTAHTRENHAKADSSVSQEQLRKLQERVEKCTQEAEKCKDQYEKMLEELNRYNPRYMEDMEQVFEGCQEAERKRLCFFKEMFLNLHQHLNLSTSESFQALYRDLYQVIMAADNQEDLKWWRNTHGPGMAMNWPQFEEWSLETQRPITKKEKSGKVADDVTLTSILPTRDGVVSQTPLQTRQGSFYQEEQNSLYDSLRAPTFVRKEDISEWSDEDTPKKYLDANGHEEDIKVPGVRVRALYDYTGQEADELSFKAGEELMKISEEDEQGWCKGRLLTGHVGLYPANYVEKVGL
Running AlphaFold prediction
> select add #9
7416 atoms, 7605 bonds, 927 residues, 9 models selected
> select subtract #9
489 atoms, 505 bonds, 56 residues, 8 models selected
> open "I:/Chimera/AF Presentation/TRPV4 AF3/TRPV4 pdb data/chicken trpv4 xray
> pdb3w9f.ent"
chicken trpv4 xray pdb3w9f.ent title:
Crystal structure of the ankyrin repeat domain of chicken TRPV4 In complex
with IP3 [more info...]
Chain information for chicken trpv4 xray pdb3w9f.ent #13
---
Chain | Description | UniProt
A B C D | vanilloid receptor-related osmotically activated channel protein | Q9DFS3_CHICK 133-382
Non-standard residues in chicken trpv4 xray pdb3w9f.ent #13
---
I3P — D-myo-inositol-1,4,5-triphosphate
70 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
7824 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> select sequence PPPILKV
701 atoms, 725 bonds, 84 residues, 12 models selected
> hide #12 models
> select add #12
10859 atoms, 11128 bonds, 1353 residues, 12 models selected
> hide #11 models
> hide #10 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> select subtract #12
648 atoms, 670 bonds, 77 residues, 11 models selected
> select add #13
9220 atoms, 8941 bonds, 2 pseudobonds, 1550 residues, 14 models selected
> select subtract #13
648 atoms, 670 bonds, 77 residues, 11 models selected
> select add #11
10806 atoms, 11073 bonds, 1346 residues, 11 models selected
> select subtract #11
595 atoms, 615 bonds, 70 residues, 10 models selected
> show #11 models
> hide #!13 models
> show #10 models
> hide #10 models
> show #10 models
> hide #11 models
> show #11 models
> hide #11 models
> show #12 models
> hide #10 models
> show #10 models
> show #11 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #12 models
> show #11 models
> hide #12 models
> hide #11 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #8 models
> show #7 models
> hide #8 models
> show #8 models
> hide #7 models
> show #7 models
> hide #7 models
> show #6 models
> show #!13 models
> hide #8 models
> hide #6 models
> select add #13.1
595 atoms, 615 bonds, 2 pseudobonds, 70 residues, 12 models selected
> select subtract #13.1
595 atoms, 615 bonds, 70 residues, 10 models selected
> select sequence PPPILKV
701 atoms, 725 bonds, 84 residues, 12 models selected
> show #12 models
> hide #12 models
> alphafold predict
> MAPEEDAGGEVLVGSFWEAGNYRRTVQRVEDGHRLCGDLISCFQERARIEKAYAQQLADWARKWRGAVEKGPQYGTLEKAWHAFFTAAERLSELHLEVREKLHGPDSERVRTWQRGAFHRPVLGGFRESRAAEDGFRKAQKPWLKRLKEVEASKKSYHTARKDEKTAQTRESHAKADSSMSQEQLRKLQERVGRCTKEAEKMKTQYEQTLAELNRYTPRYMEDMEQAFESCQAAERQRLLFFKDVLLTLHQHLDLSSSDKFHELHRDLQRGIEDASDEEDLRWWRSTHGPGMAMNWPQFEEWSLDTQRAISRKEKGGRSPDEVTLTSIVPTRDGTAPPPQSPSSPGSGQDEDWSDEESPRKAGTGVRVRALYDYAGQEADELSFRAGEELLKMSEEDEQGWCQGQLQSGRIGLYPANYVECVGA,MADPEDPRDAGDVLGDDSFPLSSLANLFEVEDTPSPAEPSRGPPGAVDGKQNLRMKFHGAFRKGPPKPMELLESTIYESSVVPAPKKAPMDSLFDYGTYRQHPSENKRWRRRVVEKPVAGTKGPAPNPPPILKVFNRPILFDIVSRGSPDGLEGLLSFLLTHKKRLTDEEFREPSTGKTCLPKALLNLSAGRNDTIPILLDIAEKTGNMREFINSPFRDVYYRGQTALHIAIERRCKHYVELLVEKGADVHAQARGRFFQPKDEGGYFYFGELPLSLAACTNQPHIVHYLTENGHKQADLRRQDSRGNTVLHALVAIADNTRENTKFVTKMYDLLLIKCAKLFPDTNLEALLNNDGLSPLMMAAKTGKIGIFQHIIRREIADEDVRHLSRKFKDWAYGPVYSSLYDLSSLDTCGEEVSVLEILVYNSKIENRHEMLAVEPINELLRDKWRKFGAVSFYISVVSYLCAMIIFTLIAYYRPMEGPPPYPYTTTIDYLRLAGEIITLLTGILFFFSNIKDLFMKKCPGVNSFFIDGSFQLLYFIYSVLVIVTAGLYLGGVEAYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMIQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCPSSESCSEDHSNCTLPTYPSCRDSQTFSTFLLDLFKLTIGMGDLEMLESAKYPGVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKHIWKLQWATTILDIERSFPLFLRRVFRSGEMVTVGKGTDGTPDRRWCFRVDEVNWSHWNQNLGIISEDPGKSDTYQYYGFSHTVGRLRRDRWSTVVPRVVELNKSCPTEDVVVPLGTMGTAEARERRHGQTPSSPL
Running AlphaFold prediction
> alphafold predict
> MAPEEDAGGEVLVGSFWEAGNYRRTVQRVEDGHRLCGDLISCFQERARIEKAYAQQLADWARKWRGAVEKGPQYGTLEKAWHAFFTAAERLSELHLEVREKLHGPDSERVRTWQRGAFHRPVLGGFRESRAAEDGFRKAQKPWLKRLKEVEASKKSYHTARKDEKTAQTRESHAKADSSMSQEQLRKLQERVGRCTKEAEKMKTQYEQTLAELNRYTPRYMEDMEQAFESCQAAERQRLLFFKDVLLTLHQHLDLSSSDKFHELHRDLQRGIEDASDEEDLRWWRSTHGPGMAMNWPQFEEWSLDTQRAISRKEKGGRSPDEVTLTSIVPTRDGTAPPPQSPSSPGSGQDEDWSDEESPRKAGTGVRVRALYDYAGQEADELSFRAGEELLKMSEEDEQGWCQGQLQSGRIGLYPANYVECVGA,MADPEDPRDAGDVLGDDSFPLSSLANLFEVEDTPSPAEPSRGPPGAVDGKQNLRMKFHGAFRKGPPKPMELLESTIYESSVVPAPKKAPMDSLFDYGTYRQHPSENKRWRRRVVEKPVAGTKGPAPNPPPILKVFNRPILFDIVSRGSPDGLEGLLSFLLTHKKRLTDEEFREPSTGKTCLPKALLNLSAGRNDTIPILLDIAEKTGNMREFINSPFRDVYYRGQTALHIAIERRCKHYVELLVEKGADVHAQARGRFFQPKDEGGYFYFGELPLSLAACTNQPHIVHYLTENGHKQADLRRQDSRGNTVLHALVAIADNTRENTKFVTKMYDLLLIKCAKLFPDTNLEALLNNDGLSPLMMAAKTGKIGIFQHIIRREIADEDVRHLSRKFKDWAYGPVYSSLYDLSSLDTCGEEVSVLEILVYNSKIENRHEMLAVEPINELLRDKWRKFGAVSFYISVVSYLCAMIIFTLIAYYRPMEGPPPYPYTTTIDYLRLAGEIITLLTGILFFFSNIKDLFMKKCPGVNSFFIDGSFQLLYFIYSVLVIVTAGLYLGGVEAYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMIQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCPSSESCSEDHSNCTLPTYPSCRDSQTFSTFLLDLFKLTIGMGDLEMLESAKYPGVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKHIWKLQWATTILDIERSFPLFLRRVFRSGEMVTVGKGTDGTPDRRWCFRVDEVNWSHWNQNLGIISEDPGKSDTYQYYGFSHTVGRLRRDRWSTVVPRVVELNKSCPTEDVVVPLGTMGTAEARERRHGQTPSSPL
Running AlphaFold prediction
> hide #!13 models
> select add #13
9273 atoms, 8996 bonds, 2 pseudobonds, 1557 residues, 15 models selected
> select sequence PPPILKV
701 atoms, 725 bonds, 84 residues, 12 models selected
> matchmaker #2-8,10-12#!13 & sel to #1/B & sel 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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.562 angstroms; (across all 7 pairs:
0.562)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.580 angstroms; (across all 7 pairs:
0.580)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.464 angstroms; (across all 7 pairs:
0.464)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.727 angstroms; (across all 7 pairs:
0.727)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#7), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.081 angstroms; (across all 7 pairs:
1.840)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#8), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 1.040 angstroms; (across all 7 pairs:
1.040)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#10), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.000 angstroms; (across all 7 pairs:
0.000)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#11), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.000 angstroms; (across all 7 pairs:
0.000)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#12), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.000 angstroms; (across all 7 pairs:
0.000)
> show #!13 models
> hide #!13.1 models
> show #11 models
> show #12 models
> hide #12 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.94197,-0.19629,0.27232,-0.22152,0.25408,0.94706,-0.19625,0.81581,-0.21939,0.25405,0.94198,-0.6692,#2,0.82896,0.39621,-0.39477,-9.9093,0.15458,0.51603,0.84251,5.993,0.53753,-0.75943,0.36652,-5.5127,#3,-0.9998,0.00068211,0.020114,1.2998,0.018775,-0.32836,0.94436,10.894,0.007249,0.94455,0.32828,5.1758,#4,-0.72935,-0.34303,-0.59193,5.7765,-0.091643,0.9064,-0.41235,-5.0923,0.67798,-0.2465,-0.69252,-33.358,#5,-0.30248,0.10235,-0.94764,0.86096,-0.69712,-0.70179,0.14672,10.207,-0.65003,0.705,0.28363,5.7454,#6,-0.28716,0.36205,0.88683,21.8,-0.54327,0.70096,-0.46208,-16.137,-0.78892,-0.61447,-0.0046004,60.162,#7,0.95383,-0.12432,0.2734,0.61676,0.17363,0.97103,-0.1642,0.84612,-0.24507,0.20409,0.94778,-2.5345,#8,0.84761,-0.41325,0.33284,-3.9316,0.4665,0.87926,-0.096294,-3.1042,-0.25286,0.23689,0.93805,1.2468,#9,0.9136,-0.17943,0.36489,14.111,0.27985,0.9285,-0.24408,22.693,-0.295,0.32511,0.89849,-2.4228,#10,0.94197,-0.19629,0.27232,-0.22152,0.25408,0.94706,-0.19625,0.81581,-0.21939,0.25405,0.94198,-0.6692,#11,0.94197,-0.19629,0.27232,-0.22152,0.25408,0.94706,-0.19625,0.81581,-0.21939,0.25405,0.94198,-0.6692,#12,0.94197,-0.19629,0.27232,-0.22152,0.25408,0.94706,-0.19625,0.81581,-0.21939,0.25405,0.94198,-0.6692
> view matrix models
> #1,0.98322,-0.10868,0.14655,-0.14784,0.12491,0.98643,-0.10654,0.37932,-0.13298,0.12306,0.98345,-0.30859,#2,0.78019,0.53213,-0.32885,-8.5921,0.13156,0.37437,0.9179,5.9105,0.61155,-0.7594,0.22207,-6.8061,#3,-0.98575,-0.13755,0.096866,1.9296,0.12437,-0.20809,0.97017,10.883,-0.11329,0.96839,0.22223,4.5286,#4,-0.80235,-0.20568,-0.56029,8.5178,0.069408,0.90022,-0.42986,-10.096,0.5928,-0.38379,-0.70802,-31.205,#5,-0.3126,-0.056062,-0.94823,1.3552,-0.73605,-0.6167,0.27911,10.321,-0.60043,0.7852,0.15152,5.1144,#6,-0.26467,0.50498,0.82155,13.189,-0.60289,0.57826,-0.54967,-11.19,-0.75264,-0.64079,0.1514,64.198,#7,0.98813,-0.029529,0.15078,0.87982,0.041116,0.99639,-0.074315,0.092096,-0.14804,0.079632,0.98577,-2.0534,#8,0.91866,-0.32911,0.21852,-4.476,0.34033,0.94019,-0.014737,-2.8643,-0.2006,0.087907,0.97572,1.5751,#9,0.9662,-0.10171,0.23687,16.773,0.14403,0.97507,-0.16881,20.249,-0.2138,0.19722,0.95676,-2.754,#10,0.98322,-0.10868,0.14655,-0.14784,0.12491,0.98643,-0.10654,0.37932,-0.13298,0.12306,0.98345,-0.30859,#11,0.98322,-0.10868,0.14655,-0.14784,0.12491,0.98643,-0.10654,0.37932,-0.13298,0.12306,0.98345,-0.30859,#12,0.98322,-0.10868,0.14655,-0.14784,0.12491,0.98643,-0.10654,0.37932,-0.13298,0.12306,0.98345,-0.30859
> select add #13
9273 atoms, 8996 bonds, 2 pseudobonds, 1557 residues, 15 models selected
> select subtract #13
701 atoms, 725 bonds, 84 residues, 12 models selected
> hide #!13 models
> show #!13 models
> select add #13
9273 atoms, 8996 bonds, 2 pseudobonds, 1557 residues, 15 models selected
> select subtract #13
701 atoms, 725 bonds, 84 residues, 12 models selected
> hide #!13 models
> hide #11 models
> show #!13 models
> show #11 models
> select add #13
9273 atoms, 8996 bonds, 2 pseudobonds, 1557 residues, 15 models selected
> select subtract #13
701 atoms, 725 bonds, 84 residues, 12 models selected
> view matrix models
> #1,0.80868,-0.32997,0.48698,-0.241,0.22276,0.93798,0.26565,-2.1264,-0.54444,-0.10635,0.83203,3.8057,#2,0.86992,0.12551,-0.47696,-11.538,0.45563,0.16567,0.87462,-0.58377,0.18878,-0.97816,0.086932,0.049979,#3,-0.96132,0.25371,-0.10721,0.33066,-0.078094,0.12219,0.98943,9.59,0.26413,0.95953,-0.097655,4.4686,#4,-0.54709,-0.56133,-0.62097,0.25366,0.14475,0.66722,-0.73067,-21.185,0.82446,-0.48962,-0.28378,-24.05,#5,-0.27726,0.37957,-0.88264,0.16138,-0.93784,-0.30655,0.16276,9.1842,-0.20879,0.8729,0.44097,5.3604,#6,-0.32116,0.083891,0.9433,36.328,-0.86005,0.39115,-0.3276,11.643,-0.39646,-0.91649,-0.05347,58.082,#7,0.83129,-0.27567,0.48266,0.18854,0.1408,0.94446,0.29692,-2.8372,-0.53771,-0.17887,0.82394,1.9367,#8,0.66853,-0.52773,0.524,-2.6269,0.38843,0.84863,0.3591,-5.1475,-0.63418,-0.036532,0.77232,8.0463,#9,0.76132,-0.29602,0.57687,8.7273,0.20973,0.9543,0.2129,18.04,-0.61352,-0.041098,0.78861,-10.337,#10,0.80868,-0.32997,0.48698,-0.241,0.22276,0.93798,0.26565,-2.1264,-0.54444,-0.10635,0.83203,3.8057,#11,0.80868,-0.32997,0.48698,-0.241,0.22276,0.93798,0.26565,-2.1264,-0.54444,-0.10635,0.83203,3.8057,#12,0.80868,-0.32997,0.48698,-0.241,0.22276,0.93798,0.26565,-2.1264,-0.54444,-0.10635,0.83203,3.8057
> matchmaker #2-8,10-12#!13 & sel to #1/B & sel 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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_1.cif, chain B (#2), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.562 angstroms; (across all 7 pairs:
0.562)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_2.cif, chain B (#3), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.580 angstroms; (across all 7 pairs:
0.580)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_3.cif, chain B (#4), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.464 angstroms; (across all 7 pairs:
0.464)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
fold_fl_chicktrpv4_sdpiiirat_model_4.cif, chain B (#5), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.727 angstroms; (across all 7 pairs:
0.727)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#7), sequence alignment
score = 35
RMSD between 5 pruned atom pairs is 1.081 angstroms; (across all 7 pairs:
1.840)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#8), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 1.040 angstroms; (across all 7 pairs:
1.040)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#10), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.000 angstroms; (across all 7 pairs:
0.000)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#11), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.000 angstroms; (across all 7 pairs:
0.000)
Matchmaker fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with Morph -
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#12), sequence alignment
score = 35
RMSD between 7 pruned atom pairs is 0.000 angstroms; (across all 7 pairs:
0.000)
> show #9 models
> hide #9 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #6 models
> view matrix models
> #1,0.41409,0.63507,0.65209,-6.9211,-0.69905,-0.23694,0.67467,6.7998,0.58297,-0.73522,0.34583,7.6665,#2,0.82474,-0.045877,0.56364,-11.533,-0.045918,-0.99885,-0.014111,4.6524,0.56364,-0.014244,-0.8259,-3.2069,#3,-0.42707,0.45706,0.7802,3.5871,0.42341,0.86348,-0.27408,5.0218,-0.79896,0.21329,-0.56229,2.7212,#4,0.088122,0.20378,-0.97504,-30.066,0.85536,-0.51712,-0.030771,-16.431,-0.51049,-0.8313,-0.21988,15.668,#5,-0.98251,0.12197,-0.14067,3.3852,0.028422,0.84495,0.5341,5.9918,0.18401,0.52076,-0.83364,2.805,#6,-0.98181,0.14526,0.1223,34.677,-0.16158,-0.97742,-0.13619,50.757,0.099758,-0.15347,0.9831,36.129,#7,0.35521,0.6466,0.67509,-7.8095,-0.67985,-0.31698,0.66131,5.0654,0.64159,-0.69386,0.327,8.2875,#8,0.47229,0.48797,0.73405,-9.5211,-0.79655,-0.1203,0.59248,11.88,0.37742,-0.86453,0.33187,7.1805,#9,0.36465,0.68044,0.63563,10.887,-0.75577,-0.18246,0.6289,-12.308,0.54391,-0.70972,0.44772,5.4584,#10,0.41409,0.63507,0.65209,-6.9211,-0.69905,-0.23694,0.67467,6.7998,0.58297,-0.73522,0.34583,7.6665,#11,0.41409,0.63507,0.65209,-6.9211,-0.69905,-0.23694,0.67467,6.7998,0.58297,-0.73522,0.34583,7.6665,#12,0.41409,0.63507,0.65209,-6.9211,-0.69905,-0.23694,0.67467,6.7998,0.58297,-0.73522,0.34583,7.6665
> view matrix models
> #1,0.20467,0.59396,0.77802,-6.7418,-0.45071,-0.64838,0.61356,9.3047,0.86889,-0.47624,0.135,6.2237,#2,0.76112,-0.2846,0.58284,-11.205,0.036107,-0.87861,-0.47618,3.6903,0.64761,0.38347,-0.65845,-3.4032,#3,-0.27327,0.64091,0.71733,3.2541,0.11795,0.76241,-0.63625,3.5441,-0.95468,-0.08926,-0.28394,4.0014,#4,0.31631,0.11301,-0.9419,-35.164,0.51997,-0.8511,0.0725,-3.2006,-0.79346,-0.5127,-0.32797,19.46,#5,-0.95439,0.29678,0.032695,3.2882,0.29834,0.94352,0.14407,4.476,0.011909,0.14726,-0.98903,3.6563,#6,-0.99544,-0.087439,0.038212,42.802,0.094593,-0.95693,0.27448,51.983,0.012566,0.27684,0.96083,20.248,#7,0.14939,0.58385,0.798,-8.0511,-0.3971,-0.70368,0.58918,8.2146,0.90553,-0.40491,0.12673,7.3552,#8,0.24751,0.48575,0.83832,-8.0137,-0.63591,-0.57136,0.51881,14.097,0.731,-0.66151,0.16748,3.3569,#9,0.14496,0.64985,0.74611,6.0199,-0.50762,-0.59843,0.61985,-12.033,0.8493,-0.46859,0.24313,14.528,#10,0.20467,0.59396,0.77802,-6.7418,-0.45071,-0.64838,0.61356,9.3047,0.86889,-0.47624,0.135,6.2237,#11,0.20467,0.59396,0.77802,-6.7418,-0.45071,-0.64838,0.61356,9.3047,0.86889,-0.47624,0.135,6.2237,#12,0.20467,0.59396,0.77802,-6.7418,-0.45071,-0.64838,0.61356,9.3047,0.86889,-0.47624,0.135,6.2237
> show #5 models
> show #4 models
> show #3 models
> show #2 models
> show #1 models
> view matrix models
> #1,-0.29862,-0.95191,0.068534,-27.53,0.92413,-0.27048,0.26984,0.71004,-0.23833,0.14392,0.96046,37.032,#2,-0.27606,-0.45645,-0.84584,-31.384,0.80577,0.36983,-0.46256,-9.2506,0.52395,-0.80924,0.2657,31.55,#3,0.056355,0.21974,-0.97393,-38.284,-0.9984,0.0087675,-0.055794,1.3771,-0.003721,0.97552,0.21988,41.716,#4,0.070303,-0.84456,0.53083,-18.477,-0.73212,-0.40513,-0.5476,7.6942,0.67754,-0.35013,-0.6468,5.2721,#5,0.7863,0.60881,-0.10526,-37.633,-0.23857,0.14203,-0.96068,0.9807,-0.56992,0.7805,0.25692,42.356,#6,0.64823,-0.6533,0.39115,-19.199,-0.23232,0.31951,0.91866,22.876,-0.72514,-0.68637,0.055338,99.578,#7,-0.21694,-0.97552,0.036048,-27.415,0.94238,-0.19965,0.26844,1.5758,-0.25467,0.092204,0.96262,35.182,#8,-0.4982,-0.86637,-0.034652,-23.578,0.81484,-0.48148,0.32282,-2.731,-0.29637,0.1326,0.94582,39.345,#9,-0.31355,-0.94273,0.11378,-50.097,0.89523,-0.25353,0.36645,13.405,-0.31661,0.21676,0.92346,32.949,#10,-0.29862,-0.95191,0.068534,-27.53,0.92413,-0.27048,0.26984,0.71004,-0.23833,0.14392,0.96046,37.032,#11,-0.29862,-0.95191,0.068534,-27.53,0.92413,-0.27048,0.26984,0.71004,-0.23833,0.14392,0.96046,37.032,#12,-0.29862,-0.95191,0.068534,-27.53,0.92413,-0.27048,0.26984,0.71004,-0.23833,0.14392,0.96046,37.032
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.27606,-0.45645,-0.84584,-29.133,0.80577,0.36983,-0.46256,-5.1898,0.52395,-0.80924,0.2657,33.553
> undo
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.29862,-0.95191,0.068534,-45.355,0.92413,-0.27048,0.26984,-16.155,-0.23833,0.14392,0.96046,25.986,#2,-0.27606,-0.45645,-0.84584,-49.209,0.80577,0.36983,-0.46256,-26.115,0.52395,-0.80924,0.2657,20.505,#3,0.056355,0.21974,-0.97393,-56.109,-0.9984,0.0087675,-0.055794,-15.488,-0.003721,0.97552,0.21988,30.671,#4,0.070303,-0.84456,0.53083,-36.302,-0.73212,-0.40513,-0.5476,-9.1706,0.67754,-0.35013,-0.6468,-5.7733,#5,0.7863,0.60881,-0.10526,-55.459,-0.23857,0.14203,-0.96068,-15.884,-0.56992,0.7805,0.25692,31.31,#6,0.64823,-0.6533,0.39115,-37.025,-0.23232,0.31951,0.91866,6.0112,-0.72514,-0.68637,0.055338,88.533,#7,-0.21694,-0.97552,0.036048,-45.24,0.94238,-0.19965,0.26844,-15.289,-0.25467,0.092204,0.96262,24.137,#8,-0.4982,-0.86637,-0.034652,-41.404,0.81484,-0.48148,0.32282,-19.596,-0.29637,0.1326,0.94582,28.299,#9,-0.31355,-0.94273,0.11378,-67.922,0.89523,-0.25353,0.36645,-3.4594,-0.31661,0.21676,0.92346,21.904,#10,-0.29862,-0.95191,0.068534,-45.355,0.92413,-0.27048,0.26984,-16.155,-0.23833,0.14392,0.96046,25.986,#11,-0.29862,-0.95191,0.068534,-45.355,0.92413,-0.27048,0.26984,-16.155,-0.23833,0.14392,0.96046,25.986,#12,-0.29862,-0.95191,0.068534,-45.355,0.92413,-0.27048,0.26984,-16.155,-0.23833,0.14392,0.96046,25.986
> view matrix models
> #1,-0.29862,-0.95191,0.068534,-47.003,0.92413,-0.27048,0.26984,-14.993,-0.23833,0.14392,0.96046,25.822,#2,-0.27606,-0.45645,-0.84584,-50.857,0.80577,0.36983,-0.46256,-24.954,0.52395,-0.80924,0.2657,20.341,#3,0.056355,0.21974,-0.97393,-57.757,-0.9984,0.0087675,-0.055794,-14.326,-0.003721,0.97552,0.21988,30.507,#4,0.070303,-0.84456,0.53083,-37.95,-0.73212,-0.40513,-0.5476,-8.0089,0.67754,-0.35013,-0.6468,-5.9376,#5,0.7863,0.60881,-0.10526,-57.107,-0.23857,0.14203,-0.96068,-14.722,-0.56992,0.7805,0.25692,31.146,#6,0.64823,-0.6533,0.39115,-38.672,-0.23232,0.31951,0.91866,7.1729,-0.72514,-0.68637,0.055338,88.368,#7,-0.21694,-0.97552,0.036048,-46.888,0.94238,-0.19965,0.26844,-14.127,-0.25467,0.092204,0.96262,23.973,#8,-0.4982,-0.86637,-0.034652,-43.052,0.81484,-0.48148,0.32282,-18.434,-0.29637,0.1326,0.94582,28.135,#9,-0.31355,-0.94273,0.11378,-69.57,0.89523,-0.25353,0.36645,-2.2977,-0.31661,0.21676,0.92346,21.739,#10,-0.29862,-0.95191,0.068534,-47.003,0.92413,-0.27048,0.26984,-14.993,-0.23833,0.14392,0.96046,25.822,#11,-0.29862,-0.95191,0.068534,-47.003,0.92413,-0.27048,0.26984,-14.993,-0.23833,0.14392,0.96046,25.822,#12,-0.29862,-0.95191,0.068534,-47.003,0.92413,-0.27048,0.26984,-14.993,-0.23833,0.14392,0.96046,25.822
> view matrix models
> #1,-0.29862,-0.95191,0.068534,-80.403,0.92413,-0.27048,0.26984,17.993,-0.23833,0.14392,0.96046,25.461,#2,-0.27606,-0.45645,-0.84584,-84.257,0.80577,0.36983,-0.46256,8.0322,0.52395,-0.80924,0.2657,19.979,#3,0.056355,0.21974,-0.97393,-91.157,-0.9984,0.0087675,-0.055794,18.66,-0.003721,0.97552,0.21988,30.145,#4,0.070303,-0.84456,0.53083,-71.35,-0.73212,-0.40513,-0.5476,24.977,0.67754,-0.35013,-0.6468,-6.2989,#5,0.7863,0.60881,-0.10526,-90.507,-0.23857,0.14203,-0.96068,18.264,-0.56992,0.7805,0.25692,30.785,#6,0.64823,-0.6533,0.39115,-72.073,-0.23232,0.31951,0.91866,40.159,-0.72514,-0.68637,0.055338,88.007,#7,-0.21694,-0.97552,0.036048,-80.288,0.94238,-0.19965,0.26844,18.859,-0.25467,0.092204,0.96262,23.611,#8,-0.4982,-0.86637,-0.034652,-76.452,0.81484,-0.48148,0.32282,14.552,-0.29637,0.1326,0.94582,27.774,#9,-0.31355,-0.94273,0.11378,-102.97,0.89523,-0.25353,0.36645,30.688,-0.31661,0.21676,0.92346,21.378,#10,-0.29862,-0.95191,0.068534,-80.403,0.92413,-0.27048,0.26984,17.993,-0.23833,0.14392,0.96046,25.461,#11,-0.29862,-0.95191,0.068534,-80.403,0.92413,-0.27048,0.26984,17.993,-0.23833,0.14392,0.96046,25.461,#12,-0.29862,-0.95191,0.068534,-80.403,0.92413,-0.27048,0.26984,17.993,-0.23833,0.14392,0.96046,25.461
> view matrix models
> #1,-0.29862,-0.95191,0.068534,-74.503,0.92413,-0.27048,0.26984,18.738,-0.23833,0.14392,0.96046,27.594,#2,-0.27606,-0.45645,-0.84584,-78.357,0.80577,0.36983,-0.46256,8.7778,0.52395,-0.80924,0.2657,22.112,#3,0.056355,0.21974,-0.97393,-85.257,-0.9984,0.0087675,-0.055794,19.405,-0.003721,0.97552,0.21988,32.279,#4,0.070303,-0.84456,0.53083,-65.45,-0.73212,-0.40513,-0.5476,25.723,0.67754,-0.35013,-0.6468,-4.1658,#5,0.7863,0.60881,-0.10526,-84.607,-0.23857,0.14203,-0.96068,19.009,-0.56992,0.7805,0.25692,32.918,#6,0.64823,-0.6533,0.39115,-66.173,-0.23232,0.31951,0.91866,40.904,-0.72514,-0.68637,0.055338,90.14,#7,-0.21694,-0.97552,0.036048,-74.388,0.94238,-0.19965,0.26844,19.604,-0.25467,0.092204,0.96262,25.744,#8,-0.4982,-0.86637,-0.034652,-70.552,0.81484,-0.48148,0.32282,15.297,-0.29637,0.1326,0.94582,29.907,#9,-0.31355,-0.94273,0.11378,-97.07,0.89523,-0.25353,0.36645,31.434,-0.31661,0.21676,0.92346,23.511,#10,-0.29862,-0.95191,0.068534,-74.503,0.92413,-0.27048,0.26984,18.738,-0.23833,0.14392,0.96046,27.594,#11,-0.29862,-0.95191,0.068534,-74.503,0.92413,-0.27048,0.26984,18.738,-0.23833,0.14392,0.96046,27.594,#12,-0.29862,-0.95191,0.068534,-74.503,0.92413,-0.27048,0.26984,18.738,-0.23833,0.14392,0.96046,27.594
> hide #1 models
> hide #3 models
> hide #2 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #11 models
> select add #12
10859 atoms, 11128 bonds, 1353 residues, 12 models selected
> select subtract #12
648 atoms, 670 bonds, 77 residues, 11 models selected
> select add #11
10806 atoms, 11073 bonds, 1346 residues, 11 models selected
> select subtract #11
595 atoms, 615 bonds, 70 residues, 10 models selected
> select add #10
10753 atoms, 11018 bonds, 1339 residues, 10 models selected
> select subtract #10
542 atoms, 560 bonds, 63 residues, 9 models selected
> select add #9
7416 atoms, 7605 bonds, 927 residues, 9 models selected
> select subtract #9
489 atoms, 505 bonds, 56 residues, 8 models selected
> select add #8
10647 atoms, 10908 bonds, 1325 residues, 8 models selected
> select subtract #8
436 atoms, 450 bonds, 49 residues, 7 models selected
> select add #7
10594 atoms, 10853 bonds, 1318 residues, 7 models selected
> select subtract #7
383 atoms, 395 bonds, 42 residues, 6 models selected
> select add #6
1530 atoms, 1555 bonds, 117 residues, 6 models selected
> select subtract #6
265 atoms, 275 bonds, 35 residues, 5 models selected
> select add #5
10423 atoms, 10678 bonds, 1304 residues, 5 models selected
> select subtract #5
212 atoms, 220 bonds, 28 residues, 4 models selected
> select add #4
10370 atoms, 10623 bonds, 1297 residues, 4 models selected
> select subtract #4
159 atoms, 165 bonds, 21 residues, 3 models selected
> select add #3
10317 atoms, 10568 bonds, 1290 residues, 3 models selected
> select subtract #3
106 atoms, 110 bonds, 14 residues, 2 models selected
> select add #2
10264 atoms, 10513 bonds, 1283 residues, 2 models selected
> select subtract #2
53 atoms, 55 bonds, 7 residues, 1 model selected
> select add #1
10211 atoms, 10458 bonds, 1276 residues, 1 model selected
> select subtract #1
Nothing selected
> show #1 models
> select add #13
8572 atoms, 8271 bonds, 2 pseudobonds, 1473 residues, 3 models selected
> view matrix models #13,1,0,0,-75.117,0,1,0,70.524,0,0,1,-1.965
> view matrix models #13,1,0,0,14.207,0,1,0,-34.057,0,0,1,91.972
> view matrix models #13,1,0,0,-49.771,0,1,0,-42.268,0,0,1,37.051
> view matrix models #13,1,0,0,-11.083,0,1,0,5.4101,0,0,1,-17.519
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.70222,0.56177,-0.43738,-27.504,-0.65274,0.7533,-0.080453,0.0046647,0.28428,0.34199,0.89567,-20.019
> view matrix models
> #13,0.97908,-0.096626,0.17909,-7.3822,-0.19211,-0.1486,0.97006,31.688,-0.06712,-0.98417,-0.16405,-25.506
> view matrix models
> #13,0.98813,0.10484,-0.1123,-14.169,0.085649,0.23088,0.96921,30.331,0.12754,-0.96732,0.21915,-17.575
> view matrix models
> #13,0.71003,-0.40788,-0.57402,-18.621,0.70345,0.37383,0.60449,29.502,-0.031978,-0.833,0.55235,-15.518
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.71003,-0.40788,-0.57402,-46.609,0.70345,0.37383,0.60449,23.888,-0.031978,-0.833,0.55235,-16.117
> view matrix models
> #13,0.71003,-0.40788,-0.57402,-44.596,0.70345,0.37383,0.60449,29.419,-0.031978,-0.833,0.55235,-14.848
> view matrix models
> #13,0.71003,-0.40788,-0.57402,-31.492,0.70345,0.37383,0.60449,84.369,-0.031978,-0.833,0.55235,85.01
> view matrix models
> #13,0.71003,-0.40788,-0.57402,-30.357,0.70345,0.37383,0.60449,85.121,-0.031978,-0.833,0.55235,84.548
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.015978,0.89073,0.45425,-36.143,0.10731,-0.45321,0.88492,92.579,0.9941,0.034604,-0.10282,75.267
> view matrix models
> #13,-0.76993,-0.47563,0.42542,-29.489,0.63772,-0.59732,0.48634,93.533,0.022797,0.64575,0.76321,71.747
> view matrix models
> #13,-0.79293,-0.067761,0.60553,-31.497,0.45025,-0.73473,0.50738,93.431,0.41052,0.67496,0.61311,73.157
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.79293,-0.067761,0.60553,-20.725,0.45025,-0.73473,0.50738,56.265,0.41052,0.67496,0.61311,48.063
> view matrix models
> #13,-0.79293,-0.067761,0.60553,-8.641,0.45025,-0.73473,0.50738,45.106,0.41052,0.67496,0.61311,69.354
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.1479,0.20642,0.96722,0.81743,0.79345,-0.55905,0.24064,42.544,0.59039,0.80303,-0.081102,58.842
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.1479,0.20642,0.96722,-18.81,0.79345,-0.55905,0.24064,22.147,0.59039,0.80303,-0.081102,25.137
> view matrix models
> #13,-0.1479,0.20642,0.96722,-18.654,0.79345,-0.55905,0.24064,21.957,0.59039,0.80303,-0.081102,25.415
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.38189,0.41765,0.82446,-25.779,0.55941,-0.60564,0.56592,25.143,0.73568,0.67732,-0.0023488,29.621
> view matrix models
> #13,-0.25877,0.6484,0.71597,-28.796,0.61735,-0.45906,0.63886,25.253,0.74291,0.60732,-0.2815,26.077
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.25877,0.6484,0.71597,-38.219,0.61735,-0.45906,0.63886,40.332,0.74291,0.60732,-0.2815,18.386
> hide #!13 models
> show #!13 models
> view matrix models
> #13,-0.25877,0.6484,0.71597,-66.819,0.61735,-0.45906,0.63886,-7.0097,0.74291,0.60732,-0.2815,19.59
> hide #1 models
> show #2 models
> hide #2 models
> show #6 models
> view matrix models
> #13,-0.25877,0.6484,0.71597,-23.464,0.61735,-0.45906,0.63886,31.395,0.74291,0.60732,-0.2815,35.784
> view matrix models
> #13,-0.25877,0.6484,0.71597,-30.751,0.61735,-0.45906,0.63886,29.365,0.74291,0.60732,-0.2815,36.266
> view matrix models
> #13,-0.25877,0.6484,0.71597,-30.865,0.61735,-0.45906,0.63886,29.276,0.74291,0.60732,-0.2815,36.232
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.14074,-0.82445,-0.54816,-32.947,0.26514,0.50206,-0.82319,-8.4317,0.95388,-0.26119,0.14793,55.074
> view matrix models
> #13,0.37829,-0.72665,0.57348,-10.819,0.90601,0.16358,-0.39036,9.0317,0.18984,0.66725,0.72023,45.523
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.37829,-0.72665,0.57348,-29.803,0.90601,0.16358,-0.39036,-23.886,0.18984,0.66725,0.72023,68.088
> view matrix models
> #13,0.37829,-0.72665,0.57348,-27.445,0.90601,0.16358,-0.39036,-22.38,0.18984,0.66725,0.72023,65.826
> view matrix models
> #13,0.37829,-0.72665,0.57348,-44.598,0.90601,0.16358,-0.39036,-16.248,0.18984,0.66725,0.72023,89.443
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.11465,-0.70846,0.69637,-45.657,0.96313,0.25103,0.096814,-8.9303,-0.2434,0.6596,0.71112,84.791
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.11465,-0.70846,0.69637,-36.601,0.96313,0.25103,0.096814,-10.672,-0.2434,0.6596,0.71112,110.86
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.20298,-0.1992,0.95871,-37.274,0.81859,-0.50274,-0.27777,-9.6057,0.53732,0.84117,0.061017,106.82
> view matrix models
> #13,-0.13253,0.55643,0.82025,-51.561,0.91352,-0.25255,0.31891,-1.9958,0.38461,0.79158,-0.47484,97.287
> view matrix models
> #13,0.071609,0.069178,0.99503,-41.126,0.96705,-0.24917,-0.052271,-7.3331,0.24432,0.96599,-0.084742,99.994
> view matrix models
> #13,-0.96478,0.24087,0.10577,-68.113,-0.17864,-0.3047,-0.93555,-32.816,-0.19312,-0.92149,0.33699,123.35
> view matrix models
> #13,-0.81961,0.56433,-0.098854,-73.464,0.056148,-0.092592,-0.99412,-33.65,-0.57017,-0.82034,0.044203,113.59
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.81961,0.56433,-0.098854,-106.51,0.056148,-0.092592,-0.99412,-23.617,-0.57017,-0.82034,0.044203,43.154
> view matrix models
> #13,-0.81961,0.56433,-0.098854,-113.36,0.056148,-0.092592,-0.99412,-25.177,-0.57017,-0.82034,0.044203,46.295
> view matrix models
> #13,-0.81961,0.56433,-0.098854,-113.75,0.056148,-0.092592,-0.99412,7.5096,-0.57017,-0.82034,0.044203,57.084
> view matrix models
> #13,-0.81961,0.56433,-0.098854,-114.01,0.056148,-0.092592,-0.99412,7.6529,-0.57017,-0.82034,0.044203,53.043
> view matrix models
> #13,-0.81961,0.56433,-0.098854,-116.61,0.056148,-0.092592,-0.99412,10.882,-0.57017,-0.82034,0.044203,56.895
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.81575,0.56811,-0.10861,-116.76,0.063527,-0.098642,-0.99309,11.045,-0.5749,-0.81702,0.044378,56.81
> view matrix models
> #13,-0.72851,0.68364,0.04378,-114.73,0.015466,0.080306,-0.99665,8.4568,-0.68486,-0.72539,-0.069077,52.815
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.72851,0.68364,0.04378,-111.27,0.015466,0.080306,-0.99665,0.74363,-0.68486,-0.72539,-0.069077,53.104
> view matrix models
> #13,-0.72851,0.68364,0.04378,-99.045,0.015466,0.080306,-0.99665,8.1764,-0.68486,-0.72539,-0.069077,48.393
> show #1 models
> view matrix models
> #13,-0.72851,0.68364,0.04378,-99.045,0.015466,0.080306,-0.99665,8.1764,-0.68486,-0.72539,-0.069077,48.393
> select sequence PPPILKV
701 atoms, 725 bonds, 84 residues, 12 models selected
> select add #6
1848 atoms, 1885 bonds, 159 residues, 12 models selected
> select add #8
12006 atoms, 12288 bonds, 1428 residues, 12 models selected
> select add #7
22164 atoms, 22691 bonds, 2697 residues, 12 models selected
> select subtract #6
20899 atoms, 21411 bonds, 2615 residues, 11 models selected
> select add #6
22164 atoms, 22691 bonds, 2697 residues, 12 models selected
> select subtract #7
11953 atoms, 12233 bonds, 1421 residues, 11 models selected
> select subtract #6
10688 atoms, 10953 bonds, 1339 residues, 10 models selected
> select subtract #8
477 atoms, 495 bonds, 63 residues, 9 models selected
> select add #9
7351 atoms, 7540 bonds, 927 residues, 9 models selected
> select add #10
17509 atoms, 17943 bonds, 2196 residues, 9 models selected
> select subtract #9
10582 atoms, 10843 bonds, 1325 residues, 8 models selected
> select add #11
20740 atoms, 21246 bonds, 2594 residues, 8 models selected
> select subtract #10
10529 atoms, 10788 bonds, 1318 residues, 7 models selected
> select subtract #11
318 atoms, 330 bonds, 42 residues, 6 models selected
> select add #12
10476 atoms, 10733 bonds, 1311 residues, 6 models selected
> select subtract #12
265 atoms, 275 bonds, 35 residues, 5 models selected
> hide #1 models
> show #1 models
> select add #5
10423 atoms, 10678 bonds, 1304 residues, 5 models selected
> select add #4
20581 atoms, 21081 bonds, 2573 residues, 5 models selected
> select subtract #5
10370 atoms, 10623 bonds, 1297 residues, 4 models selected
> select subtract #4
159 atoms, 165 bonds, 21 residues, 3 models selected
> select add #3
10317 atoms, 10568 bonds, 1290 residues, 3 models selected
> select subtract #3
106 atoms, 110 bonds, 14 residues, 2 models selected
> select add #2
10264 atoms, 10513 bonds, 1283 residues, 2 models selected
> select subtract #2
53 atoms, 55 bonds, 7 residues, 1 model selected
> select add #1
10211 atoms, 10458 bonds, 1276 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #13
8572 atoms, 8271 bonds, 2 pseudobonds, 1473 residues, 3 models selected
> view matrix models
> #13,-0.72851,0.68364,0.04378,-96.777,0.015466,0.080306,-0.99665,5.9957,-0.68486,-0.72539,-0.069077,41.209
> hide #6 models
> show #6 models
> hide #1 models
> select subtract #13
Nothing selected
> show #7 models
> select add #6
1265 atoms, 1280 bonds, 82 residues, 1 model selected
> select add #13
9837 atoms, 9551 bonds, 2 pseudobonds, 1555 residues, 4 models selected
> color sel bychain
> view matrix models
> #6,0.64823,-0.6533,0.39115,-61.917,-0.23232,0.31951,0.91866,34.874,-0.72514,-0.68637,0.055338,85.528,#13,-0.72851,0.68364,0.04378,-92.521,0.015466,0.080306,-0.99665,-0.034765,-0.68486,-0.72539,-0.069077,36.597
> hide #!13 models
> select subtract #6
8572 atoms, 8271 bonds, 2 pseudobonds, 1473 residues, 3 models selected
Drag select of 10 residues
> select add #6/B:105
8752 atoms, 8280 bonds, 2 pseudobonds, 1484 residues, 4 models selected
> select add #6/B:104
8766 atoms, 8294 bonds, 2 pseudobonds, 1485 residues, 4 models selected
> select add #6/B:103
8773 atoms, 8300 bonds, 2 pseudobonds, 1486 residues, 4 models selected
> select subtract #6/B:103
8766 atoms, 8294 bonds, 2 pseudobonds, 1485 residues, 4 models selected
> select add #6/B:102
8788 atoms, 8315 bonds, 2 pseudobonds, 1486 residues, 4 models selected
> select add #6/B:101
8802 atoms, 8328 bonds, 2 pseudobonds, 1487 residues, 4 models selected
> select add #6/B:103
8809 atoms, 8334 bonds, 2 pseudobonds, 1488 residues, 4 models selected
> color (#6 & sel) magenta
> show #!13 models
> select subtract #13
237 atoms, 63 bonds, 15 residues, 1 model selected
> select clear
> select add #13/B:385
5 atoms, 4 bonds, 1 residue, 1 model selected
> select sequence PPPILKV
701 atoms, 725 bonds, 84 residues, 12 models selected
> select add #13
9273 atoms, 8996 bonds, 2 pseudobonds, 1557 residues, 15 models selected
> select sequence PPPILKV
701 atoms, 725 bonds, 84 residues, 12 models selected
> hide #6 models
> select add #13
9273 atoms, 8996 bonds, 2 pseudobonds, 1557 residues, 15 models selected
> hide #!13 models
> show #!13 models
> hide #!13 models
> close #10-12
> show #8 models
> hide #7 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> show #6 models
> hide #6 models
> hide #7 models
> close #7
> view matrix models
> #1,-0.29862,-0.95191,0.068534,-89.935,0.92413,-0.27048,0.26984,17.085,-0.23833,0.14392,0.96046,21.1,#2,-0.27606,-0.45645,-0.84584,-93.789,0.80577,0.36983,-0.46256,7.1245,0.52395,-0.80924,0.2657,15.618,#3,0.056355,0.21974,-0.97393,-100.69,-0.9984,0.0087675,-0.055794,17.752,-0.003721,0.97552,0.21988,25.784,#4,0.070303,-0.84456,0.53083,-80.882,-0.73212,-0.40513,-0.5476,24.069,0.67754,-0.35013,-0.6468,-10.66,#5,0.7863,0.60881,-0.10526,-100.04,-0.23857,0.14203,-0.96068,17.356,-0.56992,0.7805,0.25692,26.424,#6,0.64823,-0.6533,0.39115,-77.349,-0.23232,0.31951,0.91866,33.221,-0.72514,-0.68637,0.055338,79.034,#8,-0.4982,-0.86637,-0.034652,-85.983,0.81484,-0.48148,0.32282,13.644,-0.29637,0.1326,0.94582,23.413,#9,-0.31355,-0.94273,0.11378,-112.5,0.89523,-0.25353,0.36645,29.78,-0.31661,0.21676,0.92346,17.017,#13,-0.72851,0.68364,0.04378,-107.95,0.015466,0.080306,-0.99665,-1.6881,-0.68486,-0.72539,-0.069077,30.103
> view matrix models
> #1,-0.29862,-0.95191,0.068534,-81.569,0.92413,-0.27048,0.26984,30.838,-0.23833,0.14392,0.96046,71.985,#2,-0.27606,-0.45645,-0.84584,-85.423,0.80577,0.36983,-0.46256,20.877,0.52395,-0.80924,0.2657,66.504,#3,0.056355,0.21974,-0.97393,-92.323,-0.9984,0.0087675,-0.055794,31.505,-0.003721,0.97552,0.21988,76.67,#4,0.070303,-0.84456,0.53083,-72.516,-0.73212,-0.40513,-0.5476,37.822,0.67754,-0.35013,-0.6468,40.226,#5,0.7863,0.60881,-0.10526,-91.673,-0.23857,0.14203,-0.96068,31.109,-0.56992,0.7805,0.25692,77.309,#6,0.64823,-0.6533,0.39115,-68.984,-0.23232,0.31951,0.91866,46.974,-0.72514,-0.68637,0.055338,129.92,#8,-0.4982,-0.86637,-0.034652,-77.618,0.81484,-0.48148,0.32282,27.397,-0.29637,0.1326,0.94582,74.298,#9,-0.31355,-0.94273,0.11378,-104.14,0.89523,-0.25353,0.36645,43.533,-0.31661,0.21676,0.92346,67.902,#13,-0.72851,0.68364,0.04378,-99.587,0.015466,0.080306,-0.99665,12.065,-0.68486,-0.72539,-0.069077,80.988
> select add #9
15935 atoms, 15821 bonds, 2 pseudobonds, 2393 residues, 11 models selected
> select subtract #9
9008 atoms, 8721 bonds, 2 pseudobonds, 1522 residues, 10 models selected
> close #2-5,8
> show #1 models
> show #!13 models
> show #9 models
> hide #9 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #!13 models
> show #!13 models
> select add #1
18901 atoms, 18849 bonds, 2 pseudobonds, 2756 residues, 5 models selected
> select subtract #1
8690 atoms, 8391 bonds, 2 pseudobonds, 1480 residues, 4 models selected
> select add #6
9837 atoms, 9551 bonds, 2 pseudobonds, 1555 residues, 4 models selected
> select subtract #6
8572 atoms, 8271 bonds, 2 pseudobonds, 1473 residues, 3 models selected
> view matrix models
> #13,-0.72851,0.68364,0.04378,-109.53,0.015466,0.080306,-0.99665,-36.075,-0.68486,-0.72539,-0.069077,84.072
> view matrix models
> #13,-0.72851,0.68364,0.04378,-78.601,0.015466,0.080306,-0.99665,-81.635,-0.68486,-0.72539,-0.069077,92.989
> view matrix models
> #13,-0.72851,0.68364,0.04378,-97.999,0.015466,0.080306,-0.99665,-59.485,-0.68486,-0.72539,-0.069077,94.264
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.19588,0.044907,-0.9796,-101.31,-0.34131,-0.93961,0.025176,-35.59,-0.91931,0.33928,0.19938,83.987
> view matrix models
> #13,0.031014,-0.44214,-0.89641,-92.08,0.6626,-0.66236,0.34963,-22.949,-0.74833,-0.6048,0.27242,97.625
> view matrix models
> #13,0.21709,-0.34397,-0.91354,-91.488,0.58102,-0.7065,0.40408,-22.455,-0.7844,-0.61851,0.046477,93.826
> view matrix models
> #13,0.42784,0.0085809,-0.90381,-93.084,0.7003,-0.63533,0.32547,-23.236,-0.57143,-0.77219,-0.27783,92.696
> view matrix models
> #13,0.30338,-0.43573,-0.84741,-88.49,0.69538,-0.50678,0.50954,-21.832,-0.65147,-0.74385,0.14925,98.277
> view matrix models
> #13,0.30127,-0.44486,-0.8434,-88.346,0.6968,-0.50109,0.51321,-21.824,-0.65093,-0.7423,0.15902,98.42
> view matrix models
> #13,0.27166,0.086102,-0.95853,-96.481,0.95061,-0.17936,0.25331,-26.876,-0.15011,-0.98001,-0.13057,101.84
> view matrix models
> #13,-0.8402,-0.51011,0.18397,-83.475,-0.020923,-0.3085,-0.95099,-54.755,0.54187,-0.80288,0.24853,113.17
> view matrix models
> #13,-0.88223,-0.35991,0.30353,-83.729,0.30253,-0.92734,-0.22025,-32.78,0.36075,-0.10248,0.92702,114.06
> view matrix models
> #13,-0.18545,0.96134,0.20354,-92.853,0.86449,0.25809,-0.43134,-43.555,-0.46719,0.095968,-0.87893,74.488
> select add #6
9837 atoms, 9551 bonds, 2 pseudobonds, 1555 residues, 4 models selected
> select subtract #6
8572 atoms, 8271 bonds, 2 pseudobonds, 1473 residues, 3 models selected
> select add #6
9837 atoms, 9551 bonds, 2 pseudobonds, 1555 residues, 4 models selected
> select add #1
20048 atoms, 20009 bonds, 2 pseudobonds, 2831 residues, 5 models selected
> matchmaker #1,6 & sel to #13 & sel
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 chicken trpv4 xray pdb3w9f.ent, chain A (#13) with
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1), sequence alignment
score = 1239.7
RMSD between 231 pruned atom pairs is 0.578 angstroms; (across all 255 pairs:
2.576)
Matchmaker chicken trpv4 xray pdb3w9f.ent, chain A (#13) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 15.2
RMSD between 6 pruned atom pairs is 1.222 angstroms; (across all 15 pairs:
14.037)
> view matrix models
> #1,0.021847,-0.33576,-0.94169,-44.704,0.095467,-0.93691,0.33627,-39.406,-0.99519,-0.097248,0.011585,79.453,#6,-0.38272,0.89795,0.21727,-43.129,-0.70679,-0.13313,-0.69479,-29.614,-0.59496,-0.41948,0.68561,68.743,#13,0.045352,0.30575,0.95103,-73.348,-0.62141,-0.73676,0.2665,-18.464,0.78217,-0.60307,0.15659,104.82
> view matrix models
> #1,0.68364,0.56767,-0.45869,-56.487,0.72944,-0.55181,0.40425,-44.607,-0.023626,-0.61095,-0.79132,86.391,#6,0.7815,0.62355,-0.020916,-54.227,-0.04483,0.022684,-0.99874,-30.665,-0.62229,0.78145,0.045682,90.074,#13,-0.18206,0.98256,-0.037735,-95.62,-0.97932,-0.18464,-0.08265,-41.267,-0.088176,0.021907,0.99586,67.423
> matchmaker #1,6 to #13
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 chicken trpv4 xray pdb3w9f.ent, chain A (#13) with
fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1), sequence alignment
score = 1239.7
RMSD between 231 pruned atom pairs is 0.578 angstroms; (across all 255 pairs:
2.576)
Matchmaker chicken trpv4 xray pdb3w9f.ent, chain A (#13) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 15.2
RMSD between 6 pruned atom pairs is 1.222 angstroms; (across all 15 pairs:
14.037)
> view matrix models
> #1,-0.23901,0.96514,-0.10666,-58.937,0.94963,0.25526,0.1818,-49.212,0.20269,-0.057835,-0.97753,83.074,#6,0.68323,-0.13717,0.7172,-70.255,0.72792,0.20553,-0.65413,-40.075,-0.05768,0.96899,0.24028,84.284,#13,0.69967,0.5534,-0.4519,-68.926,-0.71339,0.5758,-0.39941,-68.824,0.03917,0.60184,0.79766,45.419
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> select sequence PPPILKV
224 atoms, 230 bonds, 21 residues, 3 models selected
> matchmaker #6 & sel to #1/B & sel 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 fold_fl_chicktrpv4_sdpiiirat_model_0.cif, chain B (#1) with
6f55-assembly1.cif, chain B (#6), sequence alignment score = 35
RMSD between 4 pruned atom pairs is 0.960 angstroms; (across all 7 pairs:
3.546)
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #1 models
> hide #!13 models
> select add #13
8796 atoms, 8501 bonds, 2 pseudobonds, 1494 residues, 6 models selected
> select add #9
15670 atoms, 15546 bonds, 2 pseudobonds, 2358 residues, 6 models selected
> select subtract #9
8743 atoms, 8446 bonds, 2 pseudobonds, 1487 residues, 5 models selected
> select add #6
9890 atoms, 9606 bonds, 2 pseudobonds, 1562 residues, 5 models selected
> select add #1
20048 atoms, 20009 bonds, 2 pseudobonds, 2831 residues, 5 models selected
> show #1 models
> show #6 models
> show #!13 models
> hide #!13 models
> ui mousemode right translate
> select sequence PPPILKV
224 atoms, 230 bonds, 21 residues, 3 models selected
> color (#1,6 & sel) magenta
> select sequence TKGPAPNPPPILKV
313 atoms, 321 bonds, 28 residues, 2 models selected
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie1.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie1.mp4
> cd "I:/Chimera/AF Presentation/TRPV4 AF3"
Current working directory is: I:\Chimera\AF Presentation\TRPV4 AF3
> hide #6 models
> hide #1 models
> show #1 models
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie1.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie1.mp4
> hide #1 models
> show #6 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie1.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie1.mp4
> show #!13 models
> hide #6 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie1.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie1.mp4
> alphafold match #13/A
1 UniProt id does not have an AlphaFold database model: Q9DFS3 (chain A)
Fetching compressed AlphaFold A0A1D5PXA5 from
https://alphafold.ebi.ac.uk/files/AF-A0A1D5PXA5-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1D5PXA5 (chain
A)
AlphaFold prediction matching chicken trpv4 xray pdb3w9f.ent
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A1D5PXA5 | TRPV4_CHICK | 2.55 | 260 | 255 | 97
Opened 1 AlphaFold model
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie1.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie1.mp4
> select sequence PPPILKV
248 atoms, 253 bonds, 24 residues, 4 models selected
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat/fold_fl_chicktrpv4_sdpiiirat_model_0.cif"
Chain information for fold_fl_chicktrpv4_sdpiiirat_model_0.cif #3
---
Chain | Description
A | .
B | .
Computing secondary structure
> close #3
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat/fold_fl_chicktrpv4_sdpiiirat_model_0.cif"
Chain information for fold_fl_chicktrpv4_sdpiiirat_model_0.cif #3
---
Chain | Description
A | .
B | .
Computing secondary structure
> close #3
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred
> AF3/htrpv4nt_sdpiiish3/fold_htrpv4nt_sdpiiish3_model_0.cif"
Chain information for fold_htrpv4nt_sdpiiish3_model_0.cif #3
---
Chain | Description
A | .
B | .
Computing secondary structure
> alphafold pae #3 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred
> AF3/htrpv4nt_sdpiiish3\\\fold_htrpv4nt_sdpiiish3_full_data_0.json"
> alphafold pae #3 colorDomains true
> color bfactor #3 palette alphafold
1741 atoms, 229 residues, atom bfactor range 23.7 to 95.2
> hide #!2 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie1.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie1.mp4
> alphafold pae #3 colorDomains true
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie2.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie2.mp4
> hide #2.1 models
> select add #3
1989 atoms, 2037 bonds, 253 residues, 5 models selected
> select add #6
3136 atoms, 3197 bonds, 328 residues, 5 models selected
> select add #9
10010 atoms, 10242 bonds, 1192 residues, 5 models selected
> select subtract #9
3083 atoms, 3142 bonds, 321 residues, 4 models selected
> select subtract #6
1818 atoms, 1862 bonds, 239 residues, 3 models selected
> select add #2.1
3871 atoms, 3956 bonds, 496 residues, 3 models selected
> select subtract #2.1
1794 atoms, 1839 bonds, 236 residues, 2 models selected
> select add #1
11952 atoms, 12242 bonds, 1505 residues, 2 models selected
> select subtract #1
1741 atoms, 1784 bonds, 229 residues, 1 model selected
> contacs #3 /A to /B distance 8
Unknown command: alphafold contacs #3 /A to /B distance 8
> alphafold contacts #3 /A toAtoms /B distance 8
Interface PAE pseudobonds can only be computed for a single structure, got 4.
> color bfactor #3 palette alphafold
1741 atoms, 229 residues, atom bfactor range 23.7 to 95.2
> alphafold contacts /A toAtoms /B distance 8
Interface PAE pseudobonds can only be computed for a single structure, got 6.
> alphafold pae #3 colorDomains true
> alphafold contacts #3/A toAtoms #3/B distance 8
Found 151 residue or atom pairs within distance 8
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie3.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie3.mp4
> hide #!3 models
> show #1 models
> alphafold contacts #1/A toAtoms #1/B distance 8
Found 344 residue or atom pairs within distance 8
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie4.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie4.mp4
> color #3/B:11 lime
> color #3/A:23 magenta
> alphafold pae #1 file "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4
> First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat\\\fold_fl_chicktrpv4_sdpiiirat_full_data_0.json"
> color #1/B:504 lime
> color #1/B:5 magenta
> alphafold contacts #1 distance 8
Found 24794 residue or atom pairs within distance 8
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie5.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie5.mp4
> show #!3 models
> hide #!1 models
> color bfactor #3 palette alphafold
1741 atoms, 229 residues, atom bfactor range 23.7 to 95.2
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie6.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie6.mp4
> alphafold pae #3 colorDomains true
> alphafold contacts #3 distance 8
Found 3656 residue or atom pairs within distance 8
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie7.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie7.mp4
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/NT
> TRPV4/tryp_chick/fold_tryp_chick_model_0.cif"
Chain information for fold_tryp_chick_model_0.cif #4
---
Chain | Description
A | .
Computing secondary structure
> hide #!3 models
> alphafold pae #1 file "C:/Users/RyanRechnen/Desktop/AF Presentation/TRPV4
> First test AF3/FL TRPV4
> SdpIIIsh3/fl_chicktrpv4_sdpiiirat\\\fold_fl_chicktrpv4_sdpiiirat_full_data_0.json"
> color bfactor #1 palette alphafold
10211 atoms, 1276 residues, atom bfactor range 16.7 to 95.6
> alphafold pae #4 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/NT
> TRPV4/tryp_chick\\\fold_tryp_chick_full_data_0.json"
> color bfactor #4 palette alphafold
1034 atoms, 134 residues, atom bfactor range 37.1 to 88.4
> select sequence PPPILKV
355 atoms, 364 bonds, 64 pseudobonds, 38 residues, 8 models selected
> select sequence TKGPAPNPPPILKV
438 atoms, 449 bonds, 78 pseudobonds, 45 residues, 5 models selected
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/NT
> TRPV4/tryp_chick/fold_tryp_chick_model_1.cif" "I:/Chimera/AF
> Presentation/TRPV4 AF3/Pred AF3/NT
> TRPV4/tryp_chick/fold_tryp_chick_model_2.cif" "I:/Chimera/AF
> Presentation/TRPV4 AF3/Pred AF3/NT
> TRPV4/tryp_chick/fold_tryp_chick_model_3.cif" "I:/Chimera/AF
> Presentation/TRPV4 AF3/Pred AF3/NT
> TRPV4/tryp_chick/fold_tryp_chick_model_4.cif"
Chain information for fold_tryp_chick_model_1.cif #5
---
Chain | Description
A | .
Chain information for fold_tryp_chick_model_2.cif #7
---
Chain | Description
A | .
Chain information for fold_tryp_chick_model_3.cif #8
---
Chain | Description
A | .
Chain information for fold_tryp_chick_model_4.cif #10
---
Chain | Description
A | .
Computing secondary structure
> ui tool show "Model Panel"
> ui tool show Rotamers
> select add #6
1490 atoms, 1512 bonds, 78 pseudobonds, 113 residues, 5 models selected
> select add #4
2423 atoms, 2473 bonds, 78 pseudobonds, 233 residues, 5 models selected
> select subtract #4
1389 atoms, 1407 bonds, 78 pseudobonds, 99 residues, 4 models selected
> select subtract #6
124 atoms, 127 bonds, 78 pseudobonds, 17 residues, 3 models selected
> select add #2.1
2177 atoms, 2221 bonds, 78 pseudobonds, 274 residues, 3 models selected
> select subtract #2.1
100 atoms, 104 bonds, 78 pseudobonds, 14 residues, 2 models selected
> select add #1
10211 atoms, 10458 bonds, 24794 pseudobonds, 1276 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!1 models
> hide #4 models
> hide #5 models
> hide #7 models
> hide #8 models
> hide #10 models
> hide #!1 models
> show #!3 models
> select add #3
1741 atoms, 1784 bonds, 3656 pseudobonds, 229 residues, 2 models selected
> select #3/B:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select sequence TKGPAPNPPPILKV
842 atoms, 869 bonds, 78 pseudobonds, 101 residues, 9 models selected
> select sequence PPPILKV
571 atoms, 588 bonds, 64 pseudobonds, 66 residues, 12 models selected
> select add #1
10729 atoms, 10991 bonds, 24828 pseudobonds, 1335 residues, 12 models selected
> select add #2
12782 atoms, 13085 bonds, 24828 pseudobonds, 1592 residues, 13 models selected
> select subtract #1
2571 atoms, 2627 bonds, 34 pseudobonds, 316 residues, 11 models selected
> select subtract #2
494 atoms, 510 bonds, 34 pseudobonds, 56 residues, 9 models selected
> select add #4
1474 atoms, 1520 bonds, 34 pseudobonds, 183 residues, 9 models selected
> select subtract #4
440 atoms, 454 bonds, 34 pseudobonds, 49 residues, 8 models selected
> select add #5
1420 atoms, 1464 bonds, 34 pseudobonds, 176 residues, 8 models selected
> select subtract #5
386 atoms, 398 bonds, 34 pseudobonds, 42 residues, 7 models selected
> select add #6
1533 atoms, 1558 bonds, 34 pseudobonds, 117 residues, 7 models selected
> select subtract #6
268 atoms, 278 bonds, 34 pseudobonds, 35 residues, 6 models selected
> select add #7
1248 atoms, 1288 bonds, 34 pseudobonds, 162 residues, 6 models selected
> select subtract #7
214 atoms, 222 bonds, 34 pseudobonds, 28 residues, 5 models selected
> select add #8
1194 atoms, 1232 bonds, 34 pseudobonds, 155 residues, 5 models selected
> select subtract #8
160 atoms, 166 bonds, 34 pseudobonds, 21 residues, 4 models selected
> select add #9
7034 atoms, 7211 bonds, 34 pseudobonds, 885 residues, 4 models selected
> select subtract #9
107 atoms, 111 bonds, 34 pseudobonds, 14 residues, 3 models selected
> select add #10
1087 atoms, 1121 bonds, 34 pseudobonds, 141 residues, 3 models selected
> select subtract #10
53 atoms, 55 bonds, 34 pseudobonds, 7 residues, 2 models selected
> swapaa interactive sel PRO rotLib Dunbrack
fold_htrpv4nt_sdpiiish3_model_0.cif #3/B PRO 142: phi -77.0, psi 139.2 trans
Changed 10 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #!3/B:142 PRO criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
fold_htrpv4nt_sdpiiish3_model_0.cif #!3/B PRO 142: phi -77.0, psi 139.2 trans
Applying PRO rotamer (chi angles: 29.7 -34.4) to
fold_htrpv4nt_sdpiiish3_model_0.cif #!3/B PRO 142
> hide #!3 models
> select add #3
1741 atoms, 1784 bonds, 3656 pseudobonds, 229 residues, 2 models selected
> select subtract #3
Nothing selected
> show #4 models
> hide #4 models
> show #4 models
> select add #4
1034 atoms, 1066 bonds, 134 residues, 1 model selected
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie1.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie1.mp4
> close #5,7-8,10
> hide #4 models
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD +
> SH3 SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_0.cif" "I:/Chimera/AF
> Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_1.cif" "I:/Chimera/AF
> Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_2.cif" "I:/Chimera/AF
> Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_3.cif" "I:/Chimera/AF
> Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_4.cif"
Chain information for fold_tryp_chick_sh3_model_0.cif #5
---
Chain | Description
A | .
B | .
Chain information for fold_tryp_chick_sh3_model_1.cif #7
---
Chain | Description
A | .
B | .
Chain information for fold_tryp_chick_sh3_model_2.cif #8
---
Chain | Description
A | .
B | .
Chain information for fold_tryp_chick_sh3_model_3.cif #10
---
Chain | Description
A | .
B | .
Chain information for fold_tryp_chick_sh3_model_4.cif #11
---
Chain | Description
A | .
B | .
Computing secondary structure
> select add #5
1497 atoms, 1536 bonds, 193 residues, 1 model selected
> select add #7
2994 atoms, 3072 bonds, 386 residues, 2 models selected
> select add #8
4491 atoms, 4608 bonds, 579 residues, 3 models selected
> select add #10
5988 atoms, 6144 bonds, 772 residues, 4 models selected
> select add #11
7485 atoms, 7680 bonds, 965 residues, 5 models selected
> view orient
Color zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 0 maps.
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 5 atomic models, 0 maps.
> ui mousemode right "play coordinates"
> ui tool show "Render/Select by Attribute"
> color byattribute r:c_alpha_distance #4-11#2.1#!1,3,13 target absc palette
> 0.0691726,blue:6.27279,white:13.8214,red
39312 atoms, 5290 residues, atom c_alpha_distance range 0.0692 to 13.8
> alphafold pae #5 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_0.json"
> color bfactor #5 palette alphafold
1497 atoms, 193 residues, atom bfactor range 27.5 to 95.5
> alphafold pae #7 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_1.json"
> color bfactor #7 palette alphafold
1497 atoms, 193 residues, atom bfactor range 23.2 to 93.6
> alphafold pae #7 colorDomains true
> color #4/A:102 lime
> color #4/A:86 magenta
> alphafold pae #4 colorDomains true
> alphafold pae #8 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_2.json"
> alphafold pae #8 colorDomains true
> alphafold pae #7 colorDomains true
> alphafold pae #5 colorDomains true
> alphafold pae #10 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_3.json"
> alphafold pae #10 colorDomains true
> alphafold pae #11 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_4.json"
> alphafold pae #11 colorDomains true
> select sequence PPPILKV
625 atoms, 644 bonds, 64 pseudobonds, 73 residues, 13 models selected
> select sequence TKGPAPNPPPILKV
943 atoms, 974 bonds, 78 pseudobonds, 115 residues, 10 models selected
> matchmaker #7-8,10-11 & sel to #5/B & sel 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 fold_tryp_chick_sh3_model_0.cif, chain B (#5) with
fold_tryp_chick_sh3_model_1.cif, chain B (#7), sequence alignment score = 56.4
RMSD between 7 pruned atom pairs is 0.947 angstroms; (across all 14 pairs:
7.806)
Matchmaker fold_tryp_chick_sh3_model_0.cif, chain B (#5) with
fold_tryp_chick_sh3_model_2.cif, chain B (#8), sequence alignment score = 71.4
RMSD between 5 pruned atom pairs is 1.066 angstroms; (across all 14 pairs:
5.813)
Matchmaker fold_tryp_chick_sh3_model_0.cif, chain B (#5) with
fold_tryp_chick_sh3_model_3.cif, chain B (#10), sequence alignment score =
71.4
RMSD between 5 pruned atom pairs is 0.655 angstroms; (across all 14 pairs:
6.058)
Matchmaker fold_tryp_chick_sh3_model_0.cif, chain B (#5) with
fold_tryp_chick_sh3_model_4.cif, chain B (#11), sequence alignment score =
71.4
RMSD between 8 pruned atom pairs is 1.247 angstroms; (across all 14 pairs:
7.492)
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202508300055 (2025-08-30)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "I:\Chimera\AF Presentation\TRPV4 AF3\TRPV4 pdb data\6F55-assembly1
> SdpIIISH3 TRPV4PRD.cif\6f55-assembly1.cif" format mmcif
6f55-assembly1.cif title:
Complex structure of PACSIN SH3 domain and TRPV4 proline rich region [more
info...]
Chain information for 6f55-assembly1.cif #1
---
Chain | Description
A | PACSIN 3
B | PRR
OpenGL version: 3.3.0 Core Profile Context 25.8.1.250723
OpenGL renderer: AMD Radeon RX 7800 XT
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.9
Locale: de_DE.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 137,291,546,624
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i5-10400F CPU @ 2.90GHz
OSLanguage: de-DE
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.7.2
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.16
ChimeraX-AtomicLibrary: 14.1.23
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202508300055
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.3.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.48.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.10.6
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.3
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.19.1
fonttools: 4.59.2
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2025.4.15
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.5
matplotlib-inline: 0.1.7
msgpack: 1.1.1
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.4.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 311
pyzmq: 27.0.2
qtconsole: 5.6.1
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (2)
comment:1 by , 7 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 7 weeks ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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