Crash fetching from Toolshed

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202501230202 (2025-01-23 02:02:02 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x00000c34 (most recent call first):
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 324 in wait
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 622 in wait
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 1392 in run
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000df0 (most recent call first):
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\ssl.py", line 1134 in read
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\ssl.py", line 1278 in recv_into
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\socket.py", line 706 in readinto
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\http\client.py", line 279 in _read_status
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\http\client.py", line 318 in begin
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\http\client.py", line 1378 in getresponse
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 1352 in do_open
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 1391 in https_open
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 496 in _call_chain
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 536 in _open
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 519 in open
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 216 in urlopen
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 516 in reload_available
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 975 in run
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x000031fc (most recent call first):
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
  File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202501230202 (2025-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\26.cxs

Log from Mon Feb 3 13:59:35 2025UCSF ChimeraX version: 1.10.dev202501230202
(2025-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\TOP26_COMBINED.cxs

Log from Mon Feb 26 10:01:55 2024UCSF ChimeraX version: 1.6rc202304072249
(2023-04-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf1_90_5db12_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
conf1_90_5db12_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf2_376_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf2_376_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf2_410_67d33_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf2_410_67d33_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf3_363_mpnn3.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf3_363_mpnn3.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_134_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_134_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_154_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf4_154_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_19_mpnn13.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_19_mpnn13.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_240_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_240_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_650_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_650_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_650_mpnn4.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
conf4_650_mpnn4.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#11  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_750_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_750_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#12  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_161_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_161_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#13  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_288_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_288_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#14  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_32_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_32_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#15  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_32_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_32_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#16  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_338_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_338_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#17  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_50_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_50_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#18  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_50_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_50_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#19  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_527_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_527_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#20  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_527_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_527_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#21  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_624_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_624_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#22  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_665_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_665_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#23  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_84_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_84_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#24  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_878_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_878_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#25  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_98_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
set2conf1_98_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#26  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color bfactor palette alphafold

66156 atoms, 8502 residues, atom bfactor range 53.2 to 98.6  

> ui tool show Matchmaker

> matchmaker #2-26 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
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf1_90_5db12_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#2), sequence alignment score = 1282.5  
RMSD between 254 pruned atom pairs is 0.312 angstroms; (across all 254 pairs:
0.312)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf2_376_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#3), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.230 angstroms; (across all 254 pairs:
0.230)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf2_410_67d33_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#4), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.311 angstroms; (across all 254 pairs:
0.311)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf3_363_mpnn3.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#5), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.278 angstroms; (across all 254 pairs:
0.278)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_134_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#6), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.294 angstroms; (across all 254 pairs:
0.294)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_154_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#7), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.326 angstroms; (across all 254 pairs:
0.351)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_19_mpnn13.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#8), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.416 angstroms; (across all 254 pairs:
0.445)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_240_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#9), sequence alignment score = 1291.5  
RMSD between 253 pruned atom pairs is 0.288 angstroms; (across all 254 pairs:
0.316)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_650_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#10), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.388 angstroms; (across all 254 pairs:
0.431)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_650_mpnn4.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#11), sequence alignment score = 1282.5  
RMSD between 254 pruned atom pairs is 0.301 angstroms; (across all 254 pairs:
0.301)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_750_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#12), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.398 angstroms; (across all 254 pairs:
0.422)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_161_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#13), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.330 angstroms; (across all 254 pairs:
0.330)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_288_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#14), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.315 angstroms; (across all 254 pairs:
0.315)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_32_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#15), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.310 angstroms; (across all 254 pairs:
0.310)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_32_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#16), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.250 angstroms; (across all 254 pairs:
0.250)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_338_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#17), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.318 angstroms; (across all 254 pairs:
0.318)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_50_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#18), sequence alignment score = 1285.5  
RMSD between 254 pruned atom pairs is 0.355 angstroms; (across all 254 pairs:
0.355)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_50_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#19), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.263 angstroms; (across all 254 pairs:
0.263)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_527_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#20), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.368 angstroms; (across all 254 pairs:
0.422)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_527_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#21), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.201 angstroms; (across all 254 pairs:
0.201)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_624_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#22), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.313 angstroms; (across all 254 pairs:
0.313)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_665_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#23), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.200 angstroms; (across all 254 pairs:
0.200)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_84_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#24), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.304 angstroms; (across all 254 pairs:
0.335)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_878_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#25), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.300 angstroms; (across all 254 pairs:
0.300)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_98_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#26), sequence alignment score = 1279.5  
RMSD between 253 pruned atom pairs is 0.288 angstroms; (across all 254 pairs:
0.317)  
  

> show atoms

> color byhetero

> color byelement

> hide target m

> show #1 models

> save /Users/tigerous/Work/Jie-TRP/Design-TRPV1/Design-hTRPV1-AKRD/COMBINED-
> SELECT/TOP26_COMBINED.cxs

> show #2 models

> hide #1 models

> show #3 models

> hide #2 models

> show #4 models

> hide #3 models

> show #1 models

> hide #4 models

> save /Users/tigerous/Work/Jie-TRP/Design-TRPV1/Design-hTRPV1-AKRD/COMBINED-
> SELECT/TOP26_COMBINED.cxs

> hide #1 models

> show #26 models

> save /Users/tigerous/Work/Jie-TRP/Design-TRPV1/Design-hTRPV1-AKRD/COMBINED-
> SELECT/TOP26_COMBINED.cxs

——— End of log from Mon Feb 26 10:01:55 2024 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Selection Inspector"

[Repeated 1 time(s)]

> show #25 models

> hide #25 models

> show #25 models

> hide #25 models

> save C:/Users/zhyau/OneDrive/Desktop/26.cxs

——— End of log from Mon Feb 3 13:59:35 2025 ———

> view name session-start

opened ChimeraX session  

> show #25 models

> show #24 models

> show #23 models

> show #22 models

> show #21 models

> hide #21 models

> hide #22 models

> hide #23 models

> hide #24 models

> hide #25 models

> hide #26 models

> show #26 models

> log metadata #1

The model has no metadata

> log chains #1

Chain information for
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> ui tool show "Model Panel"

> help help:user/tools/modelpanel.html


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10.dev202501230202 (2025-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\26.cxs

Log from Mon Feb 3 13:59:35 2025UCSF ChimeraX version: 1.10.dev202501230202
(2025-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\TOP26_COMBINED.cxs

Log from Mon Feb 26 10:01:55 2024UCSF ChimeraX version: 1.6rc202304072249
(2023-04-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf1_90_5db12_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
conf1_90_5db12_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf2_376_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf2_376_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf2_410_67d33_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf2_410_67d33_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf3_363_mpnn3.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf3_363_mpnn3.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_134_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_134_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_154_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
conf4_154_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_19_mpnn13.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_19_mpnn13.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_240_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_240_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_650_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_650_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_650_mpnn4.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
conf4_650_mpnn4.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#11  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> conf4_750_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
conf4_750_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#12  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_161_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_161_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#13  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_288_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_288_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#14  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_32_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_32_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#15  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_32_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_32_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#16  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_338_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_338_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#17  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_50_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_50_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#18  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_50_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_50_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#19  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_527_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_527_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#20  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_527_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_527_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#21  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_624_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_624_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#22  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_665_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_665_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#23  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_84_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
set2conf1_84_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#24  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_878_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
set2conf1_878_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#25  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> set2conf1_98_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
set2conf1_98_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#26  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color bfactor palette alphafold

66156 atoms, 8502 residues, atom bfactor range 53.2 to 98.6  

> ui tool show Matchmaker

> matchmaker #2-26 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
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf1_90_5db12_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#2), sequence alignment score = 1282.5  
RMSD between 254 pruned atom pairs is 0.312 angstroms; (across all 254 pairs:
0.312)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf2_376_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#3), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.230 angstroms; (across all 254 pairs:
0.230)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf2_410_67d33_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#4), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.311 angstroms; (across all 254 pairs:
0.311)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf3_363_mpnn3.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#5), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.278 angstroms; (across all 254 pairs:
0.278)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_134_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#6), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.294 angstroms; (across all 254 pairs:
0.294)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_154_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#7), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.326 angstroms; (across all 254 pairs:
0.351)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_19_mpnn13.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#8), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.416 angstroms; (across all 254 pairs:
0.445)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_240_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#9), sequence alignment score = 1291.5  
RMSD between 253 pruned atom pairs is 0.288 angstroms; (across all 254 pairs:
0.316)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_650_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#10), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.388 angstroms; (across all 254 pairs:
0.431)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_650_mpnn4.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#11), sequence alignment score = 1282.5  
RMSD between 254 pruned atom pairs is 0.301 angstroms; (across all 254 pairs:
0.301)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
conf4_750_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#12), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.398 angstroms; (across all 254 pairs:
0.422)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_161_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#13), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.330 angstroms; (across all 254 pairs:
0.330)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_288_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#14), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.315 angstroms; (across all 254 pairs:
0.315)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_32_mpnn6.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#15), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.310 angstroms; (across all 254 pairs:
0.310)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_32_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#16), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.250 angstroms; (across all 254 pairs:
0.250)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_338_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#17), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.318 angstroms; (across all 254 pairs:
0.318)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_50_mpnn12.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#18), sequence alignment score = 1285.5  
RMSD between 254 pruned atom pairs is 0.355 angstroms; (across all 254 pairs:
0.355)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_50_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#19), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.263 angstroms; (across all 254 pairs:
0.263)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_527_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#20), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.368 angstroms; (across all 254 pairs:
0.422)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_527_mpnn8.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#21), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.201 angstroms; (across all 254 pairs:
0.201)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_624_mpnn5.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#22), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.313 angstroms; (across all 254 pairs:
0.313)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_665_mpnn16.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#23), sequence alignment score = 1288.5  
RMSD between 254 pruned atom pairs is 0.200 angstroms; (across all 254 pairs:
0.200)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_84_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#24), sequence alignment score = 1288.5  
RMSD between 253 pruned atom pairs is 0.304 angstroms; (across all 254 pairs:
0.335)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_878_mpnn2.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#25), sequence alignment score = 1291.5  
RMSD between 254 pruned atom pairs is 0.300 angstroms; (across all 254 pairs:
0.300)  
  
Matchmaker
conf1_163_05f68_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#1) with
set2conf1_98_mpnn10.complex_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#26), sequence alignment score = 1279.5  
RMSD between 253 pruned atom pairs is 0.288 angstroms; (across all 254 pairs:
0.317)  
  

> show atoms

> color byhetero

> color byelement

> hide target m

> show #1 models

> save /Users/tigerous/Work/Jie-TRP/Design-TRPV1/Design-hTRPV1-AKRD/COMBINED-
> SELECT/TOP26_COMBINED.cxs

> show #2 models

> hide #1 models

> show #3 models

> hide #2 models

> show #4 models

> hide #3 models

> show #1 models

> hide #4 models

> save /Users/tigerous/Work/Jie-TRP/Design-TRPV1/Design-hTRPV1-AKRD/COMBINED-
> SELECT/TOP26_COMBINED.cxs

> hide #1 models

> show #26 models

> save /Users/tigerous/Work/Jie-TRP/Design-TRPV1/Design-hTRPV1-AKRD/COMBINED-
> SELECT/TOP26_COMBINED.cxs

——— End of log from Mon Feb 26 10:01:55 2024 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Selection Inspector"

[Repeated 1 time(s)]

> show #25 models

> hide #25 models

> show #25 models

> hide #25 models

> save C:/Users/zhyau/OneDrive/Desktop/26.cxs

——— End of log from Mon Feb 3 13:59:35 2025 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 566.07
OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming F15 FX507VI_FX507VI
OS: Microsoft Windows 11 家庭版 (Build 26100)
Memory: 16,780,505,088
MaxProcessMemory: 137,438,953,344
CPU: 16 13th Gen Intel(R) Core(TM) i7-13620H
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.12.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.17
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202501230202
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    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: 1.1.2
    ChimeraX-ProfileGrids: 1.0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.15
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 2.5.1
    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: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.10
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.12
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.15.4
    fonttools: 4.55.4
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.5
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 2.2.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 5.24.1
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.2
    tcia_utils: 1.5.1
    tenacity: 9.0.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1