Save command history: No space left on device

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/TRMT-
> RNA-Met/model&map/New-model/TRMT1-tRNA-MET-1-coot-2.pdb format pdb

Chain information for TRMT1-tRNA-MET-1-coot-2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
T | No description available  
  

> set bgColor white

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting soft

> open
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/T1-D233A-Met-
> SAM/T1-D233A-Met-SAM-coot-6.pdb

Chain information for T1-D233A-Met-SAM-coot-6.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
T | No description available  
  

> open /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/TRMT-
> RNA-Met/2tRNA/TRMT1-2tRNA-predict.pdb

Chain information for TRMT1-2tRNA-predict.pdb #3  
---  
Chain | Description  
A B | No description available  
D E | No description available  
  

> color bychain

> select H

15478 atoms, 1961 residues, 2 models selected  

> delete atoms sel

> delete bonds sel

> hide #!2 models

> hide #3 models

> select (#1/A & ::polymer_type>0 ) & ((#1/T & ::polymer_type>0 ) :<4)

355 atoms, 341 bonds, 43 residues, 1 model selected  

> show sel atoms

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/B

Alignment identifier is 1/B  

> color sel purple

> select
> #1/A:76-100,165-173,187-200,213-220,223-225,239-247,262-265,270-277,287-306,332-341,405-417,419-421,425-437,448-455,462-472,492-505,518-524,542-545

1446 atoms, 1449 bonds, 183 residues, 1 model selected  

> select (#1/A#1/B & ::polymer_type>0 ) & ((#1/T & ::polymer_type>0 ) :<4)

378 atoms, 362 bonds, 46 residues, 1 model selected  

> select (#1/B & ::polymer_type>0 ) & ((#1/T & ::polymer_type>0 ) :<4)

23 atoms, 21 bonds, 3 residues, 1 model selected  

> color sel medium blue

> show sel atoms

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select (#1/A & ::polymer_type>0 ) & ((#1/T & ::polymer_type>0 ) :<4)

355 atoms, 341 bonds, 43 residues, 1 model selected  

> color sel red

> select sel :< 4

184 atoms, 188 bonds, 16 residues, 3 models selected  

> select #1/T:26

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select sel :< 5

416 atoms, 428 bonds, 37 residues, 3 models selected  

> select add #3

13604 atoms, 14201 bonds, 1489 residues, 3 models selected  

> select subtract #3

222 atoms, 229 bonds, 19 residues, 2 models selected  

> select add #2

8706 atoms, 9032 bonds, 10 pseudobonds, 999 residues, 4 models selected  

> select subtract #2

179 atoms, 182 bonds, 17 residues, 1 model selected  

> select add #1

8530 atoms, 8852 bonds, 10 pseudobonds, 984 residues, 4 models selected  

> select subtract #1

Nothing selected  

> show #!2 models

> hide #!2 models

> select #1/T:26

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select sel :< 5

416 atoms, 428 bonds, 37 residues, 3 models selected  

> select #1/T:26

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select sel :< 4

330 atoms, 341 bonds, 27 residues, 3 models selected  

> select add #3

13565 atoms, 14161 bonds, 1484 residues, 3 models selected  

> select subtract #3

183 atoms, 189 bonds, 14 residues, 2 models selected  

> select add #2

8667 atoms, 8992 bonds, 10 pseudobonds, 994 residues, 4 models selected  

> select subtract #2

140 atoms, 142 bonds, 12 residues, 1 model selected  

> select add #1

8530 atoms, 8852 bonds, 10 pseudobonds, 984 residues, 4 models selected  

> select subtract #1

Nothing selected  

> select up

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

1579 atoms, 1764 bonds, 74 residues, 1 model selected  

> select sel :< 4

4745 atoms, 5086 bonds, 333 residues, 3 models selected  

> select add #3

15828 atoms, 16594 bonds, 1643 residues, 3 models selected  

> select subtract #3

2446 atoms, 2622 bonds, 173 residues, 2 models selected  

> select add #2

10484 atoms, 10976 bonds, 10 pseudobonds, 1102 residues, 4 models selected  

> select subtract #2

1957 atoms, 2126 bonds, 120 residues, 1 model selected  

> select add #1

8530 atoms, 8852 bonds, 10 pseudobonds, 984 residues, 4 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #3 models

> select #3/A:659

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

271 atoms, 281 bonds, 40 residues, 1 model selected  

> select #3/A:594

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:584

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:573

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:545

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 1 model selected  

> select subtract #3

Nothing selected  

> hide #3 models

> show #!2 models

> select clear

> select #2/T:74

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

1579 atoms, 1764 bonds, 74 residues, 1 model selected  

> select (#2/B#2/A & ::polymer_type>0 ) & ((#2/T & ::polymer_type>0 ) :<4)

395 atoms, 381 bonds, 47 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #2/B

Alignment identifier is 2/B  

> select (#2/B#2/A & ::polymer_type>0 ) & ((#2/T & ::polymer_type>0 ) :<4)

395 atoms, 381 bonds, 47 residues, 1 model selected  

> select (#2/B#2/A & ::polymer_type>0 ) & ((#2/T & ::polymer_type>0 ) :<4)

395 atoms, 381 bonds, 47 residues, 1 model selected  

> select add #2

8527 atoms, 8850 bonds, 10 pseudobonds, 982 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select (#2/B#2/A & ::polymer_type>0 ) & ((#2/T & ::polymer_type>0 ) :<4)

395 atoms, 381 bonds, 47 residues, 1 model selected  

> select add #2

8527 atoms, 8850 bonds, 10 pseudobonds, 982 residues, 3 models selected  

> select subtract #2

Nothing selected  

> show #3 models

> hide #3 models

> hide #!2 models

> show #3 models

> hide #3 models

> open /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/TRMT-
> RNA-Met/2tRNA/P11_J229_006_sharp.mrc

Opened P11_J229_006_sharp.mrc as #4, grid size 320,320,320, pixel 0.838, shown
at level 0.0632, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.09876

> surface dust #4 size 8.38

> show #3 models

> volume #4 level 0.07212

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A #3/B

Alignment identifier is 1  

> select #3/A-B:570

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:570

18 atoms, 16 bonds, 2 residues, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> color sel orange red

> select #3/A-B:483

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:483

18 atoms, 16 bonds, 2 residues, 1 model selected  

> hide #!4 models

> show #!4 models

> volume #4 level 0.0588

> volume #4 level 0.08544

> select #3/A-B:588

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:588

18 atoms, 16 bonds, 2 residues, 1 model selected  

> hide #!4 models

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select #3/A-B:659

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:546-659

1742 atoms, 1786 bonds, 228 residues, 1 model selected  

> hide #!3 models

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 2 models selected  

> select subtract #3

Nothing selected  

> open
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/T1-apo-
> map-model/final/TRMT-Dimer-1-coot-0.pdb

Chain information for TRMT-Dimer-1-coot-0.pdb #5  
---  
Chain | Description  
A B | No description available  
  

> select add #5

6456 atoms, 6580 bonds, 10 pseudobonds, 848 residues, 3 models selected  

> color sel bychain

> select subtract #5

Nothing selected  

> ui tool show Matchmaker

> matchmaker #!1-3 to #5

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 TRMT-Dimer-1-coot-0.pdb, chain B (#5) with TRMT1-tRNA-
MET-1-coot-2.pdb, chain B (#1), sequence alignment score = 2074.7  
RMSD between 421 pruned atom pairs is 0.612 angstroms; (across all 423 pairs:
0.631)  
  
Matchmaker TRMT-Dimer-1-coot-0.pdb, chain B (#5) with T1-D233A-Met-SAM-
coot-6.pdb, chain B (#2), sequence alignment score = 2066.1  
RMSD between 410 pruned atom pairs is 0.739 angstroms; (across all 420 pairs:
0.824)  
  
Matchmaker TRMT-Dimer-1-coot-0.pdb, chain B (#5) with TRMT1-2tRNA-predict.pdb,
chain A (#3), sequence alignment score = 2049.9  
RMSD between 417 pruned atom pairs is 0.786 angstroms; (across all 423 pairs:
0.880)  
  

> matchmaker #!1-3 to #5

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 TRMT-Dimer-1-coot-0.pdb, chain B (#5) with TRMT1-tRNA-
MET-1-coot-2.pdb, chain B (#1), sequence alignment score = 2074.7  
RMSD between 421 pruned atom pairs is 0.612 angstroms; (across all 423 pairs:
0.631)  
  
Matchmaker TRMT-Dimer-1-coot-0.pdb, chain B (#5) with T1-D233A-Met-SAM-
coot-6.pdb, chain B (#2), sequence alignment score = 2066.1  
RMSD between 410 pruned atom pairs is 0.739 angstroms; (across all 420 pairs:
0.824)  
  
Matchmaker TRMT-Dimer-1-coot-0.pdb, chain B (#5) with TRMT1-2tRNA-predict.pdb,
chain A (#3), sequence alignment score = 2049.9  
RMSD between 417 pruned atom pairs is 0.786 angstroms; (across all 423 pairs:
0.880)  
  

> show #!1 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> hide #!5 models

> show #!3 models

> select #3/A-B:506

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #3/A-B:506-659

2386 atoms, 2442 bonds, 308 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for TRMT1-2tRNA-predict.pdb_A SES surface #3.2: minimum,
-16.12, mean -0.25, maximum 13.76  
Coulombic values for TRMT1-2tRNA-predict.pdb_B SES surface #3.3: minimum,
-17.83, mean -0.24, maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 4 models selected  

> select subtract #3

2 models selected  

> ui tool show "Side View"

> hide #3.3 models

> hide #3.2 models

> show #3.3 models

> transparency #3 50 target r

> transparency #3 80 target r

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A #3/B

Alignment identifier is 1  

> select #3/A-B:659

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:586-659

1096 atoms, 1126 bonds, 148 residues, 1 model selected  

> select #3/A-B:659

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:637-659

300 atoms, 310 bonds, 46 residues, 1 model selected  

> transparency #3 0 target r

> hide #3.3 models

> select #3/A-B:659

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:634-659

336 atoms, 346 bonds, 52 residues, 1 model selected  

> coulombic sel

Coulombic values for TRMT1-2tRNA-predict.pdb_A SES surface #3.2: minimum,
-16.12, mean -0.25, maximum 13.76  
Coulombic values for TRMT1-2tRNA-predict.pdb_B SES surface #3.3: minimum,
-17.83, mean -0.24, maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #3/A-B:631

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A-B:631-659

372 atoms, 382 bonds, 58 residues, 1 model selected  

> select #3/A-B:620

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #3/A-B:620-659

542 atoms, 562 bonds, 80 residues, 1 model selected  

> coulombic sel

Coulombic values for TRMT1-2tRNA-predict.pdb_A SES surface #3.2: minimum,
-16.12, mean -0.25, maximum 13.76  
Coulombic values for TRMT1-2tRNA-predict.pdb_B SES surface #3.3: minimum,
-17.83, mean -0.24, maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #3/A-B:659

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:625-659

462 atoms, 478 bonds, 70 residues, 1 model selected  

> select #3/A-B:625-659

462 atoms, 478 bonds, 70 residues, 1 model selected  

> coulombic sel

Coulombic values for TRMT1-2tRNA-predict.pdb_A SES surface #3.2: minimum,
-16.12, mean -0.25, maximum 13.76  
Coulombic values for TRMT1-2tRNA-predict.pdb_B SES surface #3.3: minimum,
-17.83, mean -0.24, maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #3/A-B:659

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:631-659

372 atoms, 382 bonds, 58 residues, 1 model selected  

> coulombic sel

Coulombic values for TRMT1-2tRNA-predict.pdb_A SES surface #3.2: minimum,
-16.12, mean -0.25, maximum 13.76  
Coulombic values for TRMT1-2tRNA-predict.pdb_B SES surface #3.3: minimum,
-17.83, mean -0.24, maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface "TRMT1-2tRNA-predict.pdb_A SES surface": minimum -28,
mean -5.432, maximum 23.34  
Map values for surface "TRMT1-2tRNA-predict.pdb_B SES surface": minimum
-28.33, mean -5.405, maximum 23.55  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Coulombic values for TRMT1-2tRNA-predict.pdb_A SES surface #3.2: minimum,
-16.12, mean -0.25, maximum 13.76  
Coulombic values for TRMT1-2tRNA-predict.pdb_B SES surface #3.3: minimum,
-17.83, mean -0.24, maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close #3.2

> close #3.3

> hide #3.1 models

> show #3.1 models

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select
> #3/A-B:68-73,76-100,165-173,187-199,213-219,239-248,262-265,270-277,287-306,332-341,405-417,425-437,448-455,462-471,492-505,510-512,518-523,537-539,542-545,573-583,594-602,607-610,617-619

3410 atoms, 3406 bonds, 426 residues, 1 model selected  

> select #3/A-B:573

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #3/A-B:573-583

194 atoms, 192 bonds, 22 residues, 1 model selected  

> coulombic sel

Coulombic values for TRMT1-2tRNA-predict.pdb_A SES surface #3.2: minimum,
-16.12, mean -0.25, maximum 13.76  
Coulombic values for TRMT1-2tRNA-predict.pdb_B SES surface #3.3: minimum,
-17.83, mean -0.24, maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 4 models selected  

> select subtract #3

2 models selected  

> select #3/A-B:541

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #3/A-B:541-659

1820 atoms, 1866 bonds, 238 residues, 1 model selected  

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 4 models selected  

> select subtract #3

2 models selected  

> close #3.2

> close #3.3

> select #3/A-B:506-507

26 atoms, 26 bonds, 4 residues, 1 model selected  

> select #3/A-B:506-659

2386 atoms, 2442 bonds, 308 residues, 1 model selected  

> coulombic sel

Coulombic values for TRMT1-2tRNA-predict.pdb_A SES surface #3.2: minimum,
-16.12, mean -0.25, maximum 13.76  
Coulombic values for TRMT1-2tRNA-predict.pdb_B SES surface #3.3: minimum,
-17.83, mean -0.24, maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #3.2 models

> show #3.2 models

> hide #3.3 models

> select subtract #3.3

1193 atoms, 1221 bonds, 154 residues, 3 models selected  

> select subtract #3.2

1 model selected  

> select add #3.2

5069 atoms, 659 residues, 1 model selected  

> select subtract #3.2

1 model selected  

> select #3/A-B:659

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:506-659

2386 atoms, 2442 bonds, 308 residues, 1 model selected  

> mlp sel

Map values for surface "TRMT1-2tRNA-predict.pdb_A SES surface": minimum -28,
mean -5.432, maximum 23.34  
Map values for surface "TRMT1-2tRNA-predict.pdb_B SES surface": minimum
-28.33, mean -5.405, maximum 23.55  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #3.3 models

> select subtract #3.3

1193 atoms, 1221 bonds, 154 residues, 3 models selected  

> select subtract #3.2

1 model selected  

> hide #3.2 models

> select #3/A-B:509

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:509-512

80 atoms, 78 bonds, 8 residues, 1 model selected  

> select #3/A-B:512

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:512

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:509

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:509-512

80 atoms, 78 bonds, 8 residues, 1 model selected  

> show sel atoms

> select #3/A-B:521

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:521

22 atoms, 20 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #3/A-B:528

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:528

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:536

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:536

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:544

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:544

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:544,546

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select #3/A-B:544,546,549-550

84 atoms, 78 bonds, 8 residues, 1 model selected  

> show sel atoms

> select #3/A-B:562

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:562

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:562

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:562-571

148 atoms, 150 bonds, 20 residues, 1 model selected  

> select #3/A-B:579

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:579-588

190 atoms, 188 bonds, 20 residues, 1 model selected  

> select #3/A-B:597

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:597-616

332 atoms, 336 bonds, 40 residues, 1 model selected  

> close #3.2

> close #3.3

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select #3/A-B:501

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #3/A-B:501-659

2480 atoms, 2540 bonds, 318 residues, 1 model selected  

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> select #3/A-B:506-507

26 atoms, 26 bonds, 4 residues, 1 model selected  

> select #3/A-B:506-526

336 atoms, 340 bonds, 42 residues, 1 model selected  

> select
> #3/A-B:68-73,76-100,165-173,187-199,213-219,239-248,262-265,270-277,287-306,332-341,405-417,425-437,448-455,462-471,492-505,510-512,518-523,537-539,542-545,573-583,594-602,607-610,617-619

3410 atoms, 3406 bonds, 426 residues, 1 model selected  

> select #3/A-B:659

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:547-659

1720 atoms, 1764 bonds, 226 residues, 1 model selected  

> select #3/A-B:546-547

30 atoms, 28 bonds, 4 residues, 1 model selected  

> select #3/A-B:541-547

108 atoms, 108 bonds, 14 residues, 1 model selected  

> select #3/A-B:528

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:528-659

2036 atoms, 2084 bonds, 264 residues, 1 model selected  

> select #3/A-B:544

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A-B:544-659

1782 atoms, 1826 bonds, 232 residues, 1 model selected  

> select add #3

13382 atoms, 13972 bonds, 1470 residues, 2 models selected  

> select subtract #3

Nothing selected  

> hide #3.1 models

> hide #!3 models

> color #!1 byhetero

> hide #!1 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 182, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 212, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 119, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 191, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 85, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open /Users/LaymanXUE/Downloads/cryosparc_P13_J117_component_000/*.mrc
> vseries true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 182, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 212, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 119, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 191, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 85, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Bad MRC grid size (0,0,0)  

> open /Users/LaymanXUE/Downloads/cryosparc_P13_J117_component_000/*.mrc
> vseries true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 182, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 212, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 119, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 191, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 85, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Bad MRC grid size (0,0,0)  

> show #!4 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 182, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 212, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 119, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 191, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 85, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> hide #!4 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 182, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 212, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 119, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 191, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 85, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device:
'/Users/LaymanXUE/Library/Application Support/ChimeraX/commands.1400.tmp'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3CH/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 49天7小时36分钟

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2719H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    biopython: 1.83
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBImages: 1.2
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.2
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 0.5
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RIBFIND: 0.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 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: 1.1.3
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    et-xmlfile: 1.1.0
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openpyxl: 3.1.2
    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.2.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyqtgraph: 0.13.3
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.31.0
    ribfind: 2.0.2
    scipy: 1.11.1
    seaborn: 0.13.2
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9