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Opened 4 hours ago
Closed 80 minutes ago
#19987 closed defect (fixed)
Minimize: 'str' object is not callable
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202603070142 (2026-03-07 01:42:04 UTC)
Description
I am trying to minimize a structure produced by AF3 but i have type error related to a string , which i guess is a bad type casting or failed transformation in another object. I have attached the structure for reproducibility
Log:
UCSF ChimeraX version: 1.12.dev202603070142 (2026-03-07)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /Users/ereboul/projects/NPF-ab-initio-
> modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement
Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement
> open NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
> select #1:25-115
1403 atoms, 1417 bonds, 91 residues, 1 model selected
> name RU1A_1 sel
> select #1:328-433
1700 atoms, 1718 bonds, 106 residues, 1 model selected
> name RU1A_2 sel
> select #1:136-229
1473 atoms, 1490 bonds, 94 residues, 1 model selected
> name RU1B_1 sel
> select #1:441-540
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> name RU1B_2 sel
> select RU1A_1
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save /path/to/output/RU1A_1.pdb selectedOnly true
Cannot save '/path/to/output/RU1A_1.pdb': Unable to open file
'/path/to/output/RU1A_1.pdb' for writing
> select RU1B_1
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save /path/to/output/RU1B_1.pdb selectedOnly true
Cannot save '/path/to/output/RU1B_1.pdb': Unable to open file
'/path/to/output/RU1B_1.pdb' for writing
> select RU1A_2
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save /path/to/output/RU1A_2.pdb selectedOnly true
Cannot save '/path/to/output/RU1A_2.pdb': Unable to open file
'/path/to/output/RU1A_2.pdb' for writing
> select RU1B_2
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save /path/to/output/RU1B_2.pdb selectedOnly true
Cannot save '/path/to/output/RU1B_2.pdb': Unable to open file
'/path/to/output/RU1B_2.pdb' for writing
> select RU1A_1
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save RU1A_1.pdb selectedOnly true
> select RU1B_1
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save RU1B_1.pdb selectedOnly true
> select RU1A_2
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save RU1A_2.pdb selectedOnly true
> select RU1B_2
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save RU1B_2.pdb selectedOnly true
> close #1
> open RU1A_1.pdb
Summary of feedback from opening RU1A_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1A_1.pdb #1
---
Chain | Description
A | No description available
> open RU1A_2.pdb
Summary of feedback from opening RU1A_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1A_2.pdb #2
---
Chain | Description
A | No description available
> open RU1B_1.pdb
Summary of feedback from opening RU1B_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1B_1.pdb #3
---
Chain | Description
A | No description available
> open RU1B_2.pdb
Summary of feedback from opening RU1B_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1B_2.pdb #4
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #3/A
Alignment identifier is 3/A
> sequence chain #4/A
Alignment identifier is 4/A
> close
> open NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
> select #1:25-115
1403 atoms, 1417 bonds, 91 residues, 1 model selected
> save RU1A_1.pdb selectedOnly true
> select clear
> open /Users/ereboul/projects/NPF-ab-initio-
> modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement/RU1A_1.pdb
Summary of feedback from opening /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement/RU1A_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19
24 messages similar to the above omitted
Chain information for RU1A_1.pdb #2
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> close #2
> select #1:25-115
1403 atoms, 1417 bonds, 91 residues, 1 model selected
> save RU1A_1.pdb selectedOnly true
> select #1:328-433
1700 atoms, 1718 bonds, 106 residues, 1 model selected
> save RU1B_1.pdb selectedOnly true
> select #1:136-229
1473 atoms, 1490 bonds, 94 residues, 1 model selected
> save RU1B_1.pdb selectedOnly true
> select #1:441-540
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save RU1B_2.pdb selectedOnly true
> close #1
> open RU1A_1.pdb
Summary of feedback from opening RU1A_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19
24 messages similar to the above omitted
Chain information for RU1A_1.pdb #1
---
Chain | Description
A | No description available
> open RU1A_2.pdb
No such file/path: RU1A_2.pdb
> open RU1B_1.pdb
Summary of feedback from opening RU1B_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1B_1.pdb #2
---
Chain | Description
A | No description available
> open RU1B_2.pdb
Summary of feedback from opening RU1B_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1B_2.pdb #3
---
Chain | Description
A | No description available
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RU1B_1.pdb, chain A (#2) with RU1A_1.pdb, chain A (#1), sequence
alignment score = 102.7
RMSD between 27 pruned atom pairs is 0.755 angstroms; (across all 90 pairs:
5.828)
> close
> open NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
> select #1:25-115
1403 atoms, 1417 bonds, 91 residues, 1 model selected
> save RU1A_1.pdb selectedOnly true
> select #1:328-433
1700 atoms, 1718 bonds, 106 residues, 1 model selected
> save RU1A_2.pdb selectedOnly true
> select #1:136-229
1473 atoms, 1490 bonds, 94 residues, 1 model selected
> save RU1B_1.pdb selectedOnly true
> select #1:441-540
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save RU1B_2.pdb selectedOnly true
> close #1
> open RU1A_1.pdb
Summary of feedback from opening RU1A_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19
24 messages similar to the above omitted
Chain information for RU1A_1.pdb #1
---
Chain | Description
A | No description available
> open RU1A_2.pdb
Summary of feedback from opening RU1A_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
25 messages similar to the above omitted
Chain information for RU1A_2.pdb #2
---
Chain | Description
A | No description available
> open RU1B_1.pdb
Summary of feedback from opening RU1B_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1B_1.pdb #3
---
Chain | Description
A | No description available
> open RU1B_2.pdb
Summary of feedback from opening RU1B_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1B_2.pdb #4
---
Chain | Description
A | No description available
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RU1A_2.pdb, chain A (#2) with RU1A_1.pdb, chain A (#1), sequence
alignment score = 106.8
RMSD between 31 pruned atom pairs is 0.895 angstroms; (across all 88 pairs:
6.092)
> matchmaker #3 to #4
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 RU1B_2.pdb, chain A (#4) with RU1B_1.pdb, chain A (#3), sequence
alignment score = 107.6
RMSD between 13 pruned atom pairs is 1.230 angstroms; (across all 86 pairs:
6.503)
> select #2 & aligned
Expected a keyword
> matchmaker #1 to #2 showAlignment true
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 RU1A_2.pdb, chain A (#2) with RU1A_1.pdb, chain A (#1), sequence
alignment score = 106.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: RU1A_1.pdb #1/A, RU1A_2.pdb
#2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 31 pruned atom pairs is 0.895 angstroms; (across all 88 pairs:
6.092)
> hide #3 models
> hide #4 models
> select #2/A:402
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:402-426
370 atoms, 372 bonds, 25 residues, 1 model selected
> select #2/A:363
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/A:363-394 #1/A:57-88
995 atoms, 1004 bonds, 64 residues, 2 models selected
MatchMaker Alignment [ID: 1] region RU1A_2.pdb, chain A..RU1A_1.pdb, chain A
[39-70] RMSD: 8.630
> select #2/A:328
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:328 #1/A:28
35 atoms, 33 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 1] region RU1A_2.pdb, chain A..RU1A_1.pdb, chain A
[4] RMSD: 0.688
> hide #1 models
> hide #2 models
> show #3 models
> show #4 models
> matchmaker #3 to #4 showAlignment true
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 RU1B_2.pdb, chain A (#4) with RU1B_1.pdb, chain A (#3), sequence
alignment score = 107.6
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: RU1B_1.pdb #3/A, RU1B_2.pdb
#4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 13 pruned atom pairs is 1.230 angstroms; (across all 86 pairs:
6.503)
> close #2
> close
> open *.pdb
Summary of feedback from opening RU1A_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19
24 messages similar to the above omitted
Summary of feedback from opening RU1A_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
25 messages similar to the above omitted
Summary of feedback from opening RU1B_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Summary of feedback from opening RU1B_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
Chain information for RU1A_1.pdb #2
---
Chain | Description
A | No description available
Chain information for RU1A_2.pdb #3
---
Chain | Description
A | No description available
Chain information for RU1B_1.pdb #4
---
Chain | Description
A | No description available
Chain information for RU1B_2.pdb #5
---
Chain | Description
A | No description available
> close
> open /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_1_chimerax_minimized.pdb /Users/ereboul/projects/NPF-ab-initio-
> modelling/neurosnap_boltz2_apo-NPF2.5/rank_2_chimerax_minimized.pdb
> /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_7_chimerax_minimized.pdb
Chain information for rank_1_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
Chain information for rank_2_chimerax_minimized.pdb #2
---
Chain | Description
A | No description available
Chain information for rank_7_chimerax_minimized.pdb #3
---
Chain | Description
A | No description available
> ui tool show "Find Cavities"
> kvfinder
23 cavities found for rank_1_chimerax_minimized.pdb #1
rank_1_chimerax_minimized.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.13 | | 837.43 | 711.31 | 3877 | 0 | 0
1.1.3 | | 807.19 | 699.71 | 3737 | 14.07 | 6.06
1.1.12 | | 227.02 | 201.07 | 1051 | 4.2 | 1.11
1.1.9 | | 126.58 | 147.25 | 586 | 4.84 | 2.32
1.1.6 | | 77.11 | 90.07 | 357 | 0 | 0
1.1.4 | | 76.25 | 83.08 | 353 | 4.24 | 1.7
1.1.16 | | 49.03 | 80.07 | 227 | 0 | 0
1.1.15 | | 43.63 | 66.31 | 202 | 0 | 0
1.1.19 | | 43.42 | 73.52 | 201 | 0 | 0
1.1.14 | | 36.5 | 54.73 | 169 | 1.7 | 0.37
1.1.21 | | 29.59 | 45.11 | 137 | 0 | 0
1.1.20 | | 28.51 | 44.2 | 132 | 0 | 0
1.1.2 | | 27.65 | 44.69 | 128 | 1.7 | 0.64
1.1.7 | | 25.92 | 45.52 | 120 | 1.34 | 0.37
1.1.10 | | 24.84 | 40.56 | 115 | 0 | 0
1.1.23 | | 21.82 | 40.63 | 101 | 0 | 0
1.1.8 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.11 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.17 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.18 | | 12.1 | 21.07 | 56 | 0.6 | 0.19
1.1.5 | | 9.29 | 18.8 | 43 | 0.6 | 0.18
1.1.22 | | 8.86 | 19.3 | 41 | 1.2 | 0.35
1.1.1 | | 7.78 | 15.17 | 36 | 1.2 | 0.27
Populating font family aliases took 109 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
31 cavities found for rank_2_chimerax_minimized.pdb #2
rank_2_chimerax_minimized.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.1.17 | | 722.09 | 660.9 | 3343 | 0 | 0
2.1.2 | | 339.98 | 345.67 | 1574 | 6.49 | 1.8
2.1.5 | | 183.38 | 215.19 | 849 | 8.38 | 3.6
2.1.16 | | 141.26 | 191.79 | 654 | 5.82 | 2.32
2.1.24 | | 112.97 | 152.87 | 523 | 0 | 0
2.1.8 | | 80.78 | 87.67 | 374 | 4.2 | 1.49
2.1.12 | | 66.31 | 84.35 | 307 | 2.08 | 0.59
2.1.6 | | 65.66 | 104.31 | 304 | 0 | 0
2.1.26 | | 59.62 | 79.55 | 276 | 0 | 0
2.1.25 | | 58.32 | 84.68 | 270 | 0 | 0
2.1.21 | | 52.27 | 77.56 | 242 | 0 | 0
2.1.4 | | 51.84 | 71.19 | 240 | 0 | 0
2.1.10 | | 44.28 | 64.98 | 205 | 2.68 | 0.85
2.1.19 | | 39.53 | 53.82 | 183 | 1.34 | 0.33
2.1.9 | | 27 | 44.51 | 125 | 0 | 0
2.1.7 | | 23.98 | 35.41 | 111 | 1.47 | 0.55
2.1.15 | | 17.28 | 36.68 | 80 | 0 | 0
2.1.20 | | 16.85 | 32.3 | 78 | 0 | 0
2.1.29 | | 16.85 | 27.01 | 78 | 1.8 | 0.57
2.1.31 | | 15.34 | 24.48 | 71 | 1.34 | 0.53
2.1.22 | | 13.61 | 25.27 | 63 | 1.2 | 0.27
2.1.1 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.3 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.11 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.13 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.14 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.23 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.27 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.28 | | 11.23 | 20.82 | 52 | 0.85 | 0.22
2.1.30 | | 8.86 | 19.38 | 41 | 1.34 | 0.36
2.1.18 | | 8.21 | 15.44 | 38 | 0.6 | 0.21
20 cavities found for rank_7_chimerax_minimized.pdb #3
rank_7_chimerax_minimized.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
3.1.13 | | 1598.4 | 1105.39 | 7400 | 18.14 | 5.62
3.1.3 | | 562.9 | 565.87 | 2606 | 16.05 | 7.27
3.1.5 | | 423.14 | 404.75 | 1959 | 9.14 | 3.19
3.1.4 | | 167.4 | 188.06 | 775 | 8.16 | 3.65
3.1.15 | | 57.24 | 80.85 | 265 | 0 | 0
3.1.17 | | 47.3 | 74.18 | 219 | 0 | 0
3.1.1 | | 28.3 | 48.73 | 131 | 0 | 0
3.1.11 | | 26.78 | 45.09 | 124 | 1.7 | 0.33
3.1.6 | | 26.14 | 44.82 | 121 | 0 | 0
3.1.19 | | 25.49 | 39.31 | 118 | 1.7 | 0.56
3.1.12 | | 19.01 | 38.34 | 88 | 0 | 0
3.1.16 | | 19.01 | 38.34 | 88 | 0 | 0
3.1.14 | | 16.85 | 32.3 | 78 | 0 | 0
3.1.18 | | 16.85 | 32.3 | 78 | 0 | 0
3.1.7 | | 12.96 | 23.28 | 60 | 1.2 | 0.35
3.1.8 | | 12.31 | 29.54 | 57 | 0 | 0
3.1.9 | | 12.31 | 29.54 | 57 | 0 | 0
3.1.10 | | 12.31 | 29.54 | 57 | 0 | 0
3.1.20 | | 9.94 | 20.83 | 46 | 1.04 | 0.44
3.1.2 | | 6.48 | 14.83 | 30 | 0.6 | 0.12
> hide #!2 models
> hide #!3 models
> close #3
> close
> open /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_1_chimerax_minimized.pdb /Users/ereboul/projects/NPF-ab-initio-
> modelling/neurosnap_boltz2_apo-NPF2.5/rank_2_chimerax_minimized.pdb
> /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_7_chimerax_minimized.pdb
Chain information for rank_1_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
Chain information for rank_2_chimerax_minimized.pdb #2
---
Chain | Description
A | No description available
Chain information for rank_7_chimerax_minimized.pdb #3
---
Chain | Description
A | No description available
> ui tool show "Find Cavities"
> kvfinder #1
23 cavities found for rank_1_chimerax_minimized.pdb #1
rank_1_chimerax_minimized.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.13 | | 837.43 | 711.31 | 3877 | 0 | 0
1.1.3 | | 807.19 | 699.71 | 3737 | 14.07 | 6.06
1.1.12 | | 227.02 | 201.07 | 1051 | 4.2 | 1.11
1.1.9 | | 126.58 | 147.25 | 586 | 4.84 | 2.32
1.1.6 | | 77.11 | 90.07 | 357 | 0 | 0
1.1.4 | | 76.25 | 83.08 | 353 | 4.24 | 1.7
1.1.16 | | 49.03 | 80.07 | 227 | 0 | 0
1.1.15 | | 43.63 | 66.31 | 202 | 0 | 0
1.1.19 | | 43.42 | 73.52 | 201 | 0 | 0
1.1.14 | | 36.5 | 54.73 | 169 | 1.7 | 0.37
1.1.21 | | 29.59 | 45.11 | 137 | 0 | 0
1.1.20 | | 28.51 | 44.2 | 132 | 0 | 0
1.1.2 | | 27.65 | 44.69 | 128 | 1.7 | 0.64
1.1.7 | | 25.92 | 45.52 | 120 | 1.34 | 0.37
1.1.10 | | 24.84 | 40.56 | 115 | 0 | 0
1.1.23 | | 21.82 | 40.63 | 101 | 0 | 0
1.1.8 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.11 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.17 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.18 | | 12.1 | 21.07 | 56 | 0.6 | 0.19
1.1.5 | | 9.29 | 18.8 | 43 | 0.6 | 0.18
1.1.22 | | 8.86 | 19.3 | 41 | 1.2 | 0.35
1.1.1 | | 7.78 | 15.17 | 36 | 1.2 | 0.27
> hide #2 models
> hide #3 models
> view #1.1.13 @< 3.5
> zoom 0.75
moved plane near -44.267412448592516 [-0.39958368 0.66184108 0.63427065]
moved plane far -44.267412448592516 [-0.39958368 0.66184108 0.63427065]
> surface #1.1.1-23 transparency 50
> ~surface #1.1
> surface #1.1.13
> show
> #!1/A:35,42-43,45-47,72,75-76,157-158,181-182,185-186,189,334,338-339,341-342,344-345,371,374-375,378,448,451-452,455,458-459,462-463,466,482-483,485-486,489-490
> select #!1/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #!1/A:459
41 atoms, 41 bonds, 2 residues, 1 model selected
> select add #!1/A:182
61 atoms, 61 bonds, 3 residues, 1 model selected
> show #2 models
> hide #!1 models
> ui tool show "Find Cavities"
> kvfinder #2 volumeCutoff 100
5 cavities found for rank_2_chimerax_minimized.pdb #2
rank_2_chimerax_minimized.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.1.4 | | 722.09 | 660.9 | 3343 | 0 | 0
2.1.1 | | 339.98 | 345.67 | 1574 | 6.49 | 1.8
2.1.2 | | 183.38 | 215.19 | 849 | 8.38 | 3.6
2.1.3 | | 141.26 | 191.79 | 654 | 5.82 | 2.32
2.1.5 | | 112.97 | 152.87 | 523 | 0 | 0
> view #2.1.4 @< 3.5
> zoom 0.75
moved plane near -41.330234783346505 [-0.11106485 -0.12389558 0.98606008]
moved plane far -41.330234783346505 [-0.11106485 -0.12389558 0.98606008]
> surface #2.1.1-5 transparency 50
> ~surface #2.1
> surface #2.1.4
> show
> #!2/A:35,38-39,42-43,45-47,71-72,75-76,156-158,160-161,178,181-182,185-186,189,338,341-342,345,371,374-375,451,455,458-459,463,479,483,486,489-490
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #3 models
> ui tool show "Find Cavities"
> kvfinder #3 volumeCutoff 100
4 cavities found for rank_7_chimerax_minimized.pdb #3
rank_7_chimerax_minimized.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
3.1.4 | | 1598.4 | 1105.39 | 7400 | 18.14 | 5.62
3.1.1 | | 562.9 | 565.87 | 2606 | 16.05 | 7.27
3.1.3 | | 423.14 | 404.75 | 1959 | 9.14 | 3.19
3.1.2 | | 167.4 | 188.06 | 775 | 8.16 | 3.65
> hide #!3 models
> open /Users/ereboul/projects/NPF-ab-initio-
> modelling/neurosnap_boltz2_NF2.5-GA1/rank_2_minimized_chimerax.pdb
Chain information for rank_2_minimized_chimerax.pdb #4
---
Chain | Description
A | No description available
> show #!2 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!1-2 to #4
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 rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_1_chimerax_minimized.pdb, chain A (#1), sequence alignment score = 2727.6
RMSD between 385 pruned atom pairs is 1.067 angstroms; (across all 560 pairs:
5.097)
Matchmaker rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_2_chimerax_minimized.pdb, chain A (#2), sequence alignment score = 2769.6
RMSD between 507 pruned atom pairs is 0.723 angstroms; (across all 560 pairs:
4.085)
> hide #!3 models
> show #!1 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!1-3 to #4
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 rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_1_chimerax_minimized.pdb, chain A (#1), sequence alignment score = 2727.6
RMSD between 385 pruned atom pairs is 1.067 angstroms; (across all 560 pairs:
5.097)
Matchmaker rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_2_chimerax_minimized.pdb, chain A (#2), sequence alignment score = 2769.6
RMSD between 507 pruned atom pairs is 0.723 angstroms; (across all 560 pairs:
4.085)
Matchmaker rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_7_chimerax_minimized.pdb, chain A (#3), sequence alignment score = 2771.4
RMSD between 264 pruned atom pairs is 1.123 angstroms; (across all 560 pairs:
6.522)
> hide #!3 models
> hide #4 models
> hide #!2 models
> close
> open *.pdb
Summary of feedback from opening RU1A_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19
24 messages similar to the above omitted
Summary of feedback from opening RU1A_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
25 messages similar to the above omitted
Summary of feedback from opening RU1B_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Summary of feedback from opening RU1B_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
Chain information for RU1A_1.pdb #2
---
Chain | Description
A | No description available
Chain information for RU1A_2.pdb #3
---
Chain | Description
A | No description available
Chain information for RU1B_1.pdb #4
---
Chain | Description
A | No description available
Chain information for RU1B_2.pdb #5
---
Chain | Description
A | No description available
> hide #1 models
> show #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:7
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:7-25
273 atoms, 276 bonds, 19 residues, 1 model selected
> select #1/A:25
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A:25-115
1403 atoms, 1417 bonds, 91 residues, 1 model selected
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #1 models
> close
> ui tool show "Molecular Dynamics Viewer"
Chain information for structure #1
---
Chain | Description
A | No description available
> open /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_1_chimerax_minimized.pdb /Users/ereboul/projects/NPF-ab-initio-
> modelling/neurosnap_boltz2_apo-NPF2.5/rank_7_chimerax_minimized.pdb
Chain information for rank_1_chimerax_minimized.pdb #2
---
Chain | Description
A | No description available
Chain information for rank_7_chimerax_minimized.pdb #3
---
Chain | Description
A | No description available
> hide #3 models
> show #3 models
> hide #!1 models
> hide #3 models
> ui tool show "Find Cavities"
> kvfinder #2 volumeCutoff 100
4 cavities found for rank_1_chimerax_minimized.pdb #2
rank_1_chimerax_minimized.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.1.4 | | 837.43 | 711.31 | 3877 | 0 | 0
2.1.1 | | 807.19 | 699.71 | 3737 | 14.07 | 6.06
2.1.3 | | 227.02 | 201.07 | 1051 | 4.2 | 1.11
2.1.2 | | 126.58 | 147.25 | 586 | 4.84 | 2.32
> view #2.1.4 @< 3.5
> zoom 0.75
moved plane near -37.78458045484981 [ 0.11486323 0.38519969 -0.91565694]
moved plane far -37.78458045484981 [ 0.11486323 0.38519969 -0.91565694]
> surface #2.1.1-4 transparency 50
> ~surface #2.1
> surface #2.1.4
> show
> #!2/A:35,42-43,45-47,72,75-76,157-158,181-182,185-186,189,334,338-339,341-342,344-345,371,374-375,378,448,451-452,455,458-459,462-463,466,482-483,485-486,489-490
> select #!2/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #!2/A:459
41 atoms, 41 bonds, 2 residues, 1 model selected
> select add #!2/A:182
61 atoms, 61 bonds, 3 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #!2/A
Alignment identifier is 2/A
> select #!2/A:178
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #!2/A:178
20 atoms, 20 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #!2/A:181
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add #!2/A:178
40 atoms, 40 bonds, 2 residues, 1 model selected
> select add #!2/A:182
60 atoms, 60 bonds, 3 residues, 1 model selected
> select #!2/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #!2/A:178
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #!2/A:178
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #!2/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #!2/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2:177
20 atoms, 20 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #!2/A:182
20 atoms, 20 bonds, 1 residue, 1 model selected
> close
> cd /Users/ereboul/projects/NPF-ab-initio-
> modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement
Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement
> open NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
> select #1:25-115
1403 atoms, 1417 bonds, 91 residues, 1 model selected
> save RU1A_1.pdb selectedOnly true
> select #1:136-229
1473 atoms, 1490 bonds, 94 residues, 1 model selected
> save RU1B.pdb selectedOnly true
> select #1:328-433
1700 atoms, 1718 bonds, 106 residues, 1 model selected
> save RU2A.pdb selectedOnly true
> select #1:441-540
1562 atoms, 1586 bonds, 100 residues, 1 model selected
> save RU2B.pdb selectedOnly true
> select #1:25-115
1403 atoms, 1417 bonds, 91 residues, 1 model selected
> save RU1A.pdb selectedOnly true
> close #1
> open RU1A.pdb
Summary of feedback from opening RU1A.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19
24 messages similar to the above omitted
Chain information for RU1A.pdb #1
---
Chain | Description
A | No description available
> open RU1B.pdb
Summary of feedback from opening RU1B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU1B.pdb #2
---
Chain | Description
A | No description available
> open RU2A.pdb
Summary of feedback from opening RU2A.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
25 messages similar to the above omitted
Chain information for RU2A.pdb #3
---
Chain | Description
A | No description available
> open RU2B.pdb
Summary of feedback from opening RU2B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20
24 messages similar to the above omitted
Chain information for RU2B.pdb #4
---
Chain | Description
A | No description available
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RU1B.pdb, chain A (#2) with RU1A.pdb, chain A (#1), sequence
alignment score = 102.7
RMSD between 27 pruned atom pairs is 0.755 angstroms; (across all 90 pairs:
5.828)
> matchmaker #3 to #4
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 RU2B.pdb, chain A (#4) with RU2A.pdb, chain A (#3), sequence
alignment score = 97.4
RMSD between 14 pruned atom pairs is 1.317 angstroms; (across all 92 pairs:
6.853)
> open /Users/ereboul/projects/NPF-ab-initio-
> modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement/NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #5
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:230
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/A:230-314
1359 atoms, 1372 bonds, 85 residues, 1 model selected
> select #5/A:325
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5/A:230-325
1540 atoms, 1554 bonds, 96 residues, 1 model selected
> select #5/A:324
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5/A:230-324
1521 atoms, 1535 bonds, 95 residues, 1 model selected
> select #5/A:230
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/A:230
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/A:314
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:314
11 atoms, 10 bonds, 1 residue, 1 model selected
> close #1-4
> color bfactor sel
11 atoms, 1 residues, atom bfactor range 73.5 to 73.5
> color bfactor sel
11 atoms, 1 residues, atom bfactor range 73.5 to 73.5
> select up
337 atoms, 338 bonds, 22 residues, 1 model selected
> select up
8784 atoms, 8887 bonds, 560 residues, 1 model selected
> color bfactor sel
8784 atoms, 560 residues, atom bfactor range 37.9 to 97.2
> select #5:434–440
Expected an objects specifier or a keyword
> select #5
8784 atoms, 8887 bonds, 560 residues, 1 model selected
> select #5:434–440
Expected an objects specifier or a keyword
> select #5:434-440
87 atoms, 88 bonds, 7 residues, 1 model selected
> select /A:560
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:541-560
340 atoms, 343 bonds, 20 residues, 1 model selected
> close
> open
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_0.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_1.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_2.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_3.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_4.cif
Chain information for fold_dlc4_rnads_drb2_drb4_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D E | .
Chain information for fold_dlc4_rnads_drb2_drb4_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
D E | .
Chain information for fold_dlc4_rnads_drb2_drb4_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
D E | .
Chain information for fold_dlc4_rnads_drb2_drb4_model_3.cif #4
---
Chain | Description
A | .
B | .
C | .
D E | .
Chain information for fold_dlc4_rnads_drb2_drb4_model_4.cif #5
---
Chain | Description
A | .
B | .
C | .
D E | .
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
> set bgColor #ffffff00
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> show protein target c
Computing secondary structure
[Repeated 4 time(s)]
> hide protein target a
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 111575 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #2 models
> color bfactor #2
22315 atoms, 2623 residues, atom bfactor range 13.7 to 91.6
> show #1 models
> hide #2 models
> color bfactor #1
22315 atoms, 2623 residues, atom bfactor range 14.7 to 91.1
> hide #1 models
> show #2 models
> hide #2 models
> show #1 models
> hide #1 models
> show #2 models
> show #1 models
> hide #2 models
> hide #1 models
> show #1 models
> select #1/C:236
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1116 atoms, 1137 bonds, 152 residues, 1 model selected
> hide sel target c
> select #1/A:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
920 atoms, 936 bonds, 119 residues, 1 model selected
> hide sel target c
> select #1/B:323
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1782 atoms, 1829 bonds, 236 residues, 1 model selected
> hide sel target c
> select #1/B
3332 atoms, 3409 bonds, 434 residues, 1 model selected
> select #1/C
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> select #1/D
1424 atoms, 1593 bonds, 66 residues, 1 model selected
> hide #1 models
> show #2 models
> select #2/D
1424 atoms, 1593 bonds, 66 residues, 1 model selected
> hide #2 models
> show #3 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> hide #5 models
> show #1 models
> select up
22315 atoms, 23065 bonds, 2623 residues, 1 model selected
> hide #1 models
> show #2 models
> select #2/B
3332 atoms, 3409 bonds, 434 residues, 1 model selected
> select up
22315 atoms, 23065 bonds, 2623 residues, 1 model selected
> select down
3332 atoms, 3409 bonds, 434 residues, 1 model selected
> select #2/A
13438 atoms, 13710 bonds, 1702 residues, 1 model selected
> select up
22315 atoms, 23065 bonds, 2623 residues, 1 model selected
> select down
13438 atoms, 13710 bonds, 1702 residues, 1 model selected
> select clear
> close
> pwd
Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement
> cd ../../
Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection
> cd ../
Current working directory is: /Users/ereboul/projects/NPF-ab-initio-modelling
> open /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_1_chimerax_minimized.pdb
Chain information for rank_1_chimerax_minimized.pdb #1
---
Chain | Description
A | No description available
> open 4OH3
4oh3 title:
Crystal structure of a nitrate transporter [more info...]
Chain information for 4oh3 #2
---
Chain | Description | UniProt
A B | Nitrate transporter 1.1 | PTR7_ARATH 1-590
Non-standard residues in 4oh3 #2
---
LMT — dodecyl-β-D-maltoside
NO3 — nitrate ion
7992 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Matchmaker
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4oh3, chain A (#2) with rank_1_chimerax_minimized.pdb, chain A
(#1), sequence alignment score = 1132
RMSD between 298 pruned atom pairs is 1.193 angstroms; (across all 493 pairs:
5.405)
> select #2/B:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
202 atoms, 205 bonds, 28 residues, 1 model selected
> select up
2026 atoms, 2067 bonds, 273 residues, 1 model selected
> select up
2126 atoms, 2165 bonds, 292 residues, 1 model selected
> select up
3078 atoms, 3138 bonds, 414 residues, 1 model selected
> select up
3128 atoms, 3190 bonds, 420 residues, 1 model selected
> select up
4062 atoms, 4150 bonds, 537 residues, 1 model selected
> select #2/B
4090 atoms, 4178 bonds, 3 pseudobonds, 539 residues, 2 models selected
> delete #2/B
> save /Users/ereboul/projects/NPF-ab-initio-modelling/NPF6.3_4OH3_crystal.pdb
> models #2
> ui tool show "Molecular Dynamics Viewer"
Chain information for structure #3
---
Chain | Description
A | No description available
> info #2
3 models
#2, 4oh3, shown
3958 atoms, 4046 bonds, 514 residues, 1 chains (A)
3 missing structure
#2.1, missing structure, shown, 3 pseudobonds
#2.1.1, labels, shown, 6 triangles
> close #3
> ui tool show "Molecular Dynamics Viewer"
Chain information for structure #3
---
Chain | Description
A | No description available
> delete solvent
> delete ligand
> delete #2 & ~protein
> close #3
> show #2 ribbons
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select clear
[Repeated 2 time(s)]
> pwd
Current working directory is: /Users/ereboul/projects/NPF-ab-initio-modelling
> cd MODELLER
Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/MODELLER
> select #2/A
3930 atoms, 4018 bonds, 3 pseudobonds, 512 residues, 2 models selected
> hide #1 models
> ui tool show "Find Cavities"
> kvfinder #2 volumeCutoff 100
2 cavities found for 4oh3 #2
4oh3 Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.2.1 | | 1165.1 | 871.46 | 5394 | 12.01 | 2.97
2.2.2 | | 298.51 | 251.56 | 1382 | 6.43 | 1.39
> view #2.2.2 @< 3.5
> zoom 0.75
moved plane near -41.243530436001585 [-0.72965792 -0.58301651 -0.35733888]
moved plane far -41.243530436001585 [-0.72965792 -0.58301651 -0.35733888]
> surface #2.2.1-2 transparency 50
> ~surface #2.2
> surface #2.2.2
> show
> #!2/A:56-57,60-61,64-67,71,131-133,135-140,361-362,364-366,368-369,534-536
> view #!2.2.1 @< 3.5
> zoom 0.75
moved plane near -62.466540726917366 [-0.76363139 -0.29706315 -0.5732544 ]
moved plane far -62.466540726917366 [-0.76363139 -0.29706315 -0.5732544 ]
> ~surface #2.2
> surface #!2.2.1
> show
> #!2/A:41,44-45,47-49,51-53,77-78,81-82,85-86,88-90,92-93,98,156-157,160,164-166,168,201,205,248-252,353,356,359-360,364,382,385,388-389,392-393,469,476,480,494,497-504,507,511
> select #2/A
3930 atoms, 4018 bonds, 3 pseudobonds, 512 residues, 2 models selected
> close #2.2
> select #2/A
3930 atoms, 4018 bonds, 3 pseudobonds, 512 residues, 2 models selected
> save 4oh3_clean.pdb selectedOnly true
> close #2
> show #1 models
> open 4oh3_clean.pdb
Summary of feedback from opening 4oh3_clean.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 2 LYS A 5 1 4
Start residue of secondary structure not found: HELIX 2 2 SER A 6 ASP A 8 1 3
Start residue of secondary structure not found: HELIX 3 3 GLY A 24 THR A 27 1
4
Start residue of secondary structure not found: HELIX 4 4 LEU A 28 MET A 47 1
20
End residue of secondary structure not found: HELIX 5 5 LEU A 49 GLU A 55 1 7
Start residue of secondary structure not found: HELIX 6 6 ASN A 61 LEU A 78 1
18
Start residue of secondary structure not found: HELIX 7 7 PRO A 79 PHE A 90 1
12
Start residue of secondary structure not found: HELIX 8 8 ASN A 92 SER A 115 1
24
Start residue of secondary structure not found: HELIX 9 9 ASN A 117 LEU A 119
1 3
Start residue of secondary structure not found: HELIX 10 10 LYS A 136 ALA A
154 1 19
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 12 12 ALA A 165 GLN A 167
1 3
Start residue of secondary structure not found: HELIX 13 13 PRO A 171 ALA A
195 1 25
Start residue of secondary structure not found: HELIX 14 14 ILE A 196 ASN A
202 1 7
Start residue of secondary structure not found: HELIX 15 15 TRP A 205 PHE A
223 1 19
Start residue of secondary structure not found: HELIX 16 16 ILE A 224 GLY A
226 1 3
Start residue of secondary structure not found: HELIX 17 17 THR A 241 MET A
252 1 12
17 messages similar to the above omitted
End residue of secondary structure not found: HELIX 35 35 VAL A 516 PHE A 540
1 25
Start residue of secondary structure not found: HELIX 36 36 PRO A 555 ASP A
557 1 3
Chain information for 4oh3_clean.pdb #2
---
Chain | Description
A | No description available
3930 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> info #2
2 models
#2, 4oh3_clean.pdb, shown
3930 atoms, 4018 bonds, 512 residues, 1 chains (A)
3 missing structure
#2.1, missing structure, shown, 3 pseudobonds
> close
> open /Users/ereboul/Downloads/9KBZ.cif
Summary of feedback from opening /Users/ereboul/Downloads/9KBZ.cif
---
note | Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
9KBZ.cif title:
Cryo-EM structure of DCL4-DRB4CTD-dsRNA complex [more info...]
Chain information for 9KBZ.cif #1
---
Chain | Description | UniProt
A | Dicer-like protein 4 | DCL4_ARATH 62-1702
B | Double-stranded RNA-binding protein 4 | DRB4_ARATH 292-355
C | RNA (57-MER) |
D | RNA (55-MER) |
Non-standard residues in 9KBZ.cif #1
---
MG — magnesium ion
> open /Users/ereboul/Downloads/emd_62235.map
Opened emd_62235.map as #2, grid size 360,360,360, pixel 0.855, shown at level
0.144, step 2, values float32
> volume #2 level 0.1708
> surface style mesh
> volume #2 level 0.3237
> volume #2 level 0.2068
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> pwd
Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/MODELLER
> cd ../../
Current working directory is: /Users/ereboul/projects
> cd drb2_modelling
Current working directory is: /Users/ereboul/projects/drb2_modelling
> select clear
> select /C
1102 atoms, 1230 bonds, 52 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> select clear
> select /D
1084 atoms, 1212 bonds, 51 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select clear
> select /A:126-1702
11290 atoms, 11519 bonds, 9 pseudobonds, 1423 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> open
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_0.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_1.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_2.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_3.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_4.cif
Chain information for fold_dlc4_rnads_drb2_drb4_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
D E | .
Chain information for fold_dlc4_rnads_drb2_drb4_model_1.cif #4
---
Chain | Description
A | .
B | .
C | .
D E | .
Chain information for fold_dlc4_rnads_drb2_drb4_model_2.cif #5
---
Chain | Description
A | .
B | .
C | .
D E | .
Chain information for fold_dlc4_rnads_drb2_drb4_model_3.cif #6
---
Chain | Description
A | .
B | .
C | .
D E | .
Chain information for fold_dlc4_rnads_drb2_drb4_model_4.cif #7
---
Chain | Description
A | .
B | .
C | .
D E | .
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #3-7 to #1
Computing secondary structure
[Repeated 4 time(s)] 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 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_0.cif,
chain A (#3), sequence alignment score = 7506.1
RMSD between 489 pruned atom pairs is 1.251 angstroms; (across all 1423 pairs:
4.154)
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_1.cif,
chain A (#4), sequence alignment score = 7500.4
RMSD between 557 pruned atom pairs is 1.247 angstroms; (across all 1423 pairs:
5.431)
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_2.cif,
chain A (#5), sequence alignment score = 7489.3
RMSD between 655 pruned atom pairs is 1.266 angstroms; (across all 1423 pairs:
3.987)
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_3.cif,
chain A (#6), sequence alignment score = 7483.3
RMSD between 575 pruned atom pairs is 1.218 angstroms; (across all 1423 pairs:
4.163)
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_4.cif,
chain A (#7), sequence alignment score = 7475.5
RMSD between 673 pruned atom pairs is 1.258 angstroms; (across all 1423 pairs:
3.878)
> hide protein target a
> hide RNA target a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select #1/C:33
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1102 atoms, 1230 bonds, 52 residues, 1 model selected
> select up
13858 atoms, 14350 bonds, 1576 residues, 1 model selected
> select down
1102 atoms, 1230 bonds, 52 residues, 1 model selected
> select add #1/D:26
1124 atoms, 1254 bonds, 53 residues, 1 model selected
> select up
2186 atoms, 2442 bonds, 103 residues, 1 model selected
> show sel target ab
> surface sel
> hide dna target a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide all target a
> show #1 target c
> show #3-7 target c
> hide #6 models
> hide #7 models
> hide #3 models
> hide #5 models
> close #3-7
> open
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_0.cif
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_1.cif
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_2.cif
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_3.cif
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_1.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_2.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_3.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> ui tool show Matchmaker
> matchmaker #3-7 to #1
Computing secondary structure
[Repeated 4 time(s)] 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 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_0.cif, chain A (#3), sequence alignment
score = 7501.3
RMSD between 568 pruned atom pairs is 1.191 angstroms; (across all 1423 pairs:
3.888)
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_1.cif, chain A (#4), sequence alignment
score = 7507.3
RMSD between 589 pruned atom pairs is 1.252 angstroms; (across all 1423 pairs:
3.219)
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_2.cif, chain A (#5), sequence alignment
score = 7512.4
RMSD between 463 pruned atom pairs is 1.159 angstroms; (across all 1423 pairs:
4.254)
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_3.cif, chain A (#6), sequence alignment
score = 7471.2
RMSD between 528 pruned atom pairs is 1.206 angstroms; (across all 1423 pairs:
4.336)
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif, chain A (#7), sequence alignment
score = 7507
RMSD between 447 pruned atom pairs is 1.203 angstroms; (across all 1423 pairs:
4.576)
> hide all target a
> show #3-7 target c
> hide #3 models
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> hide #5 models
> show #5 models
> hide #4 models
> hide #6 models
> show #6 models
> hide #5 models
> hide #7 models
> hide #!1 models
> color bfactor #6
21838 atoms, 2602 residues, atom bfactor range 15.1 to 90.8
> show #!1 models
> surface hidePatches (#!1 & sel)
> select clear
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> close #3-5
> hide #6 models
> hide #7 models
> show #7 models
> select #7/B:389
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
125 atoms, 126 bonds, 16 residues, 1 model selected
> select up
3332 atoms, 3409 bonds, 434 residues, 1 model selected
> select #7/C:208
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
159 atoms, 162 bonds, 21 residues, 1 model selected
> select up
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> show nucleic target a
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 43676 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #7 models
> show #6 models
> select #1/B
379 atoms, 389 bonds, 47 residues, 1 model selected
> select #6/D
1210 atoms, 1351 bonds, 57 residues, 1 model selected
> select #6/B
3332 atoms, 3409 bonds, 434 residues, 1 model selected
> select #1/B
379 atoms, 389 bonds, 47 residues, 1 model selected
> select #6/C:323
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
48 atoms, 49 bonds, 6 residues, 1 model selected
> select up
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> select #6/B:204
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
102 atoms, 106 bonds, 12 residues, 1 model selected
> select up
3332 atoms, 3409 bonds, 434 residues, 1 model selected
> hide #!1 models
> select #6/C:206
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
69 atoms, 71 bonds, 8 residues, 1 model selected
> select up
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/C
Alignment identifier is 6/C
> select #6/C:355
8 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/C
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> show #7 models
> show #!1 models
> hide #7 models
> select #6/C:355
8 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/C
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B
379 atoms, 389 bonds, 47 residues, 1 model selected
> select #6/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/C
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> select #6/C:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/C:307-355
396 atoms, 407 bonds, 49 residues, 1 model selected
> select #6/B:392
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
241 atoms, 241 bonds, 32 residues, 1 model selected
> select up
3332 atoms, 3409 bonds, 434 residues, 1 model selected
> hide #!1 models
> color sel byelement
> color sel orange
> select #6/A:682
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
63 atoms, 65 bonds, 7 residues, 1 model selected
> select up
13430 atoms, 13702 bonds, 1701 residues, 1 model selected
> color sel cornflower blue
> select #6/C:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/C:175
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
233 atoms, 237 bonds, 31 residues, 1 model selected
> select up
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> color sel forest green
> hide #6 models
> show #7 models
> show #6 models
> hide #6 models
> select #7/A:362
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
217 atoms, 217 bonds, 27 residues, 1 model selected
> select up
13430 atoms, 13702 bonds, 1701 residues, 1 model selected
> select #7/C:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
161 atoms, 162 bonds, 20 residues, 1 model selected
> select up
2697 atoms, 2760 bonds, 355 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #7/C
Alignment identifier is 7/C
> show #!1 models
> select #1/B
379 atoms, 389 bonds, 47 residues, 1 model selected
> select #7/C:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/C:307-355
396 atoms, 407 bonds, 49 residues, 1 model selected
> select #1/B
379 atoms, 389 bonds, 47 residues, 1 model selected
> color sel red
> select #7/C:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/C:307-355
396 atoms, 407 bonds, 49 residues, 1 model selected
> ui tool show "Minimize Structure"
> minimize #7 logEnergy true
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Deleting residues with incomplete backbones
Summary of feedback from adding hydrogens to
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7
---
notes | Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain A determined from SEQRES records
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain B
determined from SEQRES records
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain C
determined from SEQRES records
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain D
determined from SEQRES records
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain E
determined from SEQRES records
Chain-initial residues that are actual N termini:
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/A ARG 1,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/B MET 1,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/C MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/A CYS 1701,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/B ILE 434,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/C PRO 355
Chain-final residues that are not actual C termini:
2549 hydrogen bonds
20715 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 101, in minimize
run(self.session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 129, in prep
callback(session, state, structures)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep
callback(session, state, structures)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep
callback(session, state, structures)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps
callback()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 128, in <lambda>
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())
^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 45, in <lambda>
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 89, in _minimize
raise LimitationError(c_error_template(c_term, "can't find C atom"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'str' object is not callable
TypeError: 'str' object is not callable
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 89, in _minimize
raise LimitationError(c_error_template(c_term, "can't find C atom"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show Clashes
> hide #!1 models
> clashes interModel false ignoreHiddenModels true select true reveal true
480 clashes
> select clear
> ui tool show "Minimize Structure"
[Repeated 1 time(s)]
> minimize #7 logEnergy true
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Deleting residues with incomplete backbones
Summary of feedback from adding hydrogens to
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7
---
notes | Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain A determined from SEQRES records
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain B
determined from SEQRES records
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain C
determined from SEQRES records
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain D
determined from SEQRES records
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain E
determined from SEQRES records
Chain-initial residues that are actual N termini:
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/A ARG 1,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/B MET 1,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/C MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/A CYS 1701,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/B ILE 434,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/C PRO 355
Chain-final residues that are not actual C termini:
2349 hydrogen bonds
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 101, in minimize
run(self.session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 129, in prep
callback(session, state, structures)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep
callback(session, state, structures)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep
callback(session, state, structures)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps
callback()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 128, in <lambda>
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())
^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 45, in <lambda>
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 89, in _minimize
raise LimitationError(c_error_template(c_term, "can't find C atom"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'str' object is not callable
TypeError: 'str' object is not callable
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 89, in _minimize
raise LimitationError(c_error_template(c_term, "can't find C atom"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac16,9
Model Number: Z1CD000KXFN/A
Chip: Apple M4 Max
Total Number of Cores: 14 (10 Performance and 4 Efficiency)
Memory: 36 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (25D2128)
Kernel Version: Darwin 25.3.0
Time since boot: 4 jours, 22 heures et 30 minutes
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
LS32D80xU:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.1.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.5
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.64.1
ChimeraX-AtomicLibrary: 14.2.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202603070142
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.3
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.18
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.6
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.5.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
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: 1.50.3
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.4
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
MolecularDynamicsViewer: 1.6
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.17.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.3
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.6
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.4
plotly: 6.5.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.13.1
pydantic_core: 2.41.5
pydata-sphinx-theme: 0.16.1
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.0
pynmrstar: 3.5.0
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PySide6: 6.10.1
PySide6_Addons: 6.10.1
PySide6_Essentials: 6.10.1
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.22
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.1
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
shiboken6: 6.10.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.3.2
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.14.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.41.0
wcwidth: 0.6.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.23.0
File attachment: fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif
Attachments (1)
Change History (3)
by , 4 hours ago
| Attachment: | fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif added |
|---|
comment:1 by , 3 hours ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Minimize: 'str' object is not callable |
comment:2 by , 80 minutes ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Hi Etienne,
Thanks for reporting this problem. I have fixed the code and the fix will be in the next daily build.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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