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Opened 26 hours ago
Last modified 3 hours ago
#20758 assigned defect
'zone' command uses dead residue
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "T:\Donnees_pro\\_DATA_ANALYSIS\Protein_Structural_Models\MtPMT
> Pretomanid\session_3.cxs" format session
Log from Tue Jul 14 18:49:58 2026UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "T:\Donnees_pro\\_DATA_ANALYSIS\Protein_Structural_Models\MtPMT
> Pretomanid\session.cxs" format session
Log from Mon Jul 13 16:06:09 2026UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid"
Current working directory is:
T:\Donnees_pro\\_DATA_ANALYSIS\Protein_Structural_Models\MtPMT Pretomanid
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/Rv1002c_AF.pdb"
Rv1002c_AF.pdb title:
Alphafold monomer V2.0 prediction for polyprenol-phosphate-mannose-- protein
mannosyltransferase (P9WN05) [more info...]
Chain information for Rv1002c_AF.pdb #1
---
Chain | Description | UniProt
A | polyprenol-phosphate-mannose--protein mannosyltransferase | PMT_MYCTU 1-522
Computing secondary structure
> view clip false
[Repeated 1 time(s)]
> log metadata #1
Metadata for Rv1002c_AF.pdb #1
---
Title | Alphafold monomer V2.0 prediction for polyprenol-phosphate-mannose-- protein mannosyltransferase (P9WN05)
Source (natural) | Mycobacterium tuberculosis (strain ATCC 25618 / H37RV)
> log chains #1
Chain information for Rv1002c_AF.pdb #1
---
Chain | Description | UniProt
A | polyprenol-phosphate-mannose--protein mannosyltransferase | PMT_MYCTU 1-522
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/6P25.pdb"
6P25.pdb title:
Structure of S. Cerevisiae protein O-mannosyltransferase PMT1-PMT2 complex
bound to the sugar donor and A peptide acceptor [more info...]
Chain information for 6P25.pdb #2
---
Chain | Description | UniProt
A | PMT1 | PMT1_YEAST 1-817
B | PMT2 | PMT2_YEAST 1-759
D | acceptor peptide |
Non-standard residues in 6P25.pdb #2
---
CPL — 1-palmitoyl-2-linoleoyl-Sn-glycero-3-phosphocholine (palmitoyl-linoleoyl
phosphatidylcholine)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
NNM — (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl
dihydrogenphosphate
> view #2 clip false
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/D
Alignment identifier is 2/D
> select
> #2/A:35-42,46-64,77-91,100-113,134-159,162-185,188-208,213-232,236-258,262-296,310-314,368-371,438-441,455-460,504-507,532-550,560-567,586-614,620-645,652-677,682-708,714-722,738-743
3033 atoms, 3102 bonds, 378 residues, 1 model selected
> select
> #2/B:58-80,82-86,92-105,115-127,147-173,177-197,202-222,229-250,253-272,278-312,318-330,384-387,453-456,500-504,547-565,579-583,609-634,641-669,674-695,698-734
2975 atoms, 3059 bonds, 365 residues, 1 model selected
> select
> #1/A:40-59,73-87,105-117,121-147,150-161,164-171,175-206,223-236,240-263,269-276,278-302,326-344,396-414,419-430,433-436,445-467,474-503,509-515,519-521
2512 atoms, 2580 bonds, 315 residues, 1 model selected
> select clear
> select #2/A
5990 atoms, 6173 bonds, 1 pseudobond, 734 residues, 2 models selected
> ui tool show Match→Align
> msa3d #1/A#2/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
0 residue pairs aligned
Cannot generate alignment because no residues within cutoff distance
> msa3d #1/A#2/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
0 residue pairs aligned
Cannot generate alignment because no residues within cutoff distance
> ui tool show Match→Align
> msa3d #1/A#2/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
0 residue pairs aligned
Cannot generate alignment because no residues within cutoff distance
> hide #1 models
> show #1 models
> select add #1
10072 atoms, 10388 bonds, 1 pseudobond, 1256 residues, 3 models selected
> select add #2
15821 atoms, 16324 bonds, 2 pseudobonds, 1952 residues, 4 models selected
> ui tool show Match→Align
> msa3d #1/A#2/B
Match→Align cutoff: 5.0, in column if within cutoff of: any
0 residue pairs aligned
Cannot generate alignment because no residues within cutoff distance
> select subtract #2
4082 atoms, 4215 bonds, 522 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
Drag select of 14 residues
> select #1/A:452
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:406
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 522 residues
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,74.478,0,1,0,34.839,0,0,1,70.305
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.44291,-0.17838,0.87864,27.825,-0.10861,0.98347,0.14491,30.054,-0.88997,-0.031245,-0.45496,73.822
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.44291,-0.17838,0.87864,114.26,-0.10861,0.98347,0.14491,75.042,-0.88997,-0.031245,-0.45496,114.31
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.44291,-0.17838,0.87864,113.64,-0.10861,0.98347,0.14491,92.327,-0.88997,-0.031245,-0.45496,104.1
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> ui tool show Match→Align
> msa3d #1/A#2/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
10 residue pairs aligned
10 fully populated columns
Pairwise RMSDs across all fully populated columns
---
Model | 1 | 2
1 | 0.000 | 3.082
2 | 3.082 | 0.000
Overall RMSD: 3.082
Sequence lengths: 522 731
SDM (cutoff 5.0): 237.999
Q-score: 0.000
Alignment identifier is MA-1
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1
Chains used in RMSD evaluation for alignment MA-1: Rv1002c_AF.pdb #1/A,
6P25.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1
> msa3d #1/A#2/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
10 residue pairs aligned
10 fully populated columns
Pairwise RMSDs across all fully populated columns
---
Model | 1 | 2
1 | 0.000 | 3.082
2 | 3.082 | 0.000
Overall RMSD: 3.082
Sequence lengths: 522 731
SDM (cutoff 5.0): 237.999
Q-score: 0.000
Alignment identifier is MA-2
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-2
Chains used in RMSD evaluation for alignment MA-2: Rv1002c_AF.pdb #1/A,
6P25.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-2
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rv1002c_AF.pdb, chain A (#1) with 6P25.pdb, chain A (#2), sequence
alignment score = 483.1
RMSD between 263 pruned atom pairs is 1.162 angstroms; (across all 452 pairs:
6.572)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rv1002c_AF.pdb, chain A (#1) with 6P25.pdb, chain A (#2), sequence
alignment score = 483.1
RMSD between 263 pruned atom pairs is 1.162 angstroms; (across all 452 pairs:
6.572)
Drag select of 12 residues
> ui mousemode right zoom
> ui mousemode right translate
> split 6P25.pdb
Expected a structures specifier or a keyword
> split #2
Split 6P25.pdb (#2) into 3 models
Chain information for 6P25.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for 6P25.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for 6P25.pdb D #2.3
---
Chain | Description
D | No description available
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2.2 models
> hide #2.3 models
> show #2.3 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> ui tool show Matchmaker
> matchmaker #!2.2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rv1002c_AF.pdb, chain A (#1) with 6P25.pdb B, chain B (#2.2),
sequence alignment score = 391.5
RMSD between 212 pruned atom pairs is 1.262 angstroms; (across all 447 pairs:
8.242)
> undo
> show #!2.1 models
> show #!2.2 models
> hide #!2 models
> show #!2 models
> select add #2
11757 atoms, 12109 bonds, 2 pseudobonds, 1433 residues, 7 models selected
> select add #1
15821 atoms, 16324 bonds, 2 pseudobonds, 1952 residues, 7 models selected
> select subtract #1
11739 atoms, 12109 bonds, 2 pseudobonds, 1430 residues, 6 models selected
> hide #1 models
> close #2
> show #1 models
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/6P25.pdb"
6P25.pdb title:
Structure of S. Cerevisiae protein O-mannosyltransferase PMT1-PMT2 complex
bound to the sugar donor and A peptide acceptor [more info...]
Chain information for 6P25.pdb #2
---
Chain | Description | UniProt
A | PMT1 | PMT1_YEAST 1-817
B | PMT2 | PMT2_YEAST 1-759
D | acceptor peptide |
Non-standard residues in 6P25.pdb #2
---
CPL — 1-palmitoyl-2-linoleoyl-Sn-glycero-3-phosphocholine (palmitoyl-linoleoyl
phosphatidylcholine)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
NNM — (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl
dihydrogenphosphate
> split #2
Split 6P25.pdb (#2) into 3 models
Chain information for 6P25.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for 6P25.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for 6P25.pdb D #2.3
---
Chain | Description
D | No description available
> hide #!2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2 models
> show #!2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.1 models
> hide #2.3 models
> show #2.3 models
> show #!2.2 models
> hide #2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #2.3 models
> ui tool show Matchmaker
> matchmaker #1 to #2.2
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 6P25.pdb B, chain B (#2.2) with Rv1002c_AF.pdb, chain A (#1),
sequence alignment score = 391.5
RMSD between 212 pruned atom pairs is 1.262 angstroms; (across all 447 pairs:
8.242)
> matchmaker #!2.1 to #2.2
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 6P25.pdb B, chain B (#2.2) with 6P25.pdb A, chain A (#2.1),
sequence alignment score = 1308.1
RMSD between 341 pruned atom pairs is 1.056 angstroms; (across all 661 pairs:
6.791)
> matchmaker #!2.1 to #2.2
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 6P25.pdb B, chain B (#2.2) with 6P25.pdb A, chain A (#2.1),
sequence alignment score = 1308.1
RMSD between 341 pruned atom pairs is 1.056 angstroms; (across all 661 pairs:
6.791)
> show #!2.1 models
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1-20
153 atoms, 156 bonds, 20 residues, 1 model selected
> select #1/A:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:21-30
67 atoms, 69 bonds, 10 residues, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1-27
198 atoms, 203 bonds, 27 residues, 1 model selected
> delete #1/A:1:27
> ui mousemode right select
> select #2.1/A:689
7 atoms, 6 bonds, 1 residue, 1 model selected
> undo
[Repeated 2 time(s)]Undo failed, probably because structures have been
modified.
> hide sel
> delete sel
> view clip false
> hide #!2.1 models
> hide #!2.2 models
> hide #2.1.1 models
> show #2.1.1 models
> hide #!1 models
> select #2.1/A:1003@C13
1 atom, 1 residue, 1 model selected
> show #!2.2 target m
[Repeated 1 time(s)]
> select add #2
11739 atoms, 12109 bonds, 2 pseudobonds, 1430 residues, 6 models selected
> select subtract #2.1
5749 atoms, 5936 bonds, 1 pseudobond, 696 residues, 4 models selected
> select subtract #2.3
5723 atoms, 5909 bonds, 1 pseudobond, 693 residues, 3 models selected
> sequence chain #2.2/B
Alignment identifier is 2.2/B
> select subtract #2.2
1 model selected
> select add #2.2
5723 atoms, 5909 bonds, 1 pseudobond, 693 residues, 3 models selected
> select subtract #2.2.1
5723 atoms, 5909 bonds, 693 residues, 2 models selected
> select add #2.2
5723 atoms, 5909 bonds, 1 pseudobond, 693 residues, 3 models selected
> select subtract #2.2
1 model selected
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #2.1.1 models
> hide #2.2.1 models
> hide #!2.1 models
> hide #!2.2 models
> hide #2.3 models
> show #!2.1 models
> select add #2.1
5990 atoms, 6173 bonds, 1 pseudobond, 734 residues, 3 models selected
> sequence chain #2.1/A
Alignment identifier is 2.1/A
> select add #2
11739 atoms, 12109 bonds, 2 pseudobonds, 1430 residues, 6 models selected
> select subtract #2
Nothing selected
> select add #2.1
5990 atoms, 6173 bonds, 1 pseudobond, 734 residues, 2 models selected
> select subtract #2.1
Nothing selected
> select clear
[Repeated 2 time(s)]
> select #2.1/A:1003@C12
1 atom, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 1 residue, 1 model selected
> combine sel modelId #10
> hide #!2.1 models
> hide #!2 models
> hide #!10 models
> hide #10.1 models
> show #!10 models
> close #10
> select add #2.1
5990 atoms, 6173 bonds, 1 pseudobond, 734 residues, 2 models selected
> select add #2
11739 atoms, 12109 bonds, 2 pseudobonds, 1430 residues, 6 models selected
> select subtract #2
Nothing selected
> show #!2.1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 1 residue, 1 model selected
> combine sel modelId #3
> hide #!2 models
> hide #!2.1 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> hide #!3 models
> hide #3.1 models
> show #!3 models
> close #3
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> ui tool show "Model Panel"
[Repeated 1 time(s)]
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 1 residue, 1 model selected
> combine selAtoms modelID #3
Expected a keyword
> combine selAtoms modelId #3
> hide #!2 models
> hide #!2.1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #3.1 models
> close #3
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> info selection
atom id #2.1/A:1003@C3 idatm_type C3
atom id #2.1/A:1003@C2 idatm_type C3
atom id #2.1/A:1003@C5 idatm_type C3
atom id #2.1/A:1003@C6 idatm_type C3
atom id #2.1/A:1003@C9 idatm_type C3
atom id #2.1/A:1003@C8 idatm_type C2
atom id #2.1/A:1003@C7 idatm_type C2
atom id #2.1/A:1003@C31 idatm_type C3
atom id #2.1/A:1003@C12 idatm_type C2
atom id #2.1/A:1003@C14 idatm_type C3
atom id #2.1/A:1003@C16 idatm_type C3
atom id #2.1/A:1003@C17 idatm_type C2
atom id #2.1/A:1003@C18 idatm_type C2
atom id #2.1/A:1003@C19 idatm_type C3
atom id #2.1/A:1003@C20 idatm_type C3
atom id #2.1/A:1003@C22 idatm_type C2
atom id #2.1/A:1003@C23 idatm_type C2
atom id #2.1/A:1003@C28 idatm_type C2
atom id #2.1/A:1003@C29 idatm_type C3
atom id #2.1/A:1003@C30 idatm_type C3
atom id #2.1/A:1003@C11 idatm_type C3
atom id #2.1/A:1003@O1' idatm_type O3
atom id #2.1/A:1003@P idatm_type Pac
atom id #2.1/A:1003@OP idatm_type O3
atom id #2.1/A:1003@OP2 idatm_type O3-
atom id #2.1/A:1003@OP3 idatm_type O3-
atom id #2.1/A:1003@C1 idatm_type C3
atom id #2.1/A:1003@C4 idatm_type C3
atom id #2.1/A:1003@C10 idatm_type C3
atom id #2.1/A:1003@C13 idatm_type C2
atom id #2.1/A:1003@C15 idatm_type C3
atom id #2.1/A:1003@C21 idatm_type C3
atom id #2.1/A:1003@C24 idatm_type C3
atom id #2.1/A:1003@C25 idatm_type C3
atom id #2.1/A:1003@C26 idatm_type C3
atom id #2.1/A:1003@C27 idatm_type C2
atom id #2.1/A:1003@C32 idatm_type C2
atom id #2.1/A:1003@C33 idatm_type C2
atom id #2.1/A:1003@C34 idatm_type C3
atom id #2.1/A:1003@C35 idatm_type C3
atom id #2.1/A:1003@C36 idatm_type C3
atom id #2.1/A:1003@C37 idatm_type C2
atom id #2.1/A:1003@C38 idatm_type C2
atom id #2.1/A:1003@C39 idatm_type C3
atom id #2.1/A:1003@C40 idatm_type C3
> combine atoms sel modelId #3
Expected a keyword
> combine #2.2/A:1003 modelID #3
Expected a keyword
> combine #2.1/A:1003 modelID #3
Expected a keyword
> combine #2.1/A:1003 modelId #3
> hide #!2 models
> hide #!2.1 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> hide #!3 models
> close #3
> show #!2.1 models
> info selection
atom id #2.1/A:1003@C3 idatm_type C3
atom id #2.1/A:1003@C2 idatm_type C3
atom id #2.1/A:1003@C5 idatm_type C3
atom id #2.1/A:1003@C6 idatm_type C3
atom id #2.1/A:1003@C9 idatm_type C3
atom id #2.1/A:1003@C8 idatm_type C2
atom id #2.1/A:1003@C7 idatm_type C2
atom id #2.1/A:1003@C31 idatm_type C3
atom id #2.1/A:1003@C12 idatm_type C2
atom id #2.1/A:1003@C14 idatm_type C3
atom id #2.1/A:1003@C16 idatm_type C3
atom id #2.1/A:1003@C17 idatm_type C2
atom id #2.1/A:1003@C18 idatm_type C2
atom id #2.1/A:1003@C19 idatm_type C3
atom id #2.1/A:1003@C20 idatm_type C3
atom id #2.1/A:1003@C22 idatm_type C2
atom id #2.1/A:1003@C23 idatm_type C2
atom id #2.1/A:1003@C28 idatm_type C2
atom id #2.1/A:1003@C29 idatm_type C3
atom id #2.1/A:1003@C30 idatm_type C3
atom id #2.1/A:1003@C11 idatm_type C3
atom id #2.1/A:1003@O1' idatm_type O3
atom id #2.1/A:1003@P idatm_type Pac
atom id #2.1/A:1003@OP idatm_type O3
atom id #2.1/A:1003@OP2 idatm_type O3-
atom id #2.1/A:1003@OP3 idatm_type O3-
atom id #2.1/A:1003@C1 idatm_type C3
atom id #2.1/A:1003@C4 idatm_type C3
atom id #2.1/A:1003@C10 idatm_type C3
atom id #2.1/A:1003@C13 idatm_type C2
atom id #2.1/A:1003@C15 idatm_type C3
atom id #2.1/A:1003@C21 idatm_type C3
atom id #2.1/A:1003@C24 idatm_type C3
atom id #2.1/A:1003@C25 idatm_type C3
atom id #2.1/A:1003@C26 idatm_type C3
atom id #2.1/A:1003@C27 idatm_type C2
atom id #2.1/A:1003@C32 idatm_type C2
atom id #2.1/A:1003@C33 idatm_type C2
atom id #2.1/A:1003@C34 idatm_type C3
atom id #2.1/A:1003@C35 idatm_type C3
atom id #2.1/A:1003@C36 idatm_type C3
atom id #2.1/A:1003@C37 idatm_type C2
atom id #2.1/A:1003@C38 idatm_type C2
atom id #2.1/A:1003@C39 idatm_type C3
atom id #2.1/A:1003@C40 idatm_type C3
> ui tool show "Model Panel"
> save "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/session.cxs"
——— End of log from Mon Jul 13 16:06:09 2026 ———
> view name session-start
opened ChimeraX session
> info selection
atom id #2.1/A:1003@C3 idatm_type C3
atom id #2.1/A:1003@C2 idatm_type C3
atom id #2.1/A:1003@C5 idatm_type C3
atom id #2.1/A:1003@C6 idatm_type C3
atom id #2.1/A:1003@C9 idatm_type C3
atom id #2.1/A:1003@C8 idatm_type C2
atom id #2.1/A:1003@C7 idatm_type C2
atom id #2.1/A:1003@C31 idatm_type C3
atom id #2.1/A:1003@C12 idatm_type C2
atom id #2.1/A:1003@C14 idatm_type C3
atom id #2.1/A:1003@C16 idatm_type C3
atom id #2.1/A:1003@C17 idatm_type C2
atom id #2.1/A:1003@C18 idatm_type C2
atom id #2.1/A:1003@C19 idatm_type C3
atom id #2.1/A:1003@C20 idatm_type C3
atom id #2.1/A:1003@C22 idatm_type C2
atom id #2.1/A:1003@C23 idatm_type C2
atom id #2.1/A:1003@C28 idatm_type C2
atom id #2.1/A:1003@C29 idatm_type C3
atom id #2.1/A:1003@C30 idatm_type C3
atom id #2.1/A:1003@C11 idatm_type C3
atom id #2.1/A:1003@O1' idatm_type O3
atom id #2.1/A:1003@P idatm_type Pac
atom id #2.1/A:1003@OP idatm_type O3
atom id #2.1/A:1003@OP2 idatm_type O3-
atom id #2.1/A:1003@OP3 idatm_type O3-
atom id #2.1/A:1003@C1 idatm_type C3
atom id #2.1/A:1003@C4 idatm_type C3
atom id #2.1/A:1003@C10 idatm_type C3
atom id #2.1/A:1003@C13 idatm_type C2
atom id #2.1/A:1003@C15 idatm_type C3
atom id #2.1/A:1003@C21 idatm_type C3
atom id #2.1/A:1003@C24 idatm_type C3
atom id #2.1/A:1003@C25 idatm_type C3
atom id #2.1/A:1003@C26 idatm_type C3
atom id #2.1/A:1003@C27 idatm_type C2
atom id #2.1/A:1003@C32 idatm_type C2
atom id #2.1/A:1003@C33 idatm_type C2
atom id #2.1/A:1003@C34 idatm_type C3
atom id #2.1/A:1003@C35 idatm_type C3
atom id #2.1/A:1003@C36 idatm_type C3
atom id #2.1/A:1003@C37 idatm_type C2
atom id #2.1/A:1003@C38 idatm_type C2
atom id #2.1/A:1003@C39 idatm_type C3
atom id #2.1/A:1003@C40 idatm_type C3
> combine sel modelId #3
> hide #!2.1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> split sel
Did not split 6P25.pdb A, has only one piece
> ui tool show "Model Panel"
[Repeated 1 time(s)]
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 1 residue, 1 model selected
> cd T:\Donnees_pro\\_DATA_ANALYSIS\Protein_Structural_Models\MtPMT Pretomanid
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd "T:\Donnees_pro\\_DATA_ANALYSIS\Protein_Structural_Models\MtPMT
> Pretomanid"
Current working directory is:
T:\Donnees_pro\\_DATA_ANALYSIS\Protein_Structural_Models\MtPMT Pretomanid
> save dol_p.pdb atoms sel
Expected a models specifier or a keyword
> save dol_p.pdb selectOnly true
Expected a models specifier or a keyword
> info selection
atom id #3/A:1003@C3 idatm_type C3
atom id #3/A:1003@C2 idatm_type C3
atom id #3/A:1003@C5 idatm_type C3
atom id #3/A:1003@C6 idatm_type C3
atom id #3/A:1003@C9 idatm_type C3
atom id #3/A:1003@C8 idatm_type C2
atom id #3/A:1003@C7 idatm_type C2
atom id #3/A:1003@C31 idatm_type C3
atom id #3/A:1003@C12 idatm_type C2
atom id #3/A:1003@C14 idatm_type C3
atom id #3/A:1003@C16 idatm_type C3
atom id #3/A:1003@C17 idatm_type C2
atom id #3/A:1003@C18 idatm_type C2
atom id #3/A:1003@C19 idatm_type C3
atom id #3/A:1003@C20 idatm_type C3
atom id #3/A:1003@C22 idatm_type C2
atom id #3/A:1003@C23 idatm_type C2
atom id #3/A:1003@C28 idatm_type C2
atom id #3/A:1003@C29 idatm_type C3
atom id #3/A:1003@C30 idatm_type C3
atom id #3/A:1003@C11 idatm_type C3
atom id #3/A:1003@O1' idatm_type O3
atom id #3/A:1003@P idatm_type Pac
atom id #3/A:1003@OP idatm_type O3
atom id #3/A:1003@OP2 idatm_type O3-
atom id #3/A:1003@OP3 idatm_type O3-
atom id #3/A:1003@C1 idatm_type C3
atom id #3/A:1003@C4 idatm_type C3
atom id #3/A:1003@C10 idatm_type C3
atom id #3/A:1003@C13 idatm_type C2
atom id #3/A:1003@C15 idatm_type C3
atom id #3/A:1003@C21 idatm_type C3
atom id #3/A:1003@C24 idatm_type C3
atom id #3/A:1003@C25 idatm_type C3
atom id #3/A:1003@C26 idatm_type C3
atom id #3/A:1003@C27 idatm_type C2
atom id #3/A:1003@C32 idatm_type C2
atom id #3/A:1003@C33 idatm_type C2
atom id #3/A:1003@C34 idatm_type C3
atom id #3/A:1003@C35 idatm_type C3
atom id #3/A:1003@C36 idatm_type C3
atom id #3/A:1003@C37 idatm_type C2
atom id #3/A:1003@C38 idatm_type C2
atom id #3/A:1003@C39 idatm_type C3
atom id #3/A:1003@C40 idatm_type C3
> save test.pdb selectedOnly
Missing "selectedOnly" keyword's argument
> save test.pdb selectedOnly true
> open test.^pdb
Unrecognized file suffix '.^pdb'
> open test.pdb
> hide #!3 models
> hide #3.1 models
> hide #4 models
> show #!2 models
> show #!2.1 models
> hide #!2 models
> show #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 1 residue, 1 model selected
> hide #!2.1 models
> hide #!2 models
> show #4 models
> close #4
> close #3
> open dol_p.pdb
Summary of feedback from opening dol_p.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 40 PHE A 59 1 20
Start residue of secondary structure not found: HELIX 2 2 PHE A 73 LYS A 76 1
4
Start residue of secondary structure not found: HELIX 3 3 HIS A 77 ASN A 87 1
11
Start residue of secondary structure not found: HELIX 4 4 VAL A 105 PHE A 117
1 13
Start residue of secondary structure not found: HELIX 5 5 GLY A 121 SER A 147
1 27
24 messages similar to the above omitted
> select add #3
90 atoms, 88 bonds, 2 residues, 2 models selected
> select add #2.1
6035 atoms, 6217 bonds, 1 pseudobond, 735 residues, 3 models selected
> select add #2.2
11758 atoms, 12126 bonds, 2 pseudobonds, 1428 residues, 5 models selected
> select add #2.3
11784 atoms, 12153 bonds, 2 pseudobonds, 1431 residues, 6 models selected
> combine sel modelId #3
Remapping chain ID 'A' in dol_p.pdb #3 to 'C'
Computing secondary structure
Tried to add model combination #3 with the same id as another model dol_p.pdb
#3
> combine sel modelId #4
Remapping chain ID 'A' in dol_p.pdb #3 to 'C'
> hide #3 models
> close #4
> show #3 models
> show #!1 models
> show #!2.1 models
> hide #3 models
> select add #1
15668 atoms, 16164 bonds, 2 pseudobonds, 1926 residues, 7 models selected
> select add #2
15668 atoms, 16164 bonds, 2 pseudobonds, 1926 residues, 8 models selected
> select subtract #2
3929 atoms, 4055 bonds, 496 residues, 2 models selected
> select subtract #3
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> style sel stick
Changed 3884 atom styles
> show sel atoms
> select subtract #1
Nothing selected
Drag select of 2 atoms, 1 bonds
> select add #1
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> select subtract #1
Nothing selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:240@CZ3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> combine sel modelId #4
> hide #!1 models
> hide #!2 models
> hide #!2.1 models
> close #4
> show #!1 models
> show #!2.1 models
> ui mousemode right select
> select clear
> select #1/A:339@CE1
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:247@N idatm_type Npl
atom id #1/A:247@CA idatm_type C3
atom id #1/A:247@C idatm_type C2
atom id #1/A:247@CB idatm_type C3
atom id #1/A:247@O idatm_type O2
atom id #1/A:247@CG idatm_type C3
atom id #1/A:247@CD1 idatm_type C3
atom id #1/A:247@CD2 idatm_type C3
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:339@N idatm_type Npl
atom id #1/A:339@CA idatm_type C3
atom id #1/A:339@C idatm_type C2
atom id #1/A:339@CB idatm_type C3
atom id #1/A:339@O idatm_type O2
atom id #1/A:339@CG idatm_type Car
atom id #1/A:339@CD1 idatm_type Car
atom id #1/A:339@CD2 idatm_type Car
atom id #1/A:339@CE1 idatm_type Car
atom id #1/A:339@CE2 idatm_type Car
atom id #1/A:339@CZ idatm_type Car
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:244@N idatm_type Npl
atom id #1/A:244@CA idatm_type C3
atom id #1/A:244@C idatm_type C2
atom id #1/A:244@CB idatm_type C3
atom id #1/A:244@O idatm_type O2
atom id #1/A:244@CG idatm_type Car
atom id #1/A:244@CD1 idatm_type Car
atom id #1/A:244@CD2 idatm_type Car
atom id #1/A:244@CE1 idatm_type Car
atom id #1/A:244@CE2 idatm_type Car
atom id #1/A:244@OH idatm_type O3
atom id #1/A:244@CZ idatm_type Car
> select #2.1/A:655@CG
1 atom, 1 residue, 1 model selected
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:447@N idatm_type Npl
atom id #1/A:447@CA idatm_type C3
atom id #1/A:447@C idatm_type C2
atom id #1/A:447@CB idatm_type C3
atom id #1/A:447@O idatm_type O2
atom id #1/A:447@CG idatm_type Car
atom id #1/A:447@CD1 idatm_type Car
atom id #1/A:447@CD2 idatm_type Car
atom id #1/A:447@CE1 idatm_type Car
atom id #1/A:447@CE2 idatm_type Car
atom id #1/A:447@OH idatm_type O3
atom id #1/A:447@CZ idatm_type Car
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:446@N idatm_type Npl
atom id #1/A:446@CA idatm_type C3
atom id #1/A:446@C idatm_type C2
atom id #1/A:446@CB idatm_type C3
atom id #1/A:446@O idatm_type O2
atom id #1/A:446@CG idatm_type Car
atom id #1/A:446@CD1 idatm_type Car
atom id #1/A:446@CD2 idatm_type Car
atom id #1/A:446@CE1 idatm_type Car
atom id #1/A:446@CE2 idatm_type Car
atom id #1/A:446@CZ idatm_type Car
> ui mousemode right rotate
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:102@N idatm_type Npl
atom id #1/A:102@CA idatm_type C3
atom id #1/A:102@C idatm_type C2
atom id #1/A:102@CB idatm_type C3
atom id #1/A:102@O idatm_type O2
atom id #1/A:102@CG idatm_type Car
atom id #1/A:102@CD2 idatm_type Car
atom id #1/A:102@ND1 idatm_type Npl
atom id #1/A:102@CE1 idatm_type Car
atom id #1/A:102@NE2 idatm_type Npl
Drag select of 1 atoms, 2 residues
> ui mousemode right zoom
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:239@N idatm_type Npl
atom id #1/A:239@CA idatm_type C3
atom id #1/A:239@C idatm_type C2
atom id #1/A:239@CB idatm_type C3
atom id #1/A:239@O idatm_type O2
atom id #1/A:239@CG idatm_type C3
atom id #1/A:239@CD idatm_type C3
atom id #1/A:239@CE idatm_type C3
atom id #1/A:239@NZ idatm_type N3+
Drag select of 1 atoms, 2 residues
> select add #1
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> hide sel atoms
> select subtract #1
Nothing selected
> select add #1
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> show sel atoms
> select subtract #1
Nothing selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:441@N idatm_type Npl
atom id #1/A:441@CA idatm_type C3
atom id #1/A:441@C idatm_type C2
atom id #1/A:441@CB idatm_type C3
atom id #1/A:441@O idatm_type O2
atom id #1/A:441@CG idatm_type C3
atom id #1/A:441@CD idatm_type C3
atom id #1/A:441@NE idatm_type Ng+
atom id #1/A:441@NH1 idatm_type Ng+
atom id #1/A:441@NH2 idatm_type Ng+
atom id #1/A:441@CZ idatm_type C2
> select add #1
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> hide sel atoms
> select subtract #1
Nothing selected
> select #1/A:441
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:102,239,244,247,339,441,446,447
84 atoms, 82 bonds, 8 residues, 1 model selected
> style sel stick
Changed 84 atom styles
> show sel atoms
> ui mousemode right translate
> ui mousemode right rotate
> select add #1
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> show sel atoms
> select subtract #1
Nothing selected
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> info selection
atom id #1/A:240@N idatm_type Npl
atom id #1/A:240@CA idatm_type C3
atom id #1/A:240@C idatm_type C2
atom id #1/A:240@CB idatm_type C3
atom id #1/A:240@O idatm_type O2
atom id #1/A:240@CG idatm_type Car
atom id #1/A:240@CD1 idatm_type Car
atom id #1/A:240@CD2 idatm_type Car
atom id #1/A:240@CE2 idatm_type Car
atom id #1/A:240@CE3 idatm_type Car
atom id #1/A:240@NE1 idatm_type Npl
atom id #1/A:240@CH2 idatm_type Car
atom id #1/A:240@CZ2 idatm_type Car
atom id #1/A:240@CZ3 idatm_type Car
> select add #1
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
3884 atoms, 4011 bonds, 495 residues, 1 model selected
> hide sel atoms
> select #1/A:102,239,240,244,247,339,441,446,447
98 atoms, 98 bonds, 9 residues, 1 model selected
> show sel atoms
> hide #!2 models
> show #3 models
> show #2.3 models
> hide #!2.1 models
> show #!2.2 models
> save sesscion_2.csx
No known data format for file suffix '.csx'
> save sesscion_2.cxs
> hide #2.3 models
> hide #!2 models
> hide #!2.2 models
> show #2.3 models
> close session
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/test.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/test.cif
---
warnings | Unable to fetch template for 'LIG_B': will connect using distance criteria
Unknown polymer entity '1' on line 74
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
notes | Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
Fetching CCD CPL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CPL/CPL.cif
Fetching CCD NNM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/NNM/NNM.cif
Chain information for test.cif
---
Chain | Description
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
1.4/D | No description available
Computing secondary structure
[Repeated 2 time(s)]Drag select of 88 atoms, 90 bonds, 186 residues
> select add #1
15846 atoms, 16348 bonds, 2 pseudobonds, 1953 residues, 7 models selected
> select subtract #1
Nothing selected
> ui mousemode right translate
> ui mousemode right zoom
> hide #1.3.1 models
> hide #1.4.1 models
> close #1.3.1
> close #1.4.1
> hide #!1 models
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> show #!1 models
> show #1.4 models
> hide #1.4 models
> show #1.3 models
> hide #1.3 models
> show #1.2 models
> hide #1.2 models
> show #1.1 models
> select add #1
15846 atoms, 16348 bonds, 1953 residues, 5 models selected
> close #1.3
> close session
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/dock_1.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/dock_1.cif
---
warnings | Unable to fetch template for 'LIG_B': will connect using distance criteria
Unknown polymer entity '1' on line 74
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for dock_1.cif
---
Chain | Description
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
1.4/D 1.6/D | No description available
Computing secondary structure
[Repeated 2 time(s)]
> close session
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/dock_1.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/dock_1.cif
---
warnings | Unable to fetch template for 'LIG_B': will connect using distance criteria
Unknown polymer entity '1' on line 74
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for dock_1.cif
---
Chain | Description
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
1.4/D 1.6/D | No description available
Computing secondary structure
[Repeated 2 time(s)]
> hide #!1.3 models
> hide #!1.4 models
> hide #1.1 models
> hide #1.2 models
> show #!1.3 models
> close session
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/dock_1.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/dock_1.cif
---
warnings | Unable to fetch template for 'LIG_B': will connect using distance criteria
Unknown polymer entity '1' on line 74
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for dock_1.cif
---
Chain | Description
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
1.4/D 1.6/D | No description available
Computing secondary structure
[Repeated 2 time(s)]
> close session
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/dock_1.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/dock_1.cif
---
warnings | Unable to fetch template for 'LIG_B': will connect using distance criteria
Unknown polymer entity '1' on line 74
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for dock_1.cif
---
Chain | Description
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
1.4/D 1.6/D | No description available
Computing secondary structure
[Repeated 2 time(s)]
> close session
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/dock_1.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/dock_1.cif
---
warnings | Unable to fetch template for 'LIG_B': will connect using distance criteria
Unknown polymer entity '1' on line 74
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for dock_1.cif
---
Chain | Description
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
1.4/D 1.6/D | No description available
Computing secondary structure
[Repeated 2 time(s)]
> select add #1.3.1
1 pseudobond, 1 model selected
> select add #1.4.1
2 pseudobonds, 2 models selected
> close
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/dock_1.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/dock_1.cif
---
warnings | Unable to fetch template for 'LIG_B': will connect using distance criteria
Unknown polymer entity '1' on line 74
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for dock_1.cif
---
Chain | Description
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
1.4/D 1.6/D | No description available
Computing secondary structure
[Repeated 2 time(s)]
> select add #1.3.1
1 pseudobond, 1 model selected
> close #1.3.1
> close #1.4.1
> hide #1.6 models
> hide #1.5 models
> hide #1.4 models
> hide #1.3 models
> hide #1.2 models
> split dock_1.cif group
Expected a structures specifier or a keyword
> split #1
Did not split dock_1.cif, has only one piece
[Repeated 2 time(s)]Split dock_1.cif (#1.4) into 2 models
Did not split dock_1.cif, has only one piece
[Repeated 1 time(s)] Chain information for dock_1.cif B #1.4.1
---
Chain | Description
B | No description available
Chain information for dock_1.cif D #1.4.2
---
Chain | Description
D | No description available
> hide #!1.4 models
> show #!1.4 models
> show #1.4.1 models
> show #1.4.2 models
> hide #1.4.2 models
> show #1.4.2 models
> split #2
> close session
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/dock_1.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/dock_1.cif
---
warnings | Unknown polymer entity '1' on line 26
Unable to fetch template for 'LIG_B': will connect using distance criteria
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for dock_1.cif
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.2/B | No description available
1.2/D | No description available
Computing secondary structure
[Repeated 1 time(s)]
> close session
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/dock_1.cif"
Summary of feedback from opening
T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
Pretomanid/dock_1.cif
---
warnings | Unknown polymer entity '1' on line 26
Unable to fetch template for 'Pa': will connect using distance criteria
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for dock_1.cif
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.3/B | No description available
1.3/D | No description available
Computing secondary structure
[Repeated 2 time(s)]
> close #1.2.1
> close #1.3.1
> split #1
Split dock_1.cif (#1.1) into 2 models
Split dock_1.cif (#1.2) into 2 models
Split dock_1.cif (#1.3) into 2 models
Chain information for dock_1.cif A #1.1.1
---
Chain | Description
A | No description available
Chain information for dock_1.cif A #1.2.1
---
Chain | Description
A | No description available
Chain information for dock_1.cif B #1.3.1
---
Chain | Description
B | No description available
Chain information for dock_1.cif D #1.3.2
---
Chain | Description
D | No description available
> hide #!1.2 models
> hide #1.2.1 models
> hide #1.2.2 models
> hide #!1.3 models
> hide #1.3.1 models
> hide #1.3.2 models
> hide #1.1.1 models
> rename #1.1.2 Pa
> rename #1.1.1 MtPMT
> rename #1.1 MtPMT
> hide #1.1.2 models
> hide #!1.1 models
> rename #1.2 6P25
> rename #1.2.1 6P25 A
Expected a keyword
> rename #1.2.1 6P25_A
> rename #1.2.2 6P25_C
> rename #1.3 6P25_BD
> rename #1.3 .1 6P25_B
Expected a keyword
> rename #1.3 .2 6P25_D
Expected a keyword
> rename #1.3.2 6P25_D
> rename #1.3.1 6P25_B
> rename #1.2 6P25_AC
> show #!1.1 models
> show #1.1.1 models
> show #1.1.2 models
> show #!1.2 models
> show #1.2.1 models
> show #1.2.2 models
> show #!1.3 models
> show #1.3.1 models
> show #1.3.2 models
> color #1.1 #0450b2ff models
> color #1.1 #0570b2ff models
> color #1.1 #0575b2ff models
> color #1.1 #0570b2ff models
> color #1.1.2 #b21648ff
> color #1.1.2 #b21baaff
> color #1.1.2 #b214afff
> color #1.3 #9bb249ff models
> color #1.3 #9ab249ff models
> ui mousemode right "translate selected models"
> sequence chain #1.1.1/A
Alignment identifier is 1.1.1/A
> sequence chain #1.2.1/A
Alignment identifier is 1.2.1/A
> sequence chain #1.3.1/B
Alignment identifier is 1.3.1/B
> sequence chain #1.3.2/D
Alignment identifier is 1.3.2/D
> select #1.2.1/A:749
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2.1/A:726-749
208 atoms, 213 bonds, 24 residues, 1 model selected
> select #1.2.1/A:725
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1.2.1/A:722-725
37 atoms, 38 bonds, 4 residues, 1 model selected
> hide #!1.1 models
> hide #!1.3 models
> select #1.2.1/A:748-749
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #1.2.1/A:626-749
1041 atoms, 1079 bonds, 124 residues, 1 model selected
> select
> #1.2.1/A:36-41,47-63,78-90,101-113,135-160,163-174,177-184,189-207,214-231,237-257,263-295,311-313,369-371,439-441,456-459,505-507,533-549,561-566,587-613,621-639,642-644,653-655,657-676,683-703,705-707,715-721,738-741
2635 atoms, 2688 bonds, 332 residues, 1 model selected
> select #1.2.1/A:15
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2.1/A:15-104
702 atoms, 722 bonds, 90 residues, 1 model selected
> select #1.2.1/A:105
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2.1/A:105-323
1729 atoms, 1780 bonds, 219 residues, 1 model selected
> select #1.2.1/A:179-214
297 atoms, 306 bonds, 36 residues, 1 model selected
> select #1.2.1/A:179-221
353 atoms, 363 bonds, 43 residues, 1 model selected
> select #1.2.1/A:237
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1.2.1/A:237-290
444 atoms, 460 bonds, 54 residues, 1 model selected
> select #1.2.1/A:341
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2.1/A:325-341
122 atoms, 122 bonds, 17 residues, 1 model selected
> ui mousemode right select
Drag select of 139 residues
Drag select of 157 residues
Drag select of 225 residues
> hide sel
> select
> #1.2.1/A:36-41,47-63,78-90,101-113,135-160,163-174,177-184,189-207,214-231,237-257,263-295,311-313,369-371,439-441,456-459,505-507,533-549,561-566,587-613,621-639,642-644,653-655,657-676,683-703,705-707,715-721,738-741
2635 atoms, 2688 bonds, 332 residues, 1 model selected
> show #!1.1 models
> show #!1.3 models
> select add #1
15400 atoms, 15896 bonds, 1912 residues, 10 models selected
> select subtract #1
Nothing selected
> save "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/session_3.cxs"
Drag select of 128 residues, 12 atoms, 13 bonds
> select add #1
15400 atoms, 15896 bonds, 1912 residues, 10 models selected
> select subtract #1
Nothing selected
Drag select of 3 residues
> save "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/session_3.cxs"
——— End of log from Tue Jul 14 18:49:58 2026 ———
> view name session-start
opened ChimeraX session
> close session
Select a database from the database table
> open 5mm1 fromDatabase pdb format mmcif
Summary of feedback from opening 5mm1 fetched from pdb
---
notes | Fetching compressed mmCIF 5mm1 from http://files.rcsb.org/download/5mm1.cif
Fetching CCD GDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif
Fetching CCD MJC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/MJC/MJC.cif
5mm1 title:
Dolichyl phosphate mannose synthase in complex with GDP and dolichyl phosphate
mannose [more info...]
Chain information for 5mm1 #1
---
Chain | Description | UniProt
A | Dolichol monophosphate mannose synthase | Q8U4M3_PYRFU 1-352
Non-standard residues in 5mm1 #1
---
GDP — guanosine-5'-diphosphate
MJC — dolichyl phosphate mannose
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> save "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/5mm1.cif" relModel #1
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/PolyprenolPMan_C40.sdf"
> hide #!1 models
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/DolPMan_C25.mol2"
Opened DolPMan_C25.mol2 containing 1 structure (41 atoms, 41 bonds)
> open "T:/Donnees_pro/_DATA_ANALYSIS/Protein_Structural_Models/MtPMT
> Pretomanid/DolPMan_C25.sdf"
> hide #3 models
> zone label false
Traceback (most recent call last):
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 683, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 594, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 237, in mouse_drag
self._scale_range(scale)
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 223, in _scale_range
self._show_zone(r, ribbon=ribbon, log_command = 'include distances')
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 64, in _show_zone
ratoms = residue.atoms
^^^^^^^^^^^^^
File "atomic_cpp/cymol.pyx", line 1046, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 1046, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 683, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 594, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 237, in mouse_drag
self._scale_range(scale)
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 223, in _scale_range
self._show_zone(r, ribbon=ribbon, log_command = 'include distances')
File "C:\Users\viljoen\AppData\Local\Programs\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 64, in _show_zone
ratoms = residue.atoms
^^^^^^^^^^^^^
File "atomic_cpp/cymol.pyx", line 1046, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 1046, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 32.0.101.6651
OpenGL renderer: Intel(R) Graphics
OpenGL vendor: Intel
Python: 3.11.9
Locale: fr_FR.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows
Manufacturer: HP
Model: HP EliteBook 640 14 inch G11 Notebook PC
OS: Microsoft Windows 11 Entreprise LTSC (Build 26100.8655)
Memory: 16,605,532,160
MaxProcessMemory: 137,438,953,344
CPU: 14 Intel(R) Core(TM) Ultra 5 125U
OSLanguage: fr-FR
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2026.5.20
cftime: 1.6.5
charset-normalizer: 3.4.7
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: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 2.4
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
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: 1.2.2
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: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
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: 2.7.13
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: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
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: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
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: 3.18
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
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
kiwisolver: 1.5.0
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: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
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: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
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
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
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: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2026.2
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
WMI: 1.5.1
yarl: 1.24.2
Change History (1)
comment:1 by , 3 hours ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'zone' command uses dead residue |
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