'zone' command uses dead residue

[chimerax-bug-report@…]

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

[Tom Goddard]

Fixed.

The zone mouse mode gave an error when dragging to increase the zone radius for showing labels if the chosen zone residue has been deleted. Made code check for deleted residue.