Opened 2 hours ago

Closed 35 minutes ago

#20356 closed defect (fixed)

Table deleted during timer interval

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: UI Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs

Log from Wed May 20 01:32:16 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs

Log from Wed May 6 14:49:12 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs

Log from Mon May 4 20:49:57 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/bxest1.pdbqt

Chain information for bxest1.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
Opened bxest1.pdbqt containing 1 structures (2426 atoms, 2476 bonds)  

> close

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst2/bxest2.pdbqt

Chain information for bxest2.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
Opened bxest2.pdbqt containing 1 structures (1679 atoms, 1701 bonds)  

> show surfaces

> hide surfaces

> close #1

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst3/bxest3.pdbqt

Chain information for bxest3.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
Opened bxest3.pdbqt containing 1 structures (2592 atoms, 2644 bonds)  

> close

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst4/bxest4.pdbqt

Chain information for bxest4.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
Opened bxest4.pdbqt containing 1 structures (1786 atoms, 1821 bonds)  

> close #1

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/bxest1.pdbqt

Chain information for bxest1.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
Opened bxest1.pdbqt containing 1 structures (2426 atoms, 2476 bonds)  

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> lighting soft

> color #1 grey

> show surfaces

> color #1 #919191ff

> color #1 grey

> hide surfaces

> select :222,192,93,94,117,24

57 atoms, 55 bonds, 6 residues, 1 model selected  

> show sel atoms

> color select byatom

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byatom

> addh

Summary of feedback from adding hydrogens to bxest1.pdb #1  
---  
notes | No usable SEQRES records for bxest1.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ILE 248  
Chain-final residues that are not actual C termini:  
233 hydrogen bonds  
1533 hydrogens added  
  

> color byatom

> ui mousemode right select

> select clear

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed1.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.751 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -22.139  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.872  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -3.267  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -3.267  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_rigid_seed1.pdbqt containing 20 structures (1180 atoms,
1240 bonds)  

> hbonds #2.1-20 restrict #!1 & (main|ligand) twoColors true reveal true

22 hydrogen bonds found  
4 strict hydrogen bonds found  

> close #3

> close #2

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed2.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed2.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -8.274 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -22.142  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -16.013  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -6.129  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -6.129  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_rigid_seed2.pdbqt containing 20 structures (1180 atoms,
1240 bonds)  

> close #2

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.668 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -22.211  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.711  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -3.500  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -3.500  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_rigid_seed3.pdbqt containing 20 structures (1180 atoms,
1240 bonds)  

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.668 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -22.211  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.711  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -3.500  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -3.500  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_rigid_seed3.pdbqt containing 20 structures (1180 atoms,
1240 bonds)  

> close #3

> save
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/Bxest1/Seed3_11.pdb
> models #2.11

Computing secondary structure  

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/Seed3_11.pdb

> hide #!2 models

> show #!2 models

> close #3

> close #2

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed4.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed4.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.690 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -21.611  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.754  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -2.857  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -2.857  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_rigid_seed4.pdbqt containing 20 structures (1180 atoms,
1240 bonds)  

> hide #!2 target m

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed5.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed5.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.811 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -21.886  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.988  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -2.898  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -2.898  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_rigid_seed5.pdbqt containing 20 structures (1180 atoms,
1240 bonds)  

> close #2

> save
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/Bxest1/Seed5_2.pdb
> models #3.2

Computing secondary structure  

> save
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/Bxest1/Seed5_16.pdb
> models #3.16

Computing secondary structure  

> close #3

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/Seed3_11.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/Seed5_2.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/Seed5_16.pdb

> hide #2 models

> hide #3 models

> hide #4 models

> show #!1 surfaces

> select :93

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color select redd

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color select red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel red

> select clear

> select :94,24

39 atoms, 38 bonds, 2 residues, 1 model selected  

> color sel orange

> select clear

> show #2 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #3 models

> hide #3 models

> hide #2 models

> show #2 models

> show #4 models

> hide #4 models

> show #4 models

> hide #2,4#!1 surfaces

> hide #4 models

> close #3-4

> select add #2

59 atoms, 62 bonds, 1 residue, 1 model selected  

> select up

4018 atoms, 4071 bonds, 249 residues, 2 models selected  

> select down

59 atoms, 62 bonds, 1 residue, 2 models selected  

> color byatom

> color #2 #a1a1a1ff

> color #2 #00f900ff

> color byatom

> color #2 #00fdffff

> select clear

> show surfaces

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style stick

Changed 4018 atom styles  

> style sphere

Changed 4018 atom styles  

> style ball

Changed 4018 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> undo

> hide surfaces

> show surfaces

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> select add #2

59 atoms, 62 bonds, 1 residue, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 59 atom styles  

> select clear

> select add #1

3959 atoms, 4009 bonds, 248 residues, 1 model selected  

> color byatom

> select subtract #1

1 model selected  

> select add #1

3959 atoms, 4009 bonds, 248 residues, 1 model selected  

> select subtract #1

1 model selected  

> select add #1

3959 atoms, 4009 bonds, 248 residues, 1 model selected  

> select add #2

4018 atoms, 4071 bonds, 249 residues, 3 models selected  

> select subtract #2

3959 atoms, 4009 bonds, 248 residues, 2 models selected  

> select add #2

4018 atoms, 4071 bonds, 249 residues, 3 models selected  

> select subtract #1

59 atoms, 62 bonds, 1 residue, 2 models selected  

> select subtract #2

Nothing selected  

> color byatom

> hide surfaces

> show surfaces

> color #1 #919191ff

> color #1 grey

> select :93

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel red

> select :94,24

39 atoms, 38 bonds, 2 residues, 1 model selected  

> color sel orange

> select clear

> color #2 #a1a1a1ff

> color #2 #00fdffff

> color #2 #00f900ff

> color #2 #ff2600ff

> color #2 #942192ff

> color #2 white

> color #2 #0433ffff

> color #2 #00fdffff

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> graphics silhouettes false

> lighting flat

[Repeated 2 time(s)]

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> select :194

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select :194,129

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

> transparency sel 20

> transparency sel 90

> transparency sel 70

> show sel atoms

> style sel stick

Changed 24 atom styles  

> transparency sel 70

[Repeated 1 time(s)]

> select clear

> select :194,129

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

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel atoms

> select #1/A:231@OE1

1 atom, 1 residue, 1 model selected  

> select clear

> style stick

Changed 4018 atom styles  

> hide atoms

> select add #2

59 atoms, 62 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> ui mousemode right translate

> ui mousemode right "translate selected models"

> ui mousemode right translate

> select :194,129,121

46 atoms, 43 bonds, 3 residues, 1 model selected  

> transparency sel 70

> select :194,129,121,125

62 atoms, 58 bonds, 4 residues, 1 model selected  

> select :194,129,121,125,193

79 atoms, 76 bonds, 5 residues, 1 model selected  

> transparency sel 70

> transparency sel 60

> ui mousemode right select

> select clear

> select :194,129,121,125,193

79 atoms, 76 bonds, 5 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select :194,129,121,125,193,194

79 atoms, 76 bonds, 5 residues, 1 model selected  

> transparency sel 60

> select :194,129,121,125,193,194,222

96 atoms, 93 bonds, 6 residues, 1 model selected  

> transparency sel 60

> transparency sel 0

> select :194,129,121,194,222

63 atoms, 60 bonds, 4 residues, 1 model selected  

> transparency sel 60

> transparency sel 0

> select :194,129,121,194

46 atoms, 43 bonds, 3 residues, 1 model selected  

> transparency sel 60

> ui mousemode right select

> select clear

> undo

> select ~sel & ##selected

3913 atoms, 3966 bonds, 245 residues, 1 model selected  

> select down

3913 atoms, 3966 bonds, 245 residues, 2 models selected  

> select ~sel & ##selected

46 atoms, 43 bonds, 3 residues, 1 model selected  

> transparency sel 0

> select :194,129194

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select :194,129,194

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

> transparency sel 60

> select :194,129,121,194

46 atoms, 43 bonds, 3 residues, 1 model selected  

> transparency sel 60

> select clear

> ui mousemode right select

> select clear

> select :194,129,121,194

46 atoms, 43 bonds, 3 residues, 1 model selected  

> transparency sel 0

> select clear

> select #1/A:129@CA

1 atom, 1 residue, 1 model selected  

> select #1/A:129@HA3

1 atom, 1 residue, 1 model selected  

> select #1/A:129@CA

1 atom, 1 residue, 1 model selected  

> select add #1/A:129@HA3

2 atoms, 1 residue, 2 models selected  

> select add #1/A:24@CD1

3 atoms, 2 residues, 2 models selected  

> select subtract #1/A:24@CD1

2 atoms, 1 residue, 2 models selected  

> select add #1/A:24@CD1

3 atoms, 2 residues, 2 models selected  

> select subtract #1/A:24@CD1

2 atoms, 1 residue, 2 models selected  

> select add #1/A:194@HE1

3 atoms, 2 residues, 2 models selected  

> select add #1/A:194@CE

4 atoms, 2 residues, 2 models selected  

> select add #1/A:194@SD

5 atoms, 2 residues, 2 models selected  

> select add #1/A:194@CG

6 atoms, 2 residues, 2 models selected  

> select subtract #1/A:194@CG

5 atoms, 2 residues, 2 models selected  

> transparency sel 60

> select add #1/A:129@HA2

6 atoms, 2 residues, 2 models selected  

> select add #1/A:194@HE2

7 atoms, 2 residues, 2 models selected  

> select add #1/A:194@HE3

8 atoms, 2 residues, 2 models selected  

> select add #1/A:23@CA

9 atoms, 3 residues, 2 models selected  

> select subtract #1/A:23@CA

8 atoms, 2 residues, 2 models selected  

> select subtract #1/A:194@HE3

7 atoms, 2 residues, 2 models selected  

> select subtract #1/A:194@CE

6 atoms, 2 residues, 2 models selected  

> select add #1/A:194@CE

7 atoms, 2 residues, 2 models selected  

> transparency sel 60

> select :194,129,121,194

46 atoms, 43 bonds, 3 residues, 1 model selected  

> transparency sel 60

> transparency sel 50

> select clear

> save
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs

> save
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs
> includeMaps true

——— End of log from Mon May 4 20:49:57 2026 ———

> view name session-start

opened ChimeraX session  

> close #2

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed2-4.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed3-11.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed3-15.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed4-7.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed4-13.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-1.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-2.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-5.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-7.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-17.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed6-5.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed6-10.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed6-13.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed6-15.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed7-1.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-2.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-3.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-5.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-7.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-15.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-16.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed9-15.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed9-16.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed10-1.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed10-3.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed10-11.pdb

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed10-18.pdb

> hide surfaces

> show surfaces

> hide #2 models

> hide #!1 models

> hide #3 models

> show #!1 models

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> hide #13 models

> hide #12 models

> hide #14 models

> hide #15 models

> hide #16 models

> hide #17 models

> hide #18 models

> hide #20 models

> hide #19 models

> hide #21 models

> hide #22 models

> hide #23 models

> hide #24 models

> hide #25 models

> hide #26 models

> hide #27 models

> hide #28 models

> show #28 models

> show #27 models

> hide #28 models

> hide #27 models

> show #26 models

> hide #26 models

> show #25 models

> hide #25 models

> show #24 models

> hide #24 models

> show #23 models

> hide #23 models

> show #23 models

> hide #23 models

> show #24 models

> show #22 models

> hide #22 models

> show #22 models

> show #21 models

> hide #21 models

> show #21 models

> hide #21 models

> show #20 models

> hide #20 models

> show #19 models

> hide #19 models

> show #18 models

> hide #18 models

> show #17 models

> hide #17 models

> show #16 models

> hide #16 models

> show #15 models

> show #14 models

> hide #14 models

> show #14 models

> hide #14 models

> show #13 models

> hide #13 models

> show #12 models

> hide #12 models

> show #11 models

> hide #11 models

> show #10 models

> hide #10 models

> show #9 models

> hide #9 models

> show #8 models

> hide #8 models

> show #7 models

> hide #7 models

> show #6 models

> hide #6 models

> show #5 models

> hide #5 models

> show #4 models

> hide #4 models

> show #3 models

> show #2 models

> hide #2 models

> hide #3,15,22,24#!1 surfaces

> close #4-28

> close #2

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for bxest1.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: bxest1.pdb #1/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: bxest1.pdb #1/A ILE 248  
Chain-final residues that are not actual C termini:  
233 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
38 hydrogens added  
  

> hbonds reveal true

233 hydrogen bonds found  

> show surfaces

> close #3

> close #2

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.668 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -22.211  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.711  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -3.500  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -3.500  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_rigid_seed3.pdbqt containing 20 structures (1180 atoms,
1240 bonds)  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for bxest1.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: bxest1.pdb #1/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: bxest1.pdb #1/A ILE 248  
Chain-final residues that are not actual C termini:  
233 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
760 hydrogens added  
  

> hbonds #2.1-20 restrict #!1 & (main|ligand) twoColors true reveal true

19 hydrogen bonds found  
8 strict hydrogen bonds found  

> hide #2.11#!1 surfaces

> show #2.11#!1 atoms

[Repeated 1 time(s)]

> hbonds #2.11#!1 reveal true

252 hydrogen bonds found  

> hide #2.11#!1 atoms

> show #2.11#!1 atoms

> show #2.11#!1 surfaces

> hide #2.3#!1 surfaces

> select add #1

3959 atoms, 4009 bonds, 233 pseudobonds, 248 residues, 2 models selected  

> hide sel atoms

> select add #2

5899 atoms, 6009 bonds, 233 pseudobonds, 268 residues, 24 models selected  

> select subtract #1

1940 atoms, 2000 bonds, 20 residues, 22 models selected  

> select subtract #2

Nothing selected  

> hbonds #2.1-20 restrict #!1 & (main|ligand) twoColors true reveal true

19 hydrogen bonds found  
8 strict hydrogen bonds found  

> ui mousemode right select

> select #2.11/?:1@@serial_number=19

1 atom, 1 residue, 1 model selected  

> select add #1/A:93@HG

2 atoms, 1 bond, 2 residues, 2 models selected  

> select subtract #1/A:93@HG

1 atom, 1 residue, 2 models selected  

> select #1/A:93@HG

1 atom, 1 residue, 1 model selected  

> select add #2.11/?:1@@serial_number=19

2 atoms, 2 residues, 3 models selected  

> bond sel

Created 0 bonds  

> bond sel

Created 0 bonds  

> bond sel

Created 0 bonds  

> select #2.11/?:1@@serial_number=20

1 atom, 1 residue, 1 model selected  

> select #1/A:93

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:120

19 atoms, 18 bonds, 1 residue, 1 model selected  

> show sel surfaces

> select clear

> show #2.11#!1 surfaces

> save
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs

> hbonds

252 hydrogen bonds found  

> hide #2.11#!1 surfaces

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for bxest1.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: bxest1.pdb #1/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: bxest1.pdb #1/A ILE 248  
Chain-final residues that are not actual C termini:  
233 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
0 hydrogens added  
  

> show #2.11#!1 surfaces

> ui tool show ViewDock

> ui tool show H-Bonds

> hbonds reveal true

252 hydrogen bonds found  

> hide #2.11#!1 atoms

> show #2.11#!1 atoms

> close #3

> hide #2.11#!1 surfaces

> hide #2.11#!1 atoms

> select add #2

1940 atoms, 2000 bonds, 20 residues, 21 models selected  

> show sel & #2.11 atoms

> select clear

> select :79,10

33 atoms, 31 bonds, 2 residues, 1 model selected  

> select #1/A:93

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #1/A:94

30 atoms, 28 bonds, 2 residues, 2 models selected  

> select add #1/A:24

50 atoms, 48 bonds, 3 residues, 2 models selected  

> show sel atoms

> select clear

> show #2.11#!1 surfaces

> save
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs

——— End of log from Wed May 6 14:49:12 2026 ———

> view name session-start

opened ChimeraX session  

> close #2

> hide surfaces

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed1.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.751 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -22.139  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.872  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -3.267  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -3.267  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_seed1.pdbqt containing 20 structures (1180 atoms, 1240
bonds)  

> close #2

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed2.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed2.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -8.274 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -22.142  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -16.013  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -6.129  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -6.129  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_seed2.pdbqt containing 20 structures (1180 atoms, 1240
bonds)  

> close #2

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed3.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed3.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.668 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -22.211  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.711  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -3.500  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -3.500  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_seed3.pdbqt containing 20 structures (1180 atoms, 1240
bonds)  

> close #2

> open
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed4.pdbqt

Summary of feedback from opening
/Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed4.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.690 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -21.611  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -18.754  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -2.857  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -2.857  
  
955 messages similar to the above omitted  
  
Opened docked_MHET4_seed4.pdbqt containing 20 structures (1180 atoms, 1240
bonds)  

> show #2.13#!1 surfaces

> save
> /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs

——— End of log from Wed May 20 01:32:16 2026 ———

> view name session-start

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 655, in <lambda>  
QTimer.singleShot(10, lambda s=self, i=scroll_to: s.scrollTo(i))  
^^^^^^^^^^^^^  
RuntimeError: wrapped C/C++ object of type ItemTable has been deleted  
  
RuntimeError: wrapped C/C++ object of type ItemTable has been deleted  
  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 655, in  
QTimer.singleShot(10, lambda s=self, i=scroll_to: s.scrollTo(i))  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,15
      Model Number: MQKP3PP/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 13822.61.10

Software:

    System Software Overview:

      System Version: macOS 26.2 (25C56)
      Kernel Version: Darwin 25.2.0
      Time since boot: 22 days, 4 hours, 33 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2880 x 1864 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    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: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    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
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    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: 1.1.4
    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: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    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: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    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-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    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: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0

Change History (2)

comment:1 by Eric Pettersen, 72 minutes ago

Component: Unassigned → UI
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Table deleted during timer interval

comment:2 by Eric Pettersen, 35 minutes ago

Resolution: → fixed
Status: accepted → closed

Fix: ​https://github.com/RBVI/ChimeraX/commit/e2fff27bd95578ae57e586cb62ba5fe780a704ab

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