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Opened 17 hours ago
#19876 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
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.
How to cite UCSF ChimeraX
> open C:/Docking1/phenolic/2IQ7.pdbqt
Summary of feedback from opening C:/Docking1/phenolic/2IQ7.pdbqt
---
warnings | Ignored bad PDB record found on line 20857
HETATM20849 C1 NAG H . 34.531 3.292 33.938 1.00 8.21 0.167 C
Ignored bad PDB record found on line 20858
HETATM20850 C2 NAG H . 34.356 3.644 35.422 1.00 10.57 0.139 C
Ignored bad PDB record found on line 20859
HETATM20851 C3 NAG H . 33.913 2.424 36.245 1.00 10.79 0.163 C
Ignored bad PDB record found on line 20860
HETATM20852 C4 NAG H . 32.705 1.753 35.567 1.00 8.58 0.176 C
Ignored bad PDB record found on line 20861
HETATM20853 C5 NAG H . 33.032 1.456 34.098 1.00 7.59 0.174 C
394 messages similar to the above omitted
Chain information for 2IQ7.pdb #1
---
Chain | Description
A B C D E G | No description available
F | No description available
Opened 2IQ7.pdbqt containing 1 structures (20848 atoms, 21261 bonds)
> style stick
Changed 20848 atom styles
> select add #1
20848 atoms, 21261 bonds, 2372 residues, 1 model selected
> style sel stick
Changed 20848 atom styles
> show sel cartoons
Computing secondary structure
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel atoms
> select subtract #1
Nothing selected
> open C:/Docking1/phenolic/output.pdbqt
Summary of feedback from opening C:/Docking1/phenolic/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.446 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -7.199
Ignored bad PDB record found on line 4
REMARK INTER: -7.199
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
220 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (144 atoms, 297 bonds)
> color #1 #00557fff
> ui tool show H-Bonds
> hbonds sel radius 0.4 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
Atom specifier selects no atoms
> select add #1
20848 atoms, 21261 bonds, 2372 residues, 1 model selected
> select add #2
20992 atoms, 21558 bonds, 2381 residues, 11 models selected
> select subtract #1
144 atoms, 297 bonds, 9 residues, 10 models selected
> hbonds sel radius 0.4 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
Skipping possible acceptor with bad geometry: 2IQ7.pdb #1/C SER 204 O
Wrong number of grandchild atoms for phi/psi acceptor 2IQ7.pdb #1/C SER 204 O
[Repeated 5 time(s)]
Skipped 6 atom(s) with bad connectivities; see log for details
17 hydrogen bonds found
> hbonds sel radius 0.4 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
Skipping possible acceptor with bad geometry: 2IQ7.pdb #1/C SER 204 O
Wrong number of grandchild atoms for phi/psi acceptor 2IQ7.pdb #1/C SER 204 O
[Repeated 5 time(s)]
Skipped 6 atom(s) with bad connectivities; see log for details
17 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel radius 0.04 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
Skipping possible acceptor with bad geometry: 2IQ7.pdb #1/C SER 204 O
Wrong number of grandchild atoms for phi/psi acceptor 2IQ7.pdb #1/C SER 204 O
[Repeated 5 time(s)]
Skipped 6 atom(s) with bad connectivities; see log for details
17 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel radius 0.1 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
Skipping possible acceptor with bad geometry: 2IQ7.pdb #1/C SER 204 O
Wrong number of grandchild atoms for phi/psi acceptor 2IQ7.pdb #1/C SER 204 O
[Repeated 5 time(s)]
Skipped 6 atom(s) with bad connectivities; see log for details
17 hydrogen bonds found
> view #2 clip false
> view #1 clip false
> select subtract #2
Nothing selected
> view #2 clip false
> hide #3 models
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true select true
> color #ffff00 dashes 7 reveal true
38 contacts
> select add #1
20862 atoms, 21261 bonds, 2373 residues, 2 models selected
> select subtract #1
14 atoms, 1 residue, 1 model selected
> select add #2
144 atoms, 297 bonds, 9 residues, 10 models selected
> select subtract #2
Nothing selected
> view clip false
> view #2 clip false
> ui mousemode right zoom
> ui mousemode right translate
> close #2
> close
> open C:/Docking1/phenolic/3DCN.pdbqt
Chain information for 3DCN.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Opened 3DCN.pdbqt containing 1 structures (1767 atoms, 1795 bonds)
> open C:/Docking1/phenolic/output1.pdbqt
Summary of feedback from opening C:/Docking1/phenolic/output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.751 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -6.423
Ignored bad PDB record found on line 4
REMARK INTER: -6.423
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
220 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (144 atoms, 297 bonds)
> color #1 #00557fff
> ui tool show H-Bonds
> select add #2
144 atoms, 297 bonds, 9 residues, 10 models selected
> hbonds sel radius 0.1 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 3DCN.pdb #1/A GLY 201 N
11 hydrogen bonds found
> close
> open C:\Docking1\phenolic\2IQ7.pdbqt format pdbqt
Summary of feedback from opening C:\Docking1\phenolic\2IQ7.pdbqt
---
warnings | Ignored bad PDB record found on line 20857
HETATM20849 C1 NAG H . 34.531 3.292 33.938 1.00 8.21 0.167 C
Ignored bad PDB record found on line 20858
HETATM20850 C2 NAG H . 34.356 3.644 35.422 1.00 10.57 0.139 C
Ignored bad PDB record found on line 20859
HETATM20851 C3 NAG H . 33.913 2.424 36.245 1.00 10.79 0.163 C
Ignored bad PDB record found on line 20860
HETATM20852 C4 NAG H . 32.705 1.753 35.567 1.00 8.58 0.176 C
Ignored bad PDB record found on line 20861
HETATM20853 C5 NAG H . 33.032 1.456 34.098 1.00 7.59 0.174 C
394 messages similar to the above omitted
Chain information for 2IQ7.pdb #1
---
Chain | Description
A B C D E G | No description available
F | No description available
Opened 2IQ7.pdbqt containing 1 structures (20848 atoms, 21261 bonds)
> select add #1
20848 atoms, 21261 bonds, 2372 residues, 1 model selected
> show sel cartoons
Computing secondary structure
> style sel stick
Changed 20848 atom styles
> hide sel atoms
> select subtract #1
Nothing selected
> color #1 #00557fff
> open C:/Docking1/tannin/output.pdbqt
Summary of feedback from opening C:/Docking1/tannin/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -18.217 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -27.322
Ignored bad PDB record found on line 4
REMARK INTER: -34.191
Ignored bad PDB record found on line 5
REMARK INTRA: 6.869
Ignored bad PDB record found on line 6
REMARK UNBOUND: 6.869
976 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (1323 atoms, 3429 bonds)
> select add #2
1323 atoms, 3429 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.1 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
Skipping possible acceptor with bad geometry: 2IQ7.pdb #1/C SER 204 O
Wrong number of grandchild atoms for phi/psi acceptor 2IQ7.pdb #1/C SER 204 O
[Repeated 5 time(s)]
Skipped 6 atom(s) with bad connectivities; see log for details
33 hydrogen bonds found
> select subtract #2
Nothing selected
> view #2 clip false
> close #2
> close #3
> open C:/Docking1/flavonoid/output.pdbqt
Summary of feedback from opening C:/Docking1/flavonoid/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.029 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -9.029
Ignored bad PDB record found on line 4
REMARK INTER: -9.029
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
112 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (153 atoms, 337 bonds)
> select add #2
153 atoms, 337 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.1 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
0 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 intraModel false distSlop 0.3 intraMol false
> reveal true retainCurrent true
0 hydrogen bonds found
> close
> open C:\Docking1\phenolic\3DCN.pdbqt format pdbqt
Chain information for 3DCN.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Opened 3DCN.pdbqt containing 1 structures (1767 atoms, 1795 bonds)
> color #1 #00557fff
> open C:/Docking1/tannin/output1.pdbqt
Summary of feedback from opening C:/Docking1/tannin/output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -12.098 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -16.057
Ignored bad PDB record found on line 4
REMARK INTER: -22.707
Ignored bad PDB record found on line 5
REMARK INTRA: 6.650
Ignored bad PDB record found on line 6
REMARK UNBOUND: 6.650
976 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (1323 atoms, 3429 bonds)
> select add #2
1323 atoms, 3429 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.1 dashes 7 intraModel false distSlop 0.3 intraMol false
> reveal true retainCurrent true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 3DCN.pdb #1/A GLY 201 N
18 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 intraModel false distSlop 0.3 intraMol false
> reveal true retainCurrent true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 3DCN.pdb #1/A GLY 201 N
18 hydrogen bonds found
> select subtract #2
Nothing selected
> close #2
> close #3
> open C:/Docking1/flavonoid/output1.pdbqt
Summary of feedback from opening C:/Docking1/flavonoid/output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.042 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -8.042
Ignored bad PDB record found on line 4
REMARK INTER: -8.042
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
112 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (153 atoms, 337 bonds)
> select add #2
153 atoms, 337 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.1 dashes 7 intraModel false distSlop 0.3 intraMol false
> reveal true retainCurrent true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 3DCN.pdb #1/A GLY 201 N
0 hydrogen bonds found
> close
> open C:/Docking/doxycyline/6WAF.pdbqt
Summary of feedback from opening C:/Docking/doxycyline/6WAF.pdbqt
---
warnings | Ignored bad PDB record found on line 3202
HETATM 3199 S SO4 C . -10.370 -3.272 39.368 1.00188.75 0.261 S
Ignored bad PDB record found on line 3203
HETATM 3200 O1 SO4 C . -10.166 -4.136 38.209 1.00186.31 -0.565 OA
Ignored bad PDB record found on line 3204
HETATM 3201 O2 SO4 C . -9.991 -1.902 39.039 1.00188.13 -0.565 OA
Ignored bad PDB record found on line 3205
HETATM 3202 O3 SO4 C . -9.545 -3.742 40.477 1.00188.99 -0.565 OA
Ignored bad PDB record found on line 3206
HETATM 3203 O4 SO4 C . -11.779 -3.306 39.752 1.00191.98 -0.565 OA
5 messages similar to the above omitted
Chain information for 6WAF.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
Opened 6WAF.pdbqt containing 1 structures (3198 atoms, 3262 bonds)
> color #1 #aa007fff
> open C:/Docking/doxycyline/output.pdbqt
Summary of feedback from opening C:/Docking/doxycyline/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -12.139 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -9.880
Ignored bad PDB record found on line 4
REMARK INTER: -13.559
Ignored bad PDB record found on line 5
REMARK INTRA: 3.678
Ignored bad PDB record found on line 6
REMARK UNBOUND: 3.678
211 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (351 atoms, 612 bonds)
> select add #2
351 atoms, 612 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.1 dashes 7 intraModel false distSlop 0.3 intraMol false
> reveal true retainCurrent true
32 hydrogen bonds found
> hide #!2 models
> close #2
> close #3
> open C:/Docking/saponin/output.pdbqt
Summary of feedback from opening C:/Docking/saponin/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -13.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -14.102
Ignored bad PDB record found on line 4
REMARK INTER: -14.102
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
112 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (315 atoms, 656 bonds)
> select add #2
315 atoms, 656 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.1 dashes 7 intraModel false intraMol false reveal true
> retainCurrent true
1 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 intraModel false angleSlop 16.0 intraMol
> false reveal true retainCurrent true
1 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 intraModel false intraMol false reveal true
1 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 showDist true intraModel false intraMol false
> reveal true
1 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 showDist true intraMol false reveal true
1 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 showDist true reveal true
1 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 showDist true intraModel false intraMol false
> select true reveal true
1 hydrogen bonds found
> hbonds sel radius 0.1 dashes 7 showDist true intraModel false intraMol false
> select true reveal true
1 hydrogen bonds found
> hbonds sel radius 100.0 dashes 7 showDist true intraModel false intraMol
> false select true reveal true
1 hydrogen bonds found
> color #3 #ffff7fff models
> color #3.1 white models
> show all
Restriction atom specifier must not be blank
> hbonds sel radius 0.04 dashes 7 showDist true restrict #1 intraModel false
> intraMol false reveal true
0 hydrogen bonds found
> hbonds sel radius 0.04 dashes 7 showDist true restrict #2 intraModel false
> intraMol false reveal true
1 hydrogen bonds found
> select add #2
316 atoms, 656 bonds, 10 residues, 11 models selected
> select subtract #2
1 atom, 1 residue, 1 model selected
> select add #1
3198 atoms, 3262 bonds, 398 residues, 1 model selected
> select subtract #1
Nothing selected
> close #3.1
> close #3
> close #2
> hide atoms
> open C:/Docking/terpenoid/output.pdbqt
Summary of feedback from opening C:/Docking/terpenoid/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.432 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -7.432
Ignored bad PDB record found on line 4
REMARK INTER: -7.432
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
85 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (108 atoms, 252 bonds)
> select add #2
108 atoms, 252 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.04 dashes 7 showDist true restrict #2 intraModel false
> intraMol false reveal true
0 hydrogen bonds found
> ui mousemode right "mark center"
[Repeated 1 time(s)]
> ui mousemode right "mark plane"
> ui mousemode right zoom
> ui mousemode right translate
> ui tool show "Check Waters"
> hbonds interModel false reveal true restrict any name "water H-bonds"
314 hydrogen bonds found
> ~select
Nothing selected
No waters chosen
> volume step 1
No volumes specified
> undo
[Repeated 4 time(s)]Undo failed, probably because structures have been
modified.
> close
> open C:\Docking\doxycyline\6WAF.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\doxycyline\6WAF.pdbqt
---
warnings | Ignored bad PDB record found on line 3202
HETATM 3199 S SO4 C . -10.370 -3.272 39.368 1.00188.75 0.261 S
Ignored bad PDB record found on line 3203
HETATM 3200 O1 SO4 C . -10.166 -4.136 38.209 1.00186.31 -0.565 OA
Ignored bad PDB record found on line 3204
HETATM 3201 O2 SO4 C . -9.991 -1.902 39.039 1.00188.13 -0.565 OA
Ignored bad PDB record found on line 3205
HETATM 3202 O3 SO4 C . -9.545 -3.742 40.477 1.00188.99 -0.565 OA
Ignored bad PDB record found on line 3206
HETATM 3203 O4 SO4 C . -11.779 -3.306 39.752 1.00191.98 -0.565 OA
5 messages similar to the above omitted
Chain information for 6WAF.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
Opened 6WAF.pdbqt containing 1 structures (3198 atoms, 3262 bonds)
> close
> open C:/Docking/terpenoid/3KZ9.pdbqt
Summary of feedback from opening C:/Docking/terpenoid/3KZ9.pdbqt
---
warnings | Ignored bad PDB record found on line 7378
HETATM 7373 S SO4 E . 40.796 44.200 61.886 1.00112.81 0.261 S
Ignored bad PDB record found on line 7379
HETATM 7374 O1 SO4 E . 41.307 44.802 60.655 1.00112.72 -0.565 OA
Ignored bad PDB record found on line 7380
HETATM 7375 O2 SO4 E . 39.906 45.132 62.576 1.00112.49 -0.565 OA
Ignored bad PDB record found on line 7381
HETATM 7376 O3 SO4 E . 40.051 42.988 61.557 1.00113.05 -0.565 OA
Ignored bad PDB record found on line 7382
HETATM 7377 O4 SO4 E . 41.911 43.846 62.760 1.00112.77 -0.565 OA
25 messages similar to the above omitted
Chain information for 3KZ9.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Computing secondary structure
Opened 3KZ9.pdbqt containing 1 structures (7372 atoms, 7627 bonds)
> color #1 #aa007fff
> open C:/Docking/terpenoid/output1.pdbqt
Summary of feedback from opening C:/Docking/terpenoid/output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.019 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -8.019
Ignored bad PDB record found on line 4
REMARK INTER: -8.019
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
85 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (108 atoms, 252 bonds)
> hide #2.1#!1 atoms
> show #2.1#!1 atoms
> hide #2.1#!1 atoms
> select add #1
7372 atoms, 7627 bonds, 17 pseudobonds, 806 residues, 2 models selected
> hide sel atoms
> select subtract #1
Nothing selected
> select add #2
108 atoms, 252 bonds, 9 residues, 10 models selected
> show sel & #2.1 atoms
> ui tool show H-Bonds
> hbonds sel radius 0.04 dashes 7 showDist true restrict #2 intraModel false
> intraMol false reveal true
0 hydrogen bonds found
> hbonds sel radius 0.07 dashes 7 showDist true restrict #2 intraModel false
> distSlop 0.8 intraMol false reveal true
0 hydrogen bonds found
> close #2
> open C:\Docking\terpenoid\output1.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\terpenoid\output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.019 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -8.019
Ignored bad PDB record found on line 4
REMARK INTER: -8.019
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
85 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (108 atoms, 252 bonds)
> close
> open C:\Docking\terpenoid\3KZ9.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\terpenoid\3KZ9.pdbqt
---
warnings | Ignored bad PDB record found on line 7378
HETATM 7373 S SO4 E . 40.796 44.200 61.886 1.00112.81 0.261 S
Ignored bad PDB record found on line 7379
HETATM 7374 O1 SO4 E . 41.307 44.802 60.655 1.00112.72 -0.565 OA
Ignored bad PDB record found on line 7380
HETATM 7375 O2 SO4 E . 39.906 45.132 62.576 1.00112.49 -0.565 OA
Ignored bad PDB record found on line 7381
HETATM 7376 O3 SO4 E . 40.051 42.988 61.557 1.00113.05 -0.565 OA
Ignored bad PDB record found on line 7382
HETATM 7377 O4 SO4 E . 41.911 43.846 62.760 1.00112.77 -0.565 OA
25 messages similar to the above omitted
Chain information for 3KZ9.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Computing secondary structure
Opened 3KZ9.pdbqt containing 1 structures (7372 atoms, 7627 bonds)
> color #1 #aa007fff
> hide atoms
> open C:/Docking/doxycyline/output1.pdbqt
Summary of feedback from opening C:/Docking/doxycyline/output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -13.135 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -11.006
Ignored bad PDB record found on line 4
REMARK INTER: -14.671
Ignored bad PDB record found on line 5
REMARK INTRA: 3.665
Ignored bad PDB record found on line 6
REMARK UNBOUND: 3.665
211 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (351 atoms, 608 bonds)
> select add #2
351 atoms, 608 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 showDist true restrict #2 intraModel false
> distSlop 0.8 intraMol false reveal true
0 hydrogen bonds found
> hbonds sel radius 0.07 dashes 7 showDist true intraModel false distSlop 0.8
> intraMol false reveal true
33 hydrogen bonds found
> select subtract #2
Nothing selected
> select add #1
7372 atoms, 7627 bonds, 17 pseudobonds, 806 residues, 2 models selected
> remove hbond
Unknown command: remove hbond
> ui tool show ViewDock
> hbonds #!2.1-9 restrict #!1 & (main|ligand) saltOnly true select true reveal
> true
Skipping possible acceptor with bad geometry: 3KZ9.pdb #1/D GLN 138 OE1
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/D GLN 138
OE1
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: 3KZ9.pdb
#1/B ARG 10 O
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/B ARG 10 O
Skipping possible acceptor with bad geometry: 3KZ9.pdb #1/B ARG 74 O
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/B ARG 74 O
Skipping possible acceptor with bad geometry: 3KZ9.pdb #1/C ARG 74 O
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/C ARG 74 O
Skipping possible acceptor with bad geometry: 3KZ9.pdb #1/D SER 77 O
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/D SER 77 O
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: 3KZ9.pdb
#1/D SER 193 O
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/D SER 193 O
Skipping possible acceptor with bad geometry: 3KZ9.pdb #1/B ARG 74 O
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/B ARG 74 O
Skipping possible acceptor with bad geometry: 3KZ9.pdb #1/C ARG 74 O
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/C ARG 74 O
Skipping possible acceptor with bad geometry: 3KZ9.pdb #1/D GLN 138 O
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/D GLN 138 O
Skipping possible acceptor with bad geometry: 3KZ9.pdb #1/D GLN 138 OE1
Wrong number of grandchild atoms for phi/psi acceptor 3KZ9.pdb #1/D GLN 138
OE1
donor: 3KZ9.pdb #1/B MSE 101 N acceptor: 3KZ9.pdb #1/B MSE 101 O
Traceback (most recent call last):
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\viewdock\tool.py", line 262, in ok_cb
results_callback(run(self.session,
^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hide #!1 models
> show #!1 models
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> close #2
> close #3
> open C:/Docking/saponin/output1.pdbqt
Summary of feedback from opening C:/Docking/saponin/output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -13.779 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -14.584
Ignored bad PDB record found on line 4
REMARK INTER: -14.584
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
112 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (315 atoms, 661 bonds)
> clashes #2.1-9 restrict #!1 & (main|ligand) reveal true
1 clashes
> color #3 #ffff7fff models
> close #3
> select add #2
315 atoms, 661 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 showDist true intraModel false distSlop 0.8
> intraMol false reveal true
6 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 0.8 intraMol false
> reveal true
6 hydrogen bonds found
> hbonds sel radius 0.07 dashes 7 intraModel false intraMol false reveal true
3 hydrogen bonds found
> hbonds sel radius 0.07 dashes 7 intraModel false intraMol false reveal true
3 hydrogen bonds found
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 0.8 intraMol false
> reveal true
6 hydrogen bonds found
> close
> ui tool show H-Bonds
> open C:\Docking\doxycyline\6WAF.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\doxycyline\6WAF.pdbqt
---
warnings | Ignored bad PDB record found on line 3202
HETATM 3199 S SO4 C . -10.370 -3.272 39.368 1.00188.75 0.261 S
Ignored bad PDB record found on line 3203
HETATM 3200 O1 SO4 C . -10.166 -4.136 38.209 1.00186.31 -0.565 OA
Ignored bad PDB record found on line 3204
HETATM 3201 O2 SO4 C . -9.991 -1.902 39.039 1.00188.13 -0.565 OA
Ignored bad PDB record found on line 3205
HETATM 3202 O3 SO4 C . -9.545 -3.742 40.477 1.00188.99 -0.565 OA
Ignored bad PDB record found on line 3206
HETATM 3203 O4 SO4 C . -11.779 -3.306 39.752 1.00191.98 -0.565 OA
5 messages similar to the above omitted
Chain information for 6WAF.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
Opened 6WAF.pdbqt containing 1 structures (3198 atoms, 3262 bonds)
> open C:\Docking\doxycyline\output.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\doxycyline\output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -12.139 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -9.880
Ignored bad PDB record found on line 4
REMARK INTER: -13.559
Ignored bad PDB record found on line 5
REMARK INTRA: 3.678
Ignored bad PDB record found on line 6
REMARK UNBOUND: 3.678
211 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (351 atoms, 612 bonds)
> color #1 #aa557fff
> color #1 #aa007fff
> color #1 #aa557fff
> color #1 #aa007fff
> ui tool show H-Bonds
> select add #2
351 atoms, 612 bonds, 9 residues, 10 models selected
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 1.0 intraMol false
> reveal true
42 hydrogen bonds found
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 2.0 intraMol false
> reveal true
68 hydrogen bonds found
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
223 hydrogen bonds found
> close #2
> close #3
> open C:\Docking\saponin\output.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\saponin\output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -13.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -14.102
Ignored bad PDB record found on line 4
REMARK INTER: -14.102
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
112 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (315 atoms, 656 bonds)
> select add #2
315 atoms, 656 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
16 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 8.0 intraMol false
> reveal true
49 hydrogen bonds found
> ui tool show H-Bonds
> ui tool show "Find Cavities"
> kvfinder #1
25 cavities found for 6WAF.pdb #1
6WAF.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.7 | | 861.19 | 595.98 | 3987 | 9.62 | 3.11
1.1.2 | | 770.9 | 775.73 | 3569 | 13.05 | 4.77
1.1.4 | | 134.78 | 159.63 | 624 | 0 | 0
1.1.6 | | 116.64 | 143.68 | 540 | 0 | 0
1.1.3 | | 110.38 | 95.17 | 511 | 3.06 | 0.85
1.1.24 | | 78.62 | 83.05 | 364 | 4.28 | 1.89
1.1.5 | | 51.84 | 73.89 | 240 | 0 | 0
1.1.1 | | 46.66 | 62.07 | 216 | 3.23 | 1.66
1.1.20 | | 39.1 | 58.75 | 181 | 1.2 | 0.24
1.1.16 | | 37.8 | 56.29 | 175 | 3.06 | 1.17
1.1.12 | | 35.86 | 57.21 | 166 | 0 | 0
1.1.9 | | 29.59 | 31.21 | 137 | 1.8 | 0.44
1.1.18 | | 29.16 | 60.54 | 135 | 0 | 0
1.1.14 | | 24.19 | 44.47 | 112 | 0 | 0
1.1.22 | | 23.98 | 34.15 | 111 | 1.8 | 0.69
1.1.19 | | 23.54 | 34.58 | 109 | 2.16 | 0.73
1.1.15 | | 21.82 | 39.56 | 101 | 3.84 | 2.03
1.1.11 | | 17.93 | 30.75 | 83 | 1.47 | 0.45
1.1.13 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.17 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.23 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.25 | | 12.1 | 23.73 | 56 | 1.47 | 0.5
1.1.10 | | 10.58 | 24.24 | 49 | 1.7 | 0.78
1.1.21 | | 10.37 | 21.1 | 48 | 0.85 | 0.3
1.1.8 | | 8.64 | 20.22 | 40 | 1.2 | 0.49
> ui tool show "Find Cavities"
> kvfinder #1 gridSpacing 0.7 probeIn 1.6 probeOut 4.2 volumeCutoff 6
13 cavities found for 6WAF.pdb #1
6WAF.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.6 | | 760.09 | 494.22 | 2216 | 8.71 | 3.15
1.1.9 | | 464.08 | 439.34 | 1353 | 12.62 | 5.22
1.1.3 | | 108.05 | 141.08 | 315 | 0 | 0
1.1.4 | | 96.73 | 130.33 | 282 | 6.14 | 2.04
1.1.7 | | 67.23 | 86.9 | 196 | 0 | 0
1.1.2 | | 64.83 | 56.82 | 189 | 2.52 | 0.65
1.1.13 | | 57.28 | 55.96 | 167 | 3.5 | 1.33
1.1.1 | | 22.64 | 37.82 | 66 | 2.42 | 1.12
1.1.5 | | 19.55 | 40.21 | 57 | 0 | 0
1.1.10 | | 15.43 | 28.63 | 45 | 1.98 | 0.86
1.1.12 | | 10.29 | 19.49 | 30 | 0.7 | 0.05
1.1.11 | | 7.55 | 14.73 | 22 | 0.7 | 0.16
1.1.8 | | 7.2 | 10.5 | 21 | 0.7 | 0.07
> view #1.1.6 @< 3.5
> zoom 0.75
moved plane near -42.09814198522398 [-0.6189133 -0.35881948 -0.69870946]
moved plane far -42.09814198522398 [-0.6189133 -0.35881948 -0.69870946]
> surface #1.1.1-13 probeRadius 1.6 transparency 50
> ~surface #1.1
> surface #1.1.6 probeRadius 1.6
> show
> #!1/A:29-36,64,112,115-117,119-125,171/B:29-36,112,115-117,119-122,125,171,178
> select #!1 & (#!1.1.6 @< 5.0)
264 atoms, 238 bonds, 54 residues, 1 model selected
> ~select #!1 & (#!1.1.6 @< 5.0)
Nothing selected
> select #!1 & (#!1.1.6 @< 5.0)
264 atoms, 238 bonds, 54 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
13 hydrogen bonds found
> close
> open C:/Docking/doxycyline/6WAF.pdbqt
Summary of feedback from opening C:/Docking/doxycyline/6WAF.pdbqt
---
warnings | Ignored bad PDB record found on line 3202
HETATM 3199 S SO4 C . -10.370 -3.272 39.368 1.00188.75 0.261 S
Ignored bad PDB record found on line 3203
HETATM 3200 O1 SO4 C . -10.166 -4.136 38.209 1.00186.31 -0.565 OA
Ignored bad PDB record found on line 3204
HETATM 3201 O2 SO4 C . -9.991 -1.902 39.039 1.00188.13 -0.565 OA
Ignored bad PDB record found on line 3205
HETATM 3202 O3 SO4 C . -9.545 -3.742 40.477 1.00188.99 -0.565 OA
Ignored bad PDB record found on line 3206
HETATM 3203 O4 SO4 C . -11.779 -3.306 39.752 1.00191.98 -0.565 OA
5 messages similar to the above omitted
Chain information for 6WAF.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
Opened 6WAF.pdbqt containing 1 structures (3198 atoms, 3262 bonds)
> color #1 #aa007fff
> open C:/Docking/doxycyline/output.pdbqt
Summary of feedback from opening C:/Docking/doxycyline/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -12.139 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -9.880
Ignored bad PDB record found on line 4
REMARK INTER: -13.559
Ignored bad PDB record found on line 5
REMARK INTRA: 3.678
Ignored bad PDB record found on line 6
REMARK UNBOUND: 3.678
211 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (351 atoms, 612 bonds)
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
Atom specifier selects no atoms
> select add #2
351 atoms, 612 bonds, 9 residues, 10 models selected
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
223 hydrogen bonds found
> view #2 clip false
> ui mousemode right select
Drag select of 2 residues
> ui mousemode right select
Drag select of 3 atoms, 11 residues, 3 bonds
Drag select of 3 atoms, 4 bonds
> ui mousemode right rotate
> ui mousemode right select
> select #1/A:36@NH2
1 atom, 1 residue, 1 model selected
> select #1/A:36@NH2
1 atom, 1 residue, 1 model selected
Drag select of 2 atoms, 3 bonds
> remove atom
Unknown command: remove atom
> remove atm
Unknown command: remove atm
Drag select of 8 atoms, 23 residues, 7 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 8 atoms, 7 bonds
Drag select of 7 atoms, 6 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 1 atoms
> hide sel atoms
Drag select of 16 residues
> hide sel cartoons
> hide sel atoms
Drag select of 5 atoms, 4 bonds, 1 pseudobonds
> hide sel atoms
Drag select of 6 atoms, 12 residues, 5 bonds
> hide sel atoms
[Repeated 1 time(s)]Drag select of 6 atoms, 8 residues, 5 bonds
> hide sel atoms
> view #2 clip false
> select clear
> ui mousemode right translate
> ui mousemode right select
Drag select of 2 residues
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> show sel cartoons
> ui mousemode right translate
> select add #1
3198 atoms, 3262 bonds, 398 residues, 1 model selected
> select subtract #1
Nothing selected
> close #2
> close
> open C:\Docking\doxycyline\6WAF.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\doxycyline\6WAF.pdbqt
---
warnings | Ignored bad PDB record found on line 3202
HETATM 3199 S SO4 C . -10.370 -3.272 39.368 1.00188.75 0.261 S
Ignored bad PDB record found on line 3203
HETATM 3200 O1 SO4 C . -10.166 -4.136 38.209 1.00186.31 -0.565 OA
Ignored bad PDB record found on line 3204
HETATM 3201 O2 SO4 C . -9.991 -1.902 39.039 1.00188.13 -0.565 OA
Ignored bad PDB record found on line 3205
HETATM 3202 O3 SO4 C . -9.545 -3.742 40.477 1.00188.99 -0.565 OA
Ignored bad PDB record found on line 3206
HETATM 3203 O4 SO4 C . -11.779 -3.306 39.752 1.00191.98 -0.565 OA
5 messages similar to the above omitted
Chain information for 6WAF.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
Opened 6WAF.pdbqt containing 1 structures (3198 atoms, 3262 bonds)
> color #1 #aa007fff
> open C:/Docking/saponin/output.pdbqt
Summary of feedback from opening C:/Docking/saponin/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -13.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -14.102
Ignored bad PDB record found on line 4
REMARK INTER: -14.102
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
112 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (315 atoms, 656 bonds)
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
Atom specifier selects no atoms
> select add #2
315 atoms, 656 bonds, 9 residues, 10 models selected
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
16 hydrogen bonds found
> ui mousemode right select
Drag select of 37 atoms, 53 residues, 56 bonds
Drag select of 17 atoms, 21 residues, 17 bonds
> hide sel atoms
[Repeated 1 time(s)]Drag select of 3 atoms, 17 residues, 2 bonds
> hide sel atoms
Drag select of 6 atoms, 46 residues, 5 bonds
> hide sel atoms
> ui mousemode right translate
> select add #1
3198 atoms, 3262 bonds, 398 residues, 1 model selected
> select subtract #1
Nothing selected
> ui mousemode right rotate
> ui mousemode right translate
> view #1 clip false
> view #2 clip false
> close #2
> close #3
> open C:/Docking/terpenoid/output.pdbqt
Summary of feedback from opening C:/Docking/terpenoid/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.432 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -7.432
Ignored bad PDB record found on line 4
REMARK INTER: -7.432
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
85 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (108 atoms, 252 bonds)
> view clip false
> ui tool show H-Bonds
> select add #2
108 atoms, 252 bonds, 9 residues, 10 models selected
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
12 hydrogen bonds found
> ui mousemode right select
Drag select of 12 atoms, 25 residues, 10 bonds
> hide sel atoms
Drag select of 2 atoms, 22 residues, 2 bonds
> hide sel atoms
> select add #1
3198 atoms, 3262 bonds, 398 residues, 1 model selected
> select subtract #1
Nothing selected
> view #2 clip false
> select add #2
108 atoms, 252 bonds, 9 residues, 10 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.94405,-0.20882,-0.25527,2.3497,-0.055345,0.66273,-0.74681,8.9122,0.32512,0.71915,0.6141,11.26
> view matrix models
> #2,0.95095,-0.11935,-0.28539,4.1076,-0.14153,0.65249,-0.74446,10.431,0.27507,0.74834,0.60359,12.886
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.95095,-0.11935,-0.28539,4.5923,-0.14153,0.65249,-0.74446,10.289,0.27507,0.74834,0.60359,12.88
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> close #2
> close
> open C:/Docking/terpenoid/3KZ9.pdbqt
Summary of feedback from opening C:/Docking/terpenoid/3KZ9.pdbqt
---
warnings | Ignored bad PDB record found on line 7378
HETATM 7373 S SO4 E . 40.796 44.200 61.886 1.00112.81 0.261 S
Ignored bad PDB record found on line 7379
HETATM 7374 O1 SO4 E . 41.307 44.802 60.655 1.00112.72 -0.565 OA
Ignored bad PDB record found on line 7380
HETATM 7375 O2 SO4 E . 39.906 45.132 62.576 1.00112.49 -0.565 OA
Ignored bad PDB record found on line 7381
HETATM 7376 O3 SO4 E . 40.051 42.988 61.557 1.00113.05 -0.565 OA
Ignored bad PDB record found on line 7382
HETATM 7377 O4 SO4 E . 41.911 43.846 62.760 1.00112.77 -0.565 OA
25 messages similar to the above omitted
Chain information for 3KZ9.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Computing secondary structure
Opened 3KZ9.pdbqt containing 1 structures (7372 atoms, 7627 bonds)
> color #1 #aa007fff
> select add #1
7372 atoms, 7627 bonds, 17 pseudobonds, 806 residues, 2 models selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select subtract #1
Nothing selected
> open C:/Docking/terpenoid/output.pdbqt
Summary of feedback from opening C:/Docking/terpenoid/output.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.432 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -7.432
Ignored bad PDB record found on line 4
REMARK INTER: -7.432
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
85 messages similar to the above omitted
Opened output.pdbqt containing 9 structures (108 atoms, 252 bonds)
> close #2
> open C:/Docking/terpenoid/output1.pdbqt
Summary of feedback from opening C:/Docking/terpenoid/output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.019 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -8.019
Ignored bad PDB record found on line 4
REMARK INTER: -8.019
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
85 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (108 atoms, 252 bonds)
> select add #1
7372 atoms, 7627 bonds, 17 pseudobonds, 806 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> undo
Undo failed, probably because structures have been modified.
> close
> open C:\Docking\terpenoid\3KZ9.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\terpenoid\3KZ9.pdbqt
---
warnings | Ignored bad PDB record found on line 7378
HETATM 7373 S SO4 E . 40.796 44.200 61.886 1.00112.81 0.261 S
Ignored bad PDB record found on line 7379
HETATM 7374 O1 SO4 E . 41.307 44.802 60.655 1.00112.72 -0.565 OA
Ignored bad PDB record found on line 7380
HETATM 7375 O2 SO4 E . 39.906 45.132 62.576 1.00112.49 -0.565 OA
Ignored bad PDB record found on line 7381
HETATM 7376 O3 SO4 E . 40.051 42.988 61.557 1.00113.05 -0.565 OA
Ignored bad PDB record found on line 7382
HETATM 7377 O4 SO4 E . 41.911 43.846 62.760 1.00112.77 -0.565 OA
25 messages similar to the above omitted
Chain information for 3KZ9.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Computing secondary structure
Opened 3KZ9.pdbqt containing 1 structures (7372 atoms, 7627 bonds)
> color #1 #aa007fff
> hide atoms
> hide target a
> open C:\Docking\terpenoid\output1.pdbqt format pdbqt
Summary of feedback from opening C:\Docking\terpenoid\output1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.019 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -8.019
Ignored bad PDB record found on line 4
REMARK INTER: -8.019
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
85 messages similar to the above omitted
Opened output1.pdbqt containing 9 structures (108 atoms, 252 bonds)
> select add #2
108 atoms, 252 bonds, 9 residues, 10 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.76175,0.20684,0.61397,-37.68,0.001333,0.94717,-0.32074,19.885,-0.64788,0.24514,0.72122,18.346
> ui mousemode right translate
> select subtract #2
Nothing selected
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right translate
> select add #2
108 atoms, 252 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
donor: output1.pdb #2.3/? UNK 0 O acceptor: 3KZ9.pdb #1/B MSE 101 O
Traceback (most recent call last):
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\tool.py", line 53, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hbonds sel radius 0.07 dashes 7 intraModel false distSlop 5.0 intraMol false
> reveal true
donor: output1.pdb #2.3/? UNK 0 O acceptor: 3KZ9.pdb #1/B MSE 101 O
Traceback (most recent call last):
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\tool.py", line 53, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File "C:\DockingSoftware\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2115
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel
Python: 3.11.9
Locale: en_GB.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: HP
Model: HP EliteBook 820 G3
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,464,728,064
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6300U CPU @ 2.40GHz
OSLanguage: en-GB
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
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: 2026.1.4
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
comtypes: 1.4.11
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
narwhals: 2.16.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.2
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.5.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
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
pyKVFinder: 0.9.0
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
pywin32: 311
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
tomlkit: 0.14.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
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
WMI: 1.5.1
yarl: 1.22.0
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