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Opened 4 years ago
Closed 4 years ago
#6244 closed defect (fixed)
ViewdockX after rows deleted: KeyError: 'stars'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
I deleted some rows in ViewDockX Table and close the window.
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/shahryar/Desktop/Mpro_APR_ZN.pdbqt
Chain information for Mpro_APR_ZN.pdb #1
---
Chain | Description
A | No description available
Opened Mpro_APR_ZN.pdbqt containing 1 structures (2258 atoms, 2308 bonds)
> open /Users/shahryar/Desktop/out.pdbqt
Summary of feedback from opening /Users/shahryar/Desktop/out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.1 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 3 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: O1_1 and C18_21
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: O2_2 and C28_31
130 messages similar to the above omitted
Opened out.pdbqt containing 9 structures (315 atoms, 351 bonds)
> select ::name="APR"
36 atoms, 39 bonds, 1 residue, 1 model selected
> select ::name="UNK"
315 atoms, 351 bonds, 9 residues, 9 models selected
> ~select #2.1
280 atoms, 312 bonds, 8 residues, 8 models selected
> delete atoms sel
> delete bonds sel
> save "/Users/shahryar/Documents/My Projects/نوین زیست/Dr.
> Bakhtiari/Tabatabaeian/Docking/D1/D1_Mpro_APR.pdb"
> open "/Users/shahryar/Downloads/Conformer3D_CID_5892 (1).sdf"
PubChem entry 5892
> hide #2.1 models
> hide #!2 models
> hide #1 models
> hide #3 models
> show #3 models
> select #3
71 atoms, 75 bonds, 1 residue, 1 model selected
> select up
2329 atoms, 2383 bonds, 287 residues, 3 models selected
> show #1 models
> show #!2 models
> show #2.1 models
> select #2.1
35 atoms, 39 bonds, 1 residue, 1 model selected
> select #2
35 atoms, 39 bonds, 1 residue, 2 models selected
> select #1
2258 atoms, 2308 bonds, 286 residues, 1 model selected
> hide #3 models
> delete atoms sel
> delete bonds sel
> select #2
35 atoms, 39 bonds, 1 residue, 2 models selected
> delete atoms sel
> delete bonds sel
> show #3 models
> select #3
71 atoms, 75 bonds, 1 residue, 1 model selected
> ~select #3
Nothing selected
> hide #2 models
> show #2 models
> select #2
1 model selected
> hide #3 models
> delete atoms #2
> delete bonds #2
> hide #2 models
> ~select #2
Nothing selected
> select #3
71 atoms, 75 bonds, 1 residue, 1 model selected
> show #3 models
> save "/Users/shahryar/Documents/My Projects/نوین زیست/Dr.
> Bakhtiari/Tabatabaeian/Docking/NAD.pdb"
> close session
> open /Users/shahryar/Downloads/1ei7.pdb1 format pdb
1ei7.pdb1 title:
TMV coat protein refined from the 4-layer aggregate [more info...]
Chain information for 1ei7.pdb1
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A
1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B
1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B 1.21/B 1.22/B 1.23/B
1.24/B 1.25/B 1.26/B 1.27/B 1.28/B 1.29/B 1.30/B 1.31/B 1.32/B 1.33/B 1.34/B |
No description available
> close session
> select #1.1/A:1-158
Nothing selected
> open /Users/shahryar/Downloads/1ei7.pdb1 format pdb
1ei7.pdb1 title:
TMV coat protein refined from the 4-layer aggregate [more info...]
Chain information for 1ei7.pdb1
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A
1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B
1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B 1.21/B 1.22/B 1.23/B
1.24/B 1.25/B 1.26/B 1.27/B 1.28/B 1.29/B 1.30/B 1.31/B 1.32/B 1.33/B 1.34/B |
No description available
> select #1.1/A:1-158
1235 atoms, 1260 bonds, 158 residues, 1 model selected
> select #1.13/A:1-158
1235 atoms, 1260 bonds, 158 residues, 1 model selected
> select #1.10/B:201-358
1235 atoms, 1260 bonds, 158 residues, 1 model selected
> close session
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for 5btr_A.pdb #1
---
Chain | Description
A | nad-dependent protein deacetylase sirtuin-1
D | amc-containing peptide
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.2 0.000 0.000
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: P1_1 and O7_9
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: P1_1 and O9_11
Ignored bad PDB record found on line 7
REMARK 3 A between atoms: P1_1 and O10_12
526 messages similar to the above omitted
Opened out1.pdbqt containing 9 structures (477 atoms, 513 bonds)
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #2.2 models
> select #2.2
53 atoms, 57 bonds, 1 residue, 1 model selected
> show #2.2 models
> hide #2.3 models
> show #2.3 models
> hide #2.4 models
> select #2.4
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #2.5 models
> show #2.5 models
> hide #2.5 models
> select #2.5
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #2.6 models
> select #2.6
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #2.7 models
> hide #2.8 models
> hide #2.9 models
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.7
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> show #2.9 models
> show #2.8 models
> show #2.7 models
> select #2.7
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.7
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #2.2 models
> show #2.2 models
> select #2.2
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.3
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.2
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #2.4 models
> hide #2.1 models
> show #2.1 models
> hide #2.3 models
> show #2.3 models
> select #2.4
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.4
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.5
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.4
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/out_noSTL.pdbqt
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/out_noSTL.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.0 0.000 0.000
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: P1_1 and O7_9
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: P1_1 and O9_11
Ignored bad PDB record found on line 7
REMARK 3 A between atoms: P1_1 and O10_12
526 messages similar to the above omitted
Opened out_noSTL.pdbqt containing 9 structures (477 atoms, 513 bonds)
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/out_noFTL.pdbqt
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/out_noFTL.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.1 0.000 0.000
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: P1_1 and O7_9
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: P1_1 and O9_11
Ignored bad PDB record found on line 7
REMARK 3 A between atoms: P1_1 and O10_12
526 messages similar to the above omitted
Opened out_noFTL.pdbqt containing 9 structures (477 atoms, 513 bonds)
> hide #3.1 models
> show #3.1 models
> hide #3.2 models
> show #3.2 models
> hide #3.3 models
> show #3.3 models
> select #3.2
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #3.3
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #3.4 models
> show #3.4 models
> hide #3.6 models
> show #3.6 models
> select #3.6
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #3.7 models
> show #3.7 models
> hide #3.5 models
> show #3.5 models
> hide #3.4 models
> show #3.4 models
> hide #3.7 models
> show #3.7 models
> select #3.7
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #3.8 models
> show #3.8 models
> select #3.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1
3061 atoms, 3138 bonds, 5 pseudobonds, 379 residues, 3 models selected
> ~select #1
Nothing selected
> select #2.1
53 atoms, 57 bonds, 1 residue, 1 model selected
> ~select #2.1
Nothing selected
> select #2.3
53 atoms, 57 bonds, 1 residue, 1 model selected
> ~select #2.3
Nothing selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> ~select #2.8
Nothing selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #2.5 models
> hide #2.5 models
> show #2.5 models
> show #2.6 models
> select #2.5
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2.6
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3
424 atoms, 456 bonds, 8 residues, 9 models selected
> ~select #3
Nothing selected
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.2 models
> select #3.2
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #3.3 models
> select #3.3
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #3.2
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms #1-2,4#3.1,4-7,9#!3
> delete bonds #1-2,4#3.1,4-7,9#!3
> show #3.3 models
> show #3.2 models
> hide #2 models
> undo
[Repeated 9 time(s)]
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/shahryar/Desktop/movie1.mp4
Movie saved to /Users/shahryar/Desktop/movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/shahryar/Desktop/movie2.mp4
Movie saved to /Users/shahryar/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/shahryar/Desktop/movie3.mp4
Movie saved to /Users/shahryar/Desktop/movie3.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/shahryar/Desktop/movie4.mp4
Movie saved to /Users/shahryar/Desktop/movie4.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/shahryar/Desktop/movie5.mp4
Movie saved to /Users/shahryar/Desktop/movie5.mp4
> ضضعهف
Unknown command: ضضعهف
> lighting full
> lighting simple
> ui tool show "Selection Inspector"
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb format pdb
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for 5btr_A.pdb #1
---
Chain | Description
A | nad-dependent protein deacetylase sirtuin-1
D | amc-containing peptide
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #!3 models
> hide #4 models
> hide #2 models
> show #2 models
> select #2
1 model selected
> ~select #2
Nothing selected
> hide #2 models
> show #2 models
> select #2
1 model selected
> close session
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb format pdb
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for 5btr_A.pdb #1
---
Chain | Description
A | nad-dependent protein deacetylase sirtuin-1
D | amc-containing peptide
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt format pdbqt
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.2 0.000 0.000
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: P1_1 and O7_9
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: P1_1 and O9_11
Ignored bad PDB record found on line 7
REMARK 3 A between atoms: P1_1 and O10_12
526 messages similar to the above omitted
Opened out1.pdbqt containing 9 structures (477 atoms, 513 bonds)
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> hide #2.3 models
> show #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> hide #2.9 models
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.4
53 atoms, 57 bonds, 1 residue, 1 model selected
> select add #1/A
3022 atoms, 3099 bonds, 5 pseudobonds, 373 residues, 4 models selected
> select #1
3061 atoms, 3138 bonds, 5 pseudobonds, 379 residues, 3 models selected
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Alignment identifier is 1/D
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/D:0
3 atoms, 2 bonds, 1 residue, 1 model selected
> select #1/D:0-4
58 atoms, 60 bonds, 5 residues, 1 model selected
> show #2.4 models
> hide #2.4 models
> select #2.4
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.5
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.7
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2
477 atoms, 513 bonds, 9 residues, 10 models selected
> ~select #2
Nothing selected
> select #2.2
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms #1#2.1,3#!2
> delete bonds #1#2.1,3#!2
> select #2
371 atoms, 399 bonds, 7 residues, 8 models selected
> hide #!2 models
> show #!2 models
> show #2.2 models
> show #2.4 models
> hide #!2 models
> show #!2 models
> close session
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt format pdbqt
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.2 0.000 0.000
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: P1_1 and O7_9
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: P1_1 and O9_11
Ignored bad PDB record found on line 7
REMARK 3 A between atoms: P1_1 and O10_12
526 messages similar to the above omitted
Opened out1.pdbqt containing 9 structures (477 atoms, 513 bonds)
> select #1.1
53 atoms, 57 bonds, 1 residue, 1 model selected
> ~select #1.1
Nothing selected
> select #1.2
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1.4
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #1.4 models
> hide #1.5 models
> show #1.5 models
> select #1.5
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #1.5 models
> hide #1.6 models
> delete atoms #1.1,3,7-9#!1
> delete bonds #1.1,3,7-9#!1
> show #1.4 models
> show #1.5 models
> show #1.6 models
> select #1.6
53 atoms, 57 bonds, 1 residue, 1 model selected
> hide #1.6 models
> show #1.6 models
> delete atoms sel
> delete bonds sel
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb format pdb
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for 5btr_A.pdb #2
---
Chain | Description
A | nad-dependent protein deacetylase sirtuin-1
D | amc-containing peptide
> interfaces ~solvent
3 buried areas: #2/A #2/D 962, #2/A #1.4/ 458, #2/A #1.5/ 402
> ui mousemode right zoom
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "contour level"
[Repeated 1 time(s)]
> ui mousemode right "move planes"
> ui mousemode right "rotate slab"
> ui mousemode right "crop volume"
> ui mousemode right "pick blobs"
> volume appearance brain
No volumes specified
> volume appearance brain
No volumes specified
> view
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/out_noSTL.pdbqt format pdbqt
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/out_noSTL.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.0 0.000 0.000
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: P1_1 and O7_9
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: P1_1 and O9_11
Ignored bad PDB record found on line 7
REMARK 3 A between atoms: P1_1 and O10_12
526 messages similar to the above omitted
Opened out_noSTL.pdbqt containing 9 structures (477 atoms, 513 bonds)
> close session
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb format pdb
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for 5btr_A.pdb #1
---
Chain | Description
A | nad-dependent protein deacetylase sirtuin-1
D | amc-containing peptide
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt format pdbqt
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.2 0.000 0.000
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: P1_1 and O7_9
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: P1_1 and O9_11
Ignored bad PDB record found on line 7
REMARK 3 A between atoms: P1_1 and O10_12
526 messages similar to the above omitted
Opened out1.pdbqt containing 9 structures (477 atoms, 513 bonds)
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> show #2.3 models
> delete atoms
> delete bonds
> close session
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb format pdb
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/5btr_A.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for 5btr_A.pdb #1
---
Chain | Description
A | nad-dependent protein deacetylase sirtuin-1
D | amc-containing peptide
> open /Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt format pdbqt
Summary of feedback from opening
/Users/shahryar/Desktop/موقت/SIRT1_Recheck/out1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.2 0.000 0.000
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: P1_1 and O7_9
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: P1_1 and O9_11
Ignored bad PDB record found on line 7
REMARK 3 A between atoms: P1_1 and O10_12
526 messages similar to the above omitted
Opened out1.pdbqt containing 9 structures (477 atoms, 513 bonds)
> toolshed show
> ui tool show ViewDockX
> hide #2.1-9 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.4 models
> show #2.2 models
> show #2.3 models
> hide #2.3 models
> hide #2.2,4 models
> show #2.4 models
> show #2.1 models
> hide #2.4 models
> clashes #2.1-9 restrict #!1 reveal true interSubmodel true
No clashes
> clashes #2.1-9 restrict #!1 reveal true interSubmodel true
No clashes
> clashes #2.1-9 restrict #!1 reveal true interSubmodel true
No clashes
> ui tool show ViewDockX
> show #2.2 models
> hide #2.1 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> show #2.5 models
> show #2.6 models
> show #2.7 models
> show #2.9 models
> show #2.8 models
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.8
53 atoms, 57 bonds, 1 residue, 1 model selected
> select #2.9
53 atoms, 57 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 333, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 92, in _intercept
return interceptor(request_info, *args)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 382, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 380, in handle_scheme
method(query)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 486, in _cb_prune
stars = int(query["stars"][0])
KeyError: 'stars'
KeyError: 'stars'
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 486, in _cb_prune
stars = int(query["stars"][0])
See log for complete Python traceback.
OpenGL version: 4.1 NVIDIA-16.0.13
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 432.60.3.0.0
SMC Version (system): 2.19f12
Software:
System Software Overview:
System Version: macOS 11.6.2 (20G314)
Kernel Version: Darwin 20.6.0
Time since boot: 5 days 16:51
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Automatic Graphics Switching: Supported
gMux Version: 4.0.8 [3.2.8]
Metal Family: Supported, Metal GPUFamily macOS 1
NVIDIA GeForce GT 750M:
Chipset Model: NVIDIA GeForce GT 750M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 2 GB
Vendor: NVIDIA (0x10de)
Device ID: 0x0fe9
Revision ID: 0x00a2
ROM Revision: 3776
Automatic Graphics Switching: Supported
gMux Version: 4.0.8 [3.2.8]
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → ViewdockX after rows deleted: KeyError: 'stars' |
comment:2 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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