ViewdockX after rows deleted: KeyError: 'stars'

[shahriar.arab@…]

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

[pett]

Fixed in tomorrow's daily build