![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8620 closed defect (fixed)
'ModellerScoringJob' object has no attribute 'results'
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "D:\研一\CHIMERAX\HBc dimer.cxs" format session
Log from Sat Mar 4 16:01:13 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 4BMG format mmcif fromDatabase pdb
4bmg title:
Crystal structure of hexameric HBc149 Y132A [more info...]
Chain information for 4bmg #1
---
Chain | Description | UniProt
A B C D E F | CAPSID PROTEIN | CAPSD_HBVD1
4bmg mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 6775 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> sym #1 assembly 2
> view
> sym #1 assembly 3
> view
> hide #!2 models
> show #!2 models
> close #1
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> color #2 #5a5eb2ff models
> color #2 #3ab2b2ff models
> color #2 yellow models
> rainbow
[Repeated 1 time(s)]
> color orange red
> color #3.1 #19cdffff
> color #3.1 #27edffff
> color #3 #b28f8fff models
> color #3 #b2b2b2ff models
[Repeated 1 time(s)]
> color #3 #5ab2a8ff models
> color #3 #64b24eff models
Alignment identifier is 1
> close session
> open 4BMG format mmcif fromDatabase pdb
4bmg title:
Crystal structure of hexameric HBc149 Y132A [more info...]
Chain information for 4bmg #1
---
Chain | Description | UniProt
A B C D E F | CAPSID PROTEIN | CAPSD_HBVD1
4bmg mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> sym #1 assembly 1
> view
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 9033 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /C:1-143
2266 atoms, 2334 bonds, 286 residues, 2 models selected
> select /D:1-142
2250 atoms, 2318 bonds, 284 residues, 2 models selected
> select /A:1-144
1134 atoms, 1168 bonds, 144 residues, 1 model selected
> sym #1 assembly 2
> view
> select /B:1-142
2250 atoms, 2318 bonds, 284 residues, 2 models selected
> select /A:1-144
2268 atoms, 2336 bonds, 288 residues, 2 models selected
> select /C:1-143
2266 atoms, 2334 bonds, 286 residues, 2 models selected
> delete select
Missing or invalid "atoms" argument: invalid atoms specifier
> delete /A
> delete /d
> undo
Undo failed, probably because structures have been modified.
> close session
> open 4BMG format mmcif fromDatabase pdb
4bmg title:
Crystal structure of hexameric HBc149 Y132A [more info...]
Chain information for 4bmg #1
---
Chain | Description | UniProt
A B C D E F | CAPSID PROTEIN | CAPSD_HBVD1
4bmg mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 6775 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /B:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /C:1-143
1133 atoms, 1167 bonds, 143 residues, 1 model selected
> select /D:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /B:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /D:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /B:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /D:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /B:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /D:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> delete /A
> delete /C
> delete /E
> delete /F
> hide #1 models
> show #1 models
> mlp sel
Map values for surface "4bmg_D SES surface": minimum -26.95, mean -3.418,
maximum 22.06
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "4bmg_D SES surface": minimum -26.95, mean -3.418,
maximum 22.06
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> hide sel surfaces
Alignment identifier is 1/D
> ui mousemode right translate
> ui mousemode right select
Drag select of 284 residues
Alignment identifier is 1
> select add #1
2250 atoms, 2318 bonds, 284 residues, 2 models selected
> select subtract #1
1 model selected
> select clear
Drag select of 7 residues
> ui mousemode right translate
> ui mousemode right select
> select add #1
2250 atoms, 2318 bonds, 284 residues, 2 models selected
> select subtract #1
1 model selected
Drag select of 4 residues
> select clear
> distance #1/B:109@CA #2/D:120@CA
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable object and one or more atoms, got 1 atoms and 0
measurable objects
> distance #1/B:109@CA #1/D:120@CA
Distance between /B THR 109 CA and /D VAL 120 CA: 41.600Å
> distance #1/B:120@CA #1/D:109@CA
Distance between /B VAL 120 CA and /D THR 109 CA: 12.875Å
> hide #2.1 models
> show #2.1 models
> delete select
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
[Repeated 1 time(s)]
> delete pseudobonds sel
> ui mousemode right label
> label #1/D:109
> label #1/B:120
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> show (#!1 & sel) target ab
> select sel @< 5
1168 atoms, 77 bonds, 152 residues, 1 model selected
> select /B-D:109-110
36 atoms, 36 bonds, 4 residues, 1 model selected
> select /B-D:109-110
36 atoms, 36 bonds, 4 residues, 1 model selected
> select /B-D:6-10,12-18,26-44,49-75,84-133
1732 atoms, 1770 bonds, 1 pseudobond, 216 residues, 2 models selected
> select /B-D:108-109
30 atoms, 28 bonds, 4 residues, 1 model selected
> select /B-D:108-109
30 atoms, 28 bonds, 4 residues, 1 model selected
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select sel @< 5
1168 atoms, 77 bonds, 152 residues, 1 model selected
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /B-D:109-110
36 atoms, 36 bonds, 4 residues, 1 model selected
> select /B-D:109-110
36 atoms, 36 bonds, 4 residues, 1 model selected
> select /B-D:109-110
36 atoms, 36 bonds, 4 residues, 1 model selected
> select /B-D:6-10,12-18,26-44,49-75,84-133
1732 atoms, 1770 bonds, 1 pseudobond, 216 residues, 2 models selected
> select /B-D:109-110
36 atoms, 36 bonds, 4 residues, 1 model selected
> select /B-D:109-110
36 atoms, 36 bonds, 4 residues, 1 model selected
> select /B-D:6-10,12-18,26-44,49-75,84-133
1732 atoms, 1770 bonds, 1 pseudobond, 216 residues, 2 models selected
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select sel :< 5
1205 atoms, 157 bonds, 152 residues, 1 model selected
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select sel @< 5
1168 atoms, 77 bonds, 152 residues, 1 model selected
> label #1/D:109
[Repeated 2 time(s)]
> label delete residues
[Repeated 4 time(s)]
> label #1/B:134
> label delete residues
> label #1/D:109
> ui mousemode right select
> select clear
> ui mousemode right label
> label delete residues
[Repeated 1 time(s)]
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right label
> label #1/B:120
> label delete residues
> label #1/D:109
> label #1/B:120
> label #1/D:109
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui mousemode right select
> select /D:109@OG1
1 atom, 1 residue, 1 model selected
> select /D:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel @< 5
1125 atoms, 37 bonds, 142 residues, 1 model selected
> help help:user/menu.html#selectzone
> select clear
[Repeated 1 time(s)]
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /B-D:109
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /B:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /D:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel @< 5
1125 atoms, 37 bonds, 142 residues, 1 model selected
> select sel @< 3
1126 atoms, 1159 bonds, 143 residues, 1 model selected
> ui mousemode right "tape measure"
> marker segment #3 position 57.27,-18.23,10.16 toPosition 57.47,-16.96,10.79
> color yellow radius 0.1 label 1.43 labelHeight 0.2 labelColor yellow
> marker delete #3
> ui mousemode right select
> select clear
> select /B:127
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> ui mousemode right "tape measure"
> marker segment #3 position 57.27,-18.23,10.16 toPosition 56.96,-23.82,13.6
> color yellow radius 0.1 label 6.572 labelHeight 0.6572 labelColor yellow
> marker delete #3
> marker segment #3 position 55.64,-15.53,11 toPosition 55.12,-22.11,13.64
> color yellow radius 0.1 label 7.11 labelHeight 0.711 labelColor yellow
> marker delete #3
> marker segment #3 position 56.01,-18.1,11.05 toPosition 55.69,-22.25,13.3
> color yellow radius 0.1 label 4.729 labelHeight 0.4729 labelColor yellow
> marker delete #3
> hide sel target a
> ui mousemode right select
> select /D:109@CB
1 atom, 1 residue, 1 model selected
> select clear
> select /D:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel :< 1
1125 atoms, 6 bonds, 142 residues, 1 model selected
> select clear
> select /D:109@CB
1 atom, 1 residue, 1 model selected
> select clear
> select /D:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel :> 5
2173 atoms, 2237 bonds, 274 residues, 1 model selected
> select clear
> select sel :> 5
Nothing selected
> select /D:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel :> 5
2173 atoms, 2237 bonds, 274 residues, 1 model selected
> ui mousemode right translate
> select add #1
2250 atoms, 2318 bonds, 1 pseudobond, 284 residues, 4 models selected
> select subtract #1
1 model selected
> close #2
> ui mousemode right label
> label delete residues
> ui mousemode right select
> select /D:127
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /B:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /B:127
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /B:127
19 atoms, 17 bonds, 2 residues, 2 models selected
> distance #1/B:127@CA #1/D:29@CA
Distance between /B ARG 127 CA and /D ASP 29 CA: 6.172Å
> ui mousemode right label
> label #1/B:127
> label #1/D:29
> close #2
> ui mousemode right label
> label delete residues
> ui mousemode right select
> distance #1/B:120@CA #1/D:109@CA
Distance between /B VAL 120 CA and /D THR 109 CA: 12.875Å
> select clear
> ui mousemode right label
> label #1/D:109
> label #1/B:120
> ui mousemode right translate
> ui mousemode right select
> select /D:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide (#!1 & sel) target a
> select clear
Drag select of 1 residues
> select clear
> ui mousemode right translate
> select /B
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /D
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /D and /B
Expected a keyword
> select /D & /B
Nothing selected
> select /D & /B
Nothing selected
> ui mousemode right select
Drag select of 4 atoms, 284 residues, 3 bonds, 1 pseudobonds
> mlp sel
Map values for surface "4bmg_B SES surface": minimum -26.19, mean -3.336,
maximum 22.15
Map values for surface "4bmg_D SES surface": minimum -26.95, mean -3.418,
maximum 22.06
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
[Repeated 1 time(s)]
> surface style solid
> transparency 50
Drag select of 4bmg_B SES surface, 424 of 150592 triangles, 6 residues
> select clear
[Repeated 1 time(s)]Drag select of 4bmg_B SES surface, 18 of 150592 triangles,
1 residues
> ui mousemode right translate
> ui mousemode right select
> select clear
> hide surfaces
> close #2
> select /B:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right label
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui mousemode right select
> select /B:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select add /D:132
13 atoms, 11 bonds, 2 residues, 2 models selected
Drag select of 3 residues
> select clear
[Repeated 2 time(s)]
> select /B:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /D:132
13 atoms, 11 bonds, 2 residues, 2 models selected
> ui mousemode right translate
> distance #1/B:136@CA #1/D:132@CA
Distance between /B ASN 136 CA and /D ALA 132 CA: 22.489Å
> distance #1/B:132@CA #1/D:136@CA
Distance between /B ALA 132 CA and /D ASN 136 CA: 11.475Å
> close session
> open 4BMG format mmcif fromDatabase pdb
4bmg title:
Crystal structure of hexameric HBc149 Y132A [more info...]
Chain information for 4bmg #1
---
Chain | Description | UniProt
A B C D E F | CAPSID PROTEIN | CAPSD_HBVD1
4bmg mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 6775 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> distance #1/B:132@CA #1/D:136@CA
Distance between /B ALA 132 CA and /D ASN 136 CA: 11.475Å
> distance /B:136@ca /c:132@cA
Distance between /B ASN 136 CA and /C ALA 132 CA: 72.458Å
> distance /B:136@ca /A:132@cA
Distance between /B ASN 136 CA and /A ALA 132 CA: 74.673Å
> distance /B:136@ca /E:132@cA
Distance between /B ASN 136 CA and /E ALA 132 CA: 91.289Å
> distance /B:136@ca /F:132@cA
Distance between /B ASN 136 CA and /F ALA 132 CA: 61.363Å
> distance /B:132@ca /F:136@cA
Distance between /B ALA 132 CA and /F ASN 136 CA: 72.758Å
> close #2
> distance /B:132@CA /D:136@CA
Distance between /B ALA 132 CA and /D ASN 136 CA: 11.475Å
> distance /B:136@CA /D:132@CA
Distance between /B ASN 136 CA and /D ALA 132 CA: 22.489Å
> ui mousemode right label
Alignment identifier is 1
> label delete residues
> ui mousemode right translate
> ui mousemode right select
> select /D:130
7 atoms, 7 bonds, 1 residue, 1 model selected
> select sel @< 5
34 atoms, 35 bonds, 6 residues, 1 model selected
Drag select of 2 residues
> select /D:130
7 atoms, 7 bonds, 1 residue, 1 model selected
> select sel @< 8
66 atoms, 65 bonds, 11 residues, 1 model selected
> select clear
> select /D:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel CPR rotLib Dunbrack
/D ASN 136: phi -81.8, psi 104.1 trans
Changed 10 bond radii
> swapaa #!1/D:136 CPR criteria 1 rotLib Dunbrack
Using Dunbrack library
4bmg #!1/D ASN 136: phi -81.8, psi 104.1 trans
Applying PRO rotamer (chi angles: 30.1 -34.4) to 4bmg #!1/D PRO 136
> swapaa interactive sel CPR rotLib Dunbrack
/D PRO 136: phi -81.8, psi 104.1 trans
Changed 10 bond radii
> swapaa #!1/D:136 CPR criteria 1 rotLib Dunbrack
Using Dunbrack library
4bmg #!1/D PRO 136: phi -81.8, psi 104.1 trans
Applying PRO rotamer (chi angles: 30.1 -34.4) to 4bmg #!1/D PRO 136
> select clear
> select /D:136
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel TPR rotLib Dunbrack
/D PRO 136: phi -81.8, psi 104.1 trans
Changed 10 bond radii
> swapaa interactive sel CYS rotLib Dynameomics
/D PRO 136: phi -81.8, psi 104.1 trans
Changed 9 bond radii
> help help:user/tools/rotamers.html
> swapaa #!1/D:136 CYS criteria 1 rotLib Dynameomics
Using Dynameomics library
4bmg #!1/D PRO 136: phi -81.8, psi 104.1 trans
Applying CYS rotamer (chi angles: -61.0) to 4bmg #!1/D CYS 136
> swapaa interactive sel CYS rotLib Dunbrack
/D CYS 136: phi -81.8, psi 104.1 trans
Changed 9 bond radii
> swapaa #!1/D:136 CYS criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
4bmg #!1/D CYS 136: phi -81.8, psi 104.1 trans
Applying CYS rotamer (chi angles: -178.2) to 4bmg #!1/D CYS 136
> show sel target ab
> select clear
[Repeated 3 time(s)]
> select /D:136
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> ui mousemode right translate
> ui mousemode right select
> select /B:132
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel CYS rotLib Dunbrack
/B ALA 132: phi -104.5, psi -20.3 trans
Changed 9 bond radii
> swapaa #!1/B:132 CYS criteria 1 rotLib Dunbrack
Using Dunbrack library
4bmg #!1/B ALA 132: phi -104.5, psi -20.3 trans
Applying CYS rotamer (chi angles: -62.4) to 4bmg #!1/B CYS 132
> select clear
> select /B:132
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> distance /B:136@SG /D:132@SG
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable object and one or more atoms, got 0 atoms and 0
measurable objects
> select clear
> ui mousemode right "tape measure"
> marker segment #3 position 61.24,-26.89,13.29 toPosition 57.97,-37.61,4.702
> color yellow radius 0.1 label 14.12 labelHeight 1.412 labelColor yellow
> marker delete #3
> ui mousemode right translate
> distance /B:136@SA /D:132@SA
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable object and one or more atoms, got 0 atoms and 0
measurable objects
> distance /B:136@SG /D:132@SG
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable object and one or more atoms, got 0 atoms and 0
measurable objects
> select /A-F:29
48 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-F:29
48 atoms, 42 bonds, 6 residues, 1 model selected
> ui mousemode right select
> select clear
> select /D:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:127
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /D:29
19 atoms, 17 bonds, 2 residues, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel CYS rotLib Dunbrack
/B ARG 127: phi -72.0, psi -36.2 trans
Changed 9 bond radii
4bmg #!1/D ASP 29: phi -72.0, psi -36.8 trans
Changed 9 bond radii
> swapaa #!1/D:29 CYS criteria 1 rotLib Dunbrack
Using Dunbrack library
4bmg #!1/D ASP 29: phi -72.0, psi -36.8 trans
Applying CYS rotamer (chi angles: -69.5) to 4bmg #!1/D CYS 29
> swapaa #!1/B:127 CYS criteria 1 rotLib Dunbrack
Using Dunbrack library
4bmg #!1/B ARG 127: phi -72.0, psi -36.2 trans
Applying CYS rotamer (chi angles: -69.5) to 4bmg #!1/B CYS 127
> show sel target ab
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select clear
> select /D:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /B:127
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel target ab
> select clear
> ui mousemode right "tape measure"
> marker segment #3 position 58.85,-14.45,13.2 toPosition 55.02,-16.62,10.79
> color yellow radius 0.1 label 5.018 labelHeight 0.5018 labelColor yellow
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right "tape measure"
> marker segment #3 position 60.77,-16,17.26 toPosition 58.54,-21.8,10.59
> color yellow radius 0.1 label 9.113 labelHeight 0.9113 labelColor yellow
> select #1/A-F:6-10,12-18,26-44,49-75,81-133
5340 atoms, 5457 bonds, 666 residues, 1 model selected
> select #1/A-F:61
36 atoms, 33 bonds, 6 residues, 1 model selected
> select #1/A-F:61
36 atoms, 33 bonds, 6 residues, 1 model selected
> marker segment #3 position 53.43,2.605,-1.605 toPosition 51.1,6.188,-2.334
> color yellow radius 0.1 label 4.333 labelHeight 0.4333 labelColor yellow
> marker delete #3
> ui mousemode right translate
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> ui mousemode right translate
> ui mousemode right select
> close session
> open 4BMG format mmcif fromDatabase pdb
4bmg title:
Crystal structure of hexameric HBc149 Y132A [more info...]
Chain information for 4bmg #1
---
Chain | Description | UniProt
A B C D E F | CAPSID PROTEIN | CAPSD_HBVD1
4bmg mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 6775 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> delete /A
> delete /C
> delete /E
> delete /F
> save "D:/研一/CHIMERAX/HBc dimer.cxs"
——— End of log from Sat Mar 4 16:01:13 2023 ———
opened ChimeraX session
Alignment identifier is 1
> ui tool show "Modeller Comparative"
> modeller comparative 1:1 numModels 5 fast false multichain true hetPreserve
> true hydrogens true waterPreserve true
Cannot preserve water/het with more than one template per target; not
preserving
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> modeller comparative 1:1 numModels 5 fast false multichain true hetPreserve
> true hydrogens true waterPreserve true directory D:/研一/CHIMERAX
Cannot preserve water/het with more than one template per target; not
preserving
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> modeller comparative 1:1 numModels 5 fast true multichain true hetPreserve
> true hydrogens true waterPreserve true directory D:/研一/CHIMERAX
Cannot preserve water/het with more than one template per target; not
preserving
Error launching job: Invalid license key
> ui tool show "Modeller Comparative"
> modeller comparative 1:1 numModels 5 fast true multichain true hetPreserve
> true hydrogens true waterPreserve true directory D:/研一/CHIMERAX
Cannot preserve water/het with more than one template per target; not
preserving
Webservices job id: AHWJXQWITPHI8M6E
Modeller job (ID AHWJXQWITPHI8M6E) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bmg, chain B (#1) with chains_B,D, chain B (#), sequence alignment
score = 761.8
Matchmaker 4bmg, chain D (#1) with chains_B,D, chain D (#), sequence alignment
score = 729.4
RMSD between 284 pruned atom pairs is 0.163 angstroms; (across all 284 pairs:
0.163)
Associated chains_B,D chain B to chains B,D with 0 mismatches
Associated chains_B,D chain D to chains B,D with 0 mismatches
Chain information for chains_B,D
---
Chain | Description
2.1/B 2.1/D | No description available
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> hide #1 models
> hide #2.1 models
> show #2.1 models
Alignment identifier is 2
> select #2.1/B:143-144/D:297-298
66 atoms, 66 bonds, 4 residues, 1 model selected
> select #2.1/B:143-154/D:297-308
396 atoms, 400 bonds, 24 residues, 1 model selected
> close session
> open 4BMG format mmcif fromDatabase pdb
4bmg title:
Crystal structure of hexameric HBc149 Y132A [more info...]
Chain information for 4bmg #1
---
Chain | Description | UniProt
A B C D E F | CAPSID PROTEIN | CAPSD_HBVD1
4bmg mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> sym #1 assembly 1
> view
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 9033 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> close #1
> sym #2
4bmg mmCIF Assemblies
---
> log metadata #2
No models had metadata
> log chains #2
Chain information for 4bmg #2.1
---
Chain | Description | UniProt
C D | CAPSID PROTEIN | CAPSD_HBVD1
> select /C:1-143
1133 atoms, 1167 bonds, 143 residues, 1 model selected
> select /D:1-142
1125 atoms, 1159 bonds, 142 residues, 1 model selected
> select /C:1-143
1133 atoms, 1167 bonds, 143 residues, 1 model selected
Alignment identifier is 2.1/C
> select clear
> select /C:143
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:143
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Modeller Comparative"
> modeller comparative 2.1/C:1 numModels 5 fast true multichain true
> hetPreserve true hydrogens true waterPreserve true directory D:/研一/CHIMERAX
Cannot preserve water/het with more than one template per target; not
preserving
Webservices job id: Z331J86ODTRU4BSC
Modeller job (ID Z331J86ODTRU4BSC) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bmg, chain C (#2.1) with chain_C, chain C (#), sequence alignment
score = 774.4
RMSD between 143 pruned atom pairs is 0.159 angstroms; (across all 143 pairs:
0.159)
Associated chain_C chain C to chain C with 0 mismatches
Chain information for chain_C
---
Chain | Description
1.1/C | No description available
> hide #!2 models
> hide #2.1 models
> hide #1.1 models
> hide #!1 models
> show #!1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
Alignment identifier is 1
> select #1.1/C:152-153
40 atoms, 40 bonds, 2 residues, 1 model selected
> select #1.1/C:152-154
61 atoms, 62 bonds, 3 residues, 1 model selected
> select #2.1/C:143 #1.1/C:143
27 atoms, 25 bonds, 2 residues, 2 models selected
> select #2.1/C:143 #1.1/C:143-154
206 atoms, 207 bonds, 13 residues, 2 models selected
> modeller scores #1.1 refresh false
Exception in thread Thread-94:
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\threading.py", line 973, in _bootstrap_inner
self.run()
File "D:\ChimeraX\bin\lib\threading.py", line 910, in run
self._target(*self._args, **self._kwargs)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\tasks.py", line 213, in
_run_thread
self.run(*args, **kw)
TypeError: run() takes 1 positional argument but 6 were given
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 661, in
customEvent
func(*args, **kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
See log for complete Python traceback.
> modeller scores #1.1 refresh true
Exception in thread Thread-97:
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\threading.py", line 973, in _bootstrap_inner
self.run()
File "D:\ChimeraX\bin\lib\threading.py", line 910, in run
self._target(*self._args, **self._kwargs)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\tasks.py", line 213, in
_run_thread
self.run(*args, **kw)
TypeError: run() takes 1 positional argument but 6 were given
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 661, in
customEvent
func(*args, **kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
See log for complete Python traceback.
> close #1
> show #!2 models
> show #2.1 models
> ui tool show "Model Loops"
> modeller refine 2.1/C:1:all-missing numModels 5 fast false adjacentFlexible
> 1 protocol standard
Webservices job id: OQTXZZMP0P2FKCAJ
Modeller job (ID OQTXZZMP0P2FKCAJ) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bmg, chain C (#2.1) with chain_C, chain C (#), sequence alignment
score = 803.8
RMSD between 143 pruned atom pairs is 0.009 angstroms; (across all 143 pairs:
0.009)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bmg, chain C (#2.1) with chain_C, chain C (#), sequence alignment
score = 803.8
RMSD between 143 pruned atom pairs is 0.036 angstroms; (across all 143 pairs:
0.036)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bmg, chain C (#2.1) with chain_C, chain C (#), sequence alignment
score = 803.8
RMSD between 143 pruned atom pairs is 0.027 angstroms; (across all 143 pairs:
0.027)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bmg, chain C (#2.1) with chain_C, chain C (#), sequence alignment
score = 803.8
RMSD between 143 pruned atom pairs is 0.010 angstroms; (across all 143 pairs:
0.010)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bmg, chain C (#2.1) with chain_C, chain C (#), sequence alignment
score = 803.8
RMSD between 143 pruned atom pairs is 0.014 angstroms; (across all 143 pairs:
0.014)
Associated chain_C chain C to chain C with 0 mismatches
[Repeated 4 time(s)] Chain information for chain_C
---
Chain | Description
1.1/C 1.2/C 1.3/C 1.4/C 1.5/C | No description available
> modeller scores #1.1-5 refresh false
Exception in thread Thread-123:
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\threading.py", line 973, in _bootstrap_inner
Exception in thread Thread-125:
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\threading.py", line 973, in _bootstrap_inner
self.run()
File "D:\ChimeraX\bin\lib\threading.py", line 910, in run
self.run()
File "D:\ChimeraX\bin\lib\threading.py", line 910, in run
self._target(*self._args, **self._kwargs)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\tasks.py", line 213, in
_run_thread
Exception in thread Thread-127:
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\threading.py", line 973, in _bootstrap_inner
Exception in thread Thread-129:
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\threading.py", line 973, in _bootstrap_inner
self.run()
File "D:\ChimeraX\bin\lib\threading.py", line 910, in run
self.run(*args, **kw)
TypeError: run() takes 1 positional argument but 6 were given
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 661, in
customEvent
func(*args, **kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
See log for complete Python traceback.
self._target(*self._args, **self._kwargs)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\tasks.py", line 213, in
_run_thread
Exception in thread Thread-131:
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\threading.py", line 973, in _bootstrap_inner
self.run(*args, **kw)
TypeError: run() takes 1 positional argument but 6 were given
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 661, in
customEvent
func(*args, **kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
See log for complete Python traceback.
self._target(*self._args, **self._kwargs)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\tasks.py", line 213, in
_run_thread
self.run()
File "D:\ChimeraX\bin\lib\threading.py", line 910, in run
self.run()
File "D:\ChimeraX\bin\lib\threading.py", line 910, in run
self._target(*self._args, **self._kwargs)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\tasks.py", line 213, in
_run_thread
self._target(*self._args, **self._kwargs)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\tasks.py", line 213, in
_run_thread
self.run(*args, **kw)
TypeError: run() takes 1 positional argument but 6 were given
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 661, in
customEvent
func(*args, **kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
See log for complete Python traceback.
self.run(*args, **kw)
TypeError: run() takes 1 positional argument but 6 were given
self.run(*args, **kw)
TypeError: run() takes 1 positional argument but 6 were given
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 661, in
customEvent
func(*args, **kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 661, in
customEvent
func(*args, **kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
AttributeError: 'ModellerScoringJob' object has no attribute 'results'
File "D:\ChimeraX\bin\lib\site-packages\chimerax\modeller\scores.py", line
136, in on_finish
if len(self.results) > 1:
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.3616
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Acer
Model: Swift SF314-71
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,870,006,784
MaxProcessMemory: 137,438,953,344
CPU: 16 12th Gen Intel(R) Core(TM) i5-12500H
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 'ModellerScoringJob' object has no attribute 'results' |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Score fetching had not been updated for changes to core/tasks