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Opened 2 years ago
Closed 2 years ago
#9423 closed defect (fixed)
"swapaa interactive" for non-rotamer res type produces traceback
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | 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: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/15310/Desktop/7ahl.pdb
7ahl.pdb title:
Alpha-hemolysin from staphylococcus aureus [more info...]
Chain information for 7ahl.pdb #1
---
Chain | Description | UniProt
A B C D E F G | alphatoxin | HLA_STAAU 1-293
> hide atoms
> hide cartoons
> show surfaces
> show atoms
> hide surfaces
> hide cartoons
> hide atoms
> show atoms
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 22778 atom styles
> style sphere
Changed 22778 atom styles
> style ball
Changed 22778 atom styles
> style sphere
Changed 22778 atom styles
> style stick
Changed 22778 atom styles
> hide atoms
> hide cartoons
> show surfaces
> set bgColor white
> set bgColor #ffffff00
> style stick
Changed 22778 atom styles
> style stick
Changed 22778 atom styles
> style stick
Changed 22778 atom styles
> style sphere
Changed 22778 atom styles
> style sphere
Changed 22778 atom styles
> style ball
Changed 22778 atom styles
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> clip
[Repeated 1 time(s)]
> ui mousemode right "clip rotate"
[Repeated 2 time(s)]
> ui mousemode right zone
> ui mousemode right "clip rotate"
> ui mousemode right clip
> hide #!1 models
> show #!1 models
> select add #1
22778 atoms, 22324 bonds, 2869 residues, 8 models selected
> select subtract #1
7 models selected
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ARG 66
/A LYS 75
/D LYS 30
/D LYS 240
/F LYS 283
/G LYS 30
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7ahl.pdb_A SES surface #1.1: minimum, -13.59, mean -0.18,
maximum 12.86
Coulombic values for 7ahl.pdb_B SES surface #1.2: minimum, -13.03, mean 0.29,
maximum 13.02
Coulombic values for 7ahl.pdb_C SES surface #1.3: minimum, -13.46, mean 0.23,
maximum 12.96
Coulombic values for 7ahl.pdb_D SES surface #1.4: minimum, -11.79, mean 0.11,
maximum 12.41
Coulombic values for 7ahl.pdb_E SES surface #1.5: minimum, -17.53, mean 0.74,
maximum 15.61
Coulombic values for 7ahl.pdb_F SES surface #1.6: minimum, -13.58, mean 0.44,
maximum 19.70
Coulombic values for 7ahl.pdb_G SES surface #1.7: minimum, -13.80, mean 0.44,
maximum 13.88
To also show corresponding color key, enter the above coulombic command and
add key true
Alignment identifier is 1
> select
> /A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> undo
> select #1.2.1
1 model selected
> color #1.2.1 white
> select clear
> select #1.1.1
1 model selected
> select clear
> select #1.2.1
1 model selected
> color #1.2.1 dark gray
> ui tool show "Side View"
> save "C:/学习区/CXS/1 ahl.cxs"
> open C:/Users/15310/Desktop/7ahl.pdb
7ahl.pdb title:
Alpha-hemolysin from staphylococcus aureus [more info...]
Chain information for 7ahl.pdb #2
---
Chain | Description | UniProt
A B C D E F G | alphatoxin | HLA_STAAU 1-293
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> select 113
Expected an objects specifier or a keyword
> select 113
Expected an objects specifier or a keyword
> select #2/G:164@CD
1 atom, 1 residue, 1 model selected
> select #1/G:92@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> show sel surfaces
Drag select of 7ahl.pdb_A SES surface, 7ahl.pdb_B SES surface, 7ahl.pdb_C SES
surface, 7ahl.pdb_D SES surface, 7ahl.pdb_E SES surface, 7ahl.pdb_F SES
surface, 7ahl.pdb_G SES surface, 22778 atoms, 1636 bonds
> select clear
[Repeated 1 time(s)]
> show atoms
> hide atoms
> hide cartoons
> show surfaces
> hide surfaces
> show surfaces
> show cartoons
> hide cartoons
> ui tool show "Side View"
> clip
[Repeated 1 time(s)]
> clipe
Unknown command: clipe
> clip
> select /A:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> ui tool show "Side View"
> color (#!1-2 & sel) red
> select clear
[Repeated 1 time(s)]
> select #1.3.2
1 model selected
> select #1.2.2
1 model selected
> select up
2 models selected
> select up
2909 atoms, 293 residues, 4 models selected
> select up
3293 atoms, 3217 bonds, 421 residues, 4 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 4 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 10 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 11 models selected
> select down
22778 atoms, 22324 bonds, 2869 residues, 17 models selected
> select down
9 models selected
> select down
3293 atoms, 3217 bonds, 421 residues, 3 models selected
> select down
2909 atoms, 293 residues, 4 models selected
> select down
2 models selected
> select up
2909 atoms, 293 residues, 4 models selected
> select up
3293 atoms, 3217 bonds, 421 residues, 4 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 4 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 10 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 10 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 11 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 18 models selected
> color (#!1-2 & sel) forest green
> select clear
> select /A:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> color (#!1-2 & sel) red
> select /B:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> color (#!1-2 & sel) red
> select /C:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> color (#!1-2 & sel) red
> select /D:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> select /E:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> select /F:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> color (#!1-2 & sel) red
> select /G:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> color (#!1-2 & sel) red
> select /G:115
18 atoms, 16 bonds, 2 residues, 2 models selected
> color (#!1-2 & sel) yellow
> color (#!1-2 & sel) lime
> select down
18 atoms, 16 bonds, 2 residues, 4 models selected
> select down
18 atoms, 16 bonds, 2 residues, 4 models selected
> select down
18 atoms, 16 bonds, 2 residues, 4 models selected
> select up
296 atoms, 300 bonds, 32 residues, 4 models selected
> select up
5808 atoms, 5912 bonds, 586 residues, 4 models selected
> select up
6486 atoms, 6364 bonds, 812 residues, 4 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 4 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 16 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 16 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 16 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 16 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 16 models selected
> select down
14 models selected
> select down
6486 atoms, 6364 bonds, 812 residues, 2 models selected
> select down
5808 atoms, 5912 bonds, 586 residues, 4 models selected
> select down
296 atoms, 300 bonds, 32 residues, 4 models selected
> select down
18 atoms, 16 bonds, 2 residues, 4 models selected
> select up
296 atoms, 300 bonds, 32 residues, 4 models selected
> select up
5808 atoms, 5912 bonds, 586 residues, 4 models selected
> select up
6486 atoms, 6364 bonds, 812 residues, 4 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 4 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 16 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 16 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 16 models selected
> color (#!1-2 & sel) light gray
> select #1.5.1
1 model selected
> select #1.4.1
1 model selected
> select #1.5.1
1 model selected
> select #1.4.1
1 model selected
> select #1.3.1
1 model selected
> select #1.1.1
1 model selected
> select #1.7.1
1 model selected
> select #1.6.1
1 model selected
> select #1.5.1
1 model selected
> select #1.2.1
1 model selected
> select #1.4.1
1 model selected
> select #1.1.1
1 model selected
> select #1.6.1
1 model selected
> select #1.1.1
1 model selected
> color #1.1.1 cornflower blue
> select #1.1.1
1 model selected
> select #1.4.1
1 model selected
> select #1.1.1
1 model selected
> color #1.1.1 orange
> select #1.1.1
1 model selected
> select up
2891 atoms, 293 residues, 3 models selected
> select up
3245 atoms, 3179 bonds, 411 residues, 3 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 3 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 9 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 10 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 17 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 17 models selected
> color (#!1-2 & sel) dim gray
> color (#!1-2 & sel) dark gray
> select up
45556 atoms, 44648 bonds, 5738 residues, 17 models selected
> color (#!1-2 & sel) light sea green
> style sel sphere
Changed 45556 atom styles
> style sel ball
Changed 45556 atom styles
> hide sel cartoons
> style sel sphere
Changed 45556 atom styles
> select down
22778 atoms, 22324 bonds, 2869 residues, 16 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 10 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 17 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 17 models selected
> clip
> color (#!1-2 & sel) hot pink
[Repeated 1 time(s)]
> color (#!1-2 & sel) purple
> color (#!1-2 & sel) forest green
> color (#!1-2 & sel) black
> color (#!1-2 & sel) gray
> select #1.4.1
1 model selected
> color #1.4.1 orange red
> undo
> select clear
> select #1.4.1
1 model selected
> color #1.4.1 yellow
> select clear
> select #1.1.1
1 model selected
> select #1/A:10@CA
1 atom, 1 residue, 1 model selected
> select #1/B:18@H
1 atom, 1 residue, 1 model selected
> select #1/B:19@CA
1 atom, 1 residue, 1 model selected
> select #1.1.1
1 model selected
> select
45556 atoms, 44648 bonds, 5738 residues, 30 models selected
> color (#!1-2 & sel) lime
> color (#!1-2 & sel) orange
> style sel sphere
Changed 45556 atom styles
> style sel ball
Changed 45556 atom styles
> style sel sphere
Changed 45556 atom styles
> style sel sphere
Changed 45556 atom styles
> style sel sphere
Changed 45556 atom styles
> style sel sphere
Changed 45556 atom styles
> style sel sphere
Changed 45556 atom styles
> style sel sphere
Changed 45556 atom styles
> style sel sphere
Changed 45556 atom styles
> hide sel surfaces
> show sel surfaces
> show sel cartoons
> select clear
> select #1.3.1
1 model selected
> ui tool show "Side View"
> select add #1.7
2904 atoms, 293 residues, 4 models selected
> color (#!1 & sel) orange
> select subtract #1.7
2 models selected
> color #1 cyan
> clip
> color #1.3.1 forest green
> select #1.4.1
1 model selected
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
[Repeated 3 time(s)]
> undo
[Repeated 4 time(s)]
> lighting flat
> lighting full
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> ui tool show "Side View"
> color #1.3.1 cornflower blue
> undo
> save C:/学习区/CXS/切面，WT，黄色.cxs
> select #1.4.1
1 model selected
> select #1.3.1
1 model selected
> select #1.4.1
1 model selected
> select up
2 models selected
> select up
2896 atoms, 293 residues, 4 models selected
> select up
3262 atoms, 3192 bonds, 415 residues, 4 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 4 models selected
> select up
22778 atoms, 22324 bonds, 2869 residues, 10 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 11 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 18 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 18 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 18 models selected
> select down
22778 atoms, 22324 bonds, 2869 residues, 17 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 11 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 18 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 18 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 18 models selected
> select up
45556 atoms, 44648 bonds, 5738 residues, 18 models selected
> color (#!1-2 & sel) cornflower blue
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting soft
> select #1.3.1
1 model selected
> color #1.3.1 cornflower blue
> select #1.4.1
1 model selected
> color #1.4.1 yellow
> select #1/C:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> lighting simple
> select #1.3.1
1 model selected
> color #1.3.1 orange red
> select #1.7.1
1 model selected
> color #1.7.1 cornflower blue
> select #1.6.1
1 model selected
> select #1.6.1
1 model selected
> color #1.6.1 cornflower blue
> select #1.5.1
1 model selected
> color #1.5.1 cornflower blue
> select #1.4.1
1 model selected
> select #1.1.1
1 model selected
> select add #1.2.1
2 models selected
> select add #1.4.1
3 models selected
> select add #1.3.1
4 models selected
> color #1.1.1#1.2.1#1.3.1#1.4.1 cornflower blue
> select clear
> lighting full
> lighting simple
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> select /C:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> select /A,C:113
36 atoms, 32 bonds, 4 residues, 2 models selected
> select /A,C,B,D,E,F,G:113
126 atoms, 112 bonds, 14 residues, 2 models selected
> color (#!1-2 & sel) hot pink
> select clear
> select /A,C,B,D,E,F,G:115
126 atoms, 112 bonds, 14 residues, 2 models selected
> color (#!1-2 & sel) yellow
> select clear
> save "C:/学习区/CXS/切面，αHLWT 蓝色，标注113红色，115黄色.cxs"
> save C:/学习区/CXS/αHLWT切面，标注M113红色，115黄色.tif width 1128 height 693 supersample
> 3
> save C:/学习区/CXS/αHLWT切面，标注M113红色，115黄色.cxs
> save C:/学习区/CXS/αHLWT切面，标注M113红色，115黄色.tif width 2000 height 1216
> supersample 3 transparentBackground true
> select
> #1/A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> select clear
> select #1/A-G:113
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/A-G:113
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1.2.1
1 model selected
> select #1.3.1
1 model selected
> select clear
> select #1/A-G:114
56 atoms, 49 bonds, 7 residues, 1 model selected
> select #1/A-G:113-114
119 atoms, 112 bonds, 14 residues, 1 model selected
> select #1/A-G:112-113
161 atoms, 161 bonds, 14 residues, 1 model selected
> select #1/A-G:112-113
161 atoms, 161 bonds, 14 residues, 1 model selected
> select #1/A-G:113
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/A-G:113
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/A-G:113
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/A-G:101-113
1008 atoms, 1029 bonds, 91 residues, 1 model selected
> select
> #1/A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> select clear
> select #1/A-G:101-113
1008 atoms, 1029 bonds, 91 residues, 1 model selected
> select clear
> select
> #1/A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> select clear
> select #1/A-G:101-113
1008 atoms, 1029 bonds, 91 residues, 1 model selected
> select clear
> select
> #1/A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> select clear
> select #1/A-G:101-113
1008 atoms, 1029 bonds, 91 residues, 1 model selected
> select clear
> select #1/C:187@N
1 atom, 1 residue, 1 model selected
> select #1/A-G:101-113
1008 atoms, 1029 bonds, 91 residues, 1 model selected
> select
> #1/A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> select clear
> select #1/A-G:101-113
1008 atoms, 1029 bonds, 91 residues, 1 model selected
> select clear
> select #1/A-G:190
56 atoms, 49 bonds, 7 residues, 1 model selected
> select #1/A-G:181-190
742 atoms, 770 bonds, 70 residues, 1 model selected
> select
> #1/A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> select clear
> select
> #1/A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> select clear
> select
> #1/A-G:21-29,34-43,51-61,66-71,75-90,97-102,111-126,132-147,153-158,164-171,228-234,242-261,264-270,274-285,290-292
10783 atoms, 10895 bonds, 1071 residues, 1 model selected
> select #1/A-G:113-114
119 atoms, 112 bonds, 14 residues, 1 model selected
> select #1/A-G:113-120
525 atoms, 532 bonds, 56 residues, 1 model selected
> select #1/A-G:114
56 atoms, 49 bonds, 7 residues, 1 model selected
> select #1/A-G:113-114
119 atoms, 112 bonds, 14 residues, 1 model selected
> select #1/A-G:112-113
161 atoms, 161 bonds, 14 residues, 1 model selected
> select #1/A-G:112-113
161 atoms, 161 bonds, 14 residues, 1 model selected
> select #1/A-G:113-114
119 atoms, 112 bonds, 14 residues, 1 model selected
> select #1/A-G:113-114
119 atoms, 112 bonds, 14 residues, 1 model selected
> select #1/A-G:113-120
525 atoms, 532 bonds, 56 residues, 1 model selected
> select clear
> select #1/A-G:113
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/A-G:113
63 atoms, 56 bonds, 7 residues, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
7ahl.pdb #1/A MET 113: phi -155.9, psi 123.0 trans
Changed 600 bond radii
7ahl.pdb #!1/B MET 113: phi -147.8, psi 111.0 trans
Changed 600 bond radii
7ahl.pdb #!1/C MET 113: phi -144.1, psi 131.6 trans
Changed 600 bond radii
7ahl.pdb #!1/D MET 113: phi -148.1, psi 138.7 trans
Changed 600 bond radii
7ahl.pdb #!1/E MET 113: phi -146.6, psi 135.9 trans
Changed 600 bond radii
7ahl.pdb #!1/F MET 113: phi -148.0, psi 121.5 trans
Changed 600 bond radii
7ahl.pdb #!1/G MET 113: phi -133.7, psi 148.7 trans
Changed 600 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #!1/G:113 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
7ahl.pdb #!1/G MET 113: phi -133.7, psi 148.7 trans
Applying ARG rotamer (chi angles: -63.3 -69.9 -177.1 -87.5) to 7ahl.pdb #!1/G
ARG 113
> swapaa #!1/F:113 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
7ahl.pdb #!1/F MET 113: phi -148.0, psi 121.5 trans
Applying ARG rotamer (chi angles: -176.3 177.1 179.2 -179.0) to 7ahl.pdb #!1/F
ARG 113
> swapaa #!1/D:113 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
7ahl.pdb #!1/D MET 113: phi -148.1, psi 138.7 trans
Applying ARG rotamer (chi angles: -65.3 -70.3 -175.0 -84.9) to 7ahl.pdb #!1/D
ARG 113
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #!1/E:113 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
7ahl.pdb #!1/E MET 113: phi -146.6, psi 135.9 trans
Applying ARG rotamer (chi angles: -65.3 -70.3 -175.0 -84.9) to 7ahl.pdb #!1/E
ARG 113
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #!1/C:113 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
7ahl.pdb #!1/C MET 113: phi -144.1, psi 131.6 trans
Applying ARG rotamer (chi angles: -64.9 -70.2 -176.3 -85.6) to 7ahl.pdb #!1/C
ARG 113
> swapaa #!1/B:113 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
7ahl.pdb #!1/B MET 113: phi -147.8, psi 111.0 trans
Applying ARG rotamer (chi angles: -176.6 177.7 179.2 -179.6) to 7ahl.pdb #!1/B
ARG 113
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #!1/A:113 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
7ahl.pdb #!1/A MET 113: phi -155.9, psi 123.0 trans
Applying ARG rotamer (chi angles: -176.6 176.8 179.2 -178.4) to 7ahl.pdb #!1/A
ARG 113
> select #1/A-G:113-120
546 atoms, 553 bonds, 56 residues, 1 model selected
> select #1/A-G:115
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/A-G:115
63 atoms, 56 bonds, 7 residues, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Command cancelled by user
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Using Dunbrack library
Swapping 7ahl.pdb #1/A THR 115 to ALA
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 111, in launch_rotamers
run(self.session, "swapaa interactive sel %s rotLib %s" % (res_type,
lib_name))
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 147, in rotamers
rotamers = swap_res.get_rotamers(session, r, res_type=r_type, rot_lib=rot_lib,
log=log)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 204, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 42, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 204, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 416, in template_swap_res
info = Atom.idatm_info_map[tmpl_bud.idatm_type]
KeyError: ''
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 113, in launch_rotamers
run(self.session, "swapaa sel %s rotLib %s" % (res_type, lib_name))
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 40, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 49, in swap_aa
template_swap_res(res, r_type, bfactor=bfactor)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 420, in template_swap_res
raise AssertionError("Can't determine atom type information for atom %s of
residue %s" % (bud, res))
AssertionError: Can't determine atom type information for atom O of residue
7ahl.pdb #1/A THR 115
AssertionError: Can't determine atom type information for atom O of residue
7ahl.pdb #1/A THR 115
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 420, in template_swap_res
raise AssertionError("Can't determine atom type information for atom %s of
residue %s" % (bud, res))
See log for complete Python traceback.
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> undo
[Repeated 2 time(s)]Undo failed, probably because structures have been
modified.
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Using Dunbrack library
Swapping 7ahl.pdb #1/A THR 115 to ALA
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 111, in launch_rotamers
run(self.session, "swapaa interactive sel %s rotLib %s" % (res_type,
lib_name))
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 147, in rotamers
rotamers = swap_res.get_rotamers(session, r, res_type=r_type, rot_lib=rot_lib,
log=log)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 204, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 42, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 204, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 416, in template_swap_res
info = Atom.idatm_info_map[tmpl_bud.idatm_type]
KeyError: ''
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 113, in launch_rotamers
run(self.session, "swapaa sel %s rotLib %s" % (res_type, lib_name))
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 40, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 49, in swap_aa
template_swap_res(res, r_type, bfactor=bfactor)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 420, in template_swap_res
raise AssertionError("Can't determine atom type information for atom %s of
residue %s" % (bud, res))
AssertionError: Can't determine atom type information for atom O of residue
7ahl.pdb #1/A THR 115
AssertionError: Can't determine atom type information for atom O of residue
7ahl.pdb #1/A THR 115
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 420, in template_swap_res
raise AssertionError("Can't determine atom type information for atom %s of
residue %s" % (bud, res))
See log for complete Python traceback.
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Command cancelled by user
> select #1/A-G:113
84 atoms, 77 bonds, 7 residues, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
7ahl.pdb #1/A ARG 113: phi -155.9, psi 123.0 trans
Changed 600 bond radii
7ahl.pdb #!1/B ARG 113: phi -147.8, psi 111.0 trans
Changed 600 bond radii
7ahl.pdb #!1/C ARG 113: phi -144.1, psi 131.6 trans
Changed 600 bond radii
7ahl.pdb #!1/D ARG 113: phi -148.1, psi 138.7 trans
Changed 600 bond radii
7ahl.pdb #!1/E ARG 113: phi -146.6, psi 135.9 trans
Changed 600 bond radii
7ahl.pdb #!1/F ARG 113: phi -148.0, psi 121.5 trans
Changed 600 bond radii
7ahl.pdb #!1/G ARG 113: phi -133.7, psi 148.7 trans
Changed 600 bond radii
> swapaa #!1/G:113 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
7ahl.pdb #!1/G ARG 113: phi -133.7, psi 148.7 trans
Applying ARG rotamer (chi angles: -63.3 -69.9 -177.1 -87.5) to 7ahl.pdb #!1/G
ARG 113
> swapaa #!1/F:113 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
7ahl.pdb #!1/F ARG 113: phi -148.0, psi 121.5 trans
Applying ARG rotamer (chi angles: -176.3 177.1 179.2 -179.0) to 7ahl.pdb #!1/F
ARG 113
> swapaa #!1/C:113 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
7ahl.pdb #!1/C ARG 113: phi -144.1, psi 131.6 trans
Applying ARG rotamer (chi angles: -64.9 -70.2 -176.3 -85.6) to 7ahl.pdb #!1/C
ARG 113
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #!1/E:113 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
7ahl.pdb #!1/E ARG 113: phi -146.6, psi 135.9 trans
Applying ARG rotamer (chi angles: -65.3 -70.3 -175.0 -84.9) to 7ahl.pdb #!1/E
ARG 113
> swapaa #!1/D:113 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
7ahl.pdb #!1/D ARG 113: phi -148.1, psi 138.7 trans
Applying ARG rotamer (chi angles: -65.3 -70.3 -175.0 -84.9) to 7ahl.pdb #!1/D
ARG 113
> swapaa #!1/B:113 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
7ahl.pdb #!1/B ARG 113: phi -147.8, psi 111.0 trans
Applying ARG rotamer (chi angles: -176.6 177.7 179.2 -179.6) to 7ahl.pdb #!1/B
ARG 113
> swapaa #!1/A:113 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
7ahl.pdb #!1/A ARG 113: phi -155.9, psi 123.0 trans
Applying ARG rotamer (chi angles: -176.6 176.8 179.2 -178.4) to 7ahl.pdb #!1/A
ARG 113
> select #1/A-G:117
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/A-G:117
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/A-G:115
58 atoms, 51 bonds, 7 residues, 1 model selected
> select #1/A-G:115
58 atoms, 51 bonds, 7 residues, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Command cancelled by user
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Using Dunbrack library
Swapping 7ahl.pdb #1/A THR 115 to ALA
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 111, in launch_rotamers
run(self.session, "swapaa interactive sel %s rotLib %s" % (res_type,
lib_name))
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 147, in rotamers
rotamers = swap_res.get_rotamers(session, r, res_type=r_type, rot_lib=rot_lib,
log=log)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 204, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 42, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 204, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 416, in template_swap_res
info = Atom.idatm_info_map[tmpl_bud.idatm_type]
KeyError: ''
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 113, in launch_rotamers
run(self.session, "swapaa sel %s rotLib %s" % (res_type, lib_name))
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 40, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 49, in swap_aa
template_swap_res(res, r_type, bfactor=bfactor)
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 420, in template_swap_res
raise AssertionError("Can't determine atom type information for atom %s of
residue %s" % (bud, res))
AssertionError: Can't determine atom type information for atom O of residue
7ahl.pdb #1/A THR 115
AssertionError: Can't determine atom type information for atom O of residue
7ahl.pdb #1/A THR 115
File "C:\软件安装位置\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 420, in template_swap_res
raise AssertionError("Can't determine atom type information for atom %s of
residue %s" % (bud, res))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 531.68
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming F15 FX507VV_FX507VV
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,780,668,928
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i9-13900H
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → "swapaa interactive" for non-rotamer res type produces traceback |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Reproduce with:
open 7ahl
select #1/A-G:115
swapaa interactive sel ALA rotLib Dunbrack