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Opened 4 years ago
Closed 4 years ago
#5925 closed defect (fixed)
Swapaa: name 'critera' is not defined
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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-10-10.0.19042
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/Chimera/chimera.cxs"
Log from Thu Jan 13 19:48:31 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\RDV01\OneDrive -
> Sky\Documents\Personal\BBK\SAG\CW\3\PDB\6m0j.pdb" format pdb
6m0j.pdb title:
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]
Chain information for 6m0j.pdb #1
---
Chain | Description | UniProt
A | angiotensin-converting enzyme 2 | ACE2_HUMAN
E | spike protein S1 | SPIKE_SARS2
Non-standard residues in 6m0j.pdb #1
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
ZN — zinc ion
> lighting full
> color bychain
> sequence chain #1/E
Alignment identifier is 1/E
> select /E:338-343,349-353,364-370,383-388,405-410,416-422,438-443,502-505
377 atoms, 379 bonds, 47 residues, 1 model selected
> select /E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> style sel stick
Changed 4 atom styles
> style sel ball
Changed 4 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide #* target a
> show sel target ab
> undo
[Repeated 1 time(s)]
> style sel stick
Changed 4 atom styles
> show sel target ab
> show (sel-residues & sidechain) target ab
> style sel ball
Changed 4 atom styles
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel atoms
> hide sel surfaces
> hide sel cartoons
> color sel orange red
> color sel red
> select sel @< 5
41 atoms, 38 bonds, 10 residues, 1 model selected
> show sel target ab
> hide sel cartoons
> show sel cartoons
> color sel byhetero
> hide sel atoms
> show sel cartoons
> select
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> open "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/PDB/6m0j.pdb"
6m0j.pdb title:
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]
Chain information for 6m0j.pdb #2
---
Chain | Description | UniProt
A | angiotensin-converting enzyme 2 | ACE2_HUMAN
E | spike protein S1 | SPIKE_SARS2
Non-standard residues in 6m0j.pdb #2
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
ZN — zinc ion
> hide #!1 models
> show #!1 models
> close #1-2
> open "C:\Users\RDV01\OneDrive -
> Sky\Documents\Personal\BBK\SAG\CW\3\PDB\6m0j.pdb" format pdb
6m0j.pdb title:
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]
Chain information for 6m0j.pdb #1
---
Chain | Description | UniProt
A | angiotensin-converting enzyme 2 | ACE2_HUMAN
E | spike protein S1 | SPIKE_SARS2
Non-standard residues in 6m0j.pdb #1
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
ZN — zinc ion
> color byhetero
> color bychain
> color byhetero
> open "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/PDB/6m0j.pdb"
6m0j.pdb title:
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]
Chain information for 6m0j.pdb #2
---
Chain | Description | UniProt
A | angiotensin-converting enzyme 2 | ACE2_HUMAN
E | spike protein S1 | SPIKE_SARS2
Non-standard residues in 6m0j.pdb #2
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
ZN — zinc ion
> close #2
> open "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/PDB/6m0j_omicron.pdb"
6m0j_omicron.pdb title:
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]
Chain information for 6m0j_omicron.pdb #2
---
Chain | Description | UniProt
A | angiotensin-converting enzyme 2 | ACE2_HUMAN
E | spike protein S1 | SPIKE_SARS2
Non-standard residues in 6m0j_omicron.pdb #2
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
ZN — zinc ion
> select #2
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> hide #!1 models
> color sel bychain
> color sel byhetero
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ~select #1
Nothing selected
> select #2
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> sequence chain #2/E
Alignment identifier is 2/E
> select #2/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select sel @< 5
82 atoms, 76 bonds, 20 residues, 2 models selected
> show sel & #!2 atoms
> hide sel & #!2 cartoons
> select #2/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dunbrack
6m0j_omicron.pdb #2/E GLY 339: phi -56.0, psi -35.5 trans
Changed 90 bond radii
> swapaa #2/E:339 ASP criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLY 339: phi -56.0, psi -35.5 trans
Applying ASP rotamer (chi angles: -71.8 -15.3) to 6m0j_omicron.pdb #2/E ASP
339
> undo
Undo failed, probably because structures have been modified.
> close #2
> open "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/PDB/6m0j_omicron.pdb"
6m0j_omicron.pdb title:
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]
Chain information for 6m0j_omicron.pdb #2
---
Chain | Description | UniProt
A | angiotensin-converting enzyme 2 | ACE2_HUMAN
E | spike protein S1 | SPIKE_SARS2
Non-standard residues in 6m0j_omicron.pdb #2
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
ZN — zinc ion
> color #!2 bychain
> color #!2 byhetero
> sequence chain #2/E
Alignment identifier is 2/E
> select #2/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
50 atoms, 51 bonds, 6 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dunbrack
6m0j_omicron.pdb #2/E GLY 339: phi -56.0, psi -35.5 trans
Changed 90 bond radii
> swapaa #2/E:339 ASP criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLY 339: phi -56.0, psi -35.5 trans
Applying ASP rotamer (chi angles: -71.8 -15.3) to 6m0j_omicron.pdb #2/E ASP
339
> swapaa interactive sel ASP rotLib Dunbrack
6m0j_omicron.pdb #2/E ASP 339: phi -56.0, psi -35.5 trans
Changed 90 bond radii
> swapaa interactive sel ASP rotLib Dunbrack
6m0j_omicron.pdb #2/E ASP 339: phi -56.0, psi -35.5 trans
Changed 90 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #2/E:339 ASP criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
6m0j_omicron.pdb #2/E ASP 339: phi -56.0, psi -35.5 trans
Applying ASP rotamer (chi angles: -71.8 -15.3) to 6m0j_omicron.pdb #2/E ASP
339
> save "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/PDB/chimera.cxs"
> select #2/E:338-343,349-353,364-370,383-388,405-410,416-422,438-443,502-505
381 atoms, 383 bonds, 47 residues, 1 model selected
> select #2/E:339-340
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/E:339
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:339
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Updates
> view orient
[Repeated 1 time(s)]
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> set bgColor gray
> set bgColor white
> set bgColor black
> label sel atoms
> ~label sel atoms
> color sel red
> select #2
6562 atoms, 6672 bonds, 3 pseudobonds, 878 residues, 2 models selected
> color sel byhetero
[Repeated 2 time(s)]
> color sel bynucleotide
> color sel byhetero
> color sel bychain
[Repeated 1 time(s)]
> select #2/E:339
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:339
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:338-343,349-353,364-370,383-388,405-410,416-422,438-443,502-505
381 atoms, 383 bonds, 47 residues, 1 model selected
> select #2/E:368
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:368
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:371
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:371
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #2/E:371
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:371
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> ui tool show Rotamers
> swapaa interactive sel LEU rotLib Dunbrack
6m0j_omicron.pdb #2/E SER 371: phi -75.5, psi -30.4 trans
Changed 45 bond radii
> swapaa #2/E:371 LEU criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E SER 371: phi -75.5, psi -30.4 trans
Applying LEU rotamer (chi angles: -65.9 175.1) to 6m0j_omicron.pdb #2/E LEU
371
> swapaa interactive sel LEU rotLib Dunbrack
6m0j_omicron.pdb #2/E LEU 371: phi -75.5, psi -30.4 trans
Changed 45 bond radii
> select down
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 323, in forward_keystroke
run(self.session, 'select down')
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\select.py", line 138, in select_down
session.selection.demote(session)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\selection.py", line 64, in demote
self._promotion.demote_selection()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\selection.py", line 200, in demote_selection
p.demote()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1876, in demote
s.atoms.selected = self._prev_atom_sel_mask
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molc.py", line 210, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
ValueError: Values array length 6562 does not match objects array length 6564
ValueError: Values array length 6562 does not match objects array length 6564
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molc.py", line 210, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
See log for complete Python traceback.
> select #2/E:371@CA
1 atom, 1 residue, 1 model selected
> select #2/E:371
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:372-373
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/E:372-373
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/E:373
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:373
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel PRO rotLib Dunbrack
6m0j_omicron.pdb #2/E SER 373: phi -123.4, psi 4.4 trans
Changed 10 bond radii
> swapaa #2/E:373 PRO criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E SER 373: phi -123.4, psi 4.4 trans
Applying PRO rotamer (chi angles: 33.9 -36.2) to 6m0j_omicron.pdb #2/E PRO 373
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:371
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:371
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:373
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:373
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:375
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:375
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel PHE rotLib Dunbrack
6m0j_omicron.pdb #2/E SER 375: phi -84.7, psi -16.3 trans
Changed 162 bond radii
> swapaa #2/E:375 PHE criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E SER 375: phi -84.7, psi -16.3 trans
Applying PHE rotamer (chi angles: -70.7 103.3) to 6m0j_omicron.pdb #2/E PHE
375
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:338-343,349-353,364-370,383-388,405-410,416-422,438-443,502-505
381 atoms, 383 bonds, 47 residues, 1 model selected
> select #2/E:417
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:417
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A#2/A
9998 atoms, 10140 bonds, 6 pseudobonds, 1348 residues, 4 models selected
> hide sel & #!2 atoms
> hide sel & #!2 cartoons
> hide sel & #!2 surfaces
> select #2/E:417
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:417
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASN rotLib Dunbrack
6m0j_omicron.pdb #2/E LYS 417: phi -57.2, psi -42.0 trans
Changed 180 bond radii
> swapaa #2/E:417 ASN criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E LYS 417: phi -57.2, psi -42.0 trans
Applying ASN rotamer (chi angles: -73.2 -20.5) to 6m0j_omicron.pdb #2/E ASN
417
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:338-343,349-353,364-370,383-388,405-410,416-422,438-443,502-505
380 atoms, 382 bonds, 47 residues, 1 model selected
> select #2/E:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
6m0j_omicron.pdb #2/E ASN 440: phi -70.7, psi -23.8 trans
Changed 438 bond radii
> swapaa #2/E:440 LYS criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E ASN 440: phi -70.7, psi -23.8 trans
Applying LYS rotamer (chi angles: -69.0 179.6 179.8 178.5) to 6m0j_omicron.pdb
#2/E LYS 440
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:446
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/E:446
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 2 time(s)]
> hide sel cartoons
> show sel cartoons
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
6m0j_omicron.pdb #2/E GLY 446: phi 78.4, psi -20.5 trans
Changed 9 bond radii
> swapaa #2/E:446 SER criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLY 446: phi 78.4, psi -20.5 trans
Applying SER rotamer (chi angles: -59.9) to 6m0j_omicron.pdb #2/E SER 446
> color sel red
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:449-450
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/E:449-450
20 atoms, 20 bonds, 2 residues, 1 model selected
> ui tool show Rotamers
> select #2/E:414
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:414
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:459
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:459
6 atoms, 5 bonds, 1 residue, 1 model selected
> 456
Unknown command: 456
> select #2/E:477
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASN rotLib Dunbrack
6m0j_omicron.pdb #2/E SER 477: phi -95.1, psi -28.2 trans
Changed 180 bond radii
> swapaa #2/E:477 ASN criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E SER 477: phi -95.1, psi -28.2 trans
Applying ASN rotamer (chi angles: -67.3 -32.6) to 6m0j_omicron.pdb #2/E ASN
477
> show sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> show sel atoms
> select #2/E:477
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:477
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #2/E:476
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/E:476
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/E:477-478
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/E:477-478
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/E:477
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:477
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASN rotLib Dunbrack
6m0j_omicron.pdb #2/E ASN 477: phi -95.1, psi -28.2 trans
Changed 180 bond radii
> swapaa #2/E:477 ASN criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
6m0j_omicron.pdb #2/E ASN 477: phi -95.1, psi -28.2 trans
Applying ASN rotamer (chi angles: -67.3 -32.6) to 6m0j_omicron.pdb #2/E ASN
477
> select #2/E:477@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select #2/E:478
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
6m0j_omicron.pdb #2/E THR 478: phi -72.3, psi 131.1 trans
Changed 438 bond radii
> swapaa #2/E:478 LYS criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E THR 478: phi -72.3, psi 131.1 trans
Applying LYS rotamer (chi angles: -176.8 176.8 -179.9 -180.0) to
6m0j_omicron.pdb #2/E LYS 478
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:484
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Using Dunbrack library
Swapping 6m0j_omicron.pdb #2/E GLU 484 to ALA
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:496
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
6m0j_omicron.pdb #2/E GLY 496: phi -119.7, psi 95.5 trans
Changed 9 bond radii
> swapaa #2/E:496 SER criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLY 496: phi -119.7, psi 95.5 trans
Applying SER rotamer (chi angles: 177.9) to 6m0j_omicron.pdb #2/E SER 496
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:498
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Model Loops"
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
6m0j_omicron.pdb #2/E GLN 498: phi -103.5, psi 144.5 trans
Changed 9 bond radii
> swapaa #2/E:498 SER criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLN 498: phi -103.5, psi 144.5 trans
Applying SER rotamer (chi angles: 175.7) to 6m0j_omicron.pdb #2/E SER 498
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
6m0j_omicron.pdb #2/E SER 498: phi -103.5, psi 144.5 trans
Changed 9 bond radii
> swapaa #2/E:498 SER criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
6m0j_omicron.pdb #2/E SER 498: phi -103.5, psi 144.5 trans
Applying SER rotamer (chi angles: 175.7) to 6m0j_omicron.pdb #2/E SER 498
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:501
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> select #2/E:496
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:498
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:501
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel TYR rotLib Dunbrack
6m0j_omicron.pdb #2/E ASN 501: phi -61.2, psi 159.1 trans
Changed 180 bond radii
> swapaa #2/E:501 TYR criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E ASN 501: phi -61.2, psi 159.1 trans
Applying TYR rotamer (chi angles: -70.4 101.4) to 6m0j_omicron.pdb #2/E TYR
501
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel red
> select #2/E:505
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel HIS rotLib Dunbrack
6m0j_omicron.pdb #2/E TYR 505: phi -109.3, psi -3.4 trans
Changed 288 bond radii
> swapaa #2/E:505 HIS criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E TYR 505: phi -109.3, psi -3.4 trans
Applying HIS rotamer (chi angles: -63.7 -71.5) to 6m0j_omicron.pdb #2/E HIS
505
> color sel red
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> show #!1 models
> hide #!1 models
> hide #!2 models
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> show #!1 models
> select #1/A#2/A
9998 atoms, 10140 bonds, 6 pseudobonds, 1348 residues, 4 models selected
> hide sel & #!1 cartoons
> hide sel & #!1 atoms
> hide sel & #!1 surfaces
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #2
Nothing selected
> show #!2 models
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> color (#!1 & sel) magenta
> color (#!1 & sel) cyan
> hide #!2 models
> select #2/E:339
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #2
Nothing selected
> select #1/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/E:371
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #1/E:371
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:373
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:375
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:417
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:446
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #1/E:477
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:478
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #1/E:484
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:496
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:498
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:501
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/E:505
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #1
Nothing selected
> show #!2 models
> view orient
[Repeated 1 time(s)]
> view
> view orient
> ui tool show "Side View"
[Repeated 2 time(s)]
> view orient
[Repeated 4 time(s)]
> ui tool show "Side View"
> lighting full
> undo
[Repeated 2 time(s)]
> view orient
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #2
Nothing selected
> hide #!2 models
> hide #!1 models
> show #!2 models
> color #2 #55ffff transparency 0
> color #2 white transparency 0
> color #2 #55aa7f transparency 0
> undo
[Repeated 9 time(s)]
> redo
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> view orient
[Repeated 5 time(s)]
> lighting shadows false
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> save "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/PDB/test.gif" width 891 height 821
> supersample 3
> save "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/PDB/image2.gif" width 891 height 821
> supersample 3
> save "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/PDB/chimera.cxs"
——— End of log from Thu Jan 13 19:48:31 2022 ———
opened ChimeraX session
> sequence chain #1/A
Alignment identifier is 1/A
> view #1 clip false
[Repeated 1 time(s)]
> log metadata #1
No models had metadata
> log chains #1
Chain information for 6m0j.pdb #1
---
Chain | Description | UniProt
A | angiotensin-converting enzyme 2 | ACE2_HUMAN
E | spike protein S1 | SPIKE_SARS2
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> show cartoons
> select clear
> select #1/E:401
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
83 atoms, 84 bonds, 10 residues, 1 model selected
> select up
1559 atoms, 1598 bonds, 204 residues, 1 model selected
> hide #!1 models
> hide #!2 models
> show #!1 models
> select sel @< 5
3343 atoms, 3388 bonds, 452 residues, 2 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #1
Nothing selected
> show #!2 models
> select #2/E:401
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
83 atoms, 84 bonds, 10 residues, 1 model selected
> select up
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select sel @< 5
3349 atoms, 3392 bonds, 452 residues, 2 models selected
> select #2/E:493
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> select up
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select down
23 atoms, 22 bonds, 3 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> select up
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select subtract #2/E:494
1568 atoms, 1611 bonds, 203 residues, 1 model selected
> select subtract #2/E:493
1559 atoms, 1603 bonds, 202 residues, 1 model selected
> select add #2/E:493
1568 atoms, 1611 bonds, 203 residues, 1 model selected
> select add #2/E:494
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select subtract #2/E:493
1565 atoms, 1608 bonds, 203 residues, 1 model selected
> select subtract #2/E:494
1559 atoms, 1603 bonds, 202 residues, 1 model selected
> select #2/E:493
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:493
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:494
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 5 atoms, 31 residues, 4 bonds
Drag select of 24 atoms, 71 residues, 23 bonds
> select up
322 atoms, 316 bonds, 42 residues, 1 model selected
> select down
306 atoms, 24 bonds, 42 residues, 1 model selected
> select #2/E:493
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> select up
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select sel @< 5
3349 atoms, 3392 bonds, 452 residues, 2 models selected
> select #1/E#2/E
3133 atoms, 3214 bonds, 408 residues, 2 models selected
> select #2/E
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select sel @< 5
3349 atoms, 3392 bonds, 452 residues, 2 models selected
Drag select of 72 atoms, 178 residues, 67 bonds
Drag select of 48 atoms, 70 residues, 45 bonds
Drag select of 48 atoms, 135 residues, 45 bonds
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> select #2/E
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select sel @< 5
3349 atoms, 3392 bonds, 452 residues, 2 models selected
> select #1/E#2/E
3133 atoms, 3214 bonds, 408 residues, 2 models selected
> select #1/E#2/E
3133 atoms, 3214 bonds, 408 residues, 2 models selected
> hide #!1 target m
[Repeated 1 time(s)]
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #2
Nothing selected
> hide #!2 models
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #2
Nothing selected
> show #!2 models
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #2
Nothing selected
> ~select #2
Nothing selected
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> select #2/E
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select sel @< 5
3349 atoms, 3392 bonds, 452 residues, 2 models selected
> ~select #2/E
1775 atoms, 1776 bonds, 248 residues, 2 models selected
> show sel & #!2 atoms
> hide sel & #!2 cartoons
> show sel & #!2 cartoons
> color (#!2 & sel) yellow
> color (#!2 & sel) purple
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 2 models selected
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #1
Nothing selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #2/E
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select sel @< 5
3349 atoms, 3392 bonds, 452 residues, 2 models selected
> ~select #2/E
1775 atoms, 1776 bonds, 248 residues, 2 models selected
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> ~select #1
Nothing selected
> hide #!1 models
> select #2/E
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select clear
> select #2/E
1574 atoms, 1616 bonds, 204 residues, 1 model selected
> select sel @< 5
3349 atoms, 3392 bonds, 452 residues, 2 models selected
> ~select #1/E
1790 atoms, 1794 bonds, 248 residues, 2 models selected
> ~select #1
1682 atoms, 1705 bonds, 226 residues, 1 model selected
> ~select #2/E
108 atoms, 89 bonds, 22 residues, 1 model selected
> label sel attribute label_specifier
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 3 models selected
> ~select #2
Nothing selected
> save "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/Chimera/images/complex_mutations_only.gif"
> width 1341 height 830 supersample 3
> show #!1 models
> save "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/Chimera/images/complex.gif" width 1341
> height 830 supersample 3
> save "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/Chimera/complex.cxs"
> set bgColor white
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 3 models selected
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 3 models selected
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 3 models selected
> color sel byhetero
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> color sel byhetero
> undo
[Repeated 2 time(s)]
> ~select #2
Nothing selected
> save "C:/Users/RDV01/OneDrive -
> Sky/Documents/Personal/BBK/SAG/CW/3/Chimera/images/complex_white.gif" width
> 1341 height 830 supersample 3
> help help:contact.html
> ui tool show Rotamers
> hide #2.2 models
> ~select #2/E
Nothing selected
> select #2/A
4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected
> hide #!2 target m
> show #!2 target m
> hide #!1 models
> show #!1 models
> hide sel cartoons
> show sel cartoons
> hide #2/A
> hide #1/A
> hide #1/E
> hide #2/E
[Repeated 3 time(s)]
> undo
[Repeated 5 time(s)]
> hide #!2 models
> hide #!1 models
> hide #2.1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2
> hide #!2 models
> show #!2 models
> show #!2/A models
> hide #!1/A models
> hide #!2 models
> hide #!1/A models
> show #!1/A models
> hide #!1/A
[Repeated 1 time(s)]
> show #!1/A
> hide #!2 models
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 3 models selected
> ~select #2
Nothing selected
> select #1
6558 atoms, 6668 bonds, 3 pseudobonds, 878 residues, 2 models selected
> select #1/A
4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected
> hide sel
> hide sel surfaces
> hide sel cartoons
> show sel
> show sel *
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel models
> show target m
> hide target m
> show target m
> hide target m
> show #!1 target m
> ~select #1.1
4999 atoms, 5070 bonds, 674 residues, 1 model selected
> show #!2 models
> select #2
6573 atoms, 6686 bonds, 3 pseudobonds, 878 residues, 3 models selected
> hide #!1 models
> select #2/A
4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select 2/E 333
Expected an objects specifier or a keyword
> select help
Expected an objects specifier or a keyword
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #2/E:477@CB
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
17 atoms, 16 bonds, 2 residues, 1 model selected
> select add #2/E:484
22 atoms, 20 bonds, 3 residues, 1 model selected
> select up
24 atoms, 21 bonds, 4 residues, 1 model selected
> select up
30 atoms, 27 bonds, 4 residues, 1 model selected
> select add #2/E:505@CG
31 atoms, 27 bonds, 5 residues, 1 model selected
> select up
40 atoms, 37 bonds, 5 residues, 1 model selected
> select add #2/E:496
46 atoms, 42 bonds, 6 residues, 1 model selected
> select add #2/E:446
52 atoms, 47 bonds, 7 residues, 1 model selected
> select add #2/E:501@CG
53 atoms, 47 bonds, 8 residues, 1 model selected
> select up
64 atoms, 59 bonds, 8 residues, 1 model selected
> select add #2/E:375
75 atoms, 70 bonds, 9 residues, 1 model selected
> select add #2/E:440
84 atoms, 78 bonds, 10 residues, 1 model selected
> select add #2/E:498
90 atoms, 83 bonds, 11 residues, 1 model selected
> select add #2/E:339
98 atoms, 90 bonds, 12 residues, 1 model selected
> select up
100 atoms, 91 bonds, 13 residues, 1 model selected
> select up
105 atoms, 97 bonds, 13 residues, 1 model selected
> select add #2/E:371
113 atoms, 104 bonds, 14 residues, 1 model selected
> label sel attribute label_specifier
> show #2.2 models
> select #2/E:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:498
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:498
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:492-493
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/E:492-493
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/E:493
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:493
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
6m0j_omicron.pdb #2/E GLN 493 (alt loc A): phi -107.9, psi 151.2 trans
Changed 600 bond radii
> swapaa #2/E:493 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLN 493 (alt loc A): phi -107.9, psi 151.2 trans
6m0j_omicron.pdb #2/E GLN 493 (alt loc B): phi -106.7, psi 150.3 trans
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 45, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa
if len(critera) > 1:
NameError: name 'critera' is not defined
NameError: name 'critera' is not defined
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa
if len(critera) > 1:
See log for complete Python traceback.
> swapaa #2/E:493 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLN 493 (alt loc A): phi -107.9, psi 151.2 trans
6m0j_omicron.pdb #2/E GLN 493 (alt loc B): phi -106.7, psi 150.3 trans
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 45, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa
if len(critera) > 1:
NameError: name 'critera' is not defined
NameError: name 'critera' is not defined
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa
if len(critera) > 1:
See log for complete Python traceback.
> show sel atoms
> color sel red
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
6m0j_omicron.pdb #2/E GLN 493 (alt loc A): phi -107.9, psi 151.2 trans
Changed 600 bond radii
> swapaa #2/E:493 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLN 493 (alt loc A): phi -107.9, psi 151.2 trans
6m0j_omicron.pdb #2/E GLN 493 (alt loc B): phi -106.7, psi 150.3 trans
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 45, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa
if len(critera) > 1:
NameError: name 'critera' is not defined
NameError: name 'critera' is not defined
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa
if len(critera) > 1:
See log for complete Python traceback.
> swapaa #2/E:493 ARG criteria 2 rotLib Dunbrack
Using Dunbrack library
6m0j_omicron.pdb #2/E GLN 493 (alt loc A): phi -107.9, psi 151.2 trans
6m0j_omicron.pdb #2/E GLN 493 (alt loc B): phi -106.7, psi 150.3 trans
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 342, in _apply_rotamer
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 45, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa
if len(critera) > 1:
NameError: name 'critera' is not defined
NameError: name 'critera' is not defined
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\swap_res\swap_res.py", line 167, in swap_aa
if len(critera) > 1:
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 24.20.100.6136
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Laptop
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 8,511,598,592
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7300U CPU @ 2.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
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
comtypes: 1.1.10
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: 21.3
ParmEd: 3.2.0
parso: 0.8.3
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
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
pywin32: 228
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
tables: 3.6.1
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
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Swapaa: name 'critera' is not defined |
comment:2 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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