![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 22 months ago
Closed 22 months ago
#14391 closed defect (duplicate)
swapaa: DunbrackRotamerLibrary' object has no attribute 'display_name'
| 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: macOS-10.16-x86_64-i386-64bit
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 /Users/andrewperez/Downloads/6pbd.pdb
6pbd.pdb title:
Dna N6-adenine methyltransferase CCRM In complex with double-stranded DNA
oligonucleotide containing its recognition sequence gaatc [more info...]
Chain information for 6pbd.pdb #1
---
Chain | Description | UniProt
A B | modification methylase ccrmi | MTC1_CAUVC 1-358
X | DNA (5'-
D(*CP*GP*ap*TP*TP*CP*ap*ap*TP*GP*ap*ap*TP*CP*CP*CP*ap*ap*G)-3') |
Y | DNA (5'-
D(*GP*CP*TP*TP*GP*GP*GP*ap*TP*TP*CP*ap*TP*TP*GP*ap*ap*TP*C)-3') |
Non-standard residues in 6pbd.pdb #1
---
EDO — 1,2-ethanediol (ethylene glycol)
SFG — sinefungin (adenosyl-ornithine)
> set bgColor white
> lighting soft
> D31E
Unknown command: D31E
> D31E
Unknown command: D31E
> select sel @< 4
42 atoms, 35 bonds, 12 residues, 1 model selected
> select clear
> select sel @< 4
42 atoms, 35 bonds, 12 residues, 1 model selected
> show sel atoms
> ui tool show H-Bonds
> hbonds distSlop 3.4 reveal true
3131 hydrogen bonds found
> undo
[Repeated 1 time(s)]
> ui tool show H-Bonds
> hbonds interModel false distSlop 3.4 reveal true
3131 hydrogen bonds found
> select clear
> select up
3131 pseudobonds, 1 model selected
> select clear
[Repeated 1 time(s)]
> select up
3131 pseudobonds, 1 model selected
> ui tool show H-Bonds
> hbonds interModel false distSlop 3.4 select true
3131 hydrogen bonds found
> select clear
> ~hbonds
> select sel @< 4
42 atoms, 35 bonds, 12 residues, 1 model selected
> D31E
Unknown command: D31E
> select ::name="EDO"
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select /X
397 atoms, 430 bonds, 33 residues, 1 model selected
> select clear
> D31
Unknown command: D31
> AA:/ D31
Unknown command: AA:/ D31
> AA/: D31
Unknown command: AA/: D31
> AA/: D31
Unknown command: AA/: D31
> AA/ D31
Unknown command: AA/ D31
> select clear
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 9 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 9 atom styles
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel purple
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
59 atoms, 63 bonds, 6 residues, 1 model selected
> select up
642 atoms, 658 bonds, 90 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /X:11@C6
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> A/ D31
Unknown command: A/ D31
> A/ D31E
Unknown command: A/ D31E
> A/D31E
Unknown command: A/D31E
> select glu 31
Expected an objects specifier or a keyword
> select glu
Expected an objects specifier or a keyword
> select: lu
Unknown command: select: lu
> select: glu
Unknown command: select: glu
> select :glu31.E
Expected an objects specifier or a keyword
> select ::name="GLU"
269 atoms, 238 bonds, 33 residues, 1 model selected
> select clear
> select /X:11@C6
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select sel @< 4
71 atoms, 54 bonds, 23 residues, 1 model selected
> hbonds sel reveal true
37 hydrogen bonds found
> select ~sel
6108 atoms, 6165 bonds, 2 pseudobonds, 876 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select /X:11@C6
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> cofr sel
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> select ::name="GLU"
269 atoms, 238 bonds, 33 residues, 1 model selected
> show sel atoms
> select clear
> select /X:11
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
383 atoms, 430 bonds, 19 residues, 1 model selected
> select sel @< 4
602 atoms, 561 bonds, 25 pseudobonds, 102 residues, 2 models selected
> select ~sel
5577 atoms, 5573 bonds, 2 pseudobonds, 837 residues, 2 models selected
> hide sel atoms
> select /X:11@C4
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select sel @< 4
71 atoms, 54 bonds, 17 pseudobonds, 23 residues, 2 models selected
> select ::name="GLU"
269 atoms, 238 bonds, 33 residues, 1 model selected
> show sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
67 atoms, 69 bonds, 8 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:640@O
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add /X:11
31 atoms, 31 bonds, 3 residues, 1 model selected
> select up
33 atoms, 32 bonds, 4 residues, 1 model selected
> select up
43 atoms, 43 bonds, 4 residues, 1 model selected
> select up
634 atoms, 685 bonds, 52 residues, 1 model selected
> select up
2432 atoms, 2531 bonds, 280 residues, 1 model selected
> select down
634 atoms, 685 bonds, 52 residues, 1 model selected
> select add /A:179@CZ
635 atoms, 685 bonds, 53 residues, 1 model selected
> select up
645 atoms, 695 bonds, 53 residues, 1 model selected
> select add /A:663@O
646 atoms, 695 bonds, 54 residues, 1 model selected
> select add /A:192@O
647 atoms, 695 bonds, 55 residues, 1 model selected
> select add /X:111@O
648 atoms, 695 bonds, 56 residues, 1 model selected
> select add /A:193@NZ
649 atoms, 695 bonds, 57 residues, 1 model selected
> select up
665 atoms, 712 bonds, 57 residues, 1 model selected
> select ~sel
5514 atoms, 5528 bonds, 10 pseudobonds, 825 residues, 3 models selected
> hide sel atoms
> select ::name="ALA"
355 atoms, 292 bonds, 71 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ASN 145
/A LYS 147
/A ARG 148
/A ASP 154
/A GLU 162
/A GLU 259
/A ASP 260
/A ARG 268
/A LYS 294
/A THR 296
/A LEU 312
/A LYS 318
/A SER 325
/A ASP 340
/B GLU 15
/B GLN 37
/B LEU 38
/B MET 122
/B ASN 124
/B LYS 126
/B ARG 148
/B THR 175
/B GLU 177
/B ASP 184
/B GLN 186
/B GLU 241
/B GLU 244
/B SER 266
/B GLU 280
/B SER 285
/B SER 293
/B LYS 294
/B ASP 311
/B LYS 318
/B LEU 322
/B SER 325
/B LYS 338
/B THR 339
/B ASP 340
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6pbd.pdb_A SES surface #1.3: minimum, -20.06, mean -0.61,
maximum 10.43
Coulombic values for 6pbd.pdb_B SES surface #1.4: minimum, -20.34, mean 0.56,
maximum 16.59
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> color (#!1 & sel) cyan
> color sel byhetero
> ui tool show Distances
> ui tool show H-Bonds
> ui tool show Distances
> select clear
[Repeated 2 time(s)]
> select add /A:135@OE2
1 atom, 1 residue, 1 model selected
> select add /A:640@O
2 atoms, 2 residues, 2 models selected
> select add /A:135@OE1
3 atoms, 2 residues, 2 models selected
> select add /A:34@OH
4 atoms, 3 residues, 2 models selected
> select clear
> select /A:135@OE2
1 atom, 1 residue, 1 model selected
> select add /A:640@O
2 atoms, 2 residues, 2 models selected
> distance /A:135@OE2 /A:640@O
Distance between /A GLU 135 OE2 and HOH 640 O: 2.802Å
> select clear
> select add /A:135@OE1
1 atom, 1 residue, 1 model selected
> select add /A:34@OH
2 atoms, 2 residues, 1 model selected
> distance /A:135@OE1 /A:34@OH
Distance between /A GLU 135 OE1 and TYR 34 OH: 2.777Å
> save /Users/andrewperez/Desktop/image1.png supersample 3
> ui tool show "Color Key"
> ui mousemode right "color key"
> key pos 0.7,0.08
> ui tool show "Color Key"
> key blue:min white: #ed4e27:max
> key blue:min white: #ed4d27:max
> key blue:min white: #ed4d29:max
> key blue:min white: #ed4a35:max
> key blue:min white: #ed483c:max
> key blue:min white: #ed5267:max
> key blue:min white: #ed5a7e:max
> key blue:min white: #ed5fa2:max
> key blue:min white: #ed60ae:max
> key blue:min white: #ed60b6:max
> key blue:min white: #ed5fbd:max
> key blue:min white: #ed5fc1:max
> key blue:min white: #ed5fc4:max
> key blue:min white: #ed5fc6:max
> key blue:min white: #ed5fc8:max
> key blue:min white: #ed5fca:max
> key blue:min white: #ed5fcb:max
> key blue:min white: #ed5fcd:max
> key blue:min white: #ed5ed1:max
> key blue:min white: #ed5dd3:max
> key blue:min white: #ed5dd5:max
> key blue:min white: #ed5cd7:max
> key blue:min white: #ed5bd8:max
> key blue:min white: #ed5ad9:max
> key blue:min white: #ed59d9:max
> key blue:min white: #ed59da:max
> key blue:min white: #ed58d9:max
> key blue:min white: #ed58d8:max
> key blue:min white: #ed57d8:max
> key blue:min white: #ed54d7:max
> key blue:min white: #ed52d7:max
> key blue:min white: #ed4fd8:max
> key blue:min white: #ed49db:max
> key blue:min white: #ed44de:max
> key blue:min white: #ed43de:max
> key blue:min white: #ed40df:max
> key blue:min white: #ed3fdf:max
> key blue:min white: #ed3fde:max
> key blue:min white: #ed3ede:max
> key blue:min white: #ed3edd:max
> key blue:min white: #ed3ddc:max
> key blue:min white: #ed3cdb:max
> key blue:min white: #ed3ad9:max
> key blue:min white: #ed37d8:max
> key blue:min white: #ed34d5:max
> key blue:min white: #ed2fd2:max
> key blue:min white: #ed29cd:max
> key blue:min white: #ed1fc6:max
> key blue:min white: #ed1bc4:max
> key blue:min white: #ed19c3:max
> key blue:min white: #ed17c1:max
> key blue:min white: #ed16c0:max
> key blue:min white: #ed15c0:max
> key blue:min white: #ed15bf:max
> key blue:min white: #ed14be:max
> key blue:min white: #ed13bd:max
> key blue:min white: #ed12bc:max
> key blue:min white: #ed11bb:max
> key blue:min white: #ed0eba:max
> key blue:min white: #ed0bb7:max
> key blue:min white: #ed08b4:max
> key blue:min white: #ed04b0:max
> key blue:min white: #ed02ae:max
> key blue:min white: #ed00ab:max
> key blue:min white: #ed00aa:max
> key blue:min white: #ed00a5:max
> key blue:min white: #ed00a0:max
> key blue:min white: #ed009d:max
> key blue:min white: #ed009a:max
> key blue:min white: #ed0095:max
> key blue:min white: #ed0093:max
> key blue:min white: #ed0092:max
> key blue:min white: #ed008e:max
> key blue:min white: #ed008a:max
> key blue:min white: #ed0086:max
> key blue:min white: #ed0083:max
> key blue:min white: #ed007e:max
> key blue:min white: #ed007b:max
> key blue:min white: #ed0074:max
> key blue:min white: #ed0071:max
> key blue:min white: #ed006e:max
> key blue:min white: #ed006c:max
> key blue:min white: #ed0069:max
> key blue:min white: #ed0067:max
> key blue:min white: #ed0064:max
> key blue:min white: #ed0067:max
> key blue:min white: #ed0069:max
> key blue:min white: #ed006e:max
> key blue:min white: #ed0076:max
> key blue:min white: #ed007b:max
> key blue:min white: #ed0088:max
> key blue:min white: #ed008b:max
> key blue:min white: #ed0092:max
> key blue:min white: #ed0095:max
> key blue:min white: #ed0097:max
> key blue:min white: #ed009a:max
> key blue:min white: #ed009d:max
> key blue:min white: #ed00a2:max
> key blue:min white: #ed00a5:max
> key blue:min white: #ed00ab:max
> key blue:min white: #ed00af:max
> key blue:min white: #ed00b2:max
> key blue:min white: #ed00b5:max
> key blue:min white: #ed00b8:max
> key blue:min white: #ed00bb:max
> key blue:min white: #ed00bd:max
> key blue:min white: #ed00c0:max
> key blue:min white: #ed00c3:max
> key blue:min white: #ed00c7:max
> key blue:min white: #ed00cd:max
> key blue:min white: #ed00d0:max
> key blue:min white: #ed00d3:max
> key blue:min white: #ed00d5:max
> key blue:min white: #ed00d8:max
> key blue:min white: #ed00da:max
> key blue:min white: #ed00dd:max
> key blue:min white: #ed00e0:max
> key blue:min white: #ed00e2:max
> key blue:min white: #ed00e3:max
> key blue:min white: #ed00e5:max
> key blue:min white: #ed00e8:max
> key blue:min white: #ed00ea:max
> key blue:min white: #ed00eb:max
> key blue:min white: #ed00ed:max
> key blue:min white: #eb00ed:max
> key blue:min white: #e900ed:max
> key blue:min white: #e700ed:max
> key blue:min white: #e400ed:max
> key blue:min white: #dd00ed:max
> key blue:min white: #d903ed:max
> key blue:min white: #d407ed:max
> key blue:min white: #cd0ced:max
> key blue:min white: #c014ed:max
> key blue:min white: #ba17ed:max
> key blue:min white: #ae1aed:max
> key blue:min white: #aa1ced:max
> key blue:min white: #a71ded:max
> key blue:min white: #a41eed:max
> key blue:min white: #a220ed:max
> key blue:min white: #9f21ed:max
> key blue:min white: #9c22ed:max
> key blue:min white: #9a23ed:max
> key blue:min white: #9824ed:max
> key blue:min white: #9326ed:max
> key blue:min white: #9127ed:max
> key blue:min white: #8e29ed:max
> key blue:min white: #8c29ed:max
> key blue:min white: #872ced:max
> key blue:min white: #852ded:max
> key blue:min white: #832ded:max
> key blue:min white: #812ded:max
> key blue:min white: #802eed:max
> key blue:min white: #7e2fed:max
> key blue:min white: #7d2fed:max
> key blue:min white: #7c2fed:max
> key blue:min white: #7a2fed:max
> key blue:min white: #7930ed:max
> key blue:min white: #7830ed:max
> key blue:min white: #7630ed:max
> key blue:min white: #7530ed:max
> key blue:min white: #7331ed:max
> key blue:min white: #7131ed:max
> key blue:min white: #7031ed:max
> key blue:min white: #6f32ed:max
> key blue:min white: #6d32ed:max
> key blue:min white: #6e32ed:max
> key blue:min white: #6f32ed:max
> key blue:min white: #6e32ed:max
> key blue:min white: #6e31ed:max
> key blue:min white: #6d31ed:max
> key blue:min white: #6c30ed:max
> key blue:min white: #6b30ed:max
> key blue:min white: #6a2fed:max
> key blue:min white: #692fed:max
> key blue:min white: #682eed:max
> key blue:min white: #672ded:max
> key blue:min white: #672ced:max
> key blue:min white: #662bed:max
> key blue:min white: #652bed:max
> key blue:min white: #652aed:max
> key blue:min white: #6429ed:max
> key blue:min white: #6428ed:max
> key blue:min white: #6327ed:max
> key blue:min white: #6326ed:max
> key blue:min white: #6325ed:max
> key blue:min white: #6224ed:max
> key blue:min white: #6123ed:max
> key blue:min white: #6023ed:max
> key blue:min white: #5e21ed:max
> key blue:min white: #5d20ed:max
> key blue:min white: #5b1fed:max
> key blue:min white: #5a1eed:max
> key blue:min white: #591eed:max
> key blue:min white: #581ded:max
> key blue:min white: #571ded:max
> key blue:min white: #571ced:max
> key blue:min white: #571bed:max
> key blue:min white: #561aed:max
> key blue:min white: #5619ed:max
> key blue:min white: #5518ed:max
> key blue:min white: #5417ed:max
> key blue:min white: #5416ed:max
> key blue:min white: #5314ed:max
> key blue:min white: #5313ed:max
> key blue:min white: #5210ed:max
> key blue:min white: #500bed:max
> key blue:min white: #4f09ed:max
> key blue:min white: #4e07ed:max
> key blue:min white: #4d05ed:max
> key blue:min white: #4c03ed:max
> key blue:min white: #4b02ed:max
> key blue:min white: #4b01ed:max
> key blue:min white: #4a00ed:max
> key blue:min white: #4b00ed:max
> key blue:min white: #4c00ed:max
> key blue:min white: #4d00ed:max
> key blue:min white: #4e00ed:max
> key blue:min white: #4f00ed:max
> key blue:min white: #5000ed:max
> key blue:min white: #5100ed:max
> key blue:min white: #5200ed:max
> key blue:min white: #5300ed:max
> key blue:min white: #5400ed:max
> key blue:min white: #5500ed:max
> key blue:min white: #5600ed:max
> key blue:min white: #5700ed:max
> key blue:min white: #5800ed:max
> key blue:min white: #5c01ed:max
> key blue:min white: #5f02ed:max
> key blue:min white: #6303ed:max
> key blue:min white: #6a04ed:max
> key blue:min white: #6f05ed:max
> key blue:min white: #7406ed:max
> key blue:min white: #7806ed:max
> key blue:min white: #7c06ed:max
> key blue:min white: #7e07ed:max
> key blue:min white: #7f07ed:max
> key blue:min white: #8007ed:max
> key blue:min white: #8106ed:max
> key blue:min white: #8007ed:max
> key blue:min white: #7e07ed:max
> key blue:min white: #7c07ed:max
> key blue:min white: #7607ed:max
> key blue:min white: #7407ed:max
> key blue:min white: #7206ed:max
> key blue:min white: #7106ed:max
> key blue:min white: #7006ed:max
> key blue:min white: #6e06ed:max
> key blue:min white: #6d06ed:max
> key blue:min white: #6c06ed:max
> key blue:min white: #6b06ed:max
> key blue:min white: #6a06ed:max
> key blue:min white: #6906ed:max
> key blue:min white: #6806ed:max
> key blue:min white: #6705ed:max
> key blue:min white: #942192:max
> key delete
> ui mousemode right translate
> ui tool show "Basic Actions"
> ui tool show "Color Actions"
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue:min white:
> key blue:mi white:
> key blue:m white:
> key blue: white:
> key delete
> ui mousemode right translate
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> color (#!1 & sel) forest green
> color sel byhetero
> select clear
> select :glu
269 atoms, 238 bonds, 33 residues, 1 model selected
> select clear
> select ligand
58 atoms, 61 bonds, 3 residues, 1 model selected
> show sel atoms
> hide sel atoms
> save /Users/andrewperez/Desktop/image1.png supersample 3
[Repeated 1 time(s)]
> lighting full
> lighting soft
> save /Users/andrewperez/Desktop/image1.png supersample 3
> swapaa /A:135 ASP.
Using Dunbrack library
/A GLU 135: phi -133.1, psi 166.0 trans
Traceback (most recent call last):
File "/Volumes/Extreme SSD
SanDisk/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/Volumes/Extreme SSD
SanDisk/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Volumes/Extreme SSD
SanDisk/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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 "/Volumes/Extreme SSD
SanDisk/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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 "/Volumes/Extreme SSD
SanDisk/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
File "/Volumes/Extreme SSD
SanDisk/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params
return self._get_params(res_name, file_name, cache, archive)
File "/Volumes/Extreme SSD
SanDisk/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
File "/Volumes/Extreme SSD
SanDisk/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-20.6.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 522.0.0.0.0
OS Loader Version: 577.140.2~22
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.6.3 (22G436)
Kernel Version: Darwin 22.6.0
Time since boot: 4 hours, 37 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
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: 2021.10.8
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
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: 2022.2.22
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: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
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
setuptools-scm: 7.0.5
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
zipp: 3.15.0
Change History (2)
comment:1 by , 22 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → swapaa: DunbrackRotamerLibrary' object has no attribute 'display_name' |
comment:2 by , 22 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
