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Opened 7 weeks ago
Closed 7 weeks ago
#18831 closed defect (not a bug)
AddH: more than 2 coplanar positions specified
| 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-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/qianjia/Desktop/DMC1结构分析/八聚体.pdb
Chain information for 八聚体.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Computing secondary structure
> open /Users/qianjia/Desktop/hDMC1-8r2g.pdb
Chain information for hDMC1-8r2g.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
[Repeated 2 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 八聚体.pdb, chain C (#1) with hDMC1-8r2g.pdb, chain H (#2), sequence
alignment score = 856.8
RMSD between 193 pruned atom pairs is 0.806 angstroms; (across all 238 pairs:
2.946)
> hide surfaces
[Repeated 1 time(s)]
> show cartoons
> hide surfaces
[Repeated 2 time(s)]
> show cartoons
[Repeated 2 time(s)]
> hide surfaces
> color bychain
[Repeated 2 time(s)]
> hide surfaces
[Repeated 4 time(s)]
> show surfaces
> hide surfaces
> show cartoons
> color bypolymer
[Repeated 2 time(s)]
> color byhetero
[Repeated 1 time(s)]
> color bypolymer
> hide surfaces
[Repeated 4 time(s)]
> hide atoms
> color #2 #accfe8ff
> color #2 #b7da89ff
> color #1 #accfeaff
> set bgColor white
> lighting soft
> view orient
> view fit
Expected an objects specifier or a view name or a keyword
> save overlay.pdb
> save comparison.png
> rmsd
Missing or invalid "atoms" argument: empty atom specifier
> view save myview
Expected an objects specifier or a view name or a keyword
> volume hide
No volumes specified
> volume hide
No volumes specified
> set bgColor white
> view
[Repeated 3 time(s)]
> view orient
[Repeated 5 time(s)]
> save /Users/qianjia/Desktop/DMC1结构分析/比对.tif width 1091 height 829
> supersample 3 transparentBackground true
> ui tool show "Side View"
[Repeated 1 time(s)]
> color #2 #69976eff
> cd /Users/qianjia/Desktop/DMC1结构分析
Current working directory is: /Users/qianjia/Desktop/DMC1结构分析
> save /Users/qianjia/Desktop/DMC1结构分析/比对2.tif width 1092 height 830
> supersample 3 transparentBackground true
> ui tool show "Side View"
[Repeated 1 time(s)]
> view orient
> hide #2.7 models
> show #2.7 models
> hide #2.7 models
> show #2.7 models
> select add #2.6
1875 atoms, 240 residues, 1 model selected
> select subtract #2.6
1 model selected
> hide #2.9 models
> show #2.9 models
> hide #2.9 models
> show #2.9 models
> select add #2.9
1888 atoms, 241 residues, 1 model selected
> select subtract #2.9
1 model selected
> select add #2.9
1888 atoms, 241 residues, 1 model selected
> select subtract #2.9
1 model selected
> select add #2
14968 atoms, 15235 bonds, 8 pseudobonds, 1912 residues, 2 models selected
> select subtract #2
8 models selected
> save /Users/qianjia/Desktop/DMC1结构分析/比对3.tif width 1235 height 1001
> supersample 3
> save /Users/qianjia/Desktop/DMC1结构分析/比对3.tif width 1235 height 1001
> supersample 3 transparentBackground true
> hide #1.2 models
> show #1.2 models
> select add #1.2
4466 atoms, 608 residues, 1 model selected
> select add #1.3
8972 atoms, 1222 residues, 2 models selected
> select add #1.4
13418 atoms, 1834 residues, 3 models selected
> select subtract #1.4
8972 atoms, 1222 residues, 4 models selected
> select subtract #1.2
4506 atoms, 614 residues, 3 models selected
> select subtract #1.3
1 model selected
> color bychain
> color #1 #a1a1a1ff
> color #2 #83aa81ff
> color bychain
[Repeated 1 time(s)]
> color #1 #bad6f1ff
> color #2 #636363ff
> color #2 #88b286ff
> save /Users/qianjia/Desktop/DMC1结构分析/比对4.tif width 1235 height 1001
> supersample 3
> save /Users/qianjia/Desktop/DMC1结构分析/比对5.tif width 1235 height 1001
> supersample 3
> save /Users/qianjia/Desktop/DMC1结构分析/比对5.tif width 1235 height 1001
> supersample 3 transparentBackground true
> color #2 #c3a7ceff
> color #2 #a881bcff
> color #1 #9ec9e4ff
> color #2 #e9748eff
> color #2 #ffe4ebff
> color #2 #9495beff
> color #2 #a881bcff
> color #2 #e6738cff
> color #2 #eb84a4ff
> save /Users/qianjia/Desktop/DMC1结构分析/比对6.tif width 1236 height 1002
> supersample 3 transparentBackground true
> save /Users/qianjia/Desktop/DMC1结构分析/比对7.tif width 1236 height 1002
> supersample 3 transparentBackground true
> color #1 #279246ff
> view
[Repeated 7 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> save /Users/qianjia/Desktop/DMC1结构分析/比对8.tif width 1236 height 1002
> supersample 3
> view orient
> color #1 #5477b8ff
> save /Users/qianjia/Desktop/DMC1结构分析/比对9.tif width 1237 height 1003
> supersample 3 transparentBackground true
> view orient
> select add #2
14968 atoms, 15235 bonds, 8 pseudobonds, 1912 residues, 2 models selected
> select subtract #2
8 models selected
> select add #2
14968 atoms, 15235 bonds, 8 pseudobonds, 1912 residues, 2 models selected
> select subtract #2
8 models selected
> save /Users/qianjia/Desktop/DMC1结构分析/比对10.tif width 1237 height 1003
> supersample 3 transparentBackground true
> open /Users/qianjia/Desktop/DMC1结构分析/20聚体2.pdb
Chain information for 20聚体2.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Computing secondary structure
> select add #1
17834 atoms, 18078 bonds, 10 pseudobonds, 2438 residues, 2 models selected
> select subtract #1
4 models selected
> hide target m
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> coulombic #!3
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
20聚体2.pdb #3/A VAL 44
20聚体2.pdb #3/A VAL 44
20聚体2.pdb #3/A VAL 44
20聚体2.pdb #3/A VAL 44
20聚体2.pdb #3/A LYS 45
20聚体2.pdb #3/A LYS 45
20聚体2.pdb #3/A LYS 45
20聚体2.pdb #3/A LYS 45
20聚体2.pdb #3/A LYS 70
20聚体2.pdb #3/A LYS 70
20聚体2.pdb #3/A LYS 70
20聚体2.pdb #3/A LYS 70
20聚体2.pdb #3/A GLU 82
20聚体2.pdb #3/A GLU 82
20聚体2.pdb #3/A GLU 82
20聚体2.pdb #3/A GLU 82
20聚体2.pdb #3/A ARG 136
20聚体2.pdb #3/A ARG 136
20聚体2.pdb #3/A ARG 136
20聚体2.pdb #3/A ARG 136
20聚体2.pdb #3/A ARG 235
20聚体2.pdb #3/A ARG 235
20聚体2.pdb #3/A ARG 235
20聚体2.pdb #3/A ARG 235
20聚体2.pdb #3/A ASP 237
20聚体2.pdb #3/A ASP 237
20聚体2.pdb #3/A ASP 237
20聚体2.pdb #3/A ASP 237
20聚体2.pdb #3/A PHE 238
20聚体2.pdb #3/A PHE 238
20聚体2.pdb #3/A PHE 238
20聚体2.pdb #3/A PHE 238
20聚体2.pdb #3/A LEU 244
20聚体2.pdb #3/A LEU 244
20聚体2.pdb #3/A LEU 244
20聚体2.pdb #3/A LEU 244
20聚体2.pdb #3/A ASP 246
20聚体2.pdb #3/A ASP 246
20聚体2.pdb #3/A ASP 246
20聚体2.pdb #3/A ASP 246
20聚体2.pdb #3/A ARG 247
20聚体2.pdb #3/A ARG 247
20聚体2.pdb #3/A ARG 247
20聚体2.pdb #3/A ARG 247
20聚体2.pdb #3/A GLN 248
20聚体2.pdb #3/A GLN 248
20聚体2.pdb #3/A GLN 248
20聚体2.pdb #3/A GLN 248
20聚体2.pdb #3/A LYS 250
20聚体2.pdb #3/A LYS 250
20聚体2.pdb #3/A LYS 250
20聚体2.pdb #3/A LYS 250
20聚体2.pdb #3/A ASP 287
20聚体2.pdb #3/A ASP 287
20聚体2.pdb #3/A ASP 287
20聚体2.pdb #3/A ASP 287
20聚体2.pdb #3/A LYS 289
20聚体2.pdb #3/A LYS 289
20聚体2.pdb #3/A LYS 289
20聚体2.pdb #3/A LYS 289
20聚体2.pdb #3/A LYS 290
20聚体2.pdb #3/A LYS 290
20聚体2.pdb #3/A LYS 290
20聚体2.pdb #3/A LYS 290
20聚体2.pdb #3/A HIS 295
20聚体2.pdb #3/A HIS 295
20聚体2.pdb #3/A HIS 295
20聚体2.pdb #3/A HIS 295
20聚体2.pdb #3/A LYS 311
20聚体2.pdb #3/A LYS 311
20聚体2.pdb #3/A LYS 311
20聚体2.pdb #3/A LYS 311
20聚体2.pdb #3/A LYS 343
20聚体2.pdb #3/A LYS 343
20聚体2.pdb #3/A LYS 343
20聚体2.pdb #3/A LYS 343
20聚体2.pdb #3/B LEU 34
20聚体2.pdb #3/B LEU 34
20聚体2.pdb #3/B LEU 34
20聚体2.pdb #3/B LEU 34
20聚体2.pdb #3/B LYS 45
20聚体2.pdb #3/B LYS 45
20聚体2.pdb #3/B LYS 45
20聚体2.pdb #3/B LYS 45
20聚体2.pdb #3/B GLU 49
20聚体2.pdb #3/B GLU 49
20聚体2.pdb #3/B GLU 49
20聚体2.pdb #3/B GLU 49
20聚体2.pdb #3/B LYS 70
20聚体2.pdb #3/B LYS 70
20聚体2.pdb #3/B LYS 70
20聚体2.pdb #3/B LYS 70
20聚体2.pdb #3/B LEU 72
20聚体2.pdb #3/B LEU 72
20聚体2.pdb #3/B LEU 72
20聚体2.pdb #3/B LEU 72
20聚体2.pdb #3/B GLU 74
20聚体2.pdb #3/B GLU 74
20聚体2.pdb #3/B GLU 74
20聚体2.pdb #3/B GLU 74
20聚体2.pdb #3/B LYS 79
20聚体2.pdb #3/B LYS 79
20聚体2.pdb #3/B LYS 79
20聚体2.pdb #3/B LYS 79
20聚体2.pdb #3/B ILE 80
20聚体2.pdb #3/B ILE 80
20聚体2.pdb #3/B ILE 80
20聚体2.pdb #3/B ILE 80
20聚体2.pdb #3/B GLU 82
20聚体2.pdb #3/B GLU 82
20聚体2.pdb #3/B GLU 82
20聚体2.pdb #3/B GLU 82
20聚体2.pdb #3/B VAL 236
20聚体2.pdb #3/B VAL 236
20聚体2.pdb #3/B VAL 236
20聚体2.pdb #3/B VAL 236
20聚体2.pdb #3/B ASP 237
20聚体2.pdb #3/B ASP 237
20聚体2.pdb #3/B ASP 237
20聚体2.pdb #3/B ASP 237
20聚体2.pdb #3/B PHE 238
20聚体2.pdb #3/B PHE 238
20聚体2.pdb #3/B PHE 238
20聚体2.pdb #3/B PHE 238
20聚体2.pdb #3/B ARG 241
20聚体2.pdb #3/B ARG 241
20聚体2.pdb #3/B ARG 241
20聚体2.pdb #3/B ARG 241
20聚体2.pdb #3/B GLU 243
20聚体2.pdb #3/B GLU 243
20聚体2.pdb #3/B GLU 243
20聚体2.pdb #3/B GLU 243
20聚体2.pdb #3/B ARG 247
20聚体2.pdb #3/B ARG 247
20聚体2.pdb #3/B ARG 247
20聚体2.pdb #3/B ARG 247
20聚体2.pdb #3/B GLN 249
20聚体2.pdb #3/B GLN 249
20聚体2.pdb #3/B GLN 249
20聚体2.pdb #3/B GLN 249
20聚体2.pdb #3/B LYS 289
20聚体2.pdb #3/B LYS 289
20聚体2.pdb #3/B LYS 289
20聚体2.pdb #3/B LYS 289
20聚体2.pdb #3/B LYS 290
20聚体2.pdb #3/B LYS 290
20聚体2.pdb #3/B LYS 290
20聚体2.pdb #3/B LYS 290
20聚体2.pdb #3/B HIS 295
20聚体2.pdb #3/B HIS 295
20聚体2.pdb #3/B HIS 295
20聚体2.pdb #3/B HIS 295
20聚体2.pdb #3/B LYS 311
20聚体2.pdb #3/B LYS 311
20聚体2.pdb #3/B LYS 311
20聚体2.pdb #3/B LYS 311
20聚体2.pdb #3/B ASP 313
20聚体2.pdb #3/B ASP 313
20聚体2.pdb #3/B ASP 313
20聚体2.pdb #3/B ASP 313
20聚体2.pdb #3/C LEU 34
20聚体2.pdb #3/C LEU 34
20聚体2.pdb #3/C LEU 34
20聚体2.pdb #3/C LEU 34
20聚体2.pdb #3/C ILE 35
20聚体2.pdb #3/C ILE 35
20聚体2.pdb #3/C ILE 35
20聚体2.pdb #3/C ILE 35
20聚体2.pdb #3/C ASN 40
20聚体2.pdb #3/C ASN 40
20聚体2.pdb #3/C ASN 40
20聚体2.pdb #3/C ASN 40
20聚体2.pdb #3/C VAL 44
20聚体2.pdb #3/C VAL 44
20聚体2.pdb #3/C VAL 44
20聚体2.pdb #3/C VAL 44
20聚体2.pdb #3/C LYS 45
20聚体2.pdb #3/C LYS 45
20聚体2.pdb #3/C LYS 45
20聚体2.pdb #3/C LYS 45
20聚体2.pdb #3/C LYS 46
20聚体2.pdb #3/C LYS 46
20聚体2.pdb #3/C LYS 46
20聚体2.pdb #3/C LYS 46
20聚体2.pdb #3/C LEU 47
20聚体2.pdb #3/C LEU 47
20聚体2.pdb #3/C LEU 47
20聚体2.pdb #3/C LEU 47
20聚体2.pdb #3/C GLN 48
20聚体2.pdb #3/C GLN 48
20聚体2.pdb #3/C GLN 48
20聚体2.pdb #3/C GLN 48
20聚体2.pdb #3/C GLU 49
20聚体2.pdb #3/C GLU 49
20聚体2.pdb #3/C GLU 49
20聚体2.pdb #3/C GLU 49
20聚体2.pdb #3/C LYS 64
20聚体2.pdb #3/C LYS 64
20聚体2.pdb #3/C LYS 64
20聚体2.pdb #3/C LYS 64
20聚体2.pdb #3/C LYS 70
20聚体2.pdb #3/C LYS 70
20聚体2.pdb #3/C LYS 70
20聚体2.pdb #3/C LYS 70
20聚体2.pdb #3/C GLU 74
20聚体2.pdb #3/C GLU 74
20聚体2.pdb #3/C GLU 74
20聚体2.pdb #3/C GLU 74
20聚体2.pdb #3/C LYS 76
20聚体2.pdb #3/C LYS 76
20聚体2.pdb #3/C LYS 76
20聚体2.pdb #3/C LYS 76
20聚体2.pdb #3/C ILE 80
20聚体2.pdb #3/C ILE 80
20聚体2.pdb #3/C ILE 80
20聚体2.pdb #3/C ILE 80
20聚体2.pdb #3/C GLU 82
20聚体2.pdb #3/C GLU 82
20聚体2.pdb #3/C GLU 82
20聚体2.pdb #3/C GLU 82
20聚体2.pdb #3/C GLU 85
20聚体2.pdb #3/C GLU 85
20聚体2.pdb #3/C GLU 85
20聚体2.pdb #3/C GLU 85
20聚体2.pdb #3/C LYS 216
20聚体2.pdb #3/C LYS 216
20聚体2.pdb #3/C LYS 216
20聚体2.pdb #3/C LYS 216
20聚体2.pdb #3/C VAL 236
20聚体2.pdb #3/C VAL 236
20聚体2.pdb #3/C VAL 236
20聚体2.pdb #3/C VAL 236
20聚体2.pdb #3/C ASP 237
20聚体2.pdb #3/C ASP 237
20聚体2.pdb #3/C ASP 237
20聚体2.pdb #3/C ASP 237
20聚体2.pdb #3/C PHE 238
20聚体2.pdb #3/C PHE 238
20聚体2.pdb #3/C PHE 238
20聚体2.pdb #3/C PHE 238
20聚体2.pdb #3/C ARG 241
20聚体2.pdb #3/C ARG 241
20聚体2.pdb #3/C ARG 241
20聚体2.pdb #3/C ARG 241
20聚体2.pdb #3/C GLU 243
20聚体2.pdb #3/C GLU 243
20聚体2.pdb #3/C GLU 243
20聚体2.pdb #3/C GLU 243
20聚体2.pdb #3/C LYS 289
20聚体2.pdb #3/C LYS 289
20聚体2.pdb #3/C LYS 289
20聚体2.pdb #3/C LYS 289
20聚体2.pdb #3/C LYS 290
20聚体2.pdb #3/C LYS 290
20聚体2.pdb #3/C LYS 290
20聚体2.pdb #3/C LYS 290
20聚体2.pdb #3/C HIS 295
20聚体2.pdb #3/C HIS 295
20聚体2.pdb #3/C HIS 295
20聚体2.pdb #3/C HIS 295
20聚体2.pdb #3/C LYS 311
20聚体2.pdb #3/C LYS 311
20聚体2.pdb #3/C LYS 311
20聚体2.pdb #3/C LYS 311
20聚体2.pdb #3/C ASP 313
20聚体2.pdb #3/C ASP 313
20聚体2.pdb #3/C ASP 313
20聚体2.pdb #3/C ASP 313
20聚体2.pdb #3/C LYS 343
20聚体2.pdb #3/C LYS 343
20聚体2.pdb #3/C LYS 343
20聚体2.pdb #3/C LYS 343
20聚体2.pdb #3/D LEU 34
20聚体2.pdb #3/D LEU 34
20聚体2.pdb #3/D LEU 34
20聚体2.pdb #3/D LEU 34
20聚体2.pdb #3/D ILE 35
20聚体2.pdb #3/D ILE 35
20聚体2.pdb #3/D ILE 35
20聚体2.pdb #3/D ILE 35
20聚体2.pdb #3/D GLN 37
20聚体2.pdb #3/D GLN 37
20聚体2.pdb #3/D GLN 37
20聚体2.pdb #3/D GLN 37
20聚体2.pdb #3/D VAL 44
20聚体2.pdb #3/D VAL 44
20聚体2.pdb #3/D VAL 44
20聚体2.pdb #3/D VAL 44
20聚体2.pdb #3/D LYS 45
20聚体2.pdb #3/D LYS 45
20聚体2.pdb #3/D LYS 45
20聚体2.pdb #3/D LYS 45
20聚体2.pdb #3/D GLU 49
20聚体2.pdb #3/D GLU 49
20聚体2.pdb #3/D GLU 49
20聚体2.pdb #3/D GLU 49
20聚体2.pdb #3/D LYS 70
20聚体2.pdb #3/D LYS 70
20聚体2.pdb #3/D LYS 70
20聚体2.pdb #3/D LYS 70
20聚体2.pdb #3/D SER 73
20聚体2.pdb #3/D SER 73
20聚体2.pdb #3/D SER 73
20聚体2.pdb #3/D SER 73
20聚体2.pdb #3/D GLU 74
20聚体2.pdb #3/D GLU 74
20聚体2.pdb #3/D GLU 74
20聚体2.pdb #3/D GLU 74
20聚体2.pdb #3/D LYS 76
20聚体2.pdb #3/D LYS 76
20聚体2.pdb #3/D LYS 76
20聚体2.pdb #3/D LYS 76
20聚体2.pdb #3/D VAL 77
20聚体2.pdb #3/D VAL 77
20聚体2.pdb #3/D VAL 77
20聚体2.pdb #3/D VAL 77
20聚体2.pdb #3/D LYS 79
20聚体2.pdb #3/D LYS 79
20聚体2.pdb #3/D LYS 79
20聚体2.pdb #3/D LYS 79
20聚体2.pdb #3/D ILE 80
20聚体2.pdb #3/D ILE 80
20聚体2.pdb #3/D ILE 80
20聚体2.pdb #3/D ILE 80
20聚体2.pdb #3/D LYS 86
20聚体2.pdb #3/D LYS 86
20聚体2.pdb #3/D LYS 86
20聚体2.pdb #3/D LYS 86
20聚体2.pdb #3/D VAL 236
20聚体2.pdb #3/D VAL 236
20聚体2.pdb #3/D VAL 236
20聚体2.pdb #3/D VAL 236
20聚体2.pdb #3/D ASP 237
20聚体2.pdb #3/D ASP 237
20聚体2.pdb #3/D ASP 237
20聚体2.pdb #3/D ASP 237
20聚体2.pdb #3/D PHE 238
20聚体2.pdb #3/D PHE 238
20聚体2.pdb #3/D PHE 238
20聚体2.pdb #3/D PHE 238
20聚体2.pdb #3/D THR 239
20聚体2.pdb #3/D THR 239
20聚体2.pdb #3/D THR 239
20聚体2.pdb #3/D THR 239
20聚体2.pdb #3/D ARG 241
20聚体2.pdb #3/D ARG 241
20聚体2.pdb #3/D ARG 241
20聚体2.pdb #3/D ARG 241
20聚体2.pdb #3/D GLU 243
20聚体2.pdb #3/D GLU 243
20聚体2.pdb #3/D GLU 243
20聚体2.pdb #3/D GLU 243
20聚体2.pdb #3/D HIS 295
20聚体2.pdb #3/D HIS 295
20聚体2.pdb #3/D HIS 295
20聚体2.pdb #3/D HIS 295
20聚体2.pdb #3/D LYS 309
20聚体2.pdb #3/D LYS 309
20聚体2.pdb #3/D LYS 309
20聚体2.pdb #3/D LYS 309
20聚体2.pdb #3/D LYS 311
20聚体2.pdb #3/D LYS 311
20聚体2.pdb #3/D LYS 311
20聚体2.pdb #3/D LYS 311
20聚体2.pdb #3/D ASP 313
20聚体2.pdb #3/D ASP 313
20聚体2.pdb #3/D ASP 313
20聚体2.pdb #3/D ASP 313
20聚体2.pdb #3/D ASN 324
20聚体2.pdb #3/D ASN 324
20聚体2.pdb #3/D ASN 324
20聚体2.pdb #3/D ASN 324
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run
f(s)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 585, in find_hbonds
donor_hyds = hyd_positions(donor_atom)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 84, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 140, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
> coulombic #!3
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
20聚体2.pdb #3/A VAL 44
20聚体2.pdb #3/A VAL 44
20聚体2.pdb #3/A VAL 44
20聚体2.pdb #3/A VAL 44
20聚体2.pdb #3/A LYS 45
20聚体2.pdb #3/A LYS 45
20聚体2.pdb #3/A LYS 45
20聚体2.pdb #3/A LYS 45
20聚体2.pdb #3/A LYS 70
20聚体2.pdb #3/A LYS 70
20聚体2.pdb #3/A LYS 70
20聚体2.pdb #3/A LYS 70
20聚体2.pdb #3/A GLU 82
20聚体2.pdb #3/A GLU 82
20聚体2.pdb #3/A GLU 82
20聚体2.pdb #3/A GLU 82
20聚体2.pdb #3/A ARG 136
20聚体2.pdb #3/A ARG 136
20聚体2.pdb #3/A ARG 136
20聚体2.pdb #3/A ARG 136
20聚体2.pdb #3/A ARG 235
20聚体2.pdb #3/A ARG 235
20聚体2.pdb #3/A ARG 235
20聚体2.pdb #3/A ARG 235
20聚体2.pdb #3/A ASP 237
20聚体2.pdb #3/A ASP 237
20聚体2.pdb #3/A ASP 237
20聚体2.pdb #3/A ASP 237
20聚体2.pdb #3/A PHE 238
20聚体2.pdb #3/A PHE 238
20聚体2.pdb #3/A PHE 238
20聚体2.pdb #3/A PHE 238
20聚体2.pdb #3/A LEU 244
20聚体2.pdb #3/A LEU 244
20聚体2.pdb #3/A LEU 244
20聚体2.pdb #3/A LEU 244
20聚体2.pdb #3/A ASP 246
20聚体2.pdb #3/A ASP 246
20聚体2.pdb #3/A ASP 246
20聚体2.pdb #3/A ASP 246
20聚体2.pdb #3/A ARG 247
20聚体2.pdb #3/A ARG 247
20聚体2.pdb #3/A ARG 247
20聚体2.pdb #3/A ARG 247
20聚体2.pdb #3/A GLN 248
20聚体2.pdb #3/A GLN 248
20聚体2.pdb #3/A GLN 248
20聚体2.pdb #3/A GLN 248
20聚体2.pdb #3/A LYS 250
20聚体2.pdb #3/A LYS 250
20聚体2.pdb #3/A LYS 250
20聚体2.pdb #3/A LYS 250
20聚体2.pdb #3/A ASP 287
20聚体2.pdb #3/A ASP 287
20聚体2.pdb #3/A ASP 287
20聚体2.pdb #3/A ASP 287
20聚体2.pdb #3/A LYS 289
20聚体2.pdb #3/A LYS 289
20聚体2.pdb #3/A LYS 289
20聚体2.pdb #3/A LYS 289
20聚体2.pdb #3/A LYS 290
20聚体2.pdb #3/A LYS 290
20聚体2.pdb #3/A LYS 290
20聚体2.pdb #3/A LYS 290
20聚体2.pdb #3/A HIS 295
20聚体2.pdb #3/A HIS 295
20聚体2.pdb #3/A HIS 295
20聚体2.pdb #3/A HIS 295
20聚体2.pdb #3/A LYS 311
20聚体2.pdb #3/A LYS 311
20聚体2.pdb #3/A LYS 311
20聚体2.pdb #3/A LYS 311
20聚体2.pdb #3/A LYS 343
20聚体2.pdb #3/A LYS 343
20聚体2.pdb #3/A LYS 343
20聚体2.pdb #3/A LYS 343
20聚体2.pdb #3/B LEU 34
20聚体2.pdb #3/B LEU 34
20聚体2.pdb #3/B LEU 34
20聚体2.pdb #3/B LEU 34
20聚体2.pdb #3/B LYS 45
20聚体2.pdb #3/B LYS 45
20聚体2.pdb #3/B LYS 45
20聚体2.pdb #3/B LYS 45
20聚体2.pdb #3/B GLU 49
20聚体2.pdb #3/B GLU 49
20聚体2.pdb #3/B GLU 49
20聚体2.pdb #3/B GLU 49
20聚体2.pdb #3/B LYS 70
20聚体2.pdb #3/B LYS 70
20聚体2.pdb #3/B LYS 70
20聚体2.pdb #3/B LYS 70
20聚体2.pdb #3/B LEU 72
20聚体2.pdb #3/B LEU 72
20聚体2.pdb #3/B LEU 72
20聚体2.pdb #3/B LEU 72
20聚体2.pdb #3/B GLU 74
20聚体2.pdb #3/B GLU 74
20聚体2.pdb #3/B GLU 74
20聚体2.pdb #3/B GLU 74
20聚体2.pdb #3/B LYS 79
20聚体2.pdb #3/B LYS 79
20聚体2.pdb #3/B LYS 79
20聚体2.pdb #3/B LYS 79
20聚体2.pdb #3/B ILE 80
20聚体2.pdb #3/B ILE 80
20聚体2.pdb #3/B ILE 80
20聚体2.pdb #3/B ILE 80
20聚体2.pdb #3/B GLU 82
20聚体2.pdb #3/B GLU 82
20聚体2.pdb #3/B GLU 82
20聚体2.pdb #3/B GLU 82
20聚体2.pdb #3/B VAL 236
20聚体2.pdb #3/B VAL 236
20聚体2.pdb #3/B VAL 236
20聚体2.pdb #3/B VAL 236
20聚体2.pdb #3/B ASP 237
20聚体2.pdb #3/B ASP 237
20聚体2.pdb #3/B ASP 237
20聚体2.pdb #3/B ASP 237
20聚体2.pdb #3/B PHE 238
20聚体2.pdb #3/B PHE 238
20聚体2.pdb #3/B PHE 238
20聚体2.pdb #3/B PHE 238
20聚体2.pdb #3/B ARG 241
20聚体2.pdb #3/B ARG 241
20聚体2.pdb #3/B ARG 241
20聚体2.pdb #3/B ARG 241
20聚体2.pdb #3/B GLU 243
20聚体2.pdb #3/B GLU 243
20聚体2.pdb #3/B GLU 243
20聚体2.pdb #3/B GLU 243
20聚体2.pdb #3/B ARG 247
20聚体2.pdb #3/B ARG 247
20聚体2.pdb #3/B ARG 247
20聚体2.pdb #3/B ARG 247
20聚体2.pdb #3/B GLN 249
20聚体2.pdb #3/B GLN 249
20聚体2.pdb #3/B GLN 249
20聚体2.pdb #3/B GLN 249
20聚体2.pdb #3/B LYS 289
20聚体2.pdb #3/B LYS 289
20聚体2.pdb #3/B LYS 289
20聚体2.pdb #3/B LYS 289
20聚体2.pdb #3/B LYS 290
20聚体2.pdb #3/B LYS 290
20聚体2.pdb #3/B LYS 290
20聚体2.pdb #3/B LYS 290
20聚体2.pdb #3/B HIS 295
20聚体2.pdb #3/B HIS 295
20聚体2.pdb #3/B HIS 295
20聚体2.pdb #3/B HIS 295
20聚体2.pdb #3/B LYS 311
20聚体2.pdb #3/B LYS 311
20聚体2.pdb #3/B LYS 311
20聚体2.pdb #3/B LYS 311
20聚体2.pdb #3/B ASP 313
20聚体2.pdb #3/B ASP 313
20聚体2.pdb #3/B ASP 313
20聚体2.pdb #3/B ASP 313
20聚体2.pdb #3/C LEU 34
20聚体2.pdb #3/C LEU 34
20聚体2.pdb #3/C LEU 34
20聚体2.pdb #3/C LEU 34
20聚体2.pdb #3/C ILE 35
20聚体2.pdb #3/C ILE 35
20聚体2.pdb #3/C ILE 35
20聚体2.pdb #3/C ILE 35
20聚体2.pdb #3/C ASN 40
20聚体2.pdb #3/C ASN 40
20聚体2.pdb #3/C ASN 40
20聚体2.pdb #3/C ASN 40
20聚体2.pdb #3/C VAL 44
20聚体2.pdb #3/C VAL 44
20聚体2.pdb #3/C VAL 44
20聚体2.pdb #3/C VAL 44
20聚体2.pdb #3/C LYS 45
20聚体2.pdb #3/C LYS 45
20聚体2.pdb #3/C LYS 45
20聚体2.pdb #3/C LYS 45
20聚体2.pdb #3/C LYS 46
20聚体2.pdb #3/C LYS 46
20聚体2.pdb #3/C LYS 46
20聚体2.pdb #3/C LYS 46
20聚体2.pdb #3/C LEU 47
20聚体2.pdb #3/C LEU 47
20聚体2.pdb #3/C LEU 47
20聚体2.pdb #3/C LEU 47
20聚体2.pdb #3/C GLN 48
20聚体2.pdb #3/C GLN 48
20聚体2.pdb #3/C GLN 48
20聚体2.pdb #3/C GLN 48
20聚体2.pdb #3/C GLU 49
20聚体2.pdb #3/C GLU 49
20聚体2.pdb #3/C GLU 49
20聚体2.pdb #3/C GLU 49
20聚体2.pdb #3/C LYS 64
20聚体2.pdb #3/C LYS 64
20聚体2.pdb #3/C LYS 64
20聚体2.pdb #3/C LYS 64
20聚体2.pdb #3/C LYS 70
20聚体2.pdb #3/C LYS 70
20聚体2.pdb #3/C LYS 70
20聚体2.pdb #3/C LYS 70
20聚体2.pdb #3/C GLU 74
20聚体2.pdb #3/C GLU 74
20聚体2.pdb #3/C GLU 74
20聚体2.pdb #3/C GLU 74
20聚体2.pdb #3/C LYS 76
20聚体2.pdb #3/C LYS 76
20聚体2.pdb #3/C LYS 76
20聚体2.pdb #3/C LYS 76
20聚体2.pdb #3/C ILE 80
20聚体2.pdb #3/C ILE 80
20聚体2.pdb #3/C ILE 80
20聚体2.pdb #3/C ILE 80
20聚体2.pdb #3/C GLU 82
20聚体2.pdb #3/C GLU 82
20聚体2.pdb #3/C GLU 82
20聚体2.pdb #3/C GLU 82
20聚体2.pdb #3/C GLU 85
20聚体2.pdb #3/C GLU 85
20聚体2.pdb #3/C GLU 85
20聚体2.pdb #3/C GLU 85
20聚体2.pdb #3/C LYS 216
20聚体2.pdb #3/C LYS 216
20聚体2.pdb #3/C LYS 216
20聚体2.pdb #3/C LYS 216
20聚体2.pdb #3/C VAL 236
20聚体2.pdb #3/C VAL 236
20聚体2.pdb #3/C VAL 236
20聚体2.pdb #3/C VAL 236
20聚体2.pdb #3/C ASP 237
20聚体2.pdb #3/C ASP 237
20聚体2.pdb #3/C ASP 237
20聚体2.pdb #3/C ASP 237
20聚体2.pdb #3/C PHE 238
20聚体2.pdb #3/C PHE 238
20聚体2.pdb #3/C PHE 238
20聚体2.pdb #3/C PHE 238
20聚体2.pdb #3/C ARG 241
20聚体2.pdb #3/C ARG 241
20聚体2.pdb #3/C ARG 241
20聚体2.pdb #3/C ARG 241
20聚体2.pdb #3/C GLU 243
20聚体2.pdb #3/C GLU 243
20聚体2.pdb #3/C GLU 243
20聚体2.pdb #3/C GLU 243
20聚体2.pdb #3/C LYS 289
20聚体2.pdb #3/C LYS 289
20聚体2.pdb #3/C LYS 289
20聚体2.pdb #3/C LYS 289
20聚体2.pdb #3/C LYS 290
20聚体2.pdb #3/C LYS 290
20聚体2.pdb #3/C LYS 290
20聚体2.pdb #3/C LYS 290
20聚体2.pdb #3/C HIS 295
20聚体2.pdb #3/C HIS 295
20聚体2.pdb #3/C HIS 295
20聚体2.pdb #3/C HIS 295
20聚体2.pdb #3/C LYS 311
20聚体2.pdb #3/C LYS 311
20聚体2.pdb #3/C LYS 311
20聚体2.pdb #3/C LYS 311
20聚体2.pdb #3/C ASP 313
20聚体2.pdb #3/C ASP 313
20聚体2.pdb #3/C ASP 313
20聚体2.pdb #3/C ASP 313
20聚体2.pdb #3/C LYS 343
20聚体2.pdb #3/C LYS 343
20聚体2.pdb #3/C LYS 343
20聚体2.pdb #3/C LYS 343
20聚体2.pdb #3/D LEU 34
20聚体2.pdb #3/D LEU 34
20聚体2.pdb #3/D LEU 34
20聚体2.pdb #3/D LEU 34
20聚体2.pdb #3/D ILE 35
20聚体2.pdb #3/D ILE 35
20聚体2.pdb #3/D ILE 35
20聚体2.pdb #3/D ILE 35
20聚体2.pdb #3/D GLN 37
20聚体2.pdb #3/D GLN 37
20聚体2.pdb #3/D GLN 37
20聚体2.pdb #3/D GLN 37
20聚体2.pdb #3/D VAL 44
20聚体2.pdb #3/D VAL 44
20聚体2.pdb #3/D VAL 44
20聚体2.pdb #3/D VAL 44
20聚体2.pdb #3/D LYS 45
20聚体2.pdb #3/D LYS 45
20聚体2.pdb #3/D LYS 45
20聚体2.pdb #3/D LYS 45
20聚体2.pdb #3/D GLU 49
20聚体2.pdb #3/D GLU 49
20聚体2.pdb #3/D GLU 49
20聚体2.pdb #3/D GLU 49
20聚体2.pdb #3/D LYS 70
20聚体2.pdb #3/D LYS 70
20聚体2.pdb #3/D LYS 70
20聚体2.pdb #3/D LYS 70
20聚体2.pdb #3/D SER 73
20聚体2.pdb #3/D SER 73
20聚体2.pdb #3/D SER 73
20聚体2.pdb #3/D SER 73
20聚体2.pdb #3/D GLU 74
20聚体2.pdb #3/D GLU 74
20聚体2.pdb #3/D GLU 74
20聚体2.pdb #3/D GLU 74
20聚体2.pdb #3/D LYS 76
20聚体2.pdb #3/D LYS 76
20聚体2.pdb #3/D LYS 76
20聚体2.pdb #3/D LYS 76
20聚体2.pdb #3/D VAL 77
20聚体2.pdb #3/D VAL 77
20聚体2.pdb #3/D VAL 77
20聚体2.pdb #3/D VAL 77
20聚体2.pdb #3/D LYS 79
20聚体2.pdb #3/D LYS 79
20聚体2.pdb #3/D LYS 79
20聚体2.pdb #3/D LYS 79
20聚体2.pdb #3/D ILE 80
20聚体2.pdb #3/D ILE 80
20聚体2.pdb #3/D ILE 80
20聚体2.pdb #3/D ILE 80
20聚体2.pdb #3/D LYS 86
20聚体2.pdb #3/D LYS 86
20聚体2.pdb #3/D LYS 86
20聚体2.pdb #3/D LYS 86
20聚体2.pdb #3/D VAL 236
20聚体2.pdb #3/D VAL 236
20聚体2.pdb #3/D VAL 236
20聚体2.pdb #3/D VAL 236
20聚体2.pdb #3/D ASP 237
20聚体2.pdb #3/D ASP 237
20聚体2.pdb #3/D ASP 237
20聚体2.pdb #3/D ASP 237
20聚体2.pdb #3/D PHE 238
20聚体2.pdb #3/D PHE 238
20聚体2.pdb #3/D PHE 238
20聚体2.pdb #3/D PHE 238
20聚体2.pdb #3/D THR 239
20聚体2.pdb #3/D THR 239
20聚体2.pdb #3/D THR 239
20聚体2.pdb #3/D THR 239
20聚体2.pdb #3/D ARG 241
20聚体2.pdb #3/D ARG 241
20聚体2.pdb #3/D ARG 241
20聚体2.pdb #3/D ARG 241
20聚体2.pdb #3/D GLU 243
20聚体2.pdb #3/D GLU 243
20聚体2.pdb #3/D GLU 243
20聚体2.pdb #3/D GLU 243
20聚体2.pdb #3/D HIS 295
20聚体2.pdb #3/D HIS 295
20聚体2.pdb #3/D HIS 295
20聚体2.pdb #3/D HIS 295
20聚体2.pdb #3/D LYS 309
20聚体2.pdb #3/D LYS 309
20聚体2.pdb #3/D LYS 309
20聚体2.pdb #3/D LYS 309
20聚体2.pdb #3/D LYS 311
20聚体2.pdb #3/D LYS 311
20聚体2.pdb #3/D LYS 311
20聚体2.pdb #3/D LYS 311
20聚体2.pdb #3/D ASP 313
20聚体2.pdb #3/D ASP 313
20聚体2.pdb #3/D ASP 313
20聚体2.pdb #3/D ASP 313
20聚体2.pdb #3/D ASN 324
20聚体2.pdb #3/D ASN 324
20聚体2.pdb #3/D ASN 324
20聚体2.pdb #3/D ASN 324
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run
f(s)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 585, in find_hbonds
donor_hyds = hyd_positions(donor_atom)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 84, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 140, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,1
Model Number: Z12R0002RCH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 16 days, 4 hours, 17 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.1.3
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.1
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → AddH: more than 2 coplanar positions specified |
comment:2 by , 7 weeks ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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