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#18831 closed defect (not a bug)

AddH: more than 2 coplanar positions specified

Reported by:	chimerax-bug-report@…	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:        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 pett, 4 weeks ago

Component:	Unassigned → Structure Editing
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → AddH: more than 2 coplanar positions specified

comment:2 by pett, 4 weeks ago

Resolution:	→ not a bug
Status:	accepted → closed

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