PICKLUSTER: Attempted to add model Atomic interactions interface #2 to scene twice

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_PICKLUSTER-0.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 23.1.2  
[notice] To update, run:
/Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /Users/dinaschneidman/Downloads/ChimeraX_PICKLUSTER-0.1-py3-none-
any.whl  
Requirement already satisfied: ChimeraX-Core~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PICKLUSTER==0.1) (1.5)  
Requirement already satisfied: Jinja2>=3.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PICKLUSTER==0.1) (3.1.2)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PICKLUSTER==0.1) (1.24.3)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.1) (1.1)  
Requirement already satisfied: MarkupSafe>=2.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from Jinja2>=3.0->ChimeraX-PICKLUSTER==0.1) (2.1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.1) (1.2)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.1) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.1) (1.0.1)  
Installing collected packages: ChimeraX-PICKLUSTER  
Successfully installed ChimeraX-PICKLUSTER-0.1  
\---  

Successfully installed ChimeraX-PICKLUSTER-0.1  
Installed ChimeraX-PICKLUSTER (0.1)  

> open 6k15

6k15 title:  
RSC substrate-recruitment module [more info...]  
  
Chain information for 6k15 #1  
---  
Chain | Description | UniProt  
A | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST  
C | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST  
D H | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST  
E | High temperature lethal protein 1 | HTL1_YEAST  
F | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST  
G | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST  
I | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST  
J | Nuclear protein STH1/NPS1 | STH1_YEAST  
K | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST  
L | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST  
M | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST  
X | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST  
  
Non-standard residues in 6k15 #1  
---  
ZN — zinc ion  
  

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> hide atoms

> show cartoons

Cluster information for 6k15['H', 'M']  
---  
Cluster | Residues  
1 | [['H', 'ILE', 254], ['H', 'HIS', 255], ['H', 'LYS', 256], ['H', 'VAL',
257], ['H', 'TYR', 258], ['H', 'ILE', 259], ['H', 'CYS', 260], ['H', 'HIS',
261], ['H', 'THR', 262], ['H', 'CYS', 263], ['H', 'GLY', 264], ['H', 'ALA',
277], ['H', 'ASP', 279], ['H', 'THR', 280], ['H', 'ASN', 281], ['H', 'TYR',
330], ['H', 'HIS', 340], ['M', 'ILE', 37], ['M', 'VAL', 39], ['M', 'ARG', 41],
['M', 'GLN', 43], ['M', 'SER', 44], ['M', 'ASN', 45], ['M', 'GLY', 46], ['M',
'VAL', 47], ['M', 'LEU', 48], ['M', 'THR', 49]]  
2 | [['H', 'SER', 84], ['H', 'PHE', 85], ['H', 'SER', 87], ['H', 'TRP', 88],
['H', 'ILE', 97], ['H', 'ARG', 100], ['H', 'LYS', 162], ['H', 'TRP', 163],
['H', 'TYR', 168], ['H', 'GLN', 169], ['H', 'ILE', 170], ['H', 'ASP', 171],
['H', 'ARG', 173], ['H', 'THR', 174], ['H', 'LYS', 175], ['M', 'ALA', 63],
['M', 'PHE', 68], ['M', 'LEU', 71], ['M', 'THR', 75], ['M', 'ALA', 76], ['M',
'ARG', 77], ['M', 'GLY', 78], ['M', 'VAL', 79], ['M', 'ARG', 84], ['M', 'MET',
87], ['M', 'ALA', 88], ['M', 'LEU', 90], ['M', 'SER', 91], ['M', 'GLY', 92],
['M', 'ILE', 93], ['M', 'GLU', 96]]  
3 | [['H', 'ARG', 252], ['M', 'TYR', 60]]  
  
Cluster information for 6k15['D', 'M']  
---  
Cluster | Residues  
1 | [['D', 'VAL', 462], ['D', 'GLU', 466], ['M', 'ARG', 554], ['M', 'PRO',
555], ['M', 'LEU', 558]]  
2 | [['D', 'GLU', 451], ['D', 'GLU', 455], ['D', 'LEU', 459], ['M', 'LEU',
334], ['M', 'GLU', 337], ['M', 'ARG', 552]]  
3 | [['D', 'CYS', 448], ['M', 'LYS', 330]]  
4 | [['D', 'ASP', 192], ['D', 'THR', 193], ['D', 'PRO', 194], ['M', 'ARG',
77], ['M', 'GLY', 78], ['M', 'VAL', 79], ['M', 'ARG', 84], ['M', 'GLU', 96],
['M', 'TRP', 99]]  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 364, in thread_safe  
func(*args, **kw)  
File "/Users/dinaschneidman/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/PICKLUSTER/tool.py", line 103, in handle_scheme  
methods.display_atomic_interactions(self.session, chain1, chain2, int_allfunc)  
File "/Users/dinaschneidman/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/PICKLUSTER/methods.py", line 212, in
display_atomic_interactions  
session.models.add([pbg])  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 692, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model Atomic interactions interface #2 to scene
twice  
  
ValueError: Attempted to add model Atomic interactions interface #2 to scene
twice  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 692, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  
Cluster information for 6k15['D', 'M']  
---  
Cluster | Residues  
1 | [['D', 'VAL', 462], ['D', 'GLU', 466], ['M', 'ARG', 554], ['M', 'PRO',
555], ['M', 'LEU', 558]]  
2 | [['D', 'GLU', 451], ['D', 'GLU', 455], ['D', 'LEU', 459], ['M', 'LEU',
334], ['M', 'GLU', 337], ['M', 'ARG', 552]]  
3 | [['D', 'CYS', 448], ['M', 'LYS', 330]]  
4 | [['D', 'ASP', 192], ['D', 'THR', 193], ['D', 'PRO', 194], ['M', 'ARG',
77], ['M', 'GLY', 78], ['M', 'VAL', 79], ['M', 'ARG', 84], ['M', 'GLU', 96],
['M', 'TRP', 99]]  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 364, in thread_safe  
func(*args, **kw)  
File "/Users/dinaschneidman/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/PICKLUSTER/tool.py", line 103, in handle_scheme  
methods.display_atomic_interactions(self.session, chain1, chain2, int_allfunc)  
File "/Users/dinaschneidman/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/PICKLUSTER/methods.py", line 212, in
display_atomic_interactions  
session.models.add([pbg])  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 692, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model Atomic interactions interface #2 to scene
twice  
  
ValueError: Attempted to add model Atomic interactions interface #2 to scene
twice  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 692, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  

> color #2 #76d6ffff models

> color #2 #0096ffff models

> color #2 #fffc79ff models

> close #2

Cluster information for 6k15['D', 'M']  
---  
Cluster | Residues  
1 | [['D', 'VAL', 462], ['D', 'GLU', 466], ['M', 'ARG', 554], ['M', 'PRO',
555], ['M', 'LEU', 558]]  
2 | [['D', 'GLU', 451], ['D', 'GLU', 455], ['D', 'LEU', 459], ['M', 'LEU',
334], ['M', 'GLU', 337], ['M', 'ARG', 552]]  
3 | [['D', 'CYS', 448], ['M', 'LYS', 330]]  
4 | [['D', 'ASP', 192], ['D', 'THR', 193], ['D', 'PRO', 194], ['M', 'ARG',
77], ['M', 'GLY', 78], ['M', 'VAL', 79], ['M', 'ARG', 84], ['M', 'GLU', 96],
['M', 'TRP', 99]]  
  

> select add #2

71 pseudobonds, 1 model selected  

> show atoms

> hide atoms

> select subtract #2

Nothing selected  

> select add #2

71 pseudobonds, 1 model selected  

> style stick

Changed 21486 atom styles  

> style stick

Changed 21486 atom styles  

> color #2 #008f00ff models

Cluster information for 6k15['D', 'H']  
---  
Cluster | Residues  
1 | [['H', 'LEU', 73], ['H', 'ALA', 74], ['H', 'LYS', 75], ['H', 'GLN', 76],
['H', 'HIS', 78], ['H', 'PRO', 79], ['H', 'VAL', 80], ['H', 'ILE', 81], ['H',
'ILE', 82], ['H', 'PRO', 83], ['H', 'SER', 84], ['H', 'SER', 87], ['H', 'ILE',
91], ['H', 'PHE', 124], ['H', 'ILE', 126], ['H', 'ASN', 127], ['H', 'THR',
128], ['H', 'ARG', 130], ['H', 'LEU', 131], ['H', 'TYR', 168], ['H', 'ILE',
170], ['H', 'PRO', 172], ['H', 'LYS', 175], ['H', 'PRO', 176], ['H', 'SER',
177], ['H', 'LEU', 178], ['H', 'ILE', 179], ['H', 'GLY', 180], ['H', 'PRO',
181], ['H', 'PHE', 187], ['H', 'VAL', 189], ['H', 'LEU', 191], ['H', 'ASN',
233], ['H', 'TYR', 235], ['H', 'ALA', 238], ['H', 'PHE', 241], ['H', 'ASN',
242], ['H', 'LEU', 244], ['D', 'PRO', 181], ['D', 'SER', 182], ['D', 'PHE',
183], ['D', 'THR', 184], ['D', 'GLY', 185], ['D', 'HIS', 186], ['D', 'PHE',
187], ['D', 'GLN', 188], ['D', 'VAL', 189], ['D', 'VAL', 190], ['D', 'LEU',
191], ['D', 'ASP', 192], ['D', 'THR', 193], ['D', 'PRO', 194], ['D', 'GLN',
195], ['D', 'GLY', 196], ['D', 'LEU', 197], ['D', 'LYS', 198], ['D', 'PRO',
199], ['D', 'PHE', 200], ['D', 'LEU', 201], ['D', 'PRO', 202]]  
2 | [['H', 'LEU', 454], ['H', 'GLU', 455], ['H', 'GLU', 457], ['H', 'LYS',
458], ['H', 'LEU', 459], ['H', 'TYR', 461], ['H', 'VAL', 462], ['H', 'GLU',
464], ['H', 'SER', 465], ['H', 'MET', 468], ['H', 'LEU', 469], ['H', 'ASP',
471], ['H', 'ARG', 472], ['H', 'LEU', 475], ['D', 'LEU', 450], ['D', 'GLU',
451], ['D', 'GLN', 453], ['D', 'LEU', 454], ['D', 'GLU', 457], ['D', 'LYS',
458], ['D', 'TYR', 461], ['D', 'GLU', 464], ['D', 'LYS', 467], ['D', 'MET',
468], ['D', 'ASP', 471], ['D', 'ARG', 472], ['D', 'LEU', 475]]  
3 | [['H', 'GLU', 423], ['H', 'GLN', 426], ['H', 'ALA', 427], ['H', 'GLN',
430], ['H', 'VAL', 433], ['H', 'MET', 437], ['H', 'PHE', 444], ['H', 'LEU',
447], ['H', 'CYS', 448], ['H', 'LEU', 450], ['H', 'GLU', 451], ['D', 'SER',
418], ['D', 'TYR', 421], ['D', 'ILE', 422], ['D', 'SER', 425], ['D', 'GLN',
426], ['D', 'ILE', 429], ['D', 'LEU', 432], ['D', 'VAL', 433], ['D', 'THR',
436], ['D', 'LYS', 439], ['D', 'LEU', 440], ['D', 'LYS', 443], ['D', 'PHE',
444], ['D', 'LYS', 446], ['D', 'LEU', 447]]  
4 | [['H', 'GLN', 195], ['H', 'GLY', 196], ['H', 'LYS', 198], ['H', 'PRO',
199], ['H', 'PHE', 200], ['H', 'LEU', 201], ['H', 'PRO', 202], ['H', 'GLU',
203], ['D', 'ILE', 81], ['D', 'TYR', 134], ['D', 'GLN', 169], ['D', 'ILE',
170], ['D', 'ASP', 171], ['D', 'PRO', 172], ['D', 'ARG', 173], ['D', 'LYS',
175]]  
5 | [['H', 'SER', 387], ['H', 'LYS', 388], ['H', 'LEU', 389], ['H', 'CYS',
392], ['H', 'VAL', 393], ['H', 'ALA', 396], ['H', 'LEU', 400], ['H', 'LYS',
406], ['H', 'LYS', 409], ['H', 'LYS', 413], ['D', 'LYS', 388], ['D', 'LEU',
389], ['D', 'GLU', 391], ['D', 'CYS', 392], ['D', 'ALA', 396], ['D', 'VAL',
397], ['D', 'GLN', 398], ['D', 'THR', 399]]  
6 | [['H', 'LYS', 353], ['H', 'SER', 356], ['H', 'PRO', 358], ['H', 'ARG',
365], ['D', 'LYS', 221], ['D', 'LYS', 222], ['D', 'GLU', 223], ['D', 'PHE',
224]]  
7 | [['H', 'LEU', 482], ['D', 'LEU', 482]]  
8 | [['H', 'ASN', 362], ['D', 'VAL', 226], ['D', 'LYS', 231]]  
  
Interactions in clusters in 6k15['D', 'H']  
---  
Cluster | Interactions  
1 | [[['H', 'LEU', 73], ['D', 'HIS', 186]], [['H', 'LEU', 73], ['D', 'PHE',
183]], [['H', 'ALA', 74], ['D', 'PHE', 187]], [['H', 'ALA', 74], ['D', 'PHE',
183]], [['H', 'ALA', 74], ['D', 'HIS', 186]], [['H', 'ALA', 74], ['D', 'SER',
182]], [['H', 'LYS', 75], ['D', 'PHE', 187]], [['H', 'GLN', 76], ['D', 'GLN',
188]], [['H', 'GLN', 76], ['D', 'PHE', 187]], [['H', 'GLN', 76], ['D', 'HIS',
186]], [['H', 'HIS', 78], ['D', 'PHE', 187]], [['H', 'PRO', 79], ['D', 'GLN',
188]], [['H', 'VAL', 80], ['D', 'VAL', 189]], [['H', 'VAL', 80], ['D', 'VAL',
190]], [['H', 'VAL', 80], ['D', 'GLN', 188]], [['H', 'VAL', 80], ['D', 'PHE',
187]], [['H', 'ILE', 81], ['D', 'VAL', 190]], [['H', 'ILE', 81], ['D', 'LEU',
197]], [['H', 'ILE', 81], ['D', 'ASP', 192]], [['H', 'ILE', 81], ['D', 'LEU',
191]], [['H', 'ILE', 82], ['D', 'ASP', 192]], [['H', 'ILE', 82], ['D', 'LEU',
191]], [['H', 'ILE', 82], ['D', 'VAL', 190]], [['H', 'ILE', 82], ['D', 'VAL',
189]], [['H', 'PRO', 83], ['D', 'ASP', 192]], [['H', 'PRO', 83], ['D', 'LEU',
191]], [['H', 'SER', 84], ['D', 'THR', 193]], [['H', 'SER', 84], ['D', 'LEU',
191]], [['H', 'SER', 84], ['D', 'PRO', 194]], [['H', 'SER', 84], ['D', 'ASP',
192]], [['H', 'SER', 87], ['D', 'PHE', 200]], [['H', 'SER', 87], ['D', 'LEU',
191]], [['H', 'ILE', 91], ['D', 'PHE', 183]], [['H', 'ILE', 91], ['D', 'THR',
184]], [['H', 'ILE', 91], ['D', 'GLY', 185]], [['H', 'PHE', 124], ['D', 'PRO',
181]], [['H', 'ILE', 126], ['D', 'THR', 184]], [['H', 'ASN', 127], ['D',
'SER', 182]], [['H', 'ASN', 127], ['D', 'THR', 184]], [['H', 'ASN', 127],
['D', 'PHE', 183]], [['H', 'ASN', 127], ['D', 'PRO', 181]], [['H', 'THR',
128], ['D', 'PRO', 181]], [['H', 'ARG', 130], ['D', 'PHE', 187]], [['H',
'ARG', 130], ['D', 'THR', 184]], [['H', 'ARG', 130], ['D', 'VAL', 189]],
[['H', 'LEU', 131], ['D', 'PHE', 187]], [['H', 'LEU', 131], ['D', 'THR',
184]], [['H', 'LEU', 131], ['D', 'SER', 182]], [['H', 'LEU', 131], ['D',
'PRO', 181]], [['H', 'TYR', 168], ['D', 'ASP', 192]], [['H', 'ILE', 170],
['D', 'ASP', 192]], [['H', 'PRO', 172], ['D', 'LEU', 197]], [['H', 'LYS',
175], ['D', 'GLY', 196]], [['H', 'LYS', 175], ['D', 'ASP', 192]], [['H',
'LYS', 175], ['D', 'LEU', 197]], [['H', 'LYS', 175], ['D', 'THR', 193]],
[['H', 'LYS', 175], ['D', 'PRO', 194]], [['H', 'PRO', 176], ['D', 'LEU',
197]], [['H', 'PRO', 176], ['D', 'GLY', 196]], [['H', 'PRO', 176], ['D',
'GLN', 195]], [['H', 'SER', 177], ['D', 'LEU', 197]], [['H', 'SER', 177],
['D', 'GLY', 196]], [['H', 'LEU', 178], ['D', 'GLN', 195]], [['H', 'LEU',
178], ['D', 'LYS', 198]], [['H', 'LEU', 178], ['D', 'LEU', 197]], [['H',
'LEU', 178], ['D', 'GLY', 196]], [['H', 'LEU', 178], ['D', 'PRO', 199]],
[['H', 'LEU', 178], ['D', 'THR', 193]], [['H', 'ILE', 179], ['D', 'LYS',
198]], [['H', 'GLY', 180], ['D', 'LYS', 198]], [['H', 'GLY', 180], ['D',
'PRO', 199]], [['H', 'PRO', 181], ['D', 'LYS', 198]], [['H', 'PRO', 181],
['D', 'LEU', 201]], [['H', 'PRO', 181], ['D', 'PRO', 199]], [['H', 'PHE',
187], ['D', 'LEU', 201]], [['H', 'PHE', 187], ['D', 'PRO', 202]], [['H',
'VAL', 189], ['D', 'HIS', 186]], [['H', 'LEU', 191], ['D', 'HIS', 186]],
[['H', 'LEU', 191], ['D', 'PHE', 183]], [['H', 'LEU', 191], ['D', 'GLY',
185]], [['H', 'ASN', 233], ['D', 'GLN', 188]], [['H', 'TYR', 235], ['D',
'GLN', 188]], [['H', 'ALA', 238], ['D', 'PRO', 199]], [['H', 'PHE', 241],
['D', 'GLN', 188]], [['H', 'PHE', 241], ['D', 'PRO', 199]], [['H', 'PHE',
241], ['D', 'VAL', 190]], [['H', 'PHE', 241], ['D', 'LEU', 201]], [['H',
'PHE', 241], ['D', 'VAL', 189]], [['H', 'PHE', 241], ['D', 'PHE', 200]],
[['H', 'ASN', 242], ['D', 'LEU', 197]], [['H', 'ASN', 242], ['D', 'VAL',
190]], [['H', 'ASN', 242], ['D', 'PRO', 199]], [['H', 'ASN', 242], ['D',
'LYS', 198]], [['H', 'LEU', 244], ['D', 'GLN', 188]]]  
2 | [[['H', 'LEU', 454], ['D', 'LEU', 454]], [['H', 'LEU', 454], ['D', 'LEU',
450]], [['H', 'LEU', 454], ['D', 'GLU', 451]], [['H', 'GLU', 455], ['D',
'LEU', 450]], [['H', 'GLU', 455], ['D', 'LEU', 454]], [['H', 'GLU', 457],
['D', 'GLU', 457]], [['H', 'GLU', 457], ['D', 'LEU', 454]], [['H', 'LYS',
458], ['D', 'GLU', 457]], [['H', 'LYS', 458], ['D', 'GLN', 453]], [['H',
'LYS', 458], ['D', 'LEU', 454]], [['H', 'LYS', 458], ['D', 'LEU', 450]],
[['H', 'LEU', 459], ['D', 'GLU', 457]], [['H', 'TYR', 461], ['D', 'LYS',
458]], [['H', 'TYR', 461], ['D', 'GLU', 457]], [['H', 'TYR', 461], ['D',
'TYR', 461]], [['H', 'VAL', 462], ['D', 'GLU', 457]], [['H', 'GLU', 464],
['D', 'TYR', 461]], [['H', 'SER', 465], ['D', 'TYR', 461]], [['H', 'SER',
465], ['D', 'GLU', 464]], [['H', 'MET', 468], ['D', 'TYR', 461]], [['H',
'MET', 468], ['D', 'MET', 468]], [['H', 'LEU', 469], ['D', 'GLU', 464]],
[['H', 'ASP', 471], ['D', 'MET', 468]], [['H', 'ARG', 472], ['D', 'GLU',
464]], [['H', 'ARG', 472], ['D', 'LYS', 467]], [['H', 'ARG', 472], ['D',
'MET', 468]], [['H', 'ARG', 472], ['D', 'ASP', 471]], [['H', 'LEU', 475],
['D', 'LEU', 475]], [['H', 'LEU', 475], ['D', 'ARG', 472]], [['H', 'LEU',
475], ['D', 'MET', 468]]]  
3 | [[['H', 'GLU', 423], ['D', 'ILE', 422]], [['H', 'GLU', 423], ['D', 'SER',
418]], [['H', 'GLN', 426], ['D', 'GLN', 426]], [['H', 'GLN', 426], ['D',
'ILE', 422]], [['H', 'ALA', 427], ['D', 'ILE', 422]], [['H', 'GLN', 430],
['D', 'ILE', 422]], [['H', 'GLN', 430], ['D', 'ILE', 429]], [['H', 'GLN',
430], ['D', 'TYR', 421]], [['H', 'GLN', 430], ['D', 'GLN', 426]], [['H',
'GLN', 430], ['D', 'SER', 425]], [['H', 'VAL', 433], ['D', 'ILE', 429]],
[['H', 'VAL', 433], ['D', 'VAL', 433]], [['H', 'MET', 437], ['D', 'LEU',
432]], [['H', 'MET', 437], ['D', 'THR', 436]], [['H', 'PHE', 444], ['D',
'LYS', 439]], [['H', 'PHE', 444], ['D', 'LEU', 440]], [['H', 'PHE', 444],
['D', 'THR', 436]], [['H', 'PHE', 444], ['D', 'LYS', 443]], [['H', 'LEU',
447], ['D', 'LEU', 447]], [['H', 'LEU', 447], ['D', 'LYS', 443]], [['H',
'LEU', 447], ['D', 'PHE', 444]], [['H', 'CYS', 448], ['D', 'LYS', 443]],
[['H', 'LEU', 450], ['D', 'LEU', 447]], [['H', 'GLU', 451], ['D', 'LYS',
443]], [['H', 'GLU', 451], ['D', 'LEU', 447]], [['H', 'GLU', 451], ['D',
'LYS', 446]]]  
4 | [[['H', 'GLN', 195], ['D', 'PRO', 172]], [['H', 'GLN', 195], ['D', 'LYS',
175]], [['H', 'GLY', 196], ['D', 'ARG', 173]], [['H', 'GLY', 196], ['D',
'PRO', 172]], [['H', 'LYS', 198], ['D', 'PRO', 172]], [['H', 'PRO', 199],
['D', 'PRO', 172]], [['H', 'PHE', 200], ['D', 'TYR', 134]], [['H', 'PHE',
200], ['D', 'PRO', 172]], [['H', 'PHE', 200], ['D', 'ASP', 171]], [['H',
'PHE', 200], ['D', 'ILE', 170]], [['H', 'LEU', 201], ['D', 'GLN', 169]],
[['H', 'PRO', 202], ['D', 'TYR', 134]], [['H', 'PRO', 202], ['D', 'GLN',
169]], [['H', 'GLU', 203], ['D', 'GLN', 169]], [['H', 'GLU', 203], ['D',
'ILE', 81]]]  
5 | [[['H', 'SER', 387], ['D', 'LYS', 388]], [['H', 'LYS', 388], ['D', 'LEU',
389]], [['H', 'LYS', 388], ['D', 'LYS', 388]], [['H', 'LEU', 389], ['D',
'LYS', 388]], [['H', 'LEU', 389], ['D', 'CYS', 392]], [['H', 'LEU', 389],
['D', 'GLU', 391]], [['H', 'CYS', 392], ['D', 'CYS', 392]], [['H', 'CYS',
392], ['D', 'LEU', 389]], [['H', 'CYS', 392], ['D', 'LYS', 388]], [['H',
'VAL', 393], ['D', 'CYS', 392]], [['H', 'ALA', 396], ['D', 'ALA', 396]],
[['H', 'ALA', 396], ['D', 'CYS', 392]], [['H', 'LEU', 400], ['D', 'THR',
399]], [['H', 'LEU', 400], ['D', 'ALA', 396]], [['H', 'LYS', 406], ['D',
'ALA', 396]], [['H', 'LYS', 406], ['D', 'VAL', 397]], [['H', 'LYS', 406],
['D', 'THR', 399]], [['H', 'LYS', 406], ['D', 'GLN', 398]], [['H', 'LYS',
409], ['D', 'THR', 399]], [['H', 'LYS', 409], ['D', 'GLN', 398]], [['H',
'LYS', 413], ['D', 'THR', 399]]]  
6 | [[['H', 'LYS', 353], ['D', 'LYS', 222]], [['H', 'SER', 356], ['D', 'LYS',
222]], [['H', 'PRO', 358], ['D', 'PHE', 224]], [['H', 'PRO', 358], ['D',
'GLU', 223]], [['H', 'PRO', 358], ['D', 'LYS', 222]], [['H', 'ARG', 365],
['D', 'LYS', 221]], [['H', 'ARG', 365], ['D', 'GLU', 223]]]  
7 | [[['H', 'LEU', 482], ['D', 'LEU', 482]]]  
8 | [[['H', 'ASN', 362], ['D', 'LYS', 231]], [['H', 'ASN', 362], ['D', 'VAL',
226]]]  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 364, in thread_safe  
func(*args, **kw)  
File "/Users/dinaschneidman/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/PICKLUSTER/tool.py", line 103, in handle_scheme  
methods.display_atomic_interactions(self.session, chain1, chain2, int_allfunc)  
File "/Users/dinaschneidman/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/PICKLUSTER/methods.py", line 212, in
display_atomic_interactions  
session.models.add([pbg])  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 692, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model Atomic interactions interface #2 to scene
twice  
  
ValueError: Attempted to add model Atomic interactions interface #2 to scene
twice  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 692, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir8,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
      OS Loader Version: 577~129

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (a) (22E772610a)
      Kernel Version: Darwin 22.4.0
      Time since boot: 12 days, 1 hour, 52 minutes

Graphics/Displays:

    Intel UHD Graphics 617:

      Chipset Model: Intel UHD Graphics 617
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x87c0
      Revision ID: 0x0002
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
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    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
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    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
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    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
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    python-dateutil: 2.8.2
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