Opened 28 hours ago

Closed 23 hours ago

#19395 closed defect (duplicate)

PICKLUSTER treating PseudobondGroups as Structures

Reported by: chimerax-bug-report@… Owned by: Luca Genz
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.7.2-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/aaronchin/Desktop/cp12_gapa_prk.cxs

Log from Sun Oct 12 18:21:51 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6KEZ format mmcif fromDatabase pdb

6kez title:  
Crystal structure of GAPDH/CP12/PRK complex from Arabidopsis thaliana [more
info...]  
  
Chain information for 6kez #1  
---  
Chain | Description | UniProt  
A B C D E F G H | Glyceraldehyde-3-phosphate dehydrogenase GAPA1 | G3PA1_ARATH 1-336  
I J K L | Phosphoribulokinase | KPPR_ARATH 3-351  
M N O P | Calvin cycle protein CP12-2 | CP122_ARATH 2-78  
  
Non-standard residues in 6kez #1  
---  
NAD — nicotinamide-adenine-dinucleotide  
  
6kez mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> hide atoms

> hide cartoons

> show cartoons

> interfaces ~solvent

29 buried areas: A C 1983, G E 1975, F H 1961, B D 1961, H E 1466, F G 1464, A
D 1450, B C 1423, K P 1183, J M 1081, I O 1079, L N 1059, F N 892, A P 870, H
M 849, C O 837, K L 771, I J 691, L H 505, C D 460, G H 441, F E 436, A B 423,
I A 423, D P 408, E M 359, G N 352, K C 341, J F 337  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> lighting shadows false

> lighting full

> select clear

> lighting flat

Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  

> set bgColor white

> select /M-P:7-25,28-67

1751 atoms, 1767 bonds, 236 residues, 1 model selected  

> select /O:63

12 atoms, 12 bonds, 1 residue, 1 model selected  

> color sel lime

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select /O

540 atoms, 549 bonds, 72 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> style sel stick

Changed 540 atom styles  

> hide #1.1 models

> select /O:63

12 atoms, 12 bonds, 1 residue, 1 model selected  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> show #1.1 models

> select /M-P:7-25,28-67

1751 atoms, 1767 bonds, 236 residues, 1 model selected  

> select /O:11

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel lime

> select /M-P:7-25,28-67

1751 atoms, 1767 bonds, 236 residues, 1 model selected  

> select /O:46

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel lime

> select /O:49

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel lime

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select /O:49

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /O:49

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide #1.1 models

> show #1.1 models

Drag select of 4 residues  
Drag select of 1 residues  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> undo

[Repeated 8 time(s)]

> color sel lime

> select /O:49

11 atoms, 10 bonds, 1 residue, 1 model selected  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> color sel lime

> select /M-P:7-25,28-67

1751 atoms, 1767 bonds, 236 residues, 1 model selected  

> select /O:44

5 atoms, 4 bonds, 1 residue, 1 model selected  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> color sel lime

> save D:/博士相关资料/课题/蛋白质相互作用课题/suab5_plastid/画图/可解释性分析/GAPA_CP12_PRK_resual.png
> width 1979 height 1164 supersample 3

> save D:/博士相关资料/课题/蛋白质相互作用课题/suab5_plastid/画图/可解释性分析/cp12_gapa_prk.cxs

[Repeated 1 time(s)]

——— End of log from Sun Oct 12 18:21:51 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!1 models

> show #!1 models

> surface hidePatches sel

> ~label sel residues

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> hide #1.1 models

> hide sel atoms

> hide pseudobonds

[Repeated 1 time(s)]

> cartoon style #1 modeHelix tube radius

Missing "radius" keyword's argument  

> cartoon style #1 modeHelix tube radius 2

> lighting soft

> select #1 /O: 63

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel light sea green

> color sel hot pink

> color sel orange

> color sel purple

> color sel magenta

> color sel hot pink

> color sel cornflower blue

> color sel light sea green

> color sel forest green

> color sel coral

> color sel salmon

> color sel gold

[Repeated 1 time(s)]

> color sel byhetero

> show sel atoms

> style sel stick

Changed 12 atom styles  

> color sel byhetero

> select #1 /O: 11,44,46,49,63

41 atoms, 37 bonds, 5 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gold

> color sel byhetero

> show sel atoms

> style sel stick

Changed 41 atom styles  

> select clear

> show atoms

> hide atoms

> show cartoons

> cartoon style (#!1 & coil) xsection oval

> cartoon style #!1 xsection barbell modeHelix default

> cartoon style #!1 xsection rectangle modeHelix default

> cartoon style #!1 modeHelix tube sides 20

> cartoon style #!1 xsection rectangle modeHelix default

> cartoon style (#!1 & coil) xsection oval

> cartoon style #!1 xsection barbell modeHelix default

> cartoon style #!1 xsection oval modeHelix default

> ui tool show PICKLUSTER

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

Cluster information for 6kez['I', 'O']  
---  
Cluster | Residues  
1 | [['I', 'SER', 15], ['I', 'ARG', 65], ['I', 'ARG', 68], ['I', 'LYS', 69], ['I', 'LYS', 72], ['I', 'VAL', 73], ['I', 'THR', 74], ['I', 'ALA', 75], ['I', 'LEU', 76], ['I', 'TYR', 104], ['I', 'HIS', 106], ['I', 'GLY', 109], ['I', 'LYS', 157], ['I', 'ARG', 160], ['I', 'ASP', 161], ['I', 'GLU', 164], ['I', 'ARG', 165], ['I', 'HIS', 167], ['I', 'SER', 171], ['I', 'ALA', 174], ['I', 'SER', 175], ['I', 'ALA', 178], ['I', 'ARG', 179], ['I', 'ASP', 182], ['O', 'SER', 8], ['O', 'VAL', 11], ['O', 'GLU', 12], ['O', 'ILE', 15], ['O', 'GLN', 19], ['O', 'SER', 28], ['O', 'GLY', 29], ['O', 'GLU', 30], ['O', 'VAL', 32], ['O', 'ALA', 33], ['O', 'TRP', 35], ['O', 'ASP', 36], ['O', 'GLU', 37], ['O', 'GLU', 39], ['O', 'GLU', 40], ['O', 'LEU', 41], ['O', 'SER', 42], ['O', 'ALA', 43], ['O', 'ALA', 44], ['O', 'ALA', 45], ['O', 'SER', 46], ['O', 'ARG', 49]]  
2 | [['I', 'GLY', 18], ['I', 'LYS', 19], ['O', 'HIS', 47]]  
  
Cluster information for 6kez['I', 'O']  
---  
Cluster | Residues  
1 | [['I', 'GLY', 18], ['I', 'LYS', 19], ['O', 'HIS', 47]]  
2 | [['I', 'SER', 15], ['I', 'ARG', 65], ['I', 'ARG', 68], ['I', 'LYS', 69], ['I', 'LYS', 72], ['I', 'VAL', 73], ['I', 'THR', 74], ['I', 'ALA', 75], ['I', 'LEU', 76], ['I', 'TYR', 104], ['I', 'HIS', 106], ['I', 'GLY', 109], ['I', 'LYS', 157], ['I', 'ARG', 160], ['I', 'ASP', 161], ['I', 'GLU', 164], ['I', 'ARG', 165], ['I', 'HIS', 167], ['I', 'SER', 171], ['I', 'ALA', 174], ['I', 'SER', 175], ['I', 'ALA', 178], ['I', 'ARG', 179], ['I', 'ASP', 182], ['O', 'SER', 8], ['O', 'VAL', 11], ['O', 'GLU', 12], ['O', 'ILE', 15], ['O', 'GLN', 19], ['O', 'SER', 28], ['O', 'GLY', 29], ['O', 'GLU', 30], ['O', 'VAL', 32], ['O', 'ALA', 33], ['O', 'TRP', 35], ['O', 'ASP', 36], ['O', 'GLU', 37], ['O', 'GLU', 39], ['O', 'GLU', 40], ['O', 'LEU', 41], ['O', 'SER', 42], ['O', 'ALA', 43], ['O', 'ALA', 44], ['O', 'ALA', 45], ['O', 'SER', 46], ['O', 'ARG', 49]]  
  
Calculation of interface was successful  
Interactions in clusters in 6kez['I', 'O']  
---  
Cluster | Interactions  
1 | [[['I', 'GLY', 18], ['O', 'HIS', 47]], [['I', 'LYS', 19], ['O', 'HIS', 47]]]  
2 | [[['I', 'SER', 15], ['O', 'GLU', 39]], [['I', 'ARG', 65], ['O', 'LEU', 41]], [['I', 'ARG', 65], ['O', 'GLU', 40]], [['I', 'ARG', 65], ['O', 'GLU', 37]], [['I', 'ARG', 68], ['O', 'ASP', 36]], [['I', 'ARG', 68], ['O', 'GLU', 37]], [['I', 'ARG', 68], ['O', 'GLU', 40]], [['I', 'ARG', 68], ['O', 'ALA', 33]], [['I', 'LYS', 69], ['O', 'ALA', 33]], [['I', 'LYS', 69], ['O', 'GLU', 37]], [['I', 'LYS', 72], ['O', 'GLY', 29]], [['I', 'LYS', 72], ['O', 'GLU', 30]], [['I', 'LYS', 72], ['O', 'SER', 28]], [['I', 'LYS', 72], ['O', 'ALA', 33]], [['I', 'VAL', 73], ['O', 'ALA', 33]], [['I', 'VAL', 73], ['O', 'GLY', 29]], [['I', 'VAL', 73], ['O', 'ASP', 36]], [['I', 'THR', 74], ['O', 'VAL', 32]], [['I', 'THR', 74], ['O', 'ASP', 36]], [['I', 'THR', 74], ['O', 'ALA', 33]], [['I', 'ALA', 75], ['O', 'ASP', 36]], [['I', 'LEU', 76], ['O', 'ASP', 36]], [['I', 'TYR', 104], ['O', 'GLU', 40]], [['I', 'HIS', 106], ['O', 'ALA', 44]], [['I', 'HIS', 106], ['O', 'GLU', 40]], [['I', 'GLY', 109], ['O', 'GLU', 40]], [['I', 'LYS', 157], ['O', 'GLU', 39]], [['I', 'ARG', 160], ['O', 'SER', 46]], [['I', 'ASP', 161], ['O', 'SER', 42]], [['I', 'ASP', 161], ['O', 'SER', 46]], [['I', 'ASP', 161], ['O', 'ALA', 43]], [['I', 'ASP', 161], ['O', 'GLU', 39]], [['I', 'GLU', 164], ['O', 'ARG', 49]], [['I', 'GLU', 164], ['O', 'SER', 46]], [['I', 'GLU', 164], ['O', 'ALA', 45]], [['I', 'GLU', 164], ['O', 'VAL', 11]], [['I', 'GLU', 164], ['O', 'SER', 42]], [['I', 'ARG', 165], ['O', 'GLU', 12]], [['I', 'ARG', 165], ['O', 'SER', 8]], [['I', 'ARG', 165], ['O', 'VAL', 11]], [['I', 'HIS', 167], ['O', 'ILE', 15]], [['I', 'HIS', 167], ['O', 'SER', 42]], [['I', 'SER', 171], ['O', 'TRP', 35]], [['I', 'SER', 171], ['O', 'ILE', 15]], [['I', 'SER', 171], ['O', 'GLN', 19]], [['I', 'ALA', 174], ['O', 'TRP', 35]], [['I', 'SER', 175], ['O', 'TRP', 35]], [['I', 'SER', 175], ['O', 'GLU', 39]], [['I', 'ALA', 178], ['O', 'VAL', 32]], [['I', 'ALA', 178], ['O', 'TRP', 35]], [['I', 'ARG', 179], ['O', 'GLU', 39]], [['I', 'ARG', 179], ['O', 'TRP', 35]], [['I', 'ARG', 179], ['O', 'ASP', 36]], [['I', 'ASP', 182], ['O', 'VAL', 32]]]  
  

> select #1 /I :18 #1 /I :19 #1 /O :47

23 atoms, 22 bonds, 32 pseudobonds, 3 residues, 2 models selected  

> select #1 /I :18 #1 /I :19 #1 /O :47

23 atoms, 22 bonds, 32 pseudobonds, 3 residues, 2 models selected  

> select #1 /I :18 #1 /I :19 #1 /O :47

23 atoms, 22 bonds, 32 pseudobonds, 3 residues, 2 models selected  

> select #1 /I :18 #1 /I :19 #1 /O :47

23 atoms, 22 bonds, 32 pseudobonds, 3 residues, 2 models selected  

> select #1 /I :18 #1 /I :19 #1 /O :47

23 atoms, 22 bonds, 32 pseudobonds, 3 residues, 2 models selected  

> select #1 /I :18 #1 /I :19 #1 /O :47

23 atoms, 22 bonds, 32 pseudobonds, 3 residues, 2 models selected  

> select #1 /I :18 #1 /I :19 #1 /O :47

23 atoms, 22 bonds, 32 pseudobonds, 3 residues, 2 models selected  

> show sel atoms

> color sel byhetero

> hide #2 models

> show #2 models

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> color (#!1 & sel) yellow

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> label height 0.7

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> select add #2

23 atoms, 22 bonds, 415 pseudobonds, 3 residues, 2 models selected  

> select subtract #2

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select add #2

23 atoms, 22 bonds, 415 pseudobonds, 3 residues, 2 models selected  

> select subtract #2

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select clear

> ui tool show PICKLUSTER

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

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1458, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/aaronchin/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/PICKLUSTER/__init__.py", line 50, in start_tool  
return tool.PICKLUSTER(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/aaronchin/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/PICKLUSTER/tool.py",
line 63, in __init__  
for chain in model.chains:  
^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute 'chains'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'PseudobondGroup' object has no attribute 'chains'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'PseudobondGroup' object has no attribute 'chains'  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show PICKLUSTER

> select clear

[Repeated 2 time(s)]

> hide #2 models

> ui tool show PICKLUSTER

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

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1458, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/aaronchin/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/PICKLUSTER/__init__.py", line 50, in start_tool  
return tool.PICKLUSTER(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/aaronchin/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/PICKLUSTER/tool.py",
line 63, in __init__  
for chain in model.chains:  
^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute 'chains'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'PseudobondGroup' object has no attribute 'chains'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'PseudobondGroup' object has no attribute 'chains'  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-23.7.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,4
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1,4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 2094.40.1.0.0 (iBridge: 23.16.11072.0.0,0)
      OS Loader Version: 583~2317

Software:

    System Software Overview:

      System Version: macOS 15.7.2 (24G325)
      Kernel Version: Darwin 24.6.0
      Time since boot: 7天10小时33分钟

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      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: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 2.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 23 hours ago

Component: Unassigned → Third Party
Owner: set to Luca Genz
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → PICKLUSTER treating PseudobondGroups as Structures

comment:2 by Eric Pettersen, 23 hours ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #14628

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