Alphafold contacts: pseudobond group or endpoint atom(s) is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
Registration file
'C:\\\Users\\\albihlw\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\registration' has
expired  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Registration

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  

> open C:/Users/albihlw/Desktop/fold_2025_04_18_11_29.zip

Unrecognized file suffix '.zip'  

> open C:/Users/albihlw/Desktop/p2_rna/fold_2025_04_18_11_29_model_0.cif

Chain information for fold_2025_04_18_11_29_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> color bychain

> open C:/Users/albihlw/Desktop/p2_rna/fold_2025_04_18_11_29_full_data_0.json

fold_2025_04_18_11_29_full_data_0.json does not look like Mole Online json
file, does not contain Channels.  

> open
> C:/Users/albihlw/Desktop/p2_rna/fold_2025_04_18_11_29_summary_confidences_0.json

fold_2025_04_18_11_29_summary_confidences_0.json does not look like Mole
Online json file, does not contain Channels.  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> C:/Users/albihlw/Desktop/p2_rna/fold_2025_04_18_11_29_full_data_0.json

> alphafold contacts /A toResidues /B distance 3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> color #1/A:40-157 lime

> color #1/A:384-696 magenta

> color #1/A:612-616 lime

> color #1/A:88-90 magenta

> color #1/A:898-959/B:1-1 lime

> color #1/A:12-169 magenta

> close session

> open C:/Users/albihlw/Desktop/p2_rna/fold_2025_04_18_11_29_model_1.cif

Chain information for fold_2025_04_18_11_29_model_1.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> C:/Users/albihlw/Desktop/p2_rna/fold_2025_04_18_11_29_full_data_1.json

> alphafold contacts /A toResidues /B distance 5

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> alphafold contacts /A toResidues /B distance 5

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.5768
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 5420
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 16,547,975,168
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US

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[Tom Goddard]

ChimeraX 1.7 is being used to show AlphaFold 3 PAE values for contacts but AlphaFold 3 did not exist when 1.7 was released and uses PAE between atoms and residues where AlphaFold 2 only had PAE values between residues. A newer ChimeraX has to be used to look at AlphaFold 3 PAE values and contacts.