ISOLDE: itemgetter expected 1 argument, got 0

[f.ftrillo@…]

The following bug report has been submitted:
Platform:        macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
I don¡'t know

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/paco/Documents/2021-UdC/xx-
> CrazyIdeas/2024-oligoPPX/00-oligoPPP/01-PPP-1Ch/06-PPP-36Res-1Ch/fold_ppp_36res_1ch_model_0.cif

Chain information for fold_ppp_36res_1ch_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for fold_ppp_36res_1ch_model_0.cif  
---  
Chain | Description  
1.2/A | .  
  

> addh #1.2

Summary of feedback from adding hydrogens to fold_ppp_36res_1ch_model_0.cif
#1.2  
---  
notes | Termini for fold_ppp_36res_1ch_model_0.cif (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A PRO 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A PRO 36  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
254 hydrogens added  
  
Traceback (most recent call last):  
File "/Users/paco/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/paco/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py", line 80, in
problem_zones  
f = itemgetter(*noise)  
^^^^^^^^^^^^^^^^^^  
TypeError: itemgetter expected 1 argument, got 0  
  
TypeError: itemgetter expected 1 argument, got 0  
  
File "/Users/paco/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py", line 80, in
problem_zones  
f = itemgetter(*noise)  
^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: MLY43Y/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B91)
      Kernel Version: Darwin 24.1.0
      Time since boot: 2 days, 15 hours, 59 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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[pett]

Reported by Paco

[Tristan Croll]

Oops... upshot here is that the DBSCAN algorithm ISOLDE uses to find groups of problems in proximity to each other sorts everything into "clusters" and "remainder" (any issue that's too far from others to qualify as a cluster). Forgot to consider what would happen when there *is* no remainder. Amazingly, this seems to be the first time that's come up.