ISOLDE: graph: edges should be a n x 2 array of unsigned ints

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.3-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/LaymanXUE/Desktop/13A/E2P/E2P_331_UPDATE.pdb

Chain information for E2P_331_UPDATE.pdb #1  
---  
Chain | Description  
P | No description available  
  

> open
> /Users/LaymanXUE/Desktop/13A/E2P/cryosparc_P3_J765_012_volume_map_sharp.mrc

Opened cryosparc_P3_J765_012_volume_map_sharp.mrc as #2, grid size
288,288,288, pixel 1.1, shown at level 0.11, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.195

> set bgColor white

> isolde start

> set selectionWidth 4

> 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...  
ISOLDE: Corrected atom nomenclature of 69 residues in model #1 to IUPAC-IUB
standards.  
Chain information for E2P_331_UPDATE.pdb  
---  
Chain | Description  
1.2/P | No description available  
  

> clipper associate #2 toModel #1

Opened cryosparc_P3_J765_012_volume_map_sharp.mrc as #1.1.1.1, grid size
288,288,288, pixel 1.1, shown at step 1, values float32  

> isolde sim start /P,A

Loading residue template for SPM from internal database  
Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to E2P_331_UPDATE.pdb #1.2  
---  
notes | Termini for E2P_331_UPDATE.pdb (#1.2) chain P determined from SEQRES
records  
Chain-initial residues that are actual N termini: /P ARG 36  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /P GLN 1169  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /P GLN 1169  
516 hydrogen bonds  
8125 hydrogens added  
  
Fetching CCD AAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/AAC/AAC.cif  
Traceback (most recent call last):  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 190, in
_fix_button_clicked_cb  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/template_utils.py", line 338, in
fix_residue_to_match_md_template  
return trim_residue_to_md_template(residue, md_template)  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/template_utils.py", line 426, in
trim_residue_to_md_template  
rgraph = make_graph_from_residue(residue)  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "/Users/LaymanXUE/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3CH/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3 (22E252)
      Kernel Version: Darwin 22.4.0
      Time since boot: 3天13小时22分钟

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2719H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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[Tristan Croll]

Hmm... I thought I'd taken care of all the ways that could happen, but it
seems I missed one.

On Tue, Jul 4, 2023 at 1:28 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>