Foldseek: 'NoneType' object has no attribute 'query_chain'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Excellence/Desktop/q/Bacillus/querysg.pdb

Summary of feedback from opening
C:/Users/Excellence/Desktop/q/Bacillus/querysg.pdb  
---  
warning | Ignored bad PDB record found on line 1  
PARENT N/A  
  
Chain information for querysg.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> view

> color bfactor

1713 atoms, 220 residues, atom bfactor range 54.3 to 97.3  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> color bfactor

1713 atoms, 220 residues, atom bfactor range 54.3 to 97.3  

> hbonds reveal true

174 hydrogen bonds found  

> interfaces ~solvent

0 buried areas:  

> style stick

Changed 1713 atom styles  

> close session

> open C:/Users/Excellence/Desktop/q/Bacillus/PKS2/ATT.pdb

Chain information for ATT.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> open C:/Users/Excellence/Desktop/q/Bacillus/PKS2/queryATSPR.pdb

Summary of feedback from opening
C:/Users/Excellence/Desktop/q/Bacillus/PKS2/queryATSPR.pdb  
---  
warning | Ignored bad PDB record found on line 1  
PARENT N/A  
  
Chain information for queryATSPR.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open C:/Users/Excellence/Desktop/q/Bacillus/PKS2/queryNNA.pdb

Summary of feedback from opening
C:/Users/Excellence/Desktop/q/Bacillus/PKS2/queryNNA.pdb  
---  
warning | Ignored bad PDB record found on line 1  
PARENT N/A  
  
Chain information for queryNNA.pdb #3  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open C:/Users/Excellence/Desktop/q/Bacillus/PKS2/queryPNN.pdb

Summary of feedback from opening
C:/Users/Excellence/Desktop/q/Bacillus/PKS2/queryPNN.pdb  
---  
warning | Ignored bad PDB record found on line 1  
PARENT N/A  
  
Chain information for queryPNN.pdb #4  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> close session

> open C:\Users\Excellence\Desktop\q\Bacillus\PKS2\queryPNN.pdb format pdb

Summary of feedback from opening
C:\Users\Excellence\Desktop\q\Bacillus\PKS2\queryPNN.pdb  
---  
warning | Ignored bad PDB record found on line 1  
PARENT N/A  
  
Chain information for queryPNN.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> close session

> open C:/Users/Excellence/Desktop/q/Bacillus/PKS2/ATT.pdb

Chain information for ATT.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
Alignment identifier is 1/A  
Alignment identifier is 1/B  

> color bfactor

1585 atoms, 210 residues, atom bfactor range 0.1 to 99.9  

> hbonds reveal true

164 hydrogen bonds found  

> rainbow

> color bfactor

1585 atoms, 210 residues, atom bfactor range 0.1 to 99.9  

> label #1 atoms attribute element

> ~label #1 residues

> ~label #1 atoms

> label #1 text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> label height 1

> ~label #1 residues

> label #1 attribute label_specifier

> cofr frontCenter

> label #1 text ""

> style stick

Changed 1585 atom styles  

> select ligand

Nothing selected  

> select ions

Nothing selected  

> set bgColor white

> ui mousemode right "color key"

> ui mousemode right translate

> ui mousemode right label

> ui mousemode right distance

> ui mousemode right zoom

> select /A

1418 atoms, 1444 bonds, 156 pseudobonds, 190 residues, 2 models selected  

> delete /b

[Repeated 1 time(s)]

> select N3+

7 atoms, 7 residues, 1 model selected  

> select sideonly

658 atoms, 500 bonds, 25 pseudobonds, 174 residues, 2 models selected  

> undo

> label sel residues attribute number

> label sel residues attribute omega

> label sel residues attribute worm_radius

> label height 1

> label sel residues attribute seq_conservation

> label sel residues attribute psi

> label sel residues attribute phi

> label sel residues attribute number

> ui tool show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp1

Webservices job id: FBH9AR2QW0ISZ0KV  

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp2

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp3

Webservices job id: D6IAZPRHK8E8QGAM  
Webservices job id: E85BLVHM43DHO7S8  

QWindowsWindow::setGeometry: Unable to set geometry 1920x998+0+35 (frame:
1942x1054-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x974+0+34 (frame: 1942x1030-11-11) margins: 11, 45,
11, 11 minimum size: 549x665 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=846,
y=1054)))  

> ui tool show H-Bonds

QWindowsWindow::setGeometry: Unable to set geometry 1920x1527+0+35 (frame:
1942x1583-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x974+0+34 (frame: 1942x1030-11-11) margins: 11, 45,
11, 11 minimum size: 549x1018 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=846,
y=1583)))  

QWindowsWindow::setGeometry: Unable to set geometry 1920x2057+0+35 (frame:
1942x2113-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x974+0+34 (frame: 1942x1030-11-11) margins: 11, 45,
11, 11 minimum size: 549x1371 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=846,
y=2113)))  

> hbonds sel reveal true

6 hydrogen bonds found  

> select down

7 atoms, 7 residues, 1 model selected  

QWindowsWindow::setGeometry: Unable to set geometry 1920x998+0+35 (frame:
1942x1054-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x974+0+34 (frame: 1942x1030-11-11) margins: 11, 45,
11, 11 minimum size: 549x665 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=846,
y=1054)))  

> ui tool show "Similar Structures"

You must press the similar structures Search button before you can open
matching structures.  

> cofr sel

> ui tool show "Crystal Contacts"

> ui tool show Clashes

> clashes sel ignoreHiddenModels true select true color #55ff7f showDist true
> continuous true

2 clashes  

> clashes sel ignoreHiddenModels true select true color #55ff7f showDist true

2 clashes  

> ~clashes

> ui tool show "AlphaFold Error Plot"

Must choose path to predicted aligned file  

> ui tool show "Add Charges"

> addh #!1

Summary of feedback from adding hydrogens to ATT.pdb #1  
---  
notes | No usable SEQRES records for ATT.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLY 190  
159 hydrogen bonds  
/A GLY 190 is not terminus, removing H atom from 'C'  
1398 hydrogens added  
  
Closest equivalent command: addcharge sel standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Must choose path to predicted aligned file  

> ui tool show Foldseek

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 339, in _show_cluster_plot  
if r.query_chain is None:  
^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'query_chain'  
  
AttributeError: 'NoneType' object has no attribute 'query_chain'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 339, in _show_cluster_plot  
if r.query_chain is None:  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2125
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 3410
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 8,339,001,344
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10310U CPU @ 1.70GHz
OSLanguage: en-US

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    WMI: 1.5.1

[Tom Goddard]

Fixed a few days ago.

User press the Similar Structures panel Clusters button without doing a Foldseek search first.