ChimeraX bug report submission

[Zach Pearson]

The following bug report has been submitted:
Platform:        macOS-13.5-arm64-arm-64bit
ChimeraX Version: 1.7.dev202305251958 (2023-05-25 19:58:39 UTC)
Description
Log:
UCSF ChimeraX version: 1.7.dev202305251958 (2023-05-25)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5y5s format mmcif fromDatabase pdb

5y5s title:  
Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution
[more info...]  
  
Chain information for 5y5s #1  
---  
Chain | Description | UniProt  
0 2 4 6 8 B E G J N P R T V X Z | LH1 beta polypeptide | D2Z0P1_THETI 0-46  
1 3 5 7 9 A D F I K O Q S U W Y | LH1 alpha polypeptide | D2Z0P2_THETI 1-61  
C | Photosynthetic reaction center cytochrome c subunit | CYCR_THETI 1-404  
H | Photosynthetic reaction center H subunit | D2Z0P9_THETI 1-259  
L | Photosynthetic reaction center L subunit | D2Z0P3_THETI 1-281  
M | Photosynthetic reaction center M subunit | A8ASG6_THETI 1-325  
  
Non-standard residues in 5y5s #1  
---  
BCL — bacteriochlorophyll A  
BPH — bacteriopheophytin A  
CA — calcium ion  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
CRT — spirilloxanthin (rhodoviolascin)  
FE — Fe (III) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
HEC — heme C  
LDA — lauryl dimethylamine-N-oxide  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMT — dodecyl-β-D-maltoside  
MG — magnesium ion  
MQ8 — menaquinone 8 (2-methyl-3-(3,7,11,15,19,23,27,31-octamethyl-
dotriaconta-2,6,10,14,18,22,26,30-octaenyl)-[1,4]napthoquinone)  
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)  
PGV —
(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl
(11E)-octadec-11-enoate (phosphatidylglycerol, 2-vaccenoyl-1-palmitoyl-Sn-
glycerol-3-phosphoglycerol)  
SO4 — sulfate ion  
UNL — unknown ligand  
UQ8 — Ubiquinone-8
(2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]cyclohexa-2,5-diene-1,4-dione)  
  

> ui tool show shell

[Repeated 1 time(s)]

> lighting flat

> ui tool show shell

> view

> graphics silhouettes false

> lighting flat

> lighting full

> view orient

> ui tool show "Side View"

> volume showOutlineBox true

No volumes specified  

> ui tool show shell

> close

> open /Users/zjp/Downloads/fool.nrrd format nrrd

> close

> open /Users/zjp/git/rbvi/data/RIDER-1129164940/11-06-2014-1-96508/8-08100
> format dicom

Summary of feedback from opening
/Users/zjp/git/rbvi/data/RIDER-1129164940/11-06-2014-1-96508/8-08100  
---  
note | Opened 8 CT (No Description) as #1.1.1, grid size 512,512,213, pixel
0.588,0.588,1.24, shown at step 1, values int16  
  

> volume #1.1.1 showOutlineBox true

> ui tool show shell

[Repeated 1 time(s)]Traceback (most recent call last):  
File
"/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/qtconsole/console_widget.py", line 482, in eventFilter  
pos = event.globalPosition().toPoint()  
AttributeError: 'QContextMenuEvent' object has no attribute 'globalPosition'  
  
AttributeError: 'QContextMenuEvent' object has no attribute 'globalPosition'  
  
File
"/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/qtconsole/console_widget.py", line 482, in eventFilter  
pos = event.globalPosition().toPoint()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/qtconsole/console_widget.py", line 482, in eventFilter  
pos = event.globalPosition().toPoint()  
AttributeError: 'QContextMenuEvent' object has no attribute 'globalPosition'  
  
AttributeError: 'QContextMenuEvent' object has no attribute 'globalPosition'  
  
File
"/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/qtconsole/console_widget.py", line 482, in eventFilter  
pos = event.globalPosition().toPoint()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/qtconsole/console_widget.py", line 482, in eventFilter  
pos = event.globalPosition().toPoint()  
AttributeError: 'QContextMenuEvent' object has no attribute 'globalPosition'  
  
AttributeError: 'QContextMenuEvent' object has no attribute 'globalPosition'  
  
File
"/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/qtconsole/console_widget.py", line 482, in eventFilter  
pos = event.globalPosition().toPoint()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/qtconsole/console_widget.py", line 482, in eventFilter  
pos = event.globalPosition().toPoint()  
AttributeError: 'QContextMenuEvent' object has no attribute 'globalPosition'  
  
AttributeError: 'QContextMenuEvent' object has no attribute 'globalPosition'  
  
File
"/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/qtconsole/console_widget.py", line 482, in eventFilter  
pos = event.globalPosition().toPoint()  
 
  

[Zach Pearson]

Duplicate of #9068