Stick bond not circular

[tony.schaefer@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.92 (2020-02-03)
Description
Bond sticks are not circular when the bond is nearly on the z axis. I've attached a structure for acetone with the C-O bond almost on the z axis and an image for how it looks in my ChimeraX. 

Log:
> cd C:\Users\normn/Desktop

Current working directory is: C:\Users\normn\Desktop  

> toolshed show "Add to Personal Library"

UCSF ChimeraX version: 0.92 (2020-02-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimAARON-0.1-py3-none-any.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
c:\users\normn\appdata\local\ucsf\chimerax\cache\0.92\installers\chimaaron-0.1-py3-none-
any.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core>=0.1 in
c:\program files\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (0.92)  
Requirement already satisfied, skipping upgrade: scipy in c:\program
files\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (1.4.1)  
Requirement already satisfied, skipping upgrade: numpy in c:\program
files\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (1.17.4+mkl)  
Installing collected packages: ChimAARON  
Attempting uninstall: ChimAARON  
Found existing installation: ChimAARON 0.1  
Uninstalling ChimAARON-0.1:  
Successfully uninstalled ChimAARON-0.1  
Successfully installed ChimAARON-0.1  
Lock 2285563362760 acquired on
C:\Users\normn\AppData\Local\UCSF\ChimeraX\Cache\0.92\toolshed\bundle_info.cache.lock  
Lock 2285563362760 released on
C:\Users\normn\AppData\Local\UCSF\ChimeraX\Cache\0.92\toolshed\bundle_info.cache.lock  
  

WARNING: You are using pip version 20.0.1; however, version 20.0.2 is
available.  
You should consider upgrading via the 'C:\Program
Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
  

> open C:\Users\normn\Desktop\freq.log

Opened C:\Users\normn\Desktop\freq.log as a log file  

> close

> open C:\Users\normn\Desktop\freq.log

Opened C:\Users\normn\Desktop\freq.log as a log file  

> toolshed show "Visualize Normal Modes"

> toolshed show "Visualize Normal Modes"

> close #1.1

> open C:/Users/normn/Desktop/acetone.xyz

Opened C:/Users/normn/Desktop/acetone.xyz as a xyz file  

> tile

> select #1/a:1@O1

1 atom, 1 model selected  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> help trans

> transparency sel 50 target a

> transparency sel 100 target a

> select #2/a:1@O1

1 atom, 1 model selected  

> transparency sel 100 target a

> ~show #1

> ~select

Nothing selected  

> help color

Invalid "target" argument: Character 'o' is not an allowed target, must be one
of acrsbpfl  

> color sel blue halfbond false

> ~select

Nothing selected  

> graphics silhouettes true

> save image C:/Users/normn/Desktop/acetone.png width 787 height 522

> show #1

> open C:/Users/normn/Desktop/acetone.pdb

Summary of feedback from opening C:/Users/normn/Desktop/acetone.pdb  
---  
warnings | Ignored bad PDB record found on line 7  
END  
  
Ignored bad PDB record found on line 14  
END  
  

> tile

> save session C:/Users/normn/Desktop/acetone.cxs

> open C:/Users/normn/Desktop/acetone.cxs

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 398.36
OpenGL renderer: GeForce 940M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: acetone.zip

acetone.zip​

[tony.schaefer@…]

Added by email2trac

[Tom Goddard]

Fixed.

Bond drawing rotates a cylinder and when the bond points nearly exactly down it is 180 degree rotation and the rotation axis is degenerate (axis can be any direction in xy plane), and limited floating point precision led to a transform that flattened the cylinder. Changed code so cylinder is never rotated more than 90 degrees.