id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2793 Stick bond not circular tony.schaefer@… Tom Goddard "{{{ 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 }}} [attachment:""acetone.zip""] " defect closed normal Graphics fixed all ChimeraX