Error in 'angle' command if atoms are linear

[Tony Schaefer]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.4.dev202202010639 (2022-02-01 06:39:28 UTC)
Description
Error when setting angle of linear atoms

I'm guessing this has something to do with the axis of rotation. Any (non-zero) vector perpendicular to either bond should work. What I've found works is rolling the bond vector by one, then flipping the sign of the first non-zero element of the result, and crossing that with the bond vector.

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

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

> graphics selection width 2

UCSF ChimeraX version: 1.4.dev202202010639 (2022-02-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open smiles:C#N

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Translated SMILES to 3D structure via NCI web service (SMILES: C#N)  

> select /?:1@N1

1 atom, 1 residue, 1 model selected  

> select add /?:1@C1

2 atoms, 1 residue, 1 model selected  

> select add /?:1@H1

3 atoms, 1 residue, 1 model selected  

> angle sel 60

Traceback (most recent call last):  
File "E:\ChimeraX 1.4.dev202202010639\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 301, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.4.dev202202010639\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.4.dev202202010639\bin\lib\site-
packages\chimerax\std_commands\angle.py", line 110, in angle  
set_angle(*atoms, degrees, move_smaller=(move == "small"),
undo_state=undo_state)  
File "E:\ChimeraX 1.4.dev202202010639\bin\lib\site-
packages\chimerax\std_commands\angle.py", line 38, in set_angle  
if axis is None:  
UnboundLocalError: local variable 'axis' referenced before assignment  
  
UnboundLocalError: local variable 'axis' referenced before assignment  
  
File "E:\ChimeraX 1.4.dev202202010639\bin\lib\site-
packages\chimerax\std_commands\angle.py", line 38, in set_angle  
if axis is None:  
  
See log for complete Python traceback.  
  

> open smiles:C=N

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Translated SMILES to 3D structure via NCI web service (SMILES: C=N)  

> hide #1 models

> select #2/?:1@N1

1 atom, 1 residue, 1 model selected  

> select add #2/?:1@C1

2 atoms, 1 residue, 1 model selected  

> select add #2/?:1@H1

3 atoms, 1 residue, 1 model selected  

> angle sel 60

> hide #2 models

> show #1 models




OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Locale: en_US.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 17,107,529,728
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 2700X Eight-Core Processor         
OSLanguage: en-US

Installed Packages:
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[pett]

Hi Tony,

Thanks for finding this. There was already code in there for handling collinear atoms, but on the line throwing the error the variable 'axis' should have been 'prev_axis'. Fixed in tomorrow's build.

--Eric