Nucleotides: point is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/deys/Desktop/Sanjay_putLresult/putLisoG_WT/WT_Open_WT_Phenix118.pdb
> format PDB

Summary of feedback from opening
/Users/deys/Desktop/Sanjay_putLresult/putLisoG_WT/WT_Open_WT_Phenix118.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 22  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 23  
BOND : 0.008 0.164 28138  
  
Ignored bad PDB record found on line 24  
ANGLE : 1.329 21.543 38543  
  
18 messages similar to the above omitted  
  
Chain information for WT_Open_WT_Phenix118.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
N | No description available  
R | No description available  
T | No description available  
  

> nucleotides stubs

> hide #3/N

> hide #1/N

> show #1/N cartoons

> show #1/N

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder  
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder  
h = distance(p0, p1)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance  
return sqrt(distance_squared(p, q))  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared  
if len(p) == 3:  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "changes":  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared  
if len(p) == 3:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

I believe this was fixed awhile ago.