Nucleotides: asking for distance from None

[mks131@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-win_amd64.whl  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-win_amd64.whl  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-win_amd64.whl  

> help help:quickstart

Successfully installed ChimeraX-Clipper-0.12.1 ChimeraX-ISOLDE-1.0b5  
Installed ChimeraX-Clipper (0.12.1)  
Installed ChimeraX-ISOLDE (1.0b5)  
Bundle installation canceled  
Bundle installation canceled  

> open2
> C:/Users/Manoj/Downloads/relion_postprocess_job126_masked_refined_pixelsize.ccp4
> format ccp4

Opened relion_postprocess_job126_masked_refined_pixelsize.ccp4, grid size
376,376,376, pixel 0.649, shown at level 0.00472, step 2, values float32  

> toolshed show ISOLDE

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> open2
> C:/Users/Manoj/Downloads/Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb

Summary of feedback from opening <_io.textiowrapper
name="C:/Users/Manoj/Downloads/Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb"
mode="rt" encoding="utf-8">  
---  
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 : 0.006 0.070 12495  
  
Ignored bad PDB record found on line 24  
ANGLE : 0.827 8.410 18038  
  
18 messages similar to the above omitted  
  
Chain information for Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb #2  
---  
Chain | Description  
A E | No description available  
B | No description available  
C G | No description available  
D H | No description available  
F | No description available  
I | No description available  
J | No description available  
  

> volume #1 style image region 0,0,186,375,375,186 step 1 showOutlineBox true

> graphics silhouettes true

> nucleotides ladder

> nucleotides atoms

> style nucleic stick

Changed 5614 atom styles  

> nucleotides fill

> style nucleic stick

Changed 5614 atom styles  

> nucleotides tube/slab shape muffler

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> color bynucleotide

QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"  

> open2 C:/Users/Manoj/Phenix/phenix-installer-1.13-2998-intel-
> windows-x86_64/base/MapToModel_15/Lin28_maptomodel_0.pdb

Summary of feedback from opening <_io.textiowrapper
name="C:/Users/Manoj/Phenix/phenix-installer-1.13-2998-intel-
windows-x86_64/base/MapToModel_15/Lin28_maptomodel_0.pdb" mode="rt"
encoding="utf-8">  
---  
warning | Ignored bad PDB record found on line 2301  
END  
  
Chain information for Lin28_maptomodel_0.pdb #3  
---  
Chain | Description  
U | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 525, in rebuild  
_rebuild_molecule('internal', mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 652, in
_rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1237, in make_ladder  
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 733, in get_cylinder  
h = distance(p0, p1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 71, in distance  
return sqrt(distance_squared(p, q))  
File "C:\Program Files\ChimeraX\bin\lib\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 "new frame":  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 63, in distance_squared  
if len(p) == 3:  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4531
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 7348
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 8,501,149,696
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-5500U CPU @ 2.40GHz"

[Greg Couch]

This bug looks like it was fixed on April 16th, 13 days after the 0.93 release. Unfortunately, since you are using ISOLDE, you are stuck on ChimeraX 0.93 until a newer version comes out. I've reassigned this ticket to the author of ISOLDE so he can notify you when it is safe to update your version of ChimeraX.

[Tristan Croll]

Getting closer to release-ready... if you have an urgent need let me know and I can point you to a development build.

[Tristan Croll]

Sorry for the necropost - just closing out old tickets. :)