id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2278	Nucleotides: object of type 'NoneType' has no len()	tic20@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-07-27)
Description
Log:
UCSF ChimeraX version: 0.91 (2019-07-27)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/tic20/isolde/isolde/src/demo_data/3io0/before.pdb

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  

> toolshed show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn(""IPython History requires SQLite, your history will not be saved"")  

> close

> open 6h0s

Summary of feedback from opening 6h0s fetched from pdb  
---  
notes | Fetching compressed mmCIF 6h0s from
http://files.rcsb.org/download/6h0s.cif  
Fetching CCD FOX from http://ligand-expo.rcsb.org/reports/F/FOX/FOX.cif  
  
6h0s title:  
Crystal structure of the complex between the Lactococcus lactis FPG mutant
G226P and a Fapy-dG containing DNA [more info...]  
  
Chain information for 6h0s #1  
---  
Chain | Description  
A | Formamidopyrimidine-DNA glycosylase  
B | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(fox)P*TP*TP*TP*CP*TP*CP*G)-3')  
C | DNA (5'-D(*GP*CP*GP*ap*GP*ap*ap*ap*CP*ap*ap*ap*GP*A)-3')  
  
Non-standard residues in 6h0s #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
ZN — zinc ion  
  
  

> nucleotides selAtoms fill

> style nucleic & selAtoms stick

Changed 569 atom styles  

> nucleotides selAtoms slab

> style nucleic & selAtoms stick

Changed 569 atom styles  

> nucleotides selAtoms tube/slab shape box

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command ""graphics restart"" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py"", line 72, in draw_new_frame  
view.draw(check_for_changes = False)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py"", line 164, in draw  
self._draw_scene(camera, drawings)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py"", line 230, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 1418, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 1429, in _draw_multiple  
d.draw(renderer, draw_pass)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 711, in draw  
if not self.display:  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 334, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

}}}
"	defect	closed	normal		Depiction		fixed						all	ChimeraX