pb_scene_coord returning None

[vytautas.raskevicius@…]

The following bug report has been submitted:
Platform:        Linux-4.4.217-x86_64-Intel-R-_Core-TM-_i5-3570_CPU_@_3.40GHz-with-slackware-14.2
ChimeraX Version: 0.93 (2020-04-03)
Description
Just try to draw hydrogen bonds

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2
> /home/vytautas/COVID-19_docking/Q96K12/robetta_models_22767_good_fix.pdb

Chain information for robetta_models_22767_good_fix.pdb #1  
---  
Chain | Description  
A | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 2464, resource id:
8389166, major code: 40 (TranslateCoords), minor code: 0  

> open2 /home/vytautas/COVID-19_docking/Q96K12/Conformer3D_CID_5884_out.pdbqt

Opened Conformer3D_CID_5884_out.pdbqt containing 9 structures (531 atoms, 567
bonds)  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 3901, resource id:
8389175, major code: 40 (TranslateCoords), minor code: 0  

> hide #2.9 models

> hide #2.8 models

> hide #2.7 models

> hide #2.6 models

> hide #2.5 models

> hide #2.4 models

> hide #2.3 models

> hide #2.2 models

> set bgColor white

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> lighting full

> lighting simple

> lighting soft

> lighting simple

> hbonds #1#2.1

499 hydrogen bonds found  
Traceback (most recent call last):  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 63, in pbg_update  
self._update_graphics()  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "changes":  
TypeError: Cannot multiply Place times "None"  
  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 185, in _update_graphics_if_needed  
self._update_graphics(gc)  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "graphics update":  
TypeError: Cannot multiply Place times "None"  
  
File "/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3 (Core Profile) Mesa 11.2.2
OpenGL renderer: Mesa DRI Intel(R) Ivybridge Desktop 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: System manufacturer
Model: System Product Name
OS: Slackware 14.2 
Architecture: 64bit ELF
CPU: 4 Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz
Cache Size: 6144 KB
Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Xeon E3-1200 v2/3rd Gen Core processor Graphics Controller [8086:0152] (rev 09)
	Subsystem: ASUSTeK Computer Inc. P8H77-I Motherboard [1043:84ca]
	Kernel driver in use: i915

[Tom Goddard]

This was fixed a month ago. Use ChimeraX daily build.