ChimeraX bug report submission

[arik@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-07-31)
Description
Was saving out to OBJ format. Note: objects were clipped with the clip rotate tool before hand. Don't know if that matters. Intending to import into Cinema 4D, in which other attempts weren't able to be opened. STL worked. Thank you!

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.7 (2018-07-31)  
OpenGL version: 4.1 ATI-1.68.20  
OpenGL renderer: AMD Radeon Pro Vega 64 OpenGL Engine  
OpenGL vendor: ATI Technologies Inc.  
How to cite UCSF ChimeraX  

open
/Volumes/CCFV_Work/MLG_1511_561_3D_RA_March2016/MGoldbergM4600_MG/3D/STAT_DNA/1bf5.pdb

Opened PDB data containing 5117 atoms and 5297 bonds  
Chain information for 1bf5.pdb #1  
---  
Chain | Description  
A | signal transducer and activator of transcription 1-α/β  
B | DNA (5'- D(*ap*cp*ap*gp*tp*tp*tp*cp*cp*cp*gp*tp*ap*ap*ap*tp*G P*C)- 3')  
C | DNA (5'- D(*tp*gp*cp*ap*tp*tp*tp*ap*cp*gp*gp*gp*ap*ap*ap*cp*T P*G)- 3')  
  

style selAtoms sphere

Changed 5117 atom styles  

style selAtoms sphere

Changed 5117 atom styles  

style selAtoms stick

Changed 5117 atom styles  

style selAtoms sphere

Changed 5117 atom styles  

style selAtoms stick

Changed 5117 atom styles  

style selAtoms ball

Changed 5117 atom styles  

color selAtoms byhetero

color selAtoms bychain

hbonds selAtoms

Traceback (most recent call last):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/shortcuts/tool.py", line 50, in button_press_cb  
    ks.run_shortcut(keys)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/shortcuts/shortcuts.py", line 375, in run_shortcut  
    sc.run(self.session, status = self._enabled)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/shortcuts/shortcuts.py", line 272, in run  
    commands.run(s, f)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/cmd.py", line 83, in cmd_hbonds  
    result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hbond.py", line 560, in find_hbonds  
    donor_hyds = hyd_positions(donor_atom)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hydpos.py", line 39, in hyd_positions  
    bonded_locs.append(b_heavy._hb_coord)  
AttributeError: 'Atom' object has no attribute '_hb_coord'  
  

AttributeError: 'Atom' object has no attribute '_hb_coord'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hydpos.py", line 39, in hyd_positions  
bonded_locs.append(b_heavy._hb_coord)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

style selAtoms sphere

Changed 5117 atom styles  

show selAtoms ribbons

hide selAtoms ribbons

show selAtoms ribbons

hide selAtoms ribbons

show selAtoms surfaces

ui mousemode rightMode rotate

ui mousemode rightMode translate

ui mousemode rightMode zoom

ui mousemode rightMode zoom

ui mousemode rightMode zoom

ui mousemode rightMode move planes

ui mousemode rightMode place marker

ui mousemode rightMode select

ui mousemode rightMode rotate

ui mousemode rightMode translate

view orient cofr false

set silhouettes true

set silhouettes false

lighting flat

lighting flat

set silhouettes false

set silhouettes true

lighting flat

lighting full

set silhouettes false

lighting soft

lighting full

lighting soft

lighting shadows true intensity 0.5

lighting shadows false

lighting shadows true

lighting simple

lighting simple

lighting simple

lighting shadows true

lighting shadows false

lighting shadows true

lighting simple

lighting shadows true

lighting soft

lighting shadows true intensity 0.5

lighting soft

lighting shadows true intensity 0.5

lighting soft

lighting shadows true intensity 0.5

lighting soft

lighting shadows true intensity 0.5

lighting simple

lighting shadows true

lighting soft

lighting simple

lighting soft

lighting full

lighting full

lighting full

lighting soft

lighting full

lighting soft

lighting shadows true intensity 0.5

lighting shadows false

lighting shadows true

lighting simple

lighting simple

lighting shadows true

lighting simple

lighting soft

lighting shadows true intensity 0.5

lighting simple

lighting shadows true

lighting simple

lighting shadows true

lighting simple

lighting shadows true

lighting simple

lighting shadows true

lighting simple

lighting shadows true

lighting soft

lighting simple

lighting soft

lighting simple

lighting shadows true

lighting simple

lighting simple

lighting shadows true

lighting soft

lighting full

set bgColor black

set bgColor gray

set bgColor white

set bgColor black

view cofr false

color selAtoms bychain

color selAtoms byhetero

color selAtoms bychain

color selAtoms byhetero

show selAtoms surfaces

show selAtoms surfaces

hide selAtoms surfaces

hide selAtoms surfaces

show selAtoms surfaces

hide selAtoms ribbons

hide selAtoms ribbons

show selAtoms ribbons

show selAtoms ribbons

hide selAtoms

hide selAtoms

show selAtoms

show selAtoms

style selAtoms stick

Changed 5117 atom styles  

style selAtoms sphere

Changed 5117 atom styles  

style selAtoms ball

Changed 5117 atom styles  

color selAtoms byhetero

color selAtoms bychain

hbonds selAtoms

Traceback (most recent call last):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/shortcuts/tool.py", line 50, in button_press_cb  
    ks.run_shortcut(keys)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/shortcuts/shortcuts.py", line 375, in run_shortcut  
    sc.run(self.session, status = self._enabled)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/shortcuts/shortcuts.py", line 272, in run  
    commands.run(s, f)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/cmd.py", line 83, in cmd_hbonds  
    result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hbond.py", line 560, in find_hbonds  
    donor_hyds = hyd_positions(donor_atom)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hydpos.py", line 39, in hyd_positions  
    bonded_locs.append(b_heavy._hb_coord)  
AttributeError: 'Atom' object has no attribute '_hb_coord'  
  

AttributeError: 'Atom' object has no attribute '_hb_coord'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hydpos.py", line 39, in hyd_positions  
bonded_locs.append(b_heavy._hb_coord)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

ui mousemode rightMode distance

ui mousemode rightMode distance

distance /C:2011@C8 /A:629@CB

Distance between /C DG