Opened 7 years ago

Closed 7 years ago

#1220 closed defect (fixed)

Bad atomic import

Reported by: goddard@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-07-31)
Description
open 1bf5
hbonds

generates the follow error



Log:
UCSF ChimeraX version: 0.7 (2018-07-31)  
OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102  
OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open 1bf5

Summary of feedback from opening 1bf5 fetched from pdb  
---  
notes | Used PDBx fixed column width tables to speed up reading mmCIF file  
Used PDBx keywords to speed up reading mmCIF file  
  
Chain information for 1bf5 #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')  
  
1bf5 mmCIF Assemblies | 1| author_defined_assembly  

1bf5 citation:    Chen, X., Vinkemeier, U., Zhao, Y., Jeruzalmi, D., Darnell
Jr., J.E., Kuriyan, J. (1998). Crystal structure of a tyrosine phosphorylated
STAT-1 dimer bound to DNA. Cell(Cambridge,Mass.), 93, 827-839. PMID: 9630226.
DOI: 10.1016/S0092-8674(00)81443-9  
Opened mmCIF data containing 5117 atoms and 5298 bonds  

hbonds

Traceback (most recent call last):  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.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 "/Users/goddard/Desktop/ChimeraX July 31
2018.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 "/Users/goddard/Desktop/ChimeraX July 31
2018.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 "/Users/goddard/Desktop/ChimeraX July 31
2018.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 "/Users/goddard/Desktop/ChimeraX July 31
2018.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.  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Eric Pettersen, 7 years ago

Component: UnassignedCore
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionBad atomic import

comment:2 by Eric Pettersen, 7 years ago

Resolution: fixed
Status: acceptedclosed

This problem was fixed yesterday and does not occur in the current daily build. Re-install atomic.

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