Opened 7 years ago
Closed 7 years ago
#1220 closed defect (fixed)
Bad atomic import
Reported by: | Owned by: | Eric Pettersen | |
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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 , 7 years ago
Component: | Unassigned → Core |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Bad atomic import |
comment:2 by , 7 years ago
Resolution: | → fixed |
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Status: | accepted → closed |
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This problem was fixed yesterday and does not occur in the current daily build. Re-install atomic.