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Opened 6 years ago
Closed 6 years ago
#2500 closed defect (fixed)
hbonds saltOnly: 'list' object has no attribute 'elements'
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-08-24) Description used hbonds saltonly true command Log: UCSF ChimeraX version: 0.91 (2019-08-24) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/robertwingo/Dropbox/IU/Fall 2019/B530 - Macromolecular Struct & Fxn/Problem Sets/PS2/PS2_protein.pdb" PS2_protein.pdb title: Crystal structure of the zinc-dependent marr family transcriptional regulator ADCR In the Zn(II)-bound state [more info...] Chain information for #1 --- Chain | Description A B | adc operon repressor ADCR Non-standard residues in #1 --- ZN — zinc ion > select /a 1233 atoms, 1080 bonds, 9 pseudobonds, 3 models selected > color /a "dark slate gray" > color /B "slate gray" > ~select /a Nothing selected > set bgColor white > select /b 1273 atoms, 1151 bonds, 9 pseudobonds, 2 models selected > hide sel cartoons > ~select /b Nothing selected > select /A:1-145 1065 atoms, 1080 bonds, 1 pseudobond, 2 models selected Missing or invalid "chains" argument: invalid chains specifier Missing or invalid "chains" argument: invalid chains specifier Unknown command: sequence /a > sequence chain /a Alignment identifier is 1.A > ~select /a Nothing selected > select /a :2-19 144 atoms, 144 bonds, 1 model selected > color /a :2-19 red > color /a :37-48 red > color /a :53-62 red > color /a :64-78 red > color /a :81-82 red > color /a :81-82 green > color /a :81-82 "light blue" > color /a :81-82 blue > color /a :96-97 blue > color /a :101-124 red > color /a :127-145 red > ~select /a Nothing selected > select /b 1273 atoms, 1151 bonds, 9 pseudobonds, 2 models selected > show sel cartoons > color /b :2-19 red > color /b :37-48 red > color /b :53-62 red > color /b :64-78 red > color /b :81-82 blue > color /b :81-83 blue > sequence chain /b Alignment identifier is 1.B > color /b :81-84 blue > color /b :2-20 red > color /b :37-51 red > color /b :94-97 blue > color /b :101-124 red > color /b :127-146 red > color /b :147-148 lime > color /a :147-148 lime > save /Users/robertwingo/Desktop/image1.png supersample 3 > ~select /a Nothing selected > save /Users/robertwingo/Desktop/image2.png supersample 3 Unknown command: findhbond Unknown command: FindHBond > hbonds 1038 hydrogen bonds found > hbonds 1038 hydrogen bonds found > hbonds saltOnly true Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2688, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 92, in cmd_hbonds sb_donors, sb_acceptors = salt_preprocess(hbonds) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 419, in salt_preprocess ne_has_protons = numpy.any(ne.neighbors.elements.numbers == 1) AttributeError: 'list' object has no attribute 'elements' AttributeError: 'list' object has no attribute 'elements' File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 419, in salt_preprocess ne_has_protons = numpy.any(ne.neighbors.elements.numbers == 1) See log for complete Python traceback. > ~select a Expected an objects specifier or a keyword > ~select /a Nothing selected Expected a keyword > ~hbonds Missing "saltOnly" keyword's argument > hbonds saltOnly true Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2688, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 92, in cmd_hbonds sb_donors, sb_acceptors = salt_preprocess(hbonds) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 419, in salt_preprocess ne_has_protons = numpy.any(ne.neighbors.elements.numbers == 1) AttributeError: 'list' object has no attribute 'elements' AttributeError: 'list' object has no attribute 'elements' File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 419, in salt_preprocess ne_has_protons = numpy.any(ne.neighbors.elements.numbers == 1) See log for complete Python traceback. Alignment identifier is 1 Alignment identifier is 2 Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 1666, in <lambda> dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 549, in close_request tool_instance.delete() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/tool.py", line 499, in delete self.alignment.detach_viewer(self) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer self.session.alignments.destroy_alignment(self) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment alignment._destroy() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py", line 498, in _destroy aseq.match_maps[sseq].mod_handler.remove() KeyError: <chimerax.atomic.molobject.Chain object at 0x126bba7d0> KeyError: File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py", line 498, in _destroy aseq.match_maps[sseq].mod_handler.remove() See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 1666, in <lambda> dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 549, in close_request tool_instance.delete() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/tool.py", line 499, in delete self.alignment.detach_viewer(self) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer self.session.alignments.destroy_alignment(self) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment alignment._destroy() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py", line 498, in _destroy aseq.match_maps[sseq].mod_handler.remove() KeyError: <chimerax.atomic.molobject.Chain object at 0x126bba7d0> KeyError: File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py", line 498, in _destroy aseq.match_maps[sseq].mod_handler.remove() See log for complete Python traceback. > hbonds radius 3.9 1038 hydrogen bonds found > hbonds radius 4 1038 hydrogen bonds found > hbonds radius 10 1038 hydrogen bonds found > hbonds radius 0 1038 hydrogen bonds found > hbonds radius 1 1038 hydrogen bonds found Missing "radius" keyword's argument > hbonds radius 0 1038 hydrogen bonds found > hbonds 1038 hydrogen bonds found > hbonds saltOnly true Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2688, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 92, in cmd_hbonds sb_donors, sb_acceptors = salt_preprocess(hbonds) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 419, in salt_preprocess ne_has_protons = numpy.any(ne.neighbors.elements.numbers == 1) AttributeError: 'list' object has no attribute 'elements' AttributeError: 'list' object has no attribute 'elements' File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 419, in salt_preprocess ne_has_protons = numpy.any(ne.neighbors.elements.numbers == 1) See log for complete Python traceback. > hbonds showDist true 1038 hydrogen bonds found Alignment identifier is 1 > hbonds saltOnly true Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2688, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 92, in cmd_hbonds sb_donors, sb_acceptors = salt_preprocess(hbonds) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 419, in salt_preprocess ne_has_protons = numpy.any(ne.neighbors.elements.numbers == 1) AttributeError: 'list' object has no attribute 'elements' AttributeError: 'list' object has no attribute 'elements' File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py", line 419, in salt_preprocess ne_has_protons = numpy.any(ne.neighbors.elements.numbers == 1) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.9.22 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → hbonds saltOnly: 'list' object has no attribute 'elements' |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Thanks for reporting this problem. It is fixed now and the fix will be in the next daily build, but it may be a day or two before the next daily build is available because we just switched our server hardware and are working on getting our build process functioning again. When it is available, the download page will list its date as October 15th (or later).
--Eric