id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2500 hbonds saltOnly: 'list' object has no attribute 'elements' rjohnwingo@… Eric Pettersen "{{{ 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 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: 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 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: 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. }}} " defect closed normal Structure Editing fixed all ChimeraX