id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2919 """sequence chain"" fails after chain lengthened" ym337@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.4.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.91 (2019-12-17) Description I added a few aminoacids whist opening isolde. The sequence viewer was open by the time I added the amino acids. Then I closed the sequece viewer and tried to open the sequence again. The error message is attached. I couldn't save the ChimeraX session neither after that. Could you please have a look? Log: UCSF ChimeraX version: 0.91 (2019-12-17) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > select up Nothing selected > select up Nothing selected > open > /nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job879/isolde/isolde_N_module_session_4.cxs > format session Summary of feedback from opening /nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job879/isolde/isolde_N_module_session_4.cxs --- warning | restore_snapshot for ""RotamerRestraintMgr"" returned None opened ChimeraX session > sequence chain /N Alignment identifier is 1.1.N Traceback (most recent call last): File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 454, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1632, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/__init__.py"", line 40, in run_provider return _start_seq_viewer(session, ""Sequence Viewer"", alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 684, in _start_seq_viewer return SequenceViewer(session, tool_name, alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 55, in __init__ self._finalize_init(alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 174, in _finalize_init self.seq_canvas = SeqCanvas(parent, self, self.alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 184, in __init__ self.layout_alignment() File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 780, in layout_alignment self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps()) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 1602, in __init__ self.layout_lines(alignment.seqs, self.normal_label_color) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2244, in layout_lines self._layout_line(line, label_color, bli, end) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2237, in _layout_line numberings[numbering] = self._make_numbering(line, numbering) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2329, in _make_numbering x, y = self.item_aux_info[line][-1] IndexError: list index out of range Traceback (most recent call last): File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 454, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1632, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/__init__.py"", line 40, in run_provider return _start_seq_viewer(session, ""Sequence Viewer"", alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 684, in _start_seq_viewer return SequenceViewer(session, tool_name, alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 55, in __init__ self._finalize_init(alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 174, in _finalize_init self.seq_canvas = SeqCanvas(parent, self, self.alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 184, in __init__ self.layout_alignment() File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 780, in layout_alignment self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps()) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 1602, in __init__ self.layout_lines(alignment.seqs, self.normal_label_color) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2244, in layout_lines self._layout_line(line, label_color, bli, end) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2237, in _layout_line numberings[numbering] = self._make_numbering(line, numbering) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2329, in _make_numbering x, y = self.item_aux_info[line][-1] IndexError: list index out of range During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seqalign/cmd.py"", line 141, in seqalign_chain auto_associate=None, intrinsic=True) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seqalign/manager.py"", line 244, in new_alignment alignment=alignment) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 459, in run_provider ""run_provider() failed in bundle %s:\n%s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: run_provider() failed in bundle ChimeraX-SeqView: list index out of range chimerax.core.toolshed.ToolshedError: run_provider() failed in bundle ChimeraX-SeqView: list index out of range File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 459, in run_provider ""run_provider() failed in bundle %s:\n%s"" % (self.name, str(e))) See log for complete Python traceback. > sequence chain /A Alignment identifier is 1.1.A > sequence chain /N Destroying pre-existing alignment with identifier 1.1.N Traceback (most recent call last): File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seqalign/cmd.py"", line 141, in seqalign_chain auto_associate=None, intrinsic=True) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seqalign/manager.py"", line 220, in new_alignment self.destroy_alignment(self._alignments[identify_as]) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seqalign/manager.py"", line 109, in destroy_alignment alignment._destroy() File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seqalign/alignment.py"", line 501, in _destroy self._notify_observers(""destroyed"", None) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seqalign/alignment.py"", line 541, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 459, in alignment_notification self.delete() File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 489, in delete self.region_browser.destroy() AttributeError: 'SequenceViewer' object has no attribute 'region_browser' AttributeError: 'SequenceViewer' object has no attribute 'region_browser' File ""/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 489, in delete self.region_browser.destroy() See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.87.01 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation File attachment: 89422800_196038681466979_538118797567983616_n.jpg }}} [attachment:""89422800_196038681466979_538118797567983616_n.jpg""] " defect feedback normal Sequence Tristan Croll all ChimeraX