id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4400 Session trying to directly save alignment header elinteppa@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-5.4.0-70-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs > format session Log from Wed Mar 24 14:45:38 2021UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /home_pers/teppa/dEEPEN/data/UbiL/Brucella/UbiL1_Bruc_WP_008503541.1.B99990013.pdb Chain information for UbiL1_Bruc_WP_008503541.1.B99990013.pdb #1 --- Chain | Description | No description available > set bgColor white > style ligand ball Changed 0 atom styles > close session > open > /home_pers/teppa/dEEPEN/data/UbiL/Brucella/UbiL1_Bruc_WP_008503541.1.B99990013.pdb Chain information for UbiL1_Bruc_WP_008503541.1.B99990013.pdb #1 --- Chain | Description | No description available > clear Unknown command: clear > open 1pbe 1pbe title: Crystal structure of the P-hydroxybenzoate hydroxylase-substrate complex refined At 1.9 angstroms resolution. Analysis of the enzyme-substrate and enzyme-product complexes [more info...] Chain information for 1pbe #2 --- Chain | Description A | P-hydroxybenzoate hydroxylase Non-standard residues in 1pbe #2 --- FAD — flavin-adenine dinucleotide PHB — P-hydroxybenzoic acid 1pbe mmCIF Assemblies --- 1| author_and_software_defined_assembly > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker UbiL1_Bruc_WP_008503541.1.B99990013.pdb, chain (blank) (#1) with 1pbe, chain A (#2), sequence alignment score = 293.6 RMSD between 135 pruned atom pairs is 0.937 angstroms; (across all 365 pairs: 6.261) > select #2/A:38 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 42 atoms, 43 bonds, 5 residues, 1 model selected > select up 3491 atoms, 3231 bonds, 723 residues, 1 model selected > hide sel target a > hide sel cartoons > open > /home_pers/teppa/dEEPEN/data/UbiL/Brucella/UbiL1_Bruc_WP_008503541.1.B99990013.pdb Chain information for UbiL1_Bruc_WP_008503541.1.B99990013.pdb #3 --- Chain | Description | No description available > close #3 > open /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1.aln Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/seqalign/parse.py"", line 31, in open_file seqs, file_attrs, file_markups = ns['read'](session, stream) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/seqalign/io/readALN.py"", line 33, in read raise FormatSyntaxError(""First non-blank line does not start with 'CLUSTAL'"") chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start with 'CLUSTAL' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py"", line 150, in _qt_safe if data_format is None else "" format "" + StringArg.unparse(data_format.nicknames[0]))) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 100, in cmd_open return Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 154, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 389, in collated_open return func(*func_args, **func_kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/seqalign/__init__.py"", line 63, in open format_name=name.upper(), **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/seqalign/parse.py"", line 33, in open_file raise IOError(""Syntax error in %s file '%s': %s"" % (format_name, fname, err)) OSError: Syntax error in ALN file 'ubiL1.aln': First non-blank line does not start with 'CLUSTAL' OSError: Syntax error in ALN file 'ubiL1.aln': First non-blank line does not start with 'CLUSTAL' File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/seqalign/parse.py"", line 33, in open_file raise IOError(""Syntax error in %s file '%s': %s"" % (format_name, fname, err)) See log for complete Python traceback. > open /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1.aln Summary of feedback from opening /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1.aln --- notes | Alignment identifier is ubiL1.aln Associated UbiL1_Bruc_WP_008503541.1.B99990013.pdb chain (blank) to WP_008503541.1 with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment ubiL1.aln Opened 761 sequences from ubiL1.aln > color byattribute seq_conservation 6655 atoms, 1137 residues, atom seq_conservation range -1.24 to 3.29 > hide #1 models > select #2 3491 atoms, 3231 bonds, 723 residues, 1 model selected > show #1 models > hide #1 models > show sel cartoons > select ::name=""FAD"" 53 atoms, 58 bonds, 1 residue, 1 model selected > show sel atoms > hide #2 models > show #1 models > show #2 models > select #2/A:262 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 58 atoms, 58 bonds, 8 residues, 1 model selected > select up 3491 atoms, 3231 bonds, 723 residues, 1 model selected > hide sel cartoons > color byattribute seq_conservation palette blue:red:yellow 6655 atoms, 1137 residues, atom seq_conservation range -1.24 to 3.29 > color byattribute seq_conservation palette cyanmaroon 6655 atoms, 1137 residues, atom seq_conservation range -1.24 to 3.29 > show sel atoms > hide sel atoms > show sel target ab > hide sel target ab > show sel target ab > hide sel target ab > select clear > show sel atoms > style sel stick Changed 7 atom styles > style sel stick Changed 7 atom styles > style sel ball Changed 7 atom styles > hide sel cartoons > show sel atoms > style sel stick Changed 7 atom styles > style sel sphere Changed 7 atom styles > style sel ball Changed 7 atom styles > style sel ball Changed 15 atom styles > hide sel cartoons > style sel ball Changed 15 atom styles > show sel atoms > show sel cartoons > hide sel atoms > style sel sphere Changed 20 atom styles > hide sel atoms > style sel sphere Changed 20 atom styles > show sel atoms > style sel ball Changed 20 atom styles > style sel stick Changed 20 atom styles > style sel ball Changed 20 atom styles > hide sel atoms > show sel cartoons > hide #2 models > show #2 models > select #1:78 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 63 atoms, 65 bonds, 7 residues, 1 model selected > show sel atoms Drag select of 25 residues > show sel atoms > select clear > show sel atoms > style sel ball Changed 15 atom styles > style sel stick Changed 15 atom styles > style sel sphere Changed 15 atom styles > style sel stick Changed 15 atom styles > show sel atoms > select clear > select #1:52 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 108 atoms, 111 bonds, 15 residues, 1 model selected > select up 3164 atoms, 3228 bonds, 414 residues, 1 model selected > show sel atoms > style sel stick Changed 3164 atom styles > style sel sphere Changed 3164 atom styles > style sel ball Changed 3164 atom styles > hide sel cartoons > show sel cartoons > hide sel atoms > select clear > select ::name=""FAD"" 53 atoms, 58 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 53 atom styles > style sel stick Changed 53 atom styles > show sel atoms > hide sel atoms > show sel atoms > style sel sphere Changed 53 atom styles > style sel ball Changed 53 atom styles > select up 3491 atoms, 3231 bonds, 723 residues, 1 model selected > style sel stick Changed 3491 atom styles > style sel sphere Changed 3491 atom styles > style sel ball Changed 3491 atom styles > show sel cartoons > hide sel cartoons > style sel ball Changed 3491 atom styles > style sel sphere Changed 3491 atom styles > style sel stick Changed 3491 atom styles > select #1:277 5 atoms, 4 bonds, 1 residue, 1 model selected > style sel ball Changed 5 atom styles > show sel atoms > select #1:236 14 atoms, 15 bonds, 1 residue, 1 model selected > style sel ball Changed 14 atom styles > show sel atoms > select #1:221 7 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 7 atom styles > show sel atoms > select #1:226 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #1:223 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > show sel atoms > show sel atoms > show sel atoms > save /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs opened ChimeraX session > select ::name=""FAD"" 53 atoms, 58 bonds, 1 residue, 1 model selected > hide sel target a > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > show sel target ab > show sel target ab > style sel ball Changed 60 atom styles > select up 68 atoms, 73 bonds, 3 residues, 2 models selected > select up 99 atoms, 106 bonds, 7 residues, 2 models selected > select up 6655 atoms, 6459 bonds, 1137 residues, 2 models selected > style sel ball Changed 6655 atom styles > show sel target ab > hide sel target a > select clear > show sel target ab > select #1:397 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 17 atoms, 15 bonds, 2 residues, 1 model selected > select up 174 atoms, 177 bonds, 24 residues, 1 model selected > select up 3164 atoms, 3228 bonds, 414 residues, 1 model selected > style sel stick Changed 3164 atom styles > show sel atoms > hide sel atoms > show sel target ab > hide sel atoms > select clear > show sel target ab > show sel target ab > label sel attribute label_one_letter_code > select clear > select ::name=""PHB"" 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""FAD"" 53 atoms, 58 bonds, 1 residue, 1 model selected > show sel atoms > select #1:310 4 atoms, 3 bonds, 1 residue, 1 model selected > color byattribute seq_conservation palette cyanmaroon -1.24 to 1.24 Expected a keyword > color byattribute seq_conservation palette cyanmaroon range -1.24 to 1.24 > novalue yellow Invalid ""range"" argument: Need exactly 2 ','-separated numbers > color byattribute seq_conservation palette cyanmaroon range -1.24 ,1.24 > noValueColor yellow 6655 atoms, 1137 residues, atom seq_conservation range -1.24 to 3.29 > select clear > select #1:317 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select clear > select #1:197 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 48 atoms, 47 bonds, 7 residues, 1 model selected > select up 3164 atoms, 3228 bonds, 414 residues, 1 model selected > hide sel atoms > show ::seq_conservation>1.8 > ~label sel residues > label ::seq_conservation>1.8 > label height 1.3 > preset pub Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > select clear > label delete > surface > colr fromatoms Unknown command: colr fromatoms > color fromatoms > present inter Unknown command: present inter > preset inter Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f > set bgColor white > hide #!2 models > select ::name=""FAD"" 53 atoms, 58 bonds, 1 residue, 1 model selected > show #1 target ab > show #!2 models > hide #2.1 models > transparency sel 50 > select clear > select #1:187@CB 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 81 atoms, 83 bonds, 10 residues, 2 models selected > select up 3164 atoms, 3228 bonds, 414 residues, 2 models selected > transparency (#!1 & sel) 50 > hide sel atoms > select clear > transparency #1#!2 80 > transparency #1#!2 30 > save /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 53 atoms, 58 bonds, 1 residue, 1 model selected > color sel byelement > color byattribute seq_conservation palette cyanmaroon range -1.24 ,1.24 > noValueColor gray 6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to 3.29 > show ::seq_conservation>2 > surface hidePatches sel > select clear > select #1:286@CZ 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > select up 105 atoms, 106 bonds, 13 residues, 2 models selected > select up 3164 atoms, 3228 bonds, 414 residues, 2 models selected > surface hidePatches (#!1 & sel) > size stickRadius .5 Changed 6459 bond radii > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 53 atoms, 58 bonds, 1 residue, 1 model selected > size stickRadius .1 Changed 6459 bond radii > size stickRadius .2 Changed 6459 bond radii > select clear > show ::seq_conservation>2 > size stickRadius .5 Changed 6459 bond radii > select clear > select #2/A:395@N6A 1 atom, 1 residue, 1 model selected > select up 53 atoms, 58 bonds, 1 residue, 1 model selected > size stickRadius .3 Changed 6459 bond radii > color ligand byhetero > lighting soft > sequence header conservation setting style ""identity histogram"" > select ~::seq_conservation 3491 atoms, 3231 bonds, 723 residues, 1 model selected > color byattribute seq_conservation 6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range 0.0342 to 1 > select #1:32 9 atoms, 8 bonds, 1 residue, 1 model selected > sequence header conservation setting style AL2CO > color byattribute seq_conservation palette cyanmaroon range -2,3 > noValueColor yellow 6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to 3.29 > lighting flat > graphics silhouettes depthJump 0.03 > graphics silhouettes depthJump 0.06 > graphics silhouettes depthJump 0.1 > graphics silhouettes depthJump 0.01 > 0.5 Unknown command: 0.5 > graphics silhouettes depthJump 0.5 > graphics silhouettes depthJump 0.01 > lighting simple > lighting soft > lighting full > lighting full > lighting flat > lighting flat > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting flat > lighting flat > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting simple > graphics silhouettes false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > color byattribute seq_conservation palette cyanmaroon range -2,3 > noValueColor gray 6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to 3.29 > lighting soft > set bgColor gray > set bgColor black > set bgColor gray > color byattribute seq_conservation palette cyanmaroon range -2,3 > noValueColor yellow 6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to 3.29 > select #2/A:395@N6A 1 atom, 1 residue, 1 model selected > select up 53 atoms, 58 bonds, 1 residue, 1 model selected > select up 63 atoms, 68 bonds, 2 residues, 1 model selected > color sel byelement > set bgColor white > : set bg steelblue Unknown command: : set bg steelblue > set bgColor steelblue > select clear > set bgColor gray > color byattribute seq_conservation palette cyanmaroon range -2,3 > noValueColor yellow 6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to 3.29 > 2dlabels text ""UbiL-1 conservation"" color white > ui mousemode right ""move label"" > ui mousemode right ""move label"" > 2dlabels #3.1 xpos 0.526 ypos 0.787 > 2dlabels #3.1 xpos 0.539 ypos 0.953 > 2dlabels #3.1 xpos 0.495 ypos 0.947 > ui mousemode right ""move label"" > 2dlabels #3.1 xpos 0.475 ypos 0.942 > 2dlabels text ""UbiL-1 conservation"" color white size 26 > ui mousemode right ""move label"" > 2dlabels #3.2 xpos 0.064 ypos 0.593 > hide #3.2 models > show #3.2 models > close #3.2 > color byattribute seq_conservation palette cyanmaroon range -1.24 ,1.24 > noValueColor gray 6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to 3.29 > set bgColor white > graphics silhouettes true > lighting simple > lighting simple > lighting shadows true > lighting shadows false > lighting soft > lighting soft > lighting full > lighting full > lighting full > lighting flat > lighting flat > lighting soft > graphics silhouettes false > graphics silhouettes true > save /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 292, in process return copy_state(data, convert=convert) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 215, in copy_state return _copy(data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in _copy items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in _copy items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in _copy items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 210, in _copy return data.__class__(items) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/alignment_headers/conservation.py"", line 42, in __init__ super().__init__(alignment, *args, eval_while_hidden=True, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/alignment_headers/header_sequence.py"", line 47, in __init__ self.alignment = proxy(alignment) TypeError: cannot create weak reference to 'list' object During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 826, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 583, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> : cannot create weak reference to 'list' object ValueError: error processing: 'tools' -> -> : cannot create weak reference to 'list' object File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 292, in process return copy_state(data, convert=convert) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 215, in copy_state return _copy(data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in _copy items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 200, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in _copy items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in _copy items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 209, in items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py"", line 210, in _copy return data.__class__(items) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/alignment_headers/conservation.py"", line 42, in __init__ super().__init__(alignment, *args, eval_while_hidden=True, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/alignment_headers/header_sequence.py"", line 47, in __init__ self.alignment = proxy(alignment) TypeError: cannot create weak reference to 'list' object During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1574, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 102, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 113, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 48, in display run(session, cmd) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 79, in provider_save mgr).save(session, path, **provider_kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 826, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 583, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> : cannot create weak reference to 'list' object ValueError: error processing: 'tools' -> -> : cannot create weak reference to 'list' object File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 460.27.04 OpenGL renderer: Quadro M5000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUS Model: All Series OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 16 Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 125G 6.1G 117G 199M 1.7G 118G Swap: 8.0G 0B 8.0G Graphics: 05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM204GL [Quadro M5000] [10de:13f0] (rev a1) Subsystem: NVIDIA Corporation GM204GL [Quadro M5000] [10de:1152] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Sessions can't reproduce Eric Pettersen all ChimeraX