id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3347 Session saving creating arbitrary class instances chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.0rc202005292300 (2020-05-29 23:00:06 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0rc202005292300 (2020-05-29) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1qrk format mmcif fromDatabase pdb 1qrk title: Human factor XIII with strontium bound In the ion site [more info...] Chain information for 1qrk #1 --- Chain | Description A B | protein (coagulation factor XIII) Non-standard residues in 1qrk #1 --- SR — strontium ion > open 1de7 Summary of feedback from opening 1de7 fetched from pdb --- warnings | Expected gap or linking atom in AR7 /A:37 for PRO /A:36 Expected gap or connection between AR7 /A:37 and 0QE /A:38 Expected gap or linking atom in AR7 /B:37 for PRO /B:36 Expected gap or connection between AR7 /B:37 and 0QE /B:38 notes | Fetching compressed mmCIF 1de7 from http://files.rcsb.org/download/1de7.cif Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif Fetching CCD AR7 from http://ligand-expo.rcsb.org/reports/A/AR7/AR7.cif Fetching CCD 0QE from http://ligand-expo.rcsb.org/reports/0/0QE/0QE.cif 1de7 title: Interaction of factor XIII activation peptide with α-thrombin: crystal structure of the enzyme-substrate complex [more info...] Chain information for 1de7 #2 --- Chain | Description A B | factor XIII activation peptide (28-37) H K | α-thrombin (heavy chain) J L | α-thrombin (light chain) Non-standard residues in 1de7 #2 --- 0QE — chloromethane (Chloro Methyl group) NA — sodium ion 1de7 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select #2/H#2/K 4456 atoms, 4139 bonds, 14 pseudobonds, 3 models selected > hide (#!2 & sel) target a > select #2/J#2/L 491 atoms, 452 bonds, 1 model selected > hide sel target a > select #2/A#2/B 167 atoms, 154 bonds, 1 model selected > sequence chain #2/A#2/B Alignment identifier is 1 > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > sequence chain #2/A#2/B Alignment identifier is 1 > close session > open 1de7 format mmcif fromDatabase pdb Summary of feedback from opening 1de7 fetched from pdb --- warnings | Expected gap or linking atom in AR7 /A:37 for PRO /A:36 Expected gap or connection between AR7 /A:37 and 0QE /A:38 Expected gap or linking atom in AR7 /B:37 for PRO /B:36 Expected gap or connection between AR7 /B:37 and 0QE /B:38 1de7 title: Interaction of factor XIII activation peptide with α-thrombin: crystal structure of the enzyme-substrate complex [more info...] Chain information for 1de7 #1 --- Chain | Description A B | factor XIII activation peptide (28-37) H K | α-thrombin (heavy chain) J L | α-thrombin (light chain) Non-standard residues in 1de7 #1 --- 0QE — chloromethane (Chloro Methyl group) NA — sodium ion 1de7 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select /H:16-244 2014 atoms, 2068 bonds, 1 pseudobond, 2 models selected > hide (#!1 & sel) target a > select /H:16-244 2014 atoms, 2068 bonds, 1 pseudobond, 2 models selected > select /K:16-246 2017 atoms, 2071 bonds, 1 pseudobond, 2 models selected > hide (#!1 & sel) target a > select /A:28-38 77 atoms, 77 bonds, 1 model selected > cartoon sel > close session > open 1de7 format mmcif fromDatabase pdb Summary of feedback from opening 1de7 fetched from pdb --- warnings | Expected gap or linking atom in AR7 /A:37 for PRO /A:36 Expected gap or connection between AR7 /A:37 and 0QE /A:38 Expected gap or linking atom in AR7 /B:37 for PRO /B:36 Expected gap or connection between AR7 /B:37 and 0QE /B:38 1de7 title: Interaction of factor XIII activation peptide with α-thrombin: crystal structure of the enzyme-substrate complex [more info...] Chain information for 1de7 #1 --- Chain | Description A B | factor XIII activation peptide (28-37) H K | α-thrombin (heavy chain) J L | α-thrombin (light chain) Non-standard residues in 1de7 #1 --- 0QE — chloromethane (Chloro Methyl group) NA — sodium ion 1de7 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > close session > open 1bl2 Summary of feedback from opening 1bl2 fetched from pdb --- warnings | PDB entry 1BL2 has been replaced by 1QRK Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""GLY"" near line 925 Invalid residue range for struct_conf ""HELX_P1"": invalid entity ""1"", near line 546 Invalid residue range for struct_conf ""HELX_P2"": invalid entity ""1"", near line 547 Invalid residue range for struct_conf ""HELX_P3"": invalid entity ""1"", near line 548 Invalid residue range for struct_conf ""HELX_P4"": invalid entity ""1"", near line 549 Invalid residue range for struct_conf ""HELX_P5"": invalid entity ""1"", near line 550 23 messages similar to the above omitted Invalid sheet range for struct_sheet_range ""A 1"": invalid entity ""1"", near line 679 Invalid sheet range for struct_sheet_range ""A 2"": invalid entity ""1"", near line 680 Invalid sheet range for struct_sheet_range ""A 3"": invalid entity ""1"", near line 681 Invalid sheet range for struct_sheet_range ""B 1"": invalid entity ""1"", near line 682 Invalid sheet range for struct_sheet_range ""B 2"": invalid entity ""1"", near line 683 65 messages similar to the above omitted note | Fetching compressed mmCIF 1bl2 from http://files.rcsb.org/download/1bl2.cif 1bl2 title: Human factor XIII with strontium bound In the ion site [more info...] Non-standard residues in 1bl2 #1 --- SR — strontium ion > cartoon > close session > open C:\Users\alfon\Escritorio\FXIII\PDB\1GGT.pdb format pdb 1GGT.pdb title: Three-dimensional structure of A transglutaminase: human blood coagulation factor XIII [more info...] Chain information for 1GGT.pdb #1 --- Chain | Description A B | coagulation factor XIII > open 1qrk format mmcif fromDatabase pdb 1qrk title: Human factor XIII with strontium bound In the ion site [more info...] Chain information for 1qrk #2 --- Chain | Description A B | protein (coagulation factor XIII) Non-standard residues in 1qrk #2 --- SR — strontium ion > open 1ggY format mmcif fromDatabase pdb 1ggy title: Human factor XIII with ytterbium bound In the ion site [more info...] Chain information for 1ggy #3 --- Chain | Description A B | protein (coagulation factor XIII) Non-standard residues in 1ggy #3 --- YB — ytterbium (III) ion > hide #!1 models > show #!1 models > close > open 1ggu Summary of feedback from opening 1ggu fetched from pdb --- notes | Fetching compressed mmCIF 1ggu from http://files.rcsb.org/download/1ggu.cif Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif 1ggu title: Human factor XIII with calcium bound In the ion site [more info...] Chain information for 1ggu #1 --- Chain | Description A B | protein (coagulation factor XIII) Non-standard residues in 1ggu #1 --- CA — calcium ion > open 1ggY format mmcif fromDatabase pdb 1ggy title: Human factor XIII with ytterbium bound In the ion site [more info...] Chain information for 1ggy #2 --- Chain | Description A B | protein (coagulation factor XIII) Non-standard residues in 1ggy #2 --- YB — ytterbium (III) ion > open 1qrk format mmcif fromDatabase pdb 1qrk title: Human factor XIII with strontium bound In the ion site [more info...] Chain information for 1qrk #3 --- Chain | Description A B | protein (coagulation factor XIII) Non-standard residues in 1qrk #3 --- SR — strontium ion > mmaker #3 , #2 to #1 showalignment true > matchmaker #3 , #2 to #1 showalignment true Expected a keyword > mmaker #3 , #2 to #1 showAlignment true > matchmaker #3 , #2 to #1 showAlignment true Expected a keyword > mmaker #3 and #2 to #1 showAlignment true > matchmaker #3 and #2 to #1 showAlignment true Expected a keyword > mmaker #2-3 to #1 showAlignment true 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 1ggu, chain A (#1) with 1ggy, chain A (#2), sequence alignment score = 3695.4 Alignment identifier is 1 RMSD between 698 pruned atom pairs is 0.568 angstroms; (across all 701 pairs: 0.645) Matchmaker 1ggu, chain B (#1) with 1qrk, chain B (#3), sequence alignment score = 3685.2 Alignment identifier is 2 RMSD between 700 pruned atom pairs is 0.646 angstroms; (across all 704 pairs: 0.666) > surface > surface hidePatches > select sequence 314 Nothing selected > select #1/A:309 #2/A:309 14 atoms, 12 bonds, 2 models selected > select #1/A:314 #2/A:314 12 atoms, 10 bonds, 2 models selected > select #1/A:314 #2/A:314 12 atoms, 10 bonds, 2 models selected > select #1/A:313 #2/A:313 18 atoms, 16 bonds, 2 models selected Seqview [ID: 1] region Consensus [314] + 1 other block RMSD: 0.275 Seqview [ID: 1] region Consensus [314] + 2 other blocks RMSD: 0.275 Seqview [ID: 1] region Consensus [314] + 2 other blocks RMSD: 0.275 Seqview [ID: 1] region Consensus [314] + 3 other blocks RMSD: 0.245 Seqview [ID: 1] region Consensus [314] + 3 other blocks RMSD: 0.245 > select #1/A:396 #2/A:396 16 atoms, 14 bonds, 2 models selected > select #1/A:396 #2/A:396 16 atoms, 14 bonds, 2 models selected Seqview [ID: 1] region Consensus [314] + 4 other blocks RMSD: 0.245 Seqview [ID: 1] region Consensus [314] + 5 other blocks RMSD: 0.246 > color (#!1-2 & sel) magenta > show (#!1-2 & sel) target ab Seqview [ID: 2] region Consensus..1qrk, chain B [314] RMSD: 0.371 Seqview [ID: 2] region Consensus..1qrk, chain B [314] + 1 other block RMSD: 0.358 Seqview [ID: 2] region Consensus..1qrk, chain B [314] + 2 other blocks RMSD: 0.463 > color (#!1,3 & sel) red > show (#!1,3 & sel) target ab > save ""C:/Users/alfon/Escritorio/FXIII/PDB/FXII zymogen.calcium bidn and > yther bind..cxs"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 590, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 292, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 208, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' TypeError: __init__() missing 1 required positional argument: 'refresh_callback' File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\ui\gui.py"", line 1541, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\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 ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 113, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 48, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 79, in provider_save mgr).save(session, path, **provider_kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 590, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 292, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 208, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' TypeError: __init__() missing 1 required positional argument: 'refresh_callback' File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) See log for complete Python traceback. > save ""C:/Users/alfon/Escritorio/FXIII/PDB/FXII 1.cxs"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 590, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 292, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 208, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' TypeError: __init__() missing 1 required positional argument: 'refresh_callback' File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\ui\gui.py"", line 1541, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\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 ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 113, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 48, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 79, in provider_save mgr).save(session, path, **provider_kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 590, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 292, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 208, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' TypeError: __init__() missing 1 required positional argument: 'refresh_callback' File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) See log for complete Python traceback. > select #2 11569 atoms, 11562 bonds, 23 pseudobonds, 3 models selected > ~select #2 2 models selected > save C:/Users/alfon/Escritorio/FXIII/PDB/fxii.cxs Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 590, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 292, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 208, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' TypeError: __init__() missing 1 required positional argument: 'refresh_callback' File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\ui\gui.py"", line 1541, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\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 ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 113, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 48, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 79, in provider_save mgr).save(session, path, **provider_kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 590, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\session.py"", line 292, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 208, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 193, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 202, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' TypeError: __init__() missing 1 required positional argument: 'refresh_callback' File ""C:\Program Files\ChimeraX 1.0rc202005292300\bin\lib\site- packages\chimerax\core\state.py"", line 203, in _copy return data.__class__(items) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 445.87 OpenGL renderer: GeForce 940M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: HP Model: HP ENVY Notebook OS: Microsoft Windows 10 Home Single Language (Build 18363) Memory: 12,733,808,640 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Sessions fixed Eric Pettersen all ChimeraX