id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3292 "Circular dependency saving surface (""shape icosahedron""?)" chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.3.0-51-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-05-09) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0rc202005091901 (2020-05-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/mpillana/ad5_2019.pdb format pdb Chain information for ad5_2019.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F I | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O P | No description available Q | No description available R | No description available S | No description available T | No description available U V | No description available W | No description available X | No description available Y Z | No description available > split #1 Chain information for ad5_2019.pdb A #1.1 --- Chain | Description A | No description available Chain information for ad5_2019.pdb B #1.2 --- Chain | Description B | No description available Chain information for ad5_2019.pdb C #1.3 --- Chain | Description C | No description available Chain information for ad5_2019.pdb D #1.4 --- Chain | Description D | No description available Chain information for ad5_2019.pdb E #1.5 --- Chain | Description E | No description available Chain information for ad5_2019.pdb F #1.6 --- Chain | Description F | No description available Chain information for ad5_2019.pdb G #1.7 --- Chain | Description G | No description available Chain information for ad5_2019.pdb H #1.8 --- Chain | Description H | No description available Chain information for ad5_2019.pdb I #1.9 --- Chain | Description I | No description available Chain information for ad5_2019.pdb J #1.10 --- Chain | Description J | No description available Chain information for ad5_2019.pdb K #1.11 --- Chain | Description K | No description available Chain information for ad5_2019.pdb L #1.12 --- Chain | Description L | No description available Chain information for ad5_2019.pdb M #1.13 --- Chain | Description M | No description available Chain information for ad5_2019.pdb N #1.14 --- Chain | Description N | No description available Chain information for ad5_2019.pdb O #1.15 --- Chain | Description O | No description available Chain information for ad5_2019.pdb P #1.16 --- Chain | Description P | No description available Chain information for ad5_2019.pdb Q #1.17 --- Chain | Description Q | No description available Chain information for ad5_2019.pdb R #1.18 --- Chain | Description R | No description available Chain information for ad5_2019.pdb S #1.19 --- Chain | Description S | No description available Chain information for ad5_2019.pdb T #1.20 --- Chain | Description T | No description available Chain information for ad5_2019.pdb U #1.21 --- Chain | Description U | No description available Chain information for ad5_2019.pdb V #1.22 --- Chain | Description V | No description available Chain information for ad5_2019.pdb W #1.23 --- Chain | Description W | No description available Chain information for ad5_2019.pdb X #1.24 --- Chain | Description X | No description available Chain information for ad5_2019.pdb Y #1.25 --- Chain | Description Y | No description available Chain information for ad5_2019.pdb Z #1.26 --- Chain | Description Z | No description available Split ad5_2019.pdb (#1) into 26 models > lighting simple > close #1.21-23,25-26#1.1-16,24 > select #1.19 647 atoms, 653 bonds, 2 pseudobonds, 2 models selected > color (#!1.19 & sel) cyan > select #1.17 874 atoms, 884 bonds, 2 pseudobonds, 2 models selected > color (#!1.17 & sel) magenta > select #1.18 698 atoms, 706 bonds, 2 pseudobonds, 2 models selected > color (#!1.18 & sel) hot pink > select #1.20 663 atoms, 669 bonds, 2 pseudobonds, 2 models selected > color (#!1.20 & sel) purple > select clear > sym #1 I,222r > show surfaces > select #1.17.2 874 atoms, 1 model selected > color (#!1.17 & sel) magenta > select #1.18.2 698 atoms, 1 model selected > color (#!1.18 & sel) hot pink > select #1.19.2 647 atoms, 1 model selected > color (#!1.19 & sel) cyan > select #1.20.2 663 atoms, 1 model selected > color (#!1.20 & sel) purple > select clear > view orient > shape icosahedron radius 450 orientation 222r mesh true divisions 2 > view orient > toolshed show ""Side View"" > graphics silhouettes true > set bgColor white > lighting shadows true > lighting shadows false > lighting full > lighting full > lighting simple > lighting simple > distance style radius 0.11 > distance style radius 0.12 > distance style radius 0.11 > distance style radius 0.1 Alignment identifier is 1.17.Q Alignment identifier is 1.18.R Alignment identifier is 1.19.S Alignment identifier is 1.20.T > cartoon style #1.17.1 with 10 Expected a keyword > cartoon style #1.17.1 widh 10 Expected a keyword > cartoon style #1.17.1 size 10 Expected a keyword > size #1.17.1 pseudobondRadius 10 Changed 2 pseudobond radii > size #1.17.1 pseudobondRadius 1 Changed 2 pseudobond radii > size #1.18.1 pseudobondRadius 1 Changed 2 pseudobond radii > size #1.19.1 pseudobondRadius 1 Changed 2 pseudobond radii > size #1.20.1 pseudobondRadius 1 Changed 2 pseudobond radii > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting shadows true > lighting shadows false > view name facet > save /home/mpillana/AD41_MARZO_2020/IX/vijey/ad5.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 817, 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 571, in save for name, data in mgr.walk(): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 300, in walk key = next(odg) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 69, in order_dag yield from _postorder_traversal(path, d, node) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1> from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>] chimerax.core.order_dag.OrderDAGError: cycle detected, reached from ['models', , , ] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1543, 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 106, 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 117, 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 2849, 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 2849, 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 817, 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 571, in save for name, data in mgr.walk(): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 300, in walk key = next(odg) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 69, in order_dag yield from _postorder_traversal(path, d, node) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1> from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>] chimerax.core.order_dag.OrderDAGError: cycle detected, reached from ['models', , , ] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) See log for complete Python traceback. > open /home/mpillana/AD41_MARZO_2020/IX/badv3_ix_fit.pdb Chain information for badv3_ix_fit.pdb #3 --- Chain | Description K N O P R U | No description available > close #3 > open /home/mpillana/AD41_MARZO_2020/IX/all_IX_badv3_facet.pdb Chain information for all_IX_badv3_facet.pdb #3 --- Chain | Description A B C D E F G H I J K L M N O P Q R S T U | No description available > split #2 > split #3 Chain information for all_IX_badv3_facet.pdb A #3.1 --- Chain | Description A | No description available Chain information for all_IX_badv3_facet.pdb B #3.2 --- Chain | Description B | No description available Chain information for all_IX_badv3_facet.pdb C #3.3 --- Chain | Description C | No description available Chain information for all_IX_badv3_facet.pdb D #3.4 --- Chain | Description D | No description available Chain information for all_IX_badv3_facet.pdb E #3.5 --- Chain | Description E | No description available Chain information for all_IX_badv3_facet.pdb F #3.6 --- Chain | Description F | No description available Chain information for all_IX_badv3_facet.pdb G #3.7 --- Chain | Description G | No description available Chain information for all_IX_badv3_facet.pdb H #3.8 --- Chain | Description H | No description available Chain information for all_IX_badv3_facet.pdb I #3.9 --- Chain | Description I | No description available Chain information for all_IX_badv3_facet.pdb J #3.10 --- Chain | Description J | No description available Chain information for all_IX_badv3_facet.pdb K #3.11 --- Chain | Description K | No description available Chain information for all_IX_badv3_facet.pdb L #3.12 --- Chain | Description L | No description available Chain information for all_IX_badv3_facet.pdb M #3.13 --- Chain | Description M | No description available Chain information for all_IX_badv3_facet.pdb N #3.14 --- Chain | Description N | No description available Chain information for all_IX_badv3_facet.pdb O #3.15 --- Chain | Description O | No description available Chain information for all_IX_badv3_facet.pdb P #3.16 --- Chain | Description P | No description available Chain information for all_IX_badv3_facet.pdb Q #3.17 --- Chain | Description Q | No description available Chain information for all_IX_badv3_facet.pdb R #3.18 --- Chain | Description R | No description available Chain information for all_IX_badv3_facet.pdb S #3.19 --- Chain | Description S | No description available Chain information for all_IX_badv3_facet.pdb T #3.20 --- Chain | Description T | No description available Chain information for all_IX_badv3_facet.pdb U #3.21 --- Chain | Description U | No description available Split all_IX_badv3_facet.pdb (#3) into 21 models > hide #!1 models > hide #3.1 models > show #3.1 models > hide #3.2 models > hide #3.3 models > show #3.3 models > hide #3.3 models > hide #3.4 models > hide #3.5 models > hide #3.6 models > hide #3.7 models > hide #3.8 models > hide #3.9 models > hide #3.10 models > hide #3.11 models > hide #3.12 models > hide #3.13 models > hide #3.14 models > show #3.14 models > hide #3.15 models > show #3.15 models > hide #3.15 models > hide #3.16 models > show #3.16 models > hide #3.16 models > hide #3.17 models > show #3.17 models > hide #3.18 models > show #3.18 models > hide #3.19 models > hide #3.20 models > hide #3.21 models > show #3.21 models > close #3.2-13,15-16,19-20 > show #!1 models > hide #3.21 models > show #3.21 models > hide #3.17 models > show #3.17 models > hide #3.14 models > show #3.14 models > hide #3.1 models > close #3.1 > hide #3.14 models > show #3.14 models > hide #3.17 models > show #3.17 models > select #3.17 826 atoms, 838 bonds, 1 model selected > color sel cyan > select #3.14 826 atoms, 838 bonds, 1 model selected > color sel purple > select #3.17 826 atoms, 838 bonds, 1 model selected > ~select #3.17 Nothing selected > select #3.18 826 atoms, 838 bonds, 1 model selected > color sel magenta > select #3.21 826 atoms, 838 bonds, 1 model selected > color sel hot pink > select clear > sym #3 I,222r > select #3 3304 atoms, 3352 bonds, 5 models selected > show sel surfaces > hide #!1 models > show sel atoms > show sel atoms > select #3 3304 atoms, 3352 bonds, 9 models selected > select #3.14 826 atoms, 838 bonds, 2 models selected > select #3.17 826 atoms, 838 bonds, 2 models selected > ~select #3.17 1 model selected > select #3.14 826 atoms, 838 bonds, 2 models selected > color (#!3.14 & sel) purple > select #3.17.1 826 atoms, 1 model selected > color (#!3.17 & sel) cyan > select #3.18.1 826 atoms, 1 model selected > color (#!3.18 & sel) hot pink > select #3.21.1 826 atoms, 1 model selected > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select #3.21.2 1 model selected > color #3.21.2 hot pink > select #3.21.1 826 atoms, 1 model selected > color (#!3.21 & sel) hot pink > select #3.18.1 826 atoms, 1 model selected > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > color (#!3.18 & sel) magenta > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > view orient > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > open /home/mpillana/AD41_MARZO_2020/D_1292106460_model_P1V44.cif Summary of feedback from opening /home/mpillana/AD41_MARZO_2020/D_1292106460_model_P1V44.cif --- warning | Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for D_1292106460_model_P1V44.cif #4 --- Chain | Description A | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 B | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 C J | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 D I | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 E | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 F G | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 H | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 K | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 L | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41 M | Q9QAH8_ADE41 Penton protein OS=Human adenovirus F serotype 41 N | Q67716_ADE41 Pre-hexon-linking protein IIIa OS=Human adenovirus F serotype 41 O P | B5SNS9_ADE41 Pre-hexon-linking protein VIII OS=Human adenovirus F serotype 41 Q R S T | B5SNR3_ADE41 Hexon-interlacing protein OS=Human adenovirus F serotype 41 U V Y u | B5SNS4_ADE41 Pre-protein VI OS=Human adenovirus F serotype 41 W | B5SNS1_ADE41 Pre-histone-like nucleoprotein OS=Human adenovirus F serotype 41 w | B5SNS1_ADE41 Pre-histone-like nucleoprotein OS=Human adenovirus F serotype 41 > lighting simple > graphics silhouettes false > lighting shadows true > lighting shadows false > split #4 Chain information for D_1292106460_model_P1V44.cif A #4.1 --- Chain | Description A | No description available Chain information for D_1292106460_model_P1V44.cif B #4.2 --- Chain | Description B | No description available Chain information for D_1292106460_model_P1V44.cif C #4.3 --- Chain | Description C | No description available Chain information for D_1292106460_model_P1V44.cif D #4.4 --- Chain | Description D | No description available Chain information for D_1292106460_model_P1V44.cif E #4.5 --- Chain | Description E | No description available Chain information for D_1292106460_model_P1V44.cif F #4.6 --- Chain | Description F | No description available Chain information for D_1292106460_model_P1V44.cif G #4.7 --- Chain | Description G | No description available Chain information for D_1292106460_model_P1V44.cif H #4.8 --- Chain | Description H | No description available Chain information for D_1292106460_model_P1V44.cif I #4.9 --- Chain | Description I | No description available Chain information for D_1292106460_model_P1V44.cif J #4.10 --- Chain | Description J | No description available Chain information for D_1292106460_model_P1V44.cif K #4.11 --- Chain | Description K | No description available Chain information for D_1292106460_model_P1V44.cif L #4.12 --- Chain | Description L | No description available Chain information for D_1292106460_model_P1V44.cif M #4.13 --- Chain | Description M | No description available Chain information for D_1292106460_model_P1V44.cif N #4.14 --- Chain | Description N | No description available Chain information for D_1292106460_model_P1V44.cif O #4.15 --- Chain | Description O | No description available Chain information for D_1292106460_model_P1V44.cif P #4.16 --- Chain | Description P | No description available Chain information for D_1292106460_model_P1V44.cif Q #4.17 --- Chain | Description Q | No description available Chain information for D_1292106460_model_P1V44.cif R #4.18 --- Chain | Description R | No description available Chain information for D_1292106460_model_P1V44.cif S #4.19 --- Chain | Description S | No description available Chain information for D_1292106460_model_P1V44.cif T #4.20 --- Chain | Description T | No description available Chain information for D_1292106460_model_P1V44.cif U #4.21 --- Chain | Description U | No description available Chain information for D_1292106460_model_P1V44.cif V #4.22 --- Chain | Description V | No description available Chain information for D_1292106460_model_P1V44.cif W #4.23 --- Chain | Description W | No description available Chain information for D_1292106460_model_P1V44.cif Y #4.24 --- Chain | Description Y | No description available Chain information for D_1292106460_model_P1V44.cif u #4.25 --- Chain | Description u | No description available Chain information for D_1292106460_model_P1V44.cif w #4.26 --- Chain | Description w | No description available Split D_1292106460_model_P1V44.cif (#4) into 26 models > close #4.14,21-26#4.1-13,15-16 > hide #!1 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > select #4.20 365 atoms, 374 bonds, 1 model selected > color sel cyan > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select #4.17 365 atoms, 374 bonds, 1 model selected > color sel hot pink > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > color sel magenta > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select #4.18 365 atoms, 374 bonds, 1 model selected > color sel hot pink > select clear > sym #4 I,222r > hide #!3 models > show #4.17-20 surfaces > show #!3 models > hide #!3 models > select #4.17.1 365 atoms, 1 model selected > color (#!4.17 & sel) magenta > select #4.18.1 365 atoms, 1 model selected > color (#!4.18 & sel) hot pink > select #4.20.1 365 atoms, 1 model selected > color (#!4.20 & sel) cyan > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > select clear > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > show #!1 models > hide #!1 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > save /home/mpillana/AD41_MARZO_2020/IX/vijey/ix_vijey.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 817, 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 571, in save for name, data in mgr.walk(): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 300, in walk key = next(odg) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 69, in order_dag yield from _postorder_traversal(path, d, node) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1> from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>] chimerax.core.order_dag.OrderDAGError: cycle detected, reached from ['models', , , ] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1543, 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 106, 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 117, 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 2849, 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 2849, 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 817, 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 571, in save for name, data in mgr.walk(): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 300, in walk key = next(odg) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 69, in order_dag yield from _postorder_traversal(path, d, node) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1> from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>] chimerax.core.order_dag.OrderDAGError: cycle detected, reached from ['models', , , ] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.82 OpenGL renderer: GeForce MX130/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: HP Model: HP Pavilion Laptop 14-ce0xxx OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz Cache Size: 6144 KB Memory: total used free shared buff/cache available Mem: 15G 3.2G 10G 146M 1.8G 11G Swap: 2.0G 968M 1.1G Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07) Subsystem: Hewlett-Packard Company UHD Graphics 620 [103c:84ba] Kernel driver in use: i915 }}} " defect closed normal Sessions fixed Greg Couch all ChimeraX