Opened 4 years ago
Closed 4 years ago
#6329 closed defect (nonchimerax)
Saving command history: No space left on device
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Core | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open "/Users/tafegi16/Dropbox/OMPTA_Manuscript/Cryo-EM and NMR Structure and > Figures/Figure1 BAM_OMPTA/BAM_OMPTA_5LJO.cxs" Log from Thu Nov 11 15:38:00 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open "/Users/tafegi16/Desktop/Figure1 BAM_OMPTA/BAM.cxs" Log from Thu Nov 11 14:42:13 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/tafegi16/Dropbox/OMPTA_Manuscript/EM Structure/J950_BAM- > Pol8_real_space_refined-coot-13_D- > Peptide_real_space_refined_35_2_Loop1Update2021-05-05.pdb" Chain information for J950_BAM-Pol8_real_space_refined-coot-13_D- Peptide_real_space_refined_35_2_Loop1Update2021-05-05.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 | No description available > preset "overall look" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > preset cartoons/nucleotides ribbons/slabs Changed 24853 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > ui tool show "Show Sequence Viewer" > sequence chain /A Alignment identifier is 1/A > select /A:764-810 716 atoms, 728 bonds, 47 residues, 1 model selected > select /A:24-810 11921 atoms, 12067 bonds, 787 residues, 1 model selected > color sel blue > select clear > ui tool show "Show Sequence Viewer" > sequence chain /F Alignment identifier is 1/F > select /F:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select /F:1-12 97 atoms, 100 bonds, 12 residues, 1 model selected > show sel target ab > color sel orange > ui tool show "Color Actions" > color sel crimson > color sel orange red > color sel tomato > color sel dark salmon > color sel salmon > color sel sandy brown > color sel red > color sel orange red > color sel coral > select clear > select clear > select /F:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select /F:1-12 97 atoms, 100 bonds, 12 residues, 1 model selected > surface sel > ui tool show "Color Actions" > color sel light salmon > color sel salmon > color sel crimson > color sel coral > undo > undo > undo > undo > undo > undo > undo > undo > select /F:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select /F:1-12 97 atoms, 100 bonds, 12 residues, 1 model selected > surface hidePatches (#!1 & sel) > ui tool show "Color Actions" > color sel orange red > color sel sandy brown > color sel goldenrod > color sel salmon > color sel coral > color sel light salmon > color sel sandy brown > color sel crimson > color sel coral > select clear > select clear > select clear > surface > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting soft > select /A:810 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:24-810 11921 atoms, 12067 bonds, 787 residues, 1 model selected > color (#!1 & sel) blue > select clear > undo > color (#!1 & sel) medium blue > ui tool show "Color Actions" > color sel royal blue > select clear > save "/Users/tafegi16/Desktop/Figure1 BAM_OMPTA/001.jpg" width 1700 height > 1096 supersample 3 > surface hidePatches > select /A:810 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:24-810 11921 atoms, 12067 bonds, 787 residues, 1 model selected > ui tool show "Color Actions" > color sel royal blue > color sel royal blue > color sel royal blue > color sel royal blue > select clear > select /F:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select /F:1-12 97 atoms, 100 bonds, 12 residues, 1 model selected > color (#!1 & sel) byhetero > select clear > save "/Users/tafegi16/Desktop/Figure1 BAM_OMPTA/BAM_OMPTA_Fig1_Nature.pdb" > relModel #1 > open "/Users/tafegi16/Desktop/Figure1 BAM_OMPTA/BAM_OMPTA_Fig1_Nature.pdb" Chain information for BAM_OMPTA_Fig1_Nature.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available > undo > close #2 > select clear > save "/Users/tafegi16/Desktop/Figure1 BAM_OMPTA/BAM_OMPTA_Fig1_Nature.pdb" > open "/Users/tafegi16/Desktop/Figure1 BAM_OMPTA/BAM_OMPTA_Fig1_Nature.pdb" Chain information for BAM_OMPTA_Fig1_Nature.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available > close #2 > save "/Users/tafegi16/Desktop/Figure1 BAM_OMPTA/BAM.cxs" ——— End of log from Thu Nov 11 14:42:13 2021 ——— opened ChimeraX session > open "/Users/tafegi16/Dropbox/OMPTA_Manuscript/Cryo-EM Structure and > Figures/pdb files/5LJO-Iadanza et al 2016/5ljo.pdb" 5ljo.pdb title: E. Coli bam complex (bamabcde) by cryoem [more info...] Chain information for 5ljo.pdb #2 --- Chain | Description A | outer membrane protein assembly factor bama B | outer membrane protein assembly factor bamb C | outer membrane protein assembly factor bamc D | outer membrane protein assembly factor bamd E | outer membrane protein assembly factor bame > hide #!1 models > preset cartoons/nucleotides ribbons/slabs Changed 24947 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > ui tool show Matchmaker > matchmaker #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 J950_BAM-Pol8_real_space_refined-coot-13_D- Peptide_real_space_refined_35_2_Loop1Update2021-05-05.pdb, chain A (#1) with 5ljo.pdb, chain A (#2), sequence alignment score = 3831.5 RMSD between 641 pruned atom pairs is 1.187 angstroms; (across all 783 pairs: 1.823) > show #!1 models > ui tool show "Show Sequence Viewer" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:806 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/A:24-806 12102 atoms, 12245 bonds, 783 residues, 1 model selected > color sel yellow > color sel magenta > color sel dim gray > color sel red > select clear > select #2/A:762-806 708 atoms, 719 bonds, 45 residues, 1 model selected > select #2/A:24-806 12102 atoms, 12245 bonds, 783 residues, 1 model selected > ui tool show "Color Actions" > color sel gold > color sel coral > color sel spring green > color sel teal > color sel violet > color sel cyan > color sel dark green > color sel chocolate > color sel dark red > color sel orange > color sel coral > select clear Drag select of 5 atoms, 6 bonds > delete atoms sel > delete bonds sel Drag select of 2 atoms, 1 bonds > delete atoms sel > delete bonds sel Drag select of 9 atoms, 9 bonds > delete atoms sel > delete bonds sel Drag select of 17 atoms, 17 bonds > delete atoms sel > delete bonds sel Drag select of 2 atoms > delete atoms sel > delete bonds sel > select clear > select #2/A:762-806 708 atoms, 719 bonds, 45 residues, 1 model selected > select #2/A:24-806 12102 atoms, 12245 bonds, 783 residues, 1 model selected > ui tool show "Color Actions" > color sel lime > color sel fire brick > color sel royal blue > color sel turquoise > color sel dark blue > color sel light slate gray > color sel slate gray > select clear > ui tool show "Show Sequence Viewer" > sequence chain #1/F Alignment identifier is 1/F > select #1/F:5-12 65 atoms, 66 bonds, 8 residues, 1 model selected > show (#!1 & sel) target ab > select #1/F:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/F:1-12 97 atoms, 100 bonds, 12 residues, 1 model selected > show (#!1 & sel) target ab > ui tool show "Color Actions" > ui tool show "Color Actions" > color sel coral Drag select of 3 atoms, 4 bonds > color sel coral Drag select of 1 atoms, 1 bonds > color sel coral > select #1/F:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/F:1-12 97 atoms, 100 bonds, 12 residues, 1 model selected > color (#!1 & sel) byhetero Drag select of 4 atoms, 3 bonds > color (#!1 & sel) byhetero > select #1/F:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/F:1-12 97 atoms, 100 bonds, 12 residues, 1 model selected > surface (#!1 & sel) > color sel coral > select clear Drag select of J950_BAM-Pol8_real_space_refined-coot-13_D- Peptide_real_space_refined_35_2_Loop1Update2021-05-05.pdb_F SES surface, 682 of 18822 triangles, 4 atoms, 3 bonds > surface (#!1 & sel) > undo > undo > undo > hide #1.6 models > show #1.6 models > select #1.6 1356 atoms, 88 residues, 1 model selected > ~select #1.6 1 model selected > select #1.1 97 atoms, 12 residues, 1 model selected > ~select #1.1 1 model selected > select #1 24859 atoms, 25138 bonds, 1641 residues, 1 model selected > ~select #1 6 models selected > hide #1.1 models > hide #1.2 models > hide #1.3 models > hide #1.4 models > hide #1.5 models > show #1.5 models > show #1.4 models > show #1.3 models > show #1.2 models > hide #1.2 models > show #1.1 models > show #1.2 models > undo > undo > undo > undo > undo > undo > undo > undo > undo > undo > select clear > ui tool show "Show Sequence Viewer" > sequence chain #1/F Alignment identifier is 1/F > select #1/F:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/F:1-12 97 atoms, 100 bonds, 12 residues, 1 model selected > surface (#!1 & sel) > select #1/F:2 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/F:2 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/F:1-2 13 atoms, 12 bonds, 2 residues, 1 model selected > select #1/F:1-2 13 atoms, 12 bonds, 2 residues, 1 model selected > select clear Drag select of 1 atoms Drag select of 1 atoms Drag select of 1 atoms, 1 bonds > surface sel > ui tool show "Color Actions" > color sel coral > select clear > select clear Drag select of J950_BAM-Pol8_real_space_refined-coot-13_D- Peptide_real_space_refined_35_2_Loop1Update2021-05-05.pdb_F SES surface, 11 of 356 triangles, 1 atoms > undo > undo > save "/Users/tafegi16/Desktop/Figure1 BAM_OMPTA/BAM_OMPTA_5LJO.cxs" ——— End of log from Thu Nov 11 15:38:00 2021 ——— opened ChimeraX session > hide #2 models > hide #1.1 models > show #1.1 models > hide #1.3 models > show #1.3 models > show #1.2 models > hide #1.2 models > ui tool show "Show Sequence Viewer" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/B #2/B Alignment identifier is 1 > sequence chain #1/C #2/C Alignment identifier is 2 > sequence chain #1/D Alignment identifier is 1/D > sequence chain #1/E Alignment identifier is 1/E > sequence chain #1/F Destroying pre-existing alignment with identifier 1/F Alignment identifier is 1/F > select #1/A:810 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:24-810 11921 atoms, 12067 bonds, 787 residues, 1 model selected > surface (#!1 & sel) > select #1/B:22-23 #2/B:22-23 77 atoms, 77 bonds, 4 residues, 2 models selected > select #1/B:22-392 #2/B:22-392 11067 atoms, 11169 bonds, 742 residues, 2 models selected Seqview [ID: 1] region 2 chains [1-371] RMSD: 2.189 > color (#!1 & sel) purple > surface (#!1 & sel) > color (#!1 & sel) cornflower blue > ui tool show "Color Actions" > color sel royal blue > color sel royal blue > color sel orchid > color sel magenta > color sel orchid > color sel dark blue > color sel dark blue > color sel medium slate blue > select #1/C:189 #2/C:189 20 atoms, 18 bonds, 2 residues, 2 models selected > select #1/C:25-189 #2/C:25-189 4995 atoms, 5043 bonds, 330 residues, 2 models selected Seqview [ID: 2] region 2 chains [1-165] RMSD: 2.660 > surface (#!1 & sel) > ui tool show "Color Actions" > color sel blue > color sel cyan > color sel deep sky blue > select #1/D:242 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/D:26-242 3449 atoms, 3489 bonds, 217 residues, 1 model selected > color (#!1 & sel) cyan > surface (#!1 & sel) > select #1/B:348-392 #2/B:348-392 1382 atoms, 1392 bonds, 90 residues, 2 models selected > select #1/B:22-392 #2/B:22-392 11067 atoms, 11169 bonds, 742 residues, 2 models selected Seqview [ID: 1] region 2 chains [1-371] RMSD: 2.189 > ui tool show "Color Actions" > color sel deep sky blue > select #1/C:189 #2/C:189 20 atoms, 18 bonds, 2 residues, 2 models selected > select #1/C:25-189 #2/C:25-189 4995 atoms, 5043 bonds, 330 residues, 2 models selected Seqview [ID: 2] region 2 chains [1-165] RMSD: 2.660 > ui tool show "Color Actions" > color sel indigo > color sel pale violet red > color sel medium slate blue > select clear > lighting simple > lighting soft > lighting full > lighting simple > lighting soft > lighting full > lighting soft > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > select clear > save "/Users/tafegi16/Dropbox/OMPTA_Manuscript/Cryo-EM and NMR Structure and > Figures/Figure1 BAM_OMPTA/012.jpg" width 1646 height 1052 supersample 3 Traceback (most recent call last): File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb self.history_dialog.add(self._just_typed_command or cmd_text, File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/cmd_line/tool.py", line 406, in add self._history.enqueue((item, typed)) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 171, in enqueue self.save() File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 201, in save self._history.save(self._queue) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 108, in save with SaveTextFile(self._filename) as f: File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 174, in __init__ SaveFile.__init__(self, filename, open=open_text, critical=critical) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 74, in __init__ self._f = open(self._tmp_filename) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 173, in open_text return open(filename, 'w', newline=newline, encoding=encoding) OSError: [Errno 28] No space left on device: '/Users/tafegi16/Library/Application Support/ChimeraX/commands.68678.tmp' Error processing trigger "command started": OSError: [Errno 28] No space left on device: '/Users/tafegi16/Library/Application Support/ChimeraX/commands.68678.tmp' File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 173, in open_text return open(filename, 'w', newline=newline, encoding=encoding) See log for complete Python traceback. Traceback (most recent call last): File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 116, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog _dlg.display(session, **kw) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 51, in display run(session, cmd) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/image_formats/__init__.py", line 45, in save save_image(session, path, format_name, **kw) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/image_formats/save.py", line 123, in save_image i.save(path, format_name, **metadata) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/PIL/Image.py", line 2155, in save fp = builtins.open(filename, "w+b") OSError: [Errno 28] No space left on device: '/Users/tafegi16/Dropbox/OMPTA_Manuscript/Cryo-EM and NMR Structure and Figures/Figure1 BAM_OMPTA/012.jpg' OSError: [Errno 28] No space left on device: '/Users/tafegi16/Dropbox/OMPTA_Manuscript/Cryo-EM and NMR Structure and Figures/Figure1 BAM_OMPTA/012.jpg' File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/PIL/Image.py", line 2155, in save fp = builtins.open(filename, "w+b") See log for complete Python traceback. > save "/Users/tafegi16/Dropbox/OMPTA_Manuscript/Cryo-EM and NMR Structure and > Figures/Figure1 BAM_OMPTA/012.jpg" width 1546 height 988 supersample 3 Traceback (most recent call last): File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb self.history_dialog.add(self._just_typed_command or cmd_text, File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/cmd_line/tool.py", line 406, in add self._history.enqueue((item, typed)) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 171, in enqueue self.save() File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 201, in save self._history.save(self._queue) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 108, in save with SaveTextFile(self._filename) as f: File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 174, in __init__ SaveFile.__init__(self, filename, open=open_text, critical=critical) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 74, in __init__ self._f = open(self._tmp_filename) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 173, in open_text return open(filename, 'w', newline=newline, encoding=encoding) OSError: [Errno 28] No space left on device: '/Users/tafegi16/Library/Application Support/ChimeraX/commands.68678.tmp' Error processing trigger "command started": OSError: [Errno 28] No space left on device: '/Users/tafegi16/Library/Application Support/ChimeraX/commands.68678.tmp' File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 173, in open_text return open(filename, 'w', newline=newline, encoding=encoding) See log for complete Python traceback. Traceback (most recent call last): File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 116, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog _dlg.display(session, **kw) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 51, in display run(session, cmd) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/image_formats/__init__.py", line 45, in save save_image(session, path, format_name, **kw) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/image_formats/save.py", line 123, in save_image i.save(path, format_name, **metadata) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/PIL/Image.py", line 2155, in save fp = builtins.open(filename, "w+b") OSError: [Errno 28] No space left on device: '/Users/tafegi16/Dropbox/OMPTA_Manuscript/Cryo-EM and NMR Structure and Figures/Figure1 BAM_OMPTA/012.jpg' OSError: [Errno 28] No space left on device: '/Users/tafegi16/Dropbox/OMPTA_Manuscript/Cryo-EM and NMR Structure and Figures/Figure1 BAM_OMPTA/012.jpg' File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/PIL/Image.py", line 2155, in save fp = builtins.open(filename, "w+b") See log for complete Python traceback. > save /Users/tafegi16/Desktop/012.jpg width 1646 height 1052 supersample 3 Traceback (most recent call last): File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb self.history_dialog.add(self._just_typed_command or cmd_text, File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/cmd_line/tool.py", line 406, in add self._history.enqueue((item, typed)) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 171, in enqueue self.save() File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 201, in save self._history.save(self._queue) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/history.py", line 108, in save with SaveTextFile(self._filename) as f: File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 174, in __init__ SaveFile.__init__(self, filename, open=open_text, critical=critical) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 74, in __init__ self._f = open(self._tmp_filename) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 173, in open_text return open(filename, 'w', newline=newline, encoding=encoding) OSError: [Errno 28] No space left on device: '/Users/tafegi16/Library/Application Support/ChimeraX/commands.68678.tmp' Error processing trigger "command started": OSError: [Errno 28] No space left on device: '/Users/tafegi16/Library/Application Support/ChimeraX/commands.68678.tmp' File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/safesave.py", line 173, in open_text return open(filename, 'w', newline=newline, encoding=encoding) See log for complete Python traceback. Traceback (most recent call last): File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 116, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog _dlg.display(session, **kw) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py", line 51, in display run(session, cmd) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/image_formats/__init__.py", line 45, in save save_image(session, path, format_name, **kw) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/image_formats/save.py", line 123, in save_image i.save(path, format_name, **metadata) File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/PIL/Image.py", line 2155, in save fp = builtins.open(filename, "w+b") OSError: [Errno 28] No space left on device: '/Users/tafegi16/Desktop/012.jpg' OSError: [Errno 28] No space left on device: '/Users/tafegi16/Desktop/012.jpg' File "/Users/tafegi16/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/PIL/Image.py", line 2155, in save fp = builtins.open(filename, "w+b") See log for complete Python traceback. OpenGL version: 4.1 ATI-3.10.22 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac19,2 Processor Name: 6-Core Intel Core i5 Processor Speed: 3 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Memory: 16 GB Boot ROM Version: 1554.140.20.0.0 SMC Version (system): 2.47f3 Software: System Software Overview: System Version: macOS 10.15.7 (19H1323) Kernel Version: Darwin 19.6.0 Time since boot: 22 days 2:56 Graphics/Displays: Radeon Pro 560X: Chipset Model: Radeon Pro 560X Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c2 ROM Revision: 113-C981AA-042 VBIOS Version: 113-C9819A1X-009 EFI Driver Version: 01.B1.042 Metal: Supported, feature set macOS GPUFamily2 v1 Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 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: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 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: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 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: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 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: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
Component: | Unassigned → Core |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Saving command history: No space left on device |
comment:2 by , 4 years ago
Resolution: | → nonchimerax |
---|---|
Status: | accepted → closed |
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