id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5042 os.getcwd() failure saving map irina.grishkovskaya@… Tom Goddard "{{{ 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 problem occur whille saving mrc file, no problem with the saving pdb Traceback (most recent call last): File ""/Applications/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 *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map/__init__.py"", line 164, in save save_map(session, path, _name, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map/volume.py"", line 3974, in save_map save_grid_data(grids, path, session, format_name, options) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map_data/fileformats.py"", line 297, in save_grid_data if matching_grid_path(glist, path): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map_data/fileformats.py"", line 340, in matching_grid_path if realpath(gp) == rp: File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 392, in realpath return abspath(path) File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() FileNotFoundError: [Errno 2] No such file or directory FileNotFoundError: [Errno 2] No such file or directory File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() See log for complete Python traceback. /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc models #2 Unknown command: /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc models #2 save /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc models #2Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/cmd_line/tool.py"", line 280, in execute cmd.run(cmd_text) File ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map/__init__.py"", line 164, in save save_map(session, path, _name, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map/volume.py"", line 3974, in save_map save_grid_data(grids, path, session, format_name, options) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map_data/fileformats.py"", line 297, in save_grid_data if matching_grid_path(glist, path): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map_data/fileformats.py"", line 340, in matching_grid_path if realpath(gp) == rp: File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 392, in realpath return abspath(path) File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() FileNotFoundError: [Errno 2] No such file or directory FileNotFoundError: [Errno 2] No such file or directory File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() See log for complete Python traceback. Log: UCSF 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/irina.grishkovskaya/Downloads/cryosparc_P144_J2263_002_volume_map.mrc Opened cryosparc_P144_J2263_002_volume_map.mrc as #1, grid size 480,480,480, pixel 1.38, shown at level 0.263, step 2, values float32 > volume #1 step 1 > volume #1 level 0.2015 > volume flip #1 axis z Opened cryosparc_P144_J2263_002_volume_map.mrc z flip as #2, grid size 480,480,480, pixel 1.38, shown at step 1, values float32 > volume #1 level 0.1625 > volume #1 level 0.2841 > volume #1 level 0.4057 > set bgColor white > save > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/cryosparc_P144_J2263_flip.mrc > models #2 Traceback (most recent call last): File ""/Applications/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 *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/__init__.py"", line 164, in save save_map(session, path, _name, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/volume.py"", line 3974, in save_map save_grid_data(grids, path, session, format_name, options) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 297, in save_grid_data if matching_grid_path(glist, path): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 340, in matching_grid_path if realpath(gp) == rp: File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 392, in realpath return abspath(path) File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() FileNotFoundError: [Errno 2] No such file or directory FileNotFoundError: [Errno 2] No such file or directory File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() See log for complete Python traceback. > open > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/deepEMhancer_results/210803_coordinates/2108046n8k_widetargetDEv1in- > coot-18.pdb Summary of feedback from opening /Users/irina.grishkovskaya/DRG1/Bud20/Krios/deepEMhancer_results/210803_coordinates/2108046n8k_widetargetDEv1in- coot-18.pdb --- warnings | End residue of secondary structure not found: HELIX 7 7 UNK s 170 UNK s 179 1 10 Start residue of secondary structure not found: HELIX 8 8 UNK s 181 UNK s 184 1 4 Start residue of secondary structure not found: HELIX 44 44 LEU b 358 LYS b 360 1 3 End residue of secondary structure not found: HELIX 117 117 GLU I 115 THR I 130 1 16 Start residue of secondary structure not found: HELIX 239 239 SER y 231 GLU y 242 1 12 Chain information for 2108046n8k_widetargetDEv1in-coot-18.pdb #3 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available 4 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available o | No description available p | No description available q | No description available r | No description available s | No description available u | No description available v | No description available y | No description available z | No description available > hide atoms > show cartoons > transparency 50 > volume #1 level 0.3133 > volume #1 level 0.01665 > volume #1 level 0.05 > volume #1 level 0.08 > volume #1 level 0.3426 > volume #1 level 0.5 > volume #1 level 0.7626 > open > /Users/irina.grishkovskaya/DRG1/refinement/RealSpaceRefine_107/DRG1_refine_105-coot-1_real_space_refined_107.pdb Chain information for DRG1_refine_105-coot-1_real_space_refined_107.pdb #4 --- 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 G | No description available > hide atoms > show cartoons > select #4 32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right translate > hide #!1 models > hide #!2 models > hide #!3 models > show #!1 models > show #!2 models > show #!3 models > select up 32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > select up 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected > ~select #1 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 5 models selected > ~select #2 176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 3 models selected > select #3 143936 atoms, 154325 bonds, 5 pseudobonds, 12045 residues, 2 models selected > ~select #3 Nothing selected > select #4 32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,293.9,0,1,0,303.38,0,0,1,237.15 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99339,-0.031618,-0.11034,314.43,-0.021212,0.89418,-0.44721,382.73,0.1128,0.4466,0.8876,175.02 > view matrix models > #4,-0.13699,0.61646,-0.77538,474.34,-0.82664,0.36015,0.43238,447.85,0.5458,0.70019,0.46025,138.37 > view matrix models > #4,-0.53811,0.8022,0.25866,361.91,-0.40768,-0.51631,0.75314,466.5,0.73772,0.29982,0.60487,147.08 > view matrix models > #4,-0.014725,-0.93197,-0.36223,614.8,-0.97396,-0.068592,0.21607,557.7,-0.22622,0.35598,-0.9067,482.6 > view matrix models > #4,0.44051,-0.55614,-0.70474,546.4,-0.16551,-0.82187,0.54511,503.72,-0.88236,-0.12348,-0.45409,578.24 > view matrix models > #4,0.68532,0.12183,-0.71798,420.08,0.66217,-0.51458,0.54473,345.56,-0.30309,-0.84874,-0.43333,594.95 > view matrix models > #4,0.99514,-0.073317,-0.06579,313.82,0.020067,-0.50299,0.86406,389.58,-0.096442,-0.86118,-0.49907,576.87 > view matrix models > #4,0.99478,-0.07468,-0.069557,314.57,0.022447,-0.50476,0.86297,389.65,-0.099556,-0.86002,-0.50045,577.34 > view matrix models > #4,0.88258,-0.20625,-0.42252,397.2,0.2146,-0.62287,0.75232,394.44,-0.41834,-0.75465,-0.50547,607.97 > view matrix models > #4,0.77877,-0.23223,-0.58274,437.42,0.34826,-0.6126,0.70954,380.25,-0.52176,-0.75551,-0.3962,607.45 > view matrix models > #4,0.97949,0.19468,-0.051991,276.96,0.1962,-0.98022,0.025863,546.8,-0.045927,-0.035533,-0.99831,524.31 > view matrix models > #4,0.98426,0.17645,-0.0096685,272.98,0.17671,-0.98279,0.05385,546.02,-3.9982e-07,-0.054711,-0.9985,520.58 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.98426,0.17645,-0.0096685,255.63,0.17671,-0.98279,0.05385,546.06,-3.9982e-07,-0.054711,-0.9985,515.55 > view matrix models > #4,0.98426,0.17645,-0.0096685,260.55,0.17671,-0.98279,0.05385,547.49,-3.9982e-07,-0.054711,-0.9985,518.03 > view matrix models > #4,0.99514,0.091382,0.036657,264.42,0.093376,-0.994,-0.056971,575.98,0.031231,0.060117,-0.9977,497.64 > ~select #4 Nothing selected > select #4 32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.95478,0.27638,0.10959,234.36,0.24497,-0.94018,0.23676,506.8,0.16846,-0.19921,-0.96537,509.94 > view matrix models > #4,0.99171,-0.042032,-0.12142,305.21,-0.056676,-0.99118,-0.11979,605.23,-0.11531,0.12568,-0.98535,507.32 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99171,-0.042032,-0.12142,304.59,-0.056676,-0.99118,-0.11979,605.01,-0.11531,0.12568,-0.98535,506.66 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99171,-0.042032,-0.12142,359.47,-0.056676,-0.99118,-0.11979,652.22,-0.11531,0.12568,-0.98535,516.95 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.96814,0.17115,-0.18278,341.69,0.21016,-0.95225,0.22147,562.45,-0.13615,-0.25283,-0.95788,568.52 > view matrix models > #4,0.89033,-0.44312,-0.10468,426.91,0.23927,0.65094,-0.72044,466.23,0.38738,0.61638,0.68557,148.09 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.89033,-0.44312,-0.10468,362.33,0.23927,0.65094,-0.72044,437.09,0.38738,0.61638,0.68557,152.87 > ui mousemode right translate > ~select #4 Nothing selected > ui tool show ""Volume Viewer"" > ui tool show ""Fit in Map"" Fit molecule 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) to map cryosparc_P144_J2263_002_volume_map.mrc (#1) using 143936 atoms average map value = 0.325, steps = 68 shifted from previous position = 1.08 rotated from previous position = 2.49 degrees atoms outside contour = 125881, contour level = 0.76261 Position of 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) relative to cryosparc_P144_J2263_002_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99919002 -0.01132363 0.03861454 -8.92170616 0.01195645 0.99979734 -0.01619664 0.75058976 -0.03842331 0.01664522 0.99912291 6.60465751 Axis 0.37783275 0.88629030 0.26782815 Axis point 173.27376536 0.00000000 225.51392121 Rotation angle (degrees) 2.49090756 Shift along axis -0.93675914 Fit molecule 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) to map cryosparc_P144_J2263_002_volume_map.mrc (#1) using 143936 atoms average map value = 0.325, steps = 40 shifted from previous position = 0.012 rotated from previous position = 0.00439 degrees atoms outside contour = 125874, contour level = 0.76261 Position of 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) relative to cryosparc_P144_J2263_002_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99919171 -0.01136655 0.03855810 -8.88665146 0.01199727 0.99979734 -0.01616587 0.73839814 -0.03836654 0.01661540 0.99912559 6.59176319 Axis 0.37757322 0.88601453 0.26910353 Axis point 173.18551761 0.00000000 225.02471942 Rotation angle (degrees) 2.48801927 Shift along axis -0.92726337 > select #4 32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models > #4,0.89033,-0.44312,-0.10468,376.2,0.23927,0.65094,-0.72044,426.44,0.38738,0.61638,0.68557,147.83 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.70858,-0.37826,0.59568,295.93,0.65079,0.023998,-0.75888,461.13,0.27276,0.92539,0.26317,179.33 > view matrix models > #4,0.96289,-0.22263,0.15255,300,0.22664,0.36015,-0.90495,493.96,0.14653,0.90594,0.39724,181.16 > view matrix models > #4,0.85579,-0.4859,0.17753,348,0.328,0.24427,-0.91255,496.91,0.40004,0.83919,0.36842,158.97 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.85579,-0.4859,0.17753,348.37,0.328,0.24427,-0.91255,499.36,0.40004,0.83919,0.36842,159.36 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.91478,-0.40278,0.03057,348.89,0.18994,0.36212,-0.91258,502.32,0.3565,0.84062,0.40776,159.81 > ~select #4 Nothing selected Fit molecule 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) to map cryosparc_P144_J2263_002_volume_map.mrc (#1) using 143936 atoms average map value = 0.325, steps = 44 shifted from previous position = 0.00964 rotated from previous position = 0.00246 degrees atoms outside contour = 125871, contour level = 0.76261 Position of 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) relative to cryosparc_P144_J2263_002_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99919166 -0.01133239 0.03856944 -8.90422619 0.01196423 0.99979734 -0.01619065 0.76624848 -0.03837814 0.01663901 0.99912475 6.58637871 Axis 0.37804109 0.88606903 0.26826594 Axis point 172.90904166 0.00000000 225.46553009 Rotation angle (degrees) 2.48860878 Shift along axis -0.92031319 > save > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/DRG1_fit_JJ2263_P144.pdb > models #4 relModel #2 > save > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc > models #2 Traceback (most recent call last): File ""/Applications/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 *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/__init__.py"", line 164, in save save_map(session, path, _name, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/volume.py"", line 3974, in save_map save_grid_data(grids, path, session, format_name, options) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 297, in save_grid_data if matching_grid_path(glist, path): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 340, in matching_grid_path if realpath(gp) == rp: File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 392, in realpath return abspath(path) File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() FileNotFoundError: [Errno 2] No such file or directory FileNotFoundError: [Errno 2] No such file or directory File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() See log for complete Python traceback. > > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc > models #2 Unknown command: /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc models #2 > save > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc > models #2 Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/cmd_line/tool.py"", line 280, in execute cmd.run(cmd_text) File ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/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 ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/__init__.py"", line 164, in save save_map(session, path, _name, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/volume.py"", line 3974, in save_map save_grid_data(grids, path, session, format_name, options) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 297, in save_grid_data if matching_grid_path(glist, path): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 340, in matching_grid_path if realpath(gp) == rp: File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 392, in realpath return abspath(path) File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() FileNotFoundError: [Errno 2] No such file or directory FileNotFoundError: [Errno 2] No such file or directory File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() See log for complete Python traceback. OpenGL version: 4.1 ATI-3.10.19 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2,9 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 429.60.3.0.0 SMC Version (system): 2.45f4 Software: System Software Overview: System Version: macOS 10.15.7 (19H114) Kernel Version: Darwin 19.6.0 Time since boot: 17:33 Graphics/Displays: Intel HD Graphics 630: Chipset Model: Intel HD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x591b Revision ID: 0x0004 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal: Supported, feature set macOS GPUFamily2 v1 Radeon Pro 560: Chipset Model: Radeon Pro 560 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c0 ROM Revision: 113-C980AJ-927 VBIOS Version: 113-C9801AU-A02 EFI Driver Version: 01.A0.927 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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 }}} " defect closed normal Input/Output fixed all ChimeraX