id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2646 Problem starting ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' jliu321@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-07-07) Description could not start isolde properly Log: UCSF ChimeraX version: 0.91 (2019-07-07) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_Clipper-0.9.12-cp37-cp37m-macosx_10_9_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/jingliu/Library/Caches/ChimeraX/0.91/installers/ChimeraX_Clipper-0.9.12-cp37-cp37m-macosx_10_9_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in ./ChimeraX_Daily.app/Contents/lib/python3.7/site-packages (from ChimeraX- Clipper==0.9.12) (0.91) Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in ./ChimeraX_Daily.app/Contents/lib/python3.7/site-packages (from ChimeraX- Clipper==0.9.12) (1.0) Installing collected packages: ChimeraX-Clipper Found existing installation: ChimeraX-Clipper 0.9.6 Uninstalling ChimeraX-Clipper-0.9.6: Successfully uninstalled ChimeraX-Clipper-0.9.6 Successfully installed ChimeraX-Clipper-0.9.12 Lock 4711808304 acquired on /Users/jingliu/Library/Caches/ChimeraX/0.91/toolshed/bundle_info.cache.lock Lock 4711808304 released on /Users/jingliu/Library/Caches/ChimeraX/0.91/toolshed/bundle_info.cache.lock WARNING: You are using pip version 19.1.1, however version 19.3.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. > open /Users/jingliu/Downloads/201905_TrimerR/TrimerR_cryosparc/J79_map_sharp.mrc Opened J79_map_sharp.mrc, grid size 288,288,288, pixel 1.06, shown at level 0.294, step 2, values float32 > open /Users/jingliu/Downloads/201905_TrimerR/Flex-EM_3-final1_mdcg.pdb Chain information for Flex-EM_3-final1_mdcg.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > select #2 10404 atoms, 10542 bonds, 1 model selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > fitmap #2 inMap #1 Fit molecule Flex-EM_3-final1_mdcg.pdb (#2) to map J79_map_sharp.mrc (#1) using 10404 atoms average map value = 0.3294, steps = 148 shifted from previous position = 2.16 rotated from previous position = 10.4 degrees atoms outside contour = 6845, contour level = 0.40487 Position of Flex-EM_3-final1_mdcg.pdb (#2) relative to J79_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.63935431 0.38701534 0.66441342 127.21921290 -0.74141190 -0.53932397 -0.39929694 392.21193157 0.20380005 -0.74789624 0.63175688 132.69206023 Axis -0.27498813 0.36334902 -0.89014551 Axis point 122.62525403 198.23226834 0.00000000 Rotation angle (degrees) 140.66568177 Shift along axis -10.58919568 > close #1 > open /Users/jingliu/Downloads/201905_TrimerR/TrimerR_cryosparc/J79_map_invert.mrc Opened J79_map_invert.mrc, grid size 288,288,288, pixel 1.06, shown at level 0.294, step 2, values float32 > fitmap #2 inMap #1 Fit molecule Flex-EM_3-final1_mdcg.pdb (#2) to map J79_map_invert.mrc (#1) using 10404 atoms average map value = 0.3547, steps = 248 shifted from previous position = 7.68 rotated from previous position = 16.9 degrees atoms outside contour = 5342, contour level = 0.29422 Position of Flex-EM_3-final1_mdcg.pdb (#2) relative to J79_map_invert.mrc (#1) coordinates: Matrix rotation and translation -0.82384580 0.35806220 0.43939681 185.83018374 -0.56281962 -0.60863324 -0.55928494 393.73434029 0.06717271 -0.70806570 0.70294438 140.06039822 Axis -0.14813703 0.37061361 -0.91689747 Axis point 139.96683500 198.10236491 0.00000000 Rotation angle (degrees) 149.85614840 Shift along axis -10.02605002 > show selAtoms ribbons > hide selAtoms > fitmap #2 inMap #1 Fit molecule Flex-EM_3-final1_mdcg.pdb (#2) to map J79_map_invert.mrc (#1) using 10404 atoms average map value = 0.4909, steps = 232 shifted from previous position = 4.81 rotated from previous position = 21.2 degrees atoms outside contour = 6313, contour level = 0.53563 Position of Flex-EM_3-final1_mdcg.pdb (#2) relative to J79_map_invert.mrc (#1) coordinates: Matrix rotation and translation -0.96241770 -0.04262670 0.26820725 274.54743410 -0.17232026 -0.66746840 -0.72442506 356.79112391 0.20989971 -0.74341704 0.63503796 133.05969707 Axis -0.13238488 0.40643646 -0.90403742 Axis point 134.71155451 202.88359978 0.00000000 Rotation angle (degrees) 175.88663008 Shift along axis -11.62395259 > addh Summary of feedback from adding hydrogens to Flex-EM_3-final1_mdcg.pdb #2 --- warning | Unknown hybridization for atoms (C7, C6, C8, O4, O5, O7, C5, C2, C3, O3, C4, C1, O6) of residue type NAG; not adding hydrogens to them notes | No usable SEQRES records for Flex-EM_3-final1_mdcg.pdb (#2) chain A; guessing termini instead No usable SEQRES records for Flex-EM_3-final1_mdcg.pdb (#2) chain B; guessing termini instead No usable SEQRES records for Flex-EM_3-final1_mdcg.pdb (#2) chain C; guessing termini instead No usable SEQRES records for Flex-EM_3-final1_mdcg.pdb (#2) chain D; guessing termini instead No usable SEQRES records for Flex-EM_3-final1_mdcg.pdb (#2) chain E; guessing termini instead Chain-initial residues that are actual N termini: /A GLU 190, /B PRO 37, /C GLN 1, /D LYS 289, /E LEU 40 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 287, /B GLN 273, /C SER 189, /D GLN 389, /E ALA 713 Chain-final residues that are not actual C termini: 676 hydrogen bonds 10265 hydrogens added > hide HC > clipper associate #1 toModel #2 Chain information for Flex-EM_3-final1_mdcg.pdb --- Chain | Description 1.1/A | No description available 1.1/B | No description available 1.1/C | No description available 1.1/D | No description available 1.1/E | No description available > toolshed show ISOLDE > set selectionWidth 4 Traceback (most recent call last): File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 627, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1511, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/__init__.py"", line 48, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/tools.py"", line 214, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/tool.py"", line 168, in __init__ self.isolde = isolde.Isolde(self) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 307, in __init__ self._start_gui(gui) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 444, in _start_gui self._populate_menus_and_update_params() File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 543, in _populate_menus_and_update_params self._update_model_list(None, None, force=True) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 945, in _update_model_list from chimerax.clipper.symmetry import Symmetry_Manager ImportError: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-packages/chimerax/clipper/symmetry.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 1135, in run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name))) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2646, in run result = ci.function(session, **kw_args) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py"", line 337, in toolshed_show bi.start_tool(session, tool_name) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 633, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 633, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) See log for complete Python traceback. 'ISOLDE_ToolUI' object has no attribute 'isolde' > toolshed show ISOLDE > set selectionWidth 4 Traceback (most recent call last): File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 627, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1511, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/__init__.py"", line 48, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/tools.py"", line 214, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/tool.py"", line 168, in __init__ self.isolde = isolde.Isolde(self) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 307, in __init__ self._start_gui(gui) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 444, in _start_gui self._populate_menus_and_update_params() File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 543, in _populate_menus_and_update_params self._update_model_list(None, None, force=True) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 945, in _update_model_list from chimerax.clipper.symmetry import Symmetry_Manager ImportError: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-packages/chimerax/clipper/symmetry.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 1135, in run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name))) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2646, in run result = ci.function(session, **kw_args) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py"", line 337, in toolshed_show bi.start_tool(session, tool_name) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 633, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 633, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) See log for complete Python traceback. > close #1.2 > close #1.3 > close #1 'ISOLDE_ToolUI' object has no attribute 'isolde' > open /Users/jingliu/Downloads/201905_TrimerR/Flex-EM_3-final1_mdcg.pdb Chain information for Flex-EM_3-final1_mdcg.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open /Users/jingliu/Downloads/201905_TrimerR/TrimerR_cryosparc/J79_map_invert.mrc Opened J79_map_invert.mrc, grid size 288,288,288, pixel 1.06, shown at level 0.294, step 2, values float32 > select #1 10404 atoms, 10542 bonds, 1 model selected > ui mousemode rightMode ""translate selected models"" > clip off > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > fitmap #1 inMap #2 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 172 shifted from previous position = 7.34 rotated from previous position = 10.4 degrees atoms outside contour = 6147, contour level = 0.39481 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96877689 -0.07999262 0.23467529 286.36454817 -0.10566120 -0.72306311 -0.68265319 347.76606845 0.22429228 -0.68613471 0.69203477 107.52044113 Axis -0.12475411 0.37205689 -0.91978806 Axis point 137.21696848 194.54555512 0.00000000 Rotation angle (degrees) 179.20049559 Shift along axis -5.23240954 > show selAtoms ribbons > show selAtoms > hide selAtoms > fitmap #1 inMap #2 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 40 shifted from previous position = 0.0158 rotated from previous position = 0.0114 degrees atoms outside contour = 6155, contour level = 0.39481 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96877792 -0.08017917 0.23460738 286.39268876 -0.10548675 -0.72304476 -0.68269960 347.75293525 0.22436994 -0.68613227 0.69201201 107.52086499 Axis -0.12475741 0.37207079 -0.91978199 Axis point 137.21208698 194.55515490 0.00000000 Rotation angle (degrees) 179.21173543 Shift along axis -5.23665543 > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > fitmap #1 inMap #2 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 128 shifted from previous position = 1.81 rotated from previous position = 8.2 degrees atoms outside contour = 6793, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96875604 -0.08013423 0.23471304 286.36818913 -0.10558795 -0.72306067 -0.68266711 347.76792677 0.22441679 -0.68612076 0.69200824 107.51494784 Axis -0.12479908 0.37205947 -0.91978092 Axis point 137.20540833 194.55473805 0.00000000 Rotation angle (degrees) 179.20718231 Shift along axis -5.23833234 > fitmap #1 inMap #2 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 28 shifted from previous position = 0.029 rotated from previous position = 0.035 degrees atoms outside contour = 6793, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96871876 -0.07962018 0.23504161 286.26261545 -0.10616689 -0.72311543 -0.68251930 347.82732893 0.22430454 -0.68612290 0.69204251 107.51152652 Axis -0.12485720 0.37201782 -0.91978988 Axis point 137.20621067 194.53538660 0.00000000 Rotation angle (degrees) 179.17314391 Shift along axis -5.23199526 > toolshed show ""Fit in Map"" Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 48 shifted from previous position = 0.00611 rotated from previous position = 0.027 degrees atoms outside contour = 6788, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96877034 -0.07995596 0.23471480 286.35317847 -0.10571277 -0.72307020 -0.68263770 347.76879859 0.22429625 -0.68613151 0.69203665 107.51410397 Axis -0.12476591 0.37205175 -0.91978854 Axis point 137.21559175 194.54164442 0.00000000 Rotation angle (degrees) 179.19774781 Shift along axis -5.22936672 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 44 shifted from previous position = 0.00501 rotated from previous position = 0.00539 degrees atoms outside contour = 6787, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96878397 -0.08001095 0.23463981 286.37303912 -0.10562455 -0.72305889 -0.68266334 347.75990715 0.22427896 -0.68613702 0.69203679 107.52111151 Axis -0.12474074 0.37205998 -0.91978863 Axis point 137.21908685 194.54506673 0.00000000 Rotation angle (degrees) 179.20220872 Shift along axis -5.23153835 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 40 shifted from previous position = 0.0169 rotated from previous position = 0.00944 degrees atoms outside contour = 6791, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96877788 -0.08017266 0.23460978 286.39172746 -0.10549337 -0.72304386 -0.68269953 347.75355178 0.22436701 -0.68613398 0.69201127 107.52120326 Axis -0.12475730 0.37207134 -0.91978178 Axis point 137.21226940 194.55501703 0.00000000 Rotation angle (degrees) 179.21132619 Shift along axis -5.23637227 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 44 shifted from previous position = 0.0193 rotated from previous position = 0.0248 degrees atoms outside contour = 6789, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96874478 -0.07982471 0.23486496 286.31355605 -0.10590584 -0.72308861 -0.68258827 347.79626824 0.22431561 -0.68612739 0.69203446 107.51450516 Axis -0.12481224 0.37203794 -0.91978784 Axis point 137.20991275 194.54113095 0.00000000 Rotation angle (degrees) 179.18764488 Shift along axis -5.23256336 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 48 shifted from previous position = 0.00277 rotated from previous position = 0.016 degrees atoms outside contour = 6786, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96878335 -0.07999571 0.23464757 286.37023163 -0.10563951 -0.72306298 -0.68265668 347.76118925 0.22427460 -0.68613449 0.69204072 107.52038500 Axis -0.12474154 0.37205709 -0.91978969 Axis point 137.21925659 194.54410511 0.00000000 Rotation angle (degrees) 179.20126886 Shift along axis -5.23138748 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 44 shifted from previous position = 0.00291 rotated from previous position = 0.00658 degrees atoms outside contour = 6786, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96879080 -0.08009121 0.23458422 286.39019113 -0.10552978 -0.72305446 -0.68268268 347.74795806 0.22429406 -0.68613232 0.69203656 107.51881558 Axis -0.12472966 0.37206371 -0.91978862 Axis point 137.21937661 194.54617167 0.00000000 Rotation angle (degrees) 179.20766068 Shift along axis -5.23153708 Fit molecule Flex-EM_3-final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.3837, steps = 44 shifted from previous position = 0.0199 rotated from previous position = 0.00715 degrees atoms outside contour = 6793, contour level = 0.46522 Position of Flex-EM_3-final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96876651 -0.08019483 0.23464913 286.38537169 -0.10550098 -0.72305718 -0.68268425 347.75715807 0.22441250 -0.68611736 0.69201300 107.51493579 Axis -0.12478029 0.37206246 -0.91978226 Axis point 137.20743897 194.55566305 0.00000000 Rotation angle (degrees) 179.21178004 Shift along axis -5.23819610 > toolshed show ISOLDE > set selectionWidth 4 Traceback (most recent call last): File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 627, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1511, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/__init__.py"", line 48, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/tools.py"", line 214, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/tool.py"", line 168, in __init__ self.isolde = isolde.Isolde(self) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 307, in __init__ self._start_gui(gui) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 444, in _start_gui self._populate_menus_and_update_params() File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 543, in _populate_menus_and_update_params self._update_model_list(None, None, force=True) File ""/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 945, in _update_model_list from chimerax.clipper.symmetry import Symmetry_Manager ImportError: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-packages/chimerax/clipper/symmetry.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 1135, in run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name))) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2646, in run result = ci.function(session, **kw_args) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py"", line 337, in toolshed_show bi.start_tool(session, tool_name) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 633, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py) File ""/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 633, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.12 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. }}} " defect closed normal Third Party not a bug all ChimeraX