Opened 6 years ago

Closed 6 years ago

#2646 closed defect (not a bug)

Problem starting ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry'

Reported by: jliu321@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 <lambda>  
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 <lambda>  
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 <lambda>  
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.

Change History (5)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem starting ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry'

Reported by Jing Liu

in reply to:  2 ; comment:2 by Tristan Croll, 6 years ago 

I recently did some renaming of classes in the Clipper API to make it more Python-standard. Your problem should go away if you update to the latest version of ISOLDE (just go to the ToolShed and install via the links as normal).

comment:3 by Tristan Croll, 6 years ago

I'm curious here as to the reason behind Clipper upgrading at the start of this log record. Did you trigger this yourself through the Tool Shed? In general you shouldn't need to manually install/upgrade Clipper - when you install the latest ISOLDE version, the required Clipper version will be automatically fetched and installed.

in reply to:  4 ; comment:4 by jliu321@…, 6 years ago 

It could be me. I remembered that on my own laptop chimerax (installed in June), I tried to follow the tutorial and use cview command, it told me to install the clipper. When I switched to the workstation in our lab which just has a chimerax installed two days ago, I assumed that I need to install clipper. Then I installed it again manually.

Best.

Jing
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, December 5, 2019 12:32 AM
Cc: Jing Liu <jliu321@stanford.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #2646: Problem starting ISOLDE: cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry'

#2646: Problem starting ISOLDE: cannot import name 'Symmetry_Manager' from
'chimerax.clipper.symmetry'
----------------------------------+---------------------------
          Reporter:  jliu321@…    |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------

Comment (by Tristan Croll):

 I'm curious here as to the reason behind Clipper upgrading at the start of
 this log record. Did you trigger this yourself through the Tool Shed? In
 general you shouldn't need to manually install/upgrade Clipper - when you
 install the latest ISOLDE version, the required Clipper version will be
 automatically fetched and installed.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2646#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:5 by Tristan Croll, 6 years ago

Resolution: → not a bug
Status: assigned → closed

A simple version-incompatibility issue. The good news is that going in to the future it will be easier for ISOLDE and Clipper to enforce version compatibility.

Note: See TracTickets for help on using tickets.