Opened 2 years ago

Closed 2 years ago

#9418 closed defect (duplicate)

ISOLDE: various simulation-related problems

Reported by: chimerax-bug-report@… 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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/albertoestevez/Documents/P_12_DDB1_complex_KRIOS/Isolde_maps/AMBRA1_001.pdb

Chain information for AMBRA1_001.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/albertoestevez/Documents/P_12_DDB1_complex_KRIOS/cryosparc_P12_J451_006_volume_map_sharp.mrc

Opened cryosparc_P12_J451_006_volume_map_sharp.mrc as #2, grid size
312,312,312, pixel 0.835, shown at level 0.152, step 2, values float32  

> set bgColor white

> volume #2 step 1

> volume flip #2

Opened cryosparc_P12_J451_006_volume_map_sharp.mrc z flip as #3, grid size
312,312,312, pixel 0.835, shown at step 1, values float32  

> close #2

> surface dust #3 size 8.35

> surface dust #3 size 12

> volume #3 level 0.2483

> select add #1

6240 atoms, 6316 bonds, 4 pseudobonds, 398 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-4.5487,0,1,0,52.011,0,0,1,29.676

> volume #3 level 0.3305

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.85258,0.52242,0.013733,-53.876,-0.022216,0.0099756,0.9997,73.58,0.52212,-0.85263,0.020111,177.31

> view matrix models
> #1,0.016904,0.98351,0.18006,-21.611,-0.62482,-0.1302,0.76983,195.64,0.78058,-0.12552,0.61232,-14.455

> view matrix models
> #1,-0.29762,0.8514,0.4319,9.267,0.46288,-0.26698,0.84526,62.339,0.83497,0.45148,-0.31464,4.9597

> view matrix models
> #1,0.65232,0.25008,0.71549,-68.855,-0.12868,-0.89375,0.42971,265.7,0.74694,-0.37237,-0.55084,148.11

> view matrix models
> #1,0.54992,0.13216,0.82469,-52.125,0.16818,-0.9847,0.045651,280.19,0.81811,0.11359,-0.56373,77.691

> view matrix models
> #1,0.51276,0.044749,0.85736,-39.561,0.33168,-0.93143,-0.14975,273.13,0.79187,0.36116,-0.49245,41.552

> view matrix models
> #1,0.75884,-0.26877,0.59324,-2.8243,0.014351,-0.90375,-0.42781,341.42,0.65112,0.33315,-0.68194,84.212

> view matrix models
> #1,0.83024,-0.14168,0.53909,-22.65,-0.12917,-0.98973,-0.061184,331.46,0.54223,-0.018836,-0.84002,160.94

> view matrix models
> #1,0.84796,-0.11565,0.51729,-25.951,-0.15565,-0.98721,0.034422,324.21,0.5067,-0.1097,-0.85512,178.92

> view matrix models
> #1,0.78609,-0.0026655,0.61811,-43.32,-0.078602,-0.9923,0.095684,308.1,0.6131,-0.1238,-0.78025,158.64

> view matrix models
> #1,0.77184,-0.022842,0.63541,-40.736,-0.049005,-0.99852,0.023632,312.85,0.63393,-0.049378,-0.77182,145.42

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.77184,-0.022842,0.63541,-35.266,-0.049005,-0.99852,0.023632,271.3,0.63393,-0.049378,-0.77182,165.6

> view matrix models
> #1,0.77184,-0.022842,0.63541,-38.896,-0.049005,-0.99852,0.023632,271.41,0.63393,-0.049378,-0.77182,165.59

> view matrix models
> #1,0.77184,-0.022842,0.63541,-37.53,-0.049005,-0.99852,0.023632,270.85,0.63393,-0.049378,-0.77182,165.73

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.80008,0.22717,0.55522,-64.667,0.15252,-0.97214,0.17797,224.25,0.58018,-0.057706,-0.81244,178.27

> view matrix models
> #1,0.82256,0.22002,0.5244,-63.347,0.17335,-0.97525,0.13726,226.34,0.54162,-0.021999,-0.84034,181.77

> select add #3

6240 atoms, 6316 bonds, 4 pseudobonds, 398 residues, 4 models selected  

> fitmap #1 inMap #3

Fit molecule AMBRA1_001.pdb (#1) to map
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) using 6240 atoms  
average map value = 0.1294, steps = 80  
shifted from previous position = 1.61  
rotated from previous position = 5.11 degrees  
atoms outside contour = 4793, contour level = 0.33047  
  
Position of AMBRA1_001.pdb (#1) relative to
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.78094838 0.29096031 0.55268591 -71.07852355  
0.24304596 -0.95669086 0.16022250 211.55061140  
0.57536795 0.00920257 -0.81784291 169.87045335  
Axis -0.94355618 -0.14171494 -0.29936368  
Axis point 0.00000000 114.63315179 91.75943051  
Rotation angle (degrees) 175.40988260  
Shift along axis -13.76634480  
  

> ui mousemode right "move picked models"

> view matrix models #3,1,0,0,0.061814,0,1,0,0.15167,0,0,1,-0.11834

> select subtract #3

6240 atoms, 6316 bonds, 4 pseudobonds, 398 residues, 2 models selected  

> view matrix models #3,1,0,0,-0.5033,0,1,0,-0.82878,0,0,1,1.2209

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.8817,-0.29218,0.37046,10.491,-0.32706,-0.94441,0.033554,298.53,0.34006,-0.15075,-0.92824,233.31

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.8817,-0.29218,0.37046,9.7356,-0.32706,-0.94441,0.033554,299.09,0.34006,-0.15075,-0.92824,236.28

> view matrix models
> #1,0.8817,-0.29218,0.37046,9.8915,-0.32706,-0.94441,0.033554,298.48,0.34006,-0.15075,-0.92824,235.35

> fitmap #1 inMap #3

Fit molecule AMBRA1_001.pdb (#1) to map
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) using 6240 atoms  
average map value = 0.1461, steps = 72  
shifted from previous position = 2.79  
rotated from previous position = 3.61 degrees  
atoms outside contour = 4586, contour level = 0.33047  
  
Position of AMBRA1_001.pdb (#1) relative to
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.88134140 -0.27199886 0.38633400 5.38553688  
-0.33075345 -0.93908575 0.09338149 290.69254159  
0.33740109 -0.21008228 -0.91761971 239.28333050  
Axis -0.96969223 0.15636086 -0.18774518  
Axis point 0.00000000 155.45750713 107.29095447  
Rotation angle (degrees) 170.99769078  
Shift along axis -4.69366998  
  

> volume #3 level 0.6455

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99076,0.039451,0.12977,-21.636,0.035213,-0.99877,0.03479,255.9,0.13098,-0.029899,-0.99093,252.38

> view matrix models
> #1,0.97172,0.20841,0.11099,-38.824,0.21454,-0.97561,-0.046355,238.21,0.098625,0.068856,-0.99274,244.13

> view matrix models
> #1,0.99083,0.12566,0.049611,-24.019,0.12755,-0.99114,-0.036933,250.6,0.04453,0.042922,-0.99809,255.14

> view matrix models
> #1,0.99306,0.096961,0.066542,-22.462,0.10493,-0.98606,-0.12917,262.93,0.053089,0.13526,-0.98939,241.2

> fitmap #1 inMap #3

Fit molecule AMBRA1_001.pdb (#1) to map
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) using 6240 atoms  
average map value = 0.385, steps = 72  
shifted from previous position = 1.15  
rotated from previous position = 7.84 degrees  
atoms outside contour = 4675, contour level = 0.64553  
  
Position of AMBRA1_001.pdb (#1) relative to
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.99992041 -0.01166651 -0.00480124 -0.55026691  
-0.01232476 -0.98462235 -0.17426109 284.78589308  
-0.00269439 0.17430640 -0.98468777 242.22926044  
Axis 0.99997995 -0.00604419 -0.00188840  
Axis point 0.00000000 131.75553830 133.61796427  
Rotation angle (degrees) 169.96281739  
Shift along axis -2.72898200  
  

> select add #3

6240 atoms, 6316 bonds, 4 pseudobonds, 398 residues, 4 models selected  

> volume #3 level 0.3442

Alignment identifier is 1/A  

> volume #3 color #b2b2d0

> volume #3 color #c7d3db

> volume #3 color #c7d3db8d

> color #1 #d2b4d2 transparency 0

> color #1 #d268d2 transparency 0

> volume #3 level 0.2894

> isolde start

> set selectionWidth 4

Populating font family aliases took 295 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> select clear

> select /A:42

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:42-71

478 atoms, 484 bonds, 30 residues, 1 model selected  

> select /A:42

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:42-43

39 atoms, 40 bonds, 2 residues, 1 model selected  

> select /A:42

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:42-61

330 atoms, 335 bonds, 20 residues, 1 model selected  
No models are initialised for Clipper. Use the command "clipper spotlight
#{model id(s)}" to initialise (a) specific model(s).  
[Repeated 4 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
Chain information for AMBRA1_001.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> clipper associate #3 toModel #1

Opened cryosparc_P12_J451_006_volume_map_sharp.mrc z flip as #1.1.1.1, grid
size 312,312,312, pixel 0.835, shown at step 1, values float32  

> select /A:179-180

32 atoms, 31 bonds, 2 residues, 1 model selected  

> select /A:179-183

87 atoms, 86 bonds, 5 residues, 1 model selected  

> select /A:41-42

46 atoms, 47 bonds, 2 residues, 1 model selected  

> select /A:42-61

330 atoms, 335 bonds, 20 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim pause

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde cisflip #1.2/A:65

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde cisflip #1.2/A:65

Performing cis<\-->trans flip for 1 residues  

> isolde sim pause

> select /A:42

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:42-66

405 atoms, 411 bonds, 25 residues, 1 model selected  

> isolde sim resume

> isolde sim pause

> isolde sim stop

Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 1009, in _sim_end_cb  
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/cmd.py", line 109, in spotlight  
sh = get_symmetry_handler(m, create=create, auto_add_to_session=True)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 594, in __init__  
self.add_model(model, ignore_model_symmetry=ignore_model_symmetry,  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 649, in add_model  
self.set_default_atom_display(mode=self._hydrogen_mode)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 922, in set_default_atom_display  
atoms = model.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "sim terminated":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 922, in set_default_atom_display  
atoms = model.atoms  
  
See log for complete Python traceback.  
  

> select /A:66

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:66-68

52 atoms, 51 bonds, 3 residues, 1 model selected  

> select /A:62

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:62-81

314 atoms, 317 bonds, 20 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  
Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 16 does not match objects array length 24  
  
ValueError: Values array length 16 does not match objects array length 24  
  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> isolde sim pause

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select /A:42

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:42-47

108 atoms, 109 bonds, 6 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  
Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 17 does not match objects array length 24  
  
ValueError: Values array length 17 does not match objects array length 24  
  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 22 does not match objects array length 24  
  
ValueError: Values array length 22 does not match objects array length 24  
  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> close

Deleting atomic symmetry model...  
Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1038, in
_sim_end_cb  
self._pr_sim_end_cb()  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1095, in
_pr_sim_end_cb  
restraints =
self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 2382, in get_restraints  
return self._get_restraints(atoms)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 2335, in _get_restraints  
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))  
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim terminated":  
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'  
  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 2335, in _get_restraints  
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/B6C04EDA-C0D6-41B4-BA0F-1ECD2CCB1C82/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 1009, in _sim_end_cb  
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
Error processing trigger "sim terminated":  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
File "/Users/albertoestevez/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 1009, in _sim_end_cb  
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 90 days 3:29

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG HDR 4K:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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-NIHPresets: 1.1.12
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    et-xmlfile: 1.1.0
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openpyxl: 3.0.10
    openvr: 1.16.802
    packaging: 21.0
    pandas: 1.5.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    pyqtgraph: 0.13.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    seaborn: 0.12.1
    Send2Trash: 1.8.2
    SEQCROW: 1.7.1
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: various simulation-related problems

comment:2 by Eric Pettersen, 2 years ago

Resolution: → duplicate
Status: assigned → closed
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