Opened 2 years ago

Closed 2 years ago

#9417 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/cryosparc_P12_J451_006_volume_map_sharp.mrc

Opened cryosparc_P12_J451_006_volume_map_sharp.mrc as #1, grid size
312,312,312, pixel 0.835, shown at level 0.152, step 2, values float32  

> set bgColor white

> surface dust #1 size 8.35

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

Chain information for AMBRA1_001.pdb #2  
---  
Chain | Description  
A | No description available  
  

> volume flip #1

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 #1

> fitmap #2 inMap #3

Fit molecule AMBRA1_001.pdb (#2) to map
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) using 6240 atoms  
average map value = 0.138, steps = 2000  
shifted from previous position = 2.56  
rotated from previous position = 5.21 degrees  
atoms outside contour = 3857, contour level = 0.15239  
  
Position of AMBRA1_001.pdb (#2) relative to
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.99776835 -0.01178731 0.06572205 -4.63207946  
0.01582411 0.99799737 -0.06124417 5.48067821  
-0.06486853 0.06214749 0.99595671 3.37207517  
Axis 0.67881904 0.71842271 0.15189968  
Axis point 43.60094087 0.00000000 85.44249183  
Rotation angle (degrees) 5.21463801  
Shift along axis 1.30531709  
  

> surface dust #3 size 8.35

> select add #2

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

> select subtract #2

Nothing selected  

> select add #2

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

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.99777,-0.011787,0.065722,63.485,0.015824,0.998,-0.061244,-28.172,-0.064869,0.062147,0.99596,48.37

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.77134,-0.63397,-0.055803,186.4,-0.58133,-0.66618,-0.46719,308.27,0.25901,0.3928,-0.8824,167.5

> view matrix models
> #2,0.8407,-0.47895,0.25266,123.84,-0.50925,-0.54066,0.66959,159.13,-0.18409,-0.69159,-0.69844,345.08

> view matrix models
> #2,0.67089,-0.70607,0.22666,178.15,-0.74013,-0.65655,0.14545,261.29,0.046119,-0.26533,-0.96305,288.82

> view matrix models
> #2,0.66328,-0.74599,0.059642,202.44,-0.68259,-0.63572,-0.36045,306.04,0.30681,0.19837,-0.93087,191.5

> view matrix models
> #2,0.98137,-0.08149,0.174,62.832,-0.00384,-0.91374,-0.40629,257.73,0.19209,0.39805,-0.89703,177.2

> view matrix models
> #2,0.073343,-0.92766,0.36615,269.88,-0.99428,-0.096595,-0.045566,243.39,0.077638,-0.36072,-0.92944,293.3

> view matrix models
> #2,-0.10329,-0.95343,0.28338,305.36,-0.94095,0.0013145,-0.33855,255.64,0.32242,-0.30162,-0.89726,250.09

> view matrix models
> #2,-0.1652,-0.79513,0.5835,260.51,-0.90731,-0.10941,-0.40598,272.8,0.38665,-0.59648,-0.70336,258.51

> view matrix models
> #2,0.093215,-0.75537,0.64863,214.41,-0.95163,-0.25916,-0.16505,271.68,0.29278,-0.60187,-0.74299,275.82

> view matrix models
> #2,0.13357,-0.73652,0.66309,205.13,-0.96177,-0.25773,-0.092545,264.95,0.23906,-0.62539,-0.74279,285.87

> view matrix models
> #2,0.13634,-0.78131,0.60907,216.39,-0.96888,-0.23339,-0.082512,261.66,0.20662,-0.57886,-0.78881,289.15

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.13634,-0.78131,0.60907,140,-0.96888,-0.23339,-0.082512,289.57,0.20662,-0.57886,-0.78881,296.57

> view matrix models
> #2,0.13634,-0.78131,0.60907,145.7,-0.96888,-0.23339,-0.082512,304.45,0.20662,-0.57886,-0.78881,293.79

> volume #3 level 0.3031

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87452,-0.46494,0.138,59.37,-0.48323,-0.81114,0.32946,270.25,-0.04124,-0.35481,-0.93403,313.28

> view matrix models
> #2,0.86415,-0.48112,0.14755,61.774,-0.49839,-0.85881,0.11857,301.29,0.069667,-0.176,-0.98192,280.94

> view matrix models
> #2,0.68777,-0.71073,0.14773,114.42,-0.72523,-0.68165,0.096941,310.62,0.031803,-0.17381,-0.98426,285.89

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.68777,-0.71073,0.14773,114.49,-0.72523,-0.68165,0.096941,313.45,0.031803,-0.17381,-0.98426,284.44

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.72213,-0.69175,0.004045,123.16,-0.68823,-0.71784,0.10511,312.37,-0.069803,-0.078684,-0.99445,286.64

> view matrix models
> #2,0.73186,-0.66847,-0.13241,133.72,-0.66165,-0.74355,0.096759,313.09,-0.16313,0.016792,-0.98646,285.74

> view matrix models
> #2,0.72136,-0.68057,-0.12832,136.21,-0.69093,-0.71991,-0.065924,331.57,-0.047511,0.13621,-0.98954,255.55

> view matrix models
> #2,0.72631,-0.67549,-0.12718,134.78,-0.68579,-0.72466,-0.067545,331.69,-0.04654,0.13628,-0.98958,255.42

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.72631,-0.67549,-0.12718,135.04,-0.68579,-0.72466,-0.067545,330.78,-0.04654,0.13628,-0.98958,252.99

> select add #3

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

> fitmap #2 inMap #3

Fit molecule AMBRA1_001.pdb (#2) to map
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) using 6240 atoms  
average map value = 0.1439, steps = 76  
shifted from previous position = 2.65  
rotated from previous position = 8.54 degrees  
atoms outside contour = 4364, contour level = 0.30307  
  
Position of AMBRA1_001.pdb (#2) relative to
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.81289237 -0.57896080 -0.06332744 103.69962741  
-0.58185211 -0.81206800 -0.04465046 323.54438562  
-0.02557532 0.07314322 -0.99699346 260.32671075  
Axis 0.95202758 -0.30511872 -0.02336803  
Axis point 0.00000000 174.15884373 136.66705850  
Rotation angle (degrees) 176.45315253  
Shift along axis -6.07786378  
  

> volume #3 color #b2b2b263

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.70498,-0.70192,0.10153,112.77,-0.70179,-0.71108,-0.043068,326.7,0.10243,-0.04089,-0.9939,257.16,#3,0.97303,0.15527,-0.1706,6.0383,-0.15606,0.98771,0.0088758,21.003,0.16988,0.017987,0.9853,-22.778

> select subtract #3

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

> view matrix models
> #2,0.8163,-0.57563,-0.047873,98.164,-0.57741,-0.81093,-0.094864,328.85,0.015785,0.10508,-0.99434,249.8

> view matrix models
> #2,0.81362,-0.58005,-0.039582,98.183,-0.58049,-0.80667,-0.11098,330.46,0.032443,0.11327,-0.99303,246.42

> view matrix models
> #2,0.78401,-0.61839,0.054001,96.827,-0.60694,-0.78191,-0.14228,334.14,0.13021,0.078771,-0.98835,237.52

> view matrix models
> #2,0.89086,-0.44866,-0.071153,74.586,-0.45425,-0.87842,-0.14842,327.19,0.0040864,0.16454,-0.98636,242.82

> view matrix models
> #2,0.90343,-0.42756,-0.031798,65.947,-0.42874,-0.90116,-0.063918,317.58,-0.0013265,0.071378,-0.99745,256.72

> fitmap #2 inMap #3

Fit molecule AMBRA1_001.pdb (#2) to map
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) using 6240 atoms  
average map value = 0.3849, steps = 108  
shifted from previous position = 0.779  
rotated from previous position = 18.6 degrees  
atoms outside contour = 3101, contour level = 0.30307  
  
Position of AMBRA1_001.pdb (#2) relative to
cryosparc_P12_J451_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.99992281 -0.01155001 -0.00457761 -0.59922069  
-0.01217237 -0.98453250 -0.17477864 284.82630321  
-0.00248811 0.17482087 -0.98459710 242.12386243  
Axis 0.99998055 -0.00597672 -0.00178017  
Axis point 0.00000000 131.74827611 133.60462202  
Rotation angle (degrees) 169.93279665  
Shift along axis -2.73255951  
  

> isolde start

> set selectionWidth 4

Populating font family aliases took 294 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

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  
Alignment identifier is 1.2/A  

> select /A:115

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

> select /A:115-117

42 atoms, 41 bonds, 3 residues, 1 model selected  

> select /A:41-42

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

> select /A:42-58

281 atoms, 285 bonds, 17 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.2685

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim pause

> isolde sim stop

Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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:59

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:59-81

363 atoms, 367 bonds, 23 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde cisflip #1.2/A:65

Performing cis<\-->trans flip for 1 residues  
Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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 14  
  
ValueError: Values array length 17 does not match objects array length 14  
  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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.  
  
Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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 14  
  
ValueError: Values array length 17 does not match objects array length 14  
  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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

Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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 14  
  
ValueError: Values array length 17 does not match objects array length 14  
  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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 tutorial

> isolde sim resume

> isolde sim pause

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select /A:59

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:59-91

518 atoms, 523 bonds, 33 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  
[Repeated 3 time(s)]

> ui mousemode right "isolde tug selection"

> 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  

> select
> /A:42-47,59-61,67-71,77-81,87-91,98-103,110-115,119-124,129-133,140-145,152-156,159-163,172-175,183-188,194-200,216-222,251-253,259-265,275-281,290-295,300-305,311-316,330-337,347-349,351-354,367-372,380-384,389-394

2570 atoms, 2579 bonds, 154 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde cisflip #1.2/A:332

Performing cis<\-->trans flip for 1 residues  
Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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 12 does not match objects array length 14  
  
ValueError: Values array length 12 does not match objects array length 14  
  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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.  
  

> select clear

Traceback (most recent call last):  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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 14  
  
ValueError: Values array length 17 does not match objects array length 14  
  
File
"/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/C36BFDA0-3E53-4963-A80E-AE8EB00C2A45/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.  
  




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 2:59

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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