Errorpalooza

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-11-26)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.8 (2018-11-26)  
How to cite UCSF ChimeraX  

> open C:\Users\Jacobson Lab\Desktop\Aligned\aligned_right.pyc

File not found: C:\Users\Jacobson  

File not found: C:\Users\Jacobson  

> open "C:/Users/Jacobson Lab/Desktop/Aligned/aligned_right.pyc"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\ui\gui.py", line 542, in _qt_safe  
run(session, "open " + quote_if_necessary(paths[0]))  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
from_database=from_database, ignore_cache=ignore_cache, **kw))  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 117, in open  
models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
return f(*args, **kw)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\models.py", line 586, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\io.py", line 461, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\io.py", line 414, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\scripting.py", line 57, in open_python_script  
code = compile(data, file_name, 'exec')  
ValueError: source code string cannot contain null bytes  
  
ValueError: source code string cannot contain null bytes  
  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\scripting.py", line 57, in open_python_script  
code = compile(data, file_name, 'exec')  
  
See log for complete Python traceback.  
  

> open "C:\Users\Jacobson Lab\Desktop\Aligned\MRP4_MRP1bound.pdb"

MRP4_MRP1bound.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for MRP4_MRP1bound.pdb #1  
---  
Chain | Description  
A | No description available  
  
Opened cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc, grid
size 150,150,150, pixel 1.63, shown at level 0.68, step 1, values float32  
  
  
  
cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc title:  
Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) [more
info...]  
  
cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc title:  
Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) bound to
leukotriene C4 [more info...]  
  
cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MRP4-MRP1apo [more info...]  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 111, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 111, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
AttributeError: 'Volume' object has no attribute '_c_pointer'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\ui\gui.py", line 546, in _qt_safe  
session.models.open(paths)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\models.py", line 596, in open  
self.add_group(models, name=name)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\models.py", line 526, in add_group  
self.add([parent])  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\models.py", line 456, in add  
m.added_to_session(session)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2111, in added_to_session  
self._report_ensemble_chain_descriptions(session, sibs)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2343, in
_report_ensemble_chain_descriptions  
structs = AtomicStructures(ensemble)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 393, in __init__  
Collection.__init__(self, mol_pointers, AtomicStructure, AtomicStructures)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 116, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'list'>"  
  
ValueError: Collection items of unrecognized type ""  
  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 116, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  

> open "C:/Users/Jacobson Lab/Desktop/Aligned/5uja_bound.pdb"

5uja_bound.pdb title:  
Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) bound to
leukotriene C4 [more info...]  
  
Chain information for 5uja_bound.pdb #3  
---  
Chain | Description  
A | bovine multidrug resistance protein 1 (MRP1),multidrug resistance-
associated protein 1  
  

> hide #!3 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!2 models

> open "C:/Users/Jacobson Lab/Desktop/Aligned/MRP4_MRP1apo.pdb"

MRP4_MRP1apo.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MRP4-MRP1apo [more info...]  
  
Chain information for MRP4_MRP1apo.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 1859, in <lambda>  
sm.addAction(style, lambda s=style: self.representation_changed_cb(s))  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2363, in
representation_changed_cb  
self.set_map_style(v, style)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2377, in set_map_style  
if style != 'box' and v.showing_box_faces():  
AttributeError: 'NoneType' object has no attribute 'showing_box_faces'  
  
AttributeError: 'NoneType' object has no attribute 'showing_box_faces'  
  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2377, in set_map_style  
if style != 'box' and v.showing_box_faces():  
  
See log for complete Python traceback.  
  

Missing or invalid "percent" argument: Expected a number  

> transparency 70

> transparency 50

Expected an atoms specifier or a keyword  

Expected a keyword  

> transparency 30

> close

> open "C:/Users/Jacobson
Lab/Desktop/Aligned/cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc"

Opened cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc, grid
size 150,150,150, pixel 1.63, shown at level 0.68, step 1, values float32  
  
  
  
  
5uj9_apo.pdb title:  
Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) [more
info...]  
  
Chain information for 5uj9_apo.pdb #2.1  
---  
Chain | Description  
A | bovine multidrug resistance protein 1 (MRP1),multidrug resistance-
associated protein 1  
  
5uja_bound.pdb title:  
Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) bound to
leukotriene C4 [more info...]  
  
Chain information for 5uja_bound.pdb #2.2  
---  
Chain | Description  
A | bovine multidrug resistance protein 1 (MRP1),multidrug resistance-
associated protein 1  
  
MRP4_MRP1apo.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MRP4-MRP1apo [more info...]  
  
Chain information for MRP4_MRP1apo.pdb #2.3  
---  
Chain | Description  
A | No description available  
  
MRP4_MRP1bound.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for MRP4_MRP1bound.pdb #2.4  
---  
Chain | Description  
A | No description available  
  

> color selAtoms byhetero

> vr on

started SteamVR rendering  

> vr off

> vr on

started SteamVR rendering  

> transparency #1 50

> show ligand :<10

> hide HC

> select ligand

43 atoms, 42 bonds, 1 model selected  

> style selAtoms sphere

Changed 43 atom styles  

> style selAtoms ball

Changed 43 atom styles  

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.2 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> hide #!2.3 models

> show #!2.3 models

> hide #!2.3 models

> show #!2.3 models

> show #!2.3 models

> hide #!2.4 models

> show #!2.4 models

> show ligand :<5

> hide #!2.3 models

> hide #!2.1 models

> show ligand :<10

> hide HC

> meeting start

Meeting at vive or 169.230.21.39 port 52194  
Connection accepted from 169.230.21.70 port 54662  

> vr on

> show #!2.3 models

> hide #!2.3 models

> show #!2.1 models

> show #!2.3 models

> hide #!2.3 models

> show #!2.3 models

> hide #!2.3 models

> hide #!2.3 models

> show #!2.3 models

> hide #!2.3 models

> show #!2.3 models

> color selAtoms byhetero

> color selAtoms byhetero

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\core\triggerset.py", line 126, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 447, in next_frame  
self.process_controller_events()  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 476, in process_controller_events  
self.process_controller_motion()  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 497, in process_controller_motion  
hc.process_motion(self)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 1126, in process_motion  
ui.drag(window_xy)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 763, in drag  
return self._click('move', window_xy)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 770, in _click  
if self._post_mouse_event(type, window_xy) and type != 'move':  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 809, in _post_mouse_event  
w, pos = self._clicked_widget(window_xy)  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 833, in _clicked_widget  
x,y = window_xy  
TypeError: 'NoneType' object is not iterable  
  
Error processing trigger "new frame": 'NoneType' object is not iterable:  
TypeError: 'NoneType' object is not iterable  
  
File "C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site-
packages\chimerax\vive\vr.py", line 833, in _clicked_widget  
x,y = window_xy  
  
See log for complete Python traceback.  
  

> vr off

> vr on

started SteamVR rendering  

> hide #!2.2 models

> hide #!2.4 models

> hide #!2.1 models

> show #!2.2 models

> hide #!2.3 models

> show #!2.4 models

> transparency 50

> transparency 0




OpenGL version: 3.3.0 NVIDIA 391.58
OpenGL renderer: Quadro P6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

The last of many different errors was window_xy being None in vr.py

[Tom Goddard]

Reported by Wilian Coelho after a VR demo session.

This ticket includes several tracebacks.

1) The first traceback is from opening a ".pyc" file that seems to be a Chimera 1 session. It gives a very cryptic error, apparently because the byte code compiled Python 2.7 is not readable by Python 3. Did not do anything to fix this. Probably more likely for users to open a Chimera 1 Python session file -- we may want to catch that and report a useful error when that happens.

2) Second traceback was caused by choosing a PDB and MRC file from the Open File dialog. The code that logged a chain table thought the MRC was part of an ensemble because its name matched the PDB. Fixed. Also the name only matched because of a bug in our code to read multiple files -- it inadvertently overwrote the name variable. Fixed.

Still working on two additional tracebacks.

[Tom Goddard]

3) Third traceback was choosing Mesh style from Volume Viewer when no volume was opened. Fixed.

[Tom Goddard]

4) Fourth traceback was from click on gui panel in VR and then hiding the gui panel before the click was released. Fixed.