PC requires restart to launch ChimeraX a second time

[pascal.albanese@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-10-20)
Description
(Describe the actions that caused t

HI, i'm not able to open any of thew previous sessions, even the ones of the same daily build. 

In addition i have to restart my PC any time i close ChimeraX, in order to lunch it again

Thanks, 

p

Log:
UCSF ChimeraX version: 0.8 (2018-10-20)  
How to cite UCSF ChimeraX  

open D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs

open D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs

Summary of feedback from opening D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs  
---  
error | Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 590, in restore  
obj = sm.restore_snapshot(self, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 574, in restore_snapshot  
inst.seq_canvas.restore_state(session, data['seq canvas'])  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 1085, in restore_state  
header_class = bundle.get_class(class_name)  
TypeError: get_class() missing 1 required positional argument: 'logger'  
  
Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2563, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\core\commands\open.py", line 110, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 577, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 815, in open  
    session.restore(stream, path=path, resize_window=resize_window)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 596, in restore  
    self.reset()  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 410, in reset  
    sm.reset_state(container, self)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 576, in reset_state  
    for pbg in list(self.group_map.values()):  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
    return look_in_class._attr_registration.get_attr(attr_name)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
    raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 229, in _actually_resize  
    self._reformat()  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 995, in _reformat  
    self.label_width, self.font_pixels, self.numbering_widths,
self.letter_gaps())  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 1566, in __init__  
    self.layout_lines(alignment.seqs, self.normal_label_color)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2208, in layout_lines  
    self._layout_line(line, label_color, bli, end)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2158, in _layout_line  
    font=self._label_font(line))  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2098, in _label_font  
    if self.has_associated_structures(line):  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2036, in has_associated_structures  
    and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2036, in <listcomp>  
    and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
    return look_in_class._attr_registration.get_attr(attr_name)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 66, in get_attr  
    raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 66, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

open D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs format session

open D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs format session

Summary of feedback from opening D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs  
---  
error | Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 562, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 410, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 576, in reset_state  
for pbg in list(self.group_map.values()):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 529, in customEvent  
    func(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 278, in defer  
    cxcmd(session, topic)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 374, in cxcmd  
    run(session, cmd)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2563, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\core\commands\open.py", line 110, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 577, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 815, in open  
    session.restore(stream, path=path, resize_window=resize_window)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 596, in restore  
    self.reset()  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 410, in reset  
    sm.reset_state(container, self)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 576, in reset_state  
    for pbg in list(self.group_map.values()):  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
    return look_in_class._attr_registration.get_attr(attr_name)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
    raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

open "D:\UTRECHT_MS\Chimera modelling\Structural
prediction\R_18.3_docking.cxs" format session

open "D:\UTRECHT_MS\Chimera modelling\Structural
prediction\R_18.3_docking.cxs" format session

opened ChimeraX session  
Exception ignored in: <bound method Drawing.__del__ of
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x000001E5B07D26D8>>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1055, in __del__  
if not self.was_deleted:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 66, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'PseudobondGroup' object has no attribute 'was_deleted'  
Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 126, in invoke  
    return self._func(self._name, data)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 101, in _changes_handler  
    if pb.group in self.monitored_groups:  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
    return look_in_class._attr_registration.get_attr(attr_name)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
    raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError  
  
Error processing trigger "changes":  
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 72, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\view.py", line 159, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\view.py", line 198, in _draw_scene  
self._update_projection(camera, vnum)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\view.py", line 748, in _update_projection  
near_far = self.near_far_distances(camera, view_num)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\view.py", line 763, in near_far_distances  
near, far = self._near_far_bounds(cp, vd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\view.py", line 776, in _near_far_bounds  
b = self.drawing_bounds()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\view.py", line 546, in drawing_bounds  
dm.cached_drawing_bounds = b = self.drawing.bounds()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 851, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 852, in <listcomp>  
if d.display and not getattr(d, 'skip_bounds', False)]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1534, in bounds  
b = super().bounds()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 851, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 852, in <listcomp>  
if d.display and not getattr(d, 'skip_bounds', False)]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 851, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 852, in <listcomp>  
if d.display and not getattr(d, 'skip_bounds', False)]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 869, in bounds  
spos = self.get_scene_positions(displayed_only=True)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 447, in get_scene_positions  
p = dp * p  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 592, in __mul__  
places.array(), len(places))  
TypeError: Require array value type double, got float  
  




OpenGL version: 3.3.0 NVIDIA 388.75
OpenGL renderer: GeForce 940M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

The session-restore problem is already tracked in ticket #1395

[Greg Couch]

Hello,

My apologies for not following up on this earlier. Do you still "have to restart my PC any time i close ChimeraX, in order to launch it again"? If you do, then you probably need to update your graphics driver. Using ChimeraX should not require restarting your computer.