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Opened 4 years ago
Closed 4 years ago
#6614 closed defect (duplicate)
Lots of previously fixed problems
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.13.0-39-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS_vs_7CYQ.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 646, in restore_snapshot
inst._finalize_init(data['alignment'])
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 174, in _finalize_init
self.seq_canvas = SeqCanvas(parent, self, self.alignment)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 186, in __init__
self.layout_alignment()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 744, in layout_alignment
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 1546, in __init__
self.layout_lines(alignment.seqs, self.normal_label_color)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2185, in layout_lines
self._layout_line(line, label_color, bli, end)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2135, in _layout_line
font=self._label_font(line))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2074, in _label_font
if self.has_associated_structures(line):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2018, in has_associated_structures
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2018, in <listcomp>
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, 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'
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 646, in restore_snapshot
inst._finalize_init(data['alignment'])
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 174, in _finalize_init
self.seq_canvas = SeqCanvas(parent, self, self.alignment)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 186, in __init__
self.layout_alignment()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 744, in layout_alignment
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 1546, in __init__
self.layout_lines(alignment.seqs, self.normal_label_color)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2185, in layout_lines
self._layout_line(line, label_color, bli, end)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2135, in _layout_line
font=self._label_font(line))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2074, in _label_font
if self.has_associated_structures(line):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2018, in has_associated_structures
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2018, in <listcomp>
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, 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'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 629, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer
cxcmd(session, topic)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
See log for complete Python traceback.
> open "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS_vs_7CYQ.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 629, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer
cxcmd(session, topic)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
See log for complete Python traceback.
> open "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 629, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer
cxcmd(session, topic)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
See log for complete Python traceback.
> open "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS_vs_7CYQ.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
See log for complete Python traceback.
> open /home/pierre/Téléchargements/7ed5.pdb
7ed5.pdb title:
A dual mechanism of action of At-527 against sars-cov-2 polymerase [more
info...]
Chain information for 7ed5.pdb #1
---
Chain | Description
A | RNA-directed RNA polymerase
B D | NSP8
C | NSP7
I | RNA (5'-
R(P*GP*CP*up*ap*up*GP*up*GP*ap*GP*ap*up*up*ap*ap*GP*up*up*ap*U*(AT9) )-3')
J | RNA (5'-
R(P*CP*CP*CP*CP*ap*up*ap*ap*CP*up*up*ap*ap*up*CP*up*CP*ap*CP*ap*up*ap
*GP*C)-3')
Non-standard residues in 7ed5.pdb #1
---
AT9 —
[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-
oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogenphosphate (At-9010)
MG — magnesium ion
ZN — zinc ion
> style stick
Changed 11402 atom styles
> show cartoons
> show atoms
> hide cartoons
> show cartoons
> hide atoms
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 1/C
Alignment identifier is 1/I
Alignment identifier is 1/J
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> show sel atoms
> save "/home/pierre/ownCloud/Construction model/7ED5_SARS2_NSP12.cxs"
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> open /home/pierre/Téléchargements/MERS_NSP12_current_best_2.pdb
Chain information for MERS_NSP12_current_best_2.pdb #2
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_2.pdb, chain A
(#2), sequence alignment score = 3462.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7ed5.pdb #1/A,
MERS_NSP12_current_best_2.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 649 pruned atom pairs is 0.892 angstroms; (across all 924 pairs:
3.987)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, 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'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_2.pdb, chain A
(#2), sequence alignment score = 3462.9
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7ed5.pdb #1/A,
MERS_NSP12_current_best_2.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 649 pruned atom pairs is 0.892 angstroms; (across all 924 pairs:
3.987)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, 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'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_2.pdb, chain A
(#2), sequence alignment score = 3462.9
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7ed5.pdb #1/A,
MERS_NSP12_current_best_2.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 649 pruned atom pairs is 0.892 angstroms; (across all 924 pairs:
3.987)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, 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'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> hide #2 models
> select #2/A
7508 atoms, 7700 bonds, 933 residues, 1 model selected
> select #2/A
7508 atoms, 7700 bonds, 933 residues, 1 model selected
> select #1/A
7529 atoms, 7717 bonds, 18 pseudobonds, 933 residues, 2 models selected
> color (#!1 & sel) red
> select #1/B#1/D
2370 atoms, 2400 bonds, 304 residues, 1 model selected
> color sel blue
> select #1
11402 atoms, 11732 bonds, 18 pseudobonds, 1354 residues, 2 models selected
> ~select #1
Nothing selected
> select #1/C
553 atoms, 556 bonds, 72 residues, 1 model selected
> color sel lime
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> color sel byelement
> select #1
11402 atoms, 11732 bonds, 18 pseudobonds, 1354 residues, 2 models selected
> ~select #1
Nothing selected
> lighting simple
> lighting full
> lighting simple
> set bgColor white
> set bgColor black
> lighting soft
> lighting full
> lighting simple
> select #1/J
499 atoms, 555 bonds, 24 residues, 1 model selected
> nucleotides sel stubs
> style sel stick
Changed 499 atom styles
> hide sel cartoons
> hide sel atoms
> show sel atoms
> style sel ball
Changed 499 atom styles
> style sel sphere
Changed 499 atom styles
> style sel stick
Changed 499 atom styles
> nucleotides sel stubs
> nucleotides sel tube/slab shape muffler
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> nucleotides sel slab
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape muffler
> nucleotides sel stubs
> nucleotides sel ladder
> nucleotides sel ladder
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel slab
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel tube/slab shape muffler
> nucleotides sel tube/slab shape box
> show sel cartoons
> hide sel atoms
> show sel atoms
> select #1/I
451 atoms, 504 bonds, 21 residues, 1 model selected
> nucleotides sel tube/slab shape box
> show sel atoms
> select #1
11402 atoms, 11732 bonds, 18 pseudobonds, 1354 residues, 2 models selected
> ~select #1
Nothing selected
> save /home/pierre/image1.png supersample 3
> select #1/J
499 atoms, 555 bonds, 24 residues, 1 model selected
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel slab
> style nucleic & sel stick
Changed 499 atom styles
> color sel byelement
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel tube/slab shape muffler
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> nucleotides sel fill
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel tube/slab shape muffler
> nucleotides sel slab
> style nucleic & sel stick
Changed 499 atom styles
> nucleotides sel tube/slab shape box
> color sel byhetero
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel dark goldenrod
> select #1/I
451 atoms, 504 bonds, 21 residues, 1 model selected
> color sel olive
> color sel goldenrod
> select #1
11402 atoms, 11732 bonds, 18 pseudobonds, 1354 residues, 2 models selected
> ~select #1
Nothing selected
> lighting simple
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> set bgColor white
> set bgColor black
> ui tool show "Side View"
> lighting shadows true
> graphics silhouettes true
> lighting shadows false
> lighting flat
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting flat
> lighting simple
> set bgColor gray
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting flat
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting shadows true
> set bgColor black
> save /home/pierre/image2.png supersample 3
> save /home/pierre/image3.png supersample 3
> save /home/pierre/image4.png supersample 3
> lighting full
> lighting full
> lighting full
> lighting full
> lighting full
> lighting simple
> lighting full
> lighting soft
> lighting full
> save /home/pierre/image5.png supersample 3
> save /home/pierre/image6.png supersample 3
> save "/home/pierre/ownCloud/Construction model/NSP12_SARS2_AT9_NIRAN.cxs"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> close session
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 914, in <lambda>
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 633, in file_close_cb
run(session, 'close session')
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/std_commands/close.py", line 60, in close_session
session.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
See log for complete Python traceback.
> ui tool show "Blast Protein"
> show # target m
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> open /home/pierre/Téléchargements/MERS_NSP12_current_best_2.pdb format pdb
Chain information for MERS_NSP12_current_best_2.pdb #1
---
Chain | Description
A | No description available
> open "/home/pierre/ownCloud/Construction model/NSP12_SARS2_AT9_NIRAN.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 495, in delete
self.region_browser.destroy()
See log for complete Python traceback.
> open /home/pierre/Téléchargements/7ed5.pdb format pdb
7ed5.pdb title:
A dual mechanism of action of At-527 against sars-cov-2 polymerase [more
info...]
Chain information for 7ed5.pdb #1
---
Chain | Description
A | RNA-directed RNA polymerase
B D | NSP8
C | NSP7
I | RNA (5'-
R(P*GP*CP*up*ap*up*GP*up*GP*ap*GP*ap*up*up*ap*ap*GP*up*up*ap*U*(AT9) )-3')
J | RNA (5'-
R(P*CP*CP*CP*CP*ap*up*ap*ap*CP*up*up*ap*ap*up*CP*up*CP*ap*CP*ap*up*ap
*GP*C)-3')
Non-standard residues in 7ed5.pdb #1
---
AT9 —
[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-
oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogenphosphate (At-9010)
MG — magnesium ion
ZN — zinc ion
> show atoms
> show cartoons
> hide atoms
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 1/C
Alignment identifier is 1/I
Alignment identifier is 1/J
> ui tool show "Color Actions"
> color sel orange
> color sel yellow
> color sel red
> color sel orange red
> color sel tomato
> select /C
553 atoms, 556 bonds, 72 residues, 1 model selected
> color sel lime
> select /B/D
2370 atoms, 2400 bonds, 304 residues, 1 model selected
> color sel blue
> color sel medium blue
> color sel blue
> color sel medium blue
> color sel blue
> select /I
451 atoms, 504 bonds, 21 residues, 1 model selected
> color sel dark goldenrod
> select /J
499 atoms, 555 bonds, 24 residues, 1 model selected
> nucleotides sel slab
> style nucleic & sel stick
Changed 499 atom styles
> show sel atoms
> color sel olive
> color sel dark khaki
> select /I
451 atoms, 504 bonds, 21 residues, 1 model selected
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 427 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 427 atom styles
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> color sel byhetero
> color sel byelement
> hide sel atoms
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting simple
> save /home/pierre/image7.png supersample 3
> save /home/pierre/image8.png supersample 3
> save /home/pierre/image9.png supersample 3
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> show sel atoms
> save /home/pierre/image10.png supersample 3
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> hide sel atoms
> save /home/pierre/image11.png supersample 3
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> show sel atoms
> save /home/pierre/image12.png supersample 3
> save "/home/pierre/ownCloud/Construction model/NSP12_SARS2_AT9_NIRAN_v2.cxs"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 47, in display
self._current_option)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/manager.py", line 91, in
save_args_string_from_widget
provider_info.format_name, self).save_args_string_from_widget(widget)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 189, in save_args_string_from_widget
return widget.options_string()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/options.py", line 35, in options_string
raise UserError("No %s to save" % self._name.lower())
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/options.py", line 35, in options_string
raise UserError("No %s to save" % self._name.lower())
See log for complete Python traceback.
> save "/home/pierre/ownCloud/Construction model/NSP12_SARS2_AT9_NIRAN.cxs"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> select ::name="MG"
3 atoms, 3 residues, 1 model selected
> show sel atoms
> select ::name="ZN"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> open /home/pierre/Téléchargements/MERS_NSP12_current_best_10.pdb
Chain information for MERS_NSP12_current_best_10.pdb #2
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_10.pdb, chain A
(#2), sequence alignment score = 3480.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7ed5.pdb #1/A,
MERS_NSP12_current_best_10.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 700 pruned atom pairs is 0.876 angstroms; (across all 924 pairs:
4.011)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, 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'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_10.pdb, chain A
(#2), sequence alignment score = 3480.9
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7ed5.pdb #1/A,
MERS_NSP12_current_best_10.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 700 pruned atom pairs is 0.876 angstroms; (across all 924 pairs:
4.011)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, 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'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [942] RMSD: 6.114
> ui mousemode right select
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [691] RMSD: 1.794
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [693] RMSD: 0.851
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [717] RMSD: 0.256
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [718] RMSD: 0.298
> show sel atoms
> style sel ball
Changed 16 atom styles
> style sel stick
Changed 16 atom styles
> color sel cyan
> color sel magenta
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [619-624] RMSD: 3.590
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [626-628] RMSD: 0.820
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [602-609] RMSD: 0.657
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [618-627] RMSD: 2.919
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [647-654] RMSD: 4.207
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [655-656] RMSD: 0.483
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [646] RMSD: 1.095
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [645] RMSD: 1.303
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel purple
> color sel magenta
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [647-654] RMSD: 4.207
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [655-659] RMSD: 0.476
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [661-674] RMSD: 0.935
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [692-703] RMSD: 1.585
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [707-719] RMSD: 3.521
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [703-704] RMSD: 2.939
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [707-719] RMSD: 3.521
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [721-733] RMSD: 0.458
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [767-775] RMSD: 0.528
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [783-793] RMSD: 0.714
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [810] RMSD: 0.521
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [798-803] RMSD: 0.455
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [811-825] RMSD: 1.586
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [825] RMSD: 2.433
> show sel atoms
> style sel stick
Changed 18 atom styles
> color sel magenta
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [632-636] RMSD: 0.695
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [616-625] RMSD: 3.048
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [631-645] RMSD: 0.794
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [646-660] RMSD: 3.101
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [650] RMSD: 1.658
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel magenta
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [553] RMSD: 0.818
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [560] RMSD: 0.976
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [542-549] RMSD: 1.189
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [527-540] RMSD: 2.633
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [511-525] RMSD: 1.348
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [496-510] RMSD: 0.699
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [481-495] RMSD: 1.359
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [466-480] RMSD: 2.437
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [451-465] RMSD: 3.800
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [436-450] RMSD: 4.422
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [421-435] RMSD: 9.977
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [406-420] RMSD: 13.935
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [391-405] RMSD: 1.107
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [901-959] RMSD: 11.163
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [856-900] RMSD: 5.450
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [811-855] RMSD: 2.411
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [766-810] RMSD: 0.625
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [721-765] RMSD: 0.787
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [676-720] RMSD: 2.456
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [631-675] RMSD: 1.928
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [616-630] RMSD: 2.522
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [571-615] RMSD: 1.404
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [604] RMSD: 0.625
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [578] RMSD: 2.631
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [572] RMSD: 1.561
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [578] RMSD: 2.631
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [580] RMSD: 2.597
> show sel atoms
> style sel stick
Changed 22 atom styles
> color sel byelement
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [586-612] RMSD: 0.742
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [617-630] RMSD: 2.573
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [631-643] RMSD: 0.705
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [650] RMSD: 1.658
> color sel byelement
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [633-640] RMSD: 0.718
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [621-628] RMSD: 2.668
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [648-657] RMSD: 3.052
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [693-704] RMSD: 1.846
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [707-718] RMSD: 3.662
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [718] RMSD: 0.298
> color sel byhetero
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [647-656] RMSD: 3.769
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [650] RMSD: 1.658
> color sel magenta
> color sel byhetero
> color sel yellow
> color sel byelement
> color sel yellow
> color sel byhetero
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [677-688] RMSD: 0.769
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [691-704] RMSD: 1.813
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [708-719] RMSD: 3.301
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [711] RMSD: 5.739
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [718] RMSD: 0.298
> color sel yellow
> color sel byhetero
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [752-765] RMSD: 1.256
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [769-778] RMSD: 0.490
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [781-793] RMSD: 0.727
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [797-804] RMSD: 0.432
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [799-824] RMSD: 1.201
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [825] RMSD: 2.433
> color sel yellow
> color sel byhetero
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [826-898] RMSD: 4.613
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [346-389] RMSD: 0.969
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [465] RMSD: 1.754
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [466-510] RMSD: 1.661
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [511-570] RMSD: 1.600
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [616-659] RMSD: 2.378
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [723-733] RMSD: 0.451
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [739-749] RMSD: 0.374
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [706-735] RMSD: 2.566
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [718] RMSD: 0.298
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [676-705] RMSD: 1.600
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [586-615] RMSD: 0.775
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [556-571] RMSD: 0.823
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [932-959] RMSD: 11.199
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [196-285] RMSD: 0.601
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [286-360] RMSD: 0.689
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [361-435] RMSD: 7.714
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [436-495] RMSD: 3.232
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [496-555] RMSD: 1.587
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [556-615] RMSD: 1.281
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [706-750] RMSD: 2.109
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [751-825] RMSD: 1.017
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [886-900] RMSD: 2.612
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [871-885] RMSD: 8.670
> select #2/A:619
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:619
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:618@CB
1 atom, 1 residue, 1 model selected
> select #2/A:619
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select #1/A:618@CG
1 atom, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> color sel byelement
> color sel yellow
Drag select of 16 residues, 2 atoms, 1 bonds
> select #1/A:618
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:618
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select #1/A:553
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select #2/A:554
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select #1/A:545
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel yellow
> color sel byhetero
> select #2/A:546
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [189] RMSD: 0.217
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [243] RMSD: 0.247
> show sel atoms
> style sel stick
Changed 28 atom styles
> hide sel atoms
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [295] RMSD: 0.603
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [317] RMSD: 0.603
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [536] RMSD: 1.560
> show sel atoms
> style sel stick
Changed 25 atom styles
> hide sel atoms
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [598] RMSD: 0.805
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [625] RMSD: 1.042
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [721] RMSD: 0.539
> show sel atoms
> style sel stick
Changed 22 atom styles
> hide sel atoms
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [752] RMSD: 0.404
> show sel atoms
> hide sel atoms
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [768-769] RMSD: 0.640
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [772] RMSD: 0.772
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [809] RMSD: 0.491
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [820] RMSD: 0.711
> show sel atoms
> style sel stick
Changed 22 atom styles
> hide sel atoms
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [827] RMSD: 1.018
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [855] RMSD: 0.763
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [870] RMSD: 4.177
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel atoms
> style sel stick
Changed 22 atom styles
> show sel atoms
> hide sel atoms
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [886] RMSD: 3.860
> show sel atoms
> hide sel atoms
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [908] RMSD: 3.298
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_10.pdb,
chain A [678-680] RMSD: 0.603
> select clear
> select #2/A:219
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #1/A:218
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel yellow
> color sel byhetero
> select #1/A:209
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:209
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel yellow
> color sel byhetero
> select #1/A:209
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #2/A:35
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #1/A:125
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:35
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel yellow
> select #2/A:33
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:33
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #1/A:33
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel yellow
> color sel byhetero
> select #1/A:72
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> hide sel atoms
> select #2/A:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:73
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel yellow
> color sel byhetero
> select #2/A:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
MERS_NSP12_current_best_10.pdb #2/A ARG 76: phi -80.8, psi 137.5 trans
Changed 600 bond radii
> swapaa interactive sel ARG rotLib Dynameomics
MERS_NSP12_current_best_10.pdb #2/A ARG 76: phi -80.8, psi 137.5 trans
Changed 648 bond radii
> swapaa interactive sel ARG rotLib Richardson.common
MERS_NSP12_current_best_10.pdb #2/A ARG 76: phi -80.8, psi 137.5 trans
Changed 272 bond radii
> swapaa interactive sel ARG rotLib Richardson.mode
MERS_NSP12_current_best_10.pdb #2/A ARG 76: phi -80.8, psi 137.5 trans
Changed 272 bond radii
> color sel yellow
> color sel byhetero
> select #2/A:118
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #1/A:116
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:118
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:116
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel yellow
> color sel byhetero
> select #1/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> hide sel atoms
> select #1/A:118
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> select #1/A:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> hide sel atoms
> select #2/A:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> show sel atoms
> select #1/A:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel medium blue
> color sel cornflower blue
> hide sel atoms
> select #2/A:217
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:216
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> hide sel atoms
> select #2/A:218
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #1/A:217
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel yellow
> color sel byhetero
> ui tool show Distances
> select #1/A:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> hide sel atoms
> select #2/A:52
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #1/A:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel yellow
> color sel byhetero
> select #1/A:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #2/A:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #1/A:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> color sel yellow
> color sel byhetero
> select #1/A:116
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:118
11 atoms, 10 bonds, 1 residue, 1 model selected
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 47, in display
self._current_option)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/manager.py", line 91, in
save_args_string_from_widget
provider_info.format_name, self).save_args_string_from_widget(widget)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 189, in save_args_string_from_widget
return widget.options_string()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/options.py", line 35, in options_string
raise UserError("No %s to save" % self._name.lower())
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/options.py", line 35, in options_string
raise UserError("No %s to save" % self._name.lower())
See log for complete Python traceback.
> save "/home/pierre/ownCloud/Construction model/test.cxs"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 658, in take_snapshot
'region browser': self.region_browser.save_state(),
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff1b83810d0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff13f2b3050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff1b83810d0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff13f2b3050>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 510.54
OpenGL renderer: Quadro RTX 3000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7550
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 16 Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz
Cache Size: 16384 KB
Memory:
total used free shared buff/cache available
Mem: 30Gi 13Gi 5.7Gi 243Mi 12Gi 17Gi
Swap: 30Gi 231Mi 30Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics [8086:9bc4] (rev 05)
DeviceName: Onboard - Video
Subsystem: Dell Device [1028:09c3]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Lots of previously fixed problems |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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