Opened 6 years ago

Closed 6 years ago

#2949 closed defect (duplicate)

"sequence chain" fails after chain lengthened

Reported by: ym337@… 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-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.92 (2020-03-08)
Description
Hi 

I am working with ISOLDE to build my model using ChimeraX interface. 

There I had added an deleted a few sequences in chain a. This was done while the sequence viewer was closed. 

Now, when I try to view the sequence by ' sequence chain #1/a', I am getting this error (attached as screenshot)



Could you please help? I hope I don't have to start from the begining.



Log:
UCSF ChimeraX version: 0.92 (2020-03-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed
'ChimeraX_ISOLDE-1.0b4.dev2-cp37-cp37m-linux_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/home/ym337/.cache/ChimeraX/0.92/installers/ChimeraX_ISOLDE-1.0b4.dev2-cp37-cp37m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
/nfs4/suffolk/MBU/software/chimerax/chimerax-0.92/lib/python3.7/site-packages
(from ChimeraX-ISOLDE==1.0b4.dev2) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.92 in
/nfs4/suffolk/MBU/software/chimerax/chimerax-0.92/lib/python3.7/site-packages
(from ChimeraX-ISOLDE==1.0b4.dev2) (0.92)  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper==0.11.* in
/nfs4/suffolk/Homes/ym337/.local/share/ChimeraX/0.92/site-packages (from
ChimeraX-ISOLDE==1.0b4.dev2) (0.11.1)  
Installing collected packages: ChimeraX-ISOLDE  
Attempting uninstall: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0b4.dev2  
Uninstalling ChimeraX-ISOLDE-1.0b4.dev2:  
Successfully uninstalled ChimeraX-ISOLDE-1.0b4.dev2  
Successfully installed ChimeraX-ISOLDE-1.0b4.dev2  
Lock 47072785360848 acquired on
/home/ym337/.cache/ChimeraX/0.92/toolshed/bundle_info.cache.lock  
Lock 47072785360848 released on
/home/ym337/.cache/ChimeraX/0.92/toolshed/bundle_info.cache.lock  
  

> open
> /nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job1613/isolde/working_CIII_CytC_4.cxs

Summary of feedback from opening
/nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job1613/isolde/working_CIII_CytC_4.cxs  
---  
warning | restore_snapshot for "RotamerRestraintMgr" returned None  
  
opened ChimeraX session  

> sequence chain #1/c

Alignment identifier is 1.1.c  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seqalign/cmd.py", line 141, in seqalign_chain  
auto_associate=None, intrinsic=True)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 244, in new_alignment  
alignment=alignment)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 453, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1632, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/__init__.py", line 40, in run_provider  
return _start_seq_viewer(session, "Sequence Viewer", alignment)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 693, in _start_seq_viewer  
return SequenceViewer(session, tool_name, alignment)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 55, in __init__  
self._finalize_init(alignment)  
File "/usr/mbu/software/chimerax/chimerax-0.92/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/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 184, in __init__  
self.layout_alignment()  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 780, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1602, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2244, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2237, in _layout_line  
numberings[numbering] = self._make_numbering(line, numbering)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2329, in _make_numbering  
x, y = self.item_aux_info[line][-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2329, in _make_numbering  
x, y = self.item_aux_info[line][-1]  
  
See log for complete Python traceback.  
  

Unknown command: sequenchain /d  

> sequence chain #1/d

Alignment identifier is 1.1.d  

> isolde start

> set selectionWidth 4

Done loading forcefield  
Traceback (most recent call last):  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2549, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2558, in _xtal_mask_to_atoms  
atoms, 0, context, cutoff, focus=focus)  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/clipper/symmetry.py", line 930, in
isolate_and_cover_selection  
extra_padding=extra_padding)  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/clipper/maps/map_mgr.py", line 358, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/clipper/maps/mask_handler.py", line 111, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/clipper/maps/mask_handler.py", line 176, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/clipper/maps/mask_handler.py", line 176, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  

> isolde restrain distances #1/d:3-434 templateAtoms #1/a:3-434

Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/restraints/cmd.py", line 48, in restrain_distances  
model_residues, **kwargs)  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/restraints/restraint_utils.py", line 527, in
restrain_atom_distances_to_template  
session, template_residues, restrained_residues  
ValueError: not enough values to unpack (expected 2, got 0)  
  
ValueError: not enough values to unpack (expected 2, got 0)  
  
File "/home/ym337/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/restraints/restraint_utils.py", line 527, in
restrain_atom_distances_to_template  
session, template_residues, restrained_residues  
  
See log for complete Python traceback.  
  

> select #1/a

7136 atoms, 7287 bonds, 1 model selected  

> select #1/d

7142 atoms, 7293 bonds, 1 model selected  

> select clear

> select clear

Found iron-sulfur cysteine  
Found iron-sulfur cysteine  
Found iron-sulfur cysteine  

> select clear

> save working_CIII_CytC_5.cxs

Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 616, 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/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x2ba79bdd9f50> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x2ba87fd6b6d0>  
  
RuntimeError: Error while saving session data for 'tools' -> ->  
  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 616, 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/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x2ba79bdd9f50> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x2ba87fd6b6d0>  
  
RuntimeError: Error while saving session data for 'tools' -> ->  
  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> save working_CIII_CytC_5.cxs

Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 616, 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/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x2ba79bdd9f50> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x2ba87fd6b6d0>  
  
RuntimeError: Error while saving session data for 'tools' -> ->  
  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 616, 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/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x2ba79bdd9f50> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x2ba87fd6b6d0>  
  
RuntimeError: Error while saving session data for 'tools' -> ->  
  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

Empty filename passed to function  

> save session
> /work/complex_iD/ym337/Para_SC_Biochem_16Inga19/PostProcess/CIII_cytc552_wrt_job1531_job1613/isolde/working_CIII_CytC_5.cxs

Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 616, 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/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x2ba79bdd9f50> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x2ba87fd6b6d0>  
  
RuntimeError: Error while saving session data for 'tools' -> ->  
  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 616, 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/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 935, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 651, in file_save_cb  
self.save_dialog.display(self, session)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 1100, in save  
run(session, cmd)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 992, in save_session  
save(session, filename, **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x2ba79bdd9f50> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x2ba87fd6b6d0>  
  
RuntimeError: Error while saving session data for 'tools' -> ->  
  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> sequence chain #1/d

Destroying pre-existing alignment with identifier 1.1.d  
Alignment identifier is 1.1.d  

> sequence chain #1/a

Alignment identifier is 1.1.a  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seqalign/cmd.py", line 141, in seqalign_chain  
auto_associate=None, intrinsic=True)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 244, in new_alignment  
alignment=alignment)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 453, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1632, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/__init__.py", line 40, in run_provider  
return _start_seq_viewer(session, "Sequence Viewer", alignment)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 693, in _start_seq_viewer  
return SequenceViewer(session, tool_name, alignment)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 55, in __init__  
self._finalize_init(alignment)  
File "/usr/mbu/software/chimerax/chimerax-0.92/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/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 184, in __init__  
self.layout_alignment()  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 780, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1602, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2244, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2237, in _layout_line  
numberings[numbering] = self._make_numbering(line, numbering)  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2329, in _make_numbering  
x, y = self.item_aux_info[line][-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/usr/mbu/software/chimerax/chimerax-0.92/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2329, in _make_numbering  
x, y = self.item_aux_info[line][-1]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: Screenshot from 2020-03-12 14-49-03.png

Screenshot from 2020-03-12 14-49-03.png​

Attachments (1)

Screenshot from 2020-03-12 14-49-03.png​ (704.2 KB ) - added by ym337@… 6 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by ym337@…, 6 years ago

Attachment: Screenshot from 2020-03-12 14-49-03.png​ added

Added by email2trac

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → "sequence chain" fails after chain lengthened

comment:2 by Eric Pettersen, 6 years ago

Resolution: → duplicate
Status: accepted → closed
Note: See TracTickets for help on using tickets.