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#3038 closed defect (fixed)
Restoring session: 'SymmetryManager' object has no attribute '_unit_cell'
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-5.3.0-46-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.93 (2020-04-03) Description Re-opening a session saved with ISOLDE Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. > open2 /home/luca/umod/4p9A/isolde.cxs Log from Sun Apr 12 15:06:59 2020UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open2 /home/luca/umod/4p9A/alena_199_real_space_refined_featured.pdb Summary of feedback from opening <_io.textiowrapper name="/home/luca/umod/4p9A/alena_199_real_space_refined_featured.pdb" mode="rt" encoding="utf-8"> --- warnings | Ignored bad PDB record found on line 61 REMARK SECONDARY STRUCTURE ASSIGNED BY STRIDE Ignored bad PDB record found on line 112 REMARK DISULFIDE BONDS ASSIGNED BY SSBOND Chain information for alena_199_real_space_refined_featured.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > color byhetero > color byhetero > color bychain > color byhetero > open2 /home/luca/umod/4p9A/denmod_i21_map_normalized_cellfixed.ccp4 Opened denmod_i21_map_normalized_cellfixed.ccp4, grid size 146,249,249, pixel 1.06, shown at level 0.179, step 1, values float32 > volume #2 level 0.5359 > volume #2 style mesh > volume #2 color #729fcf Unknown command: assoc #2 to #1 > clipper associate #2 toModel #1 Chain information for alena_199_real_space_refined_featured.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available > close session Deleting atomic symmetry model... > isolde start > set selectionWidth 4 Done loading forcefield > close session Expected a models specifier or a keyword > open2 /home/luca/umod/4p9A/alena_199_real_space_refined_featured.pdb Summary of feedback from opening <_io.textiowrapper name="/home/luca/umod/4p9A/alena_199_real_space_refined_featured.pdb" mode="rt" encoding="utf-8"> --- warnings | Ignored bad PDB record found on line 61 REMARK SECONDARY STRUCTURE ASSIGNED BY STRIDE Ignored bad PDB record found on line 112 REMARK DISULFIDE BONDS ASSIGNED BY SSBOND Chain information for alena_199_real_space_refined_featured.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > color bychain > color byhetero > open2 /home/luca/umod/4p9A/denmod_i21_map_normalized_cellfixed.ccp4 Opened denmod_i21_map_normalized_cellfixed.ccp4, grid size 146,249,249, pixel 1.06, shown at level 0.179, step 1, values float32 > volume #2 level 0.9942 > volume #2 level 0.709 > transparency 50 > volume #2 color #729fcf > transparency 0 > transparency 50 > volume #2 level 0.4544 > clipper associate #2 toModel #1 Chain information for alena_199_real_space_refined_featured.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available > isolde start > set selectionWidth 4 Done loading forcefield > clipper spotlight radius 13.00 > clipper spotlight radius 14.00 > clipper spotlight radius 15.00 > clipper spotlight radius 16.00 > clipper spotlight radius 17.00 > clipper spotlight radius 18.00 > clipper spotlight radius 19.00 > clipper spotlight radius 20.00 > volume #1.1.1.1 level 0.6779 > save2 /home/luca/umod/4p9A/isolde.cxs Error processing trigger "end restore session": AttributeError: 'SymmetryManager' object has no attribute '_unit_cell' File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 867, in unit_cell return self._unit_cell See log for complete Python traceback. Summary of feedback from opening /home/luca/umod/4p9A/isolde.cxs --- warning | restore_snapshot for "RotamerRestraintMgr" returned None note | 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 "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1134, in _end_restore_session_cb self.add_model(self.structure) File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 594, in add_model self.spotlight_mode = spotlight_mode File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 243, in __setattr__ super(Drawing, self).__setattr__(key, value) File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 820, in spotlight_mode if self.atomic_symmetry_model is not None: File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 842, in atomic_symmetry_model return AtomicSymmetryModel(self, self.spotlight_radius, live=self.spotlight_mode, debug=self._debug) File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1197, in __init__ self.live_scrolling = live File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 243, in __setattr__ super(Drawing, self).__setattr__(key, value) File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1393, in live_scrolling self._update_box() File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1455, in _update_box symops = self._current_symops = self.unit_cell.all_symops_in_box(box_corner_xyz, grid_dim, True, self._sym_search_frequency) File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1220, in unit_cell return self.manager.unit_cell File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 867, in unit_cell return self._unit_cell AttributeError: 'SymmetryManager' object has no attribute '_unit_cell' opened ChimeraX session 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 "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1609, in _model_changed_cb self.show_selection_in_context(*self._last_context_params) AttributeError: 'AtomicSymmetryModel' object has no attribute '_last_context_params' Error processing trigger "atoms changed": AttributeError: 'AtomicSymmetryModel' object has no attribute '_last_context_params' File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1609, in _model_changed_cb self.show_selection_in_context(*self._last_context_params) See log for complete Python traceback. 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 "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1611, in _model_changed_cb self._update_sym_coords() File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1617, in _update_sym_coords res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3]) TypeError: 'NoneType' object is not subscriptable Error processing trigger "atoms changed": TypeError: 'NoneType' object is not subscriptable File "/home/luca/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1617, in _update_sym_coords res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3]) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUSTeK COMPUTER INC. Model: ROG Strix GL10CS_GL10CS OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 8 Intel(R) Core(TM) i7-9700K CPU @ 3.60GHz Cache Size: 12288 KB Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1f02] (rev a1) Subsystem: ASUSTeK Computer Inc. Device [1043:210b] Kernel driver in use: nvidia
Change History (5)
comment:1 by , 6 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Restoring session: 'SymmetryManager' object has no attribute '_unit_cell' |
comment:2 by , 6 years ago
follow-up: 3 comment:3 by , 6 years ago
Thanks!
Best, Luca
------------------------------------------------------------------------
Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Member
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jovine@ki.se<mailto:luca.jovine@ki.se>
W3: http://jovinelab.org
------------------------------------------------------------------------
On 13 Apr 2020, at 18:29, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:
#3038: Restoring session: 'SymmetryManager' object has no attribute '_unit_cell'
------------------------------------+---------------------------
Reporter: luca.jovine@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+---------------------------
Comment (by Tristan Croll):
Hmm - thanks for reporting this. Looks like I've messed up session restore
while doing some recent rearrangements... will try to get a fix out in the
next day or two.
--
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comment:4 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed. I'd like to get a couple of other things done before pushing a new build out (should be either tonight or tomorrow) but if you desperately need to get back up and running in the meantime, it's a simple fix. Just open /home/luca/.local/share/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py in an editor, and swap the order of lines 594 and 595:
self.spotlight_mode = spotlight_mode
uc = self._unit_cell = Unit_Cell(model.atoms, self.cell, self.spacegroup, self.grid)
to
uc = self._unit_cell = Unit_Cell(model.atoms, self.cell, self.spacegroup, self.grid)
self.spotlight_mode = spotlight_mode
follow-up: 5 comment:5 by , 6 years ago
Thanks - and I can certainly wait a few days, no problem at all! Best regards, Luca När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.
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Hmm - thanks for reporting this. Looks like I've messed up session restore while doing some recent rearrangements... will try to get a fix out in the next day or two.