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Opened 6 years ago
Closed 6 years ago
#2104 closed defect (fixed)
Clipper: 'NXmapHandler' object has no attribute 'set_display_style'
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-02-21) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.9 (2019-02-21) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/sshakeel/Documents/LMB/Fanconi/Paper/Images4paper/maps_models/cropped_maps_4_faster_modelling/maps_models_270219/pp_bottom_res4p97_partsubflipZori190.mrc Opened pp_bottom_res4p97_partsubflipZori190.mrc, grid size 380,380,380, pixel 1.06, shown at level 0.00422, step 2, values float32 > open /Users/sshakeel/Documents/LMB/Fanconi/Paper/Images4paper/maps_models/cropped_maps_4_faster_modelling/maps_models_270219/phenix_processing/RealSpaceRefine_51/Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4.pdb Chain information for Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4.pdb #2 --- Chain | Description G | No description available I | No description available O | No description available P | No description available > close #2 > open /Users/sshakeel/Documents/LMB/Fanconi/Paper/Images4paper/maps_models/cropped_maps_4_faster_modelling/maps_models_270219/phenix_processing/RealSpaceRefine_53/Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4_real_space_refined.pdb Chain information for Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4_real_space_refined.pdb #2 --- Chain | Description G | No description available I | No description available O | No description available P | No description available > toolshed show ISOLDE Expected a keyword Expected a keyword Chain information for Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4_real_space_refined.pdb --- Chain | Description 2.3/G | No description available 2.3/I | No description available 2.3/O | No description available 2.3/P | No description available Done loading forcefield QWidget::repaint: Recursive repaint detected > select #2.3.4 3 models selected > select #2.3.3 2 models selected > select #2.3.2 2 models selected > select #2.3.1 13 pseudobonds, 2 models selected > addh hbond true Summary of feedback from adding hydrogens to Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4_real_space_refined.pdb #2.3 --- warnings | Not adding hydrogens to /O LEU 389 CA because it is missing heavy- atom bond partners Not adding hydrogens to /O THR 390 CA because it is missing heavy-atom bond partners Not adding hydrogens to /O ILE 391 CA because it is missing heavy-atom bond partners Not adding hydrogens to /O GLN 392 CA because it is missing heavy-atom bond partners Not adding hydrogens to /O ALA 393 CA because it is missing heavy-atom bond partners 698 messages similar to the above omitted notes | No usable SEQRES records for Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4_real_space_refined.pdb (#2.3) chain G; guessing termini instead No usable SEQRES records for Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4_real_space_refined.pdb (#2.3) chain I; guessing termini instead No usable SEQRES records for Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4_real_space_refined.pdb (#2.3) chain O; guessing termini instead No usable SEQRES records for Bottom_B100_WD40_helices_nonsym_real_space_refined_sidechains_stubbed- coot-4_real_space_refined.pdb (#2.3) chain P; guessing termini instead Chain-initial residues that are actual N termini: /G ALA 1, /I ALA 1, /O LEU 389 Chain-initial residues that are not actual N termini: /G ALA 100, /G ALA 118, /G ALA 150, /I ALA 30, /I ALA 68, /I ALA 76, /I ALA 100, /I ALA 118, /I ALA 128, /I ALA 138, /I ALA 232, /I ALA 244, /I ALA 288, /P LYS 461 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /G ALA 285, /G ALA 98, /G ALA 115, /G ALA 146, /I ALA 306, /I ALA 27, /I ALA 66, /I ALA 74, /I ALA 96, /I ALA 108, /I ALA 126, /I ALA 136, /I ALA 228, /I ALA 240, /I ALA 281, /O ALA 508, /P LEU 501 150 hydrogen bonds Adding 'H' to /G ALA 100 Adding 'H' to /G ALA 118 Adding 'H' to /G ALA 150 Adding 'H' to /I ALA 30 Adding 'H' to /I ALA 68 8 messages similar to the above omitted /G ALA 285 is not terminus, removing H atom from 'C' /G ALA 98 is not terminus, removing H atom from 'C' /G ALA 115 is not terminus, removing H atom from 'C' /G ALA 146 is not terminus, removing H atom from 'C' /I ALA 306 is not terminus, removing H atom from 'C' 12 messages similar to the above omitted 681 hydrogens added Traceback (most recent call last): File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/isolde/isolde.py", line 1445, in _add_real_space_map_from_gui self.add_real_space_map(existing_volume=v, to_model=self.selected_model) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/isolde/isolde.py", line 1337, in add_real_space_map nxmap = map_mgr.nxmapset.add_nxmap_handler_from_volume(existing_volume) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 57, in add_nxmap_handler_from_volume self.set_nxmap_display_style(h) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 93, in set_nxmap_display_style nxmap_handler.set_display_style(style) AttributeError: 'NXmapHandler' object has no attribute 'set_display_style' AttributeError: 'NXmapHandler' object has no attribute 'set_display_style' File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 93, in set_nxmap_display_style nxmap_handler.set_display_style(style) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 3473, in _update_drawings v.update_drawings() File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 679, in update_drawings self._update_surfaces() File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 694, in _update_surfaces s.update_surface(show_mesh, ro) TypeError: update_surface() takes 2 positional arguments but 3 were given Error processing trigger "graphics update": update_surface() takes 2 positional arguments but 3 were given: TypeError: update_surface() takes 2 positional arguments but 3 were given File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 694, in _update_surfaces s.update_surface(show_mesh, ro) See log for complete Python traceback. > select #2.1 6 models selected > ~select #2.3 6 models selected > open /Users/sshakeel/Documents/LMB/Fanconi/Paper/Images4paper/maps_models/cropped_maps_4_faster_modelling/maps_models_270219/pp_bottom_res4p97_partsubflipZori190.mrc Opened pp_bottom_res4p97_partsubflipZori190.mrc, grid size 380,380,380, pixel 1.06, shown at level 0.00422, step 2, values float32 Traceback (most recent call last): File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/isolde/isolde.py", line 1445, in _add_real_space_map_from_gui self.add_real_space_map(existing_volume=v, to_model=self.selected_model) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/isolde/isolde.py", line 1337, in add_real_space_map nxmap = map_mgr.nxmapset.add_nxmap_handler_from_volume(existing_volume) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 57, in add_nxmap_handler_from_volume self.set_nxmap_display_style(h) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 93, in set_nxmap_display_style nxmap_handler.set_display_style(style) AttributeError: 'NXmapHandler' object has no attribute 'set_display_style' AttributeError: 'NXmapHandler' object has no attribute 'set_display_style' File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 93, in set_nxmap_display_style nxmap_handler.set_display_style(style) See log for complete Python traceback. > open /Users/sshakeel/Documents/LMB/Fanconi/Paper/Images4paper/maps_models/cropped_maps_4_faster_modelling/maps_models_270219/pp_bottom_res4p97_partsubflipZori190.mrc Opened pp_bottom_res4p97_partsubflipZori190.mrc, grid size 380,380,380, pixel 1.06, shown at level 0.00422, step 2, values float32 Traceback (most recent call last): File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/isolde/isolde.py", line 1445, in _add_real_space_map_from_gui self.add_real_space_map(existing_volume=v, to_model=self.selected_model) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/isolde/isolde.py", line 1337, in add_real_space_map nxmap = map_mgr.nxmapset.add_nxmap_handler_from_volume(existing_volume) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 57, in add_nxmap_handler_from_volume self.set_nxmap_display_style(h) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 93, in set_nxmap_display_style nxmap_handler.set_display_style(style) AttributeError: 'NXmapHandler' object has no attribute 'set_display_style' AttributeError: 'NXmapHandler' object has no attribute 'set_display_style' File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/maps/nxmapset.py", line 93, in set_nxmap_display_style nxmap_handler.set_display_style(style) See log for complete Python traceback. OpenGL version: 4.1 ATI-1.68.20 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc.
Change History (4)
comment:1 by , 6 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Clipper: 'NXmapHandler' object has no attribute 'set_display_style' |
follow-up: 2 comment:2 by , 6 years ago
I *think* this is happening because you’re using old versions of ISOLDE and Clipper I built for a workshop. There have been some API changes in ChimeraX between then and the official 0.9 release. Could you try reinstalling ISOLDE from the ToolShed (Tools/More Tools...) and see if this persists?
follow-up: 3 comment:3 by , 6 years ago
I *think* this is happening because you’re using old versions of ISOLDE and Clipper I built for a workshop. There have been some API changes in ChimeraX between then and the official 0.9 release. Could you try reinstalling ISOLDE from the ToolShed (Tools/More Tools...) and see if this persists?
comment:4 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Just cleaning up old tickets... this problem does not occur in any recent builds.
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Reported by Shabih Shakeel