id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2965 Clipper: 'XmapHandler_Live' object has no attribute 'set_display_style' folf@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-02-26) Description Install version 0.9 of ChimeraX on MacOS Mojave 10.14.6 Install Isolde Open pdb file (files are directly from phenix-1.17.1_3660) In Isolde- > load crystallographic dataset Log: UCSF ChimeraX version: 0.9 (2019-02-26) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-macosx_10_9_x86_64.whl > toolshed show ISOLDE Expected a keyword Expected a keyword Done loading forcefield > open /Users/folf/dtu/Folmer_shared/Projects/PsPL7A/CasperWork/Refine_66/PsAg17A_refine_66.pdb Summary of feedback from opening /Users/folf/dtu/Folmer_shared/Projects/PsPL7A/CasperWork/Refine_66/PsAg17A_refine_66.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-03-20 Time 07:34:33 Romance Standard Time +0100 (1584686073.30 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : D:\Phenix_PsAgl7A\AutoBuild_run_31_/exptl_fobs_phases_freeR_flags.mtz 57 messages similar to the above omitted Chain information for PsAg17A_refine_66.pdb #1 --- Chain | Description A | No description available Chain information for PsAg17A_refine_66.pdb --- Chain | Description 1.3/A | No description available QWidget::repaint: Recursive repaint detected > toolshed show '""Density Map Toolbar""' > toolshed hide '""Density Map Toolbar""' Expected a keyword > set bgColor white > set bgColor blue > set bgColor black > open /Users/folf/dtu/Folmer_shared/Projects/PsPL7A/CasperWork/Refine_66/PsAg17A_refine_66.mtz Must specify a structure model to associate with crystallographic data Must specify a structure model to associate with crystallographic data > open /Users/folf/dtu/Folmer_shared/Projects/PsPL7A/CasperWork/Refine_66/PsAg17A_refine_66.mtz Must specify a structure model to associate with crystallographic data Must specify a structure model to associate with crystallographic data Unknown command: ls > pwd Current working directory is: /Users/folf/Desktop WARNING: multiple experimental reflection datasets found: (Original-experimental-data-mapped-to-asu) F-obs, SIGF-obs, (Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered Automatically choosing ""(Original-experimental-data-mapped-to-asu) F-obs, SIGF-obs"". Traceback (most recent call last): File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 1256, in _choose_reflections_file self.add_xtal_data(filename) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 1283, in add_xtal_data xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/map_mgr.py"", line 271, in add_xmapset_from_mtz return self.add_xmapset_from_file(mtzfile, oversampling_rate) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/map_mgr.py"", line 291, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 241, in __init__ map_params) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 392, in _prepare_standard_live_maps exclude_missing_reflections=exclude_missing_reflections File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 469, in add_live_xmap contour=contour) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 436, in set_xmap_display_style xmap_handler.set_display_style(style) AttributeError: 'XmapHandler_Live' object has no attribute 'set_display_style' AttributeError: 'XmapHandler_Live' object has no attribute 'set_display_style' File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 436, in set_xmap_display_style xmap_handler.set_display_style(style) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 3489, in _update_drawings v.update_drawings() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 686, in update_drawings self._update_surfaces() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 701, 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.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 701, in _update_surfaces s.update_surface(show_mesh, ro) See log for complete Python traceback. WARNING: multiple experimental reflection datasets found: (Original-experimental-data-mapped-to-asu) F-obs, SIGF-obs, (Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered Automatically choosing ""(Original-experimental-data-mapped-to-asu) F-obs, SIGF-obs"". Traceback (most recent call last): File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 1256, in _choose_reflections_file self.add_xtal_data(filename) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 1283, in add_xtal_data xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/map_mgr.py"", line 271, in add_xmapset_from_mtz return self.add_xmapset_from_file(mtzfile, oversampling_rate) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/map_mgr.py"", line 291, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 241, in __init__ map_params) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 392, in _prepare_standard_live_maps exclude_missing_reflections=exclude_missing_reflections File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 469, in add_live_xmap contour=contour) File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 436, in set_xmap_display_style xmap_handler.set_display_style(style) AttributeError: 'XmapHandler_Live' object has no attribute 'set_display_style' AttributeError: 'XmapHandler_Live' object has no attribute 'set_display_style' File ""/Users/folf/Library/Application Support/ChimeraX/0.9/site- packages/chimerax/clipper/maps/xmapset.py"", line 436, in set_xmap_display_style xmap_handler.set_display_style(style) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.16 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc. }}} " defect closed normal Third Party fixed all ChimeraX