id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4950 KeyError in map menu ria2@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-4.19.0-17-amd64-x86_64-with-debian-10.5 ChimeraX Version: 0.91 (2019-09-21) Description Trying to save map after erase outside sphere Log: Startup Messages --- warning | could not retrieve bundle list from toolshed notes | available bundle cache has not been initialized yet Updating list of available bundles failed: Internal Server Error UCSF ChimeraX version: 0.91 (2019-09-21) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /storage/ria2/Zika/2021-02-19_Zika7/relion_processing/Refine3D/job039/run_class001.mrc Opened run_class001.mrc, grid size 400,400,400, pixel 2.2, shown at level 0.0181, step 2, values float32 > close session > open /storage/ria2/CPV/CPV-oligo15/LocalRec/run_class001_job247.mrc Opened run_class001_job247.mrc, grid size 420,420,420, pixel 1.1, shown at level 0.0456, step 2, values float32 > open /storage/ria2/CPV/CPV-oligo15/LocalRec/CPV-outershell_job247.mrc Opened CPV-outershell_job247.mrc, grid size 420,420,420, pixel 1.1, shown at level 0.0456, step 2, values float32 > toolshed show ""Map Coordinates"" > hide #!1 models > ui mousemode rightMode clip > hide #!2 models > open /storage/ria2/CPV/CPV-oligo15/phenix- refinement/RealSpaceRefine_25/VP2-DNA-hex_chID_real_space_refined_025.pdb Chain information for VP2-DNA-hex_chID_real_space_refined_025.pdb #3 --- Chain | Description A D G J M P | No description available B E H K N Q | No description available C F I L O R | No description available > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > ui mousemode rightMode clip > ui mousemode rightMode clip > ui mousemode rightMode clip > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > show cartoons > hide atoms > close #3 > open /storage/ria2/CPV/CPV-oligo15/phenix-refinement/VP2-mon-Gly29-rbuild- DNA.pdb Summary of feedback from opening /storage/ria2/CPV/CPV-oligo15/phenix- refinement/VP2-mon-Gly29-rbuild-DNA.pdb --- warnings | Ignored bad PDB record found on line 20 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.008 0.078 4477 Ignored bad PDB record found on line 23 ANGLE : 0.863 10.174 6127 Ignored bad PDB record found on line 24 CHIRALITY : 0.059 0.259 659 16 messages similar to the above omitted Chain information for VP2-mon-Gly29-rbuild-DNA.pdb #3 --- Chain | Description 1 | No description available N | No description available > close #3 > open /storage/ria2/CPV/CPV-oligo15/phenix-refinement/chains_VP2-icos- Gly29-DNA.pdb Summary of feedback from opening /storage/ria2/CPV/CPV-oligo15/phenix- refinement/chains_VP2-icos-Gly29-DNA.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 271100 messages similar to the above omitted Chain information for chains_VP2-icos-Gly29-DNA.pdb #3 --- Chain | Description a d g j m p s v | No description available a c d f g i j l m o p r s u v x y z | No description available b c e f h i k l n o q r t u w x y z | No description available b e h k n q t w | No description available > hide atoms > show cartoons > show cartoons > ui mousemode rightMode clip > hide #!1 models Expected a keyword Expected a keyword > select nucleic 12720 atoms, 14040 bonds, 1 model selected > ~ribbon ~sel > ui mousemode rightMode ""map eraser"" > display sel > show #!1 models > open /storage/ria2/CPV/CPV-oligo15/phenix-refinement/run_class001-job190.mrc Opened run_class001-job190.mrc, grid size 420,420,420, pixel 1.1, shown at level 0.0431, step 2, values float32 > hide #!1 models > volume erase #5 center 231,231,231 radius 101.87 outside true > ui mousemode rightMode clip > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > save /storage/ria2/CPV/CPV- oligo15/processing_relion31/run_class001_map190-DNAcore.mrc models #6 Traceback (most recent call last): File ""/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 871, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 601, in file_save_cb self.save_dialog.display(self, session) File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 114, in display fmt.update(session, self) File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/map/savemap.py"", line 67, in update self._map_menu.value = m File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 273, in value or (val is not None and self.value == val): File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 81, in _sleep_check self._items_change() File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 291, in _items_change prev_value = self.value File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 259, in value return self.item_map[text] KeyError: 'run_class001-job190.mrc copy #6' KeyError: 'run_class001-job190.mrc copy #6' File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 259, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 871, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 601, in file_save_cb self.save_dialog.display(self, session) File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 114, in display fmt.update(session, self) File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/map/savemap.py"", line 67, in update self._map_menu.value = m File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 273, in value or (val is not None and self.value == val): File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 259, in value return self.item_map[text] KeyError: 'run_class001-job190.mrc copy #6' KeyError: 'run_class001-job190.mrc copy #6' File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 259, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 871, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 601, in file_save_cb self.save_dialog.display(self, session) File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 114, in display fmt.update(session, self) File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/map/savemap.py"", line 67, in update self._map_menu.value = m File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 273, in value or (val is not None and self.value == val): File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 259, in value return self.item_map[text] KeyError: 'run_class001-job190.mrc copy #6' KeyError: 'run_class001-job190.mrc copy #6' File ""/opt/chimerax/daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 259, in value return self.item_map[text] See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.31 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal General Controls duplicate all ChimeraX