id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3052 Toolbar icon image save → can't access Desktop jeremy.force@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 0.94 (2020-04-14) Description Unable to take snapshot of amino acid change with highlighted surrounding interactions in green Log: UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jf119/Downloads/3zbf 2.cif"" format mmCIF 3zbf 2.cif title: Structure of Human ROS1 Kinase Domain in Complex with Crizotinib [more info...] Chain information for 3zbf 2.cif #1 --- Chain | Description A | proto-oncogene tyrosine-protein kinase ros Non-standard residues in 3zbf 2.cif #1 --- VGH — 3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine (crizotinib) > lighting soft > toolshed show ""Blast Protein"" > blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name > bp1 Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service Opal job id: appBlastProtein2Service1587003720855-1159428074 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1587003720855-1159428074 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Alignment identifier is bp1 [1] Associated 3zbf 2.cif chain A to 3ZBF_A with 0 mismatches > show target ab > hide target a > show target ab > hide target a > show sel target ab > select sel :< 5 32 atoms, 29 bonds, 1 pseudobond, 2 models selected > select sel :< 5 164 atoms, 161 bonds, 1 pseudobond, 2 models selected > select /A:1953 6 atoms, 5 bonds, 1 model selected > toolshed show Rotamers > swapaa interactive sel GLY rotLib Dunbrack > swapaa sel GLY rotLib Dunbrack Using Dunbrack library Swapping /A SER 1953 to GLY > swapaa interactive sel GLY rotLib Dunbrack > swapaa sel GLY rotLib Dunbrack Using Dunbrack library Swapping /A GLY 1953 to GLY > select sel :< 5 30 atoms, 27 bonds, 1 pseudobond, 2 models selected > undo > undo Undo failed, probably because structures have been modified. > select sel :< 5 30 atoms, 27 bonds, 1 pseudobond, 2 models selected > select sel :< 5 162 atoms, 159 bonds, 1 pseudobond, 2 models selected > show sel target ab > undo > toolshed show Rotamers > select /A:1953 4 atoms, 3 bonds, 1 model selected > select sel :< 5 30 atoms, 27 bonds, 1 pseudobond, 2 models selected > select /A:1953 4 atoms, 3 bonds, 1 model selected > select sel :< 5 30 atoms, 27 bonds, 1 pseudobond, 2 models selected > select sel :< 5 162 atoms, 159 bonds, 1 pseudobond, 2 models selected Traceback (most recent call last): File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/tool.py"", line 162, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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 ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1634, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 1170, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 375, in try_shortcut self.run_shortcut(keys) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 393, in run_shortcut sc.run(self.session, status = self._enabled) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 312, in run f(s) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 1096, in save_image path = unused_file_name(directory, basename, suffix) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 1116, in unused_file_name files = listdir(dir) PermissionError: [Errno 1] Operation not permitted: '/Users/jf119/Desktop' PermissionError: [Errno 1] Operation not permitted: '/Users/jf119/Desktop' File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 1116, in unused_file_name files = listdir(dir) See log for complete Python traceback. OpenGL version: 4.1 ATI-3.8.24 OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Platform nonchimerax Greg Couch Tom Goddard all ChimeraX