id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2795 Problem with intra-mol excluded H-bond detection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2019-12-24) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.92 (2019-12-24) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_in.pdb bcrp_az628_in.pdb title: Structure of inhibitor-bound ABCG2 [more info...] Chain information for bcrp_az628_in.pdb #1 --- Chain | Description A B | No description available Non-standard residues in bcrp_az628_in.pdb #1 --- CL — (CL) POPC — (popc) SPC — (SPC) > close session > open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_in.pdb bcrp_az628_in.pdb title: Full System [more info...] Chain information for bcrp_az628_in.pdb #1 --- Chain | Description A B | No description available Non-standard residues in bcrp_az628_in.pdb #1 --- CL — (CL) POPC — (popc) SPC — (SPC) Expected an objects specifier or a keyword > select #1/CL Nothing selected > select ::name=""CL"" 23 atoms, 1 model selected > hide ::name=""CL"" > hide ::name=""SPC"" > hide ::name=""POPC"" > hide #1 atoms > show ::name=""UNK"" Expected a keyword Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > set bgColor white > open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_out.pdb bcrp_az628_out.pdb title: Full System [more info...] Chain information for bcrp_az628_out.pdb #2 --- Chain | Description A B | No description available Non-standard residues in bcrp_az628_out.pdb #2 --- CL — (CL) POPC — (popc) SPC — (SPC) > hide ::name=""CL"" ::name=""SPC"" ::name=""POPC"" > hide #2 atoms > show ::name=""UNK"" > show #2::name=""UNK"" > show sel atoms > hide sel atoms > select ::name=""UNK"" 124 atoms, 134 bonds, 2 models selected > show sel atoms > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > close session > open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_in.pdb bcrp_az628_in.pdb title: Full System [more info...] Chain information for bcrp_az628_in.pdb #1 --- Chain | Description A B | No description available Non-standard residues in bcrp_az628_in.pdb #1 --- CL — (CL) POPC — (popc) SPC — (SPC) > open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/bcrp_az628_out.pdb bcrp_az628_out.pdb title: Full System [more info...] Chain information for bcrp_az628_out.pdb #2 --- Chain | Description A B | No description available Non-standard residues in bcrp_az628_out.pdb #2 --- CL — (CL) POPC — (popc) SPC — (SPC) > select up Nothing selected > hide ::name=""CL"" ::name=""SPC"" ::name=""POPC"" > hide atoms > show ::name=""UNK"" > toolshed show ""Side View"" > lighting soft > color ::name=""UNK"" byhetero > color ::name=""UNK"" byhetero > select #1 #2 275284 atoms, 216744 bonds, 24 pseudobonds, 4 models selected > select #1::name='UNK' 62 atoms, 67 bonds, 1 model selected > color #1::name='UNK' byhetero Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #2::name='UNK' #E97B74 > color #2::name='UNK' byhetero > color #2::name='UNK' #9C5F9F > color #2::name='UNK' byhetero > select #2 137642 atoms, 108372 bonds, 12 pseudobonds, 2 models selected > ~select #2::name='UNK' 137580 atoms, 108305 bonds, 12 pseudobonds, 2 models selected > color sel #E7C69A > color sel #E97B74 > ~select Nothing selected > select #1/B:535-551 #1/A:392-412 #1/A:536-551 #1/A:438-450 1053 atoms, 1058 bonds, 1 model selected > select #1/B:535-551 #1/A:392-412 #1/A:536-551 #1/A:438-450 #2/B:535-551 > #2/A:392-412 #2/A:536-551 #2/A:438-450 2106 atoms, 2116 bonds, 2 models selected > select ~sel 273178 atoms, 214628 bonds, 24 pseudobonds, 4 models selected > ~select ::name='UNK' 273054 atoms, 214494 bonds, 24 pseudobonds, 4 models selected > transparency sel 100 target c > ~select Nothing selected > graphics silhouettes true > toolshed show H-Bonds > hbonds intraModel false twoColors true intraMol false intraRes false 18328 hydrogen bonds found Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/tool.py"", line 49, in run_hbonds run(self.session, "" "".join(self.gui.get_command())) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py"", line 144, in cmd_hbonds precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]] UnboundLocalError: local variable 'hb' referenced before assignment UnboundLocalError: local variable 'hb' referenced before assignment File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py"", line 144, in cmd_hbonds precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]] See log for complete Python traceback. > save image /Users/Jphild/Documents/Papers/*JW- > AZ628_ABCG2/8_docking/md_az628.tif format tiff pixelSize 0.03 supersample 10 > cartoon style width 1.3 > cartoon style arrowScale 2 > lighting depthCueStart .4 depthCueEnd .8 > lighting gentle > lighting soft > graphics silhouettes width 1 > save image /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/md_az628.tif > format tiff pixelSize 0.03 supersample 10 > color #2::name='UNK' #E97B74 > color #2::name='UNK' byhetero > save image /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/md_az628.tif > format tiff pixelSize 0.03 supersample 10 > save session /Users/Jphild/Documents/Papers/*JW- > AZ628_ABCG2/9_md/md_az628.cxs Expected fewer arguments > lighting depthCueStart 1 depthCueEnd 1 > save image /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/md_az628.tif > format tiff pixelSize 0.03 supersample 10 > select #1 #2 275284 atoms, 216744 bonds, 24 pseudobonds, 4 models selected > transparency sel 0 target c > ~select Nothing selected > surface protein > hide #1 atoms > hide #2 atoms > lighting simple > lighting flat > lighting simple > show #1::name='UNK' > show #2::name='UNK' > lighting full > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting simple > transparency #1 50 > transparency #2 50 > hide #1 cartoons > hide #2 cartoons > transparency #1 100 > transparency #1 0 > hide #2 > hide #2 surfaces > show #1::name='UNK' > show #2::name='UNK' > lighting soft > view > view > lighting soft > lighting full > lighting soft > graphics silhouettes false > graphics silhouettes true > set bgColor gray > set bgColor white > lighting soft > lighting full > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting gentle > cartoon style width 1.3 > lighting depthCueStart .4 depthCueEnd .8 > lighting depthCueStart 1 depthCueEnd .8 > lighting depthCueStart 1 depthCueEnd 1 > lighting depthCueStart 0.5 depthCueEnd 1 > lighting depthCueStart 1 depthCueEnd 1 > save image /Users/Jphild/Documents/Papers/*JW- > AZ628_ABCG2/9_md/md_az628_surf)full.tif format tiff pixelSize 0.03 > supersample 10 > lighting soft > save image /Users/Jphild/Documents/Papers/*JW- > AZ628_ABCG2/9_md/md_az628_surf.tif format tiff pixelSize 0.03 supersample 10 > surface #1::name='UNK' > surface #2::name='UNK' > transparency #2.4 50 > transparency #1.4 50 > transparency #1.4 60 > transparency #2.4 60 > save image /Users/Jphild/Documents/Papers/*JW- > AZ628_ABCG2/9_md/md_az628_surf.tif format tiff pixelSize 0.03 supersample 10 > view > save image /Users/Jphild/Documents/Papers/*JW- > AZ628_ABCG2/9_md/md_az628_surf_full.tif format tiff pixelSize 0.03 > supersample 10 > save session /Users/Jphild/Documents/Papers/*JW- > AZ628_ABCG2/9_md/md_az628_surf.cxs > close session > open /Users/Jphild/Documents/Papers/*JW-AZ628_ABCG2/9_md/md_az628.cxs opened ChimeraX session > toolshed show H-Bonds > hbonds interModel false twoColors true intraMol false intraRes false 93601 hydrogen bonds found Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/tool.py"", line 49, in run_hbonds run(self.session, "" "".join(self.gui.get_command())) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py"", line 144, in cmd_hbonds precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]] UnboundLocalError: local variable 'hb' referenced before assignment UnboundLocalError: local variable 'hb' referenced before assignment File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py"", line 144, in cmd_hbonds precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]] See log for complete Python traceback. > hide #1 > hide #1 cartoons > toolshed show ""Side View"" > show #2/A:446 atoms > show #2/A:446,535,538,539,542,545 #2/B:535,538-539,542 atoms > color #2/A:446,535,538,539,542,545 #2/B:535,538-539,542 byhetero > toolshed show H-Bonds > hbonds interModel false twoColors true intraMol false intraRes false 93601 hydrogen bonds found Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/tool.py"", line 49, in run_hbonds run(self.session, "" "".join(self.gui.get_command())) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py"", line 144, in cmd_hbonds precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]] UnboundLocalError: local variable 'hb' referenced before assignment UnboundLocalError: local variable 'hb' referenced before assignment File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/hbonds/cmd.py"", line 144, in cmd_hbonds precise[:] = [hb for hb in precise is mol_map[hb[0]] != mol_map[hb[1]]] See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.4.7 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc. }}} " defect closed normal Structure Analysis fixed all ChimeraX