id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3119 pseudobond's atoms pb_scene_coord is None(?) jeremy.force@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 0.94 (2020-04-14) Description (Describe the actions that caused this problem to occur here) 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 3ZBF format mmCIF fromDatabase pdb 3zbf title: Structure of Human ROS1 Kinase Domain in Complex with Crizotinib [more info...] Chain information for 3zbf #1 --- Chain | Description A | proto-oncogene tyrosine-protein kinase ros Non-standard residues in 3zbf #1 --- VGH — 3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine (crizotinib) > preset cartoons/nucleotides ribbons/slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > select ::name=""HOH""::name=""VGH"" 167 atoms, 33 bonds, 1 model selected > delete atoms sel > delete bonds sel > color bynucleotide > color bynucleotide > select /A 2260 atoms, 2311 bonds, 2 pseudobonds, 2 models selected > rainbow sel > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > undo > redo > select 2260 atoms, 2311 bonds, 2 pseudobonds, 2 models selected > undo > preset cartoons/nucleotides ribbons/slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > show sel cartoons > show sel cartoons > show sel surfaces > hide sel surfaces > hide sel cartoons > hide sel cartoons > show sel cartoons > show sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > ~select #1 1 model selected > select #1 2260 atoms, 2311 bonds, 2 pseudobonds, 2 models selected > ~select #1 1 model selected > color bychain > color bychain > rainbow > hbonds The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A ARG 2230 N 263 hydrogen bonds found > hide atoms > show atoms > hide atoms > show atoms > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > undo > rainbow > select 2260 atoms, 2311 bonds, 265 pseudobonds, 3 models selected > show sel atoms > hide sel surfaces > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > rainbow sel > show sel atoms > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A ARG 2230 N 263 hydrogen bonds found > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A ARG 2230 N 263 hydrogen bonds found > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A ARG 2230 N 263 hydrogen bonds found > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A ARG 2230 N 263 hydrogen bonds found > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A ARG 2230 N 263 hydrogen bonds found > preset ""molecular surfaces"" ""ghostly white"" Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > toolshed show ViewDockX No suitable models found for ViewDockX > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > select 2260 atoms, 2311 bonds, 265 pseudobonds, 3 models selected > ~select #1 1 model selected > set bgColor black > set bgColor white Empty filename passed to function Empty filename passed to function > save2 ""/Users/jf119/Downloads/ROS1_no criz.pdb"" > open2 /Users/jf119/Desktop/ROS1_ATP.pdb > close session > open2 ""/Users/jf119/Desktop/ROS1 ATP/ROS1 ATP V1.pdb"" Chain information for ROS1 ATP V1.pdb #1 --- Chain | Description A | No description available > open2 ""/Users/jf119/Desktop/ROS1 ATP/ROS1_model 1.pdb"" > open2 ""/Users/jf119/Desktop/ROS1 ATP/ROS1_model 7.pdb"" > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > undo > show #3 models > select #1/A 2753 atoms, 2804 bonds, 4 pseudobonds, 2 models selected > select clear > select clear > hide #3 models > show #3 models > select #1/A 2753 atoms, 2804 bonds, 4 pseudobonds, 2 models selected > select ~sel 84 atoms, 88 bonds, 2 models selected > delete atoms sel > delete bonds sel > open2 ""/Users/jf119/Desktop/ROS1 ATP/ROS1_model 1.pdb"" > cartoon > select #1/A 2753 atoms, 2804 bonds, 4 pseudobonds, 2 models selected > cartoon style sel xsection oval modeHelix default > cartoon sel > show (sel-residues & sidechain) target ab > cartoon style sel xsection rectangle modeHelix default > cartoon style sel xsection oval modeHelix default > cartoon style sel xsection rectangle modeHelix default > preset ""molecular surfaces"" ""ghostly white"" Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > show (sel-residues & sidechain) target ab > hide sel target a > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""ghostly white"" Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""space-filling (chain colors)"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""space-filling (single color)"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""ghostly white"" Changed 2753 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""ghostly white"" Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > rainbow sel > color sel bynucleotide > mlp sel Map values for surface ""ROS1 ATP V1.pdb_A SES surface"": minimum -29.32, mean -3.722, maximum 22.64 > select clear > toolshed show Rotamers No residues selected Alignment identifier is 1.A > toolshed show Rotamers > show (sel-residues & sidechain) target ab > toolshed show Rotamers > swapaa interactive sel GLY rotLib Richardson.mode > swapaa sel GLY rotLib Richardson.mode Using Richardson.mode library Swapping ROS1 ATP V1.pdb #1/A SER 1953 to GLY > toolshed show Rotamers > swapaa interactive sel SER rotLib Richardson.mode ROS1 ATP V1.pdb #1/A GLY 1953: phi -128.8, psi none trans Changed 9 bond radii > swapaa #1/A:1953 SER criteria 1 rotLib Richardson.mode Using Richardson.mode library ROS1 ATP V1.pdb #1/A GLY 1953: phi -128.8, psi none trans Applying SER rotamer (chi angles: 64.0) to ROS1 ATP V1.pdb #1/A SER 1953 > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: ROS1 ATP V1.pdb #1/A ARG 2230 N 0 hydrogen bonds found > select #1/A 2751 atoms, 2802 bonds, 4 pseudobonds, 2 models selected > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: ROS1 ATP V1.pdb #1/A ARG 2230 N 227 hydrogen bonds found Traceback (most recent call last): File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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 ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 63, in pbg_update self._update_graphics() File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 231, in _update_positions axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 754, in pb_scene_coords v[i] = a.pb_scene_coord File ""cymol.pyx"", line 242, in chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__ File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) TypeError: Cannot multiply Place times ""None"" Error processing trigger ""changes"": TypeError: Cannot multiply Place times ""None"" File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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 ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 185, in _update_graphics_if_needed self._update_graphics(gc) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 231, in _update_positions axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 754, in pb_scene_coords v[i] = a.pb_scene_coord File ""cymol.pyx"", line 242, in chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__ File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) TypeError: Cannot multiply Place times ""None"" Error processing trigger ""graphics update"": TypeError: Cannot multiply Place times ""None"" File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) See log for complete Python traceback. > ~select #3 2751 atoms, 2802 bonds, 4 pseudobonds, 3 models selected > hide #3 models Traceback (most recent call last): File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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 ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 63, in pbg_update self._update_graphics() File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 231, in _update_positions axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 754, in pb_scene_coords v[i] = a.pb_scene_coord File ""cymol.pyx"", line 242, in chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__ File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) TypeError: Cannot multiply Place times ""None"" Error processing trigger ""model display changed"": TypeError: Cannot multiply Place times ""None"" File ""/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) 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 Graphics duplicate all ChimeraX