id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3092 pb_scene_coord returning None kasey.jividen@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-04-03) Description contact command is generating data for bonds and showing residues, but not displaying bonds: ""contacts sel intraRes true select true reveal true"" Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open2 /Users/kjividen/Desktop/103119_Cas9Sso7d_color.cxs opened ChimeraX session Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.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-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py"", line 525, in rebuild _rebuild_molecule('internal', mol) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py"", line 652, in _rebuild_molecule hide_residues = make_ladder(nd, residues, mol._ladder_params) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py"", line 1191, in make_ladder midpt = c3p0[1] + mid * (c3p1[1] - c3p0[1]) TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' Error processing trigger ""new frame"": TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py"", line 1191, in make_ladder midpt = c3p0[1] + mid * (c3p1[1] - c3p0[1]) See log for complete Python traceback. > name frozen cas9 #3/b > select cas9 10940 atoms, 10877 bonds, 18 pseudobonds, 3 models selected > surface hide cas9 > hide sel atoms > style cas9 stick Changed 10940 atom styles > color #3/B: 1116, 1134, 1166, 1185, 1202, 1275, 1286, 1301 black > select #3/B: 1116, 1134, 1166, 1185, 1202, 1275, 1286, 1301 64 atoms, 58 bonds, 1 model selected > show sel atoms > contacts sel intraRes true select true reveal true 84 contacts Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.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-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 749, 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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 749, 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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 749, 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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 749, 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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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/B: 1116, 1134, 1166, 1185, 1202, 1275, 1286, 1301 64 atoms, 58 bonds, 1 model selected Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.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-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 749, 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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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. > contacts sel intraRes true select true reveal true 84 contacts Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.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-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 749, 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 ""/Applications/ChimeraX-0.93.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 ""/Applications/ChimeraX-0.93.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 INTEL-10.36.25 OpenGL renderer: Intel HD Graphics 4000 OpenGL Engine OpenGL vendor: Intel Inc. }}} " defect closed normal Graphics duplicate all ChimeraX