id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3183 pb_scene_coord returning None vytautas.raskevicius@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-4.4.217-x86_64-Intel-R-_Core-TM-_i5-3570_CPU_@_3.40GHz-with-slackware-14.2 ChimeraX Version: 0.93 (2020-04-03) Description Just try to draw hydrogen bonds 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 > /home/vytautas/COVID-19_docking/Q96K12/robetta_models_22767_good_fix.pdb Chain information for robetta_models_22767_good_fix.pdb #1 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 2464, resource id: 8389166, major code: 40 (TranslateCoords), minor code: 0 > open2 /home/vytautas/COVID-19_docking/Q96K12/Conformer3D_CID_5884_out.pdbqt Opened Conformer3D_CID_5884_out.pdbqt containing 9 structures (531 atoms, 567 bonds) QXcbConnection: XCB error: 3 (BadWindow), sequence: 3901, resource id: 8389175, major code: 40 (TranslateCoords), minor code: 0 > hide #2.9 models > hide #2.8 models > hide #2.7 models > hide #2.6 models > hide #2.5 models > hide #2.4 models > hide #2.3 models > hide #2.2 models > set bgColor white > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > lighting full > lighting simple > lighting soft > lighting simple > hbonds #1#2.1 499 hydrogen bonds found Traceback (most recent call last): File ""/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 63, in pbg_update self._update_graphics() File ""/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File ""/home/vytautas/bin/chimerax/chimerax-0.93/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 ""/home/vytautas/bin/chimerax/chimerax-0.93/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 ""/home/vytautas/bin/chimerax/chimerax-0.93/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 ""/home/vytautas/bin/chimerax/chimerax-0.93/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 ""/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 185, in _update_graphics_if_needed self._update_graphics(gc) File ""/home/vytautas/bin/chimerax/chimerax-0.93/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File ""/home/vytautas/bin/chimerax/chimerax-0.93/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 ""/home/vytautas/bin/chimerax/chimerax-0.93/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 ""/home/vytautas/bin/chimerax/chimerax-0.93/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 ""/home/vytautas/bin/chimerax/chimerax-0.93/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: 3.3 (Core Profile) Mesa 11.2.2 OpenGL renderer: Mesa DRI Intel(R) Ivybridge Desktop OpenGL vendor: Intel Open Source Technology Center Manufacturer: System manufacturer Model: System Product Name OS: Slackware 14.2 Architecture: 64bit ELF CPU: 4 Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz Cache Size: 6144 KB Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation Xeon E3-1200 v2/3rd Gen Core processor Graphics Controller [8086:0152] (rev 09) Subsystem: ASUSTeK Computer Inc. P8H77-I Motherboard [1043:84ca] Kernel driver in use: i915 }}} " defect closed normal Graphics 0.93 duplicate all ChimeraX