id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1779 ISOLDE picking: unsupported operand type(s) for -: 'NoneType' and 'NoneType' goddard@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.8 (2018-12-17) Description Right click and drag in ISOLDE, showing demo data, produced this error. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' note | Traceback (most recent call last): File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\core\toolshed\\\\__init__.py"", line 338, in __init__ self.init_available_from_cache(logger) File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\core\toolshed\\\\__init__.py"", line 445, in init_available_from_cache abc.load_from_cache() File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\core\toolshed\available.py"", line 61, in load_from_cache b = _build_bundle(d) File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\core\toolshed\available.py"", line 242, in _build_bundle keywords = _extract_extra_keywords(keywords) File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\core\toolshed\installed.py"", line 270, in _extract_extra_keywords all_kwds = [k.strip() for k in kwds.split(',')] AttributeError: 'list' object has no attribute 'split' UCSF ChimeraX version: 0.8 (2018-12-17) How to cite UCSF ChimeraX Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl unloading module chimerax.isolde Successfully installed ChimeraX-ISOLDE-1.0b2 Installed ChimeraX-ISOLDE (1.0b2) 'clip' is a prefix of an existing command 'clipper' > toolshed show ISOLDE Summary of feedback from opening C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\isolde\demo_data\3io0\before.pdb --- warning | Ignored bad PDB record found on line 3846 END before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description A | predicted microcompartment protein before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description 1.3/A | predicted microcompartment protein > set bgColor black > ui mousemode rightMode zoom > ui mousemode rightMode zoom > vr on started SteamVR rendering > clip off VR mode select > vr off > vr off > select up 19 atoms, 18 bonds, 1 model selected > vr off reverting to start > ui mousemode rightMode zoom > select up 17 atoms, 16 bonds, 1 model selected > vr off > vr on started SteamVR rendering VR mode contour level > volume #1.1.1.3 level 0.2104 > volume #1.1.1.3 level 0.1786 > volume #1.1.1.3 level 0.1799 > volume #1.1.1.3 level 0.1752 > volume #1.1.1.3 level 0.4274 > volume #1.1.1.1 level 0.1753 Traceback (most recent call last): File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 436, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 367, in _dispatch_mouse_event f(MouseEvent(event)) File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\isolde\tugging.py"", line 95, in mouse_down pick = picking.pick_closest_to_line(self.session, x, y, self._atoms, 0.5) File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\isolde\picking.py"", line 25, in pick_closest_to_line length = numpy.linalg.norm(xyz2-xyz1) TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' File ""C:\Program Files\ChimeraX-0.8\bin\lib\site- packages\chimerax\isolde\picking.py"", line 25, in pick_closest_to_line length = numpy.linalg.norm(xyz2-xyz1) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.81 OpenGL renderer: Quadro P6000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party fixed Tom Goddard all ChimeraX