id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3122 sse.py → scipy cannot import _uarray chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: Windows-8.1-6.3.9600 ChimeraX Version: 0.94 (2020-04-28) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.94.dev202004282203 (2020-04-28) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_UI-1.0-py3-none-any.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\yonathan arfi\appdata\local\ucsf\chimerax\cache\0.94\installers\chimerax_ui-1.0-py3-none- any.whl Requirement already satisfied, skipping upgrade: ChimeraX-Core>=0.9 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-UI==1.0) (0.94.dev202004282203) Installing collected packages: ChimeraX-UI Attempting uninstall: ChimeraX-UI Found existing installation: ChimeraX-UI 1.0 Uninstalling ChimeraX-UI-1.0: Successfully uninstalled ChimeraX-UI-1.0 Successfully installed ChimeraX-UI-1.0 Lock 900644913992 acquired on C:\Users\Yonathan ARFI\AppData\Local\UCSF\ChimeraX\Cache\0.94\toolshed\bundle_info.cache.lock Lock 900644913992 released on C:\Users\Yonathan ARFI\AppData\Local\UCSF\ChimeraX\Cache\0.94\toolshed\bundle_info.cache.lock WARNING: You are using pip version 20.0.2; however, version 20.1 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. > open 6n2y format mmCIF fromDatabase pdb 6n2y title: Bacillus PS3 ATP synthase class 1 [more info...] Chain information for 6n2y #1 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | ATP synthase subunit δ a | ATP synthase subunit a b1 | ATP synthase subunit b b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2y #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > preset cartoons/nucleotides cylinders/stubs Changed 34914 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 cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\structure.py"", line 1559, in _update_graphics_if_needed s[i]._update_graphics_if_needed() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\structure.py"", line 297, in _update_graphics_if_needed self._create_ribbon_graphics() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\structure.py"", line 550, in _create_ribbon_graphics ribbons_drawing.compute_ribbons(self) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\ribbon.py"", line 586, in compute_ribbons _make_ribbon_graphics(structure, self) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\ribbon.py"", line 128, in _make_ribbon_graphics centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\ribbon.py"", line 957, in _arc_helix_geometry hc = HelixCylinder(coords[start:end]) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\sse.py"", line 185, in __init__ self._straight_optimize() File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\sse.py"", line 398, in _straight_optimize opt = OptLine(self.coords, centroid, axis) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\sse.py"", line 25, in __init__ from scipy.optimize import minimize File ""C:\Program Files\ChimeraX\bin\lib\site-packages\scipy\\__init__.py"", line 156, in from . import fft File ""C:\Program Files\ChimeraX\bin\lib\site-packages\scipy\fft\\__init__.py"", line 76, in from ._basic import ( File ""C:\Program Files\ChimeraX\bin\lib\site-packages\scipy\fft\\_basic.py"", line 1, in from scipy._lib.uarray import generate_multimethod, Dispatchable File ""C:\Program Files\ChimeraX\bin\lib\site-packages\scipy\\_lib\uarray.py"", line 27, in from ._uarray import * File ""C:\Program Files\ChimeraX\bin\lib\site- packages\scipy\\_lib\\_uarray\\__init__.py"", line 114, in from ._backend import * File ""C:\Program Files\ChimeraX\bin\lib\site- packages\scipy\\_lib\\_uarray\\_backend.py"", line 15, in from . import _uarray # type: ignore ImportError: DLL load failed: Le module spécifié est introuvable. Error processing trigger ""graphics update"": ImportError: DLL load failed: Le module spécifié est introuvable. File ""C:\Program Files\ChimeraX\bin\lib\site- packages\scipy\\_lib\\_uarray\\_backend.py"", line 15, in from . import _uarray # type: ignore See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 344.42 OpenGL renderer: GeForce GTX 965M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Micro-Star International Co., Ltd. Model: GS60 2QD OS: Microsoft Windows 8.1 (Build 9600) Memory: 8,503,721,984 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-4720HQ CPU @ 2.60GHz"" }}} " defect closed normal Build System nonchimerax Tom Goddard Eric Pettersen Conrad Huang all ChimeraX