id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3214 Tube helices broken on Windows, Scipy cannot import _uarray goddard@… Greg Couch "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.0 (2020-05-07) Description Helix tubes (Presets / Cylnders) is broken on Windows because a scipy import fails. Probably need to update or rollback scipy to fix this. Log: UCSF ChimeraX version: 1.0rc202005070439 (2020-05-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4hus format mmcif fromDatabase pdb 4hus title: Crystal structure of streptogramin group A antibiotic acetyltransferase VatA from Staphylococcus aureus in complex with virginiamycin M1 [more info...] Chain information for 4hus #1 --- Chain | Description A B C | Virginiamycin A acetyltransferase Non-standard residues in 4hus #1 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) NA — sodium ion PEG — di(hydroxyethyl)ether PGE — triethylene glycol SO4 — sulfate ion VIR — virginiamycin M1 > preset cartoons/nucleotides cylinders/stubs 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 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-May-7-2020\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\chimerax\atomic\structure.py"", line 1562, in _update_graphics_if_needed s[i]._update_graphics_if_needed() File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\chimerax\atomic\structure.py"", line 300, in _update_graphics_if_needed self._create_ribbon_graphics() File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\chimerax\atomic\structure.py"", line 553, in _create_ribbon_graphics ribbons_drawing.compute_ribbons(self) File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\chimerax\atomic\ribbon.py"", line 586, in compute_ribbons _make_ribbon_graphics(structure, self) File ""C:\Program Files\ChimeraX-May-7-2020\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-May-7-2020\bin\lib\site- packages\chimerax\atomic\ribbon.py"", line 957, in _arc_helix_geometry hc = HelixCylinder(coords[start:end]) File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\chimerax\atomic\sse.py"", line 185, in __init__ self._straight_optimize() File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\chimerax\atomic\sse.py"", line 398, in _straight_optimize opt = OptLine(self.coords, centroid, axis) File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\chimerax\atomic\sse.py"", line 25, in __init__ from scipy.optimize import minimize File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\scipy\\__init__.py"", line 156, in from . import fft File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\scipy\fft\\__init__.py"", line 76, in from ._basic import ( File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\scipy\fft\\_basic.py"", line 1, in from scipy._lib.uarray import generate_multimethod, Dispatchable File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\scipy\\_lib\uarray.py"", line 27, in from ._uarray import * File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\scipy\\_lib\\_uarray\\__init__.py"", line 114, in from ._backend import * File ""C:\Program Files\ChimeraX-May-7-2020\bin\lib\site- packages\scipy\\_lib\\_uarray\\_backend.py"", line 15, in from . import _uarray # type: ignore ImportError: DLL load failed: The specified module could not be found. Error processing trigger ""graphics update"": ImportError: DLL load failed: The specified module could not be found. File ""C:\Program Files\ChimeraX-May-7-2020\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 442.19 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Gigabyte Technology Co., Ltd. Model: Z270X-Gaming K7 OS: Microsoft Windows 10 Home (Build 18362) Memory: 17,129,693,184 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz"" }}} " defect closed normal 1.0 Depiction fixed chimera-programmers all ChimeraX