![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 5 years ago
#3227 closed defect (fixed)
Cannot import _uarray
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | 1.0rc1 |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.0rc202005150054 (2020-05-15 00:54:28 UTC) Description I tried the Cartoon tube helices tool Log: UCSF ChimeraX version: 1.0rc202005150054 (2020-05-15) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\Asus\Documents\Manuela\pubblicazioni\2020_ttd > termos\figures\xpd ts.cxs" format session Log from Sat May 16 17:26:52 2020UCSF ChimeraX version: 1.0rc202005150054 (2020-05-15) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open D:\Manuela\LAB\XPD\proteina\PDB\pdb6ro4.ent format pdb pdb6ro4.ent title: Structure of the core tfiih-xpa-DNA complex [more info...] Chain information for pdb6ro4.ent #1 --- Chain | Description A | general transcription and DNA repair factor iih helicase subunit XPB B | tfiih basal transcription factor complex helicase XPD subunit C | general transcription factor iih subunit 4 D | general transcription factor iih subunit 2 E | general transcription factor iih subunit 3 F | general transcription factor iih subunit 5 G | xeroderma pigmentosum group A-complementing protein J | DNA1 K | DNA2 Non-standard residues in pdb6ro4.ent #1 --- SF4 — iron/sulfur cluster ZN — zinc ion > sequence chain #1/A Alignment identifier is 1.A > hide surfaces > select /C:18-458 3109 atoms, 3178 bonds, 8 pseudobonds, 2 models selected > hide sel surfaces > select /D:55-387 2182 atoms, 2228 bonds, 6 pseudobonds, 2 models selected > select /D:55-387 2182 atoms, 2228 bonds, 6 pseudobonds, 2 models selected > hide sel surfaces > hide sel surfaces > select /E:8-285 1857 atoms, 1890 bonds, 6 pseudobonds, 2 models selected > hide sel surfaces > hide sel cartoons > hide sel atoms > hide sel atoms > select /A:71-720 4648 atoms, 4748 bonds, 4 pseudobonds, 2 models selected > hide sel atoms > select /C:18-458 3109 atoms, 3178 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > select /D:55-387 2182 atoms, 2228 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > select /E:8-285 1857 atoms, 1890 bonds, 6 pseudobonds, 2 models selected > select /D:55-387 2182 atoms, 2228 bonds, 6 pseudobonds, 2 models selected > select /D:55-387 2182 atoms, 2228 bonds, 6 pseudobonds, 2 models selected > select /E:8-285 1857 atoms, 1890 bonds, 6 pseudobonds, 2 models selected > select /F:4-65 490 atoms, 495 bonds, 1 model selected > hide sel atoms > select /E:8-285 1857 atoms, 1890 bonds, 6 pseudobonds, 2 models selected > select /G:104-237 1129 atoms, 1149 bonds, 1 model selected > hide sel atoms > select /J:17-35 387 atoms, 433 bonds, 1 model selected > hide sel atoms > select /K:15-42 575 atoms, 646 bonds, 1 model selected > select /K:15-42 575 atoms, 646 bonds, 1 model selected > select /K:15-42 575 atoms, 646 bonds, 1 model selected > hide sel atoms > rainbow sel > nucleotides sel fill > style nucleic & sel stick Changed 575 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 575 atom styles > show sel cartoons > select /B:1-728 5436 atoms, 5556 bonds, 2 pseudobonds, 2 models selected > show sel cartoons > hide sel surfaces > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > select /B:1-728 5436 atoms, 5556 bonds, 2 pseudobonds, 2 models selected > hide sel surfaces > hide sel atoms > hide sel cartoons > show sel cartoons > select /K:15-42 575 atoms, 646 bonds, 1 model selected > hide sel atoms > hide sel cartoons > select :ZN 6 atoms, 1 model selected > hide sel atoms > color sel byhetero > rainbow sel > select /B:1-728 5436 atoms, 5556 bonds, 2 pseudobonds, 2 models selected > color sel byhetero > rainbow sel > color sel bychain > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel tube/slab shape box > toolshed show "Color Actions" > color sel yellow > color sel yellow > select /B:1-728 5436 atoms, 5556 bonds, 2 pseudobonds, 2 models selected Alignment identifier is 1.B > color sel yellow > color sel yellow > color lime > color sel yellow > color sel red > color sel yellow > color sel red > color sel blue > color sel yellow > color sel blue > color sel red > color orange > color blue > color purple > color sel yellow > color sel cyan > color sel light sea green > color sel blue > color sel cornflower blue > color sel magenta > color sel dark gray > color sel hot pink > color sel dark gray > color sel yellow > color sel cyan > color sel light sea green > color sel blue > color sel cornflower blue > color sel yellow > color sel lime > color sel yellow > color sel red > color sel orange red > color sel orange > color sel forest green > color sel cornflower blue > color sel dark gray > color sel gray > color sel dim gray > color sel purple > color medium blue > color cornflower blue > color sel purple > color sel orange > color dark gray > color sel purple > color sel orange > style sel sphere Changed 9 atom styles > style sel sphere Changed 9 atom styles > style sel stick Changed 9 atom styles > show sel atoms > color sel red > hbonds 1439 hydrogen bonds found > style sel stick Changed 8 atom styles > color sel red > show sel atoms > color sel red > show sel atoms > style sel stick Changed 19 atom styles > hide sel atoms > color sel purple > show sel atoms > color sel red > color sel yellow > hide sel atoms > hide sel atoms > hide sel atoms > color sel purple > color sel red > show sel atoms > style sel stick Changed 11 atom styles > interfaces sel & ~solvent 0 buried areas: > interfaces sel & ~solvent 0 buried areas: > interfaces sel & ~solvent 0 buried areas: > interfaces sel & ~solvent 0 buried areas: > color red > undo > save "C:/Users/Asus/Documents/Manuela/LAB/XPD/proteina/XPD_mut ts.cxs" > cofr sel > style sel ball Changed 11 atom styles > nucleotides sel tube/slab shape box > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel ladder > nucleotides sel ladder > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel ringFill thick Changed 1 residue ring style > style sel ringFill thin Changed 1 residue ring style > style sel sphere Changed 11 atom styles > style sel sphere Changed 8 atom styles > style sel sphere Changed 9 atom styles > save "C:/Users/Asus/Documents/Manuela/LAB/XPD/proteina/XPD_mut ts_ball.cxs" > color sel yellow > show sel surfaces > color sel yellow > color sel yellow > show sel cartoons > show sel surfaces > show sel atoms > hide sel surfaces > hide sel surfaces > show sel atoms > hide sel surfaces > hide sel surfaces > hide sel surfaces > hide sel surfaces > hide sel cartoons > hide sel atoms > show sel cartoons > show sel atoms > style sel stick Changed 15 atom styles > hide sel atoms > show sel atoms > style sel sphere Changed 15 atom styles > style sel ball Changed 15 atom styles > hide sel atoms > color sel yellow > color sel orange > color sel purple > hide sel surfaces > hide sel atoms > color sel orange > style sel stick Changed 11 atom styles > show sel atoms > hide sel atoms > color sel orange > color sel orange > color sel orange > color sel orange > color sel orange > color sel orange > color sel orange > color sel orange > color sel lime > color sel orange > save "C:/Users/Asus/Documents/Manuela/LAB/XPD/proteina/XPD_mut ts_ball.cxs" > label (#!1 & sel) attribute name > label (#!1 & sel) attribute name > label (#!1 & sel) attribute label_one_letter_code > label (#!1 & sel) atoms > label (#!1 & sel) atoms text Asp673 > color sel gold > color sel indian red > color sel salmon > color sel olive > color sel lime > color sel olive > color sel forest green > color sel sea green > color sel medium sea green > color sel cyan > color sel olive drab > color sel medium sea green > color sel spring green > color sel lime green > color sel olive > color sel yellow green > color sel dark khaki > color sel yellow green > color dark khaki > undo > color sel dark khaki > color sel medium purple > color sel purple > color sel dark magenta > color sel medium violet red > color sel medium slate blue > color sel turquoise > color sel medium turquoise > color sel light sea green > color sel cornflower blue > color sel cornflower blue > color sel light sea green > color sel medium blue > color sel indigo > color sel royal blue > color sel dark violet > color sel lime > color sel olive > color sel dark khaki > color sel peru > color sel light salmon > color sel dark goldenrod > color sel yellow green > color sel orange > color sel saddle brown > color sel brown > color sel dark red > color sel crimson > color sel dark red > color sel orange red > color sel red > color sel orange red > color sel fire brick > color sel saddle brown > color sel indian red > color sel green yellow > color sel indigo > color sel dark orchid > color sel dark violet > color sel hot pink > color sel blue violet > color sel orchid > color sel medium orchid > color sel medium orchid > color sel medium violet red > color sel medium violet red > color sel dark orchid > color sel dark magenta > color sel purple > color sel medium purple > color sel dark magenta > color sel purple > color sel purple > color sel dark magenta > color sel pale violet red > color sel dark magenta > color sel dark slate gray > color sel dark magenta > color sel pale violet red > color sel dark slate gray > color sel dark olive green > color sel light cyan > color sel lavender > color sel white smoke > color sel mint cream > color sel antique white > color sel linen > color sel old lace > color sel linen > color sel lavender > color sel khaki > color sel pale goldenrod > color sel aquamarine > color sel pale turquoise > color sel powder blue > color sel light steel blue > color sel silver > color sel pale turquoise > color sel pale green > color sel red > color sel orange > color sel red > hide sel surfaces > style sel stick Changed 11 atom styles > hide sel atoms > hide sel atoms > hide sel atoms > color sel red > color sel orange > color sel purple > color sel dark gray > color sel dim gray > color sel gray > save "C:/Users/Asus/Documents/Manuela/LAB/XPD/proteina/XPD_mut ts.cxs" > volume appearance brain No volumes specified > volume appearance brain No volumes specified Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\toolbar\tool.py", line 202, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\core\toolshed\info.py", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py", line 1660, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\medical_toolbar\\__init__.py", line 22, in run_provider actions.run_provider(session, name) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\medical_toolbar\actions.py", line 17, in run_provider open_dicom(session) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\medical_toolbar\actions.py", line 22, in open_dicom session.ui.main_window.folder_open_cb(session) AttributeError: 'MainWindow' object has no attribute 'folder_open_cb' AttributeError: 'MainWindow' object has no attribute 'folder_open_cb' File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\medical_toolbar\actions.py", line 22, in open_dicom session.ui.main_window.folder_open_cb(session) See log for complete Python traceback. QFileSystemWatcher::removePaths: list is empty QFileSystemWatcher::removePaths: list is empty > save "C:/Users/Asus/Documents/Manuela/pubblicazioni/2020_ttd > termos/figures/XPD 3d.bmp" width 1169 height 334 supersample 3 > graphics silhouettes true > lighting full > set bgColor white > ~hbonds > lighting full > lighting full > lighting simple > lighting simple > lighting full > lighting simple > lighting soft > lighting soft > lighting full > lighting shadows false > graphics silhouettes false > lighting shadows true > lighting flat > lighting full > graphics silhouettes false > lighting full > lighting full > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting flat > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > lighting flat > lighting soft > graphics silhouettes false > lighting full > lighting soft > lighting simple > lighting full > color sel yellow > color sel light sea green > color sel medium turquoise > color sel medium spring green > color sel steel blue > color sel peru > color sel light salmon > color sel peru > color sel dark khaki > color sel lime > color sel olive > color sel lime > color sel green > color sel chartreuse > color sel lawn green > color sel spring green > color sel lime green > color sel forest green > color sel medium sea green > color sel sea green > color sel medium sea green > color sel olive drab > color sel cyan > color sel medium sea green > color sel forest green > color sel lime green > color sel medium sea green > color sel sea green > color sel medium sea green > color sel orange > color sel gold > color sel dark orange > color sel green yellow > color sel medium sea green > save "C:/Users/Asus/Documents/Manuela/pubblicazioni/2020_ttd > termos/figures/xpd ts.cxs" opened ChimeraX session > cartoon style (sel & coil) xsection oval > cartoon style sel xsection barbell modeHelix default > cartoon style sel modeHelix tube sides 20 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.0rc202005150054\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 1.0rc202005150054\bin\lib\site- packages\chimerax\atomic\structure.py", line 300, in _update_graphics_if_needed self._create_ribbon_graphics() File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\atomic\structure.py", line 553, in _create_ribbon_graphics ribbons_drawing.compute_ribbons(self) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\atomic\ribbon.py", line 586, in compute_ribbons _make_ribbon_graphics(structure, self) File "C:\Program Files\ChimeraX 1.0rc202005150054\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 1.0rc202005150054\bin\lib\site- packages\chimerax\atomic\ribbon.py", line 957, in _arc_helix_geometry hc = HelixCylinder(coords[start:end]) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\atomic\sse.py", line 187, in __init__ self._try_curved() File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\atomic\sse.py", line 392, in _try_curved self._curved_optimize(c_center, c_axis, c_radius) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\atomic\sse.py", line 436, in _curved_optimize opt = OptArc(self.coords, center, axis, major_radius) File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\chimerax\atomic\sse.py", line 85, in __init__ from scipy.optimize import minimize File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\scipy\\__init__.py", line 156, in <module> from . import fft File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\scipy\fft\\__init__.py", line 76, in <module> from ._basic import ( File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\scipy\fft\\_basic.py", line 1, in <module> from scipy._lib.uarray import generate_multimethod, Dispatchable File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\scipy\\_lib\uarray.py", line 27, in <module> from ._uarray import * File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\scipy\\_lib\\_uarray\\__init__.py", line 114, in <module> from ._backend import * File "C:\Program Files\ChimeraX 1.0rc202005150054\bin\lib\site- packages\scipy\\_lib\\_uarray\\_backend.py", line 15, in <module> from . import _uarray # type: ignore ImportError: DLL load failed: Impossibile trovare il modulo specificato. Error processing trigger "graphics update": ImportError: DLL load failed: Impossibile trovare il modulo specificato. File "C:\Program Files\ChimeraX 1.0rc202005150054\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 388.57 OpenGL renderer: GeForce GT 540M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUSTeK Computer Inc. Model: K53SV OS: Microsoft Windows 10 Pro (Build 18362) Memory: 6,349,930,496 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-2630QM CPU @ 2.00GHz" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8
Change History (3)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Build System |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Cannot import _uarray |
| Version: | → 1.0rc1 |
comment:2 by , 5 years ago
| Status: | assigned → feedback |
|---|
comment:3 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
No response. Internal testing shows that it was fixed.
Note:
See TracTickets
for help on using tickets.
The problem is that you need a newer Microsoft Visual C++ runtime. I've added an the Visual C++ runtime installer to the ChimeraX installer. Please reinstall the ChimeraX candidate release with the latest version. And then, please confirm that it fixes your problem.