Loading scipy: Cannot find the specified module

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-05-12)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005120742 (2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open D:\FSZH\20200929-SBT\Figure\overall_structure.cxs format session

Log from Tue Nov 10 12:53:01 2020UCSF ChimeraX version: 1.0rc202005120742
(2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open D:\\\FSZH\\\20200929-SBT\\\Figure\\\overall_structure.cxs

Log from Tue Nov 3 17:51:06 2020UCSF ChimeraX version: 1.0rc202005120742
(2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open D:\FSZH\20200929SBT\Figure\overall_structure.cxs format session

Log from Tue Nov 3 17:02:28 2020UCSF ChimeraX version: 1.0rc202005120742
(2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open D:\FSZH\20200929SBT\Figure\overall_structure.cxs format session

Log from Tue Nov 3 16:07:06 2020UCSF ChimeraX version: 1.0rc202005120742
(2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open D:\FSZH\20200929SBT\Figure\overall_structure.cxs format session

Log from Tue Nov 3 16:02:31 2020 Startup Messages  
---  
warning | Your computer has Intel graphics driver 7810 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.0rc202005120742 (2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:\\\FSZH\\\20200929SBT\\\Figure\\\realspace75_final.pdb

Summary of feedback from opening
D:\\\FSZH\\\20200929SBT\\\Figure\\\realspace75_final.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.006 0.064 19861  
  
Ignored bad PDB record found on line 23  
ANGLE : 1.577 58.089 35934  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.068 0.763 1657  
  
16 messages similar to the above omitted  
  
Chain information for realspace75_final.pdb #1  
---  
Chain | Description  
A C E | No description available  
B | No description available  
D F | No description available  
  

> preset "molecular surfaces" "ghostly white"

Changed 19555 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> set bgColor white

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> cartoon style width 0.6 thickness 0.6

> close session

> open D:\FSZH\20200929SBT\Figure\realspace75_final.pdb format pdb

Summary of feedback from opening
D:\FSZH\20200929SBT\Figure\realspace75_final.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.006 0.064 19861  
  
Ignored bad PDB record found on line 23  
ANGLE : 1.577 58.089 35934  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.068 0.763 1657  
  
16 messages similar to the above omitted  
  
Chain information for realspace75_final.pdb #1  
---  
Chain | Description  
A C E | No description available  
B | No description available  
D F | No description available  
  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> cartoon style width 1

> cartoon style width 1.2

> cartoon style width 1.5

> hide atoms

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> select #1/A

5013 atoms, 5062 bonds, 2 pseudobonds, 2 models selected  

> color slate blue

> color #1/C goldenrod

> select clear

> lighting simple

> lighting soft

> lighting full

> lighting simple

> set bgColor white

> color #1/C burly wood

> color #1/E light pink

> color #1/E lightcoral

> color #1/A medium slate blue

> color #1/A royalblue

> select clear

> color #1/A steel blue

> select clear

> color #1/C hot pink

> color #1/C burly wood

> color #1/F indian red

> color #1/F firebrick

> color #1/F tomato

> color #1/E light salmon

> select clear

> color #1/E lightcoral

> color #1/F orangered

> color #1/F coral

> color #1/D goldenrod

> select clear

> color #1/D dark goldenrod

> select clear

> view orient

> view

> view orient

> view orient

> turn x 90

> select ligand

120 atoms, 123 bonds, 1 model selected  

> show sel atoms

> color byhetero

> select clear

> select NA

Expected an objects specifier or a keyword  

> select ::name="NA"

3 atoms, 1 model selected  

> style sel sphere

Changed 3 atom styles  

> select ::name="NA"

3 atoms, 1 model selected  

> show sel atoms

> style sel sphere

Changed 3 atom styles  

> style sel ball

Changed 3 atom styles  

> style sel sphere

Changed 3 atom styles  

> select ::name="BCT"

15 atoms, 12 bonds, 1 model selected  

> style sel ball

Changed 15 atom styles  

> style sel sphere

Changed 15 atom styles  

> select clear

> select ::name="BCT"

15 atoms, 12 bonds, 1 model selected  

> style sel ball

Changed 15 atom styles  

> style sel ball

Changed 15 atom styles  

> style sel sphere

Changed 15 atom styles  

> select clear

> save D:/FSZH/20200929SBT/Figure/overall_structure.cxs

opened ChimeraX session  

> select ::name="BCT"

15 atoms, 12 bonds, 1 model selected  

> hide sel atoms

> select clear

> save D:/FSZH/20200929SBT/Figure/overall_structure.cxs

opened ChimeraX session  

> hide #1.1 models

> show #1.1 models

> select :AMP

105 atoms, 111 bonds, 1 model selected  

> color sel magenta

> color byhetero

> select clear

> save D:/FSZH/20200929SBT/Figure/overall_structure.cxs

opened ChimeraX session  
Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 1.B  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> toolshed show "Model Panel"

> color #1/A

> show #1/A color

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> list #1/A

Unknown command: list #1/A  

> show color #1/A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> save D:/FSZH/20200929SBT/Figure/overall_structure.cxs

opened ChimeraX session  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> open D:/FSZH/20200929-SBT/post052/postprocess_masked_zflip.mrc

Opened postprocess_masked_zflip.mrc, grid size 240,240,240, pixel 1.08, shown
at level 0.0124, step 1, values float32  

> volume #2 level 0.02264

> transparency 50

> volume #2 style mesh

> volume #2 style surface

> open D:/FSZH/20200929-SBT/refine049/run_class001_zflip.mrc

Opened run_class001_zflip.mrc, grid size 240,240,240, pixel 1.08, shown at
level 0.0106, step 1, values float32  

> hide #!2 models

> transparency #3.1 50

> volume #3 level 0.01315

> transparency #3.1 0

> transparency #3.1 50

> transparency #3.1 20

> transparency #3.1 80

> transparency #3.1 80

> volume #3 level 0.01201

> volume #3 level 0.01344

> save C:\Users\CyroEM\Desktop\image2.png supersample 3

> turn x 90

> turn x 180

> save C:\Users\CyroEM\Desktop\image3.png supersample 3

> save D:/FSZH/20200929-SBT/Figure/overall_structure.cxs

opened ChimeraX session  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides tube/slab shape box

> tube

Unknown command: modeller tube  

> cartoon style modeHelix tube

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.0rc202005120742\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 1.0rc202005120742\bin\lib\site-
packages\chimerax\atomic\structure.py", line 300, in
_update_graphics_if_needed  
self._create_ribbon_graphics()  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\chimerax\atomic\structure.py", line 553, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 586, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File "C:\Program Files\ChimeraX 1.0rc202005120742\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 1.0rc202005120742\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 957, in _arc_helix_geometry  
hc = HelixCylinder(coords[start:end])  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\chimerax\atomic\sse.py", line 185, in __init__  
self._straight_optimize()  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\chimerax\atomic\sse.py", line 398, in _straight_optimize  
opt = OptLine(self.coords, centroid, axis)  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\chimerax\atomic\sse.py", line 25, in __init__  
from scipy.optimize import minimize  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\scipy\\__init__.py", line 156, in <module>  
from . import fft  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\scipy\fft\\__init__.py", line 76, in <module>  
from ._basic import (  
File "C:\Program Files\ChimeraX 1.0rc202005120742\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 1.0rc202005120742\bin\lib\site-
packages\scipy\\_lib\uarray.py", line 27, in <module>  
from ._uarray import *  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\scipy\\_lib\\_uarray\\__init__.py", line 114, in <module>  
from ._backend import *  
File "C:\Program Files\ChimeraX 1.0rc202005120742\bin\lib\site-
packages\scipy\\_lib\\_uarray\\_backend.py", line 15, in <module>  
from . import _uarray # type: ignore  
ImportError: DLL load failed: 找不到指定的模块。  
  
Error processing trigger "graphics update":  
ImportError: DLL load failed: 找不到指定的模块。  
  
File "C:\Program Files\ChimeraX 1.0rc202005120742\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 - Build 26.20.100.7810
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: F0DE000LCD
OS: Microsoft Windows 10 家庭中文版 (Build 18362)
Memory: 7,931,084,800
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8400T CPU @ 1.70GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tom Goddard]

Duplicate of #3227 which was fixed in ChimeraX 1.1 by Greg Couch.