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#3567 closed defect (duplicate)

scipy can't import _uarray

Reported by:	chimerax-bug-report@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Depiction	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.0 (2020-05-09)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005091901 (2020-05-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/jites/.mgltools/PyRx/Macromolecules/5IKR/5IKR.pdbqt

Summary of feedback from opening
C:/Users/jites/.mgltools/PyRx/Macromolecules/5IKR/5IKR.pdbqt  
---  
note |  
  
  
| Chain information for 5IKR.pdbqt #1  
  
---  
  
  
Chain  
| Description  
  
  
  
  
  
A | No description available  
  
  
  
  
  
Opened 5IKR.pdbqt containing 1 structures (5430 atoms, 5562 bonds)  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> open
> C:/Users/jites/.mgltools/PyRx/Macromolecules/5IKR/originalAll3dClean_000005_out.pdbqt

Opened originalAll3dClean_000005_out.pdbqt containing 9 structures (216 atoms,
234 bonds)  

> toolshed show ViewDockX

> hide #2.2-9 models

> hbonds #2.1-9 restrict #1 reveal true interSubmodel true

6 hydrogen bonds found  

> clashes #2.1-9 restrict #1 reveal true interSubmodel true

1 clashes  

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.3 models

> hide #2.3 models

> show #2.4 models

> hide #2.4 models

> show #2.1 models

> close #2

> open
> C:/Users/jites/.mgltools/PyRx/Macromolecules/5IKR/originalAll3dClean_000045_out.pdbqt

Opened originalAll3dClean_000045_out.pdbqt containing 9 structures (225 atoms,
243 bonds)  

> toolshed show ViewDockX

> hide #2.2-9 models

> hbonds #2.1-9 restrict #1 reveal true interSubmodel true

4 hydrogen bonds found  

> clashes #2.1-9 restrict #1 reveal true interSubmodel true

1 clashes  

> select up

2 atoms, 1 bond, 1 model selected  

> select up

25 atoms, 27 bonds, 1 model selected  

> select #1/A:134

14 atoms, 14 bonds, 1 model selected  

> select up

16 atoms, 15 bonds, 2 models selected  

> select up

39 atoms, 41 bonds, 2 models selected  

> select up

168 atoms, 174 bonds, 2 models selected  

> select up

5455 atoms, 5589 bonds, 2 models selected  

> toolshed show Contacts

> contacts sel restrict both intraModel false intraMol false

44 contacts  

> contacts sel restrict both intraModel false intraMol false

44 contacts  

> open 5IKR

Summary of feedback from opening 5IKR fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "NAG" near line 19167  
notes | Fetching compressed mmCIF 5ikr from
http://files.rcsb.org/download/5ikr.cif  
Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif  
Fetching CCD ID8 from http://ligand-expo.rcsb.org/reports/I/ID8/ID8.cif  
Fetching CCD COH from http://ligand-expo.rcsb.org/reports/C/COH/COH.cif  
Fetching CCD BOG from http://ligand-expo.rcsb.org/reports/B/BOG/BOG.cif  
Fetching CCD NH4 from http://ligand-expo.rcsb.org/reports/N/NH4/NH4.cif  
  
5ikr title:  
The Structure of Mefenamic Acid Bound to Human Cyclooxygenase-2 [more info...]  
  
Chain information for 5ikr #6  
---  
Chain | Description  
A B | Prostaglandin G/H synthase 2  
  
Non-standard residues in 5ikr #6  
---  
BOG — octyl beta-D-glucopyranoside  
COH — protoporphyrin IX containing Co  
ID8 — 2-[(2,3-dimethylphenyl)amino]benzoic acid (mefenamic acid)  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
NH4 — ammonium ion  
  

> matchmaker #6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5IKR.pdbqt, chain A (#1) with 5ikr, chain A (#6), sequence
alignment score = 2923.4  
RMSD between 551 pruned atom pairs is 0.000 angstroms; (across all 551 pairs:
0.000)  
  

> matchmaker #6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5IKR.pdbqt, chain A (#1) with 5ikr, chain A (#6), sequence
alignment score = 2923.4  
RMSD between 551 pruned atom pairs is 0.000 angstroms; (across all 551 pairs:
0.000)  
  

> select ::name="ID8"

64 atoms, 66 bonds, 1 model selected  

> hide #2.1 models

> show #2.2 models

> hbonds #2.1-9 restrict #1#!6 reveal true interSubmodel true

11 hydrogen bonds found  

> close #6

> hbonds #2.1-9 restrict #1 reveal true interSubmodel true

4 hydrogen bonds found  

> hide #2.2 models

> show #2.1 models

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.3 models

> hide #2.3 models

> show #2.2 models

> hide #2.2 models

> show #2.1 models

> select protein

5430 atoms, 5562 bonds, 1 model selected  

> show sel surfaces

> mlp sel

Map values for surface "5IKR.pdbqt_A SES surface": minimum -30.14, mean
-4.174, maximum 24.05  

> color bfactor sel

5430 atoms, 551 residues, 1 surfaces, atom bfactor range 0 to 121  

> color sel byhetero

> color bfactor sel

5430 atoms, 551 residues, 1 surfaces, atom bfactor range 0 to 121  

> color sel bychain

> rainbow sel

> mlp sel

Map values for surface "5IKR.pdbqt_A SES surface": minimum -30.14, mean
-4.174, maximum 24.05  

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select clear

> select up

2 atoms, 1 bond, 1 model selected  

> select up

25 atoms, 27 bonds, 1 model selected  

> style sel sphere

Changed 25 atom styles  

> style sel ball

Changed 25 atom styles  

> color sel byhetero

> rainbow sel

> color bfactor sel

25 atoms, 1 residues, atom bfactor range 0 to 0  

> mlp sel

mlp: no amino acids specified  

> color sel byhetero

> color sel bychain

> color sel byhetero

> color sel bychain

> color sel bychain

> rainbow sel

> color bfactor sel

25 atoms, 1 residues, atom bfactor range 0 to 0  

> mlp sel

mlp: no amino acids specified  

> color sel bynucleotide

> color sel byhetero

> color sel bychain

> color sel byhetero

> interfaces sel & ~solvent

0 buried areas:  

> select clear

> save E:/IBIS/graphics/interaction.jpg width 1340 height 785 supersample 3

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> hide #2.1#!1 cartoons

> show #2.1#!1 atoms

> hide #2.1#!1 atoms

> show #2.1#!1 cartoons

> view

> preset "initial styles" "original look"

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

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> preset "initial styles" cartoon

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

> preset cartoons/nucleotides ribbons/slabs

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
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides licorice/ovals

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 default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> 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 1.0rc202005091901\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.0rc202005091901\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 1.0rc202005091901\bin\lib\site-
packages\chimerax\atomic\structure.py", line 300, in
_update_graphics_if_needed  
self._create_ribbon_graphics()  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\chimerax\atomic\structure.py", line 553, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 586, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File "C:\Program Files\ChimeraX 1.0rc202005091901\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 1.0rc202005091901\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 957, in _arc_helix_geometry  
hc = HelixCylinder(coords[start:end])  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\chimerax\atomic\sse.py", line 185, in __init__  
self._straight_optimize()  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\chimerax\atomic\sse.py", line 398, in _straight_optimize  
opt = OptLine(self.coords, centroid, axis)  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\chimerax\atomic\sse.py", line 25, in __init__  
from scipy.optimize import minimize  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\scipy\\__init__.py", line 156, in <module>  
from . import fft  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\scipy\fft\\__init__.py", line 76, in <module>  
from ._basic import (  
File "C:\Program Files\ChimeraX 1.0rc202005091901\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 1.0rc202005091901\bin\lib\site-
packages\scipy\\_lib\uarray.py", line 27, in <module>  
from ._uarray import *  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\scipy\\_lib\\_uarray\\__init__.py", line 114, in <module>  
from ._backend import *  
File "C:\Program Files\ChimeraX 1.0rc202005091901\bin\lib\site-
packages\scipy\\_lib\\_uarray\\_backend.py", line 15, in <module>  
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 1.0rc202005091901\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 451.67
OpenGL renderer: GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Acer
Model: Aspire A515-51G
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 8,459,489,280
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz"

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Depiction
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → scipy can't import _uarray

comment:2 by Eric Pettersen, 5 years ago

Resolution:	→ duplicate
Status:	assigned → closed

duplicate of #3214 (but see #3481)

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