Context Navigation

← Previous Ticket
Next Ticket →

#14385 closed defect (nonchimerax)

read_full_array: Permission denied

Reported by:	tim.passchier@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Volume Data	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: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Unsure why the session will not reopen. I've had similar problems before

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\DELL\Documents\Temp Uni of Leeds\ThesisDesktop\Figures\In
> Progress Chapter 5\localres.cxs" format session

Opened relion_locres_filtered.mrc as #1, grid size 360,360,360, pixel 1.07,
shown at level 0.0576, step 1, values float32  
Opened relion_locres.mrc as #2, grid size 360,360,360, pixel 1.07, shown at
level 26.1, step 1, values float32  
Unable to restore session, resetting.  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 713, in restore  
obj = sm.restore_snapshot(self, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 406, in restore_snapshot  
c.set_vertex_colors()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 230, in set_vertex_colors  
s.vertex_colors = self.vertex_colors(report_stats)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 200, in vertex_colors  
values, outside = self.volume_values()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 267, in volume_values  
return self.offset_values(v, n, tf)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 275, in offset_values  
values, outside = self.vertex_values(v, xf)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 308, in vertex_values  
values, outside = v.interpolated_values(vertices, vertex_xform,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 1436, in interpolated_values  
matrix, p2m_transform = self.matrix_and_transform(point_xform,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 1621, in matrix_and_transform  
matrix = self.matrix(step=step, subregion=subregion)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\mrc\mrc_grid.py", line 44, in read_matrix  
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\mrc\mrc_format.py", line 284, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 27, in read_array  
m = read_full_array(path, byte_offset, full_size,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 84, in read_full_array  
file.readinto(b)  
PermissionError: [Errno 13] Permission denied  

Log from Sun Dec 18 14:59:27 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\DELL\Documents\Temp Uni of Leeds\EM\20200302 EM
> Processing\LocalRes\job513\relion_locres_filtered.mrc" format mrc

Opened relion_locres_filtered.mrc as #1, grid size 360,360,360, pixel 1.07,
shown at level 0.0576, step 2, values float32  

> open "C:\Users\DELL\Documents\Temp Uni of Leeds\EM\20200302 EM
> Processing\LocalRes\job513\relion_locres.mrc" format mrc

Opened relion_locres.mrc as #2, grid size 360,360,360, pixel 1.07, shown at
level 26.1, step 2, values float32  

> volume #1 step 1

> volume #2 step 1

> set bgColor white

> lighting soft

> hide #!2 models

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette #ff0000:#ff7f7f:#ffffff:#7f7fff:#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> color sample #1.1 map #2 palette
> 3.409,#ff0000:3.763,#ffff00:4.116,#ffffff:4.469,#00ff00:4.822,#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> ui tool show "Side View"

QWindowsWindow::setGeometry: Unable to set geometry 3840x2256+0+57 (frame:
3872x2344-16-15) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3840x2004+0+56 (frame: 3872x2092-16-16) margins: 16, 72,
16, 16 minimum size: 399x752 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=1229,2344 maxtrack=0,0)  

> color sample #1.1 map #2 palette #ff0000:#ff7f7f:#ffffff:#7f7fff:#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> color sample #1.1 map #2 palette
> 3.4,#ff0000:3.75,#ff7f7f:4.1,#ffffff:4.5,#7f7fff:4.9,#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> color sample #1.1 map #2 palette
> 3.4,#ff0000:3.75,#ff7f7f:4.1,#ffffff:4.5,#7f7fff:4.9,#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> view orient

> key red:3.40 #ff7f7f:3.75 white:4.10 #7f7fff:4.50 blue:4.90

> ui tool show "Color Key"

> ui mousemode left "color key"

> key red:3.40 #ff7f7f:3.75 white:4.10 #7f7fff: blue:4.90

> key red:3.40 #ff7f7f: white:4.10 #7f7fff: blue:4.90

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key fontSize 15

> key fontSize 14

> key fontSize 13

> key fontSize 12

> key fontSize 11

> key fontSize 10

> key red:3.40 #ff7f7f: white:4.10 #7f7fff: blue:4.9

> key red:3.40 #ff7f7f: white:4.1 #7f7fff: blue:4.9

> key red:3.4 #ff7f7f: white:4.1 #7f7fff: blue:4.9

> key pos 0.725202,0.0476309

> key size 0.25000,0.04000

> key size 0.25000,0.03000

> ui mousemode left rotate

> save C:\Users\DELL\Desktop\image219.png supersample 3

> save "C:/Users/DELL/Documents/Temp Uni of Leeds/ThesisDesktop/Figures/In
> Progress Chapter 5/localres.cxs"

\u2014\u2014\u2014 End of log from Sun Dec 18 14:59:27 2022 \u2014\u2014\u2014

opened ChimeraX session  

> open "C:/Users/DELL/Documents/Temp Uni of Leeds/EM/PDB_Deposition/SciRep
> Files/postprocess_masked.mrc"

Opened postprocess_masked.mrc as #1, grid size 360,360,360, pixel 1.07, shown
at level 0.03, step 2, values float32  

> volume #1 step 1

> open "C:/Users/DELL/Documents/Temp Uni of Leeds/ThesisDesktop/Figures/In
> Progress Chapter 5/localres.cxs"

Opened relion_locres_filtered.mrc as #1, grid size 360,360,360, pixel 1.07,
shown at level 0.0576, step 1, values float32  
Opened relion_locres.mrc as #2, grid size 360,360,360, pixel 1.07, shown at
level 26.1, step 1, values float32  
Unable to restore session, resetting.  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 713, in restore  
obj = sm.restore_snapshot(self, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 406, in restore_snapshot  
c.set_vertex_colors()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 230, in set_vertex_colors  
s.vertex_colors = self.vertex_colors(report_stats)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 200, in vertex_colors  
values, outside = self.volume_values()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 267, in volume_values  
return self.offset_values(v, n, tf)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 275, in offset_values  
values, outside = self.vertex_values(v, xf)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 308, in vertex_values  
values, outside = v.interpolated_values(vertices, vertex_xform,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 1436, in interpolated_values  
matrix, p2m_transform = self.matrix_and_transform(point_xform,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 1621, in matrix_and_transform  
matrix = self.matrix(step=step, subregion=subregion)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\mrc\mrc_grid.py", line 44, in read_matrix  
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\mrc\mrc_format.py", line 284, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 27, in read_array  
m = read_full_array(path, byte_offset, full_size,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 84, in read_full_array  
file.readinto(b)  
PermissionError: [Errno 13] Permission denied  

Log from Sun Dec 18 14:59:27 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\DELL\Documents\Temp Uni of Leeds\EM\20200302 EM
> Processing\LocalRes\job513\relion_locres_filtered.mrc" format mrc

Opened relion_locres_filtered.mrc as #1, grid size 360,360,360, pixel 1.07,
shown at level 0.0576, step 2, values float32  

> open "C:\Users\DELL\Documents\Temp Uni of Leeds\EM\20200302 EM
> Processing\LocalRes\job513\relion_locres.mrc" format mrc

Opened relion_locres.mrc as #2, grid size 360,360,360, pixel 1.07, shown at
level 26.1, step 2, values float32  

> volume #1 step 1

> volume #2 step 1

> set bgColor white

> lighting soft

> hide #!2 models

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette #ff0000:#ff7f7f:#ffffff:#7f7fff:#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> color sample #1.1 map #2 palette
> 3.409,#ff0000:3.763,#ffff00:4.116,#ffffff:4.469,#00ff00:4.822,#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> ui tool show "Side View"

QWindowsWindow::setGeometry: Unable to set geometry 3840x2256+0+57 (frame:
3872x2344-16-15) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3840x2004+0+56 (frame: 3872x2092-16-16) margins: 16, 72,
16, 16 minimum size: 399x752 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=1229,2344 maxtrack=0,0)  

> color sample #1.1 map #2 palette #ff0000:#ff7f7f:#ffffff:#7f7fff:#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> color sample #1.1 map #2 palette
> 3.4,#ff0000:3.75,#ff7f7f:4.1,#ffffff:4.5,#7f7fff:4.9,#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> color sample #1.1 map #2 palette
> 3.4,#ff0000:3.75,#ff7f7f:4.1,#ffffff:4.5,#7f7fff:4.9,#0000ff

Map values for surface "surface": minimum 3.409, mean 3.649, maximum 4.822  

> view orient

> key red:3.40 #ff7f7f:3.75 white:4.10 #7f7fff:4.50 blue:4.90

> ui tool show "Color Key"

> ui mousemode left "color key"

> key red:3.40 #ff7f7f:3.75 white:4.10 #7f7fff: blue:4.90

> key red:3.40 #ff7f7f: white:4.10 #7f7fff: blue:4.90

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key fontSize 15

> key fontSize 14

> key fontSize 13

> key fontSize 12

> key fontSize 11

> key fontSize 10

> key red:3.40 #ff7f7f: white:4.10 #7f7fff: blue:4.9

> key red:3.40 #ff7f7f: white:4.1 #7f7fff: blue:4.9

> key red:3.4 #ff7f7f: white:4.1 #7f7fff: blue:4.9

> key pos 0.725202,0.0476309

> key size 0.25000,0.04000

> key size 0.25000,0.03000

> ui mousemode left rotate

> save C:\Users\DELL\Desktop\image219.png supersample 3

> save "C:/Users/DELL/Documents/Temp Uni of Leeds/ThesisDesktop/Figures/In
> Progress Chapter 5/localres.cxs"

\u2014\u2014\u2014 End of log from Sun Dec 18 14:59:27 2022 \u2014\u2014\u2014

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 532.09
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 15 7590
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 16,893,698,048
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-US
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
   alabaster: 0.7.12
   appdirs: 1.4.4
   Babel: 2.9.1
   backcall: 0.2.0
   blockdiag: 2.0.1
   certifi: 2020.12.5
   cftime: 1.5.0
   chardet: 3.0.4
   ChimeraX-AddCharge: 1.0.1
   ChimeraX-AddH: 2.1.6
   ChimeraX-AlignmentAlgorithms: 2.0
   ChimeraX-AlignmentHdrs: 3.2
   ChimeraX-AlignmentMatrices: 2.0
   ChimeraX-Alignments: 2.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.0
   ChimeraX-Atomic: 1.13.2
   ChimeraX-AtomicLibrary: 3.1.3
   ChimeraX-AtomSearch: 2.0
   ChimeraX-AtomSearchLibrary: 1.0
   ChimeraX-AxesPlanes: 2.0
   ChimeraX-BasicActions: 1.1
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 1.1
   ChimeraX-BondRot: 2.0
   ChimeraX-BugReporter: 1.0
   ChimeraX-BuildStructure: 2.5.2
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.1
   ChimeraX-ButtonPanel: 1.0
   ChimeraX-CageBuilder: 1.0
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.1
   ChimeraX-ChemGroup: 2.0
   ChimeraX-Clashes: 2.1
   ChimeraX-Clipper: 0.16.0
   ChimeraX-ColorActions: 1.0
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.2.1
   ChimeraX-CommandLine: 1.1.4
   ChimeraX-ConnectStructure: 2.0
   ChimeraX-Contacts: 1.0
   ChimeraX-Core: 1.2.5
   ChimeraX-CoreFormats: 1.0
   ChimeraX-coulombic: 1.1.1
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0
   ChimeraX-DataFormats: 1.1
   ChimeraX-Dicom: 1.0
   ChimeraX-DistMonitor: 1.1.3
   ChimeraX-DistUI: 1.0
   ChimeraX-Dssp: 2.0
   ChimeraX-EMDB-SFF: 1.0
   ChimeraX-ExperimentalCommands: 1.0
   ChimeraX-FileHistory: 1.0
   ChimeraX-FunctionKey: 1.0
   ChimeraX-Geometry: 1.1
   ChimeraX-gltf: 1.0
   ChimeraX-Graphics: 1.0
   ChimeraX-Hbonds: 2.1
   ChimeraX-Help: 1.1
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.0
   ChimeraX-ImageFormats: 1.1
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.1
   ChimeraX-Label: 1.0
   ChimeraX-ListInfo: 1.1.1
   ChimeraX-Log: 1.1.2
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.8.1
   ChimeraX-Map: 1.0.2
   ChimeraX-MapData: 2.0
   ChimeraX-MapEraser: 1.0
   ChimeraX-MapFilter: 2.0
   ChimeraX-MapFit: 2.0
   ChimeraX-MapSeries: 2.0
   ChimeraX-Markers: 1.0
   ChimeraX-Mask: 1.0
   ChimeraX-MatchMaker: 1.2.1
   ChimeraX-MDcrds: 2.2
   ChimeraX-MedicalToolbar: 1.0.1
   ChimeraX-Meeting: 1.0
   ChimeraX-MLP: 1.1
   ChimeraX-mmCIF: 2.3
   ChimeraX-MMTF: 2.1
   ChimeraX-Modeller: 1.0.1
   ChimeraX-ModelPanel: 1.0.1
   ChimeraX-ModelSeries: 1.0
   ChimeraX-Mol2: 2.0
   ChimeraX-Morph: 1.0
   ChimeraX-MouseModes: 1.1
   ChimeraX-Movie: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nucleotides: 2.0.1
   ChimeraX-OpenCommand: 1.5
   ChimeraX-PDB: 2.4.1
   ChimeraX-PDBBio: 1.0
   ChimeraX-PDBLibrary: 1.0.1
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.0.1
   ChimeraX-PubChem: 2.0.1
   ChimeraX-ReadPbonds: 1.0
   ChimeraX-Registration: 1.1
   ChimeraX-RemoteControl: 1.0
   ChimeraX-ResidueFit: 1.0
   ChimeraX-RestServer: 1.1
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 2.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.4
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-SDF: 2.0
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0
   ChimeraX-SeqView: 2.3
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0
   ChimeraX-Shortcuts: 1.0
   ChimeraX-ShowAttr: 1.0
   ChimeraX-ShowSequences: 1.0
   ChimeraX-SideView: 1.0
   ChimeraX-Smiles: 2.0.1
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.3.1
   ChimeraX-STL: 1.0
   ChimeraX-Storm: 1.0
   ChimeraX-Struts: 1.0
   ChimeraX-Surface: 1.0
   ChimeraX-SwapAA: 2.0
   ChimeraX-SwapRes: 2.1
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.0.1
   ChimeraX-ToolshedUtils: 1.2
   ChimeraX-Tug: 1.0
   ChimeraX-UI: 1.7.6
   ChimeraX-uniprot: 2.1
   ChimeraX-UnitCell: 1.0
   ChimeraX-ViewDockX: 1.0
   ChimeraX-Vive: 1.1
   ChimeraX-VolumeMenu: 1.0
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0
   ChimeraX-WebServices: 1.0
   ChimeraX-Zone: 1.0
   colorama: 0.4.3
   comtypes: 1.1.7
   cxservices: 1.0
   cycler: 0.10.0
   Cython: 0.29.21
   decorator: 5.0.9
   distlib: 0.3.1
   docutils: 0.16
   filelock: 3.0.12
   funcparserlib: 0.3.6
   grako: 3.16.5
   h5py: 2.10.0
   html2text: 2020.1.16
   idna: 2.10
   ihm: 0.17
   imagecodecs: 2020.5.30
   imagesize: 1.2.0
   ipykernel: 5.3.4
   ipython: 7.18.1
   ipython-genutils: 0.2.0
   jedi: 0.17.2
   Jinja2: 2.11.2
   jupyter-client: 6.1.7
   jupyter-core: 4.7.1
   kiwisolver: 1.3.1
   line-profiler: 2.1.2
   lxml: 4.6.2
   lz4: 3.1.0
   MarkupSafe: 2.0.1
   matplotlib: 3.3.2
   msgpack: 1.0.0
   netCDF4: 1.5.4
   networkx: 2.5
   numexpr: 2.7.3
   numpy: 1.19.2
   numpydoc: 1.1.0
   openvr: 1.14.1501
   packaging: 20.9
   ParmEd: 3.2.0
   parso: 0.7.1
   pickleshare: 0.7.5
   Pillow: 7.2.0
   pip: 21.0.1
   pkginfo: 1.5.0.1
   prompt-toolkit: 3.0.18
   psutil: 5.7.2
   pycollada: 0.7.1
   pydicom: 2.0.0
   Pygments: 2.7.1
   PyOpenGL: 3.1.5
   PyOpenGL-accelerate: 3.1.5
   pyparsing: 2.4.7
   PyQt5-commercial: 5.15.2
   PyQt5-sip: 12.8.1
   PyQtWebEngine-commercial: 5.15.2
   python-dateutil: 2.8.1
   pytz: 2021.1
   pywin32: 228
   pyzmq: 22.0.3
   qtconsole: 4.7.7
   QtPy: 1.9.0
   RandomWords: 0.3.0
   requests: 2.24.0
   scipy: 1.5.2
   setuptools: 50.3.2
   sfftk-rw: 0.6.7.dev1
   six: 1.15.0
   snowballstemmer: 2.1.0
   sortedcontainers: 2.2.2
   Sphinx: 3.2.1
   sphinxcontrib-applehelp: 1.0.2
   sphinxcontrib-blockdiag: 2.0.0
   sphinxcontrib-devhelp: 1.0.2
   sphinxcontrib-htmlhelp: 2.0.0
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.3
   sphinxcontrib-serializinghtml: 1.1.5
   suds-jurko: 0.6
   tables: 3.6.1
   tifffile: 2020.9.3
   tinyarray: 1.2.3
   tornado: 6.1
   traitlets: 5.0.5
   urllib3: 1.25.11
   wcwidth: 0.2.5
   webcolors: 1.11.1
   wheel: 0.36.0
   wheel-filename: 1.3.0
   WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 21 months ago

Component:	Unassigned → Volume Data
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → read_full_array: Permission denied

comment:2 by Tom Goddard, 21 months ago

Resolution:	→ nonchimerax
Status:	assigned → closed

The error message is because your session is trying to open a map file that it does not have permission to open.

Unfortunately the error message does not say what file has the problem. But the traceback shows it is being used to color a surface so it is probably a local resolution map. Not sure how your permission to read the map file was changed, but you would have to fix it in order to open the session.

File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 84, in read_full_array  
file.readinto(b)  
PermissionError: [Errno 13] Permission denied

Note: See TracTickets for help on using tickets.

Download in other formats: