Opened 6 years ago

Closed 6 years ago

#2371 closed defect (duplicate)

FileNotFoundError re-reading map file

Reported by: chimerax-bug-report@… 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-10-10.0.17763
ChimeraX Version: 0.9 (2019-04-13)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-04-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/pochopien/Desktop/EMBO-Presentation/session-GCN-7.cxs

opened ChimeraX session  

> surface dust #1

> surface dust #2

> surface dust #3

> surface dust #4

> surface dust #5

> surface dust #6

> surface dust #7

> surface dust #8

> surface dust #9

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part1_gauss1.5.mrc

Opened GCN1-part1_gauss1.5.mrc, grid size 600,600,600, pixel 1.08, shown at
level -2.63e-06, step 4, values float32  

> surface dust #10

> hide #!6 models

> hide #!8 models

> view 1

> lighting flat

> lighting flat

> set silhouettes false

> set silhouettes true

> lighting simple

> lighting shadows true

> lighting soft

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part2_gauss1.5.mrc

Opened GCN1-part2_gauss1.5.mrc, grid size 600,600,600, pixel 1.08, shown at
level -2.02e-06, step 4, values float32  

> surface dust #11

> view 1

> save "C:\\\Users\\\pochopien\\\Desktop\\\image14.png" supersample 3

> view 2

> save "C:\\\Users\\\pochopien\\\Desktop\\\image15.png" supersample 3

> view 3

> view 4

> save "C:\\\Users\\\pochopien\\\Desktop\\\image16.png" supersample 3

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part1_gauss1.2.mrc

Opened GCN1-part1_gauss1.2.mrc, grid size 600,600,600, pixel 1.08, shown at
level -2.77e-06, step 4, values float32  

> surface dust #12

> view 1

> hide #!12 models

> show #!10 models

> hide #!10 models

> show #!12 models

> save "C:\\\Users\\\pochopien\\\Desktop\\\image17.png" supersample 3

> close #12

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part1_gauss1.mrc

Opened GCN1-part1_gauss1.mrc, grid size 600,600,600, pixel 1.08, shown at
level -2.01e-06, step 4, values float32  

> surface dust #12

> save "C:\\\Users\\\pochopien\\\Desktop\\\image18.png" supersample 3

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part2_gauss1.mrc

Opened GCN1-part2_gauss1.mrc, grid size 600,600,600, pixel 1.08, shown at
level -1.5e-06, step 4, values float32  

> surface dust #10

> save "C:\\\Users\\\pochopien\\\Desktop\\\image14.png" supersample 3

> view 2

> save "C:\\\Users\\\pochopien\\\Desktop\\\image15.png" supersample 3

> view 4

> save "C:\\\Users\\\pochopien\\\Desktop\\\image16.png" supersample 3

> close #12 #10

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part1_lowpass8.mrc

Opened GCN1-part1_lowpass8.mrc, grid size 600,600,600, pixel 1.08, shown at
level 0.000124, step 4, values float32  

> surface dust #10

> view 1

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part1_lowpass6.mrc

Opened GCN1-part1_lowpass6.mrc, grid size 600,600,600, pixel 1.08, shown at
level 0.000206, step 4, values float32  

> surface dust #10

> surface dust #11

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part1_lowpass7.mrc

Opened GCN1-part1_lowpass7.mrc, grid size 600,600,600, pixel 1.08, shown at
level 0.000157, step 4, values float32  

> surface dust #10

> hide #!11 models

> show #!10 models

> hide #!10 models

> close #10

> show #!11 models

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part2_lowpass8.mrc

Opened GCN1-part2_lowpass8.mrc, grid size 600,600,600, pixel 1.08, shown at
level 5.92e-05, step 4, values float32  

> surface dust #10

> open C:/Users/pochopien/Desktop/EMBO-Presentation/GCN-
volumes/GCN1-part2_lowpass7.mrc

Opened GCN1-part2_lowpass7.mrc, grid size 600,600,600, pixel 1.08, shown at
level 7.52e-05, step 4, values float32  

> surface dust #10

> view 1

> view 1

> save "C:\\\Users\\\pochopien\\\Desktop\\\image17.png" supersample 3

> view 2

> save "C:\\\Users\\\pochopien\\\Desktop\\\image18.png" supersample 3

> view 4

> save "C:\\\Users\\\pochopien\\\Desktop\\\image19.png" supersample 3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2172, in mousePressEvent  
cb(event)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\histogram.py", line 337, in select_marker_cb  
cb(self.markers[i])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2236, in selected_marker_cb  
self.select_data_cb()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2230, in select_data_cb  
d.redisplay_needed_cb()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 304, in redisplay_needed_cb  
self.redisplay_needed()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 330, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 374, in
show_using_dialog_settings  
dr.show()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 662, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1664, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1179, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1203, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\griddata.py", line 248, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\map\data\mrc\mrc_format.py", line 287, in read_matrix  
progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 28, in read_array  
type, byte_swap, progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2176, in mouseMoveEvent  
cb(event)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\histogram.py", line 386, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2243, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2230, in select_data_cb  
d.redisplay_needed_cb()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 304, in redisplay_needed_cb  
self.redisplay_needed()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 330, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 374, in
show_using_dialog_settings  
dr.show()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 662, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1664, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1179, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1203, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\griddata.py", line 248, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\map\data\mrc\mrc_format.py", line 287, in read_matrix  
progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 28, in read_array  
type, byte_swap, progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2176, in mouseMoveEvent  
cb(event)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\histogram.py", line 386, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2243, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2230, in select_data_cb  
d.redisplay_needed_cb()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 304, in redisplay_needed_cb  
self.redisplay_needed()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 330, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 374, in
show_using_dialog_settings  
dr.show()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 662, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1664, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1179, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1203, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\griddata.py", line 248, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\map\data\mrc\mrc_format.py", line 287, in read_matrix  
progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 28, in read_array  
type, byte_swap, progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2176, in mouseMoveEvent  
cb(event)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\histogram.py", line 386, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2243, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2230, in select_data_cb  
d.redisplay_needed_cb()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 304, in redisplay_needed_cb  
self.redisplay_needed()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 330, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 374, in
show_using_dialog_settings  
dr.show()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 662, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1664, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1179, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1203, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\griddata.py", line 248, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\map\data\mrc\mrc_format.py", line 287, in read_matrix  
progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 28, in read_array  
type, byte_swap, progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2176, in mouseMoveEvent  
cb(event)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\histogram.py", line 386, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2243, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 2230, in select_data_cb  
d.redisplay_needed_cb()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 304, in redisplay_needed_cb  
self.redisplay_needed()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 330, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\volume_viewer.py", line 374, in
show_using_dialog_settings  
dr.show()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 662, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1664, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1179, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1203, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\griddata.py", line 248, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\map\data\mrc\mrc_format.py", line 287, in read_matrix  
progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 28, in read_array  
type, byte_swap, progress)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\pochopien\\\Desktop\\\EMBO-Presentation\\\GCN-
volumes\\\GCN1-part1_lowpass6.mrc'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\readarray.py", line 74, in read_full_array  
file = open(path, 'rb')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 10.18.10.4252
OpenGL renderer: Intel(R) HD Graphics 2500
OpenGL vendor: Intel

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → FileNotFoundError re-reading map file

comment:2 by Tom Goddard, 6 years ago

Resolution: → duplicate
Status: assigned → closed

Newer ChimeraX versions give a user-friendly error message describing this problem.

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