Changing lighting of MRC volume: 'numpy.float64' object cannot be interpreted as an integer

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-46-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: 'list' object has no attribute
'split'  

> open /home/eugenio/Scrivania/cristal3.rec.nad

Unrecognized file suffix '.nad'  

Unrecognized file suffix '.nad'  

> open /home/eugenio/Scrivania/ift1d5_8inv.mrc

Summary of feedback from opening /home/eugenio/Scrivania/ift1d5_8inv.mrc  
---  
note | /home/eugenio/Scrivania/ift1d5_8inv.mrc: invalid cell angles 0,0,0 must
be between 0 and 180.  
  
Opened ift1d5_8inv.mrc, grid size 1600,1494,149, pixel 1, shown at step 1,
values uint8  

> lighting shadows false

> lighting soft

> ui mousemode rightMode translate

> ui mousemode rightMode zoom

> movie record

> turn y 2 180

> wait 180

> movie encode /home/eugenio/movie1.mp4

Movie saved to /home/eugenio/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /home/eugenio/movie2.mp4

Movie saved to /home/eugenio/movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /home/eugenio/movie3.mp4

Movie saved to /home/eugenio/movie3.mp4  
  

> ui mousemode rightMode select

> ui mousemode rightMode zoom

> movie record

> turn y 2 180

> wait 180

> movie encode /home/eugenio/movie4.mp4

Movie saved to /home/eugenio/movie4.mp4  
  

> ui mousemode rightMode zoom

> ui mousemode rightMode select

> ui mousemode rightMode select

> ui mousemode rightMode translate selected models

> set silhouettes true

> set silhouettes false

> show selAtoms ribbons

> color selAtoms byhetero

> lighting simple

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 3377, in _update_drawings  
v.update_drawings()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 656, in update_drawings  
self._keep_displayed_data = self.displayed_matrices()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 1588, in displayed_matrices  
matrices.append(self.matrix_plane(axis, omijk[axis], read_matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 1182, in matrix_plane  
m = self.region_matrix((ijk_min, ijk_max, ijk_step), read_matrix)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 1131, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/griddata.py", line 248, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/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 "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/mrc/mrc_format.py", line 287, in read_matrix  
progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/readarray.py", line 31, in read_array  
matrix = allocate_array(ijk_size, type, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/readarray.py", line 203, in allocate_array  
m = alloc(shape, value_type)  
TypeError: 'numpy.float64' object cannot be interpreted as an integer  
  
Error processing trigger "graphics update": 'numpy.float64' object cannot be
interpreted as an integer:  
TypeError: 'numpy.float64' object cannot be interpreted as an integer  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/readarray.py", line 203, in allocate_array  
m = alloc(shape, value_type)  
  
See log for complete Python traceback.  
  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/updateloop.py", line 72, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 159, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 217, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1360, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1371, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/grayscale.py", line 237, in draw  
pd = self.make_planes(axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/grayscale.py", line 293, in make_planes  
d = self.make_ortho_planes()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/grayscale.py", line 335, in make_ortho_planes  
d = self.make_planes_drawing(planes)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/grayscale.py", line 368, in make_planes_drawing  
textures.append(self.texture_plane(k, axis))  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/grayscale.py", line 386, in texture_plane  
d = self.color_plane(k, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/grayscale.py", line 404, in color_plane  
p = self.get_color_plane(axis, k)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/solid.py", line 211, in get_color_plane  
return self.color_values(axis, plane, cmap, cmap_range)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/solid.py", line 228, in color_values  
m = self.matrix_plane(axis, plane)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 1182, in matrix_plane  
m = self.region_matrix((ijk_min, ijk_max, ijk_step), read_matrix)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 1131, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/griddata.py", line 248, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/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 "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/mrc/mrc_format.py", line 287, in read_matrix  
progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/readarray.py", line 31, in read_array  
matrix = allocate_array(ijk_size, type, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/map/data/readarray.py", line 203, in allocate_array  
m = alloc(shape, value_type)  
TypeError: 'numpy.float64' object cannot be interpreted as an integer  
  




OpenGL version: 3.3.0 NVIDIA 390.116
OpenGL renderer: Quadro 600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Fixed. Duplicate of #1600.