Loading volume data: ModuleNotFoundError: No module named 'chimera'

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-22)
Description
Specifying a volume region with xmin > xmax gives this error.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-01-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 0557 fromDatabase emdb

Opened emd_0557.map, grid size 400,400,400, pixel 1.05, shown at level 0.0747,
step 2, values float32  

> volume #1 region 167,0,0,135,290,299

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/readarray.py", line 203, in allocate_array  
m = alloc(shape, value_type)  
ValueError: negative dimensions are not allowed  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3631, in _update_drawings  
v.update_drawings()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 689, in update_drawings  
self._update_surfaces()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 712, in _update_surfaces  
s.update_surface(ro)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1942, in update_surface  
matrix = v.matrix()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1134, in matrix  
m = self.region_matrix(r, read_matrix)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1158, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/griddata.py", line 249, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/mrc/mrc_format.py", line 287, in read_matrix  
progress)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/readarray.py", line 31, in read_array  
matrix = allocate_array(ijk_size, type, ijk_step, progress)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/readarray.py", line 206, in allocate_array  
report_memory_error(msize, value_type)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/readarray.py", line 227, in report_memory_error  
from chimera import replyobj, CancelOperation  
ModuleNotFoundError: No module named 'chimera'  
  
Error processing trigger "graphics update":  
ModuleNotFoundError: No module named 'chimera'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/readarray.py", line 227, in report_memory_error  
from chimera import replyobj, CancelOperation  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

Fixed.

Fixed memory error reporting, and also issue user error if volume command region option has minimum axis values larger than maximum axis values.