id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2775 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. }}} " defect closed normal Volume Data fixed all ChimeraX