id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1812 Changing lighting of MRC volume: 'numpy.float64' object cannot be interpreted as an integer chimerax-bug-report@… Tom Goddard "{{{ 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 }}} " defect closed normal Volume Data 0.8 duplicate all ChimeraX