id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2371 FileNotFoundError re-reading map file chimerax-bug-report@… Tom Goddard "{{{ 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 }}} " defect closed normal Volume Data duplicate all ChimeraX