id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3137 SeggerX and save dialog need updating jaremko@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.93 (2020-04-03) Description Cannot save segmentation regions from the volume>segment map feature Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. > open ""C:\Users\mattj\Google Drive\CSHL\papers\x108\figures\fig4\ORC- > dna_orientation.cxs"" format session Log from Mon May 4 14:35:38 2020 > ui mousemode rightMode zoom > set bgColor white > hide all atoms > show all cartoons > color /a #55c087 > color /b #ffe255 > color /c #f6986c > color /d #6b80bc > color /e #aa7fba > lighting soft > lighting depthCue false > cartoon suppressBackboneDisplay false > graphics silhouettes true UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\\\Users\\\mattj\\\Google > Drive\\\CSHL\\\papers\\\x108\\\figures\\\fig4\\\ORC-dna_orientation.cxs"" opened ChimeraX session > close session > open ""C:\Users\mattj\Google Drive\CSHL\papers\x108\figures\fig4\ORC- > dna_orientation.cxs"" opened ChimeraX session > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > volume #1.1 level 0.008997 > surface dust all > hide #!1.1 models > show #!1.2 models > volume #1.2 level 0.009721 > hide #!1.2 models > show #!1.1 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > volume #1.1 level 0.01048 > surface dust all > volume #1.1 level 0.01059 > show #!1.2 models > hide #!1.2 models > view list Named views: dna-conforms > hide #!1.1 models > show #!1.2 models Expected an objects specifier or a view name or a keyword > save session ""C:/Users/mattj/Google Drive/CSHL/papers/x108/figures/fig4/ORC- > dna_orientation.cxs"" > toolshed show ""Segment Map"" > hide #!1.2 models > show #!1.1 models Segmenting run_it025_class001.mrc, density threshold 0.010587 Showing run_it025_class001.seg - 0 regions, 0 surfaces Showing 47 region surfaces 937 watershed regions, grouped to 47 regions Ungrouped to 4 regions > select clear Ungrouped to 4 regions > select clear Ungrouped to 13 regions, but did not show all surfaces, see Options > select clear Ungrouped to 17 regions, but did not show all surfaces, see Options > select clear > select #1.1 2 models selected > select clear > select #1.1 2 models selected > hide #!2 models > show #!2 models Smoothing and grouping, standard deviation 5 voxels Showing 25 region surfaces Got 25 regions after smoothing 5 voxels. Ungrouped to 36 regions Grouped 5 regions > color sel red Grouped 55 regions > color sel #b2b2b2 > view list Named views: dna-conforms > view dna-conforms > select clear > hide #!2 models > view dna-conforms > select clear > hide #!1.1 models > show #!1.1 models > toolshed show ""Show Volume Menu"" > save session ""C:/Users/mattj/Google Drive/CSHL/papers/x108/figures/fig4/ORC- > dna_orientation.cxs"" Summary of feedback from opening C:\Users\mattj\Google Drive\CSHL\papers\x108\figures\fig4\ORC-dna_orientation.cxs --- note | Showing run_it025_class001.seg - 2 regions, 2 surfaces opened ChimeraX session > hide #!2 models Segmenting run_it025_class003.mrc, density threshold 0.009721 Showing run_it025_class003.seg - 0 regions, 0 surfaces Showing 47 region surfaces 811 watershed regions, grouped to 47 regions > hide #!2 models > show #!2 models Ungrouped to 4 regions > select clear Ungrouped to 3 regions > select clear Ungrouped to 7 regions > select clear > select clear Ungrouped to 4 regions > select clear Grouped 6 regions Grouped 55 regions > color sel #b2b2b2 > color sel red > select clear > view list Named views: dna-conforms > view dna-conforms > hide #!2 models > surface dust all > save session ""C:/Users/mattj/Google Drive/CSHL/papers/x108/figures/fig4/ORC- > dna_orientation.cxs"" > surface dust all > volume all hide > volume #1.1 show > volume #1.1 level 0.0106 > view dna-conforms > hide #!1.1 models > show #!1.2 models Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1156, in SaveSegmentation self.SaveSegmentationAs() File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1167, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog AttributeError: 'MainWindow' object has no attribute 'save_dialog' AttributeError: 'MainWindow' object has no attribute 'save_dialog' File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1167, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog AttributeError: 'MainWindow' object has no attribute 'save_dialog' AttributeError: 'MainWindow' object has no attribute 'save_dialog' File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1167, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog AttributeError: 'MainWindow' object has no attribute 'save_dialog' AttributeError: 'MainWindow' object has no attribute 'save_dialog' File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1156, in SaveSegmentation self.SaveSegmentationAs() File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1167, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog AttributeError: 'MainWindow' object has no attribute 'save_dialog' AttributeError: 'MainWindow' object has no attribute 'save_dialog' File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog See log for complete Python traceback. > show #!2 models Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1167, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog AttributeError: 'MainWindow' object has no attribute 'save_dialog' AttributeError: 'MainWindow' object has no attribute 'save_dialog' File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1156, in SaveSegmentation self.SaveSegmentationAs() File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1167, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog AttributeError: 'MainWindow' object has no attribute 'save_dialog' AttributeError: 'MainWindow' object has no attribute 'save_dialog' File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog See log for complete Python traceback. > hide #!2 models > save image ""C:/Users/mattj/Google Drive/CSHL/papers/x108/figures/fig4/ORC- > dna_orientation2.png"" width 2000 supersample 4 transparentBackground true > hide #!1.2 models > show #!1.1 models > toolshed show ""Segment Map"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segment_dialog.py"", line 1167, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog AttributeError: 'MainWindow' object has no attribute 'save_dialog' AttributeError: 'MainWindow' object has no attribute 'save_dialog' File ""C:\Program Files\ChimeraX_20200403\bin\lib\site- packages\chimerax\segger\segfile.py"", line 172, in show_save_dialog sd = mw.save_dialog See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 442.92 OpenGL renderer: GeForce GTX 1050 Ti with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: LENOVO Model: 20MFCTO1WW OS: Microsoft Windows 10 Pro (Build 18362) Memory: 33,922,240,512 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-8850H CPU @ 2.60GHz"" }}} " defect closed normal Input/Output fixed Eric Pettersen all ChimeraX