id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2450 Various segmentation problems jaremko@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.91 (2019-09-27) Description Map segmentation does not group/ungroup properly with selections. Regrouping selected segments will only undo the previous ungroup. Also, we can't selective color segments like in Chimera. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' > ui mousemode rightMode zoom > lighting soft > graphics silhouettes true > hide atoms > show cartoons UCSF ChimeraX version: 0.91 (2019-09-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r391.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r392.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r401.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r407.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r478.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r487.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1804.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1808.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1836.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1845.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1849.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1856.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1865.mrc C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1869.mrc Opened job141_run_class001__r391.mrc, grid size 320,320,320, pixel 1.07, shown at level 1.58e-06, step 2, values float32 > volume all step 1 > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > 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 #!1.4 models > show #!1.4 models > hide #!1.5 models > show #!1.5 models > hide #!1.7 models > show #!1.7 models > hide #!1.7 models > show #!1.7 models > hide #!1.8 models > show #!1.8 models > hide #!1.9 models > show #!1.9 models > hide #!1.9 models > show #!1.9 models > hide #!1.11 models > show #!1.11 models > close session > open C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/run_class001.mrc Opened run_class001.mrc, grid size 320,320,320, pixel 1.07, shown at level 0.00453, step 2, values float32 > surface dust #1 > toolshed show ""Segment Map"" Segmenting run_class001.mrc, density threshold 0.008591 Showing run_class001.seg - 0 regions, 0 surfaces Showing 46 region surfaces 930 watershed regions, grouped to 46 regions > hide #!2 models > show #!2 models > hide #!1 models Ungrouped to 3 regions > select clear Ungrouped to 3 regions > select clear Ungrouped to 5 regions > select clear Smoothing and grouping, standard deviation 5 voxels Showing 27 region surfaces Got 27 regions after smoothing 5 voxels. Ungrouped to 39 regions Ungrouped to 6 regions > color sel red > select clear > select clear > toolshed show ""Measure and Color Blobs"" > select clear > open C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job140/job141_run_DNA- red.seg Traceback (most recent call last): File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\ui\gui.py"", line 599, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths])) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\commands\open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\models.py"", line 637, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\io.py"", line 489, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\io.py"", line 445, in open_data models, status = open_func(*args, **kw) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\segger\segfile.py"", line 116, in open_segmentation seg = read_segmentation(session, path, open = True) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\segger\segfile.py"", line 303, in read_segmentation raise ValueError('Segmentation file format is not ""segger""') ValueError: Segmentation file format is not ""segger"" ValueError: Segmentation file format is not ""segger"" File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\segger\segfile.py"", line 303, in read_segmentation raise ValueError('Segmentation file format is not ""segger""') See log for complete Python traceback. > select clear > open C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job140/job141_run_class001.seg Traceback (most recent call last): File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\ui\gui.py"", line 599, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths])) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\commands\open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\models.py"", line 637, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\io.py"", line 489, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\core\io.py"", line 445, in open_data models, status = open_func(*args, **kw) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\segger\segfile.py"", line 116, in open_segmentation seg = read_segmentation(session, path, open = True) File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\segger\segfile.py"", line 303, in read_segmentation raise ValueError('Segmentation file format is not ""segger""') ValueError: Segmentation file format is not ""segger"" ValueError: Segmentation file format is not ""segger"" File ""C:\Program Files\ChimeraX-20190927\bin\lib\site- packages\chimerax\segger\segfile.py"", line 303, in read_segmentation raise ValueError('Segmentation file format is not ""segger""') See log for complete Python traceback. > select clear > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models Smoothing and grouping, standard deviation 5 voxels Showing 27 region surfaces Got 27 regions after smoothing 5 voxels. OpenGL version: 3.3.0 NVIDIA 430.86 OpenGL renderer: GeForce GTX 1050 Ti with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data fixed all ChimeraX