id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10349 Segger: fmap.data is None rslack@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.0-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/rslack/Downloads/5j2m.pdb format pdb Summary of feedback from opening /Users/rslack/Downloads/5j2m.pdb --- warning | Cannot find LINK/SSBOND atom SG in residue MRG /P:817 5j2m.pdb title: Hiv-1 reverse transcriptase In complex with DNA and EFDA-triphosphate, A translocation-defective RT inhibitor [more info...] Chain information for 5j2m.pdb #1 --- Chain | Description | UniProt A | PR160GAG-POL | POL_HV1H2 1-560 B | PR160GAG-POL | POL_HV1H2 1-440 P | DNA (5'- D(*ap*CP*ap*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*G)-3') | T | DNA (27-mer) | Non-standard residues in 5j2m.pdb #1 --- 6FN — 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogentriphosphate) MG — magnesium ion MRG — N2-(3-mercaptopropyl)-2'-deoxyguanosine-5'-monophosphate > open ""/Users/rslack/Library/CloudStorage/OneDrive- > EmoryUniversity/Documents/Data/3D > Maps/cryosparc_P11_J21_004_volume_map_sharp.mrc"" Opened cryosparc_P11_J21_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.84, shown at level 0.0658, step 1, values float32 > ui tool show ""Segment Map"" Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold 0.065843 Showing 48 region surfaces 1150 watershed regions, grouped to 48 regions Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 48 regions, 48 surfaces > ui tool show ""Fit to Segments"" > select #1:P,T #3 49 models selected > ui tool show ""Fit to Segments"" Simulating map res 4.000, grid 2.000 > molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false Opened 5j2m.pdb map 4 as #4, grid size 45,59,70, pixel 2, shown at level 0.103, step 1, values float32 Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size 256,256,256, pixel 0.84, shown at step 1, values float32 Top score: 0.54351, z-score: 17.45630 (avg: 0.4723, stdev: 0.0041) Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size 256,256,256, pixel 0.84, shown at step 1, values float32 Top score: 0.54351, z-score: 17.45630 (avg: 0.4723, stdev: 0.0041) Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size 256,256,256, pixel 0.84, shown at step 1, values float32 Generating Laplace version of cryosparc_P11_J21_004_volume_map_sharp.mrc Opened cryosparc_P11_J21_004_volume_map_sharp.mrc Laplacian as #6, grid size 256,256,256, pixel 0.84, shown at step 1, values float32 Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size 256,256,256, pixel 0.84, shown at step 1, values float32 Top score: 0.54351, z-score: 17.45630 (avg: 0.4723, stdev: 0.0041) > show #!4 models > select subtract #3 Nothing selected > hide #!6 models > hide #!4 models > hide #!3 models > hide #!1 models > close #4 > show #!6 models > close #6 > show #!3 models > show #!1 models > volume #2 level 0.4721 > volume #2 level 0.09354 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2233, in FitMapToSelRGroup mm = fmap.data.matrix() AttributeError: 'NoneType' object has no attribute 'matrix' AttributeError: 'NoneType' object has no attribute 'matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2233, in FitMapToSelRGroup mm = fmap.data.matrix() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2571, in FitMapToRegionsAroundSel self.FitMapToGroupsAround ( fmap, smod, regs, dmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2485, in FitMapToGroupsAround tvol = self.MapVolume ( fmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() AttributeError: 'NoneType' object has no attribute 'matrix' AttributeError: 'NoneType' object has no attribute 'matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() See log for complete Python traceback. > select #1:P,T #3 49 models selected Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2571, in FitMapToRegionsAroundSel self.FitMapToGroupsAround ( fmap, smod, regs, dmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2485, in FitMapToGroupsAround tvol = self.MapVolume ( fmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() AttributeError: 'NoneType' object has no attribute 'matrix' AttributeError: 'NoneType' object has no attribute 'matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2571, in FitMapToRegionsAroundSel self.FitMapToGroupsAround ( fmap, smod, regs, dmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2485, in FitMapToGroupsAround tvol = self.MapVolume ( fmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() AttributeError: 'NoneType' object has no attribute 'matrix' AttributeError: 'NoneType' object has no attribute 'matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() See log for complete Python traceback. > hide #!2 models Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2571, in FitMapToRegionsAroundSel self.FitMapToGroupsAround ( fmap, smod, regs, dmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2485, in FitMapToGroupsAround tvol = self.MapVolume ( fmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() AttributeError: 'NoneType' object has no attribute 'matrix' AttributeError: 'NoneType' object has no attribute 'matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() See log for complete Python traceback. Simulating map res 4.000, grid 2.000 > molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false Opened 5j2m.pdb map 4 as #4, grid size 45,59,70, pixel 2, shown at level 0.103, step 1, values float32 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2571, in FitMapToRegionsAroundSel self.FitMapToGroupsAround ( fmap, smod, regs, dmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2485, in FitMapToGroupsAround tvol = self.MapVolume ( fmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() AttributeError: 'NoneType' object has no attribute 'matrix' AttributeError: 'NoneType' object has no attribute 'matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2571, in FitMapToRegionsAroundSel self.FitMapToGroupsAround ( fmap, smod, regs, dmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2485, in FitMapToGroupsAround tvol = self.MapVolume ( fmap ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() AttributeError: 'NoneType' object has no attribute 'matrix' AttributeError: 'NoneType' object has no attribute 'matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2735, in MapVolume mm = fmap.data.matrix() See log for complete Python traceback. > ui tool show ""Fit to Segments"" Simulating map res 4.000, grid 2.000 > molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false Opened 5j2m.pdb map 4 as #5, grid size 45,59,70, pixel 2, shown at level 0.103, step 1, values float32 Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #6, grid size 256,256,256, pixel 0.84, shown at step 1, values float32 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1856, in FitToEachRegion self.saFitMapToPoints ( fmap, tpoints, to_map ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1894, in saFitMapToPoints fpoints, fpoint_weights = fit_points(fmap) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 5187, in fit_points mat = fmap.data.full_matrix() AttributeError: 'NoneType' object has no attribute 'full_matrix' AttributeError: 'NoneType' object has no attribute 'full_matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 5187, in fit_points mat = fmap.data.full_matrix() See log for complete Python traceback. Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #7, grid size 256,256,256, pixel 0.84, shown at step 1, values float32 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1856, in FitToEachRegion self.saFitMapToPoints ( fmap, tpoints, to_map ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1894, in saFitMapToPoints fpoints, fpoint_weights = fit_points(fmap) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 5187, in fit_points mat = fmap.data.full_matrix() AttributeError: 'NoneType' object has no attribute 'full_matrix' AttributeError: 'NoneType' object has no attribute 'full_matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 5187, in fit_points mat = fmap.data.full_matrix() See log for complete Python traceback. > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > ui tool show ""Fit in Map"" > hide #!7 models > hide #!6 models > show #!6 models > show #!7 models > hide #!7 models > hide #!6 models > select add #6 51 models selected > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > select subtract #6 49 models selected > select subtract #3 Nothing selected > fitmap #1 inMap #2 Fit molecule 5j2m.pdb (#1) to map cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) using 9107 atoms average map value = 0.06842, steps = 368 shifted from previous position = 0.174 rotated from previous position = 4.12 degrees atoms outside contour = 6316, contour level = 0.093545 Position of 5j2m.pdb (#1) relative to cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.90579566 -0.42349283 0.01371294 108.24317464 -0.42283294 -0.90552390 -0.03519623 109.21757910 0.02732274 0.02608231 -0.99928634 107.86680013 Axis 0.97615891 -0.21680238 0.01051207 Axis point 0.00000000 65.76877451 54.37363323 Rotation angle (degrees) 178.20132833 Shift along axis 83.11781112 > fitmap #1 inMap #2 Fit molecule 5j2m.pdb (#1) to map cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) using 9107 atoms average map value = 0.06842, steps = 48 shifted from previous position = 0.00316 rotated from previous position = 0.0129 degrees atoms outside contour = 6321, contour level = 0.093545 Position of 5j2m.pdb (#1) relative to cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.90589116 -0.42328889 0.01370113 108.24541315 -0.42262906 -0.90561864 -0.03520733 109.21576377 0.02731086 0.02610351 -0.99928611 107.86550289 Axis 0.97618337 -0.21669254 0.01050574 Axis point 0.00000000 65.76132119 54.37376691 Rotation angle (degrees) 178.20042523 Shift along axis 83.13433797 > volume #2 color #b2b2b264 > volume #2 color #b2b2b263 > volume #2 level 0.1585 > hide #!1 models > show #!1 models > volume #2 level 0.09671 > show #!3 models > hide #!2 models Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold 0.096714 Showing 43 region surfaces 686 watershed regions, grouped to 43 regions Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 43 regions, 43 surfaces > undo [Repeated 1 time(s)] > close #7 > close #6 Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold 0.096714 Only showing 60 of 161 regions. Showing 60 of 161 region surfaces 686 watershed regions, grouped to 161 regions Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 161 regions, 60 surfaces Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold 0.096714 Only showing 60 of 177 regions. Showing 60 of 177 region surfaces 686 watershed regions, grouped to 177 regions Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 177 regions, 60 surfaces Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold 0.096714 Only showing 60 of 220 regions. Showing 60 of 220 region surfaces 686 watershed regions, grouped to 220 regions Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 220 regions, 60 surfaces Please select one or more regions to align the structure to > select #1:P,T #3 61 models selected > show #!5 models > hide #!5 models > select #1:P,T #3 61 models selected > fitmap #1 inMap #2 Fit molecule 5j2m.pdb (#1) to map cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) using 9107 atoms average map value = 0.06842, steps = 48 shifted from previous position = 0.0196 rotated from previous position = 0.00826 degrees atoms outside contour = 6496, contour level = 0.096714 Position of 5j2m.pdb (#1) relative to cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.90583612 -0.42340809 0.01365693 108.23291295 -0.42275042 -0.90556348 -0.03516901 109.22922796 0.02725806 0.02608389 -0.99928806 107.87222570 Axis 0.97616928 -0.21675719 0.01048104 Axis point 0.00000000 65.77113954 54.37772399 Rotation angle (degrees) 178.20210042 Shift along axis 83.10803736 Opened 5j2m.pdb map 3 as #4, grid size 83,111,134, pixel 1, shown at level 0.11, step 1, values float32 > fitmap #1 inMap #2 resolution 3 metric correlation Fit map 5j2m.pdb map 3 in map cryosparc_P11_J21_004_volume_map_sharp.mrc using 100006 points correlation = 0.5642, correlation about mean = 0.06559, overlap = 3847 steps = 56, shift = 0.263, angle = 0.78 degrees Position of 5j2m.pdb map 3 (#4) relative to cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.90112104 -0.43300705 0.02204002 107.98669030 -0.43216567 -0.90113064 -0.03458889 109.13954834 0.03483817 0.02164384 -0.99915857 107.86114815 Axis 0.97496166 -0.22189403 0.01458776 Axis point 0.00000000 66.06940147 54.06555959 Rotation angle (degrees) 178.34745060 Shift along axis 82.63892115 Average map value = 0.06837 for 9107 atoms, 6492 outside contour > ui tool show ""Fit in Map"" Average map value = 0.06837 for 9107 atoms, 6492 outside contour Opened 5j2m.pdb map 2.5 as #4, grid size 96,130,158, pixel 0.833, shown at level 0.13, step 1, values float32 > fitmap #1 inMap #2 resolution 2.5 Fit map 5j2m.pdb map 2.5 in map cryosparc_P11_J21_004_volume_map_sharp.mrc using 129371 points correlation = 0.5485, correlation about mean = 0.04106, overlap = 6702 steps = 88, shift = 0.419, angle = 1.59 degrees Position of 5j2m.pdb map 2.5 (#4) relative to cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.91140064 -0.41143390 0.00842775 108.37658117 -0.41087370 -0.91092548 -0.03738410 109.27819215 0.02305814 0.03060915 -0.99926543 107.92542679 Axis 0.97759241 -0.21035259 0.00805433 Axis point 0.00000000 65.34492294 54.64526088 Rotation angle (degrees) 178.00708779 Shift along axis 83.83043989 Average map value = 0.06839 for 9107 atoms, 6468 outside contour > fitmap #1 inMap #2 resolution 2.5 metric correlation Fit map 5j2m.pdb map 2.5 in map cryosparc_P11_J21_004_volume_map_sharp.mrc using 129371 points correlation = 0.5491, correlation about mean = 0.04132, overlap = 6692 steps = 68, shift = 0.622, angle = 1.49 degrees Position of 5j2m.pdb map 2.5 (#4) relative to cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.90194890 -0.43128140 0.02201220 107.79126841 -0.43044093 -0.90195612 -0.03457973 109.13593252 0.03476763 0.02171420 -0.99915950 107.77168914 Axis 0.97517395 -0.22096106 0.01455937 Axis point 0.00000000 65.99124410 54.02394178 Rotation angle (degrees) 178.34601149 Shift along axis 82.56953292 Average map value = 0.06835 for 9107 atoms, 6497 outside contour > fitmap #1 inMap #2 resolution 2.5 Fit map 5j2m.pdb map 2.5 in map cryosparc_P11_J21_004_volume_map_sharp.mrc using 129371 points correlation = 0.5485, correlation about mean = 0.04107, overlap = 6702 steps = 84, shift = 0.61, angle = 1.46 degrees Position of 5j2m.pdb map 2.5 (#4) relative to cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.91117467 -0.41193341 0.00846085 108.36504776 -0.41137696 -0.91070722 -0.03716670 109.27506747 0.02301556 0.03038475 -0.99927326 107.92186501 Axis 0.97753469 -0.21062072 0.00805235 Axis point 0.00000000 65.36378798 54.63648794 Rotation angle (degrees) 178.01992522 Shift along axis 83.78402463 Average map value = 0.06839 for 9107 atoms, 6471 outside contour [Repeated 1 time(s)]Correlation = 0.5485, Correlation about mean = 0.04107, Overlap = 6702 > ui tool show ""Fit to Segments"" Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size 256,256,256, pixel 0.84, shown at step 1, values float32 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1856, in FitToEachRegion self.saFitMapToPoints ( fmap, tpoints, to_map ) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1894, in saFitMapToPoints fpoints, fpoint_weights = fit_points(fmap) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 5187, in fit_points mat = fmap.data.full_matrix() AttributeError: 'NoneType' object has no attribute 'full_matrix' AttributeError: 'NoneType' object has no attribute 'full_matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 5187, in fit_points mat = fmap.data.full_matrix() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 289, in _fit self.Fit() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 1335, in Fit func() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2233, in FitMapToSelRGroup mm = fmap.data.matrix() AttributeError: 'NoneType' object has no attribute 'matrix' AttributeError: 'NoneType' object has no attribute 'matrix' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/segger/fit_dialog.py"", line 2233, in FitMapToSelRGroup mm = fmap.data.matrix() See log for complete Python traceback. OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGQ3LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 10 days, 12 hours, 15 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-OpenCommands: 1.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 MolecularDynamicsViewer: 1.4 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Volume Data duplicate all ChimeraX