id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6846 Crash removing dock widget chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. 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All rights reserved. > open GATA4_ZnF2_mutated_from_4hc7_fit_in_relion_J106_map.cxs Opened relion_j106_run_class001.mrc as #1, grid size 256,256,256, pixel 1.32, shown at level 0.0151, step 1, values float32 Opened relion_j107_postprocessed_of_j106.mrc as #3, grid size 256,256,256, pixel 1.32, shown at level 0.0328, step 1, values float32 Log from Thu May 12 16:52:27 2022 > alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6 > alias cylinders cartoon style protein modeh tube rad 2 sides 24 > alias licorice car style protein modeh default arrows f xsect oval width 1 > thick 1 UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open cryosparc_P43_J205_008_volume_map_sharp.mrc Opened cryosparc_P43_J205_008_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.31, shown at level 0.103, step 1, values float32 > volume #1 level 0.1982 > volume #1 level 0.1409 > volume #1 level 0.3829 > volume #1 level 0.2428 > open > /largedata/zhou/cryosparc_projects/FoxA1_ALBN1_Nuc186/P43/J205/cryosparc_P43_J205_008_volume_map.mrc No such file/path: /largedata/zhou/cryosparc_projects/FoxA1_ALBN1_Nuc186/P43/J205/cryosparc_P43_J205_008_volume_map.mrc > open > /Users/zhoub2/Volumes/helix_zhoub2/RELION_proj/GATA4_ALBN1_Nuc186_FoxA1_20220421/Refine3D/job106/run_class001.mrc Opened run_class001.mrc as #2, grid size 256,256,256, pixel 1.32, shown at level 0.00557, step 1, values float32 > close #1 > volume #2 level 0.01588 > volume #2 level 0.01397 > open /Users/zhoub2/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/projects/GATA4/GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb Chain information for GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb #1 --- Chain | Description A | No description available > fitmap #1 inMap #2 Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map run_class001.mrc (#2) using 351 atoms average map value = 0.01742, steps = 80 shifted from previous position = 3.62 rotated from previous position = 13.4 degrees atoms outside contour = 207, contour level = 0.013971 Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.98601583 0.02057341 0.16537691 -29.66066787 0.00646053 0.98688576 -0.16129091 23.87844932 -0.16652642 0.16010382 0.97295206 2.30958235 Axis 0.69531834 0.71805305 -0.03053238 Axis point -13.30669656 0.00000000 163.30880604 Rotation angle (degrees) 13.36262942 Shift along axis -3.54812989 > select #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-0.16273,0,1,0,-0.0043412,0,0,1,0.33885 > ~select #2 Nothing selected > undo [Repeated 2 time(s)] > select #1 351 atoms, 355 bonds, 4 pseudobonds, 53 residues, 2 models selected > view matrix models > #1,0.98602,0.020573,0.16538,-26.308,0.0064605,0.98689,-0.16129,22.705,-0.16653,0.1601,0.97295,-2.6993 > view matrix models > #1,0.98602,0.020573,0.16538,-25.584,0.0064605,0.98689,-0.16129,23.451,-0.16653,0.1601,0.97295,-1.3066 > fitmap #1 inMap #2 Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map run_class001.mrc (#2) using 351 atoms average map value = 0.01741, steps = 124 shifted from previous position = 5.43 rotated from previous position = 0.524 degrees atoms outside contour = 203, contour level = 0.013971 Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.98518791 0.02887895 0.16902898 -31.80172581 -0.00116414 0.98682040 -0.16181513 25.40778115 -0.17147430 0.15922154 0.97223715 3.53922793 Axis 0.68459313 0.72610460 -0.06406525 Axis point -8.69698109 0.00000000 173.00639626 Rotation angle (degrees) 13.56053659 Shift along axis -3.54927763 > view matrix models > #1,0.98519,0.028879,0.16903,-28.625,-0.0011641,0.98682,-0.16182,23.284,-0.17147,0.15922,0.97224,0.052983 > fitmap #1 inMap #2 Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map run_class001.mrc (#2) using 351 atoms average map value = 0.01742, steps = 92 shifted from previous position = 5.19 rotated from previous position = 0.232 degrees atoms outside contour = 204, contour level = 0.013971 Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.98562027 0.02537279 0.16705961 -30.83922830 0.00191167 0.98692460 -0.16117128 24.70795920 -0.16896460 0.15917304 0.97268438 3.01484266 Axis 0.68913856 0.72286981 -0.05047056 Axis point -10.54866682 0.00000000 169.07269384 Rotation angle (degrees) 13.43980924 Shift along axis -3.54402426 > view matrix models > #1,0.98562,0.025373,0.16706,-25.954,0.0019117,0.98692,-0.16117,24.347,-0.16896,0.15917,0.97268,-2.69 > view matrix models > #1,0.85016,0.14263,0.50684,-73.882,-0.024161,0.97217,-0.23305,42.09,-0.52597,0.18588,0.82994,81.492 > view matrix models > #1,0.82994,0.55679,0.034416,-87.76,-0.51734,0.79129,-0.3259,189.48,-0.20869,0.25267,0.94478,-11.271 > view matrix models > #1,0.94617,0.27969,0.16287,-69.789,-0.31275,0.91962,0.23768,41.636,-0.083299,-0.27583,0.95759,74.587 > view matrix models > #1,0.94617,0.27969,0.16287,-69.028,-0.31275,0.91962,0.23768,41.5,-0.083299,-0.27583,0.95759,75.848 > fitmap #1 inMap #2 Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map run_class001.mrc (#2) using 351 atoms average map value = 0.0165, steps = 180 shifted from previous position = 12.9 rotated from previous position = 26.9 degrees atoms outside contour = 218, contour level = 0.013971 Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.95850114 0.28234253 0.03947496 -61.40358064 -0.26845940 0.94049602 -0.20831897 91.49853928 -0.09594334 0.18907654 0.97726401 -16.71162069 Axis 0.57380380 0.19553198 -0.79530903 Axis point 288.01724337 251.57748700 0.00000000 Rotation angle (degrees) 20.26005521 Shift along axis -4.05181396 > undo > view matrix models > #1,0.94617,0.27969,0.16287,-72.011,-0.31275,0.91962,0.23768,40.896,-0.083299,-0.27583,0.95759,79.144 > fitmap #1 inMap #2 Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map run_class001.mrc (#2) using 351 atoms average map value = 0.0165, steps = 176 shifted from previous position = 9.25 rotated from previous position = 27 degrees atoms outside contour = 218, contour level = 0.013971 Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.95865158 0.28192375 0.03880920 -61.24041715 -0.26812819 0.94048416 -0.20879853 91.51130099 -0.09536471 0.18975920 0.97718832 -16.95148052 Axis 0.57562358 0.19378289 -0.79442161 Axis point 288.45388091 251.25730687 0.00000000 Rotation angle (degrees) 20.25485103 Shift along axis -4.05148146 > undo > show sel atoms > hide sel atoms > show sel cartoons > show sel atoms > hide sel cartoons > view matrix models > #1,0.94617,0.27969,0.16287,-74.686,-0.31275,0.91962,0.23768,40.817,-0.083299,-0.27583,0.95759,78.205 > view matrix models > #1,0.94617,0.27969,0.16287,-73.72,-0.31275,0.91962,0.23768,40.108,-0.083299,-0.27583,0.95759,79.66 > volume #2 color #ffffb2c9 > lighting soft > lighting simple > lighting full > lighting simple > view matrix models > #1,0.94417,0.26332,0.19798,-74.93,-0.31042,0.91236,0.26689,36.978,-0.11035,-0.31345,0.94317,94.945 > view matrix models > #1,0.94417,0.26332,0.19798,-74.57,-0.31042,0.91236,0.26689,37.629,-0.11035,-0.31345,0.94317,92.35 > view matrix models > #1,0.94417,0.26332,0.19798,-71.788,-0.31042,0.91236,0.26689,34.971,-0.11035,-0.31345,0.94317,91.545 > view matrix models > #1,0.96671,0.24262,-0.081259,-31.483,-0.23494,0.96748,0.093744,33.671,0.10136,-0.071532,0.99227,-7.7423 > view matrix models > #1,0.96671,0.24262,-0.081259,-30.666,-0.23494,0.96748,0.093744,34.458,0.10136,-0.071532,0.99227,-6.1126 > view matrix models > #1,0.99376,0.073426,-0.083904,0.32666,-0.061704,0.98897,0.13464,-9.5036,0.092865,-0.12862,0.98734,8.3383 > view matrix models > #1,0.98562,0.10378,-0.13336,2.6066,-0.07581,0.97688,0.1999,-13.626,0.15102,-0.18691,0.9707,11.836 > view matrix models > #1,0.98562,0.10378,-0.13336,3.488,-0.07581,0.97688,0.1999,-12.865,0.15102,-0.18691,0.9707,11.635 > view matrix models > #1,0.97908,0.16947,-0.11258,-12.163,-0.14985,0.97494,0.16444,6.9814,0.13763,-0.14413,0.97994,3.8305 > fitmap #1 inMap #2 Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map run_class001.mrc (#2) using 351 atoms average map value = 0.01523, steps = 76 shifted from previous position = 0.719 rotated from previous position = 12.6 degrees atoms outside contour = 151, contour level = 0.013971 Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.99833250 0.00426001 -0.05756792 10.99393893 -0.00313856 0.99980382 0.01955690 -3.68263610 0.05763994 -0.01934361 0.99815002 -10.11234833 Axis -0.31932000 -0.94569887 -0.06073213 Axis point 180.88787044 0.00000000 188.98551510 Rotation angle (degrees) 3.49213291 Shift along axis 0.58622456 > color #2 #33ffff models transparency 0 > color #2 cyan models transparency 0 > color #2 #006666 models transparency 0 > color #2 #33ffff models transparency 0 > lighting soft > select clear > select /A:402@ZN 1 atom, 1 residue, 1 model selected > delete sel > open > /Users/zhoub2/Volumes/helix_zhoub2/RELION_proj/GATA4_ALBN1_Nuc186_FoxA1_20220421/MaskCreate/job103/mask.mrc Opened mask.mrc as #3, grid size 256,256,256, pixel 1.32, shown at level 1, step 1, values float32 > volume #3 level 1 [Repeated 1 time(s)] > open > /Users/zhoub2/Volumes/helix_zhoub2/RELION_proj/GATA4_ALBN1_Nuc186_FoxA1_20220421/PostProcess/job107/postprocess.mrc Opened postprocess.mrc as #4, grid size 256,256,256, pixel 1.32, shown at level 0.00868, step 1, values float32 > close #3 > volume #4 level 0.0179 > volume #4 level 0.01585 > volume #4 level 0.02046 > volume #4 level 0.07269 > volume #4 level 0.02046 > volume #4 level 0.01431 > volume #4 level 0.02199 > hide #!1 models > show #!1 models > hide #!2 models > hide #!4 models > show #!2 models > color #2 #33ffff8f models > color #2 #33ffffcb models > lighting simple > volume #2 level 0.01168 > volume #4 level 0.02609 > volume #2 level 0.01168 > volume #2 level 0.01473 > pwd Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive- NationalInstitutesofHealth/projects/FoxA1/FoxA1_ALBN1_Nuc186/model_building > cd ../../GATA4 Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > cd ../../ Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive- NationalInstitutesofHealth/projects/FoxA1 > cd .. Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive- NationalInstitutesofHealth/projects > cd GATA4 Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive- NationalInstitutesofHealth/projects/GATA4 > save relion_j106_run_class001.mrc #2 > save GATA3_ZnF2_4hc7_fit_relion_j106_run_class001.pdb #1 > volume #4 level 0.02456 > open /Users/zhoub2/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/projects/GATA4/GATA4_ZnF2_mutated_from_4hc7_fit_relion_j106_run_class001-coot-0.pdb Summary of feedback from opening /Users/zhoub2/Library/CloudStorage/OneDrive- NationalInstitutesofHealth/projects/GATA4/GATA4_ZnF2_mutated_from_4hc7_fit_relion_j106_run_class001-coot-0.pdb --- warnings | End residue of secondary structure not found: HELIX 1 1 CYS A 339 ASN A 350 1 12 End residue of secondary structure not found: HELIX 2 2 PRO A 354 LYS A 358 1 5 Chain information for GATA4_ZnF2_mutated_from_4hc7_fit_relion_j106_run_class001-coot-0.pdb #3 --- Chain | Description A | No description available > close #1 > show atoms > ui tool show AlphaFold > alphafold predict #3 Running AlphaFold prediction [Repeated 2 time(s)] > volume #4 level 0.02772 > volume #2 level 0.01395 > show cartoons > hide atoms > open > /Users/zhoub2/Volumes/helix_zhoub2/RELION_proj/GATA4_ALBN1_Nuc186_FoxA1_20220421/MaskCreate/job103/mask.mrc Opened mask.mrc as #1, grid size 256,256,256, pixel 1.32, shown at level 1, step 1, values float32 > volume #1 level 1 > volume #4 level 0.003466 > volume #4 level 0.007684 > close #1 > volume #4 level 0.03278 > show cartoons > color #3 #330033 transparency 0 > color #3 #663366 transparency 0 > color zone #2 near #3 distance 3 > lighting soft > set bgColor white > color zone #2 near #3 distance 2 > color zone #2 near #3 distance 3 > volume #2 color #6666cc > color zone #2 near #3 distance 3 > volume #2 color #00ccff > color zone #2 near #3 distance 3 > color #3 #006600 transparency 0 > color zone #2 near #3 distance 3 > color #3 #cc3300 transparency 0 > color zone #2 near #3 distance 3 > color #3 #993300 transparency 0 > color zone #2 near #3 distance 3 > color #3 #cc9966 transparency 0 > color zone #2 near #3 distance 3 > hide #!3 models > volume #2 level 0.01509 > rename #2 id #2 > rename #2 id #1 > rename #3 id #2 > rename #4 id #3 > rename #1 relion_j106_run_class001.mrc > rename #3 relion_j107_postprocessed_of_j106.mrc > save /Users/zhoub2/NIH- > OneDrive/projects/GATA4/GATA4_ZnF2_mutated_from_4hc7_fit_in_relion_J106_map.cxs > pwd Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive- NationalInstitutesofHealth/projects/GATA4 > save relion_j107_postprocessed_of_j106.mrc #3 > save relion_j106_run_class001.mrc #1 > save /Users/zhoub2/NIH- > OneDrive/projects/GATA4/GATA4_ZnF2_mutated_from_4hc7_fit_in_relion_J106_map.cxs [Repeated 1 time(s)] ——— End of log from Thu May 12 16:52:27 2022 ——— opened ChimeraX session OpenGL version: 4.1 ATI-4.8.15 OpenGL renderer: AMD Radeon R9 M395X OpenGL 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