id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15713 Session save: int too big to convert chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/helical_rise_multiply.cxs"" Opened 4rise_10z.mrc as #1, grid size 288,288,288, pixel 0.83, shown at level 0.00993, step 1, values float32 Opened 4rise_50z.mrc as #2, grid size 288,288,288, pixel 0.83, shown at level 0.00993, step 1, values float32 Opened 2rise_10z.mrc as #3, grid size 288,288,288, pixel 0.83, shown at level 0.00496, step 1, values float32 Opened 2rise_50z.mrc as #4, grid size 288,288,288, pixel 0.83, shown at level 0.00315, step 1, values float32 Opened postprocess_masked.mrc as #5, grid size 288,288,288, pixel 0.83, shown at level 0.00325, step 1, values float32 Opened postprocess_masked.mrc as #6, grid size 288,288,288, pixel 0.83, shown at level 0.00268, step 1, values float32 Log from Tue May 21 15:52:22 2024UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/rise_compare.cxs"" > To Restore session: > > * update Atomic bundle to version 1.49.1 or newer (have 1.41.5) > Unable to restore session: need to update bundle > open ""D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/rise_compare.cxs"" > To Restore session: > > * update Atomic bundle to version 1.49.1 or newer (have 1.41.5) > Unable to restore session: need to update bundle > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/4rise/job117/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #1, grid size 288,288,288, pixel 0.83, shown at level 0.000553, step 2, values float32 > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/4rise/job115/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #2, grid size 288,288,288, pixel 0.83, shown at level 0.0034, step 2, values float32 > volume #1 step 1 > volume #2 step 1 > volume #1 level 0.006669 > volume #2 level 0.01094 > hide #!2 models > ui tool show ""Side View"" > open ""D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/rise_compare.cxs"" > To Restore session: > > * update Atomic bundle to version 1.49.1 or newer (have 1.41.5) > Unable to restore session: need to update bundle > volume #1 level 0.005302 > volume #1 level 0.005 > show #!2 models > hide #!1 models > volume #2 level 0.005 > volume #2 level 0.009271 > volume #2 level 0.008769 > volume #2 level 0.006507 > volume #2 level 0.01317 > rename #1 4rise_10z.mrc > rename #2 4rise_50z.mrc > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/2rise/job094/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #3, grid size 288,288,288, pixel 0.83, shown at level 0.000603, step 2, values float32 > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/2rise/job105/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #4, grid size 288,288,288, pixel 0.83, shown at level 0.00315, step 2, values float32 > volume #3 step 1 > volume #4 step 1 > hide #!2 models > volume #3 level 0.004373 > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!4 models > volume #3 level 0.005482 > rename #3 2rise_10z.mrc > rename #4 2rise_50z.mrc > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/3rise/job090/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #5, grid size 288,288,288, pixel 0.83, shown at level 0.00056, step 2, values float32 > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/3rise/job103/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #6, grid size 288,288,288, pixel 0.83, shown at level 0.00268, step 2, values float32 > hide #!3 models > hide #!5 models > show #!5 models > hide #!6 models > volume #5 step 1 > volume #6 step 1 > volume #5 level 0.0005602 > volume #5 level 0.0004992 > volume #5 level 0.001659 > volume #5 level 0.001964 > volume #5 level 0.002148 > volume #5 level 0.00288 > volume #5 level 0.002941 > volume #5 level 0.003002 > volume #5 level 0.003063 > volume #5 level 0.003124 > volume #5 level 0.003247 > volume #5 level 0.003308 > volume #5 level 0.003369 > volume #5 level 0.00343 > volume #5 level 0.003491 > volume #5 level 0.003552 > volume #5 level 0.003613 > volume #5 level 0.002941 > show #!3 models > hide #!5 models > volume #3 level 0.004669 > volume #3 level 0.004964 > hide #!3 models > show #!5 models > volume #5 level 0.003247 > hide #!5 models > show #!2 models > show #!1 models > hide #!1 models > set bgColor white > set bgColor #ffffff00 > color #2 #3791d5ff models > color #2 #5500ffff models > color #2 #3385ffff models > color #2 #5555ffff models > transparency #2.1 50 > volume #2 level 0.01161 > volume #2 level 0.009926 > save ""D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/4rise/side_view.png"" > width 2000 height 1402 supersample 3 transparentBackground true > show #!1 models > hide #!2 models > color #1 #5555ffff models > select add #1 4 models selected > transparency sel 50 > select subtract #1 Nothing selected > volume #1 level 0.00993 > save ""D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/4rise/top_view.png"" > width 2000 height 1402 supersample 3 transparentBackground true > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/helical_rise_multiply.cxs"" ——— End of log from Tue May 21 15:52:22 2024 ——— opened ChimeraX session > hide #!1 models > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/1rise/job072/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #7, grid size 288,288,288, pixel 0.83, shown at level 0.000553, step 2, values float32 > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/1rise/job107/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #8, grid size 288,288,288, pixel 0.83, shown at level 0.00313, step 2, values float32 > hide #!7 models > rename #8 1rise_50z.mrc > rename #7 1rise_10z.mrc > volume #8 step 1 > volume #7 step 1 > volume #8 level 0.007868 > volume #8 level 0.007 > volume #8 level 0.008 > hide #!8 models > show #!7 models > volume #7 level 0.0008 > volume #7 level 0.008 > open ""D:/PTB129_Tracer/mutiply_helical rise/FDDNP/FDDNP_1rise_favor90.pdb"" Chain information for FDDNP_1rise_favor90.pdb #9 --- Chain | Description A B C D E F G H I J K L | No description available > style stick Changed 3050 atom styles > hide #!7 models > show #!7 models > color #9 #adadadff > hide #!7 models > hide #9 models > show #!8 models > select #8 4 models selected > ui tool show ""Segment Map"" Segmenting 1rise_50z.mrc, density threshold 0.008000 Showing 176 region surfaces 1919 watershed regions, grouped to 176 regions Showing 1rise_50z.seg - 176 regions, 176 surfaces > ui tool show ""Side View"" > select #10.2 1 model selected Ungrouped to 13 regions Ungrouped to 28 regions Ungrouped to 31 regions Ungrouped to 8 regions Ungrouped to 0 regions > select #10.233 1 model selected > select add #10.223 2 models selected > select add #10.220 3 models selected > select add #10.231 4 models selected > select add #10.186 5 models selected > select add #10.209 6 models selected Grouped 6 regions > select #10.183 1 model selected > select #10.184 1 model selected > select add #10.25 2 models selected > select #10.25 1 model selected > select add #10.46 2 models selected > select add #10.32 3 models selected > select add #10.21 4 models selected Ungrouped to 17 regions Ungrouped to 40 regions Ungrouped to 19 regions Ungrouped to 6 regions Ungrouped to 0 regions > select #10.183 1 model selected > select add #10.184 2 models selected > select add #10.252 3 models selected > select add #10.185 4 models selected > select add #10.255 5 models selected > select add #10.274 6 models selected > select add #10.220 7 models selected > select add #10.266 8 models selected Grouped 8 regions > select #10.209 1 model selected > select add #10.183 2 models selected Grouped 2 regions > select #10.85 1 model selected > select add #10.44 2 models selected > select add #10.24 3 models selected > select add #10.41 4 models selected > select add #10.1 5 models selected > select subtract #10.1 4 models selected > select add #10.1 5 models selected Ungrouped to 25 regions Ungrouped to 47 regions Ungrouped to 59 regions Ungrouped to 22 regions Ungrouped to 0 regions > select #10.183 1 model selected > select add #10.345 2 models selected > select add #10.371 3 models selected > select add #10.209 4 models selected > select add #10.360 5 models selected > select add #10.357 6 models selected > select add #10.274 7 models selected Grouped 7 regions > select #10.368 1 model selected > select add #10.286 2 models selected > select add #10.365 3 models selected > select add #10.338 4 models selected > select add #10.185 5 models selected > select add #10.282 6 models selected > select add #10.183 7 models selected Grouped 7 regions > select #10.335 1 model selected > select add #10.316 2 models selected > select add #10.183 3 models selected > select #10.335 1 model selected > select add #10.183 2 models selected Grouped 2 regions > select #10.12 1 model selected Ungrouped to 6 regions Ungrouped to 18 regions Ungrouped to 30 regions Ungrouped to 4 regions Ungrouped to 0 regions Ungrouped to 206 regions > select #10.378 1 model selected > select add #10.387 2 models selected > select add #10.273 3 models selected > select add #10.185 4 models selected Grouped 4 regions > select add #10.380 2 models selected > select #10.455 1 model selected > select add #10.510 2 models selected > select add #10.508 3 models selected > select add #10.402 4 models selected > select add #10.400 5 models selected > select add #10.408 6 models selected > select add #10.407 7 models selected > select add #10.572 8 models selected Ungrouped to 19 regions Ungrouped to 30 regions Ungrouped to 8 regions Ungrouped to 0 regions Ungrouped to 474 regions > select #10.380 1 model selected > select #10.3 1 model selected > select add #10.380 2 models selected > select add #10.83 3 models selected > select add #10.18 4 models selected > select add #10.87 5 models selected > select add #10.73 6 models selected > select add #10.78 7 models selected Grouped 7 regions > select #10.15 1 model selected > select add #10.50 2 models selected > select add #10.29 3 models selected > select add #10.837 4 models selected > select add #10.817 5 models selected Drag select of 899, 10 of 760 triangles, 2428, 9 of 1468 triangles, 893, 12 of 588 triangles, 2427, 15 of 1268 triangles, 8 1rise_50z.mrc > select #10.50 1 model selected > select add #10.15 2 models selected > select add #10.3 3 models selected Grouped 3 regions > select #10.29 1 model selected > select #10.837 1 model selected > select add #10.817 2 models selected > select add #10.1000 3 models selected > select add #10.1023 4 models selected > select add #10.747 5 models selected > select add #10.845 6 models selected > select add #10.847 7 models selected > select add #10.768 8 models selected Ungrouped to 27 regions Ungrouped to 8 regions Ungrouped to 0 regions Ungrouped to 954 regions > select #10.3 1 model selected > select #10.3 1 model selected > select #10.3 1 model selected > select add #10.29 2 models selected > select add #10.68 3 models selected > select add #10.48 4 models selected > select add #10.45 5 models selected > select add #10.56 6 models selected > select add #10.65 7 models selected > select add #10.52 8 models selected > select add #10.64 9 models selected > select add #10.15 10 models selected > select subtract #10.64 9 models selected > select add #10.61 10 models selected > select add #10.1333 11 models selected > select add #10.1229 12 models selected > select add #10.1061 13 models selected Grouped 13 regions > select #10.1559 1 model selected > select add #10.1211 2 models selected > select add #10.3 3 models selected Grouped 3 regions > select add #10.183 2 models selected Grouped 2 regions Opened 1rise_50z_imasked as #11, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > close #11 > close #10 > close #12-1514 > hide #8.1 models > show #8.1 models > hide #!8 models > show #!8 models Segmenting 1rise_50z.mrc, density threshold 0.008000 Showing 176 region surfaces 1919 watershed regions, grouped to 176 regions Showing 1rise_50z.seg - 176 regions, 176 surfaces > select #10.2 1 model selected Ungrouped to 13 regions Ungrouped to 28 regions Ungrouped to 31 regions Ungrouped to 8 regions Ungrouped to 0 regions > select #10.233 1 model selected > select add #10.226 2 models selected > select add #10.180 3 models selected > select add #10.227 4 models selected > select add #10.232 5 models selected > select add #10.216 6 models selected > select add #10.220 7 models selected > select add #10.25 8 models selected > select subtract #10.25 7 models selected Grouped 7 regions > select #10.40 1 model selected > select #10.25 1 model selected > select add #10.46 2 models selected > select add #10.32 3 models selected > select add #10.21 4 models selected > select add #10.85 5 models selected > select add #10.44 6 models selected Ungrouped to 22 regions Ungrouped to 47 regions Ungrouped to 27 regions Ungrouped to 10 regions Ungrouped to 0 regions > select #10.259 1 model selected > select add #10.285 2 models selected > select add #10.284 3 models selected > select add #10.272 4 models selected > select add #10.223 5 models selected > select add #10.266 6 models selected > select add #10.288 7 models selected > select add #10.238 8 models selected > select add #10.208 9 models selected > select add #10.179 10 models selected Grouped 10 regions > select #10.24 1 model selected > select add #10.41 2 models selected > select add #10.1 3 models selected Ungrouped to 20 regions Ungrouped to 40 regions Ungrouped to 51 regions Ungrouped to 18 regions Ungrouped to 0 regions > select #10.272 1 model selected > select #10.179 1 model selected > select add #10.272 2 models selected > select add #10.294 3 models selected > select add #10.369 4 models selected > select add #10.341 5 models selected > select add #10.285 6 models selected > select add #10.230 7 models selected > select add #10.351 8 models selected > select add #10.336 9 models selected > select add #10.357 10 models selected > select add #10.363 11 models selected > select add #10.339 12 models selected Grouped 12 regions > select #10.10 1 model selected > select add #10.19 2 models selected Ungrouped to 15 regions Ungrouped to 31 regions Ungrouped to 33 regions Ungrouped to 10 regions Ungrouped to 0 regions > select #10.351 1 model selected > select add #10.10 2 models selected > select add #10.413 3 models selected > select add #10.395 4 models selected > select add #10.376 5 models selected > select add #10.332 6 models selected Grouped 6 regions > select #10.405 1 model selected > select #10.18 1 model selected > select add #10.83 2 models selected > select add #10.20 3 models selected > select add #10.87 4 models selected Ungrouped to 12 regions Ungrouped to 23 regions Ungrouped to 30 regions Ungrouped to 6 regions Ungrouped to 0 regions Ungrouped to 185 regions > select #10.10 1 model selected Drag select of 2734, 13 of 2444 triangles, 460, 9 of 472 triangles, 2378, 6 of 3328 triangles, 2745, 17 of 2484 triangles, 8 1rise_50z.mrc > select add #10.444 8 models selected > select clear > select #10.405 1 model selected > select add #10.10 2 models selected > select add #10.444 3 models selected > select add #10.433 4 models selected > select add #10.442 5 models selected > select add #10.437 6 models selected > select add #10.394 7 models selected > select add #10.447 8 models selected > select add #10.388 9 models selected Grouped 9 regions > select #10.600 1 model selected > select add #10.604 2 models selected > select add #10.590 3 models selected > select add #10.591 4 models selected > select add #10.573 5 models selected > select add #10.572 6 models selected > select add #10.477 7 models selected > select add #10.460 8 models selected Ungrouped to 20 regions Ungrouped to 28 regions Ungrouped to 8 regions Ungrouped to 0 regions Ungrouped to 452 regions > select #10.3 1 model selected > select #10.3 1 model selected > select add #10.90 2 models selected > select add #10.10 3 models selected > select add #10.39 4 models selected > select add #10.75 5 models selected > select add #10.80 6 models selected > select add #10.6 7 models selected > select add #10.63 8 models selected Grouped 8 regions > select #10.779 1 model selected > select add #10.123 2 models selected > select add #10.635 3 models selected > select add #10.630 4 models selected Ungrouped to 13 regions Ungrouped to 2 regions Ungrouped to 0 regions Ungrouped to 934 regions > select #10.50 1 model selected > select #10.50 1 model selected > select add #10.39 2 models selected > select add #10.10 3 models selected > select add #10.51 4 models selected > select add #10.30 5 models selected > select add #10.3 6 models selected Grouped 6 regions > select #10.179 1 model selected > select add #10.3 2 models selected Grouped 2 regions Opened 1rise_50z_imasked as #11, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 Opened 1rise_50z_imasked as #12, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > hide #!10 models > hide #!8 models > hide #8.1 models > color #11 #aaff00ff models > color #12 #ffaa7fff models > show #9 models > color #9 #aaff00ff > color #9,11-12 lime > color #12 #ffaa7fff models > color #11 #aaff00ff models > select add #10 1514 models selected > select subtract #10 Nothing selected > select add #11 2 models selected > transparency sel 50 > transparency sel 90 > transparency sel 100 > graphics silhouettes true > select clear > select add #9 3050 atoms, 3099 bonds, 409 residues, 1 model selected > color sel lime > color sel byhetero > select clear > select add #12 2 models selected > transparency sel 50 > select /M:1@H122 1 atom, 1 residue, 1 model selected > select up 38 atoms, 39 bonds, 1 residue, 1 model selected > select up 3050 atoms, 3099 bonds, 409 residues, 1 model selected > hide H > color sel orange > color sel lime > color sel byhetero > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 38 atoms, 39 bonds, 1 residue, 1 model selected > color sel orange > color sel byhetero > select /M:1@C08 1 atom, 1 residue, 1 model selected > select /M:1@C08 1 atom, 1 residue, 1 model selected > select up 38 atoms, 39 bonds, 1 residue, 1 model selected > combine sel > hide #9 models > select add #9 3050 atoms, 3099 bonds, 409 residues, 1 model selected > select subtract #9 Nothing selected > select add #13 3050 atoms, 3099 bonds, 409 residues, 1 model selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models #13,1,0,0,-0.0791,0,1,0,0.31015,0,0,1,-4.4418 > ui tool show ""Fit in Map"" > fitmap #13 inMap #12 Fit molecule copy of FDDNP_1rise_favor90.pdb (#13) to map 1rise_50z_imasked (#12) using 3050 atoms average map value = 0.001092, steps = 64 shifted from previous position = 0.668 rotated from previous position = 2.44 degrees atoms outside contour = 3039, contour level = 0.008 Position of copy of FDDNP_1rise_favor90.pdb (#13) relative to 1rise_50z_imasked (#12) coordinates: Matrix rotation and translation 0.99911079 -0.04196330 0.00408738 5.16899461 0.04193728 0.99910065 0.00625669 -5.45418359 -0.00434626 -0.00607972 0.99997207 -3.44104713 Axis -0.14475786 0.09896195 0.98450581 Axis point 121.26268057 104.47979130 0.00000000 Rotation angle (degrees) 2.44214139 Shift along axis -4.67574015 > fitmap #13 inMap #12 Fit molecule copy of FDDNP_1rise_favor90.pdb (#13) to map 1rise_50z_imasked (#12) using 3050 atoms average map value = 0.001094, steps = 28 shifted from previous position = 0.0209 rotated from previous position = 0.0481 degrees atoms outside contour = 3040, contour level = 0.008 Position of copy of FDDNP_1rise_favor90.pdb (#13) relative to 1rise_50z_imasked (#12) coordinates: Matrix rotation and translation 0.99910194 -0.04223026 0.00345214 5.27966429 0.04220633 0.99908621 0.00673569 -5.53972106 -0.00373344 -0.00658394 0.99997136 -3.43321978 Axis -0.15527277 0.08376548 0.98431383 Axis point 124.27679533 105.23234611 0.00000000 Rotation angle (degrees) 2.45823262 Shift along axis -4.66319119 > fitmap #13 inMap #12 Fit molecule copy of FDDNP_1rise_favor90.pdb (#13) to map 1rise_50z_imasked (#12) using 3050 atoms average map value = 0.001092, steps = 48 shifted from previous position = 0.0235 rotated from previous position = 0.051 degrees atoms outside contour = 3039, contour level = 0.008 Position of copy of FDDNP_1rise_favor90.pdb (#13) relative to 1rise_50z_imasked (#12) coordinates: Matrix rotation and translation 0.99911104 -0.04195193 0.00414289 5.16125221 0.04192562 0.99910121 0.00624690 -5.45068059 -0.00440123 -0.00606765 0.99997191 -3.43856783 Axis -0.14452645 0.10027586 0.98440686 Axis point 121.05802671 104.34847552 0.00000000 Rotation angle (degrees) 2.44171621 Shift along axis -4.67745884 > hide #!11 models Drag select of 215 atoms, 210 bonds > select up 237 atoms, 211 bonds, 50 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 17 atoms, 10 bonds, 3 pseudobonds > select up 20 atoms, 10 bonds, 3 pseudobonds, 9 residues, 2 models selected > select up 44 atoms, 32 bonds, 3 pseudobonds, 9 residues, 2 models selected > select up 77 atoms, 66 bonds, 3 pseudobonds, 15 residues, 2 models selected > select up 355 atoms, 349 bonds, 3 pseudobonds, 57 residues, 2 models selected > delete atoms (#!13 & sel) > delete bonds (#!13 & sel) Drag select of 10 atoms, 3 bonds, 5 pseudobonds > select up 16 atoms, 7 bonds, 5 pseudobonds, 6 residues, 2 models selected > select up 124 atoms, 109 bonds, 5 pseudobonds, 23 residues, 2 models selected > select up 338 atoms, 333 bonds, 5 pseudobonds, 47 residues, 2 models selected > select up 497 atoms, 495 bonds, 5 pseudobonds, 67 residues, 2 models selected > delete atoms (#!13 & sel) > delete bonds (#!13 & sel) Drag select of 284 atoms, 309 bonds > select up 316 atoms, 312 bonds, 53 residues, 1 model selected > select up 412 atoms, 411 bonds, 53 residues, 1 model selected > select up 818 atoms, 822 bonds, 112 residues, 1 model selected > select up 1502 atoms, 1525 bonds, 204 residues, 1 model selected > select up 1961 atoms, 1987 bonds, 264 residues, 1 model selected > select down 1502 atoms, 1525 bonds, 204 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 11 atoms, 8 bonds > select up 14 atoms, 8 bonds, 7 residues, 1 model selected > select up 35 atoms, 27 bonds, 7 residues, 1 model selected > select up 98 atoms, 93 bonds, 18 residues, 1 model selected > select up 421 atoms, 423 bonds, 59 residues, 1 model selected > select up 459 atoms, 462 bonds, 60 residues, 1 model selected > select down 421 atoms, 423 bonds, 59 residues, 1 model selected > delete atoms sel > delete bonds sel > show #9 models > show #!11 models > select #9/M:1@C08 1 atom, 1 residue, 1 model selected > select up 38 atoms, 39 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > graphics silhouettes true width 5 > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/1rise_sideview_mode.png"" width 2000 height 1426 supersample > 3 > hide #!12 models > hide #!13 models > hide #!11 models > hide #9 models > show #!5 models > hide #!5 models > show #!4 models > volume #4 level 0.007373 > volume #4 level 0.006967 > volume #4 level 0.006642 > volume #4 level 0.006317 > volume #4 level 0.005749 > volume #5 level 0.00575 > show #!5 models > hide #!4 models > hide #!5 models > show #!4 models Segmenting 2rise_50z.mrc, density threshold 0.005749 Showing 171 region surfaces 1994 watershed regions, grouped to 171 regions Showing 2rise_50z.seg - 171 regions, 171 surfaces > select #10.12 1 model selected > select add #10.34 2 models selected Ungrouped to 7 regions Ungrouped to 20 regions Ungrouped to 40 regions Ungrouped to 10 regions Ungrouped to 0 regions > select #10.208 1 model selected > select add #10.197 2 models selected > select add #10.203 3 models selected > select add #10.224 4 models selected > select add #10.201 5 models selected Drag select of 3004, 6 of 1536 triangles, 4 2rise_50z.mrc > select add #10.1 9 models selected > select #10.172 1 model selected > select add #10.201 2 models selected > select add #10.224 3 models selected > select add #10.203 4 models selected > select add #10.197 5 models selected > select add #10.208 6 models selected Grouped 6 regions > select #10.26 1 model selected > select add #10.30 2 models selected > select add #10.36 3 models selected Ungrouped to 11 regions Ungrouped to 29 regions Ungrouped to 30 regions Ungrouped to 6 regions Ungrouped to 0 regions > select #10.264 1 model selected > select add #10.172 2 models selected > select add #10.237 3 models selected > select add #10.252 4 models selected > select add #10.244 5 models selected > select add #10.262 6 models selected > select add #10.255 7 models selected Grouped 7 regions > select #10.28 1 model selected > select add #10.33 2 models selected Ungrouped to 8 regions Ungrouped to 18 regions Ungrouped to 25 regions Ungrouped to 0 regions Ungrouped to 258 regions > select #10.172 1 model selected > select add #10.287 2 models selected > select add #10.270 3 models selected > select add #10.237 4 models selected > select add #10.277 5 models selected > select add #10.440 6 models selected > select subtract #10.440 5 models selected Grouped 5 regions > select #10.440 1 model selected > select add #10.439 2 models selected > select add #10.538 3 models selected > select add #10.539 4 models selected > select add #10.452 5 models selected > select add #10.449 6 models selected > select add #10.490 7 models selected > select add #10.491 8 models selected Ungrouped to 17 regions Ungrouped to 36 regions Ungrouped to 9 regions Ungrouped to 0 regions > select #10.56 1 model selected > select add #10.61 2 models selected > select add #10.1 3 models selected > select add #10.42 4 models selected > select add #10.24 5 models selected > select add #10.47 6 models selected > select add #10.60 7 models selected > select add #10.32 8 models selected > select add #10.64 9 models selected > select add #10.487 10 models selected > select subtract #10.487 9 models selected Grouped 9 regions > select #10.487 1 model selected > select add #10.489 2 models selected Ungrouped to 6 regions Ungrouped to 13 regions Ungrouped to 0 regions > select #10.1 1 model selected > select add #10.66 2 models selected > select add #10.56 3 models selected > select add #10.51 4 models selected Grouped 4 regions > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > select #10.422 1 model selected Ungrouped to 7 regions Ungrouped to 12 regions Ungrouped to 4 regions > select #10.56 1 model selected > select add #10.71 2 models selected > select add #10.73 3 models selected Grouped 3 regions > select #10.423 1 model selected > select add #10.421 2 models selected > select add #10.301 3 models selected > select add #10.300 4 models selected > select add #10.314 5 models selected > select add #10.315 6 models selected > select add #10.475 7 models selected Ungrouped to 14 regions Ungrouped to 37 regions Ungrouped to 4 regions Ungrouped to 0 regions > select #10.421 1 model selected > select add #10.108 2 models selected > select add #10.96 3 models selected > select add #10.300 4 models selected > select add #10.142 5 models selected > select add #10.95 6 models selected > select add #10.315 7 models selected > select add #10.16 8 models selected Grouped 8 regions > select #10.478 1 model selected > select add #10.406 2 models selected > select add #10.404 3 models selected > select add #10.321 4 models selected Ungrouped to 10 regions Ungrouped to 16 regions Ungrouped to 2 regions > select #10.85 1 model selected > select add #10.487 2 models selected > select add #10.108 3 models selected > select add #10.475 4 models selected > select add #10.16 5 models selected Grouped 5 regions > select #10.319 1 model selected > select add #10.431 2 models selected > select add #10.429 3 models selected > select add #10.375 4 models selected Ungrouped to 11 regions Ungrouped to 17 regions Ungrouped to 4 regions > select #10.16 1 model selected > select add #10.319 2 models selected > select add #10.340 3 models selected > select add #10.548 4 models selected > select #10.548 1 model selected > select add #10.319 2 models selected > select add #10.16 3 models selected > select add #10.546 4 models selected > select add #10.552 5 models selected Grouped 5 regions > select #10.374 1 model selected > select add #10.356 2 models selected > select add #10.355 3 models selected > select add #10.353 4 models selected > select add #10.352 5 models selected Ungrouped to 12 regions Ungrouped to 21 regions Ungrouped to 8 regions > select #10.16 1 model selected > select add #10.564 2 models selected > select add #10.352 3 models selected > select add #10.561 4 models selected > select add #10.555 5 models selected > select add #10.569 6 models selected > select add #10.467 7 models selected Grouped 7 regions > select #10.464 1 model selected > select add #10.466 2 models selected Ungrouped to 7 regions Ungrouped to 14 regions Ungrouped to 0 regions > select #10.570 1 model selected > select add #10.561 2 models selected > select add #10.575 3 models selected > select add #10.16 4 models selected Grouped 4 regions Grouped 1 regions > select #10.16 1 model selected Ungrouped to 1 regions Ungrouped to 4 regions Ungrouped to 7 regions [Repeated 1 time(s)] > select #10.467 1 model selected > select add #10.374 2 models selected > select add #10.16 3 models selected > select add #10.353 4 models selected > select subtract #10.353 3 models selected > select add #10.561 4 models selected > select add #10.575 5 models selected > select add #10.554 6 models selected Grouped 6 regions > select #10.352 1 model selected > select add #10.555 2 models selected > select add #10.583 3 models selected > select add #10.581 4 models selected > select add #10.585 5 models selected > select add #10.16 6 models selected Grouped 6 regions > select #10.582 1 model selected > select add #10.16 2 models selected Grouped 2 regions > select #10.584 1 model selected > select add #10.16 2 models selected Grouped 2 regions > select #10.468 1 model selected Ungrouped to 2 regions Ungrouped to 8 regions Ungrouped to 5 regions > select #10.16 1 model selected > select add #10.353 2 models selected > select #10.353 1 model selected Ungrouped to 3 regions Ungrouped to 0 regions Ungrouped to 442 regions > select #10.16 1 model selected > select #10.579 1 model selected > select add #10.16 2 models selected Grouped 2 regions > select add #10.1 2 models selected Grouped 2 regions Opened 2rise_50z_imasked as #14, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 Opened 2rise_50z_imasked as #15, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > hide #!10 models > hide #!14 models > show #!14 models > hide #!15 models > show #!15 models > hide #!4 models > hide #!14 models > show #!14 models > hide #!15 models > show #!15 models > select add #15 875 models selected > select subtract #15 873 models selected > select add #15 875 models selected > select subtract #15 873 models selected > select add #14 875 models selected > surface dust #14 size 8.3 > color #14 #aaff00ff models > color #15 #ffaa7fff models > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/2rise_sideview_mode.png"" width 2000 height 1426 supersample > 3 > graphics silhouettes true width 1 > graphics silhouettes true width 3 > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/2rise_sideview_mode.png"" width 2000 height 1426 supersample > 3 > hide #!14 models > hide #!15 models > show #!5 models > hide #!5 models > show #!3 models > hide #!3 models > show #!3 models Segmenting 2rise_10z.mrc, density threshold 0.004964 Showing 28 region surfaces 543 watershed regions, grouped to 28 regions Showing 2rise_10z.seg - 28 regions, 28 surfaces > select clear > select #10.1 1 model selected Ungrouped to 10 regions Ungrouped to 33 regions Ungrouped to 43 regions Ungrouped to 5 regions > select #10.76 1 model selected > select add #10.79 2 models selected > select add #10.84 3 models selected > select add #10.70 4 models selected > select add #10.75 5 models selected > select add #10.30 6 models selected Grouped 6 regions > select #10.30 1 model selected > select #10.87 1 model selected > select add #10.30 2 models selected Grouped 2 regions > select #10.9 1 model selected > select add #10.3 2 models selected Ungrouped to 7 regions Ungrouped to 28 regions Ungrouped to 50 regions Ungrouped to 15 regions Ungrouped to 0 regions Ungrouped to 40 regions > select #10.134 1 model selected > select #10.135 1 model selected > select add #10.157 2 models selected > select add #10.141 3 models selected > select add #10.154 4 models selected > select add #10.127 5 models selected > select add #10.120 6 models selected > select add #10.134 7 models selected Grouped 7 regions > select add #10.30 2 models selected Grouped 2 regions Opened 2rise_10z_imasked as #16, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 Opened 2rise_10z_imasked as #17, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > hide #!10 models > hide #!3 models > select add #16 167 models selected > select subtract #16 165 models selected > select add #16 167 models selected > surface dust #16 size 8.3 > color #16 #aaff00ff models > color #17 #ffaa7fff models > select clear > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/2rise_topview_mode.png"" width 1318 height 940 supersample 3 > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/2rise_topview_mode.png"" width 2000 height 1426 supersample 3 > hide #!17 models > hide #!16 models > show #!1 models > show #!2 models > hide #!1 models Segmenting 4rise_50z.mrc, density threshold 0.009926 Showing 90 region surfaces 1414 watershed regions, grouped to 90 regions Showing 4rise_50z.seg - 90 regions, 90 surfaces > select #10.19 1 model selected > select add #10.53 2 models selected > select add #10.9 3 models selected Ungrouped to 16 regions Ungrouped to 41 regions Ungrouped to 26 regions Ungrouped to 6 regions > select #10.101 1 model selected > select add #10.131 2 models selected > select add #10.96 3 models selected Grouped 3 regions > select #10.97 1 model selected > select add #10.74 2 models selected > select add #10.156 3 models selected > select add #10.3 4 models selected > select add #10.71 5 models selected Ungrouped to 16 regions Ungrouped to 28 regions Ungrouped to 20 regions Ungrouped to 10 regions Ungrouped to 0 regions Ungrouped to 267 regions > select #10.174 1 model selected > select add #10.156 2 models selected > select add #10.163 3 models selected > select add #10.181 4 models selected > select add #10.162 5 models selected > select add #10.184 6 models selected > select add #10.91 7 models selected Grouped 7 regions > select #10.137 1 model selected Ungrouped to 0 regions Ungrouped to 584 regions > select #10.25 1 model selected > select add #10.566 2 models selected > select add #10.755 3 models selected > select add #10.275 4 models selected > select subtract #10.275 3 models selected > select add #10.275 4 models selected > select add #10.547 5 models selected > select add #10.950 6 models selected > select add #10.849 7 models selected > select add #10.306 8 models selected > select add #10.918 9 models selected Ungrouped to 19 regions Ungrouped to 2 regions Ungrouped to 0 regions > select #10.1 1 model selected > select add #10.84 2 models selected > select add #10.82 3 models selected > select add #10.755 4 models selected > select add #10.68 5 models selected > select add #10.73 6 models selected > select add #10.849 7 models selected > select add #10.79 8 models selected > select add #10.608 9 models selected > select subtract #10.608 8 models selected Grouped 8 regions > select #10.608 1 model selected > select add #10.468 2 models selected > select add #10.649 3 models selected Ungrouped to 6 regions Ungrouped to 0 regions > select #10.82 1 model selected > select add #10.468 2 models selected > select add #10.68 3 models selected Grouped 3 regions > select #10.5 1 model selected > select #10.524 1 model selected Ungrouped to 2 regions > select #10.82 1 model selected > select add #10.5 2 models selected Grouped 2 regions > select #10.112 1 model selected > select add #10.141 2 models selected > select #10.141 1 model selected Ungrouped to 0 regions Ungrouped to 696 regions > select #10.543 1 model selected > select #10.112 1 model selected > select add #10.141 2 models selected Grouped 2 regions > select #10.880 1 model selected > select add #10.1035 2 models selected > select add #10.1484 3 models selected > select add #10.918 4 models selected Grouped 4 regions > select add #10.892 2 models selected > select add #10.1132 3 models selected > select add #10.500 4 models selected Grouped 4 regions > select #10.1485 1 model selected > select add #10.7 2 models selected > select add #10.451 3 models selected > select add #10.1280 4 models selected Grouped 4 regions > select #10.1022 1 model selected Grouped 1 regions > select add #10.597 2 models selected > select add #10.1281 3 models selected > select #10.7 1 model selected > select add #10.15 2 models selected Grouped 2 regions > select #10.334 1 model selected > select #10.806 1 model selected > select add #10.36 2 models selected > select add #10.1045 3 models selected > select add #10.1009 4 models selected > select add #10.641 5 models selected > select add #10.645 6 models selected > select add #10.1087 7 models selected > select add #10.310 8 models selected > select subtract #10.310 7 models selected > select add #10.7 8 models selected Grouped 8 regions Ungrouped to 8 regions > select subtract #10.29 7 models selected Grouped 7 regions > select #10.1404 1 model selected > select add #10.1385 2 models selected > select add #10.321 3 models selected > select subtract #10.321 2 models selected > select add #10.7 3 models selected Grouped 3 regions > select #10.1135 1 model selected > select add #10.5 2 models selected Ungrouped to 4 regions Ungrouped to 0 regions Ungrouped to 356 regions Ungrouped to 16 regions > select #10.17 1 model selected > select add #10.18 2 models selected > select add #10.16 3 models selected > select subtract #10.16 2 models selected > select add #10.28 3 models selected > select add #10.34 4 models selected > select add #10.556 5 models selected > hide #!2 models > select #10.23 1 model selected > select #10.181 1 model selected > select add #10.23 2 models selected Grouped 2 regions > select #10.1008 1 model selected Ungrouped to 0 regions > select #10.1 1 model selected > select #10.822 1 model selected Ungrouped to 0 regions > select #10.556 1 model selected > select add #10.1 2 models selected Grouped 2 regions > select #10.34 1 model selected > select add #10.28 2 models selected > select add #10.1 3 models selected Grouped 3 regions > select #10.18 1 model selected > select add #10.17 2 models selected > select add #10.16 3 models selected > select subtract #10.16 2 models selected > select add #10.689 3 models selected > select add #10.1 4 models selected > select subtract #10.1 3 models selected > select subtract #10.689 2 models selected > select add #10.1 3 models selected Grouped 3 regions > select #10.16 1 model selected Ungrouped to 0 regions > select #10.1 1 model selected Opened 4rise_50z_imasked as #18, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 Opened 4rise_50z_imasked as #19, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > hide #!10 models > color #18 #ffaa7f80 models > color #18 #aaff7f80 models > color #18 #aaff0080 models > color #19 #ffaa7f80 models > select add #19 1386 models selected > select add #18 1389 models selected > transparency sel & #18.1#19.1 0 > graphics silhouettes true width 1 > select clear > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/4rise_sideview_mode.png"" width 2000 height 1426 supersample > 3 > hide #14.1 models > hide #!18 models > show #!16 models > hide #!19 models > show #!14 models > hide #!14 models > hide #!16 models > show #!1 models Segmenting 4rise_10z.mrc, density threshold 0.009930 Showing 24 region surfaces 365 watershed regions, grouped to 24 regions Showing 4rise_10z.seg - 24 regions, 24 surfaces > select #10.7 1 model selected > select add #10.2 2 models selected > select add #10.15 3 models selected > select add #10.3 4 models selected Ungrouped to 26 regions Ungrouped to 42 regions Ungrouped to 39 regions Ungrouped to 8 regions > select #10.77 1 model selected > select add #10.69 2 models selected > select add #10.50 3 models selected > select add #10.89 4 models selected > select add #10.92 5 models selected Grouped 5 regions > select #10.66 1 model selected > select add #10.25 2 models selected Grouped 2 regions > select #10.13 1 model selected > select add #10.8 2 models selected > select #10.1 1 model selected > select subtract #10.1 Nothing selected > select #10.13 1 model selected > select add #10.1 2 models selected Ungrouped to 9 regions Ungrouped to 33 regions Ungrouped to 31 regions Ungrouped to 8 regions Ungrouped to 0 regions > select #10.50 1 model selected > select add #10.132 2 models selected > select add #10.83 3 models selected > select add #10.145 4 models selected > select add #10.17 5 models selected > select #10.17 1 model selected Ungrouped to 2 regions Ungrouped to 5 regions Ungrouped to 0 regions > select #10.83 1 model selected > select add #10.145 2 models selected > select add #10.134 3 models selected > select add #10.132 4 models selected > select add #10.50 5 models selected Grouped 5 regions > select #10.142 1 model selected Ungrouped to 0 regions Ungrouped to 27 regions > select #10.142 1 model selected > select #10.34 1 model selected > select add #10.25 2 models selected Grouped 2 regions Opened 4rise_10z_imasked as #20, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 Opened 4rise_10z_imasked as #21, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > hide #!10 models > color #20 #ffaa7f80 models > color #20 #aaff7f80 models > color #20 #aaff0080 models > color #21 #ffaa7f80 models > hide #!1 models > select add #20 167 models selected > surface dust #20 size 8.3 > select add #21 169 models selected > transparency sel & #20.1#21.1 0 > select clear > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/4rise_topview_mode.png"" width 2000 height 1426 supersample 3 > show #!5 models > show #!6 models > hide #!20 models > hide #!21 models > hide #!6 models > show #!6 models > close #6 > open ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/3rise/job103/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #6, grid size 288,288,288, pixel 0.83, shown at level 0.00268, step 2, values float32 > volume #6 step 1 > volume #6 level 0.0057 > hide #!15 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > select #6 2 models selected > ui tool show ""Segment Map"" Segmenting postprocess_masked.mrc, density threshold 0.005700 Showing 100 region surfaces 1643 watershed regions, grouped to 100 regions Showing postprocess_masked.seg - 100 regions, 100 surfaces > select #10.4 1 model selected > select add #10.3 2 models selected Ungrouped to 8 regions Ungrouped to 25 regions Ungrouped to 31 regions Ungrouped to 16 regions Ungrouped to 0 regions > select #10.140 1 model selected > select add #10.142 2 models selected > select add #10.144 3 models selected > select add #10.130 4 models selected Drag select of 2471, 19 of 13844 triangles, 2451, 20 of 13236 triangles, 2423, 13 of 12620 triangles, 2370, 12 of 8956 triangles, 2454, 6 of 7948 triangles, 2286, 5 of 7328 triangles, 2472, 26 of 5384 triangles, 2318, 13 of 3992 triangles, 228, 6 of 444 triangles, 6 postprocess_masked.mrc > select add #10.101 16 models selected > select subtract #10.134 15 models selected > select subtract #10.101 14 models selected > select subtract #10.8 13 models selected > select add #10.134 14 models selected > select add #10.101 15 models selected Grouped 13 regions > select #10.27 1 model selected > select add #10.26 2 models selected > select add #10.38 3 models selected > select add #10.28 4 models selected Ungrouped to 19 regions Ungrouped to 47 regions Ungrouped to 71 regions Ungrouped to 15 regions Ungrouped to 0 regions > select #10.13 1 model selected > select #10.13 1 model selected > select #10.13 1 model selected Ungrouped to 13 regions Ungrouped to 29 regions Ungrouped to 62 regions Ungrouped to 46 regions Ungrouped to 22 regions > select #10.193 1 model selected > select add #10.69 2 models selected > select add #10.180 3 models selected > select add #10.182 4 models selected > select add #10.195 5 models selected > select add #10.181 6 models selected > select add #10.210 7 models selected Drag select of 415, 5 of 452 triangles Drag select of 2388, 12 of 2880 triangles, 582, 14 of 1032 triangles, 595, 6 of 720 triangles, 6 postprocess_masked.mrc > select add #10.224 14 models selected > select add #10.23 15 models selected Drag select of 2442, 6 of 8848 triangles > select #10.224 1 model selected > select #10.237 1 model selected > select add #10.224 2 models selected > select add #10.240 3 models selected > select add #10.218 4 models selected > select add #10.210 5 models selected > select add #10.181 6 models selected > select add #10.195 7 models selected > select add #10.182 8 models selected > select add #10.180 9 models selected > select add #10.69 10 models selected > select add #10.193 11 models selected Grouped 11 regions > select add #10.251 2 models selected > select add #10.154 3 models selected > select add #10.101 4 models selected > select add #10.217 5 models selected Grouped 5 regions > select add #10.31 2 models selected > select add #10.22 3 models selected > select add #10.41 4 models selected Ungrouped to 18 regions Ungrouped to 49 regions Ungrouped to 46 regions Ungrouped to 10 regions Ungrouped to 0 regions > select #10.193 1 model selected > select #10.402 1 model selected > select add #10.395 2 models selected > select add #10.398 3 models selected > select add #10.399 4 models selected > select add #10.403 5 models selected > select add #10.400 6 models selected > select add #10.396 7 models selected > select add #10.394 8 models selected > select add #10.404 9 models selected > select add #10.401 10 models selected > select add #10.397 11 models selected > select add #10.182 12 models selected > select add #10.195 13 models selected Grouped 13 regions > select add #10.217 2 models selected > select add #10.193 3 models selected > select add #10.237 4 models selected > select add #10.424 5 models selected > select add #10.413 6 models selected > select add #10.407 7 models selected > select add #10.375 8 models selected > select add #10.210 9 models selected > select add #10.433 10 models selected > select add #10.418 11 models selected > select add #10.410 12 models selected > select add #10.20 13 models selected > select subtract #10.20 12 models selected Grouped 12 regions > select #10.20 1 model selected > select add #10.50 2 models selected Ungrouped to 9 regions Ungrouped to 36 regions Ungrouped to 18 regions Ungrouped to 7 regions Ungrouped to 0 regions > select #10.423 1 model selected Drag select of 6 postprocess_masked.mrc > select add #10.418 4 models selected > select #10.423 1 model selected > select add #10.452 2 models selected > select add #10.418 3 models selected > select add #10.182 4 models selected Grouped 4 regions > view matrix models #10.182,1,0,0,-38.62,0,1,0,19.924,0,0,1,6.4525 > view matrix models #10.182,1,0,0,-50.591,0,1,0,22.235,0,0,1,8.0171 > view matrix models #10.182,1,0,0,-57.967,0,1,0,22.058,0,0,1,8.801 > view matrix models #10.182,1,0,0,-70.67,0,1,0,25.968,0,0,1,10.625 > undo [Repeated 3 time(s)] > select clear > select #10.1 1 model selected > select add #10.12 2 models selected > select subtract #10.1 1 model selected Ungrouped to 5 regions Ungrouped to 14 regions Ungrouped to 18 regions Ungrouped to 11 regions Ungrouped to 0 regions > select #10.1 1 model selected Ungrouped to 3 regions Ungrouped to 16 regions Ungrouped to 29 regions Ungrouped to 21 regions > select #10.498 1 model selected > select add #10.473 2 models selected > select add #10.468 3 models selected > select add #10.513 4 models selected > select add #10.24 5 models selected > select subtract #10.24 4 models selected Grouped 4 regions > select #10.24 1 model selected > select add #10.25 2 models selected Ungrouped to 9 regions Ungrouped to 30 regions Ungrouped to 32 regions Ungrouped to 8 regions Ungrouped to 0 regions Ungrouped to 144 regions > select #10.423 1 model selected > select add #10.573 2 models selected > select add #10.580 3 models selected > select add #10.582 4 models selected > select add #10.568 5 models selected > select add #10.500 6 models selected > select add #10.577 7 models selected > select add #10.277 8 models selected > select add #10.341 9 models selected Grouped 9 regions > select #10.660 1 model selected > select add #10.682 2 models selected > select add #10.685 3 models selected > select add #10.643 4 models selected Ungrouped to 17 regions Ungrouped to 33 regions Ungrouped to 19 regions Ungrouped to 0 regions Ungrouped to 337 regions > select #10.66 1 model selected > select add #10.72 2 models selected > select add #10.46 3 models selected > select add #10.52 4 models selected > select add #10.56 5 models selected > select add #10.915 6 models selected > select add #10.740 7 models selected > select add #10.34 8 models selected > select subtract #10.915 7 models selected > select subtract #10.740 6 models selected > select add #10.2 7 models selected Grouped 7 regions > select #10.916 1 model selected > select add #10.835 2 models selected > select add #10.831 3 models selected > select add #10.832 4 models selected > select add #10.1040 5 models selected Ungrouped to 18 regions Ungrouped to 8 regions Ungrouped to 0 regions Ungrouped to 581 regions Ungrouped to 466 regions > select #10.81 1 model selected > select #10.81 1 model selected > select #10.72 1 model selected > select add #10.81 2 models selected > select add #10.2 3 models selected > select add #10.49 4 models selected > select add #10.60 5 models selected > select add #10.52 6 models selected Grouped 6 regions > select #10.1210 1 model selected > select add #10.2 2 models selected Grouped 2 regions > select #10.663 1 model selected > select #10.719 1 model selected > select add #10.663 2 models selected > select add #10.2 3 models selected Grouped 3 regions > select clear > select #10.2 1 model selected > select add #10.182 2 models selected Grouped 2 regions Opened postprocess_masked_imasked as #22, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 Opened postprocess_masked_imasked as #23, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > hide #!10 models > hide #!6 models > select add #23 1592 models selected > select subtract #23 1590 models selected > select add #22 1592 models selected > surface dust #22 size 8.3 > color #22 #aaff00ff models > color #23 #ffaa7fff models > select clear > graphics silhouettes true width 3 > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/3rise_sideview_mode.png"" width 2000 height 1426 supersample > 3 > hide #!22 models > hide #!23 models > show #!5 models Segmenting postprocess_masked.mrc, density threshold 0.005750 Showing 21 region surfaces 359 watershed regions, grouped to 21 regions Showing postprocess_masked.seg - 21 regions, 21 surfaces > select #10.7 1 model selected > select add #10.2 2 models selected > select add #10.8 3 models selected Ungrouped to 17 regions Ungrouped to 38 regions Ungrouped to 65 regions Ungrouped to 20 regions Ungrouped to 0 regions Ungrouped to 28 regions > select #10.78 1 model selected > select add #10.74 2 models selected > select add #10.36 3 models selected > select add #10.37 4 models selected > select subtract #10.37 3 models selected > select add #10.112 4 models selected > select add #10.35 5 models selected > select subtract #10.35 4 models selected > select add #10.83 5 models selected > select add #10.135 6 models selected > select add #10.92 7 models selected > select subtract #10.135 6 models selected > select add #10.114 7 models selected > select subtract #10.114 6 models selected > select add #10.134 7 models selected > select add #10.100 8 models selected > select subtract #10.100 7 models selected Grouped 7 regions > select #10.37 1 model selected Ungrouped to 3 regions [Repeated 1 time(s)]Ungrouped to 0 regions > select #10.5 1 model selected > select #10.35 1 model selected Ungrouped to 5 regions Ungrouped to 12 regions Ungrouped to 4 regions > select #10.93 1 model selected > select add #10.35 2 models selected > select add #10.1 3 models selected > select subtract #10.1 2 models selected > select add #10.5 3 models selected > select add #10.1 4 models selected Grouped 4 regions > select #10.100 1 model selected Ungrouped to 4 regions Ungrouped to 10 regions Ungrouped to 2 regions Ungrouped to 0 regions > select #10.1 1 model selected Ungrouped to 4 regions Ungrouped to 7 regions Ungrouped to 5 regions Ungrouped to 6 regions > select #10.100 1 model selected > select add #10.168 2 models selected > select add #10.159 3 models selected > select add #10.135 4 models selected > select subtract #10.135 3 models selected > select add #10.1 4 models selected Grouped 4 regions > select #10.135 1 model selected Ungrouped to 4 regions Ungrouped to 16 regions Ungrouped to 7 regions Ungrouped to 0 regions > select #10.1 1 model selected > select add #10.183 2 models selected Grouped 2 regions > select #10.114 1 model selected Ungrouped to 2 regions Ungrouped to 4 regions Ungrouped to 2 regions Ungrouped to 0 regions > select #10.114 1 model selected > select add #10.1 2 models selected > select subtract #10.1 1 model selected > select add #10.1 2 models selected > select add #10.83 3 models selected > select add #10.158 4 models selected > select add #10.92 5 models selected > select add #10.157 6 models selected > select add #10.160 7 models selected > select add #10.156 8 models selected Grouped 8 regions > select add #10.153 2 models selected Grouped 2 regions Opened postprocess_masked_imasked as #24, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 Opened postprocess_masked_imasked as #25, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > hide #!5 models > hide #!10 models > color #24 #aaff7fff models > hide #!25 models > show #!25 models > color #25 #ffaa7fff models > select clear > select add #24 2 models selected > surface dust #24 size 8.3 > select clear > select add #25 2 models selected > select add #24 4 models selected > transparency sel 50 > transparency sel 0 > select clear > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/3rise_topview_mode.png"" width 2000 height 1426 supersample 3 > hide #!25 models > hide #!24 models > show #!23 models > show #!22 models > hide #!23 models > hide #!22 models > show #!21 models > show #!20 models > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/4rise_topview_mode.png"" width 2000 height 1426 supersample 3 > hide #!21 models > hide #!20 models > show #!24 models > color #24 #aaff00ff models > show #!25 models > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/3rise_topview_mode.png"" width 2000 height 1426 supersample 3 > save ""D:/PTB129_Tracer/mutiply_helical > rise/real_FDDNP/helical_rise_multiply_NEW.cxs"" Traceback (most recent call last): File ""msgpack\\_packer.pyx"", line 177, in msgpack._cmsgpack.Packer._pack OverflowError: int too big to convert During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 630, in save fserialize(stream, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\serialize.py"", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File ""msgpack\\_packer.pyx"", line 294, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 300, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 297, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 231, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 184, in msgpack._cmsgpack.Packer._pack File ""stringsource"", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File ""src\\_serialize.pyx"", line 251, in chimerax.core._serialize._encode_ext RuntimeError: Can't convert object of type: RuntimeError: Can't convert object of type: File ""src\\_serialize.pyx"", line 251, in chimerax.core._serialize._encode_ext See log for complete Python traceback. Traceback (most recent call last): File ""msgpack\\_packer.pyx"", line 177, in msgpack._cmsgpack.Packer._pack OverflowError: int too big to convert During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 630, in save fserialize(stream, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\serialize.py"", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File ""msgpack\\_packer.pyx"", line 294, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 300, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 297, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 231, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 184, in msgpack._cmsgpack.Packer._pack File ""stringsource"", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File ""src\\_serialize.pyx"", line 251, in chimerax.core._serialize._encode_ext RuntimeError: Can't convert object of type: RuntimeError: Can't convert object of type: File ""src\\_serialize.pyx"", line 251, in chimerax.core._serialize._encode_ext See log for complete Python traceback. > save ""D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/1.cxs"" includeMaps > true Traceback (most recent call last): File ""msgpack\\_packer.pyx"", line 177, in msgpack._cmsgpack.Packer._pack OverflowError: int too big to convert During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 630, in save fserialize(stream, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\serialize.py"", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File ""msgpack\\_packer.pyx"", line 294, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 300, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 297, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 231, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 184, in msgpack._cmsgpack.Packer._pack File ""stringsource"", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File ""src\\_serialize.pyx"", line 251, in chimerax.core._serialize._encode_ext RuntimeError: Can't convert object of type: RuntimeError: Can't convert object of type: File ""src\\_serialize.pyx"", line 251, in chimerax.core._serialize._encode_ext See log for complete Python traceback. Traceback (most recent call last): File ""msgpack\\_packer.pyx"", line 177, in msgpack._cmsgpack.Packer._pack OverflowError: int too big to convert During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 630, in save fserialize(stream, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\serialize.py"", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File ""msgpack\\_packer.pyx"", line 294, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 300, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 297, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 231, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 184, in msgpack._cmsgpack.Packer._pack File ""stringsource"", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File ""src\\_serialize.pyx"", line 251, in chimerax.core._serialize._encode_ext RuntimeError: Can't convert object of type: RuntimeError: Can't convert object of type: File ""src\\_serialize.pyx"", line 251, in chimerax.core._serialize._encode_ext See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 474.80 OpenGL renderer: NVIDIA GeForce GT 730/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: zh_CN.cp936 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: LENOVO Model: 90L0CTO1WW OS: Microsoft Windows 10 专业版 (Build 19045) Memory: 17,106,743,296 MaxProcessMemory: 137,438,953,344 CPU: 12 AMD Ryzen 5 3600 6-Core Processor OSLanguage: zh-CN Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.11.0 }}} " defect closed normal Sessions limitation Tom Goddard all ChimeraX