id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16686 Matrix is None ymazor@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description this error pops up when i past the following list of commands: ""cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" open ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" open ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" open ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" open ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" volume flip #* axis y open ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" #### open ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"" volume #8 level 0.02292 step 4 volume #5,6,7 level 0.1 step 1 set bg white graphics silhouettes t width 3 lighting depthCue f hide #5,6,7,8 hide #9"". it doent not pop up when i just past the commands line by line, so it might be some hidden character in my text editor. does really bother me too much. Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > vop flip axis y > volume flip axis y Missing or invalid ""volumes"" argument: invalid density maps specifier > vop #* flip axis y > volume #* flipNormals axis y Invalid ""flipNormals"" argument: Expected true or false (or 1 or 0) > vop #1 flip axis y > volume #1 flipNormals axis y Invalid ""flipNormals"" argument: Expected true or false (or 1 or 0) > volume flip #1 axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #4, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > close #4 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #4, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > volume #8 level 0.427 > volume #8 level 0.02778 > hide #!8 models > volume #7 level 0.07085 > hide #!7 models > hide #!6 models > hide #!5 models > set bgColor white > show #!5 models > volume #5 level 0.1243 > show #!8 models > volume #8 style mesh > volume #8 step 4 > volume #5 level 0.1765 > volume #5 color #ff2600 > volume #5 level 0.19 > volume #5 level 0.18 > volume #5 level 0.07108 > volume #5 level 0.1608 > volume #5 level 0.18 > volume #5 level 0.08028 > volume #5 level 0.18 > show #!6 models > volume #6 level 0.18 > volume #6 level 0.1225 > volume #6 color #0433ff > volume #6 level 0.1184 > hide #!6 models > show #!7 models > volume #7 level 0.1106 > volume #7 color #ededed > volume #7 color #4f8f00 > volume #7 level 0.104 > volume #6 level 0.1093 > show #!5 models > hide #!6 models > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_PSI_ISIA_MDpaper/data/7umh.cif"" 7umh.cif title: Energetic robustness to large scale structural dynamics in a photosynthetic supercomplex [more info...] Chain information for 7umh.cif #9 --- Chain | Description | UniProt A H a | Photosystem I P700 chlorophyll a apoprotein A1 | PSAA_SYNY3 1-751 B G b | Photosystem I P700 chlorophyll a apoprotein A2 | PSAB_SYNY3 1-731 C N c | Photosystem I iron-sulfur center | PSAC_SYNY3 1-81 D P d | Photosystem I reaction center subunit II | PSAD_SYNY3 1-141 E O e | Photosystem I reaction center subunit IV | PSAE_SYNY3 1-74 F Q f | Photosystem I reaction center subunit III | PSAF_SYNY3 -21-143 I R i | Photosystem I reaction center subunit VIII | PSAI_SYNY3 1-40 J S j | Photosystem I reaction center subunit IX | PSAJ_SYNY3 1-40 K T k | Photosystem I reaction center subunit PsaK 1 | PSAK1_SYNY3 -1-84 L U l | Photosystem I reaction center subunit XI | PSAL_SYNY3 1-157 M V m | Photosystem I reaction center subunit XII | PSAM_SYNY3 1-31 W X Y Z g h n o p q r s t u v w x y | Iron stress-induced chlorophyll-binding protein | ISIA_SYNY3 1-342 Non-standard residues in 7umh.cif #9 --- BCR — β-carotene CA — calcium ion CL0 — chlorophyll A isomer CLA — chlorophyll A ECH — beta,beta-caroten-4-one (echinenone) LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole LMG — 1,2-distearoyl-monogalactosyl-diglyceride LMT — dodecyl-β-D-maltoside LMU — dodecyl-α-D-maltoside LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol ((3R,3'R)-β,β-carotene-3,3'-diol; lutein) PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone) SF4 — iron/sulfur cluster > volume #5 level 0.08412 > select add #9 140516 atoms, 145848 bonds, 2511 pseudobonds, 14006 residues, 2 models selected > ui mousemode right ""rotate selected models"" > hide sel atoms > show sel cartoons Computing secondary structure > view matrix models > #9,0.49432,-0.12016,0.86093,-43.401,-0.18429,0.9534,0.23888,0.081789,-0.84952,-0.27674,0.44914,351.15 > view matrix models > #9,0.17244,0.2131,0.96169,-67.736,-0.27894,0.94692,-0.15981,102.87,-0.9447,-0.24069,0.22273,409.72 > view matrix models > #9,0.017751,0.18369,0.98282,-33.111,-0.26444,0.94884,-0.17256,102.01,-0.96424,-0.25683,0.065418,449.45 > view matrix models > #9,0.034018,0.10029,0.99438,-20.976,-0.27072,0.95868,-0.087433,83.829,-0.96206,-0.26622,0.059764,452.16 > ui tool show ""Fit in Map"" > fitmap #9 inMap #5 Fit molecule 7umh.cif (#9) to map cryosparc_P12_J162_006_volume_map.mrc y flip (#5) using 140516 atoms average map value = 0.06217, steps = 172 shifted from previous position = 14 rotated from previous position = 5.53 degrees atoms outside contour = 114985, contour level = 0.084118 Position of 7umh.cif (#9) relative to cryosparc_P12_J162_006_volume_map.mrc y flip (#5) coordinates: Matrix rotation and translation 0.01475667 0.00763461 0.99986197 6.96886961 -0.25092361 0.96799986 -0.00368802 71.41186245 -0.96789441 -0.25083456 0.01620016 465.27162126 Axis -0.12357329 0.98387832 -0.12927913 Axis point 244.90083051 0.00000000 233.20723933 Rotation angle (degrees) 90.02988868 Shift along axis 9.24950593 > save ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/7umh_docked_J162_flipped.pdb"" > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/7umh_docked_J162_flipped.pdb"" Chain information for 7umh_docked_J162_flipped.pdb #10 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h n o p q r s t u v w x y | No description available > close #9 > close #10 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/7umh_docked_J162_flipped.pdb"" Chain information for 7umh_docked_J162_flipped.pdb #9 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h n o p q r s t u v w x y | No description available > hide #!8 models > hide #!9 models > show #!9 models > hide atoms > show cartoons > select /g,Z,Y,X,W,y 22449 atoms, 23417 bonds, 426 pseudobonds, 2147 residues, 2 models selected > view matrix models > #9,0.99663,-0.068917,-0.044377,25.838,0.069216,0.99759,0.0052272,-15.52,0.04391,-0.0082812,0.999,-7.393 > view matrix models > #9,0.9901,-0.13975,-0.013096,36.545,0.14001,0.9899,0.022085,-32.688,0.0098775,-0.0237,0.99967,3.2967 > view matrix models > #9,0.94877,-0.1662,0.26871,-9.0726,0.24247,-0.1623,-0.95649,415.85,0.20258,0.97264,-0.11369,-24.471 > view matrix models > #9,0.95822,-0.096802,0.26915,-26.895,0.25266,-0.15457,-0.95513,411.61,0.13406,0.98323,-0.12366,-9.9301 > view matrix models > #9,0.96931,-0.008812,0.24567,-44.141,0.19914,-0.55779,-0.80574,482.25,0.14413,0.82993,-0.53892,111.73 > view matrix models > #9,0.99526,-0.078815,0.056911,6.62,0.0033171,-0.55754,-0.83014,529.71,0.097158,0.8264,-0.55464,126.05 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.99526,-0.078815,0.056911,6.2844,0.0033171,-0.55754,-0.83014,522.34,0.097158,0.8264,-0.55464,130.99 > view matrix models > #9,0.99526,-0.078815,0.056911,10.408,0.0033171,-0.55754,-0.83014,521.92,0.097158,0.8264,-0.55464,130.76 > fitmap #9 inMap #5 Fit molecule 7umh_docked_J162_flipped.pdb (#9) to map cryosparc_P12_J162_006_volume_map.mrc y flip (#5) using 140516 atoms average map value = 0.06222, steps = 184 shifted from previous position = 6.28 rotated from previous position = 5.66 degrees atoms outside contour = 114853, contour level = 0.084118 Position of 7umh_docked_J162_flipped.pdb (#9) relative to cryosparc_P12_J162_006_volume_map.mrc y flip (#5) coordinates: Matrix rotation and translation 0.99958280 -0.01992303 0.02091151 0.08034984 0.00821963 -0.49785256 -0.86722273 513.83082799 0.02768855 0.86703281 -0.49748110 120.55967771 Axis 0.99986073 -0.00390721 0.01622526 Axis point 0.00000000 222.00967612 209.05030722 Rotation angle (degrees) 119.85953886 Shift along axis 0.02880414 > select /g,Z,Y,X,W,y,h 26076 atoms, 27204 bonds, 495 pseudobonds, 2497 residues, 2 models selected > select /r,q,p,o,n,x,w,s,u,t,v 41274 atoms, 43050 bonds, 784 pseudobonds, 3941 residues, 2 models selected > delete /r,q,p,o,n,x,w,s,u,t,v > save ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" > close #7 > close #9 > close #8 > close > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #4, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #7, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #8 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > hide atoms > hide #!6 models > hide #!7 models > hide #!8 models > hide #!4 models > hide #!5 models > show #!7 models > volume #7 level 0.02292 > volume #7 step 4 > show #!8 models > show target a > volume #7 style mesh > close #7 > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > volume #7 level 0.02292 step 4 > hide #!7 models > hide #!6 models > volume #8 level 0.02292 step 4 > volume #8 style mesh > volume #5,6,7 level 0.1 step 1 Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. > ui mousemode right translate > view matrix view matrix camera -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0 > hide target s > hide #* target s > hide #!5 models > show #!5 models > show #!4 models > show #!3 models > show #!1 models > show #!2 models > show #!6 models > show #!7 models > hide #* target s > hide #1,2,3,4 target s > hide #1,2,3,4,5 target s > hide #1,2,3,4,5,6 target s > hide #1,2,3,4,5,6,7,8 target s > show #!9 > show #!9 models > hide #1 models > hide #* models > show /A,B,C,D,E,F,I,J,K,L,M target s > show #9/A,B,C,D,E,F,I,J,K,L,M target s > show #!9 models > hide #9 target a > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > show /A,B,C,D,E,F,I,J,K,L,M target s > transparency #1 100 target s > save DC_AB_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /a,b,c,d,e,f,i,j,k,l,m target s > transparency #1 100 target s > save DC_ab_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /H,G,N,U,Q,S,V,P,O,T,R target s > transparency #1 100 target s > save DC_GH_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /g target s > transparency #1 100 target s > save DC_g_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Z target s > transparency #1 100 target s > save DC_Z_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > transparency #1 100 target s > save DC_1Y_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /X target s > transparency #1 100 target s > save DC_X_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /W target s > transparency #1 100 target s > save DC_W_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /y target s > transparency #1 100 target s > save DC_y_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > transparency #1 100 target s > save DC_h_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide #* models > show #!9 models > hide #9 target a > show /A,B,C,D,E,F,I,J,K,L,M target s > transparency #9 100 target s > save DC_AB_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /a,b,c,d,e,f,i,j,k,l,m target s > transparency #9 100 target s > save DC_ab_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /H,G,N,U,Q,S,V,P,O,T,R target s > transparency #9 100 target s > save DC_GH_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /g target s > transparency #9 100 target s > save DC_g_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Z target s > transparency #9 100 target s > save DC_Z_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > transparency #9 100 target s > save DC_1Y_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /X target s > transparency #9 100 target s > save DC_X_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /W target s > transparency #9 100 target s > save DC_W_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /y target s > transparency #9 100 target s > save DC_y_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > transparency #9 100 target s > save DC_h_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide #* models > show #!9 models > hide #9 target a > show /A,B,C,D,E,F,I,J,K,L,M target s > transparency #9 100 target s > save DC_1AB_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /a,b,c,d,e,f,i,j,k,l,m target s > transparency #9 100 target s > save DC_ab_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /H,G,N,U,Q,S,V,P,O,T,R target s > transparency #9 100 target s > save DC_GH_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /g target s > transparency #9 100 target s > save DC_g_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Z target s > transparency #9 100 target s > save DC_Z_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > transparency #9 100 target s > save DC_1Y_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /X target s > transparency #9 100 target s > save DC_X_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /W target s > transparency #9 100 target s > save DC_W_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /y target s > transparency #9 100 target s > save DC_y_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > transparency #9 100 target s > save DC_h_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > show #!8 models > hide #!9 models > show #8 target s > color #8 #76d6ffff models > volume #8 level 0.2092 > show #!9 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide #5 target s > hide #8 > hide #5,6,7,8 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > show /A,B,C,D,E,F,I,J,K,L,M target s > hide #5,6,7,8,9 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > show /A,B,C,D,E,F,I,J,K,L,M target s > transparency #9 100 target s > save DC_1AB_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /a,b,c,d,e,f,i,j,k,l,m target s > transparency #9 100 target s > save DC_ab_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /H,G,N,U,Q,S,V,P,O,T,R target s > transparency #9 100 target s > save DC_GH_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /g target s > transparency #9 100 target s > save DC_g_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Z target s > transparency #9 100 target s > save DC_Z_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > transparency #9 100 target s > save DC_1Y_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /X target s > transparency #9 100 target s > save DC_X_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /W target s > transparency #9 100 target s > save DC_W_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /y target s > transparency #9 100 target s > save DC_y_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > transparency #9 100 target s > save DC_h_outline.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show #8 target s > show #8 > color #8 #C71585 > transparency #8 90 target s > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > save DC_7IsiA_mask_outline.png format png width 1200 height 1200 supersample > 4 transparentBackground true > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > show #8 > color #8 dodger blue > transparency #8 80 target s > save DC_7IsiA_mask_outline.png format png width 1200 height 1200 supersample > 4 transparentBackground true > transparency #8 60 target s > save DC_7IsiA_mask_outline.png format png width 1200 height 1200 supersample > 4 transparentBackground true > ui tool show ""Side View"" > view matrix view matrix camera -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0 > show #8 > color #8 dodger blue > transparency #8 50 target s > save DC_7IsiA_mask_outline.png format png width 1200 height 1200 supersample > 4 transparentBackground true > show #!5 models > show #5 > transparency #8 90 target s > volume #5 level 0.09822 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > view matrix view matrix camera -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0 > hide #!5 models > show #!6 models > show #6 > volume #6 level 0.09081 > volume #6 level 0.08868 > hide #!6 models > show #!5 models > show #!6 models > hide #!6 models > hide #!5 models > show #!7 models > select ~sel & ##selected Nothing selected > show #7 > volume #7 level 0.09082 > volume #7 level 0.09036 > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > show #!5 models > volume #5 level 0.1309 > volume #5 level 0.09346 > hide #!5 models > show #!6 models > volume #5 level 0.09822 > hide #!5 models > volume #6 level 0.09081 > show #5,6,7 > volume #5 level 0.09822 > volume #6 level 0.08868 > volume #7 level 0.09036 > volume mask #5,6,7 surfaces #8 Opened cryosparc_P12_J162_006_volume_map.mrc y flip masked as #10, grid size 121,337,211, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip masked as #11, grid size 121,337,211, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip masked as #12, grid size 121,337,211, pixel 0.86, shown at step 1, values float32 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide #8,9 > !show #8,9 Unknown command: !show #8,9 > hide #8 > hide > hide target s > hide #* > hide #* target s > hide #10 > hide #10,11,12 > show #10 > volume #10 level 0.1042 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > color #10 grey > save J162_masked.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide #10 > show #11 > color #11 gold [Repeated 1 time(s)] > volume #11 level 0.09752 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > save J163_masked.png format png width 1200 height 1200 supersample 4 > transparentBackground true > √ Unknown command: √ > hide #11 > show #12 > color #12 red > volume #12 level 0.08577 > save J164_masked.png format png width 1200 height 1200 supersample 4 > transparentBackground true > show /Z target s > volume #12 level 0.111 > show /Y target s > hide /Y target s > hide /X target s > hide /x target s > show /x target s > show /X target s > hide /X target s > show /y target s > hide /y target s > show /h target s > hide /h target s > hide /W target s > show /W target s > hide /W target s > show /g target s > hide #!12 models > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide target s > show /g target s > color /g #045a8d target s > transparency #9 100 target s > save DC_g_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide target s > show /g target s > color /g #045a8d target s > transparency #9 0 target s > save DC_g_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > help help:user/preferences.html#startup > lighting flat [Repeated 1 time(s)] > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide target s > show /g target s > color /g #045a8d target s > transparency #9 0 target s > save DC_g_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > transparency #9 100 target s > lighting flat > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 [Repeated 1 time(s)] > hide target s > show /Z target s > color /Z #045a8d target s > transparency #9 0 target s > save DC_Z_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > show cartoons > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide atoms > hide cartoons > hide target s > show /Y target s > color /Y #045a8d target s > transparency #9 75 target s > save DC_Y_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > color /h #045a8d target s > transparency #9 75 target s > save DC_h_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > color /Y #045a8d target s > transparency #9 25 target s > save DC_Y_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > color /h #045a8d target s > transparency #9 25 target s > save DC_h_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide target s > show /Y target s > color /Y #045a8d target s > transparency #9 25 target s > save DC_Y_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > color /h #045a8d target s > transparency #9 25 target s > save DC_h_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/DC_h_50_color.png"" Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF, I, RGB) > lighting flat > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide target s > show /g target s > color /g #045a8d target s > transparency #9 0 target s > save DC_g_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Z target s > color /Z #045a8d target s > transparency #9 0 target s > save DC_Z_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > color /Y #0570b0 target s > transparency #9 0 target s > save DC_Y_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > color /h #0570b0 target s > transparency #9 0 target s > save DC_h_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > lighting flat > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide target s > show /g target s > color /g #045a8d target s > transparency #9 0 target s > save DC_g_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Z target s > color /Z #045a8d target s > transparency #9 0 target s > save DC_Z_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > color /Y #3690c0 target s > transparency #9 0 target s > save DC_Y_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > color /h #3690c0 target s > transparency #9 0 target s > save DC_h_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > graphics silhouettes true width 3 > graphics silhouettes true width 1 > graphics silhouettes true width 2 [Repeated 1 time(s)] > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide target s > show /g target s > color /g #045a8d target s > transparency #9 0 target s > save DC_g_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Z target s > color /Z #045a8d target s > transparency #9 0 target s > save DC_Z_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > color /Y #3690c0 target s > transparency #9 0 target s > save DC_Y_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /h target s > color /h #3690c0 target s > transparency #9 0 target s > save DC_h_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > volume #12 level 0.09312 > volume #11 level 0.1106 > hide target s > save DC_Z_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /Y target s > color /Y #045a8d target s > transparency #9 0 target s > save DC_Y_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /X target s > color /X #045a8d target s > transparency #9 0 target s > save DC_X_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide target s > show /Y target s > color /Y #045a8d target s > transparency #9 0 target s > save DC_Y_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /X target s > color /X #045a8d target s > transparency #9 0 target s > save DC_X_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > volume #11 level 0.1092 > save DC_X_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > hide target s > show /W target s > color /W #045a8d target s > transparency #9 0 target s > save DC_W_full_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > volume #11 level 0.09646 > volume #11 level 0.1085 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 [Repeated 1 time(s)] > hide target s > show /y target s > color /y #3690c0 target s > transparency #9 0 target s > save DC_y1_50_color.png format png width 1200 height 1200 supersample 4 > transparentBackground true > volume #10 level 0.1321 > hide target s > volume #10 level 0.1321 > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #1 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > save AB.pdb format pdb models /A,B,C,D,E,F,I,J,K,L,M selectedOnly true > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb"" [Repeated 2 time(s)] > select /A,B,C,D,E,F,I,J,K,L,M 24368 atoms, 25199 bonds, 410 pseudobonds, 2501 residues, 2 models selected > save AB.pdb format pdb models #1 > ~select Nothing selected > hide #!1 models > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb"" Chain information for AB.pdb #2 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > close #2 > show #!1 models > select /A,B,C,D,E,F,I,J,K,L,M 24368 atoms, 25199 bonds, 410 pseudobonds, 2501 residues, 2 models selected > save AB.pdb format pdb models #1 selectedOnly true > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb"" Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb --- warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4 Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26 1 8 Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33 1 3 Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71 1 33 Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) Cannot find LINK/SSBOND residue ILE (282 ) 70 messages similar to the above omitted Chain information for AB.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available > hide #!1 models > close #2 > select /a,b,c,d,e,f,i,j,k,l,m 24413 atoms, 25195 bonds, 407 pseudobonds, 2550 residues, 2 models selected > save ab1.pdb format pdb models #1 selectedOnly true > select /H,G,N,U,Q,S,V,P,O,T,R 24385 atoms, 25200 bonds, 408 pseudobonds, 2517 residues, 2 models selected > save GH.pdb format pdb models #1 selectedOnly true > select /g 3777 atoms, 3938 bonds, 71 pseudobonds, 356 residues, 2 models selected > save g.pdb format pdb models #1 selectedOnly true > select /Z 3777 atoms, 3940 bonds, 71 pseudobonds, 359 residues, 2 models selected > save Z.pdb format pdb models #1 selectedOnly true > select /X 3768 atoms, 3929 bonds, 72 pseudobonds, 361 residues, 2 models selected > save X.pdb format pdb models #1 selectedOnly true > select /W 3684 atoms, 3845 bonds, 71 pseudobonds, 358 residues, 2 models selected > save W.pdb format pdb models #1 selectedOnly true > select /y 3621 atoms, 3781 bonds, 69 pseudobonds, 350 residues, 2 models selected > save y1.pdb format pdb models #1 selectedOnly true > select /h 3627 atoms, 3787 bonds, 69 pseudobonds, 350 residues, 2 models selected > save h.pdb format pdb models #1 selectedOnly true > close #1 > open /Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb '/Users/yuvalmazor/ASU' has no suffix > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"" Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb --- warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4 Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26 1 8 Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33 1 3 Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71 1 33 Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) Cannot find LINK/SSBOND residue ILE (282 ) 70 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 364 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) Cannot find LINK/SSBOND residue ILE (282 ) 72 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 485 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 484 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASN (17 ) Cannot find LINK/SSBOND residue ILE (282 ) Cannot find LINK/SSBOND residue GLN (316 ) 73 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 486 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) 96 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue ASP (56 ) Cannot find LINK/SSBOND residue ASN (17 ) 96 messages similar to the above omitted Chain information for AB.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available Chain information for GH.pdb #2 --- Chain | Description G | No description available H | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available Chain information for W.pdb #3 --- Chain | Description W | No description available Chain information for X.pdb #4 --- Chain | Description X | No description available Chain information for Z.pdb #5 --- Chain | Description Z | No description available Chain information for ab1.pdb #6 --- Chain | Description a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available i | No description available j | No description available k | No description available l | No description available m | No description available Chain information for g.pdb #7 --- Chain | Description g | No description available Chain information for h.pdb #8 --- Chain | Description h | No description available Chain information for y1.pdb #9 --- Chain | Description y | No description available > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #1 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > select /A,B,C,D,E,F,I,J,K,L,M 24368 atoms, 25199 bonds, 410 pseudobonds, 2501 residues, 2 models selected > save AB.pdb format pdb models #1 selectedOnly true > select /a,b,c,d,e,f,i,j,k,l,m 24413 atoms, 25195 bonds, 407 pseudobonds, 2550 residues, 2 models selected > save ab1.pdb format pdb models #1 selectedOnly true > select /H,G,N,U,Q,S,V,P,O,T,R 24385 atoms, 25200 bonds, 408 pseudobonds, 2517 residues, 2 models selected > save GH.pdb format pdb models #1 selectedOnly true > select /g 3777 atoms, 3938 bonds, 71 pseudobonds, 356 residues, 2 models selected > save g.pdb format pdb models #1 selectedOnly true > select /Z 3777 atoms, 3940 bonds, 71 pseudobonds, 359 residues, 2 models selected > save Z.pdb format pdb models #1 selectedOnly true > select /X 3768 atoms, 3929 bonds, 72 pseudobonds, 361 residues, 2 models selected > save X.pdb format pdb models #1 selectedOnly true > select /Y 3822 atoms, 3984 bonds, 72 pseudobonds, 363 residues, 2 models selected > save Y.pdb format pdb models #1 selectedOnly true > select /W 3684 atoms, 3845 bonds, 71 pseudobonds, 358 residues, 2 models selected > save W.pdb format pdb models #1 selectedOnly true > select /y 3621 atoms, 3781 bonds, 69 pseudobonds, 350 residues, 2 models selected > save y1.pdb format pdb models #1 selectedOnly true > select /h 3627 atoms, 3787 bonds, 69 pseudobonds, 350 residues, 2 models selected > save h.pdb format pdb models #1 selectedOnly true > close #1 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"" Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb --- warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4 Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26 1 8 Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33 1 3 Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71 1 33 Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue GLN (123 ) Cannot find LINK/SSBOND residue THR (497 ) Cannot find LINK/SSBOND residue ASP (93 ) 70 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 364 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 72 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 485 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 484 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 73 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 486 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Chain information for AB.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available Chain information for GH.pdb #2 --- Chain | Description G | No description available H | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available Chain information for W.pdb #3 --- Chain | Description W | No description available Chain information for X.pdb #4 --- Chain | Description X | No description available Chain information for Y.pdb #5 --- Chain | Description Y | No description available Chain information for Z.pdb #6 --- Chain | Description Z | No description available Chain information for ab1.pdb #7 --- Chain | Description a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available i | No description available j | No description available k | No description available l | No description available m | No description available Chain information for g.pdb #8 --- Chain | Description g | No description available Chain information for h.pdb #9 --- Chain | Description h | No description available Chain information for y1.pdb #10 --- Chain | Description y | No description available > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"" Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb --- warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4 Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26 1 8 Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33 1 3 Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71 1 33 Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue GLN (123 ) Cannot find LINK/SSBOND residue THR (497 ) Cannot find LINK/SSBOND residue ASP (93 ) 70 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 364 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 72 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 485 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 484 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 73 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 486 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Chain information for AB.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available Chain information for GH.pdb #10 --- Chain | Description G | No description available H | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available Chain information for W.pdb #11 --- Chain | Description W | No description available Chain information for X.pdb #12 --- Chain | Description X | No description available Chain information for Y.pdb #13 --- Chain | Description Y | No description available Chain information for Z.pdb #14 --- Chain | Description Z | No description available Chain information for ab1.pdb #15 --- Chain | Description a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available i | No description available j | No description available k | No description available l | No description available m | No description available Chain information for g.pdb #16 --- Chain | Description g | No description available Chain information for h.pdb #17 --- Chain | Description h | No description available Chain information for y1.pdb #18 --- Chain | Description y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5,6,7,8,9 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide #5 > hide #6,7 > hide #5,6,7,8,9 > hide #5,6,7,8 > hide #9-18 [Repeated 1 time(s)] > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"" Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb --- warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4 Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26 1 8 Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33 1 3 Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71 1 33 Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue GLN (123 ) Cannot find LINK/SSBOND residue THR (497 ) Cannot find LINK/SSBOND residue ASP (93 ) 70 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 364 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 72 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 485 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 484 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 73 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 486 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Chain information for AB.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available Chain information for GH.pdb #10 --- Chain | Description G | No description available H | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available Chain information for W.pdb #11 --- Chain | Description W | No description available Chain information for X.pdb #12 --- Chain | Description X | No description available Chain information for Y.pdb #13 --- Chain | Description Y | No description available Chain information for Z.pdb #14 --- Chain | Description Z | No description available Chain information for ab1.pdb #15 --- Chain | Description a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available i | No description available j | No description available k | No description available l | No description available m | No description available Chain information for g.pdb #16 --- Chain | Description g | No description available Chain information for h.pdb #17 --- Chain | Description h | No description available Chain information for y1.pdb #18 --- Chain | Description y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5-8 > hide #9-11 > hide #12-18 > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > hide #12-18 target c > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"" Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb --- warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4 Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26 1 8 Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33 1 3 Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71 1 33 Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue GLN (123 ) Cannot find LINK/SSBOND residue THR (497 ) Cannot find LINK/SSBOND residue ASP (93 ) 70 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 364 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 72 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 485 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 484 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 73 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 486 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Chain information for AB.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available Chain information for GH.pdb #10 --- Chain | Description G | No description available H | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available Chain information for W.pdb #11 --- Chain | Description W | No description available Chain information for X.pdb #12 --- Chain | Description X | No description available Chain information for Y.pdb #13 --- Chain | Description Y | No description available Chain information for Z.pdb #14 --- Chain | Description Z | No description available Chain information for ab1.pdb #15 --- Chain | Description a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available i | No description available j | No description available k | No description available l | No description available m | No description available Chain information for g.pdb #16 --- Chain | Description g | No description available Chain information for h.pdb #17 --- Chain | Description h | No description available Chain information for y1.pdb #18 --- Chain | Description y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5-8 > hide #9-18 > hide #9-18 target c Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"" Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb --- warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4 Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26 1 8 Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33 1 3 Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71 1 33 Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue GLN (123 ) Cannot find LINK/SSBOND residue THR (497 ) Cannot find LINK/SSBOND residue ASP (93 ) 70 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 364 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 72 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 485 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 484 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 73 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 486 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Chain information for AB.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available Chain information for GH.pdb #10 --- Chain | Description G | No description available H | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available Chain information for W.pdb #11 --- Chain | Description W | No description available Chain information for X.pdb #12 --- Chain | Description X | No description available Chain information for Y.pdb #13 --- Chain | Description Y | No description available Chain information for Z.pdb #14 --- Chain | Description Z | No description available Chain information for ab1.pdb #15 --- Chain | Description a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available i | No description available j | No description available k | No description available l | No description available m | No description available Chain information for g.pdb #16 --- Chain | Description g | No description available Chain information for h.pdb #17 --- Chain | Description h | No description available Chain information for y1.pdb #18 --- Chain | Description y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5-8 > show #9-18 target c > hide #9-18 > hide #9-18 target c Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"" Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb --- warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4 Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26 1 8 Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33 1 3 Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71 1 33 Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue GLN (123 ) Cannot find LINK/SSBOND residue THR (497 ) Cannot find LINK/SSBOND residue ASP (93 ) 70 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 364 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 72 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 485 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 484 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 93 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 483 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 368 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) Cannot find LINK/SSBOND residue CLA (1237 ) 73 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 94 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 486 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1 4 Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1 32 Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105 1 6 Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126 1 4 487 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1012 ) Cannot find LINK/SSBOND residue CLA (1139 ) 96 messages similar to the above omitted Chain information for AB.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available Chain information for GH.pdb #10 --- Chain | Description G | No description available H | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available Chain information for W.pdb #11 --- Chain | Description W | No description available Chain information for X.pdb #12 --- Chain | Description X | No description available Chain information for Y.pdb #13 --- Chain | Description Y | No description available Chain information for Z.pdb #14 --- Chain | Description Z | No description available Chain information for ab1.pdb #15 --- Chain | Description a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available i | No description available j | No description available k | No description available l | No description available m | No description available Chain information for g.pdb #16 --- Chain | Description g | No description available Chain information for h.pdb #17 --- Chain | Description h | No description available Chain information for y1.pdb #18 --- Chain | Description y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5-8 > hide #9-18 > hide #9-18 target c > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > show /A,B,C,D,E,F,I,J,K,L,M target s > transparency #9 100 target s > show /A,B,C,D,E,F,I,J,K,L,M target s > show /a,b,c,d,e,f,i,j,k,l,m target s > transparency #9-18 100 target s > graphics selection color black width 3 > graphics silhouettes false > graphics selection color black width 3 > select /a,b 34889 atoms, 36186 bonds, 724 pseudobonds, 3395 residues, 4 models selected > select /A,B 17435 atoms, 18095 bonds, 363 pseudobonds, 1686 residues, 2 models selected > select /a,b 34889 atoms, 36186 bonds, 724 pseudobonds, 3395 residues, 4 models selected > graphics silhouettes true > graphics silhouettes true depthJump 0.1 > graphics silhouettes true depthJump 0.01 > graphics silhouettes true depthJump 0.02 > graphics silhouettes true depthJump 0.03 > graphics silhouettes true depthJump 0.04 > graphics silhouettes true depthJump 0.05 > graphics silhouettes true depthJump 0.06 > graphics silhouettes true depthJump 0.07 > show #9-18 target s > transparency #9-18 100 target s > graphics silhouettes true depthJump 0.01 > graphics silhouettes true depthJump 0.02 > close > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/7umh_docked_J162_flipped.pdb"" Chain information for 7umh_docked_J162_flipped.pdb #1 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h n o p q r s t u v w x y | No description available > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" format > swissdock Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb --- warnings | Ignored bad PDB record found on line 2 Ignored bad PDB record found on line 4 Ignored bad PDB record found on line 6 Ignored bad PDB record found on line 8 Ignored bad PDB record found on line 10 1611 messages similar to the above omitted Start residue of secondary structure not found: HELIX 41 41 GLN B 10 ALA B 13 1 4 Start residue of secondary structure not found: HELIX 42 42 ARG B 19 ALA B 26 1 8 Start residue of secondary structure not found: HELIX 43 43 PHE B 31 THR B 33 1 3 Start residue of secondary structure not found: HELIX 44 44 GLU B 39 GLN B 71 1 33 Start residue of secondary structure not found: HELIX 45 45 PHE B 74 TRP B 77 1 4 456 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CYS (10 ) Cannot find LINK/SSBOND residue CLA (1221 ) Cannot find LINK/SSBOND residue CLA (1216 ) 97 messages similar to the above omitted Ignored bad PDB record found on line 3 Ignored bad PDB record found on line 6 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 Ignored bad PDB record found on line 15 535 messages similar to the above omitted Chain information for PSI_IsiADC_docked_J162_flipped.pdb --- Chain | Description 2.1/A | No description available 2.2/B 2.7/G 2.28/b | No description available 2.3/C 2.14/N 2.29/c | No description available 2.4/D 2.16/P 2.30/d | No description available 2.5/E 2.15/O 2.31/e | No description available 2.6/F 2.17/Q 2.32/f | No description available 2.8/H 2.27/a | No description available 2.9/I 2.18/R 2.35/i | No description available 2.10/J 2.19/S 2.36/j | No description available 2.11/K 2.20/T 2.37/k | No description available 2.12/L 2.21/U 2.38/l | No description available 2.13/M 2.22/V 2.39/m | No description available 2.23/W | No description available 2.24/X | No description available 2.25/Y | No description available 2.26/Z | No description available 2.33/g | No description available 2.34/h 2.40/y | No description available Computing secondary structure [Repeated 38 time(s)] > viewdockx #2.1-40 No suitable models found for ViewDockX > hide #!1 models > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5-8 > hide #9-18 > hide #9-18 target c > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5-8 > hide #9 Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5,6,7,8 > hide #9 Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. > view matrix camera > -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53 > close > cd ""/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"" Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"" Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512, pixel 0.86, shown at level 0.076, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"" Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512, pixel 0.86, shown at level 0.071, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"" Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512, pixel 0.86, shown at level 0.0691, step 2, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"" Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size 512,512,512, pixel 0.86, shown at level 1, step 2, values float32 > volume flip #* axis y Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size 512,512,512, pixel 0.86, shown at step 1, values float32 > open ""/Users/yuvalmazor/ASU Dropbox/Yuval > Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"" Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9 --- Chain | Description A H a | No description available B G b | No description available C N c | No description available D P d | No description available E O e | No description available F Q f | No description available I R i | No description available J S j | No description available K T k | No description available L U l | No description available M V m | No description available W X Y Z g h y | No description available > volume #8 level 0.02292 step 4 > volume #5,6,7 level 0.1 step 1 > set bgColor white > graphics silhouettes true width 3 > lighting depthCue false > hide #5,6,7,8 > hide #9 Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2751, in update_cb s.update_histogram(rm, m, rz, delay = 0) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2759, in update_histogram s = v.matrix_value_statistics(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1736, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 41, in matrix mf = flip_matrix(m, self.axes) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_filter/flip.py"", line 89, in flip_matrix m = m[:,::-1,:] ~^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: Z14W00106LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 7 days, 20 hours, 46 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Volume Data duplicate all ChimeraX