id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16349 Session save: Unable to restore objects of IHMModel class in ChimeraX-IHM bundle ccaffalett@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.7.6-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > surface cap false Log from Wed Nov 20 14:01:59 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > surface cap false Log from Wed Nov 20 13:53:26 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > surface cap false Log from Wed Nov 20 13:43:19 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f-assembly1.cif format > mmcif 7n9f-assembly1.cif title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f-assembly1.cif #1 --- Chain | Description 0 0-2 0-3 0-4 0-5 0-6 0-7 0-8 Y Y-2 Y-3 Y-4 Y-5 Y-6 Y-7 Y-8 | Nucleoporin NUP170 1 1-2 1-3 1-4 1-5 1-6 1-7 1-8 Z Z-2 Z-3 Z-4 Z-5 Z-6 Z-7 Z-8 | Nucleoporin NUP157 5 5-2 5-3 5-4 5-5 5-6 5-7 5-8 6 6-2 6-3 6-4 6-5 6-6 6-7 6-8 | orphans bound to Nup192 NTD A A-2 A-3 A-4 A-5 A-6 A-7 A-8 D D-2 D-3 D-4 D-5 D-6 D-7 D-8 G G-2 G-3 G-4 G-5 G-6 G-7 G-8 J J-2 J-3 J-4 J-5 J-6 J-7 J-8 y y-2 y-3 y-4 y-5 y-6 y-7 y-8 z z-2 z-3 z-4 z-5 z-6 z-7 z-8 | Nucleoporin NSP1 B B-2 B-3 B-4 B-5 B-6 B-7 B-8 E E-2 E-3 E-4 E-5 E-6 E-7 E-8 H H-2 H-3 H-4 H-5 H-6 H-7 H-8 K K-2 K-3 K-4 K-5 K-6 K-7 K-8 | Nucleoporin NUP57 C C-2 C-3 C-4 C-5 C-6 C-7 C-8 F F-2 F-3 F-4 F-5 F-6 F-7 F-8 I I-2 I-3 I-4 I-5 I-6 I-7 I-8 L L-2 L-3 L-4 L-5 L-6 L-7 L-8 | Nucleoporin NUP49/NSP49 M M-2 M-3 M-4 M-5 M-6 M-7 M-8 O O-2 O-3 O-4 O-5 O-6 O-7 O-8 | Nucleoporin NUP192 N N-2 N-3 N-4 N-5 N-6 N-7 N-8 P P-2 P-3 P-4 P-5 P-6 P-7 P-8 | Nucleoporin NUP188 Q Q-2 Q-3 Q-4 Q-5 Q-6 Q-7 Q-8 R R-2 R-3 R-4 R-5 R-6 R-7 R-8 S S-2 S-3 S-4 S-5 S-6 S-7 S-8 T T-2 T-3 T-4 T-5 T-6 T-7 T-8 | Nucleoporin NIC96 U U-2 U-3 U-4 U-5 U-6 U-7 U-8 W W-2 W-3 W-4 W-5 W-6 W-7 W-8 | Nucleoporin NUP53 V V-2 V-3 V-4 V-5 V-6 V-7 V-8 X X-2 X-3 X-4 X-5 X-6 X-7 X-8 | Nucleoporin ASM4 a a-2 a-3 a-4 a-5 a-6 a-7 a-8 h h-2 h-3 h-4 h-5 h-6 h-7 h-8 | Nucleoporin NUP120 b b-2 b-3 b-4 b-5 b-6 b-7 b-8 i i-2 i-3 i-4 i-5 i-6 i-7 i-8 | Nucleoporin NUP85 c c-2 c-3 c-4 c-5 c-6 c-7 c-8 j j-2 j-3 j-4 j-5 j-6 j-7 j-8 | Nucleoporin 145c d d-2 d-3 d-4 d-5 d-6 d-7 d-8 k k-2 k-3 k-4 k-5 k-6 k-7 k-8 | Protein transport protein SEC13 e e-2 e-3 e-4 e-5 e-6 e-7 e-8 l l-2 l-3 l-4 l-5 l-6 l-7 l-8 | Nucleoporin SEH1 f f-2 f-3 f-4 f-5 f-6 f-7 f-8 m m-2 m-3 m-4 m-5 m-6 m-7 m-8 | Nucleoporin NUP84 g g-2 g-3 g-4 g-5 g-6 g-7 g-8 n n-2 n-3 n-4 n-5 n-6 n-7 n-8 | Nucleoporin NUP133 o o-2 o-3 o-4 o-5 o-6 o-7 o-8 p p-2 p-3 p-4 p-5 p-6 p-7 p-8 q q-2 q-3 q-4 q-5 q-6 q-7 q-8 r r-2 r-3 r-4 r-5 r-6 r-7 r-8 s s-2 s-3 s-4 s-5 s-6 s-7 s-8 t t-2 t-3 t-4 t-5 t-6 t-7 t-8 | Dynein light chain 1, cytoplasmic u u-2 u-3 u-4 u-5 u-6 u-7 u-8 v v-2 v-3 v-4 v-5 v-6 v-7 v-8 | Nucleoporin NUP82 w w-2 w-3 w-4 w-5 w-6 w-7 w-8 x x-2 x-3 x-4 x-5 x-6 x-7 x-8 | Nucleoporin NUP159 > select #1//chain_id='0-2' 8762 atoms, 8935 bonds, 16 pseudobonds, 1085 residues, 2 models selected > close session > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_44377.map Opened emd_44377.map as #1, grid size 224,224,224, pixel 10, shown at level 602, step 1, values float32 > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_24258.map Opened emd_24258.map as #2, grid size 320,320,320, pixel 6.74, shown at level 2.39e+03, step 2, values float32 > close session > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_44377.map Opened emd_44377.map as #1, grid size 224,224,224, pixel 10, shown at level 602, step 1, values float32 > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_24258.map Opened emd_24258.map as #2, grid size 320,320,320, pixel 6.74, shown at level 2.39e+03, step 2, values float32 > volume #1 level 546.9 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit map emd_24258.map in map emd_44377.map using 40960 points correlation = 0.9861, correlation about mean = 0.06355, overlap = 6.451e+10 steps = 80, shift = 76.1, angle = 0.996 degrees Position of emd_24258.map (#2) relative to emd_44377.map (#1) coordinates: Matrix rotation and translation 0.99984878 -0.01739011 0.00009221 60.45971098 0.01739012 0.99984878 -0.00009214 23.11965642 -0.00009059 0.00009373 0.99999999 48.17366686 Axis 0.00534419 0.00525559 0.99997191 Axis point -1284.57791189 3472.90248415 0.00000000 Rotation angle (degrees) 0.99645830 Shift along axis 48.61692897 > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f.cif 7n9f.cif title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f.cif #3 --- Chain | Description | UniProt 0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502 1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391 5 6 | orphans bound to Nup192 NTD | A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823 B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541 C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472 M O | Nucleoporin NUP192 | NU192_YEAST 1-1683 N P | Nucleoporin NUP188 | NU188_YEAST 1-1655 Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839 U W | Nucleoporin NUP53 | NUP53_YEAST 1-475 V X | Nucleoporin ASM4 | NUP59_YEAST 1-528 a h | Nucleoporin NUP120 | NU120_YEAST 1-1037 b i | Nucleoporin NUP85 | NUP85_YEAST 1-744 c j | Nucleoporin 145c | NU145_YEAST 0-797 d k | Protein transport protein SEC13 | SEC13_YEAST 1-297 e l | Nucleoporin SEH1 | SEH1_YEAST 1-349 f m | Nucleoporin NUP84 | NUP84_YEAST 1-726 g n | Nucleoporin NUP133 | NU133_YEAST 1-1157 o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92 u v | Nucleoporin NUP82 | NUP82_YEAST 1-713 w x | Nucleoporin NUP159 | NU159_YEAST 1-1460 7n9f.cif mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f.cif 7n9f.cif title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f.cif #4 --- Chain | Description | UniProt 0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502 1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391 5 6 | orphans bound to Nup192 NTD | A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823 B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541 C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472 M O | Nucleoporin NUP192 | NU192_YEAST 1-1683 N P | Nucleoporin NUP188 | NU188_YEAST 1-1655 Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839 U W | Nucleoporin NUP53 | NUP53_YEAST 1-475 V X | Nucleoporin ASM4 | NUP59_YEAST 1-528 a h | Nucleoporin NUP120 | NU120_YEAST 1-1037 b i | Nucleoporin NUP85 | NUP85_YEAST 1-744 c j | Nucleoporin 145c | NU145_YEAST 0-797 d k | Protein transport protein SEC13 | SEC13_YEAST 1-297 e l | Nucleoporin SEH1 | SEH1_YEAST 1-349 f m | Nucleoporin NUP84 | NUP84_YEAST 1-726 g n | Nucleoporin NUP133 | NU133_YEAST 1-1157 o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92 u v | Nucleoporin NUP82 | NUP82_YEAST 1-713 w x | Nucleoporin NUP159 | NU159_YEAST 1-1460 7n9f.cif mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f.cif 7n9f.cif title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f.cif #5 --- Chain | Description | UniProt 0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502 1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391 5 6 | orphans bound to Nup192 NTD | A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823 B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541 C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472 M O | Nucleoporin NUP192 | NU192_YEAST 1-1683 N P | Nucleoporin NUP188 | NU188_YEAST 1-1655 Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839 U W | Nucleoporin NUP53 | NUP53_YEAST 1-475 V X | Nucleoporin ASM4 | NUP59_YEAST 1-528 a h | Nucleoporin NUP120 | NU120_YEAST 1-1037 b i | Nucleoporin NUP85 | NUP85_YEAST 1-744 c j | Nucleoporin 145c | NU145_YEAST 0-797 d k | Protein transport protein SEC13 | SEC13_YEAST 1-297 e l | Nucleoporin SEH1 | SEH1_YEAST 1-349 f m | Nucleoporin NUP84 | NUP84_YEAST 1-726 g n | Nucleoporin NUP133 | NU133_YEAST 1-1157 o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92 u v | Nucleoporin NUP82 | NUP82_YEAST 1-713 w x | Nucleoporin NUP159 | NU159_YEAST 1-1460 7n9f.cif mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > select add #3 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,332.91,0,1,0,20.318,0,0,1,-5.3855 > view matrix models > #3,0.99231,0.097816,-0.075787,281.18,-0.096948,0.99518,0.015061,114.49,0.076895,-0.0075977,0.99701,-73.193 > view matrix models > #3,0.93157,0.29189,-0.21673,216.69,-0.29404,0.95552,0.022994,376.12,0.2138,0.042307,0.97596,-270.65 > select add #4 425924 atoms, 433552 bonds, 520 pseudobonds, 54142 residues, 4 models selected > select add #5 638886 atoms, 650328 bonds, 780 pseudobonds, 81213 residues, 6 models selected > select subtract #3 425924 atoms, 433552 bonds, 520 pseudobonds, 54142 residues, 4 models selected > select subtract #4 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > view matrix models > #5,0.13979,0.62998,-0.76393,1128.9,-0.90342,0.39696,0.16205,1726.7,0.40534,0.66749,0.62462,-976.83 > view matrix models > #5,0.13979,0.62998,-0.76393,156.09,-0.90342,0.39696,0.16205,1727.7,0.40534,0.66749,0.62462,-882.4 > view matrix models > #5,-0.19914,0.49993,-0.84286,802.98,-0.030293,0.85654,0.5152,-293.99,0.9795,0.12813,-0.15543,188.48 > view matrix models > #5,0.57032,0.77293,-0.27807,-1069,-0.099713,0.40116,0.91056,11.541,0.81535,-0.49158,0.30586,765.96 > view matrix models > #5,0.82807,0.38852,0.40418,-1545.2,-0.4548,0.043964,0.88951,948.78,0.32782,-0.92039,0.2131,2033.2 > view matrix models > #5,0.82807,0.38852,0.40418,-1529,-0.4548,0.043964,0.88951,918.58,0.32782,-0.92039,0.2131,1992.3 > view matrix models > #5,0.47203,0.78578,-0.39967,-828.9,-0.057563,0.47986,0.87546,-141.43,0.8797,-0.39023,0.27174,543.58 > view matrix models > #5,0.73779,0.67498,0.0079163,-1410.4,-0.22456,0.23437,0.94586,323.94,0.63658,-0.69963,0.32449,1205.9 > view matrix models > #5,0.82564,0.45794,0.32957,-1545.4,-0.40557,0.075632,0.91093,794.29,0.39223,-0.88576,0.24817,1831.9 > view matrix models > #5,0.82564,0.45794,0.32957,-1800,-0.40557,0.075632,0.91093,1078,0.39223,-0.88576,0.24817,1871.3 > view matrix models > #5,0.94612,0.32382,-0.0025781,-1353.4,-0.323,0.94311,-0.078764,817.07,-0.023074,0.075352,0.99689,36.829 > view matrix models > #5,0.37061,-0.72379,-0.58204,1481.6,0.87375,0.48422,-0.045781,179.42,0.31497,-0.49159,0.81187,728.51 > view matrix models > #5,0.37061,-0.72379,-0.58204,2078.5,0.87375,0.48422,-0.045781,-212.77,0.31497,-0.49159,0.81187,758.53 > fitmap #3 inMap #2 Fit molecule 7n9f.cif (#3) to map emd_24258.map (#2) using 212962 atoms average map value = 2115, steps = 176 shifted from previous position = 50.5 rotated from previous position = 13.2 degrees atoms outside contour = 140343, contour level = 2391.2 Position of 7n9f.cif (#3) relative to emd_24258.map (#2) coordinates: Matrix rotation and translation 0.92945983 0.36243945 -0.06886273 -116.10096073 -0.34287256 0.91754294 0.20137864 212.45270598 0.13617207 -0.16356221 0.97708985 50.12065917 Axis -0.44495516 -0.24998926 -0.85995365 Axis point 474.73234442 467.42312556 0.00000000 Rotation angle (degrees) 24.21031404 Shift along axis -44.55261677 > select subtract #5 Nothing selected > select add #3 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > view matrix models > #3,0.93529,0.34641,-0.072264,15.655,-0.32667,0.92372,0.20006,215.51,0.13606,-0.16351,0.97711,116.1 > hide #!1 models > view matrix models > #3,0.95615,0.29204,-0.02205,17.462,-0.27231,0.91422,0.30007,58.096,0.10779,-0.28091,0.95366,347.96 > view matrix models > #3,0.69236,0.71307,0.11036,-476.86,-0.70333,0.63277,0.32392,913.09,0.16115,-0.30189,0.93963,337.85 > view matrix models > #3,0.69236,0.71307,0.11036,-479.45,-0.70333,0.63277,0.32392,862.93,0.16115,-0.30189,0.93963,341.42 > view matrix models > #3,0.69236,0.71307,0.11036,-440.11,-0.70333,0.63277,0.32392,880.1,0.16115,-0.30189,0.93963,404.55 > view matrix models > #3,0.62772,0.74154,0.23684,-556.38,-0.77841,0.5951,0.19984,1157.3,0.007251,-0.3098,0.95077,568.87 > view matrix models > #3,0.62772,0.74154,0.23684,-643.67,-0.77841,0.5951,0.19984,1121.6,0.007251,-0.3098,0.95077,658.17 > view matrix models > #3,0.62772,0.74154,0.23684,-633.46,-0.77841,0.5951,0.19984,1129.6,0.007251,-0.3098,0.95077,646.21 > view matrix models > #3,0.62772,0.74154,0.23684,-661.37,-0.77841,0.5951,0.19984,1112.4,0.007251,-0.3098,0.95077,570.74 > fitmap #3 inMap #2 Fit molecule 7n9f.cif (#3) to map emd_24258.map (#2) using 212962 atoms average map value = 2862, steps = 112 shifted from previous position = 47.4 rotated from previous position = 19.3 degrees atoms outside contour = 35046, contour level = 2391.2 Position of 7n9f.cif (#3) relative to emd_24258.map (#2) coordinates: Matrix rotation and translation 0.70658642 0.70762285 0.00235119 -449.35213366 -0.70762602 0.70658659 0.00089799 1078.61889656 -0.00102589 -0.00229827 0.99999683 6.06599978 Axis -0.00225843 0.00238620 -0.99999460 Axis point 1075.98219962 1081.17694879 0.00000000 Rotation angle (degrees) 45.04226974 Shift along axis -2.47733962 > select subtract #3 Nothing selected > select add #4 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > view matrix models #4,1,0,0,26.536,0,1,0,47.263,0,0,1,44.723 > fitmap #4 inMap #2 Fit molecule 7n9f.cif (#4) to map emd_24258.map (#2) using 212962 atoms average map value = 2871, steps = 56 shifted from previous position = 11 rotated from previous position = 0.941 degrees atoms outside contour = 34855, contour level = 2391.2 Position of 7n9f.cif (#4) relative to emd_24258.map (#2) coordinates: Matrix rotation and translation 0.99999885 0.00114017 0.00099620 -2.57990797 -0.00114232 0.99999701 0.00216166 -1.17888329 -0.00099373 -0.00216280 0.99999717 5.79943458 Axis -0.81914189 0.37693344 -0.43235141 Axis point 0.00000000 2513.31418847 402.63344871 Rotation angle (degrees) 0.15123977 Shift along axis -0.83844360 > select subtract #4 Nothing selected > select add #3 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > select subtract #3 Nothing selected > select add #5 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > view matrix models > #5,0.37061,-0.72379,-0.58204,2123.1,0.87375,0.48422,-0.045781,-224.15,0.31497,-0.49159,0.81187,726.18 > view matrix models > #5,0.30598,-0.89844,-0.31494,2150.3,0.88713,0.38912,-0.24817,132.37,0.34551,-0.20346,0.91609,145.97 > view matrix models > #5,0.61099,-0.78258,-0.11941,1428.9,0.78483,0.61855,-0.037984,-337.76,0.10359,-0.07051,0.99212,121.37 > view matrix models > #5,0.50736,-0.84303,-0.1786,1697.3,0.85178,0.4592,0.25219,-500.65,-0.13059,-0.28008,0.95105,731.49 > view matrix models > #5,0.50736,-0.84303,-0.1786,1742.2,0.85178,0.4592,0.25219,-521.1,-0.13059,-0.28008,0.95105,691.36 > view matrix models > #5,0.71936,-0.67636,-0.15828,1243.3,0.69247,0.68029,0.24017,-666.05,-0.054768,-0.28238,0.95774,605.85 > view matrix models > #5,0.71936,-0.67636,-0.15828,1253.1,0.69247,0.68029,0.24017,-644.84,-0.054768,-0.28238,0.95774,604.25 > view matrix models > #5,0.71936,-0.67636,-0.15828,1247.9,0.69247,0.68029,0.24017,-643.48,-0.054768,-0.28238,0.95774,607.03 > view matrix models > #5,0.70776,-0.70305,-0.069303,1199.4,0.69774,0.68029,0.22444,-631.3,-0.11064,-0.2072,0.97202,538.78 > view matrix models > #5,0.70776,-0.70305,-0.069303,1174.4,0.69774,0.68029,0.22444,-621.98,-0.11064,-0.2072,0.97202,536.92 > view matrix models > #5,0.68208,-0.72904,0.057118,1097.5,0.71331,0.68049,0.1677,-574.76,-0.16113,-0.073639,0.98418,378.26 > view matrix models > #5,0.68208,-0.72904,0.057118,1109,0.71331,0.68049,0.1677,-559.15,-0.16113,-0.073639,0.98418,378.81 > view matrix models > #5,0.68208,-0.72904,0.057118,1107.9,0.71331,0.68049,0.1677,-558.77,-0.16113,-0.073639,0.98418,369.37 > view matrix models > #5,0.6549,-0.75534,0.023812,1214,0.73279,0.64243,0.22427,-587,-0.1847,-0.12943,0.97424,489.07 > view matrix models > #5,0.6549,-0.75534,0.023812,1203.7,0.73279,0.64243,0.22427,-598.15,-0.1847,-0.12943,0.97424,489.68 > fitmap #5 inMap #2 Fit molecule 7n9f.cif (#5) to map emd_24258.map (#2) using 212962 atoms average map value = 2862, steps = 92 shifted from previous position = 25.7 rotated from previous position = 13.2 degrees atoms outside contour = 35069, contour level = 2391.2 Position of 7n9f.cif (#5) relative to emd_24258.map (#2) coordinates: Matrix rotation and translation 0.70751221 -0.70670073 -0.00074287 1078.16466692 0.70669984 0.70750854 0.00264523 -449.54964958 -0.00134380 -0.00239652 0.99999622 6.55126791 Axis -0.00356708 0.00042516 0.99999355 Axis point 1082.18964062 1077.74952127 0.00000000 Rotation angle (degrees) 44.96744127 Shift along axis 2.51419243 > select subtract #5 Nothing selected > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Crm1_Heatmap_ChimeraX_DRAFT_v1.cxs > show #!1 models > volume #1 level 529.9 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > fitmap #5 inMap #1 Fit molecule 7n9f.cif (#5) to map emd_44377.map (#1) using 212962 atoms average map value = 555, steps = 48 shifted from previous position = 8.24 rotated from previous position = 1.61 degrees atoms outside contour = 57642, contour level = 529.93 Position of 7n9f.cif (#5) relative to emd_44377.map (#1) coordinates: Matrix rotation and translation 0.70601190 -0.70800128 -0.01677437 1128.99189637 0.70819672 0.70573878 0.01975280 -426.28067637 -0.00214668 -0.02582527 0.99966416 90.80002114 Axis -0.03216504 -0.01032295 0.99942926 Axis point 1078.64961737 1149.39643329 0.00000000 Rotation angle (degrees) 45.11327599 Shift along axis 58.83460409 > fitmap #4 inMap #1 Fit molecule 7n9f.cif (#4) to map emd_44377.map (#1) using 212962 atoms average map value = 557, steps = 44 shifted from previous position = 8.28 rotated from previous position = 1.55 degrees atoms outside contour = 56392, contour level = 529.93 Position of 7n9f.cif (#4) relative to emd_44377.map (#1) coordinates: Matrix rotation and translation 0.99999764 -0.00210404 0.00054134 35.38651442 0.00208974 0.99968092 0.02517320 20.23063752 -0.00059413 -0.02517201 0.99968296 88.18196735 Axis -0.99629685 0.02247002 0.08299207 Axis point -0.00000000 3603.64127489 -782.51170502 Rotation angle (degrees) 1.44779880 Shift along axis -27.48248616 > fitmap #3 inMap #1 Fit molecule 7n9f.cif (#3) to map emd_44377.map (#1) using 212962 atoms average map value = 555, steps = 44 shifted from previous position = 8.22 rotated from previous position = 1.62 degrees atoms outside contour = 57697, contour level = 529.93 Position of 7n9f.cif (#3) relative to emd_44377.map (#1) coordinates: Matrix rotation and translation 0.70801949 0.70591856 0.01968205 -426.37738416 -0.70619045 0.70781533 0.01710297 1111.05761122 -0.00185795 -0.02600852 0.99966000 90.81758167 Axis -0.03051210 0.01524491 -0.99941813 Axis point 1130.21428920 1074.10914627 0.00000000 Rotation angle (degrees) 44.94806750 Shift along axis -60.81709851 > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Crm1_Heatmap_ChimeraX_DRAFT_v1b_fitin2024map.cxs > hide #!2 models > select add #1 2 models selected > select add #3 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 4 models selected > select add #4 425924 atoms, 433552 bonds, 520 pseudobonds, 54142 residues, 6 models selected > select add #5 638886 atoms, 650328 bonds, 780 pseudobonds, 81213 residues, 8 models selected Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic models, 1 maps. > select subtract #5 425924 atoms, 433552 bonds, 520 pseudobonds, 54142 residues, 6 models selected > select subtract #4 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 4 models selected > color zone #1 near sel & #3 distance 60 > select subtract #3 2 models selected > select add #4 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 4 models selected > color zone #1 near sel & #4 distance 60 > select subtract #4 2 models selected > select add #5 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 4 models selected > color zone #1 near sel & #5 distance 60 > color zone #1 near #3-5 distance 60 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > set bgColor white > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Crm1_Heatmap_ChimeraX_DRAFT_v2b_fitin2024map.cxs ——— End of log from Wed Nov 20 13:43:19 2024 ——— opened ChimeraX session > color zone #1 near #3-5 distance 60 > set bgColor white > lighting full > lighting shadows false > graphics silhouettes true > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Crm1_Heatmap_ChimeraX_DRAFT_v3b_fitin2024map.cxs ——— End of log from Wed Nov 20 13:53:26 2024 ——— opened ChimeraX session > color zone #1 near #3-5 distance 60 > lighting full > lighting shadows false > graphics silhouettes false > graphics silhouettes true > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Crm1_Heatmap_ChimeraX_DRAFT_v4b_fitin2024map.cxs > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/PDB-DEV/9a8m.cif format ihm Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive- rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/PDB-DEV/9a8m.cif --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 80815 messages similar to the above omitted No mmCIF models found. notes | aligned Y-dimer-modified-aligned.pdb H, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 Entities and chains for 9a8m --- Entity | Chains Nucleoporin NUP1 | C Nucleoporin NUP120 | H, I Nucleoporin NUP133 | U, V Nucleoporin NUP145C | M, N Nucleoporin NUP2 | D, E Nucleoporin NUP60 | F, G Nucleoporin NUP84 | S, T Nucleoporin NUP85 | J, L, K Nucleoporin SEH1 | Q, R Protein transport protein SEC13 | O, P Unknown MLP Protein | A, B Opened Yeast_1_BR_v4_center_ng80.mrc 3D electron microscopy as #6.2.2, grid size 172,172,172, pixel 10, shown at level 5.46e-11, step 1, values float32 Opened LPD_mlp1-mlp2.mrc as #6.3.1.2.1, grid size 71,63,91, pixel 10, shown at level 0.016, step 1, values float32 Opened LPD_mlp1-mlp2.mrc as #6.3.1.2.2, grid size 71,63,91, pixel 10, shown at level 0.016, step 1, values float32 Opened LPD_nup1.mrc as #6.3.1.2.3, grid size 101,86,63, pixel 10, shown at level 0.000497, step 1, values float32 Opened LPD_nup2.0.mrc as #6.3.1.2.4, grid size 66,57,60, pixel 10, shown at level 0.000433, step 1, values float32 Opened LPD_nup2.0.mrc as #6.3.1.2.5, grid size 66,57,60, pixel 10, shown at level 0.000433, step 1, values float32 Opened LPD_nup60.0.mrc as #6.3.1.2.6, grid size 79,60,62, pixel 10, shown at level 0.00321, step 1, values float32 Opened LPD_nup60.1.mrc as #6.3.1.2.7, grid size 79,61,63, pixel 10, shown at level 0.00323, step 1, values float32 Opened IHM file /Users/chris/Library/CloudStorage/OneDrive- rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/PDB-DEV/9a8m.cif 15 xray and nmr models 2459 DSS crosslinks 1 electron microscopy images 2 sphere models 7 localization maps > select subtract #5 Nothing selected > select add #6 104595 atoms, 80783 bonds, 30073 pseudobonds, 35235 residues, 73 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,1921.6,0,1,0,1191.3,0,0,1,833.31 > view matrix models > #6,-0.31949,-0.94677,0.039494,2342.3,0.83056,-0.29985,-0.46932,1636.5,0.45618,-0.11714,0.88214,855.33 > view matrix models > #6,0.15176,0.053614,0.98696,2288.4,0.9788,-0.1471,-0.14252,1709.2,0.13755,0.98767,-0.074802,-94.311 > view matrix models > #6,-0.80908,-0.13988,0.57081,2167.7,0.55402,0.14255,0.82021,1984.3,-0.1961,0.97985,-0.037842,-84.193 > view matrix models > #6,-0.80908,-0.13988,0.57081,2237.4,0.55402,0.14255,0.82021,2018.8,-0.1961,0.97985,-0.037842,-269.58 > select subtract #6.1 25468 atoms, 30034 pseudobonds, 25468 residues, 29 models selected > select subtract #6.2 25468 atoms, 30034 pseudobonds, 25468 residues, 25 models selected > hide #!6.2 models > hide #!6.1 models > show #!6.2 models > hide #!6.2 models > view matrix models > #6,-0.39717,0.8723,-0.28521,1430.9,0.57544,0.4788,0.66304,1794.2,0.71493,0.099223,-0.69212,-44.795 > hide #!6.3.1 models > show #!6.3.1 models > hide #!6.3 models > show #!6.3 models > show #!6.1 models > hide #!6.1 models > hide #!6.1.1-15 target m > hide #!6.2 target m > hide #6.2.1#!6.2.2 target m > hide #6.2.1 models > show #!6.2.2 models > hide #6.2.2.1 models > hide #!6.2.2 models > view matrix models > #6,-0.097823,0.97468,-0.20106,1415.7,-0.3054,0.16288,0.93819,2034.7,0.94719,0.15318,0.28173,286.74 > view matrix models > #6,-0.19288,-0.87668,-0.44072,2233.3,-0.35994,-0.35463,0.86295,2259.5,-0.91282,0.32508,-0.24715,-43.668 > view matrix models > #6,-0.43835,-0.74796,-0.4984,2152.9,-0.42707,-0.31459,0.84773,2235.1,-0.79086,0.58446,-0.18153,-165.03 > view matrix models > #6,0.9721,0.23267,0.02965,1810.9,-0.015506,-0.062385,0.99793,2151.8,0.23404,-0.97055,-0.057036,688 > view matrix models > #6,0.33029,-0.89857,-0.28894,2276,-0.21307,-0.36919,0.9046,2275,-0.91952,-0.23721,-0.3134,189.85 > view matrix models > #6,-0.84711,0.021647,-0.53097,1742.5,-0.53052,-0.092235,0.84264,2118,-0.030734,0.9955,0.089618,-287.48 > hide #6.3.1.1.1 models > hide #!6.3.1.1 models > show #!6.3.1.1 models > hide #!6.3.1.1 models > show #!6.3.1.1 models > show #6.3.1.1.1 models > hide #6.3.1.1.1 models > view matrix models > #6,-0.053452,-0.91329,-0.40379,2261.9,-0.32126,-0.36714,0.87293,2268.2,-0.94548,0.17638,-0.27378,-0.22578 > view matrix models > #6,-0.053452,-0.91329,-0.40379,2244.2,-0.32126,-0.36714,0.87293,2269.8,-0.94548,0.17638,-0.27378,442.96 > hide #!6.3.1.2 models > view matrix models > #6,-0.053452,-0.91329,-0.40379,2136.5,-0.32126,-0.36714,0.87293,2235.8,-0.94548,0.17638,-0.27378,188.93 > view matrix models > #6,0.9312,0.19215,-0.30974,1590.7,-0.19123,-0.46588,-0.86393,1575.7,-0.31031,0.86373,-0.39709,-224.93 > view matrix models > #6,0.72913,0.38789,-0.56383,1406.3,0.53461,-0.83719,0.1154,2106.7,-0.42727,-0.38557,-0.81779,208.91 > view matrix models > #6,-0.91506,0.091117,0.3929,2026.3,0.085018,-0.90868,0.40874,2284.5,0.39426,0.40742,0.82375,445.24 > view matrix models > #6,-0.91506,0.091117,0.3929,1277.3,0.085018,-0.90868,0.40874,2166.7,0.39426,0.40742,0.82375,780.14 > view matrix models > #6,0.79419,0.41151,-0.44712,689.31,-0.44008,0.89689,0.043784,1186.8,0.41903,0.16199,0.8934,924.04 > view matrix models > #6,-0.084311,0.22645,0.97037,1398.5,-0.47155,0.84882,-0.23906,1097.5,-0.8778,-0.47773,0.03522,956.99 > view matrix models > #6,0.76203,0.38958,-0.51724,673.34,-0.42833,0.90232,0.048573,1185.5,0.48564,0.18454,0.85446,893.82 > view matrix models > #6,0.8634,0.47406,-0.17263,766.13,-0.47842,0.87794,0.01814,1187.7,0.16016,0.066928,0.98482,1020.9 > view matrix models > #6,0.8634,0.47406,-0.17263,882.92,-0.47842,0.87794,0.01814,1182.4,0.16016,0.066928,0.98482,1109.9 > view matrix models > #6,0.8634,0.47406,-0.17263,786.34,-0.47842,0.87794,0.01814,1193.9,0.16016,0.066928,0.98482,1099.4 > view matrix models > #6,0.8634,0.47406,-0.17263,814.32,-0.47842,0.87794,0.01814,1188.1,0.16016,0.066928,0.98482,1080.3 > ui tool show ""Fit in Map"" > view matrix models > #6,0.8634,0.47406,-0.17263,832.8,-0.47842,0.87794,0.01814,1185.3,0.16016,0.066928,0.98482,1077.6 > view matrix models > #6,0.90465,0.27065,-0.32917,864.56,-0.29404,0.95553,-0.02243,1121.5,0.30846,0.11708,0.944,1028.8 > view matrix models > #6,0.92309,0.31931,-0.21434,886.55,-0.32893,0.9443,-0.0098596,1133.9,0.19925,0.079604,0.97671,1066.1 > view matrix models > #6,0.93717,0.12769,-0.32467,932.83,-0.15052,0.98753,-0.04609,1088.6,0.31473,0.092064,0.9447,1040.7 > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Crm1_Heatmap_ChimeraX_DRAFT_v5b_fitin2024map.cxs ——— End of log from Wed Nov 20 14:01:59 2024 ——— opened ChimeraX session > close session > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/PDB-DEV/9a8n.cif format ihm Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive- rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/PDB-DEV/9a8n.cif --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 603451 messages similar to the above omitted No mmCIF models found. notes | aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb D, 274 residues, rms 1.348 aligned Y-dimer-modified-aligned.pdb O, 274 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb E, 307 residues, rms 1.357 aligned Y-dimer-modified-aligned.pdb P, 307 residues, rms 1.368 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb F, 649 residues, rms 1.344 aligned Y-dimer-modified-aligned.pdb Q, 649 residues, rms 1.342 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb G, 1062 residues, rms 1.337 aligned Y-dimer-modified-aligned.pdb R, 1030 residues, rms 1.339 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb A, 1006 residues, rms 1.382 aligned Y-dimer-modified-aligned.pdb L, 1006 residues, rms 1.379 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb B, 675 residues, rms 1.353 aligned Y-dimer-modified-aligned.pdb M, 670 residues, rms 1.359 aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 aligned Y-dimer-modified-aligned.pdb N, 594 residues, rms 1.316 aligned Y-dimer-modified-aligned.pdb C, 594 residues, rms 1.346 Entities and chains for 9a8n --- Entity | Chains Nucleoporin NUP1 | Q, X, R, S, T, U, V, W Nucleoporin NUP120 | BE, BT, BS, BH, BG, BF, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR Nucleoporin NUP133 | EW, FL, FK, EZ, EY, EX, FA, FB, FC, FD, FE, FF, FG, FH, FI, FJ Nucleoporin NUP145C | CK, CZ, CY, CN, CM, CL, CO, CP, CQ, CR, CS, CT, CU, CV, CW, CX Nucleoporin NUP2 | Y, AN, AM, AB, AA, Z, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL Nucleoporin NUP60 | AO, BD, BC, AR, AQ, AP, AS, AT, AU, AV, AW, AX, AY, AZ, BA, BB Nucleoporin NUP84 | EG, EV, EU, EJ, EI, EH, EK, EL, EM, EN, EO, EP, EQ, ER, ES, ET Nucleoporin NUP85 | BU, CJ, CI, BX, BW, BV, BY, BZ, CA, CB, CC, CD, CE, CF, CG, CH Nucleoporin SEH1 | DQ, EF, EE, DT, DS, DR, DU, DV, DW, DX, DY, DZ, EA, EB, EC, ED Protein transport protein SEC13 | DA, DB, DC, DD, DE, DF, DG, DH, DI, DJ, DK, DL, DM, DN, DO, DP Unknown MLP Protein | A, P, O, D, C, B, E, F, G, H, I, J, K, L, M, N Opened Yeast_Final_Double_center.mrc 3D electron microscopy as #1.2.2, grid size 224,224,224, pixel 10, shown at level 599, step 1, values float32 Opened LPD_mlp1-mlp2_C8_0.mrc as #1.3.2.1, grid size 71,63,91, pixel 10, shown at level 0.016, step 1, values float32 Opened LPD_mlp1-mlp2_C8_0.mrc as #1.3.2.2, grid size 71,63,91, pixel 10, shown at level 0.016, step 1, values float32 Opened LPD_mlp1-mlp2_C8_1.mrc as #1.3.2.3, grid size 71,63,91, pixel 10, shown at level 0.0155, step 1, values float32 Opened LPD_mlp1-mlp2_C8_1.mrc as #1.3.2.4, grid size 71,63,91, pixel 10, shown at level 0.0155, step 1, values float32 Opened LPD_mlp1-mlp2_C8_2.mrc as #1.3.2.5, grid size 71,63,91, pixel 10, shown at level 0.0156, step 1, values float32 Opened LPD_mlp1-mlp2_C8_2.mrc as #1.3.2.6, grid size 71,63,91, pixel 10, shown at level 0.0156, step 1, values float32 Opened LPD_mlp1-mlp2_C8_3.mrc as #1.3.2.7, grid size 71,63,91, pixel 10, shown at level 0.0154, step 1, values float32 Opened LPD_mlp1-mlp2_C8_3.mrc as #1.3.2.8, grid size 71,63,91, pixel 10, shown at level 0.0154, step 1, values float32 Opened LPD_mlp1-mlp2_C8_4.mrc as #1.3.2.9, grid size 71,63,91, pixel 10, shown at level 0.0156, step 1, values float32 Opened LPD_mlp1-mlp2_C8_4.mrc as #1.3.2.10, grid size 71,63,91, pixel 10, shown at level 0.0156, step 1, values float32 Opened LPD_mlp1-mlp2_C8_5.mrc as #1.3.2.11, grid size 71,63,91, pixel 10, shown at level 0.0155, step 1, values float32 Opened LPD_mlp1-mlp2_C8_5.mrc as #1.3.2.12, grid size 71,63,91, pixel 10, shown at level 0.0155, step 1, values float32 Opened LPD_mlp1-mlp2_C8_6.mrc as #1.3.2.13, grid size 71,63,91, pixel 10, shown at level 0.0156, step 1, values float32 Opened LPD_mlp1-mlp2_C8_6.mrc as #1.3.2.14, grid size 71,63,91, pixel 10, shown at level 0.0156, step 1, values float32 Opened LPD_mlp1-mlp2_C8_7.mrc as #1.3.2.15, grid size 71,63,91, pixel 10, shown at level 0.0154, step 1, values float32 Opened LPD_mlp1-mlp2_C8_7.mrc as #1.3.2.16, grid size 71,63,91, pixel 10, shown at level 0.0154, step 1, values float32 Opened LPD_nup1_C8_0.mrc as #1.3.2.17, grid size 101,86,63, pixel 10, shown at level 0.000497, step 1, values float32 Opened LPD_nup1_C8_1.mrc as #1.3.2.18, grid size 101,86,63, pixel 10, shown at level 0.00049, step 1, values float32 Opened LPD_nup1_C8_2.mrc as #1.3.2.19, grid size 101,86,63, pixel 10, shown at level 0.000489, step 1, values float32 Opened LPD_nup1_C8_3.mrc as #1.3.2.20, grid size 101,86,63, pixel 10, shown at level 0.00049, step 1, values float32 Opened LPD_nup1_C8_4.mrc as #1.3.2.21, grid size 101,86,63, pixel 10, shown at level 0.000488, step 1, values float32 Opened LPD_nup1_C8_5.mrc as #1.3.2.22, grid size 101,86,63, pixel 10, shown at level 0.00049, step 1, values float32 Opened LPD_nup1_C8_6.mrc as #1.3.2.23, grid size 101,86,63, pixel 10, shown at level 0.00049, step 1, values float32 Opened LPD_nup1_C8_7.mrc as #1.3.2.24, grid size 101,86,63, pixel 10, shown at level 0.000489, step 1, values float32 Opened LPD_nup2.0_C8_0.mrc as #1.3.2.25, grid size 66,57,60, pixel 10, shown at level 0.000433, step 1, values float32 Opened LPD_nup2.1_C8_0.mrc as #1.3.2.26, grid size 62,60,64, pixel 10, shown at level 0.00044, step 1, values float32 Opened LPD_nup2.0_C8_1.mrc as #1.3.2.27, grid size 66,57,60, pixel 10, shown at level 0.000419, step 1, values float32 Opened LPD_nup2.1_C8_1.mrc as #1.3.2.28, grid size 62,60,64, pixel 10, shown at level 0.000429, step 1, values float32 Opened LPD_nup2.0_C8_2.mrc as #1.3.2.29, grid size 66,57,60, pixel 10, shown at level 0.000417, step 1, values float32 Opened LPD_nup2.1_C8_2.mrc as #1.3.2.30, grid size 62,60,64, pixel 10, shown at level 0.000426, step 1, values float32 Opened LPD_nup2.0_C8_3.mrc as #1.3.2.31, grid size 66,57,60, pixel 10, shown at level 0.000418, step 1, values float32 Opened LPD_nup2.1_C8_3.mrc as #1.3.2.32, grid size 62,60,64, pixel 10, shown at level 0.000432, step 1, values float32 Opened LPD_nup2.0_C8_4.mrc as #1.3.2.33, grid size 66,57,60, pixel 10, shown at level 0.000424, step 1, values float32 Opened LPD_nup2.1_C8_4.mrc as #1.3.2.34, grid size 62,60,64, pixel 10, shown at level 0.000433, step 1, values float32 Opened LPD_nup2.0_C8_5.mrc as #1.3.2.35, grid size 66,57,60, pixel 10, shown at level 0.000421, step 1, values float32 Opened LPD_nup2.1_C8_5.mrc as #1.3.2.36, grid size 62,60,64, pixel 10, shown at level 0.000429, step 1, values float32 Opened LPD_nup2.0_C8_6.mrc as #1.3.2.37, grid size 66,57,60, pixel 10, shown at level 0.000417, step 1, values float32 Opened LPD_nup2.1_C8_6.mrc as #1.3.2.38, grid size 62,60,64, pixel 10, shown at level 0.000426, step 1, values float32 Opened LPD_nup2.0_C8_7.mrc as #1.3.2.39, grid size 66,57,60, pixel 10, shown at level 0.000422, step 1, values float32 Opened LPD_nup2.1_C8_7.mrc as #1.3.2.40, grid size 62,60,64, pixel 10, shown at level 0.000429, step 1, values float32 Opened LPD_nup60.0_C8_0.mrc as #1.3.2.41, grid size 79,60,62, pixel 10, shown at level 0.00321, step 1, values float32 Opened LPD_nup60.1_C8_0.mrc as #1.3.2.42, grid size 79,61,63, pixel 10, shown at level 0.00323, step 1, values float32 Opened LPD_nup60.0_C8_1.mrc as #1.3.2.43, grid size 79,60,62, pixel 10, shown at level 0.00316, step 1, values float32 Opened LPD_nup60.1_C8_1.mrc as #1.3.2.44, grid size 79,61,63, pixel 10, shown at level 0.00318, step 1, values float32 Opened LPD_nup60.0_C8_2.mrc as #1.3.2.45, grid size 79,60,62, pixel 10, shown at level 0.00314, step 1, values float32 Opened LPD_nup60.1_C8_2.mrc as #1.3.2.46, grid size 79,61,63, pixel 10, shown at level 0.00317, step 1, values float32 Opened LPD_nup60.0_C8_3.mrc as #1.3.2.47, grid size 79,60,62, pixel 10, shown at level 0.00315, step 1, values float32 Opened LPD_nup60.1_C8_3.mrc as #1.3.2.48, grid size 79,61,63, pixel 10, shown at level 0.00317, step 1, values float32 Opened LPD_nup60.0_C8_4.mrc as #1.3.2.49, grid size 79,60,62, pixel 10, shown at level 0.00314, step 1, values float32 Opened LPD_nup60.1_C8_4.mrc as #1.3.2.50, grid size 79,61,63, pixel 10, shown at level 0.00317, step 1, values float32 Opened LPD_nup60.0_C8_5.mrc as #1.3.2.51, grid size 79,60,62, pixel 10, shown at level 0.00315, step 1, values float32 Opened LPD_nup60.1_C8_5.mrc as #1.3.2.52, grid size 79,61,63, pixel 10, shown at level 0.00319, step 1, values float32 Opened LPD_nup60.0_C8_6.mrc as #1.3.2.53, grid size 79,60,62, pixel 10, shown at level 0.00313, step 1, values float32 Opened LPD_nup60.1_C8_6.mrc as #1.3.2.54, grid size 79,61,63, pixel 10, shown at level 0.00317, step 1, values float32 Opened LPD_nup60.0_C8_7.mrc as #1.3.2.55, grid size 79,60,62, pixel 10, shown at level 0.00314, step 1, values float32 Opened LPD_nup60.1_C8_7.mrc as #1.3.2.56, grid size 79,61,63, pixel 10, shown at level 0.0032, step 1, values float32 Opened IHM file /Users/chris/Library/CloudStorage/OneDrive- rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/PDB-DEV/9a8n.cif 112 xray and nmr models 12843 DSS crosslinks 1 electron microscopy images 1 sphere models 56 localization maps > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_24258.map Opened emd_24258.map as #2, grid size 320,320,320, pixel 6.74, shown at level 2.39e+03, step 2, values float32 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-1201.3,0,1,0,-723.28,0,0,1,-1065.5 > volume #1.2.2 level 595.4 > volume #1.2.2 level 575.1 > volume #1.2.2 level 560.4 > view matrix models #2,1,0,0,-1105.7,0,1,0,-1084.9,0,0,1,-1097.4 > view matrix models #2,1,0,0,-1078.3,0,1,0,-1096,0,0,1,-1097.5 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1.2.2 Fit map emd_24258.map in map Yeast_Final_Double_center.mrc 3D electron microscopy using 40960 points correlation = 0.9865, correlation about mean = 0.07074, overlap = 6.416e+10 steps = 64, shift = 36.1, angle = 1.11 degrees Position of emd_24258.map (#2) relative to Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) coordinates: Matrix rotation and translation 0.99981163 -0.01940899 0.00002041 -1052.26031032 0.01940899 0.99981163 0.00001888 -1094.13015589 -0.00002077 -0.00001848 1.00000000 -1069.75511552 Axis -0.00096222 0.00106087 0.99999897 Axis point 55781.90725988 -54809.52336780 0.00000000 Rotation angle (degrees) 1.11212425 Shift along axis -1069.90224301 > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f.cif 7n9f.cif title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f.cif #3 --- Chain | Description | UniProt 0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502 1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391 5 6 | orphans bound to Nup192 NTD | A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823 B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541 C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472 M O | Nucleoporin NUP192 | NU192_YEAST 1-1683 N P | Nucleoporin NUP188 | NU188_YEAST 1-1655 Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839 U W | Nucleoporin NUP53 | NUP53_YEAST 1-475 V X | Nucleoporin ASM4 | NUP59_YEAST 1-528 a h | Nucleoporin NUP120 | NU120_YEAST 1-1037 b i | Nucleoporin NUP85 | NUP85_YEAST 1-744 c j | Nucleoporin 145c | NU145_YEAST 0-797 d k | Protein transport protein SEC13 | SEC13_YEAST 1-297 e l | Nucleoporin SEH1 | SEH1_YEAST 1-349 f m | Nucleoporin NUP84 | NUP84_YEAST 1-726 g n | Nucleoporin NUP133 | NU133_YEAST 1-1157 o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92 u v | Nucleoporin NUP82 | NUP82_YEAST 1-713 w x | Nucleoporin NUP159 | NU159_YEAST 1-1460 7n9f.cif mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f.cif 7n9f.cif title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f.cif #4 --- Chain | Description | UniProt 0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502 1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391 5 6 | orphans bound to Nup192 NTD | A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823 B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541 C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472 M O | Nucleoporin NUP192 | NU192_YEAST 1-1683 N P | Nucleoporin NUP188 | NU188_YEAST 1-1655 Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839 U W | Nucleoporin NUP53 | NUP53_YEAST 1-475 V X | Nucleoporin ASM4 | NUP59_YEAST 1-528 a h | Nucleoporin NUP120 | NU120_YEAST 1-1037 b i | Nucleoporin NUP85 | NUP85_YEAST 1-744 c j | Nucleoporin 145c | NU145_YEAST 0-797 d k | Protein transport protein SEC13 | SEC13_YEAST 1-297 e l | Nucleoporin SEH1 | SEH1_YEAST 1-349 f m | Nucleoporin NUP84 | NUP84_YEAST 1-726 g n | Nucleoporin NUP133 | NU133_YEAST 1-1157 o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92 u v | Nucleoporin NUP82 | NUP82_YEAST 1-713 w x | Nucleoporin NUP159 | NU159_YEAST 1-1460 7n9f.cif mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f.cif 7n9f.cif title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f.cif #5 --- Chain | Description | UniProt 0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502 1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391 5 6 | orphans bound to Nup192 NTD | A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823 B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541 C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472 M O | Nucleoporin NUP192 | NU192_YEAST 1-1683 N P | Nucleoporin NUP188 | NU188_YEAST 1-1655 Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839 U W | Nucleoporin NUP53 | NUP53_YEAST 1-475 V X | Nucleoporin ASM4 | NUP59_YEAST 1-528 a h | Nucleoporin NUP120 | NU120_YEAST 1-1037 b i | Nucleoporin NUP85 | NUP85_YEAST 1-744 c j | Nucleoporin 145c | NU145_YEAST 0-797 d k | Protein transport protein SEC13 | SEC13_YEAST 1-297 e l | Nucleoporin SEH1 | SEH1_YEAST 1-349 f m | Nucleoporin NUP84 | NUP84_YEAST 1-726 g n | Nucleoporin NUP133 | NU133_YEAST 1-1157 o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92 u v | Nucleoporin NUP82 | NUP82_YEAST 1-713 w x | Nucleoporin NUP159 | NU159_YEAST 1-1460 7n9f.cif mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > select subtract #2 Nothing selected > select add #3 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > view matrix models #3,1,0,0,-936.48,0,1,0,-1205.6,0,0,1,-147.05 > view matrix models #3,1,0,0,-852.13,0,1,0,-1614.1,0,0,1,-784.58 > view matrix models #3,1,0,0,-1089,0,1,0,-980.67,0,0,1,-970.5 > view matrix models #3,1,0,0,-1085.6,0,1,0,-1020.3,0,0,1,-1119.7 > view matrix models #3,1,0,0,-1098.2,0,1,0,-1010,0,0,1,-1066.2 > hide #!1 models > view matrix models #3,1,0,0,-1097.7,0,1,0,-1045.3,0,0,1,-1067.1 > fitmap #3 inMap #1.2.2 Fit molecule 7n9f.cif (#3) to map Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) using 212962 atoms average map value = 555.6, steps = 72 shifted from previous position = 24.6 rotated from previous position = 2.01 degrees atoms outside contour = 81017, contour level = 560.37 Position of 7n9f.cif (#3) relative to Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) coordinates: Matrix rotation and translation 0.99993624 -0.01090030 0.00294899 -1069.61423952 0.01079652 0.99939122 0.03317562 -1111.88056062 -0.00330882 -0.03314167 0.99944519 -1014.65586556 Axis -0.94662752 0.08932526 0.30970524 Axis point 0.00000000 -36789.71522458 34452.59359448 Rotation angle (degrees) 2.00737799 Shift along axis 598.96301937 > show #!1 models > fitmap #3 inMap #1.2.2 Fit molecule 7n9f.cif (#3) to map Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) using 212962 atoms average map value = 555.6, steps = 48 shifted from previous position = 0.0105 rotated from previous position = 0.0066 degrees atoms outside contour = 81016, contour level = 560.37 Position of 7n9f.cif (#3) relative to Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) coordinates: Matrix rotation and translation 0.99993553 -0.01094715 0.00301619 -1069.62253899 0.01084139 0.99939341 0.03309489 -1111.83700330 -0.00337665 -0.03306006 0.99944766 -1014.70306828 Axis -0.94583481 0.09140018 0.31151647 Axis point 0.00000000 -36866.91962036 34560.09781096 Rotation angle (degrees) 2.00414093 Shift along axis 593.96741677 > hide #!1 models > select subtract #3 Nothing selected > select add #4 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > view matrix models #4,1,0,0,-1383,0,1,0,-1488,0,0,1,-358.03 > view matrix models #4,1,0,0,-1128.8,0,1,0,-1522.8,0,0,1,-925.63 > view matrix models #4,1,0,0,-1463,0,1,0,-1211.8,0,0,1,-943.38 > view matrix models > #4,0.79379,-0.60561,0.055993,-402.5,0.60645,0.79512,0.0026256,-1560.2,-0.046111,0.031873,0.99843,-939.62 > view matrix models > #4,0.63162,-0.77175,0.073901,-1.1599,0.77323,0.63401,0.012174,-1509.8,-0.056249,0.049454,0.99719,-953.54 > view matrix models > #4,0.63162,-0.77175,0.073901,148.21,0.77323,0.63401,0.012174,-1466.4,-0.056249,0.049454,0.99719,-960.81 > view matrix models > #4,0.63162,-0.77175,0.073901,69.759,0.77323,0.63401,0.012174,-1473.6,-0.056249,0.049454,0.99719,-958.31 > view matrix models > #4,0.63162,-0.77175,0.073901,85.452,0.77323,0.63401,0.012174,-1481.6,-0.056249,0.049454,0.99719,-1058.2 > view matrix models > #4,0.63162,-0.77175,0.073901,85.836,0.77323,0.63401,0.012174,-1484.5,-0.056249,0.049454,0.99719,-1081.1 > fitmap #4 inMap #1.2.2 Fit molecule 7n9f.cif (#4) to map Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) using 212962 atoms average map value = 553.4, steps = 80 shifted from previous position = 11.6 rotated from previous position = 7.59 degrees atoms outside contour = 83798, contour level = 560.37 Position of 7n9f.cif (#4) relative to Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) coordinates: Matrix rotation and translation 0.70061119 -0.71322896 -0.02117519 31.71296578 0.71352708 0.70008708 0.02751674 -1547.28240758 -0.00480126 -0.03438760 0.99939703 -1011.13181626 Axis -0.04334454 -0.01146479 0.99899440 Axis point 1851.15690808 -792.98004840 0.00000000 Rotation angle (degrees) 45.56917212 Shift along axis -993.75033209 > select subtract #4 Nothing selected > select add #5 212962 atoms, 216776 bonds, 260 pseudobonds, 27071 residues, 2 models selected > view matrix models #5,1,0,0,-1235.8,0,1,0,-1912.7,0,0,1,-289.62 > view matrix models > #5,0.37812,0.36444,-0.851,-148.16,0.40501,0.76149,0.50606,-2564.8,0.83246,-0.53602,0.14034,589.23 > view matrix models > #5,-0.88852,-0.019426,-0.45843,1338.7,0.34309,-0.69155,-0.63565,959.8,-0.30468,-0.72207,0.62112,1542.5 > view matrix models > #5,-0.11779,-0.64809,-0.7524,1781.4,0.86573,0.30413,-0.39751,-1354.6,0.48645,-0.69819,0.52525,766.44 > view matrix models > #5,-0.033017,-0.9364,-0.34938,1663.8,0.92172,0.10664,-0.37291,-1148.2,0.38645,-0.33434,0.85958,-47.036 > view matrix models > #5,-0.033017,-0.9364,-0.34938,1866.4,0.92172,0.10664,-0.37291,-772.48,0.38645,-0.33434,0.85958,-544.86 > view matrix models > #5,-0.31642,0.7663,-0.55916,-129.67,0.94391,0.31298,-0.10522,-1406.9,0.094377,-0.56109,-0.82236,2010.8 > view matrix models > #5,-0.2735,-0.54786,-0.7906,2044.9,0.93136,0.054538,-0.35999,-719.8,0.24034,-0.83479,0.49534,770.17 > view matrix models > #5,-0.2735,-0.54786,-0.7906,1517,0.93136,0.054538,-0.35999,-756.34,0.24034,-0.83479,0.49534,603.64 > view matrix models > #5,-0.090274,-0.68433,-0.72356,1447.9,0.91212,0.23488,-0.33595,-1031.7,0.39985,-0.69031,0.60299,95.253 > view matrix models > #5,-0.36974,-0.70161,-0.60913,1644,0.92327,-0.20387,-0.3256,-401.48,0.10426,-0.68278,0.72315,265.18 > view matrix models > #5,-0.36974,-0.70161,-0.60913,1785.3,0.92327,-0.20387,-0.3256,-319.55,0.10426,-0.68278,0.72315,130.04 > view matrix models > #5,-0.36974,-0.70161,-0.60913,1712.1,0.92327,-0.20387,-0.3256,-341.09,0.10426,-0.68278,0.72315,200.1 > view matrix models > #5,-0.36256,-0.84661,-0.38961,1671.9,0.91788,-0.252,-0.30657,-285.13,0.16137,-0.46877,0.86846,-344.64 > view matrix models > #5,-0.25045,-0.88196,-0.39927,1615.3,0.96601,-0.25495,-0.042779,-631.02,-0.064064,-0.39641,0.91584,-264.22 > view matrix models > #5,-0.31293,-0.93439,-0.17028,1501.2,0.9493,-0.30202,-0.087274,-492.57,0.03012,-0.18896,0.98152,-748.84 > view matrix models > #5,0.005153,-0.9882,-0.15308,1220.6,0.9809,0.034762,-0.19138,-910.54,0.19444,-0.14917,0.9695,-970.86 > fitmap #4 inMap #1.2.2 Fit molecule 7n9f.cif (#4) to map Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) using 212962 atoms average map value = 553.4, steps = 40 shifted from previous position = 0.0795 rotated from previous position = 0.00868 degrees atoms outside contour = 83846, contour level = 560.37 Position of 7n9f.cif (#4) relative to Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) coordinates: Matrix rotation and translation 0.70070438 -0.71313527 -0.02124718 31.58199529 0.71343600 0.70018048 0.02750181 -1547.37580376 -0.00473565 -0.03442914 0.99939591 -1011.10998669 Axis -0.04336870 -0.01156261 0.99899222 Axis point 1851.64615408 -793.25395170 0.00000000 Rotation angle (degrees) 45.56173083 Shift along axis -993.56898320 > view matrix models > #5,0.005153,-0.9882,-0.15308,1227.9,0.9809,0.034762,-0.19138,-893.22,0.19444,-0.14917,0.9695,-987.73 > view matrix models > #5,0.005153,-0.9882,-0.15308,1243.8,0.9809,0.034762,-0.19138,-874.81,0.19444,-0.14917,0.9695,-984.6 > view matrix models > #5,0.014566,-0.99405,-0.10797,1191.3,0.9968,0.022918,-0.076525,-1004.3,0.078544,-0.10651,0.9912,-948.38 > view matrix models > #5,0.014566,-0.99405,-0.10797,1175.3,0.9968,0.022918,-0.076525,-1045.2,0.078544,-0.10651,0.9912,-949.6 > view matrix models > #5,0.014566,-0.99405,-0.10797,1185.3,0.9968,0.022918,-0.076525,-1028.6,0.078544,-0.10651,0.9912,-947.16 > fitmap #4 inMap #1.2.2 Fit molecule 7n9f.cif (#4) to map Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) using 212962 atoms average map value = 553.4, steps = 40 shifted from previous position = 0.0117 rotated from previous position = 0.0121 degrees atoms outside contour = 83869, contour level = 560.37 Position of 7n9f.cif (#4) relative to Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) coordinates: Matrix rotation and translation 0.70082848 -0.71301112 -0.02132078 31.35338781 0.71331404 0.70030105 0.02759546 -1547.53149777 -0.00474490 -0.03454809 0.99939176 -1010.91739422 Axis -0.04352476 -0.01160959 0.99898489 Axis point 1852.14628284 -793.80069072 0.00000000 Rotation angle (degrees) 45.55207986 Shift along axis -993.28964666 > fitmap #4 inMap #2 Fit molecule 7n9f.cif (#4) to map emd_24258.map (#2) using 212962 atoms average map value = 2862, steps = 52 shifted from previous position = 8.49 rotated from previous position = 1.93 degrees atoms outside contour = 35069, contour level = 2391.2 Position of 7n9f.cif (#4) relative to emd_24258.map (#2) coordinates: Matrix rotation and translation 0.70756802 -0.70664469 -0.00087275 1078.15591157 0.70664410 0.70756414 0.00266486 -449.58900710 -0.00126558 -0.00250230 0.99999606 6.62116940 Axis -0.00365610 0.00027795 0.99999328 Axis point 1082.29345079 1077.86564240 0.00000000 Rotation angle (degrees) 44.96293081 Shift along axis 2.55431358 > fitmap #4 inMap #1.2.2 Fit molecule 7n9f.cif (#4) to map Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) using 212962 atoms average map value = 553.4, steps = 52 shifted from previous position = 8.47 rotated from previous position = 1.92 degrees atoms outside contour = 83865, contour level = 560.37 Position of 7n9f.cif (#4) relative to Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) coordinates: Matrix rotation and translation 0.70071787 -0.71312106 -0.02127930 31.59281420 0.71342302 0.70019464 0.02747813 -1547.38102054 -0.00469558 -0.03443556 0.99939588 -1011.13063362 Axis -0.04335743 -0.01161339 0.99899212 Axis point 1851.77284639 -793.25350921 0.00000000 Rotation angle (degrees) 45.56062324 Shift along axis -993.51098807 > fitmap #5 inMap #1.2.2 Fit molecule 7n9f.cif (#5) to map Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) using 212962 atoms average map value = 555.5, steps = 60 shifted from previous position = 39.7 rotated from previous position = 6.53 degrees atoms outside contour = 81046, contour level = 560.37 Position of 7n9f.cif (#5) relative to Yeast_Final_Double_center.mrc 3D electron microscopy (#1.2.2) coordinates: Matrix rotation and translation -0.01066503 -0.99940647 -0.03275672 1121.46752634 0.99993848 -0.01075924 0.00270072 -1069.62633600 -0.00305154 -0.03272590 0.99945972 -1015.52658935 Axis -0.01771437 -0.01485348 0.99973275 Axis point 1088.33856592 3.46877444 0.00000000 Rotation angle (degrees) 90.62925045 Shift along axis -1019.23361021 > hide #!2 models > show #!1 models > hide #!1.1#!1.1.1-112 target m > hide #1.2.1 target m > hide #!1.2 target m > hide #1.2.1 models > hide #!1.3.1 target m > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.3.2.1-16 target m > volume #1.2.2 level 475 > color zone #1 near #3-5 distance 60 > hide #!3 models > hide #!4 models > hide #!5 models > lighting flat > lighting full > lighting shadows false > graphics silhouettes false > graphics silhouettes true > ui tool show ""Side View"" > surface cap true [Repeated 1 time(s)] > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Version_3_DRAFTv6b.png > width 2841 height 2160 supersample 4 transparentBackground true > lighting flat > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Version_3_DRAFTv6b-flat.png > width 2841 height 2160 supersample 4 transparentBackground true > show #!5 models > show #!4 models > show #!3 models > transparency (#!5 & sel) 30 > select subtract #5 Nothing selected > transparency #3-5#1.2.2#1.3.2.17-56#!1#!1.2-3#!1.3.2 70 > hide #!3 models > hide #!4 models > hide #!5 models > save /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/ChimeraX_Sessions/2024_1120_Crm1_Heatmap_ChimeraX_DRAFT_v6b_fitin2024map.cxs > includeMaps true Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 273, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 310, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/state.py"", line 232, in copy_state return _copy(data) ^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/state.py"", line 230, in _copy return convert(data) ^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 309, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 281, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 154, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of IHMModel class in ChimeraX-IHM bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 922, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 646, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 277, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'LPD_mlp1-mlp2_C8_1.mrc' -> 'Localization map ensemble 1' -> 'Result models': Unable to restore objects of IHMModel class in ChimeraX-IHM bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'LPD_mlp1-mlp2_C8_1.mrc' -> 'Localization map ensemble 1' -> 'Result models': Unable to restore objects of IHMModel class in ChimeraX-IHM bundle because the class name is not listed in the name to class table for session restore File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 277, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 273, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 310, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/state.py"", line 232, in copy_state return _copy(data) ^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/state.py"", line 230, in _copy return convert(data) ^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 309, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 281, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 154, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of IHMModel class in ChimeraX-IHM bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 127, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 138, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 62, in display run(session, cmd) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 101, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core_formats/__init__.py"", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 922, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 646, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 277, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'LPD_mlp1-mlp2_C8_1.mrc' -> 'Localization map ensemble 1' -> 'Result models': Unable to restore objects of IHMModel class in ChimeraX-IHM bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'LPD_mlp1-mlp2_C8_1.mrc' -> 'Localization map ensemble 1' -> 'Result models': Unable to restore objects of IHMModel class in ChimeraX-IHM bundle because the class name is not listed in the name to class table for session restore File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 277, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 540.120.3~37 Software: System Software Overview: System Version: macOS 12.7.6 (21H1320) Kernel Version: Darwin 21.6.0 Time since boot: 26 days 20:50 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect assigned normal Sessions all ChimeraX