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Opened 12 months ago
Last modified 12 months ago
#16349 assigned defect
Session save: Unable to restore objects of IHMModel class in ChimeraX-IHM bundle
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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 <listcomp>
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' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x16c9315d0> ->
<chimerax.surface.colorzone.ZoneColor object at 0x16a133f90> ->
<chimerax.map.volume.VolumeSurface object at 0x17c502450> 'surface' ->
<chimerax.map.volume.Volume object at 0x17c502b90> 'LPD_mlp1-mlp2_C8_1.mrc' ->
<chimerax.core.models.Model object at 0x17c508390> 'Localization map ensemble
1' -> <chimerax.core.models.Model object at 0x17c531150> '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 <listcomp>
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>
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' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x16c9315d0> ->
<chimerax.surface.colorzone.ZoneColor object at 0x16a133f90> ->
<chimerax.map.volume.VolumeSurface object at 0x17c502450> 'surface' ->
<chimerax.map.volume.Volume object at 0x17c502b90> 'LPD_mlp1-mlp2_C8_1.mrc' ->
<chimerax.core.models.Model object at 0x17c508390> 'Localization map ensemble
1' -> <chimerax.core.models.Model object at 0x17c531150> '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
Change History (2)
comment:1 by , 12 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session save: Unable to restore objects of IHMModel class in ChimeraX-IHM bundle |
comment:2 by , 12 months ago
ChimeraX does not support session saving of IHM (PDBDev) models. The IHM specification is so complex and our effort to visualize those files never got any funding so we were not able to implement session saving. But the ChimeraX code is supposed to behave better and simply save the data in the scene that can be saved while omitting the rest. I will try to improve the code to do that with the IHM models. I'm not sure it is a better result, because you will later look at that session and see it is missing the IHM data.
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Reported by Chris Caffalette