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Opened 4 weeks ago
Closed 4 weeks ago
#19308 closed defect (duplicate)
Orthoplanes: 'NoneType' object has no attribute 'image_colors'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202509040038 (2025-09-04 00:38:56 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11.dev202509040038 (2025-09-04)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/Tetramer_goodmodel_01_05Nov25.cxs
> format session
Opened cryosparc_P1_J482_004_volume_map.mrc as #2, grid size 352,352,352,
pixel 0.846, shown at level 0.0906, step 2, values float32
Log from Wed Nov 5 23:47:55 2025UCSF ChimeraX version: 1.11.dev202509040038
(2025-09-04)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramer_02_withouttickoncopymaps.cxs
> format session
Opened cryosparc_P1_J482_004_volume_map.mrc as #2, grid size 352,352,352,
pixel 0.846, shown at level 0.0906, step 2, values float32
Log from Wed Nov 5 22:22:09 2025UCSF ChimeraX version: 1.11.dev202509040038
(2025-09-04)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/madhurikanavalli/Desktop/test/dimerfit_Kasia.cxs
Error opening map "/Users/madhurikanavalli/3u1k.cif": File 3u1k.cif, format
mrc
MRC header value nsymbt (1869770030) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Log from Fri Aug 30 15:18:41 2024 Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/madhurikanavalli/Downloads/cryosparc_P1_J138_004_volume_map
> (1).mrc" format mrc
No such file/path:
/Users/madhurikanavalli/Downloads/cryosparc_P1_J138_004_volume_map (1).mrc
> open "/Users/madhurikanavalli/Downloads/AF-Q8TCS8-F1-model_v4 (1).pdb"
AF-Q8TCS8-F1-model_v4 (1).pdb title:
Alphafold monomer V2.0 prediction for polyribonucleotide
nucleotidyltransferase 1, mitochondrial (Q8TCS8) [more info...]
Chain information for AF-Q8TCS8-F1-model_v4 (1).pdb #1
---
Chain | Description | UniProt
A | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 1-783
> open
> /Users/madhurikanavalli/Downloads/cryosparc_P1_J138_004_volume_map_sharp.mrc
Opened cryosparc_P1_J138_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.846, shown at level 0.062, step 2, values float32
> hide #1 models
> close #1
> volume #2 level 0.0941
> open /Users/madhurikanavalli/Desktop/ImageProcessing/5zf6.pdb
5zf6.pdb title:
Crystal structure of the dimeric human pnpase [more info...]
Chain information for 5zf6.pdb #1
---
Chain | Description | UniProt
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669
> transparency 50
> lighting soft
> lighting full
> lighting soft
> select add #2
2 models selected
> hide #!2 models
> show #!2 models
> select subtract #2
Nothing selected
> select add #1
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.56827,-0.43732,-0.69701,64.748,0.67429,0.73298,0.089865,-55.904,0.47159,-0.52106,0.7114,-23.186
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.56827,-0.43732,-0.69701,66.837,0.67429,0.73298,0.089865,-22.52,0.47159,-0.52106,0.7114,54.916
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.81909,0.51893,0.24453,138.84,-0.017183,-0.44828,0.89373,21.948,0.5734,0.72785,0.3761,42.804
> view matrix models
> #1,-0.69127,0.68715,0.22353,126.9,0.39929,0.10542,0.91074,-19.908,0.60225,0.71883,-0.34725,65.002
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #1,-0.69127,0.68715,0.22353,135.47,0.39929,0.10542,0.91074,90.055,0.60225,0.71883,-0.34725,57.169
> view matrix models
> #1,-0.69127,0.68715,0.22353,190.44,0.39929,0.10542,0.91074,101.05,0.60225,0.71883,-0.34725,59.234
> view matrix models
> #1,-0.69127,0.68715,0.22353,191.18,0.39929,0.10542,0.91074,83.012,0.60225,0.71883,-0.34725,60.929
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 196
shifted from previous position = 5.16
rotated from previous position = 14.4 degrees
atoms outside contour = 4870, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53017153 0.78333170 0.32451439 175.24914037
0.58899671 0.06493505 0.80552239 67.47116186
0.60991887 0.61820295 -0.49580651 64.01082743
Axis -0.47685384 -0.72654616 -0.49471314
Axis point 66.66011786 0.00000000 15.64936506
Rotation angle (degrees) 168.67279119
Shift along axis -164.25613670
> open /Users/madhurikanavalli/Downloads/5zf6.pdb
5zf6.pdb title:
Crystal structure of the dimeric human pnpase [more info...]
Chain information for 5zf6.pdb #3
---
Chain | Description | UniProt
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669
> select add #3
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> ui mousemode right "rotate selected models"
> select subtract #1
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.685,0.71791,0.124,127.29,-0.51455,-0.59723,0.61526,41.137,0.51576,0.35765,0.77851,-39.683
> view matrix models
> #3,-0.40337,0.91499,-0.0086238,106,0.40236,0.18583,0.89642,-54.028,0.82182,0.35812,-0.44312,-23.78
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.76019,0.5729,-0.30642,149.86,-0.04323,-0.51519,-0.85599,50.769,-0.64826,-0.63747,0.41641,81.316
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.76019,0.5729,-0.30642,192.58,-0.04323,-0.51519,-0.85599,144.15,-0.64826,-0.63747,0.41641,196.86
> view matrix models
> #3,-0.76019,0.5729,-0.30642,192.59,-0.04323,-0.51519,-0.85599,144.19,-0.64826,-0.63747,0.41641,196.87
> view matrix models
> #3,-0.76019,0.5729,-0.30642,209.85,-0.04323,-0.51519,-0.85599,187.07,-0.64826,-0.63747,0.41641,235.74
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.75983,0.62964,-0.16191,204.25,-0.13348,-0.39483,-0.90901,194.93,-0.63628,-0.66908,0.38404,236.22
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.75983,0.62964,-0.16191,211.78,-0.13348,-0.39483,-0.90901,195.69,-0.63628,-0.66908,0.38404,232.58
> select add #1
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> select subtract #1
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select add #2
8555 atoms, 8618 bonds, 1174 residues, 3 models selected
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 120
shifted from previous position = 0.0129
rotated from previous position = 0.00865 degrees
atoms outside contour = 4870, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53020886 0.78332789 0.32446259 175.25676778
0.58887934 0.06490056 0.80561097 67.48406251
0.60999974 0.61821139 -0.49569646 63.98889300
Axis -0.47682626 -0.72653104 -0.49476193
Axis point 66.66315130 -0.00000000 15.63552486
Rotation angle (degrees) 168.66721693
Shift along axis -164.25556328
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 1156
shifted from previous position = 0.0206
rotated from previous position = 0.00782 degrees
atoms outside contour = 4870, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53016613 0.78336587 0.32444072 175.24849006
0.58881022 0.06481730 0.80566819 67.49077469
0.61010360 0.61817200 -0.49561777 63.99770693
Axis -0.47684108 -0.72649898 -0.49479473
Axis point 66.65580950 0.00000000 15.63768479
Rotation angle (degrees) 168.66165391
Shift along axis -164.26338558
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1094, steps = 2000
shifted from previous position = 0.221
rotated from previous position = 0.156 degrees
atoms outside contour = 4865, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.52957137 0.78285031 0.32664898 175.11992042
0.59076847 0.06403733 0.80429586 67.16427833
0.60872554 0.61890598 -0.49639562 64.14667933
Axis -0.47735255 -0.72630697 -0.49458339
Axis point 66.63691808 0.00000000 15.73667756
Rotation angle (degrees) 168.80285345
Shift along axis -164.10170605
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 288
shifted from previous position = 0.225
rotated from previous position = 0.154 degrees
atoms outside contour = 4870, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53019581 0.78335894 0.32440896 175.25546840
0.58887005 0.06493539 0.80561496 67.48903760
0.61002006 0.61816840 -0.49572509 63.99117885
Axis -0.47682923 -0.72654156 -0.49474361
Axis point 66.66110864 0.00000000 15.63745351
Rotation angle (degrees) 168.66440970
Shift along axis -164.25974808
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 232
shifted from previous position = 0.00354
rotated from previous position = 0.00252 degrees
atoms outside contour = 4871, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53020339 0.78336172 0.32438985 175.25781259
0.58883600 0.06492688 0.80564053 67.48885321
0.61004634 0.61816576 -0.49569604 63.99054098
Axis -0.47682257 -0.72653754 -0.49475594
Axis point 66.66291520 -0.00000000 15.63787915
Rotation angle (degrees) 168.66252058
Shift along axis -164.25976573
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 256
shifted from previous position = 0.0121
rotated from previous position = 0.00748 degrees
atoms outside contour = 4870, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53021450 0.78340257 0.32427304 175.25068399
0.58880860 0.06502852 0.80565236 67.48701037
0.61006313 0.61810331 -0.49575323 63.99276039
Axis -0.47680987 -0.72657013 -0.49472032
Axis point 66.66124227 0.00000000 15.64470854
Rotation angle (degrees) 168.65766312
Shift along axis -164.25382012
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 592
shifted from previous position = 0.0158
rotated from previous position = 0.0135 degrees
atoms outside contour = 4866, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53013987 0.78336565 0.32448417 175.24674236
0.58888115 0.06482254 0.80561593 67.48555859
0.61005796 0.61817174 -0.49567428 64.00228754
Axis -0.47686010 -0.72650285 -0.49477071
Axis point 66.65490167 0.00000000 15.64048878
Rotation angle (degrees) 168.66529813
Shift along axis -164.26308627
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 424
shifted from previous position = 0.0048
rotated from previous position = 0.00415 degrees
atoms outside contour = 4866, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53018618 0.78335667 0.32443018 175.25208806
0.58883675 0.06487179 0.80564442 67.48445550
0.61006056 0.61817795 -0.49566332 63.99813793
Axis -0.47683273 -0.72651883 -0.49477363
Axis point 66.66006680 0.00000000 15.64100041
Rotation angle (degrees) 168.66327461
Shift along axis -164.25925025
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.11, steps = 2000
shifted from previous position = 0.0762
rotated from previous position = 0.165 degrees
atoms outside contour = 4884, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53048495 0.78362459 0.32329279 175.29799081
0.58666724 0.06409689 0.80728752 67.68716888
0.61188829 0.61791917 -0.49372931 63.80010561
Axis -0.47649839 -0.72617881 -0.49559421
Axis point 66.65973389 0.00000000 15.50596390
Rotation angle (degrees) 168.53856685
Shift along axis -164.30116055
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 2000
shifted from previous position = 0.0839
rotated from previous position = 0.144 degrees
atoms outside contour = 4865, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53008745 0.78332676 0.32466363 175.23978220
0.58861806 0.06432765 0.80584783 67.49400517
0.61035733 0.61827270 -0.49517956 63.99461111
Axis -0.47687716 -0.72632656 -0.49501302
Axis point 66.64699995 0.00000000 15.62216883
Rotation angle (degrees) 168.65768665
Shift along axis -164.26870487
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 644
shifted from previous position = 0.0503
rotated from previous position = 0.0463 degrees
atoms outside contour = 4866, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53018602 0.78335265 0.32444013 175.24810216
0.58896280 0.06498915 0.80554282 67.47147274
0.60993902 0.61817071 -0.49582191 64.00371416
Axis -0.47684122 -0.72656297 -0.49470061
Axis point 66.66109101 0.00000000 15.64899309
Rotation angle (degrees) 168.66926053
Shift along axis -164.25046913
> select subtract #2
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #3
Nothing selected
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 536
shifted from previous position = 0.00749
rotated from previous position = 0.0178 degrees
atoms outside contour = 4870, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53026340 0.78337387 0.32426241 175.26231884
0.58871526 0.06498576 0.80572402 67.49295778
0.61011070 0.61814418 -0.49564372 63.98242363
Axis -0.47678032 -0.72655381 -0.49477277
Axis point 66.66763886 0.00000000 15.63730709
Rotation angle (degrees) 168.65506434
Shift along axis -164.25565097
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 1228
shifted from previous position = 0.0152
rotated from previous position = 0.0139 degrees
atoms outside contour = 4868, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53017306 0.78334486 0.32448013 175.24906746
0.58880624 0.06477853 0.80567422 67.49336568
0.61010142 0.61820269 -0.49558217 63.99493089
Axis -0.47683947 -0.72648633 -0.49481484
Axis point 66.65525002 0.00000000 15.63335671
Rotation angle (degrees) 168.66312652
Shift along axis -164.26432228
> select add #3
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> view matrix models
> #3,-0.75983,0.62964,-0.16191,211.45,-0.13348,-0.39483,-0.90901,195.61,-0.63628,-0.66908,0.38404,229.67
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 1612
shifted from previous position = 0.00572
rotated from previous position = 0.00235 degrees
atoms outside contour = 4866, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53017195 0.78332985 0.32451818 175.25199022
0.58882446 0.06475693 0.80566264 67.48991761
0.61008479 0.61822398 -0.49557609 63.99297271
Axis -0.47684301 -0.72648001 -0.49482072
Axis point 66.65742493 0.00000000 15.63211166
Rotation angle (degrees) 168.66522554
Shift along axis -164.26281069
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 1316
shifted from previous position = 0.0116
rotated from previous position = 0.00894 degrees
atoms outside contour = 4869, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53019294 0.78333241 0.32447772 175.24972531
0.58889169 0.06488422 0.80560326 67.47923889
0.61000166 0.61820739 -0.49569910 63.99592466
Axis -0.47683532 -0.72652561 -0.49476117
Axis point 66.66002577 0.00000000 15.63982371
Rotation angle (degrees) 168.66766242
Shift along axis -164.25335202
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1099, steps = 2000
shifted from previous position = 0.176
rotated from previous position = 0.345 degrees
atoms outside contour = 4900, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53086010 0.78435805 0.32088940 175.35137069
0.58432492 0.06452559 0.80895045 67.89601905
0.61380122 0.61694319 -0.49257402 63.64064322
Axis -0.47605165 -0.72622856 -0.49595051
Axis point 66.67562044 0.00000000 15.44865974
Rotation angle (degrees) 168.36557671
Shift along axis -164.34694642
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 448
shifted from previous position = 0.18
rotated from previous position = 0.346 degrees
atoms outside contour = 4871, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53022396 0.78333692 0.32441613 175.25810721
0.58890184 0.06498377 0.80558781 67.48045204
0.60996489 0.61819122 -0.49576451 63.99022697
Axis -0.47681825 -0.72655995 -0.49472719
Axis point 66.66563091 0.00000000 15.63997000
Rotation angle (degrees) 168.66720688
Shift along axis -164.25256331
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 608
shifted from previous position = 0.00455
rotated from previous position = 0.00172 degrees
atoms outside contour = 4871, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53022740 0.78334400 0.32439340 175.25531311
0.58888033 0.06498821 0.80560318 67.48409621
0.60998267 0.61818178 -0.49575440 63.98898197
Axis -0.47681416 -0.72656058 -0.49473021
Axis point 66.66354227 0.00000000 15.63878071
Rotation angle (degrees) 168.66558797
Shift along axis -164.25278098
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 952
shifted from previous position = 0.0198
rotated from previous position = 0.0253 degrees
atoms outside contour = 4864, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53016383 0.78326739 0.32468217 175.24708520
0.58882646 0.06458350 0.80567510 67.48844552
0.61008992 0.61832125 -0.49544840 63.98628800
Axis -0.47685500 -0.72642282 -0.49489311
Axis point 66.65381088 0.00000000 15.62105041
Rotation angle (degrees) 168.67071089
Shift along axis -164.25896936
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 64
shifted from previous position = 0.0148
rotated from previous position = 0.0251 degrees
atoms outside contour = 4870, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53020351 0.78337851 0.32434911 175.25525365
0.58883378 0.06496663 0.80563894 67.49212990
0.61004836 0.61814032 -0.49572527 63.98995244
Axis -0.47682037 -0.72655051 -0.49473902
Axis point 66.66105482 0.00000000 15.63827816
Rotation angle (degrees) 168.66100586
Shift along axis -164.26004271
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.11, steps = 2000
shifted from previous position = 0.0976
rotated from previous position = 0.221 degrees
atoms outside contour = 4868, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53030190 0.78341623 0.32409705 175.26282770
0.58634766 0.06279337 0.80762207 67.66774149
0.61235309 0.61831707 -0.49265372 63.78303703
Axis -0.47660457 -0.72572909 -0.49615055
Axis point 66.63683922 -0.00000000 15.46103341
Rotation angle (degrees) 168.54504031
Shift along axis -164.28550219
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 452
shifted from previous position = 0.103
rotated from previous position = 0.228 degrees
atoms outside contour = 4873, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53023999 0.78337185 0.32430556 175.25600756
0.58888164 0.06509041 0.80559397 67.48261123
0.60997046 0.61813573 -0.49582684 63.99489971
Axis -0.47680398 -0.72659468 -0.49468993
Axis point 66.66524331 0.00000000 15.64651192
Rotation angle (degrees) 168.66308535
Shift along axis -164.25290123
Average map value = 0.1101 for 8555 atoms, 4873 outside contour
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 468
shifted from previous position = 0.0215
rotated from previous position = 0.0236 degrees
atoms outside contour = 4871, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53022549 0.78333267 0.32442389 175.26120378
0.58869596 0.06476843 0.80575562 67.51017249
0.61016227 0.61821920 -0.49548665 63.97828856
Axis -0.47680497 -0.72648012 -0.49485721
Axis point 66.65954664 0.00000000 15.62105020
Rotation angle (degrees) 168.65831877
Shift along axis -164.27032823
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.75983,0.62964,-0.16191,211.35,-0.13348,-0.39483,-0.90901,195.66,-0.63628,-0.66908,0.38404,229.11
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.90104,0.41237,0.13447,215.67,-0.29508,-0.35557,-0.88685,207.87,-0.31789,-0.83876,0.44206,202.71
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 1032
shifted from previous position = 0.0229
rotated from previous position = 0.0182 degrees
atoms outside contour = 4867, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53018707 0.78332483 0.32450560 175.24771623
0.58892855 0.06488799 0.80557601 67.47459733
0.60997117 0.61821660 -0.49572513 63.99835587
Axis -0.47684177 -0.72652827 -0.49475104
Axis point 66.65970814 0.00000000 15.64161582
Rotation angle (degrees) 168.67005183
Shift along axis -164.25088775
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 1664
shifted from previous position = 0.0186
rotated from previous position = 0.0171 degrees
atoms outside contour = 4870, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53022877 0.78335427 0.32436637 175.26165080
0.58869921 0.06483364 0.80574800 67.50564141
0.61015628 0.61818500 -0.49553670 63.97927276
Axis -0.47680080 -0.72650180 -0.49482939
Axis point 66.66175547 -0.00000000 15.62607931
Rotation angle (degrees) 168.65658943
Shift along axis -164.26669023
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 644
shifted from previous position = 0.00609
rotated from previous position = 0.0107 degrees
atoms outside contour = 4869, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53021367 0.78337477 0.32434154 175.25632282
0.58880640 0.06495516 0.80565988 67.49569086
0.61006597 0.61814626 -0.49569620 63.99027421
Axis -0.47681347 -0.72654591 -0.49475242
Axis point 66.66093857 0.00000000 15.63720472
Rotation angle (degrees) 168.65992061
Shift along axis -164.26263689
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1092, steps = 2000
shifted from previous position = 0.317
rotated from previous position = 0.649 degrees
atoms outside contour = 4884, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53069682 0.78334548 0.32362130 175.24667359
0.59519461 0.07260582 0.80029480 67.09333677
0.60341053 0.61733156 -0.50477469 64.56830683
Axis -0.47694847 -0.72935438 -0.49047156
Axis point 66.74526995 0.00000000 16.15781383
Rotation angle (degrees) 168.94179545
Shift along axis -164.18736942
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1092, steps = 2000
shifted from previous position = 0.49
rotated from previous position = 0.92 degrees
atoms outside contour = 4936, contour level = 0.0941
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53116199 0.78451417 0.32000698 175.45737218
0.58405988 0.06541926 0.80907007 68.06310467
0.61379231 0.61665050 -0.49295147 63.69301951
Axis -0.47584743 -0.72652173 -0.49571704
Axis point 66.69465830 0.00000000 15.45750434
Rotation angle (degrees) 168.33516879
Shift along axis -164.51398071
> ui tool show "Fit in Map"
> view matrix models
> #3,-0.82929,0.50215,0.2452,204.87,-0.51079,-0.50318,-0.69707,221.16,-0.22665,-0.70332,0.67378,185.65
> volume #2 level 0.1033
> color #3 #e17cd6ff
> color #3 #e15cdaff
> view matrix models
> #3,-0.31693,0.8998,0.29986,155.65,-0.87959,-0.39711,0.26196,218.08,0.35479,-0.18073,0.91731,122.78
> view matrix models
> #3,-0.42234,0.64566,0.6362,156.08,-0.74681,0.14992,-0.64792,231.27,-0.51371,-0.74876,0.41887,218.7
> view matrix models
> #3,-0.43035,0.65719,0.61879,157.19,-0.61572,0.28756,-0.73362,221.62,-0.66006,-0.69672,0.28089,234.91
> view matrix models
> #3,-0.43231,0.66215,0.6121,157.52,-0.55808,0.33671,-0.7584,217.08,-0.70827,-0.66947,0.22397,240.52
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.43231,0.66215,0.6121,160.72,-0.55808,0.33671,-0.7584,219.01,-0.70827,-0.66947,0.22397,239.83
> view matrix models
> #3,-0.43231,0.66215,0.6121,159.28,-0.55808,0.33671,-0.7584,218.31,-0.70827,-0.66947,0.22397,240.9
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1097, steps = 2000
shifted from previous position = 0.352
rotated from previous position = 0.512 degrees
atoms outside contour = 5164, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.52938973 0.78232018 0.32820976 175.20180548
0.58937752 0.06086670 0.80556153 67.55099551
0.61023000 0.61989546 -0.49330413 63.76830767
Axis -0.47742766 -0.72519584 -0.49613891
Axis point 66.56518497 0.00000000 15.32623750
Rotation angle (degrees) 168.78774324
Shift along axis -164.27182856
> view matrix models
> #3,-0.43231,0.66215,0.6121,149.22,-0.55808,0.33671,-0.7584,293.13,-0.70827,-0.66947,0.22397,224.36
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.32146,-0.80003,-0.50657,141.97,0.63696,-0.21316,0.74085,149.61,-0.70068,-0.56081,0.44107,215.08
> ui mousemode right "move picked models"
> view matrix models
> #3,0.32146,-0.80003,-0.50657,152.54,0.63696,-0.21316,0.74085,70.881,-0.70068,-0.56081,0.44107,232.12
> view matrix models #2,1,0,0,0.49818,0,1,0,-1.9443,0,0,1,-0.027411
> view matrix models
> #3,0.32146,-0.80003,-0.50657,152.17,0.63696,-0.21316,0.74085,71.821,-0.70068,-0.56081,0.44107,231.13
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 444
shifted from previous position = 2.05
rotated from previous position = 0.272 degrees
atoms outside contour = 5177, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53014537 0.78341422 0.32435791 175.24973781
0.58901723 0.06509488 0.80549448 67.46874039
0.60992178 0.61808157 -0.49595422 64.01644841
Axis -0.47685986 -0.72659856 -0.49463037
Axis point 66.66173550 0.00000000 15.66125669
Rotation angle (degrees) 168.66720919
Shift along axis -164.25673514
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.109, steps = 2000
shifted from previous position = 0.364
rotated from previous position = 0.268 degrees
atoms outside contour = 5184, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.52953165 0.78373063 0.32459593 175.22933259
0.58649074 0.06178533 0.80759593 67.65591347
0.61288240 0.61802012 -0.49236805 64.00402190
Axis -0.47700270 -0.72537431 -0.49628674
Axis point 66.58693830 0.00000000 15.55380403
Rotation angle (degrees) 168.53813576
Shift along axis -164.42507401
> hide #!1 models
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 880
shifted from previous position = 0.36
rotated from previous position = 0.25 degrees
atoms outside contour = 5168, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53016490 0.78326941 0.32467554 175.24946771
0.58893795 0.06470422 0.80558392 67.47703695
0.60998137 0.61830606 -0.49560099 63.99897669
Axis -0.47686117 -0.72646748 -0.49482160
Axis point 66.65753160 0.00000000 15.63292089
Rotation angle (degrees) 168.67551546
Shift along axis -164.25761625
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 956
shifted from previous position = 0.00538
rotated from previous position = 0.0193 degrees
atoms outside contour = 5176, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53015255 0.78339221 0.32439933 175.25212537
0.58891863 0.06495837 0.80557759 67.47860241
0.61001075 0.61812382 -0.49579211 64.00549538
Axis -0.47685229 -0.72654962 -0.49470956
Axis point 66.66066154 0.00000000 15.64936302
Rotation angle (degrees) 168.66452359
Shift along axis -164.26006100
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 112
shifted from previous position = 0.00517
rotated from previous position = 0.00997 degrees
atoms outside contour = 5171, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53016501 0.78334523 0.32449237 175.25164793
0.58886816 0.06482196 0.80562547 67.48756934
0.61004864 0.61819767 -0.49565340 63.99723866
Axis -0.47684777 -0.72650305 -0.49478230
Axis point 66.65766971 0.00000000 15.63680662
Rotation angle (degrees) 168.66600557
Shift along axis -164.26298379
> view matrix models #2,1,0,0,-2.1044,0,1,0,-5.9865,0,0,1,-10.395
> view matrix models
> #3,0.32146,-0.80003,-0.50657,166.64,0.63696,-0.21316,0.74085,116.98,-0.70068,-0.56081,0.44107,217.96
> view matrix models
> #3,0.32146,-0.80003,-0.50657,169.54,0.63696,-0.21316,0.74085,125.06,-0.70068,-0.56081,0.44107,218.42
> open /Users/madhurikanavalli/Desktop/ImageProcessing/5zf6.pdb
5zf6.pdb title:
Crystal structure of the dimeric human pnpase [more info...]
Chain information for 5zf6.pdb #4
---
Chain | Description | UniProt
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669
> view matrix models
> #3,0.32146,-0.80003,-0.50657,148.43,0.63696,-0.21316,0.74085,63.647,-0.70068,-0.56081,0.44107,223.56
> view matrix models #2,1,0,0,48.511,0,1,0,45.019,0,0,1,20.98
> select subtract #3
Nothing selected
> select add #4
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> view matrix models #4,1,0,0,83.657,0,1,0,133.4,0,0,1,74.498
> view matrix models #2,1,0,0,52.3,0,1,0,49.451,0,0,1,28.52
> select add #3
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> select subtract #4
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> view matrix models
> #3,0.32146,-0.80003,-0.50657,136.64,0.63696,-0.21316,0.74085,-37.639,-0.70068,-0.56081,0.44107,316.42
> select add #4
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> select subtract #3
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> view matrix models #4,1,0,0,100.21,0,1,0,119.24,0,0,1,167.97
> view matrix models #4,1,0,0,94.426,0,1,0,100.65,0,0,1,171.22
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.41408,0.1075,0.90387,111.26,-0.67576,0.70158,0.22613,152.77,-0.60983,-0.70443,0.36315,251.95
> view matrix models
> #4,-0.63644,0.71625,0.28624,212.21,-0.65653,-0.30824,-0.68845,194.26,-0.40487,-0.62608,0.66641,223.7
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.63644,0.71625,0.28624,224.74,-0.65653,-0.30824,-0.68845,278.34,-0.40487,-0.62608,0.66641,230.36
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.005866, steps = 116
shifted from previous position = 9.15
rotated from previous position = 11.8 degrees
atoms outside contour = 8423, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.37376363 0.83073250 0.41253395 113.00914844
0.60330567 -0.12008129 0.78841788 24.18980167
0.70450196 0.54356600 -0.45630361 26.46495607
Axis -0.55176955 -0.65794495 -0.51250250
Axis point 48.12014517 0.00000000 9.13310885
Rotation angle (degrees) 167.18059467
Shift along axis -91.83392043
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.005866, steps = 48
shifted from previous position = 0.00372
rotated from previous position = 0.00364 degrees
atoms outside contour = 8423, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.37380897 0.83073280 0.41249227 113.01657042
0.60329402 -0.12002284 0.78843569 24.18865946
0.70448788 0.54357845 -0.45631052 26.46914319
Axis -0.55174775 -0.65796676 -0.51249795
Axis point 48.12488148 0.00000000 9.13684441
Rotation angle (degrees) 167.17979429
Shift along axis -91.83735467
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.005864, steps = 40
shifted from previous position = 0.0173
rotated from previous position = 0.0226 degrees
atoms outside contour = 8423, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.37355182 0.83072501 0.41274083 112.98007958
0.60330989 -0.12040454 0.78836535 24.20207343
0.70461068 0.54350594 -0.45620727 26.44217135
Axis -0.55186913 -0.65782221 -0.51255283
Axis point 48.09869868 0.00000000 9.11163823
Rotation angle (degrees) 167.18254641
Shift along axis -91.82388905
> view matrix models
> #4,-0.63644,0.71625,0.28624,225.3,-0.65653,-0.30824,-0.68845,281.25,-0.40487,-0.62608,0.66641,228.09
> view matrix models
> #4,-0.63644,0.71625,0.28624,236.94,-0.65653,-0.30824,-0.68845,284.6,-0.40487,-0.62608,0.66641,231.87
> view matrix models
> #4,-0.63644,0.71625,0.28624,236.34,-0.65653,-0.30824,-0.68845,283.78,-0.40487,-0.62608,0.66641,229.07
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.45017,0.42924,0.78301,207.48,-0.89014,-0.14629,-0.43156,292.56,-0.070696,-0.89126,0.44794,211.86
> view matrix models
> #4,0.34045,-0.89658,0.28327,174.58,-0.051672,0.28297,0.95774,170.65,-0.93884,-0.34069,0.050008,290.91
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.005866, steps = 44
shifted from previous position = 0.0178
rotated from previous position = 0.0233 degrees
atoms outside contour = 8423, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.37380507 0.83073257 0.41249627 113.01405219
0.60332324 -0.12000649 0.78841582 24.18430772
0.70446493 0.54358241 -0.45634124 26.47196139
Axis -0.55175121 -0.65797420 -0.51248469
Axis point 48.12483337 0.00000000 9.13955270
Rotation angle (degrees) 167.18114524
Shift along axis -91.83476585
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.005865, steps = 44
shifted from previous position = 0.0162
rotated from previous position = 0.0104 degrees
atoms outside contour = 8423, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.37367588 0.83073709 0.41260419 112.99497364
0.60333702 -0.12017770 0.78837920 24.19299418
0.70452167 0.54353768 -0.45630693 26.45239851
Axis -0.55181172 -0.65790916 -0.51250304
Axis point 48.11098906 0.00000000 9.12355336
Rotation angle (degrees) 167.18214242
Shift along axis -91.82567741
> view matrix models
> #4,0.43664,-0.89777,0.05801,174.22,0.24953,0.18281,0.95095,147.04,-0.86434,-0.40075,0.30385,276.84
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.43664,-0.89777,0.05801,174.07,0.24953,0.18281,0.95095,141.74,-0.86434,-0.40075,0.30385,275.58
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.005865, steps = 64
shifted from previous position = 0.000311
rotated from previous position = 0.00048 degrees
atoms outside contour = 8423, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.37368007 0.83073787 0.41259884 112.99539390
0.60333786 -0.12016939 0.78837982 24.19256137
0.70451872 0.54353833 -0.45631070 26.45291856
Axis -0.55180974 -0.65791232 -0.51250111
Axis point 48.11140469 0.00000000 9.12410653
Rotation angle (degrees) 167.18209740
Shift along axis -91.82569332
> ui tool show "Fit in Map"
> select add #1
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> show #!1 models
> view matrix models
> #1,-0.37368,0.83074,0.4126,173.74,0.60334,-0.12017,0.78838,115.48,0.70452,0.54354,-0.45631,93.202,#4,0.43664,-0.89777,0.05801,182.52,0.24953,0.18281,0.95095,183.58,-0.86434,-0.40075,0.30385,313.81
> select subtract #1
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.04826, steps = 208
shifted from previous position = 24.3
rotated from previous position = 13.9 degrees
atoms outside contour = 7062, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53783333 0.72307022 0.43347983 159.00633082
0.47779001 -0.16220016 0.86337003 75.07630856
0.69458766 0.67146152 -0.25823907 50.90548584
Axis -0.47220498 -0.64247495 -0.60352994
Axis point 55.27447343 0.00000000 -2.91680074
Rotation angle (degrees) 168.27557772
Shift along axis -154.04121419
> view matrix models
> #4,0.43664,-0.89777,0.05801,191.01,0.24953,0.18281,0.95095,146.47,-0.86434,-0.40075,0.30385,280.45
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.04826, steps = 44
shifted from previous position = 0.00861
rotated from previous position = 0.0257 degrees
atoms outside contour = 7058, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53794322 0.72292001 0.43359400 159.01744152
0.47809988 -0.16198800 0.86323832 75.04555828
0.69428928 0.67167443 -0.25848763 50.93543074
Axis -0.47217660 -0.64257525 -0.60344536
Axis point 55.28749168 -0.00000000 -2.88908802
Rotation angle (degrees) 168.29621721
Shift along axis -154.04348260
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.04827, steps = 44
shifted from previous position = 0.0189
rotated from previous position = 0.0343 degrees
atoms outside contour = 7055, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53786107 0.72305980 0.43346279 159.01065126
0.47765769 -0.16229540 0.86342535 75.09640503
0.69465717 0.67144972 -0.25808270 50.89975282
Axis -0.47218320 -0.64243364 -0.60359096
Axis point 55.27191933 0.00000000 -2.93139955
Rotation angle (degrees) 168.27087076
Shift along axis -154.04924535
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.04826, steps = 56
shifted from previous position = 0.00275
rotated from previous position = 0.00863 degrees
atoms outside contour = 7058, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53789045 0.72301563 0.43350002 159.01318424
0.47776580 -0.16222232 0.86337927 75.08570285
0.69456008 0.67151495 -0.25817430 50.90982184
Axis -0.47217744 -0.64246791 -0.60355899
Axis point 55.27562048 0.00000000 -2.92169624
Rotation angle (degrees) 168.27762248
Shift along axis -154.04967314
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.04827, steps = 48
shifted from previous position = 0.00193
rotated from previous position = 0.00615 degrees
atoms outside contour = 7058, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53789039 0.72302397 0.43348618 159.01244545
0.47768494 -0.16228399 0.86341242 75.09257148
0.69461574 0.67149106 -0.25808666 50.90376590
Axis -0.47217206 -0.64244065 -0.60359221
Axis point 55.27392700 -0.00000000 -2.92888590
Rotation angle (degrees) 168.27395306
Shift along axis -154.04887104
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.04827, steps = 64
shifted from previous position = 0.00548
rotated from previous position = 0.00426 degrees
atoms outside contour = 7055, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53785442 0.72306533 0.43346182 159.01147157
0.47764879 -0.16230580 0.86342832 75.10035018
0.69466845 0.67144125 -0.25807439 50.90069383
Axis -0.47218581 -0.64242903 -0.60359383
Axis point 55.27087759 0.00000000 -2.93287966
Rotation angle (degrees) 168.27022770
Shift along axis -154.05294973
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.04827, steps = 60
shifted from previous position = 0.00642
rotated from previous position = 0.00609 degrees
atoms outside contour = 7058, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53785882 0.72305154 0.43347937 159.00964336
0.47772910 -0.16224717 0.86339490 75.08872707
0.69460982 0.67147027 -0.25815669 50.90531403
Axis -0.47218929 -0.64245532 -0.60356311
Axis point 55.27291232 0.00000000 -2.92451182
Rotation angle (degrees) 168.27418388
Shift along axis -154.04837304
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.04826, steps = 64
shifted from previous position = 0.0135
rotated from previous position = 0.016 degrees
atoms outside contour = 7058, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53787316 0.72300698 0.43353588 159.01006466
0.47794254 -0.16210192 0.86330406 75.06071540
0.69445186 0.67155333 -0.25836552 50.91864025
Axis -0.47219782 -0.64252143 -0.60348607
Axis point 55.27987228 0.00000000 -2.90357183
Rotation angle (degrees) 168.28517374
Shift along axis -154.04101345
> view matrix models
> #4,0.43664,-0.89777,0.05801,173.3,0.24953,0.18281,0.95095,144.52,-0.86434,-0.40075,0.30385,283.13
> select add #1
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> select subtract #4
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> view matrix models
> #1,-0.53787,0.72301,0.43354,223.6,0.47794,-0.1621,0.8633,124.88,0.69445,0.67155,-0.25837,77.874
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 1948
shifted from previous position = 2.6
rotated from previous position = 15.7 degrees
atoms outside contour = 5173, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53017143 0.78335704 0.32445337 175.25064083
0.58878998 0.06478821 0.80568533 67.49213641
0.61011852 0.61818624 -0.49558164 63.99599175
Axis -0.47683791 -0.72648873 -0.49481283
Axis point 66.65667254 0.00000000 15.63558830
Rotation angle (degrees) 168.66140010
Shift along axis -164.26446361
> view matrix models
> #1,-0.53017,0.78336,0.32445,226.92,0.58879,0.064788,0.80569,120.46,0.61012,0.61819,-0.49558,88.341
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 72
shifted from previous position = 1.36
rotated from previous position = 2.65 degrees
atoms outside contour = 6643, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56226080 0.77257068 0.29495311 179.14945505
0.55854681 0.09176525 0.82438134 73.22777991
0.60982640 0.62826243 -0.48311289 60.26848266
Axis -0.45793431 -0.73522379 -0.49974208
Axis point 68.44102626 0.00000000 12.84484093
Rotation angle (degrees) 167.63525506
Shift along axis -165.99618459
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 36
shifted from previous position = 0.00222
rotated from previous position = 0.00186 degrees
atoms outside contour = 6642, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56226149 0.77257686 0.29493559 179.14943502
0.55852256 0.09175953 0.82439841 73.23090250
0.60984799 0.62825566 -0.48309445 60.26745267
Axis -0.45793130 -0.73522087 -0.49974913
Axis point 68.44054400 0.00000000 12.84382814
Rotation angle (degrees) 167.63364557
Shift along axis -165.99762925
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 40
shifted from previous position = 0.00382
rotated from previous position = 0.0119 degrees
atoms outside contour = 6642, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56223213 0.77266158 0.29476960 179.15426710
0.55851228 0.09190124 0.82438959 73.22780149
0.60988447 0.62813076 -0.48321081 60.26856723
Axis -0.45793558 -0.73526530 -0.49967984
Axis point 68.44506902 0.00000000 12.85475786
Rotation angle (degrees) 167.62632816
Shift along axis -165.99796253
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 40
shifted from previous position = 0.00189
rotated from previous position = 0.0083 degrees
atoms outside contour = 6642, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56225259 0.77260149 0.29488805 179.15076237
0.55852481 0.09180506 0.82439182 73.22832142
0.60985413 0.62821873 -0.48313473 60.26809457
Axis -0.45793313 -0.73523542 -0.49972606
Axis point 68.44223141 0.00000000 12.84779765
Rotation angle (degrees) 167.63175258
Shift along axis -165.99666188
> select subtract #1
Nothing selected
> select #1/A:306
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:307
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:308
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:306
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2
2 models selected
> select subtract #2
Nothing selected
> select #2
2 models selected
> select subtract #2
Nothing selected
> select #2
2 models selected
> select #2
2 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> select sequence 301-306
Nothing selected
> select sequence 301-306
Nothing selected
> select sequence 301-306
Nothing selected
> help help:user/findseq.html
> ui tool show "Show Sequence Viewer"
> select add #3
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> select subtract #3
Nothing selected
> select add #1
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #3
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #4
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #3/A #3/B #4/A #4/B
Alignment identifier is 1
> select
> #1/A-B:125-142,164-180,205-212,222-224,237-267,280-301,305-328,332-356,450-462,482-499,534-540,567-593,613-636,653-666
> #3/A-B:125-142,164-180,205-212,222-224,237-267,280-301,305-328,332-356,450-462,482-499,534-540,567-593,613-636,653-666
> #4/A-B:125-142,164-180,205-212,222-224,237-267,280-301,305-328,332-356,450-462,482-499,534-540,567-593,613-636,653-666
11616 atoms, 11709 bonds, 1491 residues, 3 models selected
> show #!2 models
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 40
shifted from previous position = 0.0117
rotated from previous position = 0.00722 degrees
atoms outside contour = 6640, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56224533 0.77263148 0.29482329 179.15688679
0.55843537 0.09177590 0.82445565 73.23754273
0.60994272 0.62818610 -0.48306532 60.24856479
Axis -0.45792677 -0.73522163 -0.49975217
Axis point 68.44493944 0.00000000 12.83776309
Rotation angle (degrees) 167.62539970
Shift along axis -165.99591072
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 40
shifted from previous position = 0.00404
rotated from previous position = 0.0179 degrees
atoms outside contour = 6642, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56227457 0.77250264 0.29510503 179.14987129
0.55852816 0.09159555 0.82441285 73.23691669
0.60983079 0.62837085 -0.48296633 60.25085966
Axis -0.45793476 -0.73516833 -0.49982326
Axis point 68.43835304 0.00000000 12.82457642
Rotation angle (degrees) 167.64019313
Shift along axis -165.99519523
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 40
shifted from previous position = 0.00252
rotated from previous position = 0.00579 degrees
atoms outside contour = 6643, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56226280 0.77254581 0.29501442 179.14915690
0.55849019 0.09164317 0.82443328 73.23928513
0.60987642 0.62831083 -0.48298680 60.24865553
Axis -0.45793277 -0.73518163 -0.49980551
Axis point 68.43839047 0.00000000 12.82706773
Rotation angle (degrees) 167.63498549
Shift along axis -165.99505628
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 44
shifted from previous position = 0.0109
rotated from previous position = 0.00848 degrees
atoms outside contour = 6643, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56228174 0.77250668 0.29508080 179.14693278
0.55858918 0.09169034 0.82436097 73.22718572
0.60976829 0.62835206 -0.48306968 60.26918749
Axis -0.45793423 -0.73520218 -0.49977394
Axis point 68.43867717 0.00000000 12.83878493
Rotation angle (degrees) 167.64229799
Shift along axis -165.99526915
> select add #3
16299 atoms, 16424 bonds, 2168 residues, 3 models selected
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 48
shifted from previous position = 0.00251
rotated from previous position = 0.00327 degrees
atoms outside contour = 6644, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56227363 0.77253040 0.29503414 179.14739408
0.55858437 0.09172832 0.82436000 73.22579110
0.60978018 0.62831735 -0.48309982 60.27170015
Axis -0.45793523 -0.73521399 -0.49975566
Axis point 68.43952822 -0.00000000 12.84303370
Rotation angle (degrees) 167.64016407
Shift along axis -165.99565204
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 40
shifted from previous position = 0.00106
rotated from previous position = 0.00975 degrees
atoms outside contour = 6643, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56225268 0.77260373 0.29488202 179.15110347
0.55852278 0.09180948 0.82439270 73.22831911
0.60985591 0.62821532 -0.48313691 60.26806007
Axis -0.45793261 -0.73523677 -0.49972454
Axis point 68.44249251 0.00000000 12.84809670
Rotation angle (degrees) 167.63146412
Shift along axis -165.99671418
> select add #4
20982 atoms, 21139 bonds, 2845 residues, 3 models selected
> select subtract #4
12427 atoms, 12521 bonds, 1671 residues, 2 models selected
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.0603, steps = 40
shifted from previous position = 0.0118
rotated from previous position = 0.00691 degrees
atoms outside contour = 6640, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56224678 0.77262775 0.29483032 179.15681735
0.55843723 0.09177153 0.82445488 73.23752923
0.60993969 0.62819133 -0.48306235 60.24853618
Axis -0.45792659 -0.73522035 -0.49975421
Axis point 68.44485428 0.00000000 12.83738565
Rotation angle (degrees) 167.62577932
Shift along axis -165.99585229
> select add #1
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> select subtract #1
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select add #1
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> view matrix models
> #1,-0.56225,0.77263,0.29483,231.16,0.55844,0.091772,0.82445,121.3,0.60994,0.62819,-0.48306,94.371,#3,0.32146,-0.80003,-0.50657,136.35,0.63696,-0.21316,0.74085,-39.027,-0.70068,-0.56081,0.44107,322.02
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.1101, steps = 252
shifted from previous position = 3.7
rotated from previous position = 2.65 degrees
atoms outside contour = 5173, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53022950 0.78334634 0.32438432 175.25685423
0.58887827 0.06499723 0.80560396 67.48236203
0.60998283 0.61817787 -0.49575909 63.99041146
Axis -0.47681259 -0.72656353 -0.49472739
Axis point 66.66494214 0.00000000 15.64059965
Rotation angle (degrees) 168.66526300
Shift along axis -164.25270661
> view matrix models
> #1,-0.53023,0.78335,0.32438,227.93,0.58888,0.064997,0.8056,120.21,0.60998,0.61818,-0.49576,94.092,#3,0.32146,-0.80003,-0.50657,136.72,0.63696,-0.21316,0.74085,-35.748,-0.70068,-0.56081,0.44107,323.6
> select subtract #3
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> fitmap #1 inMap #2
Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms
average map value = 0.06778, steps = 88
shifted from previous position = 4.08
rotated from previous position = 2.46 degrees
atoms outside contour = 6341, contour level = 0.10328
Position of 5zf6.pdb (#1) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.56182390 0.76213390 0.32172320 177.76957181
0.56503217 0.06947264 0.82213879 70.72361557
0.60422889 0.64368118 -0.46966157 68.59500191
Axis -0.46000085 -0.72820014 -0.50805883
Axis point 67.67791239 0.00000000 16.37816490
Rotation angle (degrees) 168.81513008
Shift along axis -168.12539753
> close #3
> open
> /Users/madhurikanavalli/Desktop/ImageProcessing/kasiafiles/hPNP_dimer_5zf6_fit_tetramer2.pdb
hPNP_dimer_5zf6_fit_tetramer2.pdb title:
Crystal structure of the dimeric human pnpase [more info...]
Chain information for hPNP_dimer_5zf6_fit_tetramer2.pdb #3
---
Chain | Description | UniProt
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669
[deleted to fit within ticket limits]
> combine #4..1 #4.2
Expected a keyword
> combine #4.1 #4.2
> select add #7
30425 atoms, 30650 bonds, 4176 residues, 5 models selected
> select subtract #7
21870 atoms, 22032 bonds, 3002 residues, 4 models selected
> select add #7
30425 atoms, 30650 bonds, 4176 residues, 5 models selected
> select subtract #7
21870 atoms, 22032 bonds, 3002 residues, 4 models selected
> select subtract #6
13315 atoms, 13414 bonds, 1828 residues, 3 models selected
> select subtract #5
4760 atoms, 4796 bonds, 654 residues, 2 models selected
> select add #1
12883 atoms, 12975 bonds, 1771 residues, 2 models selected
> select add #3
17110 atoms, 17236 bonds, 2348 residues, 4 models selected
> select subtract #3
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #5
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select add #8
17110 atoms, 17236 bonds, 2348 residues, 2 models selected
> combine #5 #8
Remapping chain ID 'A' in combination #8 to 'C'
Remapping chain ID 'B' in combination #8 to 'D'
> select subtract #8
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #7
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #9
17110 atoms, 17236 bonds, 2348 residues, 1 model selected
> select subtract #9
Nothing selected
> close #1
> close #3
> close #4
> hide #5 models
> close #5
> show #!6 models
> hide #!6 models
> close #6
> hide #7 models
> show #7 models
> select add #7
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #7
Nothing selected
> close #7
> select add #8
8555 atoms, 8618 bonds, 1174 residues, 1 model selected
> select subtract #8
Nothing selected
> close #8
> select add #9
17110 atoms, 17236 bonds, 2348 residues, 1 model selected
> select subtract #9
Nothing selected
> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramerfit_J482_goodone.pdb
> relModel #2
> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramerfit_J482_good02.pdb
> relModel #9
> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/Tetramer_goodmodel_01_05Nov25.cxs
> includeMaps true
——— End of log from Wed Nov 5 23:47:55 2025 ———
> view name session-start
opened ChimeraX session
> hide #9 models
> ui tool show "Fit Loops"
> show #9 models
> ui tool show "Fit Loops"
No selected amino-acid residues or missing-structure pseudobonds in
combination #9
> open
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_0.cif
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_1.cif
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_2.cif
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_3.cif
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_4.cif
Chain information for fold_s1domain_model_0.cif #1
---
Chain | Description
A | .
Chain information for fold_s1domain_model_1.cif #3
---
Chain | Description
A | .
Chain information for fold_s1domain_model_2.cif #4
---
Chain | Description
A | .
Chain information for fold_s1domain_model_3.cif #5
---
Chain | Description
A | .
Chain information for fold_s1domain_model_4.cif #6
---
Chain | Description
A | .
Computing secondary structure
[Repeated 4 time(s)]
> hide #9 models
> tile
6 models tiled
> hide #!2 models
> show #!2 models
> color #3 #7a81ffff
> color #3 #0433ffff
> select add #3
522 atoms, 529 bonds, 65 residues, 1 model selected
> view matrix models #3,1,0,0,167.58,0,1,0,54.796,0,0,1,204.78
> view matrix models #3,1,0,0,165.39,0,1,0,115.67,0,0,1,225.25
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-2.0304,0,1,0,-3.9698,0,0,1,-16.281
> view matrix models #2,1,0,0,-2.6783,0,1,0,2.0885,0,0,1,-17.199
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.32589,0.91906,-0.22164,161.57,-0.87579,0.20518,-0.43692,116.43,-0.35608,0.3365,0.87177,223.66
> view matrix models
> #3,0.56547,-0.7859,-0.25021,166.9,0.82291,0.55799,0.10713,118.68,0.055423,-0.26647,0.96225,226.17
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.56547,-0.7859,-0.25021,163.29,0.82291,0.55799,0.10713,131.17,0.055423,-0.26647,0.96225,208.64
> view matrix models
> #3,0.29541,0.69457,0.65597,155.91,-0.92197,0.38722,0.0051959,144.72,-0.2504,-0.60633,0.75477,209.92
> view matrix models
> #3,0.79695,-0.604,0.0075442,161.41,0.52088,0.6935,0.49774,151.3,-0.30587,-0.39275,0.86729,210.32
> view matrix models
> #3,0.46843,-0.85689,-0.21519,160.99,0.82693,0.33948,0.44827,160.63,-0.31106,-0.38793,0.86761,210.1
> view matrix models
> #3,-0.34505,0.91726,0.19892,154.61,-0.88742,-0.24981,-0.38741,149.7,-0.30566,-0.3102,0.90019,211.43
> view matrix models
> #3,0.66119,0.61943,0.42324,159.05,-0.59559,0.77644,-0.20593,116.72,-0.45618,-0.11592,0.8823,203.44
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule fold_s1domain_model_0.cif (#1) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms
average map value = 0.0003632, steps = 356
shifted from previous position = 4.22
rotated from previous position = 14.5 degrees
atoms outside contour = 522, contour level = 0.090619
Position of fold_s1domain_model_0.cif (#1) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.97213948 0.21632806 0.09026078 182.36500636
-0.20718521 0.97309809 -0.10076905 2.02323771
-0.10963177 0.07926087 0.99080704 169.96457072
Axis 0.35881954 0.39840796 -0.84410878
Axis point 279.68301149 -935.07624490 0.00000000
Rotation angle (degrees) 14.52865421
Shift along axis -77.22638618
> fitmap #1 inMap #2
Fit molecule fold_s1domain_model_0.cif (#1) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms
average map value = 0.000365, steps = 100
shifted from previous position = 0.137
rotated from previous position = 0.599 degrees
atoms outside contour = 522, contour level = 0.090619
Position of fold_s1domain_model_0.cif (#1) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.97288387 0.20994836 0.09704977 182.50082645
-0.19979031 0.97422533 -0.10473222 2.03411083
-0.11653670 0.08250268 0.98975376 169.89241874
Axis 0.37555154 0.42840695 -0.82184459
Axis point 284.35086060 -958.13936528 0.00000000
Rotation angle (degrees) 14.43490420
Shift along axis -70.21527182
> fitmap #3 inMap #2
Fit molecule fold_s1domain_model_1.cif (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms
average map value = 0.07067, steps = 164
shifted from previous position = 8.32
rotated from previous position = 39.5 degrees
atoms outside contour = 363, contour level = 0.090619
Position of fold_s1domain_model_1.cif (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.92043171 -0.33817014 -0.19607755 159.00664102
0.31899036 0.93970634 -0.12327665 125.40584612
0.22594381 0.05092090 0.97280854 218.61730845
Axis 0.21769478 -0.52740033 0.82125385
Axis point -542.84900192 502.64006802 0.00000000
Rotation angle (degrees) 23.58417039
Shift along axis 148.01613600
> fitmap #4 inMap #2
Fit molecule fold_s1domain_model_2.cif (#4) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms
average map value = -0.001537, steps = 80
shifted from previous position = 0.947
rotated from previous position = 11.5 degrees
atoms outside contour = 522, contour level = 0.090619
Position of fold_s1domain_model_2.cif (#4) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.98137074 -0.01475330 -0.19155629 124.31223336
0.00382580 0.99835020 -0.05729090 166.97625539
0.19208549 0.05549076 0.97980811 25.02135082
Axis 0.28173775 -0.95836828 0.04641208
Axis point -72.08236990 0.00000000 838.11125119
Rotation angle (degrees) 11.54594279
Shift along axis -123.84000488
> volume #2 level 0.07472
> view matrix models
> #3,-0.67188,0.62554,0.39658,156.11,-0.55661,-0.77969,0.28683,98.367,0.48863,-0.028029,0.87204,213.25
> style sel ball
Changed 522 atom styles
> style sel sphere
Changed 522 atom styles
> show sel surfaces
> view matrix models
> #3,-0.76709,0.51052,0.38851,156.55,-0.43671,-0.85915,0.26672,89.922,0.46996,0.034932,0.882,210.08
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.7899,0.60735,-0.084731,156.46,-0.59625,-0.72837,0.33758,88.914,0.14331,0.31717,0.93748,208.03
> view matrix models
> #3,-0.66024,0.41001,0.62926,157.09,-0.37315,-0.90619,0.19893,90.332,0.6518,-0.10346,0.7513,211.23
> view matrix models
> #3,0.35613,-0.51243,-0.7814,164.32,-0.36034,0.69624,-0.62081,86.3,0.86216,0.50267,0.063305,210.69
> view matrix models
> #3,0.22649,-0.61697,-0.75369,164.12,-0.74129,0.39275,-0.54427,85.701,0.63181,0.68198,-0.3684,209.58
> view matrix models
> #3,0.4365,-0.66898,-0.60161,164.96,-0.60804,0.27351,-0.74531,86.654,0.66314,0.69112,-0.28738,209.62
> hide sel surfaces
> view matrix models
> #3,0.19536,-0.53018,-0.82507,164.33,-0.68664,0.52674,-0.50106,85.416,0.70026,0.66442,-0.26114,209.74
> view matrix models
> #3,0.35707,-0.66519,-0.65576,164.84,-0.63986,0.33727,-0.69053,86.324,0.6805,0.66617,-0.3052,209.76
> view matrix models
> #3,0.3911,-0.62689,-0.67384,164.84,-0.65268,0.32728,-0.6833,86.311,0.64888,0.70704,-0.28116,209.53
> view matrix models
> #3,0.50296,-0.58623,-0.63512,164.94,-0.61625,0.27201,-0.73908,86.63,0.60603,0.76312,-0.22446,209.2
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.50296,-0.58623,-0.63512,159.63,-0.61625,0.27201,-0.73908,149.03,0.60603,0.76312,-0.22446,209.13
> view matrix models
> #3,0.50296,-0.58623,-0.63512,160.92,-0.61625,0.27201,-0.73908,148.39,0.60603,0.76312,-0.22446,217.66
> view matrix models
> #3,0.50296,-0.58623,-0.63512,160.7,-0.61625,0.27201,-0.73908,148.47,0.60603,0.76312,-0.22446,216.16
> view matrix models
> #3,-0.45496,0.52695,-0.71787,152.27,-0.45166,0.55821,0.696,166.64,0.76747,0.64088,-0.015958,206.6
> fitmap #4 inMap #2
Fit molecule fold_s1domain_model_2.cif (#4) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms
average map value = -0.0004006, steps = 88
shifted from previous position = 1.25
rotated from previous position = 6.05 degrees
atoms outside contour = 522, contour level = 0.074721
Position of fold_s1domain_model_2.cif (#4) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99147668 0.01049450 -0.12986092 116.82021270
-0.00708136 0.99961796 0.02671695 137.03591507
0.13009169 -0.02556964 0.99117221 26.84154122
Axis -0.19675787 -0.97821877 -0.06613911
Axis point -80.51316555 0.00000000 664.24143651
Rotation angle (degrees) 7.63549261
Shift along axis -158.81167600
> fitmap #3 inMap #2
Fit molecule fold_s1domain_model_1.cif (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms
average map value = 0.07284, steps = 144
shifted from previous position = 9.14
rotated from previous position = 32.2 degrees
atoms outside contour = 318, contour level = 0.074721
Position of fold_s1domain_model_1.cif (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
-0.51872333 0.27009097 -0.81115779 162.49967762
-0.72798453 0.35795974 0.58472501 168.27559607
0.44829078 0.89382084 0.01093998 212.26586284
Axis 0.18888415 -0.76963145 -0.60991001
Axis point 77.24806995 0.00000000 108.85630195
Rotation angle (degrees) 125.09345631
Shift along axis -228.27965129
> view matrix models
> #3,0.87466,-0.27955,-0.396,157.61,-0.41844,-0.023029,-0.90795,126.96,0.2447,0.95985,-0.13712,199.83
> view matrix models
> #3,0.7064,-0.4253,0.56579,157.56,0.3865,-0.43789,-0.81171,108.84,0.59297,0.79207,-0.14495,197.91
> fitmap #3 inMap #2
Fit molecule fold_s1domain_model_1.cif (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms
average map value = 0.057, steps = 140
shifted from previous position = 8.64
rotated from previous position = 40 degrees
atoms outside contour = 355, contour level = 0.074721
Position of fold_s1domain_model_1.cif (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
-0.87064244 -0.19188813 -0.45294667 134.31464498
-0.49130252 0.29321200 0.82015154 169.18135869
-0.02456795 0.93659258 -0.34955793 220.00413042
Axis 0.21746043 -0.80002225 -0.55917382
Axis point 82.32214637 0.00000000 66.57043206
Rotation angle (degrees) 164.47081111
Shift along axis -229.16128017
> view matrix models
> #3,0.95229,0.22388,0.20741,154.09,-0.28611,0.41832,0.86206,83.875,0.10624,-0.88028,0.46241,224.1
> open Q8TCS8 fromDatabase alphafold_pae format pae
Fetching an AlphaFold database PAE file requires specifying the structure to
associate. For example "open P29474 from alphafold_pae structure #1"
> open /Users/madhurikanavalli/Downloads/AF-Q8TCS8-F1-model_v6.pdb
AF-Q8TCS8-F1-model_v6.pdb title:
Alphafold monomer V2.0 prediction for polyribonucleotide
nucleotidyltransferase 1, mitochondrial (Q8TCS8) [more info...]
Chain information for AF-Q8TCS8-F1-model_v6.pdb #7
---
Chain | Description | UniProt
A | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 1-783
Computing secondary structure
> hide #!3 models
> select subtract #3
1 model selected
> hide #6 models
> hide #!2 models
> show #!2 models
> hide #1 models
> close #1
> close #6
> close #5
> close #4
> select add #7
6032 atoms, 6129 bonds, 783 residues, 1 model selected
> view matrix models
> #7,0.93203,-0.33526,0.13754,27.703,-0.3055,-0.5228,0.79584,135.27,-0.19491,-0.78376,-0.58968,172.48
> view matrix models
> #7,0.99383,0.081244,-0.075482,18.858,0.10523,-0.47615,0.87304,113.59,0.034988,-0.8756,-0.48177,159.02
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> view matrix models
> #7,0.99383,0.081244,-0.075482,17.188,0.10523,-0.47615,0.87304,122.02,0.034988,-0.8756,-0.48177,152.46
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.96007,-0.2796,-0.0089378,326.83,0.13649,-0.44028,-0.88742,273.98,0.24419,-0.85321,0.46087,83.166
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.88144,0.35786,-0.30822,1.7984,0.34471,0.93357,0.098144,71.119,0.32287,-0.019738,-0.94624,110.86
> view matrix models
> #7,-0.099404,0.88065,-0.46322,0.9821,0.94473,0.22969,0.23394,71.545,0.31242,-0.41436,-0.85481,105.94
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.76785,-0.43102,-0.47394,-6.4138,-0.52462,0.84765,0.079073,63.133,0.36766,0.30936,-0.877,107.93
> view matrix models
> #7,-0.33896,-0.93514,-0.10302,5.3628,-0.91127,0.35356,-0.21114,50.667,0.23387,0.022309,-0.97201,103.39
> view matrix models
> #7,0.12187,-0.96241,-0.24272,2.542,-0.96457,-0.05719,-0.25755,47.564,0.23399,0.2655,-0.93528,105.4
> view matrix models
> #7,-0.20108,-0.97283,-0.11478,5.3796,-0.68218,0.22315,-0.6963,35.543,0.70299,-0.061709,-0.70852,113.32
> fitmap #7 inMap #2
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#7) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 6032 atoms
average map value = -5.856e-05, steps = 368
shifted from previous position = 2.09
rotated from previous position = 5.84 degrees
atoms outside contour = 6032, contour level = 0.074721
Position of AF-Q8TCS8-F1-model_v6.pdb (#7) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.08710074 -0.92938392 0.35869061 59.59075313
-0.79201574 -0.28300142 -0.54094475 16.28119012
0.60425532 -0.23697192 -0.76073634 160.17750188
Axis 0.73385821 -0.59284799 0.33163743
Axis point 0.00000000 22.84851283 71.47256607
Rotation angle (degrees) 168.04719174
Shift along axis 87.19974831
> view matrix models
> #7,-0.17868,-0.97881,-0.10005,6.648,-0.7608,0.20193,-0.61677,36.832,0.62391,-0.034088,-0.78076,112.96
> view matrix models
> #7,-0.20095,-0.96996,0.13707,14.191,-0.86316,0.10916,-0.493,40.09,0.46323,-0.21738,-0.85917,109.21
> view matrix models
> #7,-0.10038,-0.9943,0.035932,11.249,-0.86855,0.069951,-0.49065,40.01,0.48534,-0.080459,-0.87062,109.4
> ui mousemode right "move picked models"
> view matrix models
> #7,-0.10038,-0.9943,0.035932,7.572,-0.86855,0.069951,-0.49065,29.368,0.48534,-0.080459,-0.87062,77.9
> view matrix models
> #2,0.85656,0.43699,0.27448,-91.905,-0.45132,0.89228,-0.012127,31.709,-0.25021,-0.11349,0.96152,-24.5
> view matrix models
> #7,0.10537,-0.99398,0.030033,12.071,-0.94351,-0.10947,-0.31273,46.098,0.31413,0.0046163,-0.94937,108.85
> view matrix models
> #7,-0.56765,-0.71499,-0.40811,-7.3912,-0.38128,0.66768,-0.6394,71.402,0.72966,-0.20735,-0.65162,110.98
> view matrix models
> #2,0.93609,0.26905,0.22662,-77.448,-0.28402,0.95816,0.035632,19.557,-0.20755,-0.097718,0.97333,-57.413
> view matrix models
> #2,0.93609,0.26905,0.22662,-77.709,-0.28402,0.95816,0.035632,24.136,-0.20755,-0.097718,0.97333,-56.529
> view matrix models
> #7,0.039543,-0.98518,0.16692,17.982,-0.87376,-0.11513,-0.47253,24.985,0.48474,-0.12716,-0.86536,114.25
> view matrix models
> #2,0.93609,0.26905,0.22662,-72.357,-0.28402,0.95816,0.035632,7.0311,-0.20755,-0.097718,0.97333,-29.712
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.097094,-0.9571,0.27301,20.96,-0.44484,-0.20365,-0.87215,13.504,0.89033,-0.20613,-0.40599,130.24
> view matrix models
> #7,-0.07236,-0.95607,0.28407,21.412,-0.44804,-0.2233,-0.86568,13.632,0.89108,-0.18992,-0.4122,130.1
> ui mousemode right "move picked models"
> view matrix models
> #7,-0.07236,-0.95607,0.28407,15.841,-0.44804,-0.2233,-0.86568,68.667,0.89108,-0.18992,-0.4122,123.93
> view matrix models
> #7,-0.31735,-0.94146,-0.11376,0.63703,-0.20623,0.18561,-0.96074,85.778,0.92561,-0.28142,-0.25306,128.41
> view matrix models
> #7,0.29795,0.52938,-0.79435,-11.389,0.3903,0.69185,0.60746,91.578,0.87114,-0.49103,-0.00047747,123.65
> view matrix models
> #2,-0.0079881,0.99894,0.04544,-17.486,-0.99199,-0.0021879,-0.12629,318.3,-0.12606,-0.046085,0.99095,-56.337
> view matrix models
> #7,-0.1715,0.44788,-0.87749,-17.133,0.40556,0.84381,0.35143,88.21,0.89784,-0.29561,-0.32636,109.47
> view matrix models
> #7,-0.1715,0.44788,-0.87749,-17.408,0.40556,0.84381,0.35143,90.261,0.89784,-0.29561,-0.32636,108.77
> view matrix models
> #7,-0.19986,0.45505,-0.86775,-15.159,0.30662,0.87018,0.38571,82.163,0.93061,-0.18898,-0.31344,118.36
> view matrix models
> #7,-0.19986,0.45505,-0.86775,-19.12,0.30662,0.87018,0.38571,99.076,0.93061,-0.18898,-0.31344,101
> view matrix models
> #7,-0.19986,0.45505,-0.86775,-20.753,0.30662,0.87018,0.38571,106.14,0.93061,-0.18898,-0.31344,93.903
> view matrix models
> #7,-0.19986,0.45505,-0.86775,-14.691,0.30662,0.87018,0.38571,84.809,0.93061,-0.18898,-0.31344,123.13
> view matrix models
> #7,-0.19986,0.45505,-0.86775,-19.112,0.30662,0.87018,0.38571,85.454,0.93061,-0.18898,-0.31344,93.102
> view matrix models
> #7,-0.44672,-0.85339,-0.26864,-7.3842,-0.29981,0.4257,-0.85375,105.34,0.84294,-0.30085,-0.44603,111.24
> close session
> open
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramerfit_J482_goodone.pdb
> format pdb
Chain information for tetramerfit_J482_goodone.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
> view matrix models #1,1,0,0,29.011,0,1,0,-2.0292,0,0,1,-1.0087
> view matrix models #1,1,0,0,23.646,0,1,0,-0.29777,0,0,1,-1.2033
> view matrix models #1,1,0,0,15.181,0,1,0,-4.4582,0,0,1,-0.91014
> view matrix models #1,1,0,0,-15.467,0,1,0,-15.673,0,0,1,15.003
> view matrix models #1,1,0,0,-18.434,0,1,0,-4.2218,0,0,1,-10.466
> view matrix models #1,1,0,0,-39.086,0,1,0,-2.3932,0,0,1,-42.474
> view matrix models #1,1,0,0,-7.3595,0,1,0,2.1169,0,0,1,-20.622
> view matrix models #1,1,0,0,56.725,0,1,0,-22.296,0,0,1,-11.337
> view matrix models #1,1,0,0,58.82,0,1,0,-0.298,0,0,1,12.068
> close session
> open /Users/madhurikanavalli/Downloads/cryosparc_P1_J482_004_volume_map.mrc
Opened cryosparc_P1_J482_004_volume_map.mrc as #1, grid size 352,352,352,
pixel 0.846, shown at level 0.0477, step 2, values float32
> volume #1 level 0.06529
> volume #1 level 0.09016
> volume #1 level 0.06115
> open /Users/madhurikanavalli/Downloads/AF-Q8TCS8-F1-model_v6.pdb
AF-Q8TCS8-F1-model_v6.pdb title:
Alphafold monomer V2.0 prediction for polyribonucleotide
nucleotidyltransferase 1, mitochondrial (Q8TCS8) [more info...]
Chain information for AF-Q8TCS8-F1-model_v6.pdb #2
---
Chain | Description | UniProt
A | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 1-783
Computing secondary structure
> tile
2 models tiled
> select add #2
6032 atoms, 6129 bonds, 783 residues, 1 model selected
> view matrix models #2,1,0,0,132.15,0,1,0,269.68,0,0,1,174.53
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.42944,0.66337,0.61279,141.41,0.035656,-0.69047,0.72248,301.34,0.90239,-0.28841,-0.32017,144.99
> transparency 50
> view matrix models
> #2,0.63269,0.58288,0.50986,140.27,0.123,-0.72566,0.67697,300.82,0.76458,-0.3656,-0.53081,138.86
> view matrix models
> #2,0.60082,0.75463,0.26374,132.09,0.39851,-0.56876,0.71952,302.55,0.69297,-0.32719,-0.64245,135.08
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.60082,0.75463,0.26374,148.79,0.39851,-0.56876,0.71952,180.76,0.69297,-0.32719,-0.64245,188.93
> view matrix models
> #2,0.6614,0.18966,0.72565,161.37,0.2615,-0.9651,0.0139,190.89,0.70297,0.18057,-0.68792,178.28
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.19924,0.94382,-0.26363,126.11,0.83456,-0.022419,0.55046,202.79,0.51363,-0.32969,-0.79215,177.72
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.19924,0.94382,-0.26363,128.38,0.83456,-0.022419,0.55046,186.45,0.51363,-0.32969,-0.79215,184.65
> view matrix models
> #2,0.58266,0.81137,0.046707,142.97,0.47764,-0.38837,0.78805,177.72,0.65754,-0.43686,-0.61384,190.77
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.57664,0.24616,0.77903,167.09,-0.2162,-0.87356,0.43606,167.17,0.78787,-0.41988,-0.45051,195.95
> view matrix models
> #2,0.76261,0.6462,-0.029199,143.01,0.45171,-0.4997,0.73909,176.95,0.46301,-0.57683,-0.67297,188.94
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.76261,0.6462,-0.029199,142.26,0.45171,-0.4997,0.73909,182.18,0.46301,-0.57683,-0.67297,186.98
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.8634,0.49418,-0.10162,141.85,0.3123,-0.3653,0.87694,184.3,0.39625,-0.78889,-0.46973,193.67
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.72969,0.68377,0.0039503,132.51,0.33003,-0.35725,0.87376,248.15,0.59886,-0.63627,-0.48634,180.84
> view matrix models
> #2,0.066442,0.43084,-0.89998,103.3,0.93501,0.288,0.2069,257.15,0.34834,-0.85524,-0.3837,150.16
> view matrix models
> #2,0.23351,-0.30901,0.92195,156.19,-0.87131,-0.48737,0.057337,254.89,0.43161,-0.81669,-0.38305,176.46
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.80143,0.40414,0.44089,141.31,0.16742,-0.85928,0.48333,275.26,0.57418,-0.31354,-0.75631,163.52
> view matrix models
> #2,0.84875,0.50355,0.16142,133.15,0.28808,-0.6963,0.65741,279.7,0.44344,-0.51147,-0.73604,164.66
> view matrix models
> #2,0.86791,0.39835,0.29673,137.73,0.20619,-0.83241,0.51438,276.16,0.45191,-0.38525,-0.80459,161.95
> view matrix models
> #2,0.86632,0.49881,-0.026064,128.07,0.28331,-0.44774,0.84809,283.3,0.41136,-0.74211,-0.5292,171.77
> view matrix models
> #2,0.49235,0.85007,0.18702,129.46,0.42603,-0.42273,0.79988,282.62,0.75901,-0.31414,-0.57028,169.77
> view matrix models
> #2,0.85019,0.48331,0.20878,134.61,0.064393,-0.48905,0.86988,282.92,0.52253,-0.72611,-0.4469,174.6
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.85019,0.48331,0.20878,150.49,0.064393,-0.48905,0.86988,188.61,0.52253,-0.72611,-0.4469,184.74
> view matrix models
> #2,0.64449,0.16707,0.74614,168.48,-0.5504,-0.576,0.60439,164.48,0.53075,-0.80019,-0.27927,193.65
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.76356,0.63639,0.10946,148.31,0.32497,-0.52519,0.78649,174.28,0.558,-0.56497,-0.60782,183.09
> view matrix models
> #2,0.73909,0.6609,-0.13024,141.34,0.49027,-0.39519,0.77682,174.09,0.46193,-0.63799,-0.6161,182.8
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.73909,0.6609,-0.13024,139.59,0.49027,-0.39519,0.77682,180.83,0.46193,-0.63799,-0.6161,188.6
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.54319,0.83658,-0.071278,138.91,0.55669,-0.29531,0.77646,180.54,0.62852,-0.46144,-0.62613,188.1
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.75355,0.36167,0.54895,167.57,-0.16644,-0.70289,0.69155,141.22,0.63597,-0.61249,-0.46947,186.49
> view matrix models
> #2,-0.30331,-0.83983,0.45021,143.72,-0.74643,-0.084284,-0.66011,224.32,0.59232,-0.53627,-0.60131,183.9
> view matrix models
> #2,0.58684,-0.34812,0.73105,150.57,-0.47667,-0.87836,-0.035635,264.27,0.65453,-0.32756,-0.6814,180.79
> view matrix models
> #2,0.58684,-0.34812,0.73105,148.38,-0.47667,-0.87836,-0.035635,276.44,0.65453,-0.32756,-0.6814,180.97
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.63354,0.76624,0.10724,123.81,0.39183,-0.43726,0.80949,302.01,0.66715,-0.47082,-0.57726,184.9
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.63354,0.76624,0.10724,144.96,0.39183,-0.43726,0.80949,181.31,0.66715,-0.47082,-0.57726,189.07
> view matrix models
> #2,0.71133,0.30401,0.63372,164.61,-0.18947,-0.78531,0.5894,164.41,0.67684,-0.53933,-0.50101,194.83
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 6032 atoms
average map value = 0.04859, steps = 152
shifted from previous position = 3.28
rotated from previous position = 5.39 degrees
atoms outside contour = 4287, contour level = 0.06115
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.56426932 0.76409521 0.31266369 143.04419452
0.21814827 -0.50324783 0.83615363 170.83785223
0.79624833 -0.40360881 -0.45065337 194.48298911
Axis -0.86191870 -0.33620203 -0.37955810
Axis point 0.00000000 81.61235096 44.75810236
Rotation angle (degrees) 134.01255267
Shift along axis -254.54609246
> view matrix models
> #2,0.3492,0.93478,0.065211,136.26,0.66686,-0.2968,0.68352,191.6,0.6583,-0.1952,-0.72701,180.45
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.89941,-0.31265,0.30546,154.53,-0.35641,-0.92913,0.098419,173.65,0.25305,-0.19739,-0.9471,171.99
> view matrix models
> #2,0.83384,0.55193,-0.008982,139.59,0.4892,-0.73133,0.47523,187.7,0.25573,-0.40066,-0.87981,175.24
> view matrix models
> #2,0.64415,0.75125,0.14382,141.39,0.64873,-0.63619,0.41762,186.39,0.40524,-0.17572,-0.89717,174.12
> ui mousemode right "move picked models"
> view matrix models
> #1,0.87519,0.38044,-0.29884,-2.3734,-0.45145,0.86428,-0.22185,170.72,0.17388,0.32907,0.92816,-69.898
> volume #1 level 0.1131
> volume #1 level 0.07917
> view matrix models
> #2,-0.10638,-0.94919,0.29618,133.6,-0.9431,0.0019433,-0.3325,286.13,0.31503,-0.3147,-0.89539,123
> select #1/A:760-783
Nothing selected
> select #2/A:760-783
180 atoms, 180 bonds, 24 residues, 1 model selected
> delete sel
> select #2/1-598
Nothing selected
> select #2/A:1-598
4596 atoms, 4670 bonds, 598 residues, 1 model selected
> delete sel
> ui mousemode right "rotate selected models"
> select add #2
1256 atoms, 1277 bonds, 161 residues, 1 model selected
> view matrix models
> #2,0.6471,0.64962,0.39906,131.95,-0.0059555,-0.5191,0.85469,367.73,0.76238,-0.55545,-0.33205,150
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.6471,0.64962,0.39906,125.43,-0.0059555,-0.5191,0.85469,234.19,0.76238,-0.55545,-0.33205,186.89
> view matrix models
> #2,0.52432,0.60365,0.60057,138.39,0.096076,-0.74273,0.66266,241.7,0.84608,-0.28975,-0.44743,177.45
> view matrix models
> #2,0.58461,0.53787,0.60739,138.89,-0.0034217,-0.74701,0.6648,246.96,0.81131,-0.39073,-0.43487,176.3
> ui mousemode right "move picked models"
> view matrix models
> #1,0.99119,-0.014958,-0.1316,23.999,0.0189,0.99941,0.028756,83.761,0.13109,-0.030989,0.99089,-73.95
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.58461,0.53787,0.60739,147.74,-0.0034217,-0.74701,0.6648,281.09,0.81131,-0.39073,-0.43487,122.35
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 1256 atoms
average map value = 0.05979, steps = 140
shifted from previous position = 3.87
rotated from previous position = 19.7 degrees
atoms outside contour = 892, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.69579863 0.56968136 0.43740983 146.46213387
-0.14760186 -0.48259090 0.86331897 199.16111950
0.70290675 -0.66525869 -0.25170006 197.09026824
Axis -0.89429762 -0.15532954 -0.41964808
Axis point 0.00000000 116.56159785 13.49387603
Rotation angle (degrees) 121.28170019
Shift along axis -244.62489409
> view matrix models
> #2,0.64344,0.55251,0.52983,143.2,-0.18754,-0.55726,0.80888,290.18,0.74217,-0.61983,-0.25495,141.57
> view matrix models
> #2,0.31612,0.83453,-0.45126,95.295,0.56826,0.21433,0.79445,277.99,0.75971,-0.50757,-0.40647,132.89
> view matrix models
> #2,-0.86195,-0.25115,-0.44043,128.41,-0.093041,0.93229,-0.34954,173.5,0.49839,-0.2603,-0.82695,98.206
> view matrix models
> #2,0.65233,0.046187,0.75653,156.98,-0.2638,-0.9219,0.28375,231.83,0.71055,-0.38467,-0.5892,137.62
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.81295,-0.58161,0.028996,122.48,-0.56819,-0.78132,0.25828,234.38,-0.12756,-0.22645,-0.96563,130.95
> view matrix models
> #2,-0.96437,-0.16164,-0.20942,136.53,-0.11386,0.96816,-0.22294,185.23,0.23878,-0.19116,-0.95207,125.06
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.96437,-0.16164,-0.20942,138.86,-0.11386,0.96816,-0.22294,195.83,0.23878,-0.19116,-0.95207,110.89
> view matrix models
> #2,0.78818,0.14656,0.59774,147.24,-0.054142,-0.95095,0.30456,271.11,0.61306,-0.27241,-0.74159,120.56
> view matrix models
> #2,0.92372,0.30232,0.23524,127.49,-0.038846,0.68486,-0.72764,196.22,-0.38109,0.663,0.64437,183.01
> view matrix models
> #2,0.92372,0.30232,0.23524,121.11,-0.038846,0.68486,-0.72764,201.1,-0.38109,0.663,0.64437,222.65
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.13548,-0.69196,-0.70912,99.679,-0.31493,-0.64852,0.69299,291.92,-0.93939,0.31721,-0.13006,195.35
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.13548,-0.69196,-0.70912,105.56,-0.31493,-0.64852,0.69299,261.53,-0.93939,0.31721,-0.13006,158.07
> view matrix models
> #2,-0.31376,-0.10292,-0.94391,84.999,-0.37062,-0.90198,0.22155,314.04,-0.87418,0.41934,0.24486,213.94
> view matrix models
> #2,0.23037,-0.936,-0.26616,124.75,-0.098671,-0.29457,0.95052,259,-0.96809,-0.19271,-0.16022,160.32
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.51055,-0.83648,-0.19907,122.5,-0.11184,-0.29416,0.94919,259.15,-0.85254,-0.46235,-0.24374,156.56
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.51055,-0.83648,-0.19907,122.82,-0.11184,-0.29416,0.94919,256.93,-0.85254,-0.46235,-0.24374,154.51
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.4007,-0.62248,-0.67228,111.87,-0.21408,-0.64984,0.7293,250.64,-0.89085,0.43616,0.12713,165.9
> ui mousemode right "translate selected models"
[Repeated 2 time(s)]
> view matrix models
> #2,-0.4007,-0.62248,-0.67228,113.93,-0.21408,-0.64984,0.7293,255.19,-0.89085,0.43616,0.12713,153.24
> ui tool show "Map Filter"
> volume gaussian #1 sDev 0.42
Opened cryosparc_P1_J482_004_volume_map.mrc gaussian as #3, grid size
352,352,352, pixel 0.846, shown at step 1, values float32
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 1256 atoms
average map value = 0.04212, steps = 80
shifted from previous position = 5.77
rotated from previous position = 6.87 degrees
atoms outside contour = 1022, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.14765691 -0.51103760 -0.84678093 101.20040909
0.33912440 0.77810326 -0.52872480 135.10645661
0.92908129 -0.36523397 0.05841302 88.77346607
Axis 0.08275295 -0.89887510 0.43032024
Axis point -0.71225091 0.00000000 127.79384097
Rotation angle (degrees) 98.94987464
Shift along axis -74.86817754
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> view matrix models
> #2,-0.45927,-0.66663,-0.58709,119.96,-0.13295,-0.60189,0.78744,265.8,-0.87829,0.4397,0.1878,186.5
> hide #!3 models
> close #3
> view matrix models
> #2,0.77415,0.41998,-0.4736,92.737,-0.24702,-0.48843,-0.83691,197.65,-0.58281,0.76488,-0.27438,166.01
> view matrix models
> #2,0.75644,0.34979,0.55267,145.43,0.10707,0.76736,-0.63222,187.93,-0.64524,0.53741,0.54301,220.16
> view matrix models
> #2,0.70708,-0.70671,-0.024594,127.59,-0.32887,-0.35943,0.8733,284.08,-0.62601,-0.6094,-0.48656,169.56
> view matrix models
> #2,0.70708,-0.70671,-0.024594,129.66,-0.32887,-0.35943,0.8733,293.52,-0.62601,-0.6094,-0.48656,156.99
> view matrix models
> #2,0.99039,-0.12068,-0.067563,115.55,-0.028314,-0.65509,0.75502,280.22,-0.13537,-0.74586,-0.65221,150.64
> show #!1 models
> transparency 0
> transparency 50
> view matrix models
> #2,0.8449,0.48463,0.22644,131.66,0.11966,-0.58382,0.80302,264.44,0.52137,-0.65138,-0.55126,117.9
> view matrix models
> #2,0.38736,0.91086,0.1424,130.54,0.57477,-0.35937,0.73518,271.04,0.72083,-0.20294,-0.66274,108.58
> view matrix models
> #2,-0.38746,-0.87366,-0.29427,135.28,0.3028,-0.42209,0.85449,293.62,-0.87074,0.24197,0.42809,205.05
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.17337,-0.56863,-0.80411,96.434,-0.65603,-0.67565,0.33634,285.56,-0.73455,0.46921,-0.49018,153.04
> view matrix models
> #2,0.86201,-0.50664,0.016077,126.55,-0.38189,-0.62824,0.67785,298.11,-0.33332,-0.59045,-0.73503,143.5
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.86201,-0.50664,0.016077,128.49,-0.38189,-0.62824,0.67785,285.93,-0.33332,-0.59045,-0.73503,131.16
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 1256 atoms
average map value = 0.06804, steps = 208
shifted from previous position = 4.34
rotated from previous position = 49.4 degrees
atoms outside contour = 775, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.04261260 0.99909171 -0.00032583 124.39404394
0.54482783 -0.02351097 -0.83821837 104.44003070
-0.83746464 0.03554113 -0.54533477 199.64463617
Axis 0.67601140 0.64767865 -0.35145548
Axis point 0.00000000 -69.26766377 146.15003188
Rotation angle (degrees) 139.73972107
Shift along axis 81.56916779
> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/S1_KH_AF_Q8TCS8.pdb
> select #2/A:599-680
634 atoms, 645 bonds, 82 residues, 1 model selected
> select #2/A:599-678
625 atoms, 636 bonds, 80 residues, 1 model selected
> delete sel
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms
average map value = 0.08786, steps = 116
shifted from previous position = 6.49
rotated from previous position = 8.34 degrees
atoms outside contour = 299, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.08642435 0.98758308 -0.13118947 114.63946268
0.49800827 -0.15687479 -0.85286471 106.34543108
-0.86285503 0.00837483 -0.50538229 203.22585816
Axis 0.69930517 0.59409431 -0.39752262
Axis point 0.00000000 -51.69253347 151.23207638
Rotation angle (degrees) 141.99121366
Shift along axis 62.56030846
> select add #2
631 atoms, 640 bonds, 81 residues, 1 model selected
> view matrix models
> #2,-0.12421,-0.93788,0.32398,174.03,-0.66983,0.32014,0.66996,284.8,-0.73205,-0.13379,-0.66798,133.24
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms
average map value = 0.06691, steps = 176
shifted from previous position = 13.3
rotated from previous position = 44.4 degrees
atoms outside contour = 409, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.08570214 0.84446583 0.52870857 166.53390201
0.80947457 0.25036444 -0.53110145 116.83892504
-0.58086681 0.47349266 -0.66211680 176.42251434
Axis 0.67098439 0.74110306 -0.02337122
Axis point 85.33225300 0.00000000 79.05264705
Rotation angle (degrees) 131.53099228
Shift along axis 194.20812316
> undo
> ui tool show "Fit Loops"
> select #2/A:678-750
568 atoms, 576 bonds, 72 residues, 1 model selected
> help help:user/selection.html
> select #2/A:678-759
631 atoms, 640 bonds, 81 residues, 1 model selected
> select add #1
631 atoms, 640 bonds, 81 residues, 3 models selected
> ui tool show "Fit Loops"
> select #2/A:678-759
631 atoms, 640 bonds, 81 residues, 1 model selected
> view matrix models
> #2,-0.080102,0.99257,0.091628,132.2,0.78592,0.11943,-0.60668,151.24,-0.61311,0.023417,-0.78965,108.42
> view matrix models
> #2,-0.72601,0.14287,0.67268,201.64,0.41779,0.8686,0.26644,223.05,-0.54622,0.47448,-0.6903,110.38
> view matrix models
> #2,0.41003,-0.81571,-0.40804,121.18,-0.77968,-0.54561,0.30724,268.36,-0.47325,0.19216,-0.85971,105.09
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms
average map value = 0.06322, steps = 88
shifted from previous position = 3.4
rotated from previous position = 9.25 degrees
atoms outside contour = 424, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.03035950 0.89245803 0.45010791 155.53133934
0.87362537 0.19510483 -0.44577237 120.58172191
-0.48565132 0.40675911 -0.77375062 165.41563616
Axis 0.67339426 0.73913388 -0.01487547
Axis point 63.44943971 0.00000000 77.49031568
Rotation angle (degrees) 140.72740844
Shift along axis 191.39931233
> view matrix models
> #2,-0.2609,0.80697,0.52985,161.6,-0.79532,-0.49076,0.35582,304.63,0.54717,-0.32857,0.76984,238.37
> view matrix models
> #2,-0.2609,0.80697,0.52985,162.1,-0.79532,-0.49076,0.35582,311.26,0.54717,-0.32857,0.76984,235.39
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.79732,-0.18475,-0.57458,82.674,0.32329,0.93464,0.14809,246.3,0.50967,-0.30383,0.80494,238.13
> view matrix models
> #2,-0.26525,0.76742,0.5837,166.72,0.96297,0.1805,0.2003,251.51,0.048357,0.61522,-0.78687,118.67
> view matrix models
> #2,-0.5306,0.57497,0.62279,178.59,0.83975,0.45646,0.29404,255.22,-0.11521,0.67901,-0.72503,125.08
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.5306,0.57497,0.62279,182.25,0.83975,0.45646,0.29404,229.39,-0.11521,0.67901,-0.72503,101.71
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms
average map value = 0.07811, steps = 376
shifted from previous position = 14.4
rotated from previous position = 20.2 degrees
atoms outside contour = 373, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07173609 0.89418681 0.44190955 152.95290020
0.99703897 0.07659145 0.00687161 107.65452962
-0.02770198 0.44109399 -0.89703339 138.81763398
Axis 0.67028894 0.72491753 0.15876812
Axis point 38.94893660 -0.00000000 55.65097782
Rotation angle (degrees) 161.10063978
Shift along axis 202.60310684
> fitmap #2 inMap #1
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms
average map value = 0.07811, steps = 60
shifted from previous position = 0.00204
rotated from previous position = 0.0118 degrees
atoms outside contour = 372, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07176106 0.89413760 0.44200504 152.95957123
0.99704175 0.07653997 0.00703955 107.66663533
-0.02753672 0.44120265 -0.89698504 138.81658330
Axis 0.67028233 0.72490165 0.15886848
Axis point 38.94180658 0.00000000 55.64258504
Rotation angle (degrees) 161.10312462
Shift along axis 202.62739965
> fitmap #2 inMap #1 search 100
Found 87 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (87 of 100).
Average map values and times found:
0.08675 (1), 0.0858 (1), 0.08496 (1), 0.08402 (1), 0.08091 (1), 0.07993 (1),
0.07989 (1), 0.07882 (1), 0.07649 (1), 0.07503 (1), 0.07278 (1), 0.07178 (1),
0.07137 (1), 0.07135 (1), 0.07125 (1), 0.07038 (1), 0.06968 (1), 0.0696 (1),
0.06958 (1), 0.06919 (1), 0.06882 (1), 0.06881 (1), 0.06872 (1), 0.06856 (1),
0.06817 (1), 0.06804 (1), 0.06775 (1), 0.067 (1), 0.06694 (1), 0.06685 (1),
0.06679 (1), 0.06644 (1), 0.06608 (1), 0.06546 (1), 0.06522 (1), 0.06505 (1),
0.06501 (1), 0.06456 (1), 0.06449 (1), 0.06445 (1), 0.06412 (1), 0.06391 (1),
0.06383 (1), 0.06328 (1), 0.06317 (1), 0.06302 (1), 0.06279 (1), 0.06259 (1),
0.06247 (1), 0.06224 (1), 0.06208 (1), 0.06175 (1), 0.06135 (1), 0.06096 (1),
0.06089 (1), 0.06063 (1), 0.06061 (1), 0.06049 (1), 0.06034 (1), 0.06004 (1),
0.05993 (1), 0.05944 (1), 0.05883 (1), 0.05862 (1), 0.05856 (1), 0.05812 (1),
0.05806 (1), 0.05762 (1), 0.05748 (1), 0.05743 (1), 0.05698 (1), 0.05681 (1),
0.05641 (1), 0.05503 (1), 0.05483 (1), 0.05464 (1), 0.05438 (1), 0.05405 (1),
0.05346 (1), 0.05336 (1), 0.05331 (1), 0.05263 (1), 0.05247 (1), 0.05073 (1),
0.04919 (1), 0.04544 (1), 0.0362 (1)
Best fit found:
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms
average map value = 0.08675, steps = 68
shifted from previous position = 1.68
rotated from previous position = 1.81 degrees
atoms outside contour = 358, contour level = 0.079169
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.70736822 -0.65675968 0.26133708 180.10612296
0.21398252 -0.15340721 -0.96471646 104.42350305
0.67367783 0.73833129 0.03201965 146.82400859
Axis 0.87037715 -0.21073512 0.44501049
Axis point 0.00000000 47.11093603 95.62601638
Rotation angle (degrees) 101.94716792
Shift along axis 200.09277743
Found 87 fits.
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #10 models
> hide #2 models
> select subtract #2
Nothing selected
> select add #10
631 atoms, 640 bonds, 81 residues, 1 model selected
> view matrix models
> #10,-0.76824,-0.34676,-0.53812,99.406,-0.30813,-0.53651,0.78563,251.71,-0.56113,0.76936,0.30532,130.5
> view matrix models
> #10,0.0083816,-0.32273,-0.94645,48.86,-0.68359,-0.69264,0.23013,270.4,-0.72982,0.64506,-0.22642,136.05
> view matrix models
> #10,0.40111,0.42379,-0.8121,36.805,-0.50188,-0.63997,-0.58186,252.21,-0.76631,0.64097,-0.044006,144.17
> view matrix models
> #10,0.42445,0.50945,-0.74854,38.601,0.14388,-0.85414,-0.49974,187.19,-0.89395,0.10441,-0.43584,131.32
> view matrix models
> #10,0.14263,0.44845,0.88235,158.31,0.50713,0.73245,-0.45424,158.91,-0.84999,0.51225,-0.12295,150.79
> view matrix models
> #10,-0.53518,0.37484,0.75702,165.86,0.57045,0.82133,-0.0034073,164.81,-0.62304,0.43002,-0.65338,103.74
> view matrix models
> #10,-0.3295,0.66242,0.67278,141.81,0.70653,0.64567,-0.2897,186.36,-0.6263,0.37989,-0.68076,156.02
Desktop color scheme is dark
> close session
> open /Users/madhurikanavalli/Downloads/cryosparc_P1_J275_004_volume_map.mrc
Opened cryosparc_P1_J275_004_volume_map.mrc as #1, grid size 450,450,450,
pixel 0.846, shown at level 0.00835, step 2, values float32
> volume #1 level 0.03433
> open /Users/madhurikanavalli/Downloads/cryosparc_P1_J482_004_volume_map.mrc
Opened cryosparc_P1_J482_004_volume_map.mrc as #2, grid size 352,352,352,
pixel 0.846, shown at level 0.0477, step 2, values float32
> tile
2 models tiled
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11B0002QZE/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0.1 (25A362)
Kernel Version: Darwin 25.0.0
Time since boot: 2 days, 4 hours, 32 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.7.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.16
ChimeraX-AtomicLibrary: 14.1.23
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-clix: 0.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202509040038
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.1
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-maskChains: 1.4
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.9
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.3.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.48.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.3.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.10.6
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.3
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
finufft: 2.4.1
fonttools: 4.59.2
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2025.4.15
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.5
matplotlib-inline: 0.1.7
msgpack: 1.1.1
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.4.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.2
qtconsole: 5.6.1
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 4 weeks ago
| Component: | Unassigned → DICOM |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Orthoplanes: 'NoneType' object has no attribute 'image_colors' |
comment:2 by , 4 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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