Orthoplanes: 'NoneType' object has no attribute 'image_colors'

[chimerax-bug-report@…]

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  
  

> select add #3

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> select subtract #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #3

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models #3,1,0,0,-29.495,0,1,0,-74.165,0,0,1,7.8615

> view matrix models #3,1,0,0,-30.191,0,1,0,-73.496,0,0,1,19.042

> select add #4

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> view matrix models
> #4,0.43664,-0.89777,0.05801,169.54,0.24953,0.18281,0.95095,76.564,-0.86434,-0.40075,0.30385,338.08,#3,1,0,0,-33.957,0,1,0,-141.45,0,0,1,73.984

> select subtract #4

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models #3,1,0,0,-6.382,0,1,0,-37.244,0,0,1,78.169

> view matrix models #3,1,0,0,7.1074,0,1,0,14.723,0,0,1,79.588

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.39782,0.91744,-0.0062689,97.728,0.85434,0.36795,-0.36705,23.539,-0.33444,-0.15137,-0.93018,435.14

> hide #!4 models

> view matrix models
> #3,-0.64157,-0.026449,-0.76661,423.28,0.15277,0.97498,-0.16149,13.079,0.7517,-0.22072,-0.62148,203.2

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.64157,-0.026449,-0.76661,427.84,0.15277,0.97498,-0.16149,14.341,0.7517,-0.22072,-0.62148,195.08

> 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 = 44  
shifted from previous position = 0.014  
rotated from previous position = 0.0147 degrees  
atoms outside contour = 6338, 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  
-0.56177320 0.76214508 0.32178525 177.76212068  
0.56493063 0.06925504 0.82222693 70.73071438  
0.60437096 0.64369139 -0.46946473 68.59002634  
Axis -0.46002220 -0.72812228 -0.50815109  
Axis point 67.67059892 0.00000000 16.36862818  
Rotation angle (degrees) 168.81070899  
Shift along axis -168.12922648  
  

> 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 = 44  
shifted from previous position = 0.00118  
rotated from previous position = 0.00555 degrees  
atoms outside contour = 6338, 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  
-0.56180042 0.76212365 0.32178849 177.76456401  
0.56497732 0.06932409 0.82218903 70.72650702  
0.60430201 0.64370934 -0.46952888 68.59710591  
Axis -0.46001209 -0.72814803 -0.50812333  
Axis point 67.67325732 0.00000000 16.37390083  
Rotation angle (degrees) 168.81400533  
Shift along axis -168.12900552  
  

> 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 = 44  
shifted from previous position = 0.0011  
rotated from previous position = 0.00219 degrees  
atoms outside contour = 6340, 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  
-0.56181677 0.76211115 0.32178954 177.76628394  
0.56499162 0.06935189 0.82217686 70.72533923  
0.60427344 0.64372114 -0.46954946 68.59902440  
Axis -0.46000509 -0.72815841 -0.50811479  
Axis point 67.67475916 0.00000000 16.37531817  
Rotation angle (degrees) 168.81535483  
Shift along axis -168.12882574  
  

> view matrix models
> #3,-0.64157,-0.026449,-0.76661,428.14,0.15277,0.97498,-0.16149,13.695,0.7517,-0.22072,-0.62148,197.78

> view matrix models
> #3,-0.64157,-0.026449,-0.76661,429.22,0.15277,0.97498,-0.16149,10.389,0.7517,-0.22072,-0.62148,201.96

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.91507,0.12718,-0.38272,398.89,0.29913,0.85053,-0.43258,43.498,0.2705,-0.51032,-0.81633,372.32

> view matrix models
> #3,-0.93066,0.25206,-0.26522,362.41,0.34092,0.86054,-0.37847,26.413,0.13284,-0.44264,-0.8868,395.06

> 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 = 44  
shifted from previous position = 0.00109  
rotated from previous position = 0.0011 degrees  
atoms outside contour = 6339, 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  
-0.56180508 0.76212041 0.32178802 177.76501259  
0.56498774 0.06933961 0.82218056 70.72555730  
0.60428793 0.64371150 -0.46954404 68.59878002  
Axis -0.46001046 -0.72815376 -0.50811660  
Axis point 67.67377478 0.00000000 16.37519960  
Rotation angle (degrees) 168.81464010  
Shift along axis -168.12902480  
  

> 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 = 44  
shifted from previous position = 0.0013  
rotated from previous position = 0.00174 degrees  
atoms outside contour = 6340, 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  
-0.56182107 0.76210821 0.32178898 177.76676058  
0.56499631 0.06936111 0.82217285 70.72493750  
0.60426505 0.64372363 -0.46955686 68.59974743  
Axis -0.46000327 -0.72816181 -0.50811158  
Axis point 67.67518917 0.00000000 16.37588980  
Rotation angle (degrees) 168.81572170  
Shift along axis -168.12881525  
  

> 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 = 44  
shifted from previous position = 0.0015  
rotated from previous position = 0.00184 degrees  
atoms outside contour = 6339, 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  
-0.56180367 0.76212182 0.32178714 177.76486802  
0.56498749 0.06933911 0.82218077 70.72556637  
0.60428947 0.64370988 -0.46954426 68.59886768  
Axis -0.46001109 -0.72815353 -0.50811636  
Axis point 67.67366634 -0.00000000 16.37528860  
Rotation angle (degrees) 168.81453944  
Shift along axis -168.12908826  
  

> 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 = 44  
shifted from previous position = 0.00161  
rotated from previous position = 0.00195 degrees  
atoms outside contour = 6340, 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  
-0.56182168 0.76210791 0.32178865 177.76684825  
0.56499718 0.06936289 0.82217211 70.72490535  
0.60426368 0.64372379 -0.46955839 68.59980313  
Axis -0.46000301 -0.72816245 -0.50811088  
Axis point 67.67525750 0.00000000 16.37595603  
Rotation angle (degrees) 168.81577332  
Shift along axis -168.12881302  
  

> 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 = 44  
shifted from previous position = 0.0017  
rotated from previous position = 0.00202 degrees  
atoms outside contour = 6339, 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  
-0.56180300 0.76212254 0.32178662 177.76481731  
0.56498709 0.06933868 0.82218108 70.72559720  
0.60429047 0.64370908 -0.46954407 68.59886938  
Axis -0.46001136 -0.72815335 -0.50811637  
Axis point 67.67362036 0.00000000 16.37530466  
Rotation angle (degrees) 168.81447555  
Shift along axis -168.12912509  
  

> 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 = 44  
shifted from previous position = 0.00172  
rotated from previous position = 0.00207 degrees  
atoms outside contour = 6340, 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  
-0.56182263 0.76210752 0.32178790 177.76699161  
0.56499677 0.06936407 0.82217229 70.72494421  
0.60426317 0.64372412 -0.46955859 68.59983213  
Axis -0.46000248 -0.72816286 -0.50811078  
Axis point 67.67535296 0.00000000 16.37598872  
Rotation angle (degrees) 168.81576963  
Shift along axis -168.12884954  
  

> 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 = 44  
shifted from previous position = 0.00176  
rotated from previous position = 0.00204 degrees  
atoms outside contour = 6338, 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  
-0.56180310 0.76212248 0.32178657 177.76482158  
0.56498745 0.06933920 0.82218079 70.72554566  
0.60429004 0.64370910 -0.46954462 68.59896224  
Axis -0.46001133 -0.72815354 -0.50811613  
Axis point 67.67363504 0.00000000 16.37537496  
Rotation angle (degrees) 168.81449424  
Shift along axis -168.12912781  
  

> select add #1

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> view matrix models
> #1,-0.14985,0.98863,0.012626,183.06,0.38156,0.046045,0.9232,139.05,0.91212,0.14316,-0.38412,80.456,#3,-0.71358,-0.03176,-0.69986,455.85,0.2007,0.94783,-0.24765,11.335,0.67121,-0.31718,-0.66998,236.49

> view matrix models
> #1,0.70687,0.28057,0.64932,108.08,0.4226,-0.90364,-0.069595,177.3,0.56723,0.3236,-0.75732,116.2,#3,0.34115,0.69223,-0.63595,112.39,0.88425,-0.0067957,0.46696,-46.86,0.31892,-0.72165,-0.61442,370.77

> view matrix models
> #1,0.148,-0.90826,0.39135,209.41,0.70956,0.37316,0.59772,89.53,-0.68892,0.18923,0.6997,243.87,#3,0.63093,0.4315,0.64478,-110.94,0.29194,0.63795,-0.7126,129.47,-0.71882,0.63783,0.27653,139.68

> select add #2

17110 atoms, 17236 bonds, 2348 residues, 4 models selected  

> hide #!3 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 = 0.04801, steps = 284  
shifted from previous position = 22  
rotated from previous position = 25 degrees  
atoms outside contour = 7189, 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  
0.38285300 -0.90468146 0.18701612 126.18295836  
0.48235861 0.36841712 0.79473202 61.45913081  
-0.78787927 -0.21405670 0.57743049 239.44909763  
Axis -0.51134765 0.49416737 0.70308050  
Axis point 154.24471051 110.10948885 0.00000000  
Rotation angle (degrees) 80.54050570  
Shift along axis 134.19972853  
  

> view matrix models
> #2,0.9936,0.053643,0.099376,30.867,-0.051054,0.99829,-0.028415,60.494,-0.10073,0.023159,0.99464,39.57,#1,0.32798,-0.9004,0.28583,183.34,0.48438,0.42006,0.76742,108.6,-0.81105,-0.11325,0.57391,266.45,#3,0.57112,0.52635,0.62991,-115.99,0.27965,0.5967,-0.75216,145.55,-0.77176,0.60573,0.19359,168.43

> select subtract #3

8555 atoms, 8618 bonds, 1174 residues, 3 models selected  

> view matrix models
> #2,0.96755,0.032451,0.25059,15.256,-0.015944,0.99758,-0.067624,60.534,-0.25218,0.061434,0.96573,59.216,#1,0.18865,-0.91701,0.35144,199.34,0.52837,0.39643,0.75078,103.64,-0.82779,0.044056,0.5593,262.41

> select subtract #2

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #1,0.64787,-0.38882,0.65504,144.54,0.036303,0.8747,0.4833,147.87,-0.76089,-0.28934,0.58081,260.13

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.64787,-0.38882,0.65504,135.53,0.036303,0.8747,0.4833,160.4,-0.76089,-0.28934,0.58081,260.02

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.23258,-0.84668,0.47859,181.53,0.70575,0.48551,0.51595,108.3,-0.6692,0.21777,0.71046,241.92

> view matrix models
> #1,0.49293,-0.85966,-0.13421,180.79,0.52373,0.16999,0.83475,116.43,-0.69478,-0.48176,0.53402,258.42

> ui mousemode right "move picked models"

> view matrix models
> #2,0.96755,0.032451,0.25059,16.908,-0.015944,0.99758,-0.067624,59.82,-0.25218,0.061434,0.96573,63.354

> 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 = 0.1297, steps = 808  
shifted from previous position = 2.33  
rotated from previous position = 6.32 degrees  
atoms outside contour = 4645, 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  
0.57319897 -0.77448652 -0.26760710 116.68481785  
0.55163281 0.12322629 0.82493425 69.43518167  
-0.60592423 -0.62047232 0.49786536 223.43458404  
Axis -0.72613777 0.16996245 0.66621070  
Axis point 0.00000000 179.57744939 122.33493989  
Rotation angle (degrees) 84.42519184  
Shift along axis 75.92663194  
  

> select subtract #1

Nothing selected  

> ui tool show "Model Loops"

> ui tool show "Fit to Segments"

Density map not found or not selected  
[Repeated 3 time(s)]

> select add #2

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 = 0.1297, steps = 144  
shifted from previous position = 0.0143  
rotated from previous position = 0.0137 degrees  
atoms outside contour = 4641, 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  
0.57308626 -0.77449802 -0.26781512 116.69540535  
0.55179062 0.12306769 0.82485238 69.42161691  
-0.60588715 -0.62048944 0.49788915 223.41907541  
Axis -0.72609643 0.16983726 0.66628768  
Axis point 0.00000000 179.54103153 122.34637292  
Rotation angle (degrees) 84.43231602  
Shift along axis 75.91963727  
  

> 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 = 0.129, steps = 2000  
shifted from previous position = 0.23  
rotated from previous position = 0.448 degrees  
atoms outside contour = 4639, 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  
0.57258795 -0.77437910 -0.26922116 116.75226867  
0.54793977 0.11719931 0.82826706 69.68325907  
-0.60984017 -0.62177272 0.49142002 223.76402791  
Axis -0.72801419 0.17101288 0.66389000  
Axis point 0.00000000 179.16562442 122.41380851  
Rotation angle (degrees) 84.80166483  
Shift along axis 75.47412571  
  

> 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 = 0.1277, steps = 2000  
shifted from previous position = 0.609  
rotated from previous position = 0.904 degrees  
atoms outside contour = 4682, 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  
0.57348064 -0.77417828 -0.26789537 116.57776864  
0.55651791 0.12818804 0.82088709 68.70481792  
-0.60117198 -0.61985143 0.50435745 223.01355175  
Axis -0.72422213 0.16752956 0.66890669  
Axis point 0.00000000 179.52079300 122.52462323  
Rotation angle (degrees) 84.08729719  
Shift along axis 76.25714444  
  

> 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 = 0.129, steps = 2000  
shifted from previous position = 0.398  
rotated from previous position = 0.192 degrees  
atoms outside contour = 4689, 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  
0.57102733 -0.77539121 -0.26962241 116.96381429  
0.55768186 0.12537938 0.82053089 68.95823782  
-0.60242736 -0.61890909 0.50401667 222.89061469  
Axis -0.72336130 0.16724436 0.66990877  
Axis point 0.00000000 179.32454376 122.64471433  
Rotation angle (degrees) 84.24863936  
Shift along axis 76.24215771  
  

> hide #!1 models

> show #!1 models

> select add #1

8555 atoms, 8618 bonds, 1174 residues, 3 models selected  

> ui tool show "Show Sequence Viewer"

> select subtract #2

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> hide #!2 models

> select subtract #1

Nothing selected  

> select #1/A

4328 atoms, 4357 bonds, 597 residues, 1 model selected  

> select #1/B

4227 atoms, 4261 bonds, 577 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

[Repeated 1 time(s)]

> select add #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> select subtract #1

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B

Alignment identifier is 1/B  

> select #1/B:300

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/B:300-304

46 atoms, 47 bonds, 5 residues, 1 model selected  

> select #1/B:299-300

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #1/B:295-300

50 atoms, 51 bonds, 6 residues, 1 model selected  

> select #1/B:295

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:285-295

96 atoms, 97 bonds, 11 residues, 1 model selected  

> select #1/B:285

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/B:280-285

46 atoms, 46 bonds, 6 residues, 1 model selected  

> select #1/B:279

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:279-319

343 atoms, 350 bonds, 41 residues, 1 model selected  

> select #1/B:320

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/B:320-322

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select #1/B:277-278

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #1/B:277-288

100 atoms, 104 bonds, 12 residues, 1 model selected  

> select #1/B:277-278

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #1/B:277-307

263 atoms, 271 bonds, 31 residues, 1 model selected  

> select #1/B:279-319

343 atoms, 350 bonds, 41 residues, 1 model selected  

> select #1/B:277

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/B:277-335

498 atoms, 510 bonds, 59 residues, 1 model selected  

> select add #2

498 atoms, 510 bonds, 59 residues, 3 models selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> ui tool show "Fit to Segments"

Density map not found or not selected  
[Repeated 6 time(s)]

> select subtract #2

498 atoms, 510 bonds, 59 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 = 0.1289, steps = 2000  
shifted from previous position = 0.257  
rotated from previous position = 0.915 degrees  
atoms outside contour = 4632, 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  
0.57267166 -0.77461823 -0.26835379 116.74682003  
0.54692091 0.11716150 0.82894553 69.74141727  
-0.61067559 -0.62148191 0.49074998 223.83938491  
Axis -0.72818810 0.17186290 0.66347964  
Axis point 0.00000000 179.26106398 122.43296113  
Rotation angle (degrees) 84.81961892  
Shift along axis 75.48519232  
  

> select add #2

498 atoms, 510 bonds, 59 residues, 3 models selected  

> ui tool show "Fit to Segments"

Simulating map res 4.000, grid 2.000  

> molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 5zf6.pdb map 4 as #5, grid size 47,52,63, pixel 2, shown at level
0.104, step 1, values float32  
Please select an open structure to fit  

> select subtract #2

498 atoms, 510 bonds, 59 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 = 0.1276, steps = 2000  
shifted from previous position = 0.642  
rotated from previous position = 1.03 degrees  
atoms outside contour = 4675, 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  
0.95624965 0.12601838 -0.26401886 146.56566194  
0.23327279 0.21618286 0.94807635 145.55677599  
0.17655140 -0.96818610 0.17732813 184.05932290  
Axis -0.97312742 -0.22373293 0.05446655  
Axis point 0.00000000 174.29413134 29.54554523  
Rotation angle (degrees) 79.92830613  
Shift along axis -165.16783062  
  

> 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 = 0.1291, steps = 2000  
shifted from previous position = 0.427  
rotated from previous position = 0.28 degrees  
atoms outside contour = 4695, 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  
0.95531248 0.12439245 -0.26815027 146.59108838  
0.23788270 0.21497353 0.94720546 145.90157205  
0.17547042 -0.96866552 0.17577609 183.80822404  
Axis -0.97260592 -0.22520729 0.05761416  
Axis point 0.00000000 174.33443147 29.64460255  
Rotation angle (degrees) 80.03590204  
Shift along axis -164.84350294  
  

> 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 = 0.129, steps = 2000  
shifted from previous position = 0.223  
rotated from previous position = 0.829 degrees  
atoms outside contour = 4631, 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  
0.95523491 0.12627846 -0.26754441 146.55435334  
0.23947844 0.20095469 0.94987751 145.96486274  
0.17371337 -0.97142727 0.16171797 183.59795330  
Axis -0.97302339 -0.22347009 0.05732887  
Axis point 0.00000000 172.59699771 30.26934598  
Rotation angle (degrees) 80.85382484  
Shift along axis -164.69413167  
  

> select add #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 = 0.1276, steps = 2000  
shifted from previous position = 0.578  
rotated from previous position = 0.903 degrees  
atoms outside contour = 4673, 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  
0.95643333 0.12570810 -0.26350093 146.62391692  
0.23300137 0.21516139 0.94837541 145.55544584  
0.17591370 -0.96845394 0.17649737 184.00030683  
Axis -0.97326919 -0.22311257 0.05447811  
Axis point 0.00000000 174.18154237 29.52131391  
Rotation angle (degrees) 79.97685109  
Shift along axis -165.15580209  
  

> 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 = 0.1291, steps = 2000  
shifted from previous position = 0.363  
rotated from previous position = 0.352 degrees  
atoms outside contour = 4685, 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  
0.95497719 0.12448000 -0.26930149 146.60547981  
0.23896831 0.21519467 0.94688193 145.87389672  
0.17582011 -0.96860517 0.17575923 183.82784665  
Axis -0.97239968 -0.22596660 0.05812015  
Axis point 0.00000000 174.33808153 29.77706094  
Rotation angle (degrees) 80.03971295  
Shift along axis -164.83764797  
  

> volume gaussian #1 sDev 2

[Repeated 1 time(s)]

> hide #!2 models

> select subtract #1

Nothing selected  

> select :260-320

3024 atoms, 3078 bonds, 366 residues, 3 models selected  

> select add #3

10571 atoms, 10670 bonds, 1418 residues, 3 models selected  

> select add #4

18118 atoms, 18262 bonds, 2470 residues, 3 models selected  

> select subtract #4

9563 atoms, 9644 bonds, 1296 residues, 2 models selected  

> select subtract #3

1008 atoms, 1026 bonds, 122 residues, 1 model selected  

> select add #2

1008 atoms, 1026 bonds, 122 residues, 3 models selected  

> show #!2 models

> hide #!1 models

> volume guassian #1 stdev 2

Expected a density maps specifier or a keyword  

> select subtract #2

1008 atoms, 1026 bonds, 122 residues, 1 model selected  

> show #!1 models

> select add #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> select subtract #1

Nothing selected  

> hide #!2 models

> select :270-312

2172 atoms, 2226 bonds, 258 residues, 3 models selected  

> select :270-320

2568 atoms, 2622 bonds, 306 residues, 3 models selected  

> select add #2

2568 atoms, 2622 bonds, 306 residues, 5 models selected  

> show #!2 models

> select subtract #2

2568 atoms, 2622 bonds, 306 residues, 3 models selected  

> fitmap #1 inMap #5

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6588, steps = 44  
shifted from previous position = 0.251  
rotated from previous position = 0.917 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of 5zf6.pdb (#1) relative to 5zf6.pdb map 4 (#5) coordinates:  
Matrix rotation and translation  
0.99999998 -0.00021839 -0.00002624 -0.00561747  
0.00021838 0.99999996 -0.00015664 -0.02705654  
0.00002627 0.00015663 0.99999999 -0.00142914  
Axis 0.58007012 -0.09724114 0.80874150  
Axis point 124.68665962 -20.99976529 -0.00000000  
Rotation angle (degrees) 0.01547148  
Shift along axis -0.00178332  
  

> 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 = 0.1297, steps = 192  
shifted from previous position = 0.223  
rotated from previous position = 0.497 degrees  
atoms outside contour = 4641, 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  
0.95551911 0.12624268 -0.26654456 146.57951723  
0.23725555 0.20782832 0.94895584 145.98336518  
0.17519424 -0.96998462 0.16863216 183.82012764  
Axis -0.97296776 -0.22397652 0.05628729  
Axis point 0.00000000 173.45562784 29.89819058  
Rotation angle (degrees) 80.44526139  
Shift along axis -164.96725473  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1297, steps = 116  
shifted from previous position = 0.00753  
rotated from previous position = 0.0169 degrees  
atoms outside contour = 4645, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1297, steps = 340  
shifted from previous position = 0.00951  
rotated from previous position = 0.0154 degrees  
atoms outside contour = 4645, contour level = 0.10328  
  

> fitmap #1 inMap #5 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6588, steps = 44  
shifted from previous position = 0.233  
rotated from previous position = 0.48 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> select add #1

10267 atoms, 10366 bonds, 1378 residues, 3 models selected  

> select subtract #1

1712 atoms, 1748 bonds, 204 residues, 2 models selected  

> volume #2 color #b2b2b268

> volume #2 color #b2b2b269

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B

Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> select #1/B:268-269

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #1/B:268-288

174 atoms, 179 bonds, 21 residues, 1 model selected  

> select
> #1/B:125-142,164-180,207-212,222-224,237-267,280-299,305-328,332-356,450-462,482-499,534-540,567-593,622-636,653-666

1850 atoms, 1864 bonds, 238 residues, 1 model selected  

> select clear

> select #1/B:304

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/B:304-305

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #1/B:304

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/B:304-322

157 atoms, 157 bonds, 19 residues, 1 model selected  

> select #1/B:331-332

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #1/B:302-332

262 atoms, 265 bonds, 31 residues, 1 model selected  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1297, steps = 232  
shifted from previous position = 0.214  
rotated from previous position = 0.47 degrees  
atoms outside contour = 4639, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1291, steps = 2000  
shifted from previous position = 0.0958  
rotated from previous position = 0.454 degrees  
atoms outside contour = 4687, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.25  
rotated from previous position = 0.875 degrees  
atoms outside contour = 4630, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1277, steps = 2000  
shifted from previous position = 0.604  
rotated from previous position = 0.954 degrees  
atoms outside contour = 4674, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1291, steps = 2000  
shifted from previous position = 0.392  
rotated from previous position = 0.273 degrees  
atoms outside contour = 4688, contour level = 0.10328  
  

> ui mousemode right "rotate selected models"

> select add #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #1,0.9936,-0.094139,-0.062377,209.56,0.083684,0.24289,0.96644,190.72,-0.075829,-0.96548,0.24921,212.87

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1297, steps = 408  
shifted from previous position = 0.0525  
rotated from previous position = 7.42 degrees  
atoms outside contour = 4643, contour level = 0.10328  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B

Alignment identifier is 1/B  

> select :200-320

5772 atoms, 5862 bonds, 726 residues, 3 models selected  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1289, steps = 2000  
shifted from previous position = 0.251  
rotated from previous position = 0.502 degrees  
atoms outside contour = 4632, contour level = 0.10328  
  

> fitmap #1 inMap #5 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0131  
rotated from previous position = 0.0174 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #1 inMap #5 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6588, steps = 40  
shifted from previous position = 0.0121  
rotated from previous position = 0.00956 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #1 inMap #5 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0371  
rotated from previous position = 0.0128 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #4 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.000603, steps = 96  
shifted from previous position = 1.87  
rotated from previous position = 3.83 degrees  
atoms outside contour = 8554, contour level = 0.10328  
  

> fitmap #4 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.0006029, steps = 44  
shifted from previous position = 0.00257  
rotated from previous position = 0.00598 degrees  
atoms outside contour = 8554, contour level = 0.10328  
  

> select add #3

12403 atoms, 12526 bonds, 1658 residues, 3 models selected  

> select add #4

19034 atoms, 19190 bonds, 2590 residues, 3 models selected  

> select subtract #4

10479 atoms, 10572 bonds, 1416 residues, 2 models selected  

> select subtract #3

1924 atoms, 1954 bonds, 242 residues, 1 model selected  

> fitmap #4 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.0006029, steps = 48  
shifted from previous position = 0.00238  
rotated from previous position = 0.0048 degrees  
atoms outside contour = 8554, contour level = 0.10328  
  

> select add #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> select subtract #1

Nothing selected  

> open /Users/madhurikanavalli/Downloads/hPNP_dimer_5zf6_fit_tetramer1.pdb

hPNP_dimer_5zf6_fit_tetramer1.pdb title:  
Crystal structure of the dimeric human pnpase [more info...]  
  
Chain information for hPNP_dimer_5zf6_fit_tetramer1.pdb #6  
---  
Chain | Description | UniProt  
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669  
  

> hide #!1 models

> select add #2

2 models selected  

> select subtract #2

Nothing selected  

> select add #6

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> select add #2

8555 atoms, 8618 bonds, 1174 residues, 3 models selected  

> fitmap #4 inMap #2

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.0006029, steps = 44  
shifted from previous position = 0.00473  
rotated from previous position = 0.0042 degrees  
atoms outside contour = 8554, contour level = 0.10328  
  
Position of 5zf6.pdb (#4) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.63645764 -0.77048569 -0.03568582 78.12947023  
0.21006805 0.12863727 0.96918722 38.53015783  
-0.74215436 -0.62434307 0.24372659 302.42254591  
Axis -0.79677289 0.35323770 0.49028163  
Axis point -0.00000000 196.41371757 173.14599918  
Rotation angle (degrees) 89.74728167  
Shift along axis 99.63108047  
  

> fitmap #4 inMap #2

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.0006032, steps = 48  
shifted from previous position = 0.00496  
rotated from previous position = 0.0115 degrees  
atoms outside contour = 8554, contour level = 0.10328  
  
Position of 5zf6.pdb (#4) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.63656824 -0.77038796 -0.03582278 78.12779013  
0.21013537 0.12856732 0.96918191 38.52558497  
-0.74204044 -0.62447805 0.24372763 302.41095664  
Axis -0.79683780 0.35311230 0.49026648  
Axis point 0.00000000 196.39377529 173.12757133  
Rotation angle (degrees) 89.74608769  
Shift along axis 99.61063610  
  

> select subtract #2

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> fitmap #4 inMap #2

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.0006032, steps = 48  
shifted from previous position = 0.0201  
rotated from previous position = 0.0227 degrees  
atoms outside contour = 8554, contour level = 0.10328  
  
Position of 5zf6.pdb (#4) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.63632725 -0.77059781 -0.03559006 78.13063330  
0.21006324 0.12869982 0.96917996 38.51852128  
-0.74226752 -0.62419178 0.24376948 302.43743598  
Axis -0.79669358 0.35334215 0.49033527  
Axis point 0.00000000 196.42606613 173.17892989  
Rotation angle (degrees) 89.74799671  
Shift along axis 99.65978425  
  

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1265, steps = 2000  
shifted from previous position = 26.4  
rotated from previous position = 14.9 degrees  
atoms outside contour = 4568, contour level = 0.10328  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99998715 0.00501254 -0.00076596 -38.39780829  
-0.00499658 0.99979573 0.01958429 -41.08711100  
0.00086397 -0.01958021 0.99980792 -27.19225070  
Axis -0.96807371 -0.04028867 -0.24740679  
Axis point 0.00000000 -832.72852867 1995.56199881  
Rotation angle (degrees) 1.15906129  
Shift along axis 45.55480119  
  

> fitmap #6 inMap #5

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 80  
shifted from previous position = 6.92  
rotated from previous position = 21.3 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
(#5) coordinates:  
Matrix rotation and translation  
0.97042337 0.22451382 -0.08872453 -205.64095764  
-0.06918024 -0.09348358 -0.99321444 243.81703053  
-0.23128466 0.96997648 -0.07518673 -124.63683134  
Axis 0.98645360 0.07163285 -0.14757381  
Axis point 0.00000000 197.87770362 39.67267018  
Rotation angle (degrees) 95.68869835  
Shift along axis -166.99682276  
  

> select subtract #6

Nothing selected  

> hide #!6 models

> color #6 #db5f27ff

> color #6 #db7553ff

> color #6 #db9a8cff

> color #6 #db7a33ff

> color #6 #db5b31ff

> color #6 #db4122ff

> show #!6 models

> ui tool show "Show Sequence Viewer"

> sequence chain #6/B

Alignment identifier is 6/B  

> hide #!2 models

> select #6/B:293

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #6/B:293-363

599 atoms, 609 bonds, 71 residues, 1 model selected  

> select #6/B:270

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #6/B:270-369

837 atoms, 853 bonds, 100 residues, 1 model selected  

> select add #2

837 atoms, 853 bonds, 100 residues, 3 models selected  

> show #!2 models

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0331  
rotated from previous position = 0.0118 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0336  
rotated from previous position = 0.00485 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.03  
rotated from previous position = 0.0369 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.00753  
rotated from previous position = 0.00808 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6588, steps = 44  
shifted from previous position = 0.0101  
rotated from previous position = 0.0526 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0172  
rotated from previous position = 0.00948 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0295  
rotated from previous position = 0.0068 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0301  
rotated from previous position = 0.033 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.00827  
rotated from previous position = 0.00575 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6588, steps = 44  
shifted from previous position = 0.0134  
rotated from previous position = 0.0519 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 36  
shifted from previous position = 0.0421  
rotated from previous position = 0.0115 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.033  
rotated from previous position = 0.048 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.00797  
rotated from previous position = 0.0109 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6588, steps = 44  
shifted from previous position = 0.0483  
rotated from previous position = 0.047 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> select subtract #2

837 atoms, 853 bonds, 100 residues, 1 model selected  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6588, steps = 28  
shifted from previous position = 0.0141  
rotated from previous position = 0.00276 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> select #6/B:297-300

30 atoms, 30 bonds, 4 residues, 1 model selected  

> select #6/B:235-300

536 atoms, 546 bonds, 66 residues, 1 model selected  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1275, steps = 2000  
shifted from previous position = 0.591  
rotated from previous position = 0.862 degrees  
atoms outside contour = 4676, contour level = 0.10328  
  

> select #6/B:213

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #6/B:213-306

747 atoms, 760 bonds, 94 residues, 1 model selected  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.31  
rotated from previous position = 0.339 degrees  
atoms outside contour = 4685, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.349  
rotated from previous position = 0.98 degrees  
atoms outside contour = 4646, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1277, steps = 2000  
shifted from previous position = 0.633  
rotated from previous position = 0.897 degrees  
atoms outside contour = 4681, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.41  
rotated from previous position = 0.127 degrees  
atoms outside contour = 4685, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1287, steps = 2000  
shifted from previous position = 0.256  
rotated from previous position = 0.952 degrees  
atoms outside contour = 4632, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1277, steps = 2000  
shifted from previous position = 0.662  
rotated from previous position = 1.12 degrees  
atoms outside contour = 4683, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1291, steps = 2000  
shifted from previous position = 0.449  
rotated from previous position = 0.373 degrees  
atoms outside contour = 4684, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.167  
rotated from previous position = 0.682 degrees  
atoms outside contour = 4646, contour level = 0.10328  
  

> select #6/B:182

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #6/B:182-304

964 atoms, 983 bonds, 123 residues, 1 model selected  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1275, steps = 2000  
shifted from previous position = 0.548  
rotated from previous position = 0.789 degrees  
atoms outside contour = 4671, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.33  
rotated from previous position = 0.366 degrees  
atoms outside contour = 4685, contour level = 0.10328  
  

> fitmap #6 inMap #5 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 44  
shifted from previous position = 0.3  
rotated from previous position = 0.943 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1275, steps = 2000  
shifted from previous position = 0.595  
rotated from previous position = 0.908 degrees  
atoms outside contour = 4673, contour level = 0.10328  
  

> select #6/B:290

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #6/B:290-291

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #6/B:302

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #6/B:302-373

597 atoms, 605 bonds, 72 residues, 1 model selected  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.319  
rotated from previous position = 0.348 degrees  
atoms outside contour = 4688, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.331  
rotated from previous position = 0.953 degrees  
atoms outside contour = 4637, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1278, steps = 2000  
shifted from previous position = 0.601  
rotated from previous position = 0.815 degrees  
atoms outside contour = 4675, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.403  
rotated from previous position = 0.116 degrees  
atoms outside contour = 4686, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1287, steps = 2000  
shifted from previous position = 0.254  
rotated from previous position = 0.971 degrees  
atoms outside contour = 4636, contour level = 0.10328  
  

> select clear

> show #!4 models

> select add #4

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #4,0.41896,-0.90784,0.01751,172.56,0.15936,0.092502,0.98288,84.02,-0.89391,-0.40899,0.18343,344.93

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.41896,-0.90784,0.01751,178.41,0.15936,0.092502,0.98288,144.07,-0.89391,-0.40899,0.18343,218.26

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.42775,0.90035,0.079962,224.76,0.60709,0.22062,0.76339,113.04,0.66968,0.37509,-0.64097,107.87

> view matrix models
> #4,-0.18295,0.98312,0.003384,206.1,0.40212,0.071688,0.91278,126.6,0.89712,0.16835,-0.40844,83.19

> hide #!6 models

> show #!6 models

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1277, steps = 2000  
shifted from previous position = 0.66  
rotated from previous position = 1.14 degrees  
atoms outside contour = 4682, contour level = 0.10328  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98050817 -0.05115886 -0.18970108 13.07808380  
-0.00988416 0.95144047 -0.30767407 32.79012008  
0.19622954 0.30355198 0.93238949 -110.39635553  
Axis 0.84418066 -0.53301911 0.05700559  
Axis point 0.00000000 367.20770125 26.56375354  
Rotation angle (degrees) 21.22450246  
Shift along axis -12.73070479  
  

> view matrix models
> #4,-0.08736,0.99518,0.044597,196.53,0.42306,-0.0034671,0.90609,126.01,0.90188,0.098024,-0.42072,84.082

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.08736,0.99518,0.044597,191.27,0.42306,-0.0034671,0.90609,129.79,0.90188,0.098024,-0.42072,71.859

> view matrix models
> #4,-0.08736,0.99518,0.044597,183.77,0.42306,-0.0034671,0.90609,130.43,0.90188,0.098024,-0.42072,77.917

> 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 = 0.1277, steps = 2000  
shifted from previous position = 0.621  
rotated from previous position = 1.01 degrees  
atoms outside contour = 4676, 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  
0.97947769 0.14877998 -0.13597045 146.59186252  
0.10549263 0.19640199 0.97483206 145.59322335  
0.17174037 -0.96917014 0.17667618 184.27065038  
Axis -0.98746437 -0.15630305 -0.02198800  
Axis point 0.00000000 170.41082713 18.63330543  
Rotation angle (degrees) 79.84696577  
Shift along axis -171.56264926  
  

> fitmap #4 inMap #2

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.111, steps = 1076  
shifted from previous position = 4.65  
rotated from previous position = 13.2 degrees  
atoms outside contour = 5073, contour level = 0.10328  
  
Position of 5zf6.pdb (#4) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.36553432 0.89395507 0.25928552 159.59107335  
0.35313265 -0.12454696 0.92724612 89.23861751  
0.86120960 0.43050246 -0.27015854 37.52485026  
Axis -0.52316181 -0.63393602 -0.56958480  
Axis point 53.81283798 -0.00000000 -6.36388496  
Rotation angle (degrees) 151.65683196  
Shift along axis -161.43711324  
  

> fitmap #5 inMap #2

Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
13249 points  
correlation = 0.5788, correlation about mean = 0.198, overlap = 733.5  
steps = 2000, shift = 0.484, angle = 0.682 degrees  
  
Position of 5zf6.pdb map 4 (#5) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.95807999 0.12330246 -0.25861017 146.85960897  
0.23030716 0.20545224 0.95118241 145.69179160  
0.17041517 -0.97086861 0.16844224 183.83696417  
Axis -0.97454450 -0.21753027 0.05425498  
Axis point 0.00000000 173.40314082 29.37698708  
Rotation angle (degrees) 80.44541010  
Shift along axis -164.83952771  
  

> select add #1

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> show #!1 models

> hide #!6 models

> select subtract #4

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> fitmap #5 inMap #2

Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
13249 points  
correlation = 0.5837, correlation about mean = 0.2048, overlap = 738.4  
steps = 2000, shift = 0.311, angle = 0.305 degrees  
  
Position of 5zf6.pdb map 4 (#5) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.95689175 0.12490398 -0.26221586 146.68598283  
0.23295357 0.20914731 0.94973155 145.87551846  
0.17346699 -0.96987442 0.17103451 183.65499502  
Axis -0.97373187 -0.22100279 0.05480881  
Axis point 0.00000000 173.59451621 29.35452178  
Rotation angle (degrees) 80.29724460  
Shift along axis -165.00580142  
  

> fitmap #5 inMap #2

Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
13249 points  
correlation = 0.5802, correlation about mean = 0.2023, overlap = 737.3  
steps = 2000, shift = 0.297, angle = 0.896 degrees  
  
Position of 5zf6.pdb map 4 (#5) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.95523339 0.12648677 -0.26745139 146.55407822  
0.24029680 0.19565106 0.95077763 145.98961234  
0.17258794 -0.97248226 0.15649806 183.41632773  
Axis -0.97319253 -0.22266517 0.05758923  
Axis point 0.00000000 171.93881899 30.45197129  
Rotation angle (degrees) 81.15909876  
Shift along axis -164.56933019  
  

> 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 = 0.1291, steps = 2000  
shifted from previous position = 0.392  
rotated from previous position = 0.273 degrees  
atoms outside contour = 4687, 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  
0.97915094 0.14700446 -0.14018954 146.62405858  
0.11011085 0.19584575 0.97443318 145.92300788  
0.17070156 -0.96955356 0.17557577 184.05988413  
Axis -0.98727891 -0.15789008 -0.01873690  
Axis point 0.00000000 170.57529358 18.76382801  
Rotation angle (degrees) 79.90468443  
Shift along axis -171.24734835  
  

> fitmap #3 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.02577, steps = 116  
shifted from previous position = 8.58  
rotated from previous position = 7.99 degrees  
atoms outside contour = 7667, contour level = 0.10328  
  
Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#3) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.68645478 0.37419295 0.62350577 -153.15730085  
0.19540344 0.73097981 -0.65382413 67.23553836  
-0.70042652 0.57065588 0.42866600 94.59887008  
Axis 0.67568241 0.73056133 -0.09865815  
Axis point -12.74486076 0.00000000 170.20042114  
Rotation angle (degrees) 64.97268395  
Shift along axis -63.69895833  
  

> fitmap #4 inMap #2

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.111, steps = 628  
shifted from previous position = 0.0142  
rotated from previous position = 0.0153 degrees  
atoms outside contour = 5070, contour level = 0.10328  
  
Position of 5zf6.pdb (#4) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.36562224 0.89396097 0.25914118 159.60672611  
0.35289438 -0.12448775 0.92734478 89.24870916  
0.86126995 0.43050734 -0.26995831 37.49952053  
Axis -0.52308545 -0.63393934 -0.56965124  
Axis point 53.83227055 0.00000000 -6.37339730  
Rotation angle (degrees) 151.64648359  
Shift along axis -161.42787146  
  

> fitmap #5 inMap #2

Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
13249 points  
correlation = 0.5788, correlation about mean = 0.198, overlap = 733.5  
steps = 2000, shift = 0.601, angle = 0.852 degrees  
  
Position of 5zf6.pdb map 4 (#5) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.95808182 0.12330121 -0.25860399 146.85969531  
0.23030239 0.20544566 0.95118499 145.69187618  
0.17041133 -0.97087016 0.16843719 183.83677193  
Axis -0.97454577 -0.21752501 0.05425315  
Axis point 0.00000000 173.40254461 29.37657817  
Rotation angle (degrees) 80.44569473  
Shift along axis -164.83939909  
  

> fitmap #5 inMap #2

Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
13249 points  
correlation = 0.5837, correlation about mean = 0.2048, overlap = 738.4  
steps = 2000, shift = 0.311, angle = 0.306 degrees  
  
Position of 5zf6.pdb map 4 (#5) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.95689295 0.12490402 -0.26221149 146.68601347  
0.23294922 0.20914729 0.94973262 145.87546726  
0.17346624 -0.96987442 0.17103528 183.65508357  
Axis -0.97373258 -0.22100023 0.05480660  
Axis point 0.00000000 173.59456162 29.35417238  
Rotation angle (degrees) 80.29718783  
Shift along axis -165.00595139  
  

> select add #6

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> show #!5 models

> hide #!5 models

> select add #4

25665 atoms, 25854 bonds, 3522 residues, 3 models selected  

> select subtract #4

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> select subtract #6

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> select add #6

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> select subtract #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> fitmap #6 inMap #5

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6588, steps = 48  
shifted from previous position = 0.493  
rotated from previous position = 0.363 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
(#5) coordinates:  
Matrix rotation and translation  
0.97055165 0.22364863 -0.08950306 -205.36240728  
-0.06949210 -0.09581212 -0.99297075 244.22612919  
-0.23065202 0.96994914 -0.07744880 -124.28462420  
Axis 0.98654027 0.07093980 -0.14732906  
Axis point 0.00000000 197.65683581 39.75508724  
Rotation angle (degrees) 95.81718147  
Shift along axis -166.96219566  
  

> fitmap #6 inMap #5

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.019  
rotated from previous position = 0.00359 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
(#5) coordinates:  
Matrix rotation and translation  
0.97055020 0.22365652 -0.08949909 -205.37186328  
-0.06950193 -0.09575101 -0.99297595 244.20964705  
-0.23065517 0.96995336 -0.07738660 -124.28250667  
Axis 0.98653885 0.07094293 -0.14733704  
Axis point 0.00000000 197.65379741 39.75494966  
Rotation angle (degrees) 95.81367267  
Shift along axis -166.97095635  
  

> fitmap #6 inMap #5

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0306  
rotated from previous position = 0.00975 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
(#5) coordinates:  
Matrix rotation and translation  
0.97055232 0.22364004 -0.08951726 -205.34348872  
-0.06955967 -0.09559197 -0.99298723 244.19422434  
-0.23062884 0.96997285 -0.07722068 -124.30528679  
Axis 0.98653781 0.07091938 -0.14735532  
Axis point 0.00000000 197.66396599 39.75351657  
Rotation angle (degrees) 95.80425393  
Shift along axis -166.94396819  
  

> fitmap #1 inMap #5

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6588, steps = 48  
shifted from previous position = 0.161  
rotated from previous position = 0.509 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of 5zf6.pdb (#1) relative to 5zf6.pdb map 4 (#5) coordinates:  
Matrix rotation and translation  
0.99145298 0.01667906 0.12939396 0.08470249  
-0.01973646 0.99955465 0.02238229 -0.25108805  
-0.12896302 -0.02474477 0.99134063 0.07775739  
Axis -0.17774891 0.97444383 -0.13734824  
Axis point 0.33249228 0.00000000 -0.26118801  
Rotation angle (degrees) 7.61791888  
Shift along axis -0.27040682  
  

> fitmap #1 inMap #5

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0407  
rotated from previous position = 0.0102 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of 5zf6.pdb (#1) relative to 5zf6.pdb map 4 (#5) coordinates:  
Matrix rotation and translation  
0.99146916 0.01666799 0.12927133 0.06971343  
-0.01970608 0.99955802 0.02225820 -0.21745944  
-0.12884319 -0.02461575 0.99135942 0.06043299  
Axis -0.17698575 0.97458383 -0.13734048  
Axis point 0.23490649 0.00000000 -0.20536492  
Rotation angle (degrees) 7.60962745  
Shift along axis -0.23257063  
  

> fitmap #3 inMap #5

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#3) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.1347, steps = 208  
shifted from previous position = 25.2  
rotated from previous position = 35.7 degrees  
atoms outside contour = 6498, contour level = 0.10406  
  
Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#3) relative to 5zf6.pdb map 4
(#5) coordinates:  
Matrix rotation and translation  
0.77158106 0.62513280 0.11777791 -289.07448145  
0.63513719 -0.74671117 -0.19754285 78.40770373  
-0.03554444 0.22722545 -0.97319329 91.27335582  
Axis 0.94037000 0.33943148 0.02214813  
Axis point 0.00000000 85.49559070 58.83183688  
Rotation angle (degrees) 166.94703469  
Shift along axis -243.20139227  
  

> fitmap #4 inMap #5

Fit molecule 5zf6.pdb (#4) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.1942, steps = 288  
shifted from previous position = 83.6  
rotated from previous position = 22.3 degrees  
atoms outside contour = 4391, contour level = 0.10406  
  
Position of 5zf6.pdb (#4) relative to 5zf6.pdb map 4 (#5) coordinates:  
Matrix rotation and translation  
0.19636392 0.91428712 0.35428840 -37.79820017  
-0.65264442 -0.14778711 0.74311118 24.99961702  
0.73177624 -0.37714458 0.56768433 -77.46490126  
Axis -0.57073182 -0.19231708 -0.79829777  
Axis point 29.48192807 18.18756670 0.00000000  
Rotation angle (degrees) 101.06190229  
Shift along axis 78.60484018  
  

> show #!6 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> fitmap #6 inMap #5

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.025  
rotated from previous position = 0.006 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
(#5) coordinates:  
Matrix rotation and translation  
0.97055420 0.22364475 -0.08948515 -205.36895267  
-0.06950521 -0.09568124 -0.99298245 244.19933684  
-0.23063735 0.96996296 -0.07731936 -124.29858846  
Axis 0.98653982 0.07094047 -0.14733171  
Axis point 0.00000000 197.65981342 39.75092422  
Rotation angle (degrees) 95.80961211  
Shift along axis -166.96791002  
  

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1297, steps = 224  
shifted from previous position = 0.231  
rotated from previous position = 0.288 degrees  
atoms outside contour = 4645, contour level = 0.10328  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98003837 -0.05662787 -0.19057303 14.34462696  
-0.00335724 0.95372551 -0.30065992 30.04155398  
0.19878009 0.29529806 0.93449748 -109.97811233  
Axis 0.83483592 -0.54541761 0.07462310  
Axis point 0.00000000 373.57563125 19.53424803  
Rotation angle (degrees) 20.91184972  
Shift along axis -12.61669073  
  

> select subtract #6

Nothing selected  

> hide #!6 models

> show #!1 models

> fitmap #1 inMap #5

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6589, steps = 44  
shifted from previous position = 0.026  
rotated from previous position = 0.0331 degrees  
atoms outside contour = 0, contour level = 0.10406  
  
Position of 5zf6.pdb (#1) relative to 5zf6.pdb map 4 (#5) coordinates:  
Matrix rotation and translation  
0.99146060 0.01666840 0.12933693 0.08477383  
-0.01963405 0.99957196 0.02168854 -0.22398077  
-0.12892005 -0.02404274 0.99136349 0.08044059  
Axis -0.17271744 0.97538220 -0.13710670  
Axis point 0.38468345 0.00000000 -0.30402781  
Rotation angle (degrees) 7.60758331  
Shift along axis -0.24413772  
  

> fitmap #1 inMap #5 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms  
average map value = 0.6589, steps = 40  
shifted from previous position = 0.0313  
rotated from previous position = 0.0104 degrees  
atoms outside contour = 0, contour level = 0.10406  
  

> ui tool show "Fit in Map"

> close #5

> select :200-320

7696 atoms, 7816 bonds, 968 residues, 4 models selected  

> select :250-350

6712 atoms, 6840 bonds, 808 residues, 4 models selected  

> select :270-350

5440 atoms, 5560 bonds, 648 residues, 4 models selected  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1289, steps = 2000  
shifted from previous position = 0.175  
rotated from previous position = 0.694 degrees  
atoms outside contour = 4632, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 48  
shifted from previous position = 0.142  
rotated from previous position = 0 degrees  
atoms outside contour = 4629, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 40  
shifted from previous position = 0.0151  
rotated from previous position = 0 degrees  
atoms outside contour = 4630, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 40  
shifted from previous position = 0.0142  
rotated from previous position = 0 degrees  
atoms outside contour = 4629, contour level = 0.10328  
  

> select clear

> select add #2

2 models selected  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 40  
shifted from previous position = 0.0141  
rotated from previous position = 0 degrees  
atoms outside contour = 4630, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 40  
shifted from previous position = 0.0156  
rotated from previous position = 0 degrees  
atoms outside contour = 4629, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 36  
shifted from previous position = 0.00098  
rotated from previous position = 0 degrees  
atoms outside contour = 4629, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 36  
shifted from previous position = 0.000935  
rotated from previous position = 0 degrees  
atoms outside contour = 4630, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 28  
shifted from previous position = 0.00984  
rotated from previous position = 0 degrees  
atoms outside contour = 4631, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1293, steps = 40  
shifted from previous position = 0.00416  
rotated from previous position = 0 degrees  
atoms outside contour = 4629, contour level = 0.10328  
  

> fitmap #4 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.111, steps = 40  
shifted from previous position = 0.012  
rotated from previous position = 0 degrees  
atoms outside contour = 5072, contour level = 0.10328  
  

> select subtract #2

Nothing selected  

> fitmap #4 inMap #2 moveWholeMolecules false rotate false

Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.111, steps = 28  
shifted from previous position = 0.0186  
rotated from previous position = 0 degrees  
atoms outside contour = 5074, contour level = 0.10328  
  

> hide /B ribbons

> select clear

> show /B ribbons

> select :301-310

704 atoms, 712 bonds, 80 residues, 4 models selected  

> select :301-3330

20188 atoms, 20216 bonds, 2848 residues, 4 models selected  

> select :301-310

704 atoms, 712 bonds, 80 residues, 4 models selected  

> select :301-350

3360 atoms, 3416 bonds, 400 residues, 4 models selected  

> set bgColor white

> lighting soft

[Repeated 2 time(s)]

> volume #2 color #6d6d6d69

> volume #2 color #b6b6b669

> set bgColor black

> close #4

> open
> /Users/madhurikanavalli/Desktop/Madhuri/Downloads/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 #4  
---  
Chain | Description | UniProt  
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669  
  

> fitmap #4 inMap #2 moveWholeMolecules false rotate false

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.06485, steps = 92  
shifted from previous position = 12  
rotated from previous position = 0 degrees  
atoms outside contour = 6477, contour level = 0.10328  
  

> close #3

> show #!6 models

> fitmap #6 inMap #2 moveWholeMolecules false rotate false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1297, steps = 40  
shifted from previous position = 0.0105  
rotated from previous position = 0 degrees  
atoms outside contour = 4642, contour level = 0.10328  
  

> fitmap #6 inMap #2 moveWholeMolecules false rotate false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1297, steps = 40  
shifted from previous position = 0.00663  
rotated from previous position = 0 degrees  
atoms outside contour = 4644, contour level = 0.10328  
  

> select add #6

9395 atoms, 9472 bonds, 1274 residues, 2 models selected  

> fitmap #6 inMap #2 moveWholeMolecules false rotate false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1297, steps = 40  
shifted from previous position = 0.0111  
rotated from previous position = 0 degrees  
atoms outside contour = 4642, contour level = 0.10328  
  

> close #4

> open /Users/madhurikanavalli/Downloads/hPNP_dimer_5zf6_fit_tetramer1.pdb

hPNP_dimer_5zf6_fit_tetramer1.pdb title:  
Crystal structure of the dimeric human pnpase [more info...]  
  
Chain information for hPNP_dimer_5zf6_fit_tetramer1.pdb #3  
---  
Chain | Description | UniProt  
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669  
  

> view matrix models
> #1,0.994,-0.094744,-0.054626,186.44,0.077109,0.25294,0.9644,196.21,-0.077554,-0.96283,0.25873,175.8,#6,0.99794,0.050158,0.040032,-19.038,-0.032417,0.93235,-0.36009,102.59,-0.055385,0.35805,0.93206,-81.741

> undo

> hide #!6 models

> select subtract #6

840 atoms, 854 bonds, 100 residues, 1 model selected  

> hide #!1 models

> 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  

> view matrix models #3,1,0,0,1.8097,0,1,0,0.23566,0,0,1,-36.997

> view matrix models #3,1,0,0,35.394,0,1,0,-3.855,0,0,1,-64.467

> view matrix models #3,1,0,0,29.376,0,1,0,4.2566,0,0,1,1.29

> fitmap #3 inMap #2 moveWholeMolecules false rotate false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.0719, steps = 92  
shifted from previous position = 9.37  
rotated from previous position = 0 degrees  
atoms outside contour = 6159, contour level = 0.10328  
  

> view matrix models #3,1,0,0,31.644,0,1,0,5.3303,0,0,1,3.0727

> fitmap #3 inMap #2 moveWholeMolecules false rotate false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.07189, steps = 48  
shifted from previous position = 3.09  
rotated from previous position = 0 degrees  
atoms outside contour = 6159, contour level = 0.10328  
  

> view matrix models #3,1,0,0,34.027,0,1,0,1.7493,0,0,1,4.222

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.927,0.099914,0.3615,-47.503,-0.090663,0.99497,-0.042509,27.476,-0.36393,0.0066319,0.9314,81.127

> fitmap #3 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1263, steps = 2000  
shifted from previous position = 3.7  
rotated from previous position = 7.87 degrees  
atoms outside contour = 4616, contour level = 0.10328  
  

> fitmap #3 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1261, steps = 2000  
shifted from previous position = 0.241  
rotated from previous position = 0.799 degrees  
atoms outside contour = 4569, contour level = 0.10328  
  

> volume #2 color #9c9c9c69

> volume #2 color #8e8e8e69

> volume #2 color #4c4c4c69

> volume #2 color #ffffff69

> volume #2 color #adadad69

> color #3 #c76be1ff

> color #3 #ba49e1ff

> color #3 #e119e0ff

> color #3 #e121bdff

> select subtract #3

Nothing selected  

> fitmap #3 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1249, steps = 2000  
shifted from previous position = 0.637  
rotated from previous position = 1.01 degrees  
atoms outside contour = 4588, contour level = 0.10328  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99026797 0.07877011 0.11473715 -66.08205858  
-0.08429553 0.99546348 0.04412174 -36.13256533  
-0.11074116 -0.05336418 0.99241557 6.84643690  
Axis -0.33063295 0.76473153 -0.55305292  
Axis point -27.14208933 0.00000000 601.21610338  
Rotation angle (degrees) 8.47762549  
Shift along axis -9.56924816  
  

> hide #!3 models

> show #!1 models

> select add #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> show #!3 models

> select add #3

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> color #3 #24cbd8ff

> color #3 #b4d827ff

> select subtract #3

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> hide #!3 models

> hide #!1 models

> show #!1 models

> color #3 #4264d8ff

> color #1 #6d61d7ff

> select subtract #1

Nothing selected  

> select #1/B

4227 atoms, 4261 bonds, 577 residues, 1 model selected  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1297, steps = 340  
shifted from previous position = 0.209  
rotated from previous position = 0.503 degrees  
atoms outside contour = 4642, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1297, steps = 504  
shifted from previous position = 0.0115  
rotated from previous position = 0.0127 degrees  
atoms outside contour = 4645, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1297, steps = 348  
shifted from previous position = 0.00671  
rotated from previous position = 0.0114 degrees  
atoms outside contour = 4646, contour level = 0.10328  
  

> select add #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> select subtract #1

Nothing selected  

> color #1 #2322d7ff

> color #1 #304bd7ff

> color #1 #405cd7ff

> select #1/A-B:293

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A-B:293-367

1256 atoms, 1276 bonds, 150 residues, 1 model selected  

> hide /chain bonds

[Repeated 1 time(s)]

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.129, steps = 2000  
shifted from previous position = 0.217  
rotated from previous position = 0.341 degrees  
atoms outside contour = 4649, contour level = 0.10328  
  

> fitmap #1 inMap #2 moveWholeMolecules false

Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
(#2) using 8555 atoms  
average map value = 0.1275, steps = 2000  
shifted from previous position = 0.536  
rotated from previous position = 0.764 degrees  
atoms outside contour = 4674, contour level = 0.10328  
  

> select add #6

9811 atoms, 9894 bonds, 1324 residues, 2 models selected  

> show #!6 models

> hide #!6 models

> select subtract #6

1256 atoms, 1276 bonds, 150 residues, 1 model selected  

> select add #3

9811 atoms, 9894 bonds, 1324 residues, 2 models selected  

> show #!3 models

> show #!6 models

> select add #6

18366 atoms, 18512 bonds, 2498 residues, 3 models selected  

> hide #!3 models

> select subtract #3

9811 atoms, 9894 bonds, 1324 residues, 2 models selected  

> select add #1

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> view matrix models
> #1,0.96064,0.23479,0.14849,209.24,-0.19007,0.16566,0.96769,190.25,0.2026,-0.95783,0.20377,213.18,#6,0.92816,0.21046,-0.30695,60.885,-0.29394,0.92042,-0.25774,126.04,0.22828,0.32945,0.91616,-88.788

> undo

> select subtract #1

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> hide #!1 models

> view matrix models
> #6,-0.27804,-0.71665,-0.63961,531.76,-0.24176,0.69664,-0.67546,247.87,0.92965,-0.033174,-0.36695,123.49

> view matrix models
> #6,-0.80854,-0.29339,-0.51009,522.64,0.17861,0.70359,-0.68779,171.01,0.56068,-0.64722,-0.51647,340.29

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.80854,-0.29339,-0.51009,480.38,0.17861,0.70359,-0.68779,178.26,0.56068,-0.64722,-0.51647,288.18

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.04021, steps = 244  
shifted from previous position = 22.5  
rotated from previous position = 9.8 degrees  
atoms outside contour = 7262, contour level = 0.10328  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.35639,-0.29895,-0.88522,483.61,-0.004137,0.94793,-0.31846,84.725,0.93433,-0.10983,-0.33907,84.393

> view matrix models
> #6,-0.25916,-0.51199,-0.81897,494.96,0.10101,0.82892,-0.55017,138.34,0.96054,-0.22531,-0.16311,65.902

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.04682, steps = 180  
shifted from previous position = 9.55  
rotated from previous position = 14.6 degrees  
atoms outside contour = 7079, contour level = 0.10328  
  

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.04682, steps = 44  
shifted from previous position = 0.0919  
rotated from previous position = 0.204 degrees  
atoms outside contour = 7090, contour level = 0.10328  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.49668241 -0.45211172 -0.74087892 460.77188640  
0.15262355 0.79481607 -0.58734441 94.44318983  
0.85440777 -0.40479921 -0.32576827 117.80701656  
Axis 0.10639077 -0.92976301 0.35245106  
Axis point 200.17990455 0.00000000 217.14121089  
Rotation angle (degrees) 120.91843476  
Shift along axis 2.73329794  
  

> view matrix models
> #6,-0.52907,-0.0047689,-0.84857,450.01,0.53325,0.77601,-0.33683,33.426,0.6601,-0.6307,-0.40802,241.83

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.52907,-0.0047689,-0.84857,424.69,0.53325,0.77601,-0.33683,-64.127,0.6601,-0.6307,-0.40802,233.02

> view matrix models
> #6,-0.52907,-0.0047689,-0.84857,427.56,0.53325,0.77601,-0.33683,-69.035,0.6601,-0.6307,-0.40802,240.81

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.76339,-0.51264,-0.39298,467.55,-0.13914,0.72461,-0.67496,120.5,0.63077,-0.46058,-0.62449,258.25

> view matrix models
> #6,-0.86546,-0.26374,-0.42593,444.28,0.16092,0.65879,-0.73491,96.05,0.47442,-0.70458,-0.52772,309.8

> view matrix models
> #6,-0.28971,-0.90683,-0.30614,446.12,-0.56931,0.42039,-0.70651,254.69,0.76939,-0.030393,-0.63806,157.46

> view matrix models
> #6,0.071191,-0.22599,-0.97153,396.1,-0.32791,0.91456,-0.23676,25.444,0.94202,0.33543,-0.0089961,-69.223

> view matrix models
> #6,-0.62244,0.01769,-0.78247,425.02,-0.32291,0.90489,0.27732,-79.49,0.71295,0.42528,-0.55752,64.459

> view matrix models
> #6,-0.22541,0.34331,-0.91177,325.38,-0.19676,0.90053,0.38772,-122.1,0.95419,0.26679,-0.13544,-32.26

> view matrix models
> #6,-0.41827,-0.28212,-0.8634,464.59,-0.64872,0.75811,0.066552,44.931,0.63578,0.58794,-0.50012,34.704

> view matrix models
> #6,-0.25107,0.40226,-0.88043,312.05,-0.2867,0.83785,0.46456,-111.4,0.92454,0.36905,-0.095032,-54.949

> view matrix models
> #6,-0.76906,0.13581,-0.62458,394.31,-0.1572,0.90696,0.39079,-130.42,0.61954,0.39873,-0.67616,109.21

> view matrix models
> #6,-0.98343,0.03782,-0.1773,355.7,-0.074325,0.80792,0.58458,-165.32,0.16536,0.58807,-0.79172,171.87

> view matrix models
> #6,-0.39477,0.68819,-0.60873,225.86,0.36199,0.72545,0.58539,-221.49,0.84446,0.010739,-0.5355,116.29

> view matrix models
> #6,-0.79966,0.075061,-0.59575,404.81,-0.040684,0.9831,0.17847,-120.08,0.59908,0.16695,-0.78309,178.16

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = -0.0005825, steps = 96  
shifted from previous position = 3.28  
rotated from previous position = 3.03 degrees  
atoms outside contour = 8555, contour level = 0.10328  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.92490882 -0.02938852 -0.37905143 356.59797481  
-0.08084042 0.98941082 0.12054485 -153.92939959  
0.37149495 0.14213567 -0.91749057 213.28677900  
Axis 0.02868764 -0.99724791 -0.06836393  
Axis point 154.19781165 0.00000000 146.42433529  
Rotation angle (degrees) 157.89477035  
Shift along axis 149.15460281  
  

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = -0.0005823, steps = 28  
shifted from previous position = 0.00579  
rotated from previous position = 0.00269 degrees  
atoms outside contour = 8555, contour level = 0.10328  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.92492308 -0.02936526 -0.37901843 356.58713815  
-0.08080731 0.98941435 0.12053802 -153.93925469  
0.37146665 0.14211586 -0.91750510 213.29930744  
Axis 0.02867275 -0.99724885 -0.06835648  
Axis point 154.19422266 0.00000000 146.42639014  
Rotation angle (degrees) 157.89669311  
Shift along axis 149.15968848  
  

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.80444,0.039308,-0.59273,388.5,-0.090985,0.97788,0.18834,-22.775,0.58702,0.20543,-0.78307,177.39

> volume #2 level 0.0888

> volume #2 level 0.09242

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.03454, steps = 280  
shifted from previous position = 32.1  
rotated from previous position = 34.8 degrees  
atoms outside contour = 7410, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.90947492 -0.41561998 0.01074203 352.97733471  
-0.39427535 0.87038984 0.29490417 -29.46763984  
-0.13191783 0.26397263 -0.95546645 264.47171436  
Axis -0.20966712 0.96700906 0.14468300  
Axis point 178.52191521 0.00000000 127.95705739  
Rotation angle (degrees) 175.76982332  
Shift along axis -64.23865431  
  

> view matrix models
> #6,-0.92581,-0.30774,-0.21947,427.56,-0.3699,0.85706,0.35863,24.591,0.077733,0.41321,-0.90731,235.42

> view matrix models
> #6,-0.92581,-0.30774,-0.21947,445.36,-0.3699,0.85706,0.35863,22.611,0.077733,0.41321,-0.90731,226.52

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.06286, steps = 200  
shifted from previous position = 6.44  
rotated from previous position = 25.2 degrees  
atoms outside contour = 6186, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.94057101 -0.15322448 -0.30306507 389.01736554  
-0.21329908 0.96098057 0.17612448 -31.15370261  
0.26425307 0.23030108 -0.93655311 208.49710154  
Axis 0.09453969 -0.98998612 -0.10483186  
Axis point 177.25741183 0.00000000 134.32900383  
Rotation angle (degrees) 163.34977424  
Shift along axis 45.76217553  
  

> select subtract #6

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #6

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #6,-0.76191,-0.0097647,-0.64761,446.5,-0.20035,0.9544,0.22132,8.908,0.61591,0.29837,-0.72912,128.23

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 324  
shifted from previous position = 1.84  
rotated from previous position = 10.5 degrees  
atoms outside contour = 4725, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.94065942 0.02845456 -0.33815704 363.23421540  
-0.02966661 0.98576805 0.16547275 -62.67392798  
0.33805287 0.16568547 -0.92642786 207.49334626  
Axis 0.00031343 -0.99632647 -0.08563563  
Axis point 163.06221544 0.00000000 138.31429213  
Rotation angle (degrees) 160.16262663  
Shift along axis 44.78871788  
  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.64462,0.060699,-0.76209,438.99,-0.16555,0.96211,0.21666,3.6667,0.74636,0.26583,-0.61015,89.225

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 232  
shifted from previous position = 1.12  
rotated from previous position = 16.6 degrees  
atoms outside contour = 4726, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.94065481 0.02863395 -0.33815474 363.19518707  
-0.02945052 0.98578726 0.16539693 -62.69088648  
0.33808460 0.16554025 -0.92644224 207.53053559  
Axis 0.00021116 -0.99633143 -0.08557825  
Axis point 163.04229456 0.00000000 138.32992186  
Rotation angle (degrees) 160.16182981  
Shift along axis 44.77749212  
  

> view matrix models
> #6,-0.88604,0.038516,-0.462,420.9,-0.03934,0.9867,0.15771,-9.4885,0.46193,0.15791,-0.87275,210.25

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 192  
shifted from previous position = 0.498  
rotated from previous position = 8.14 degrees  
atoms outside contour = 4728, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.94066665 0.02855601 -0.33812838 363.20627610  
-0.02957366 0.98576223 0.16552410 -62.69813440  
0.33804090 0.16570270 -0.92642915 207.49987033  
Axis 0.00026316 -0.99632498 -0.08565318  
Axis point 163.05029791 0.00000000 138.31495884  
Rotation angle (degrees) 160.16383770  
Shift along axis 44.79027516  
  

> view matrix models
> #6,-0.72409,0.17019,-0.66837,412.13,-0.025472,0.96182,0.2725,-30.744,0.68923,0.21434,-0.69211,125.17

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 776  
shifted from previous position = 0.661  
rotated from previous position = 9.75 degrees  
atoms outside contour = 4722, contour level = 0.092417  
  

> select subtract #6

Nothing selected  

> select add #6

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #6,-0.76187,-0.15221,-0.6296,471.01,-0.29458,0.94708,0.12751,45.668,0.57687,0.28261,-0.76639,145.88

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.76187,-0.15221,-0.6296,471.34,-0.29458,0.94708,0.12751,43.678,0.57687,0.28261,-0.76639,146.42

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.06236, steps = 84  
shifted from previous position = 2.22  
rotated from previous position = 3.59 degrees  
atoms outside contour = 6255, contour level = 0.092417  
  

> select subtract #6

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #6

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #6,-0.6777,0.059786,-0.73291,439.37,-0.22546,0.93179,0.28449,3.074,0.69992,0.35804,-0.61799,81.912

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.6777,0.059786,-0.73291,439.44,-0.22546,0.93179,0.28449,2.7263,0.69992,0.35804,-0.61799,83.451

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 920  
shifted from previous position = 3.95  
rotated from previous position = 10.1 degrees  
atoms outside contour = 4722, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.88994782 0.04420559 -0.45391491 374.83079362  
-0.05717949 0.97662253 0.20721711 -63.35120865  
0.45246368 0.21036704 -0.86661544 168.59587277  
Axis 0.00345373 -0.99379614 -0.11116337  
Axis point 166.22449866 0.00000000 133.32450793  
Rotation angle (degrees) 152.86952298  
Shift along axis 45.51106552  
  

> select subtract #6

Nothing selected  

> hide #!2 models

> undo

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 116  
shifted from previous position = 0.00709  
rotated from previous position = 0.00318 degrees  
atoms outside contour = 4727, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.88993311 0.04424511 -0.45393989 374.82642072  
-0.05716226 0.97661562 0.20725443 -63.36706439  
0.45249479 0.21039081 -0.86659343 168.57997819  
Axis 0.00343866 -0.99379426 -0.11118072  
Axis point 166.22292888 0.00000000 133.32090242  
Rotation angle (degrees) 152.86765033  
Shift along axis 45.51987962  
  

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 568  
shifted from previous position = 0.0114  
rotated from previous position = 0.0123 degrees  
atoms outside contour = 4724, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.88993442 0.04404381 -0.45395691 374.86893906  
-0.05737351 0.97660900 0.20722726 -63.32915866  
0.45246548 0.21046377 -0.86659101 168.55952594  
Axis 0.00354848 -0.99379250 -0.11119295  
Axis point 166.24336123 0.00000000 133.31298230  
Rotation angle (degrees) 152.86799669  
Shift along axis 45.52362736  
  

> select add #6

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> fitmap #6 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 180  
shifted from previous position = 0.0152  
rotated from previous position = 0.00465 degrees  
atoms outside contour = 4732, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.88993786 0.04410294 -0.45394442 374.85142718  
-0.05729523 0.97661769 0.20720798 -63.34867632  
0.45246863 0.21041107 -0.86660217 168.58221982  
Axis 0.00351189 -0.99379482 -0.11117335  
Axis point 166.23335059 0.00000000 133.32210930  
Rotation angle (degrees) 152.86836781  
Shift along axis 45.53017211  
  

> select :605-635

1296 atoms, 1317 bonds, 171 residues, 3 models selected  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 344  
shifted from previous position = 0.0176  
rotated from previous position = 0.0105 degrees  
atoms outside contour = 4729, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 196  
shifted from previous position = 0.0146  
rotated from previous position = 0.00622 degrees  
atoms outside contour = 4723, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 180  
shifted from previous position = 0.0248  
rotated from previous position = 0.0219 degrees  
atoms outside contour = 4722, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 548  
shifted from previous position = 0.0148  
rotated from previous position = 0.00714 degrees  
atoms outside contour = 4725, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 312  
shifted from previous position = 0.0297  
rotated from previous position = 0.0316 degrees  
atoms outside contour = 4729, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 128  
shifted from previous position = 0.00953  
rotated from previous position = 0.0083 degrees  
atoms outside contour = 4725, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 208  
shifted from previous position = 0.0222  
rotated from previous position = 0.0184 degrees  
atoms outside contour = 4724, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 220  
shifted from previous position = 0.0138  
rotated from previous position = 0.00774 degrees  
atoms outside contour = 4725, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 1912  
shifted from previous position = 0.0151  
rotated from previous position = 0.00815 degrees  
atoms outside contour = 4724, contour level = 0.092417  
  

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 388  
shifted from previous position = 0.0217  
rotated from previous position = 0.0192 degrees  
atoms outside contour = 4728, contour level = 0.092417  
  

> view matrix models
> #1,0.994,-0.094744,-0.054626,207.02,0.077109,0.25294,0.9644,190.31,-0.077554,-0.96283,0.25873,213.32,#6,-0.74953,0.12709,-0.64965,417.13,-0.073566,0.95933,0.27255,-21.057,0.65787,0.25208,-0.7097,128.14,#3,0.92765,0.095145,0.36114,-49.146,-0.092392,0.99541,-0.024925,24.061,-0.36185,-0.010244,0.93218,84.812

> fitmap #6 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.111, steps = 448  
shifted from previous position = 2.71  
rotated from previous position = 0.0121 degrees  
atoms outside contour = 4721, contour level = 0.092417  
  

> select add #6

9419 atoms, 9496 bonds, 1288 residues, 3 models selected  

> select add #3

17542 atoms, 17675 bonds, 2405 residues, 3 models selected  

> select subtract #6

8987 atoms, 9057 bonds, 1231 residues, 2 models selected  

> hide #!6 models

> hide #!2 models

> 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 subtract #3

Nothing selected  

> show #!3 models

> show #!1 models

> hide #!1 models

> show #!6 models

> select add #6

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> select add #3

17110 atoms, 17236 bonds, 2348 residues, 2 models selected  

> 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 #4  
---  
Chain | Description | UniProt  
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669  
  

> hide #!6 models

> select subtract #6

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> show #!2 models

> select add #2

8555 atoms, 8618 bonds, 1174 residues, 3 models selected  

> select add #4

17110 atoms, 17236 bonds, 2348 residues, 4 models selected  

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1262, steps = 2000  
shifted from previous position = 2.56  
rotated from previous position = 0.165 degrees  
atoms outside contour = 4321, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99008565 0.08020231 0.11531698 -66.56585309  
-0.08547902 0.99547290 0.04155783 -35.70187256  
-0.11146190 -0.05100299 0.99245904 6.18707679  
Axis -0.31300845 0.76688716 -0.56027654  
Axis point -35.49371356 -0.00000000 601.36159142  
Rotation angle (degrees) 8.50274218  
Shift along axis -10.01010685  
  

> fitmap #3 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1265, steps = 2000  
shifted from previous position = 0.239  
rotated from previous position = 0.818 degrees  
atoms outside contour = 4303, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99012491 0.07955173 0.11543040 -66.35338000  
-0.08323899 0.99615079 0.02747518 -33.39555135  
-0.11280039 -0.03681217 0.99293552 3.37679073  
Axis -0.22351799 0.79352600 -0.56600018  
Axis point -75.44975106 0.00000000 594.67655370  
Rotation angle (degrees) 8.26825993  
Shift along axis -13.58032821  
  

> fitmap #4 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1106, steps = 296  
shifted from previous position = 11.4  
rotated from previous position = 15 degrees  
atoms outside contour = 4757, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99975115 0.02225007 0.00160437 -42.37113273  
-0.02229050 0.99922195 0.03253675 -39.86667288  
-0.00087917 -0.03256442 0.99946925 -26.34167349  
Axis -0.82491227 0.03146955 -0.56438411  
Axis point 0.00000000 12.03996179 1272.54105826  
Rotation angle (degrees) 2.26144694  
Shift along axis 48.56470264  
  

> select subtract #4

8555 atoms, 8618 bonds, 1174 residues, 3 models selected  

> select subtract #3

2 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #3

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #3,0.88251,0.23211,0.40903,-75.275,-0.21961,0.97246,-0.078009,62.282,-0.41588,-0.020986,0.90918,100.45

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.88251,0.23211,0.40903,-75.557,-0.21961,0.97246,-0.078009,61.908,-0.41588,-0.020986,0.90918,99.178

> fitmap #3 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.127, steps = 272  
shifted from previous position = 1.55  
rotated from previous position = 8.41 degrees  
atoms outside contour = 4288, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98988621 0.08222609 0.11560346 -66.94222621  
-0.08667313 0.99565733 0.03397417 -34.07262077  
-0.11230787 -0.04365027 0.99271426 4.88957146  
Axis -0.26393700 0.77493934 -0.57428763  
Axis point -54.45818067 0.00000000 600.65902030  
Rotation angle (degrees) 8.45607029  
Shift along axis -11.54370437  
  

> select subtract #3

Nothing selected  

> select add #4

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #4,0.96636,0.045793,0.25307,-32.02,-0.038117,0.99865,-0.035156,22.745,-0.25434,0.024327,0.96681,48.2

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.98649,-0.13285,0.095881,19.07,0.13318,0.99109,0.0030574,-13.022,-0.095433,0.009753,0.99539,17.369

> fitmap #3 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1267, steps = 2000  
shifted from previous position = 0.231  
rotated from previous position = 0.209 degrees  
atoms outside contour = 4265, contour level = 0.092417  
  

> fitmap #3 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1257, steps = 2000  
shifted from previous position = 0.153  
rotated from previous position = 0.802 degrees  
atoms outside contour = 4316, contour level = 0.092417  
  

> select subtract #4

Nothing selected  

> select add #4

8555 atoms, 8618 bonds, 1174 residues, 1 model selected  

> view matrix models
> #4,0.98865,0.077128,0.12895,-24.965,-0.061721,0.99092,-0.11949,40.165,-0.13699,0.11017,0.98443,7.9262

> fitmap #3 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1256, steps = 2000  
shifted from previous position = 0.447  
rotated from previous position = 0.959 degrees  
atoms outside contour = 4316, contour level = 0.092417  
  

> fitmap #3 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1267, steps = 2000  
shifted from previous position = 0.369  
rotated from previous position = 0.333 degrees  
atoms outside contour = 4261, contour level = 0.092417  
  

> fitmap #4 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1106, steps = 464  
shifted from previous position = 2.2  
rotated from previous position = 8.71 degrees  
atoms outside contour = 4757, contour level = 0.092417  
  
Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) relative to
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99975184 0.02221316 0.00168369 -42.37411242  
-0.02225622 0.99922206 0.03255658 -39.87679425  
-0.00095919 -0.03258598 0.99946848 -26.32053100  
Axis -0.82544529 0.03348892 -0.56348786  
Axis point 0.00000000 9.69649265 1274.93904155  
Rotation angle (degrees) 2.26142362  
Shift along axis 48.47338052  
  

> select subtract #4

Nothing selected  

> ui tool show "Fit to Segments"

> select #1/A-B:293

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A-B:293-367

1256 atoms, 1276 bonds, 150 residues, 1 model selected  

> select add #4

9811 atoms, 9894 bonds, 1324 residues, 2 models selected  

> select subtract #4

1256 atoms, 1276 bonds, 150 residues, 1 model selected  

> select :605-635

1728 atoms, 1756 bonds, 228 residues, 4 models selected  

> fitmap #4 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1106, steps = 776  
shifted from previous position = 0.00595  
rotated from previous position = 0.00471 degrees  
atoms outside contour = 4758, contour level = 0.092417  
  

> fitmap #4 inMap #2 moveWholeMolecules false

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms  
average map value = 0.1106, steps = 384  
shifted from previous position = 0.0135  
rotated from previous position = 0.0157 degrees  
atoms outside contour = 4757, contour level = 0.092417  
  

> cd /Users/madhurikanavalli/Desktop/test

Current working directory is: /Users/madhurikanavalli/Desktop/test  

> save /Users/madhurikanavalli/Desktop/test/dimerfit_Kasia.cxs

——— End of log from Fri Aug 30 15:18:41 2024 ———

> view name session-start

opened ChimeraX session  

> 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  

> volume #2 level 0.1132

> set bgColor white

> volume #2 level 0.1025

> volume #2 level 0.1001

> volume #2 level 0.08461

> select add #4

9851 atoms, 9935 bonds, 1345 residues, 4 models selected  

> select subtract #4

1296 atoms, 1317 bonds, 171 residues, 3 models selected  

> select add #3

9419 atoms, 9496 bonds, 1288 residues, 3 models selected  

> select subtract #3

864 atoms, 878 bonds, 114 residues, 2 models selected  

> select add #3

9419 atoms, 9496 bonds, 1288 residues, 3 models selected  

> select add #6

17542 atoms, 17675 bonds, 2405 residues, 3 models selected  

> view matrix models
> #1,0.994,-0.094744,-0.054626,190.68,0.077109,0.25294,0.9644,136.09,-0.077554,-0.96283,0.25873,179.49,#6,-0.74953,0.12709,-0.64965,400.79,-0.073566,0.95933,0.27255,-75.279,0.65787,0.25208,-0.7097,94.31,#3,0.92681,0.10093,0.36172,-64.082,-0.094651,0.99489,-0.035082,-27.656,-0.36341,-0.0017227,0.93163,49.036

> view matrix models
> #1,0.994,-0.094744,-0.054626,189.74,0.077109,0.25294,0.9644,121.52,-0.077554,-0.96283,0.25873,187.27,#6,-0.74953,0.12709,-0.64965,399.84,-0.073566,0.95933,0.27255,-89.852,0.65787,0.25208,-0.7097,102.09,#3,0.92681,0.10093,0.36172,-65.027,-0.094651,0.99489,-0.035082,-42.229,-0.36341,-0.0017227,0.93163,56.814

> view matrix models
> #1,0.994,-0.094744,-0.054626,191.44,0.077109,0.25294,0.9644,104.17,-0.077554,-0.96283,0.25873,210.37,#6,-0.74953,0.12709,-0.64965,401.54,-0.073566,0.95933,0.27255,-107.2,0.65787,0.25208,-0.7097,125.19,#3,0.92681,0.10093,0.36172,-63.324,-0.094651,0.99489,-0.035082,-59.577,-0.36341,-0.0017227,0.93163,79.914

> view matrix models
> #1,0.994,-0.094744,-0.054626,189.26,0.077109,0.25294,0.9644,133.92,-0.077554,-0.96283,0.25873,174.38,#6,-0.74953,0.12709,-0.64965,399.36,-0.073566,0.95933,0.27255,-77.452,0.65787,0.25208,-0.7097,89.203,#3,0.92681,0.10093,0.36172,-65.504,-0.094651,0.99489,-0.035082,-29.83,-0.36341,-0.0017227,0.93163,43.928

> view matrix models
> #1,0.994,-0.094744,-0.054626,160.99,0.077109,0.25294,0.9644,160.74,-0.077554,-0.96283,0.25873,187.51,#6,-0.74953,0.12709,-0.64965,371.09,-0.073566,0.95933,0.27255,-50.634,0.65787,0.25208,-0.7097,102.33,#3,0.92681,0.10093,0.36172,-93.774,-0.094651,0.99489,-0.035082,-3.0112,-0.36341,-0.0017227,0.93163,57.056

> view matrix models
> #1,0.994,-0.094744,-0.054626,162.53,0.077109,0.25294,0.9644,159.38,-0.077554,-0.96283,0.25873,186.26,#6,-0.74953,0.12709,-0.64965,372.63,-0.073566,0.95933,0.27255,-51.991,0.65787,0.25208,-0.7097,101.08,#3,0.92681,0.10093,0.36172,-92.239,-0.094651,0.99489,-0.035082,-4.368,-0.36341,-0.0017227,0.93163,55.803

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.92939,-0.058623,-0.36441,164.52,0.36859,0.096106,0.92461,157.81,-0.019182,-0.99364,0.11093,186.66,#6,-0.76215,-0.18968,-0.61899,435.59,-0.22171,0.97477,-0.025711,12.579,0.60825,0.11764,-0.78498,147.92,#3,0.94763,-0.1971,0.25131,-14.75,0.152,0.97036,0.18786,-90.399,-0.28088,-0.13982,0.9495,64.215

> view matrix models
> #1,0.96327,-0.086547,0.2542,161.13,-0.18677,0.46424,0.86579,161.41,-0.19294,-0.88147,0.43103,186.05,#6,-0.68636,0.42515,-0.59005,291.88,0.0013985,0.8121,0.58352,-77.28,0.72726,0.39968,-0.55798,37.696,#3,0.82694,0.39195,0.40316,-139.78,-0.26967,0.90562,-0.32731,105.56,-0.4934,0.16195,0.85459,63.291

Desktop color scheme is dark  

> lighting full

> view matrix models
> #1,0.92599,0.2946,-0.23612,163.44,0.14324,0.30452,0.94167,158.98,0.34932,-0.9058,0.23979,183.4,#6,-0.94666,-0.068404,-0.31488,406.44,-0.15974,0.9483,0.27424,-33.373,0.27984,0.30991,-0.90865,188.22,#3,0.99828,0.01072,-0.057691,0.50116,-0.0147,0.99751,-0.069014,-12.047,0.056808,0.069743,0.99595,-46.681

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.92599,0.2946,-0.23612,161.4,0.14324,0.30452,0.94167,143.18,0.34932,-0.9058,0.23979,186.35,#6,-0.94666,-0.068404,-0.31488,404.41,-0.15974,0.9483,0.27424,-49.176,0.27984,0.30991,-0.90865,191.17,#3,0.99828,0.01072,-0.057691,-1.5331,-0.0147,0.99751,-0.069014,-27.85,0.056808,0.069743,0.99595,-43.732

> show #!6 models

> hide #!6 models

> select add #4

26097 atoms, 26293 bonds, 3579 residues, 4 models selected  

> select subtract #3

17542 atoms, 17675 bonds, 2405 residues, 3 models selected  

> view matrix models
> #1,0.92599,0.2946,-0.23612,159.75,0.14324,0.30452,0.94167,90.273,0.34932,-0.9058,0.23979,167.09,#6,-0.94666,-0.068404,-0.31488,402.75,-0.15974,0.9483,0.27424,-102.08,0.27984,0.30991,-0.90865,171.91,#4,0.96635,0.045752,0.25314,-33.638,-0.038077,0.99866,-0.035137,-30.414,-0.25441,0.024315,0.96679,26.911

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.61907,0.58221,-0.52704,153.93,0.26992,0.47248,0.83899,79.331,0.73749,-0.66166,0.13535,146.15,#6,-0.9085,-0.41347,0.060664,407.35,-0.37329,0.86818,0.32698,-61.974,-0.18786,0.27441,-0.94308,255.17,#4,0.96004,-0.20089,-0.19484,74.965,0.18128,0.97681,-0.11393,-56.416,0.2132,0.074054,0.9742,-70.527

> view matrix models
> #1,0.6268,0.5183,-0.58179,160.01,0.301,0.52764,0.79435,76.265,0.71869,-0.67302,0.17472,146.07,#6,-0.88524,-0.46514,-0.002032,427.41,-0.43651,0.82923,0.34904,-47.779,-0.16067,0.30987,-0.9371,241.9,#4,0.95184,-0.26949,-0.14617,82.582,0.24844,0.95738,-0.14729,-60.738,0.17964,0.10388,0.97823,-70.376

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.6268,0.5183,-0.58179,139.9,0.301,0.52764,0.79435,59.265,0.71869,-0.67302,0.17472,146.39,#6,-0.88524,-0.46514,-0.002032,407.3,-0.43651,0.82923,0.34904,-64.778,-0.16067,0.30987,-0.9371,242.23,#4,0.95184,-0.26949,-0.14617,62.471,0.24844,0.95738,-0.14729,-77.738,0.17964,0.10388,0.97823,-70.05

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.56833,0.70828,-0.41874,122.46,0.33149,0.26869,0.90439,73.602,0.75307,-0.6528,-0.082087,152.32,#6,-0.92587,-0.31765,0.2046,341.15,-0.29507,0.9461,0.13355,-72.727,-0.23599,0.063284,-0.96969,316.14,#4,0.9477,-0.072153,-0.31091,49.129,0.10669,0.98969,0.09553,-90.672,0.30081,-0.1237,0.94563,-45.794

> view matrix models
> #1,0.54644,0.67075,-0.50149,128.07,0.28728,0.41234,0.86455,65.478,0.78668,-0.61649,0.032625,145.6,#6,-0.89812,-0.40253,0.17703,361.73,-0.34868,0.89718,0.27108,-78.956,-0.26794,0.18173,-0.94614,289.19,#4,0.93818,-0.1649,-0.30435,67.269,0.15659,0.98631,-0.051703,-79.126,0.30871,0.00084819,0.95115,-71.212

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.54644,0.67075,-0.50149,108.49,0.28728,0.41234,0.86455,68.46,0.78668,-0.61649,0.032625,139.36,#6,-0.89812,-0.40253,0.17703,342.14,-0.34868,0.89718,0.27108,-75.973,-0.26794,0.18173,-0.94614,282.95,#4,0.93818,-0.1649,-0.30435,47.685,0.15659,0.98631,-0.051703,-76.143,0.30871,0.00084819,0.95115,-77.451

> view matrix models
> #1,0.54644,0.67075,-0.50149,111.2,0.28728,0.41234,0.86455,87.267,0.78668,-0.61649,0.032625,138.22,#6,-0.89812,-0.40253,0.17703,344.86,-0.34868,0.89718,0.27108,-57.167,-0.26794,0.18173,-0.94614,281.81,#4,0.93818,-0.1649,-0.30435,50.401,0.15659,0.98631,-0.051703,-57.337,0.30871,0.00084819,0.95115,-78.588

> select subtract #4

8987 atoms, 9057 bonds, 1231 residues, 2 models selected  

> select add #3

17542 atoms, 17675 bonds, 2405 residues, 3 models selected  

> view matrix models
> #1,0.54644,0.67075,-0.50149,93.636,0.28728,0.41234,0.86455,86.962,0.78668,-0.61649,0.032625,135.05,#6,-0.89812,-0.40253,0.17703,327.29,-0.34868,0.89718,0.27108,-57.471,-0.26794,0.18173,-0.94614,278.64,#3,0.99828,0.01072,-0.057691,-19.1,-0.0147,0.99751,-0.069014,-28.154,0.056808,0.069743,0.99595,-46.902

> transparency 50

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 8555 atoms  
average map value = 0.1145, steps = 1280  
shifted from previous position = 3.75  
rotated from previous position = 12.3 degrees  
atoms outside contour = 4232, contour level = 0.084608  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99192569 0.06320433 0.10994826 -62.72498723  
-0.06914256 0.99629928 0.05105907 -41.19333953  
-0.10631421 -0.05824891 0.99262497 10.91865642  
Axis -0.39589431 0.78326468 -0.47933718  
Axis point 2.83869525 0.00000000 616.31281519  
Rotation angle (degrees) 7.93513801  
Shift along axis -12.66654047  
  

> view matrix models
> #1,0.54644,0.67075,-0.50149,93.206,0.28728,0.41234,0.86455,84.978,0.78668,-0.61649,0.032625,131.42,#6,-0.89812,-0.40253,0.17703,326.86,-0.34868,0.89718,0.27108,-59.456,-0.26794,0.18173,-0.94614,275.01,#3,0.99193,0.063204,0.10995,-63.155,-0.069143,0.9963,0.051059,-43.178,-0.10631,-0.058249,0.99262,7.289

> view matrix models
> #1,0.54644,0.67075,-0.50149,92.22,0.28728,0.41234,0.86455,84.636,0.78668,-0.61649,0.032625,131.84,#6,-0.89812,-0.40253,0.17703,325.88,-0.34868,0.89718,0.27108,-59.798,-0.26794,0.18173,-0.94614,275.43,#3,0.99193,0.063204,0.10995,-64.141,-0.069143,0.9963,0.051059,-43.52,-0.10631,-0.058249,0.99262,7.7078

> select subtract #3

8987 atoms, 9057 bonds, 1231 residues, 2 models selected  

> view matrix models
> #1,0.54644,0.67075,-0.50149,94.529,0.28728,0.41234,0.86455,85.746,0.78668,-0.61649,0.032625,118.28,#6,-0.89812,-0.40253,0.17703,328.18,-0.34868,0.89718,0.27108,-58.687,-0.26794,0.18173,-0.94614,261.87

> view matrix models
> #1,0.54644,0.67075,-0.50149,96.546,0.28728,0.41234,0.86455,85.767,0.78668,-0.61649,0.032625,105.23,#6,-0.89812,-0.40253,0.17703,330.2,-0.34868,0.89718,0.27108,-58.666,-0.26794,0.18173,-0.94614,248.82

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.54644,0.67075,-0.50149,96.546,0.28728,0.41234,0.86455,85.767,0.78668,-0.61649,0.032625,105.23,#6,-0.89812,-0.40253,0.17703,330.2,-0.34868,0.89718,0.27108,-58.666,-0.26794,0.18173,-0.94614,248.82

> ui mousemode right "rotate selected models"

> select add #3

17542 atoms, 17675 bonds, 2405 residues, 3 models selected  

> view matrix models
> #1,0.42372,0.78352,-0.45449,107.25,0.26163,0.3745,0.88955,88.23,0.86718,-0.49583,-0.04631,97.495,#6,-0.85867,-0.37985,0.3441,306.29,-0.30263,0.91759,0.25776,-67.573,-0.41366,0.1172,-0.90286,276.9,#3,0.99096,0.12353,-0.052365,-41.689,-0.12099,0.99143,0.049217,-32.923,0.057996,-0.042437,0.99741,-25.732

> view matrix models
> #1,0.48037,0.80395,-0.35057,97.566,0.14733,0.32006,0.93587,99.935,0.8646,-0.50122,0.035301,95.294,#6,-0.90139,-0.26766,0.34038,283.39,-0.17286,0.94315,0.28389,-90.096,-0.39701,0.19706,-0.89641,254.77,#3,0.97189,0.23512,-0.012238,-68.434,-0.23532,0.97172,-0.019439,5.7376,0.0073212,0.021773,0.99974,-29.674

> fitmap #3 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 8555 atoms  
average map value = 0.1145, steps = 1020  
shifted from previous position = 4.13  
rotated from previous position = 12.7 degrees  
atoms outside contour = 4240, contour level = 0.084608  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99191155 0.06335532 0.10998890 -62.76825757  
-0.06928609 0.99629434 0.05096082 -41.15660376  
-0.10635268 -0.05816933 0.99262552 10.90286608  
Axis -0.39506002 0.78317416 -0.48017268  
Axis point 2.56900071 0.00000000 616.37826305  
Rotation angle (degrees) 7.93898321  
Shift along axis -12.67081790  
  

> fitmap #4 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 8555 atoms  
average map value = 0.1047, steps = 804  
shifted from previous position = 5.34  
rotated from previous position = 20.5 degrees  
atoms outside contour = 4422, contour level = 0.084608  
  
Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999092 0.00412006 0.00108643 -39.00797240  
-0.00412304 0.99998770 0.00275780 -38.99266428  
-0.00107505 -0.00276225 0.99999561 -27.76974191  
Axis -0.54366522 0.21288185 -0.81185556  
Axis point -11301.91372520 4764.89551107 0.00000000  
Rotation angle (degrees) 0.29087494  
Shift along axis 35.45146656  
  

> view matrix models
> #1,0.50877,0.851,-0.13021,86.529,-0.0070294,0.15535,0.98783,117.65,0.86087,-0.50167,0.08502,94.082,#6,-0.92059,-0.046384,0.38776,226.11,0.053879,0.96834,0.24375,-116.88,-0.38679,0.24528,-0.88895,241.01,#3,0.94978,0.28585,0.12733,-102.22,-0.28518,0.95818,-0.023838,20.523,-0.12882,-0.013672,0.99157,6.4689

> view matrix models
> #1,0.41106,0.90215,0.13096,88.402,-0.17226,-0.0642,0.98296,139.1,0.89519,-0.42661,0.12901,87.865,#6,-0.83536,0.19218,0.51502,146.98,0.31322,0.93634,0.15865,-129.07,-0.45175,0.29384,-0.84237,231.83,#3,0.84686,0.53103,0.029017,-110.99,-0.52691,0.84518,-0.089589,99.508,-0.0721,0.06058,0.99556,-18.965

> view matrix models
> #1,0.55394,0.75066,-0.36008,90.156,0.13096,0.34855,0.9281,101.72,0.82219,-0.56127,0.09477,98.841,#6,-0.93074,-0.26307,0.25401,292.43,-0.17738,0.9322,0.31551,-89.483,-0.31979,0.2486,-0.91429,235.23,#3,0.97925,0.042796,0.19808,-74.97,-0.048572,0.99852,0.024389,-39.72,-0.19674,-0.033504,0.97988,24.918

> view matrix models
> #1,0.5673,0.82189,-0.051582,77.636,0.043048,0.032954,0.99853,113.04,0.82238,-0.56869,-0.016686,102.58,#6,-0.93958,0.041873,0.33975,209.96,0.086342,0.98939,0.11684,-115.11,-0.33126,0.13911,-0.93323,265.4,#3,0.91484,0.35307,0.196,-123.47,-0.3723,0.92541,0.070709,22.647,-0.15642,-0.13766,0.97805,38.388

> view matrix models
> #1,0.49291,0.78746,-0.37005,96.979,0.077493,0.38389,0.92012,107.63,0.86662,-0.48221,0.1282,91.779,#6,-0.90459,-0.28436,0.31758,289.78,-0.15616,0.91426,0.37381,-92.017,-0.39665,0.28855,-0.87144,229.77,#3,0.99105,0.040677,0.12712,-61.789,-0.035989,0.99859,-0.038956,-28.701,-0.12853,0.034033,0.99112,-2.7827

> fitmap #3 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 8555 atoms  
average map value = 0.1145, steps = 1148  
shifted from previous position = 0.0468  
rotated from previous position = 5.6 degrees  
atoms outside contour = 4238, contour level = 0.084608  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99191901 0.06352370 0.10982442 -62.76919098  
-0.06945569 0.99627767 0.05105578 -41.13025537  
-0.10617237 -0.05827113 0.99263885 10.89172991  
Axis -0.39581462 0.78200954 -0.48144768  
Axis point 2.83716672 0.00000000 617.02824957  
Rotation angle (degrees) 7.93812928  
Shift along axis -12.56308662  
  

> hide #!4 models

> split #3

Split hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) into 2 models  
Chain information for hPNP_dimer_5zf6_fit_tetramer1.pdb A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for hPNP_dimer_5zf6_fit_tetramer1.pdb B #3.2  
---  
Chain | Description  
B | No description available  
  

> select add #3.2

13214 atoms, 13318 bonds, 1808 residues, 3 models selected  

> select subtract #3.2

8987 atoms, 9057 bonds, 1231 residues, 2 models selected  

> select add #3.1

13315 atoms, 13414 bonds, 1828 residues, 3 models selected  

> view matrix models
> #1,0.63866,0.76924,-0.019308,72.947,-0.11384,0.11928,0.98631,131.14,0.76102,-0.62772,0.16375,104.77,#6,-0.96168,0.087149,0.25996,211.37,0.16026,0.94797,0.27507,-124.61,-0.22246,0.30619,-0.92561,212.03,#3.1,0.87837,0.37425,0.29732,-138.47,-0.38698,0.92193,-0.017224,45.309,-0.28055,-0.099926,0.95462,58.624

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.63866,0.76924,-0.019308,72.084,-0.11384,0.11928,0.98631,125.49,0.76102,-0.62772,0.16375,100.68,#6,-0.96168,0.087149,0.25996,210.51,0.16026,0.94797,0.27507,-130.26,-0.22246,0.30619,-0.92561,207.94,#3.1,0.87837,0.37425,0.29732,-139.33,-0.38698,0.92193,-0.017224,39.653,-0.28055,-0.099926,0.95462,54.532

> view matrix models
> #1,0.63866,0.76924,-0.019308,72.54,-0.11384,0.11928,0.98631,126.82,0.76102,-0.62772,0.16375,102,#6,-0.96168,0.087149,0.25996,210.96,0.16026,0.94797,0.27507,-128.93,-0.22246,0.30619,-0.92561,209.26,#3.1,0.87837,0.37425,0.29732,-138.87,-0.38698,0.92193,-0.017224,40.985,-0.28055,-0.099926,0.95462,55.849

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.72286,0.68885,-0.054338,64.422,-0.094506,0.17646,0.97976,124.12,0.6845,-0.7031,0.19266,111.02,#6,-0.98739,0.06889,0.14254,227.23,0.11061,0.94433,0.30983,-125.74,-0.11326,0.32169,-0.94005,195.53,#3.1,0.86215,0.31108,0.39992,-145.84,-0.33042,0.94358,-0.021645,27.528,-0.38409,-0.11348,0.9163,85.446

> view matrix models
> #1,0.49021,0.82777,-0.27293,94.401,-0.20452,0.41364,0.88717,136.23,0.84727,-0.37908,0.37207,84.985,#6,-0.91222,-0.18982,0.36306,263.96,0.048035,0.83052,0.55491,-111.5,-0.40687,0.52364,-0.74851,162.13,#3.1,0.98015,0.16795,0.1053,-79.273,-0.14126,0.96443,-0.22342,31.317,-0.13908,0.20411,0.96902,-29.133

> fitmap #3.1 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb A (#3.1) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 4328 atoms  
average map value = 0.1678, steps = 136  
shifted from previous position = 3.69  
rotated from previous position = 14.6 degrees  
atoms outside contour = 1115, contour level = 0.084608  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb A (#3.1) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99674815 0.00855406 -0.08012447 -16.33333536  
-0.03149945 0.95659060 -0.28972780 24.97205938  
0.07416797 0.29130952 0.95374937 -82.05312532  
Axis 0.96436593 -0.25608401 -0.06647806  
Axis point 0.00000000 289.92437323 27.99933406  
Rotation angle (degrees) 17.53291000  
Shift along axis -16.69152470  
  

> volume #2 color #d783ff

> transparency 50

> volume #2 level 0.1528

> fitmap #3.1 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb A (#3.1) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 4328 atoms  
average map value = 0.1678, steps = 48  
shifted from previous position = 0.00201  
rotated from previous position = 0.0151 degrees  
atoms outside contour = 2432, contour level = 0.15284  
  
Position of hPNP_dimer_5zf6_fit_tetramer1.pdb A (#3.1) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99676224 0.00853600 -0.07995103 -16.36893175  
-0.03144631 0.95653366 -0.28992148 25.01195907  
0.07400108 0.29149695 0.95370506 -82.04786196  
Axis 0.96455693 -0.25540226 -0.06632955  
Axis point 0.00000000 289.73990669 28.09020522  
Rotation angle (degrees) 17.54119628  
Shift along axis -16.73467989  
  
Must specify one map, got 0  

> correlation #3.1 #1

Unknown command: correlation #3.1 #1  

> correlation

Unknown command: correlation  

> crossfade correlation #3.1 #1

Expected an integer >= 1 or a keyword  

> crosscorrelation #3.1 #1

Unknown command: crosscorrelation #3.1 #1  

> crosscorrelation #3.1 #1

Unknown command: measure crosscorrelation #3.1 #1  

> volume #2 level 0.09062

Must specify one map, got 0  
Must specify one map, got 0  

> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramer_02_withouttickoncopymaps.cxs
> includeMaps true

> combine #3.1 #3.2

Cell requested for row 6 is out of bounds for table with 9 rows! Resizing
table model.  

> select add #5

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> select subtract #4.1

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> hide #4.1 models

> show #4.1 models

> select subtract #4.1

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> select add #4

30425 atoms, 30650 bonds, 4176 residues, 5 models selected  

> hide #!4 models

> hide #4.1 models

> show #!4 models

> hide #!4 models

> select subtract #5

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> hide #5 models

> show #5 models

> select add #5

30425 atoms, 30650 bonds, 4176 residues, 5 models selected  

> select subtract #5

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> select add #5

30425 atoms, 30650 bonds, 4176 residues, 5 models selected  

> select subtract #5

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> select add #5

30425 atoms, 30650 bonds, 4176 residues, 5 models selected  

> select subtract #5

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> select add #5

30425 atoms, 30650 bonds, 4176 residues, 5 models selected  

> hide #3.2 models

> select subtract #5

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> select add #5

30425 atoms, 30650 bonds, 4176 residues, 5 models selected  

> select subtract #5

21870 atoms, 22032 bonds, 3002 residues, 4 models selected  

> select add #5

30425 atoms, 30650 bonds, 4176 residues, 5 models selected  

> combine #3.1 #3.2

> save /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/9kjr_ChainA.pdb
> models #7 relModel #7

> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramer_02_withouttickoncopymaps.cxs
> includeMaps true

——— End of log from Wed Nov 5 22:22:09 2025 ———

> view name session-start

opened ChimeraX session  

> show #!4 models

> split #420

> split #4

Split hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) into 2 models  
Chain information for hPNP_dimer_5zf6_fit_tetramer2.pdb A #4.1  
---  
Chain | Description  
A | No description available  
  
Chain information for hPNP_dimer_5zf6_fit_tetramer2.pdb B #4.2  
---  
Chain | Description  
B | No description available  
  

> ui tool show "Fit in Map"

> fitmap #4.1 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb A (#4.1) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 4328 atoms  
average map value = 0.1511, steps = 156  
shifted from previous position = 8.94  
rotated from previous position = 22.3 degrees  
atoms outside contour = 1422, contour level = 0.090619  
  
Position of hPNP_dimer_5zf6_fit_tetramer2.pdb A (#4.1) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98383867 0.06125938 0.16825207 -71.95682366  
-0.00104748 0.94160854 -0.33670796 23.75307981  
-0.17905411 0.33109007 0.92645507 -46.53042246  
Axis 0.88416501 0.45983359 -0.08249432  
Axis point 0.00000000 176.40808408 106.68048095  
Rotation angle (degrees) 22.18778127  
Shift along axis -48.86074587  
  

> fitmap #4.2 inMap #2

Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb B (#4.2) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 4227 atoms  
average map value = 0.1559, steps = 64  
shifted from previous position = 0.136  
rotated from previous position = 0.638 degrees  
atoms outside contour = 1298, contour level = 0.090619  
  
Position of hPNP_dimer_5zf6_fit_tetramer2.pdb B (#4.2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99994145 0.01081390 0.00039510 -39.96225052  
-0.01081776 0.99987385 0.01163050 -39.04984188  
-0.00026928 -0.01163409 0.99993229 -26.51523205  
Axis -0.73218070 0.02090926 -0.68078942  
Axis point 0.00000000 421.54756264 3445.69864868  
Rotation angle (degrees) 0.91030714  
Shift along axis 46.49437443  
  

> 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  

> ui tool show "Fit in Map"

> fitmap #9 inMap #2

Fit molecule combination (#9) to map cryosparc_P1_J482_004_volume_map.mrc (#2)
using 17110 atoms  
average map value = 0.1624, steps = 40  
shifted from previous position = 0.0105  
rotated from previous position = 0.0179 degrees  
atoms outside contour = 5081, contour level = 0.090619  
  
Position of combination (#9) relative to cryosparc_P1_J482_004_volume_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99677155 0.00841415 -0.07984782 -16.35861534  
-0.03128020 0.95661300 -0.28967760 24.91875018  
0.07394607 0.29124004 0.95378781 -82.00725740  
Axis 0.96459426 -0.25536960 -0.06591113  
Axis point 0.00000000 289.78873675 27.86332375  
Rotation angle (degrees) 17.52489761  
Shift along axis -16.73772692  
  
3 fitting solutions  
map LLG values: 8337.62, 7701.22, 6592.3  
map CC values: 0.470138, 0.462942, 0.453086  
Structure being fitting was deleted during fitting  

> fitmap #9 inMap #2

Fit molecule combination (#9) to map cryosparc_P1_J482_004_volume_map.mrc (#2)
using 17110 atoms  
average map value = 0.1624, steps = 28  
shifted from previous position = 0.00445  
rotated from previous position = 0.00924 degrees  
atoms outside contour = 5084, contour level = 0.090619  
  
Position of combination (#9) relative to cryosparc_P1_J482_004_volume_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99677091 0.00841606 -0.07985550 -16.36004039  
-0.03129617 0.95656606 -0.28983084 24.95280027  
0.07394783 0.29139412 0.95374062 -82.02900446  
Axis 0.96462399 -0.25525810 -0.06590799  
Axis point 0.00000000 289.72640149 27.92910851  
Rotation angle (degrees) 17.53391181  
Shift along axis -16.74432522  
  

> ui tool show "Local EM Fitting"

Must specify exactly two half maps for fitting  

> marker #1 position 148.92,149.032,146.818 radius 85.3724 color 100,65,0,50

> phenix emplaceLocal #9 mapData #2 resolution 2.89 center
> 148.92,149.032,146.818 showSharpenedMap true applySymmetry true

> fitmap #9 inMap #2

Fit molecule combination (#9) to map full_map.mrc (#2) using 17110 atoms  
average map value = 0.1624, steps = 40  
shifted from previous position = 0.00356  
rotated from previous position = 0.00812 degrees  
atoms outside contour = 5087, contour level = 0.090619  
  
Position of combination (#9) relative to full_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99677175 0.00841491 -0.07984519 -16.36118948  
-0.03128162 0.95660725 -0.28969641 24.92316279  
0.07394272 0.29125888 0.95378232 -82.01007710  
Axis 0.96460083 -0.25534485 -0.06591093  
Axis point 0.00000000 289.78204090 27.87084986  
Rotation angle (degrees) 17.52594735  
Shift along axis -16.74065741  
  

> fitmap #9 inMap #2

Fit molecule combination (#9) to map full_map.mrc (#2) using 17110 atoms  
average map value = 0.1624, steps = 36  
shifted from previous position = 0.0164  
rotated from previous position = 0.0104 degrees  
atoms outside contour = 5079, contour level = 0.090619  
  
Position of combination (#9) relative to full_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99677020 0.00841017 -0.07986500 -16.35926930  
-0.03129626 0.95655446 -0.28986911 24.98117285  
0.07395737 0.29143236 0.95372819 -82.03523509  
Axis 0.96462564 -0.25525654 -0.06588981  
Axis point 0.00000000 289.72375643 28.00553313  
Rotation angle (degrees) 17.53626351  
Shift along axis -16.75189263  
  

> fitmap #9 inMap #2

Fit molecule combination (#9) to map full_map.mrc (#2) using 17110 atoms  
average map value = 0.1624, steps = 28  
shifted from previous position = 0.00407  
rotated from previous position = 0.00828 degrees  
atoms outside contour = 5078, contour level = 0.090619  
  
Position of combination (#9) relative to full_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99676918 0.00840904 -0.07987785 -16.35356732  
-0.03128828 0.95659639 -0.28973157 24.95081470  
0.07397450 0.29129474 0.95376890 -82.01823274  
Axis 0.96458259 -0.25541580 -0.06590293  
Axis point 0.00000000 289.78740937 27.94598913  
Rotation angle (degrees) 17.52850147  
Shift along axis -16.74195661  
  

> fitmap #9 inMap #2

Fit molecule combination (#9) to map full_map.mrc (#2) using 17110 atoms  
average map value = 0.1624, steps = 40  
shifted from previous position = 0.00239  
rotated from previous position = 0.0102 degrees  
atoms outside contour = 5078, contour level = 0.090619  
  
Position of combination (#9) relative to full_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99676909 0.00840565 -0.07987936 -16.35380451  
-0.03129860 0.95654476 -0.28990085 24.98950003  
0.07397138 0.29146432 0.95371734 -82.04196402  
Axis 0.96462163 -0.25527460 -0.06587868  
Axis point 0.00000000 289.71779582 28.02336784  
Rotation angle (degrees) 17.53832295  
Shift along axis -16.74960133  
  
4 fitting solutions  
map LLG values: 29197.6, 28909.3, 24169.4, 23982.6  
map CC values: 0.544118, 0.540111, 0.48663, 0.483889  
Opened sharpened local map as #1, grid size 223,223,223, pixel 0.846, shown at
level 0.000877, step 1, values float32  

> measure symmetry #2

No symmetry found for full_map.mrc  

Could not determine symmetry for full_map.mrc #2  
  
If you know the symmetry of the map, you can create symmetry copies of the
structure with the sym command and then combine the symmetry copies into a
single structure with the combine command  

> ui tool show "Model Panel"

> hide #!2 models

> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/Phenix_localfit_sharpenedmap.pdb
> relModel #1

> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/phenix_Localfit_sharpenmap.cxs

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: 1 day, 8 hours, 57 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