ChimeraX bug report submission

[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  

> hide #9 models

> ui tool show "Fit Loops"

> show #9 models

> ui tool show "Fit Loops"

No selected amino-acid residues or missing-structure pseudobonds in
combination #9  

> open
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_0.cif
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_1.cif
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_2.cif
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_3.cif
> /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_4.cif

Chain information for fold_s1domain_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Chain information for fold_s1domain_model_1.cif #3  
---  
Chain | Description  
A | .  
  
Chain information for fold_s1domain_model_2.cif #4  
---  
Chain | Description  
A | .  
  
Chain information for fold_s1domain_model_3.cif #5  
---  
Chain | Description  
A | .  
  
Chain information for fold_s1domain_model_4.cif #6  
---  
Chain | Description  
A | .  
  
Computing secondary structure  
[Repeated 4 time(s)]

> hide #9 models

> tile

6 models tiled  

> hide #!2 models

> show #!2 models

> color #3 #7a81ffff

> color #3 #0433ffff

> select add #3

522 atoms, 529 bonds, 65 residues, 1 model selected  

> view matrix models #3,1,0,0,167.58,0,1,0,54.796,0,0,1,204.78

> view matrix models #3,1,0,0,165.39,0,1,0,115.67,0,0,1,225.25

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-2.0304,0,1,0,-3.9698,0,0,1,-16.281

> view matrix models #2,1,0,0,-2.6783,0,1,0,2.0885,0,0,1,-17.199

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.32589,0.91906,-0.22164,161.57,-0.87579,0.20518,-0.43692,116.43,-0.35608,0.3365,0.87177,223.66

> view matrix models
> #3,0.56547,-0.7859,-0.25021,166.9,0.82291,0.55799,0.10713,118.68,0.055423,-0.26647,0.96225,226.17

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.56547,-0.7859,-0.25021,163.29,0.82291,0.55799,0.10713,131.17,0.055423,-0.26647,0.96225,208.64

> view matrix models
> #3,0.29541,0.69457,0.65597,155.91,-0.92197,0.38722,0.0051959,144.72,-0.2504,-0.60633,0.75477,209.92

> view matrix models
> #3,0.79695,-0.604,0.0075442,161.41,0.52088,0.6935,0.49774,151.3,-0.30587,-0.39275,0.86729,210.32

> view matrix models
> #3,0.46843,-0.85689,-0.21519,160.99,0.82693,0.33948,0.44827,160.63,-0.31106,-0.38793,0.86761,210.1

> view matrix models
> #3,-0.34505,0.91726,0.19892,154.61,-0.88742,-0.24981,-0.38741,149.7,-0.30566,-0.3102,0.90019,211.43

> view matrix models
> #3,0.66119,0.61943,0.42324,159.05,-0.59559,0.77644,-0.20593,116.72,-0.45618,-0.11592,0.8823,203.44

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit molecule fold_s1domain_model_0.cif (#1) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms  
average map value = 0.0003632, steps = 356  
shifted from previous position = 4.22  
rotated from previous position = 14.5 degrees  
atoms outside contour = 522, contour level = 0.090619  
  
Position of fold_s1domain_model_0.cif (#1) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97213948 0.21632806 0.09026078 182.36500636  
-0.20718521 0.97309809 -0.10076905 2.02323771  
-0.10963177 0.07926087 0.99080704 169.96457072  
Axis 0.35881954 0.39840796 -0.84410878  
Axis point 279.68301149 -935.07624490 0.00000000  
Rotation angle (degrees) 14.52865421  
Shift along axis -77.22638618  
  

> fitmap #1 inMap #2

Fit molecule fold_s1domain_model_0.cif (#1) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms  
average map value = 0.000365, steps = 100  
shifted from previous position = 0.137  
rotated from previous position = 0.599 degrees  
atoms outside contour = 522, contour level = 0.090619  
  
Position of fold_s1domain_model_0.cif (#1) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97288387 0.20994836 0.09704977 182.50082645  
-0.19979031 0.97422533 -0.10473222 2.03411083  
-0.11653670 0.08250268 0.98975376 169.89241874  
Axis 0.37555154 0.42840695 -0.82184459  
Axis point 284.35086060 -958.13936528 0.00000000  
Rotation angle (degrees) 14.43490420  
Shift along axis -70.21527182  
  

> fitmap #3 inMap #2

Fit molecule fold_s1domain_model_1.cif (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms  
average map value = 0.07067, steps = 164  
shifted from previous position = 8.32  
rotated from previous position = 39.5 degrees  
atoms outside contour = 363, contour level = 0.090619  
  
Position of fold_s1domain_model_1.cif (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.92043171 -0.33817014 -0.19607755 159.00664102  
0.31899036 0.93970634 -0.12327665 125.40584612  
0.22594381 0.05092090 0.97280854 218.61730845  
Axis 0.21769478 -0.52740033 0.82125385  
Axis point -542.84900192 502.64006802 0.00000000  
Rotation angle (degrees) 23.58417039  
Shift along axis 148.01613600  
  

> fitmap #4 inMap #2

Fit molecule fold_s1domain_model_2.cif (#4) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms  
average map value = -0.001537, steps = 80  
shifted from previous position = 0.947  
rotated from previous position = 11.5 degrees  
atoms outside contour = 522, contour level = 0.090619  
  
Position of fold_s1domain_model_2.cif (#4) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98137074 -0.01475330 -0.19155629 124.31223336  
0.00382580 0.99835020 -0.05729090 166.97625539  
0.19208549 0.05549076 0.97980811 25.02135082  
Axis 0.28173775 -0.95836828 0.04641208  
Axis point -72.08236990 0.00000000 838.11125119  
Rotation angle (degrees) 11.54594279  
Shift along axis -123.84000488  
  

> volume #2 level 0.07472

> view matrix models
> #3,-0.67188,0.62554,0.39658,156.11,-0.55661,-0.77969,0.28683,98.367,0.48863,-0.028029,0.87204,213.25

> style sel ball

Changed 522 atom styles  

> style sel sphere

Changed 522 atom styles  

> show sel surfaces

> view matrix models
> #3,-0.76709,0.51052,0.38851,156.55,-0.43671,-0.85915,0.26672,89.922,0.46996,0.034932,0.882,210.08

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.7899,0.60735,-0.084731,156.46,-0.59625,-0.72837,0.33758,88.914,0.14331,0.31717,0.93748,208.03

> view matrix models
> #3,-0.66024,0.41001,0.62926,157.09,-0.37315,-0.90619,0.19893,90.332,0.6518,-0.10346,0.7513,211.23

> view matrix models
> #3,0.35613,-0.51243,-0.7814,164.32,-0.36034,0.69624,-0.62081,86.3,0.86216,0.50267,0.063305,210.69

> view matrix models
> #3,0.22649,-0.61697,-0.75369,164.12,-0.74129,0.39275,-0.54427,85.701,0.63181,0.68198,-0.3684,209.58

> view matrix models
> #3,0.4365,-0.66898,-0.60161,164.96,-0.60804,0.27351,-0.74531,86.654,0.66314,0.69112,-0.28738,209.62

> hide sel surfaces

> view matrix models
> #3,0.19536,-0.53018,-0.82507,164.33,-0.68664,0.52674,-0.50106,85.416,0.70026,0.66442,-0.26114,209.74

> view matrix models
> #3,0.35707,-0.66519,-0.65576,164.84,-0.63986,0.33727,-0.69053,86.324,0.6805,0.66617,-0.3052,209.76

> view matrix models
> #3,0.3911,-0.62689,-0.67384,164.84,-0.65268,0.32728,-0.6833,86.311,0.64888,0.70704,-0.28116,209.53

> view matrix models
> #3,0.50296,-0.58623,-0.63512,164.94,-0.61625,0.27201,-0.73908,86.63,0.60603,0.76312,-0.22446,209.2

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.50296,-0.58623,-0.63512,159.63,-0.61625,0.27201,-0.73908,149.03,0.60603,0.76312,-0.22446,209.13

> view matrix models
> #3,0.50296,-0.58623,-0.63512,160.92,-0.61625,0.27201,-0.73908,148.39,0.60603,0.76312,-0.22446,217.66

> view matrix models
> #3,0.50296,-0.58623,-0.63512,160.7,-0.61625,0.27201,-0.73908,148.47,0.60603,0.76312,-0.22446,216.16

> view matrix models
> #3,-0.45496,0.52695,-0.71787,152.27,-0.45166,0.55821,0.696,166.64,0.76747,0.64088,-0.015958,206.6

> fitmap #4 inMap #2

Fit molecule fold_s1domain_model_2.cif (#4) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms  
average map value = -0.0004006, steps = 88  
shifted from previous position = 1.25  
rotated from previous position = 6.05 degrees  
atoms outside contour = 522, contour level = 0.074721  
  
Position of fold_s1domain_model_2.cif (#4) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99147668 0.01049450 -0.12986092 116.82021270  
-0.00708136 0.99961796 0.02671695 137.03591507  
0.13009169 -0.02556964 0.99117221 26.84154122  
Axis -0.19675787 -0.97821877 -0.06613911  
Axis point -80.51316555 0.00000000 664.24143651  
Rotation angle (degrees) 7.63549261  
Shift along axis -158.81167600  
  

> fitmap #3 inMap #2

Fit molecule fold_s1domain_model_1.cif (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms  
average map value = 0.07284, steps = 144  
shifted from previous position = 9.14  
rotated from previous position = 32.2 degrees  
atoms outside contour = 318, contour level = 0.074721  
  
Position of fold_s1domain_model_1.cif (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.51872333 0.27009097 -0.81115779 162.49967762  
-0.72798453 0.35795974 0.58472501 168.27559607  
0.44829078 0.89382084 0.01093998 212.26586284  
Axis 0.18888415 -0.76963145 -0.60991001  
Axis point 77.24806995 0.00000000 108.85630195  
Rotation angle (degrees) 125.09345631  
Shift along axis -228.27965129  
  

> view matrix models
> #3,0.87466,-0.27955,-0.396,157.61,-0.41844,-0.023029,-0.90795,126.96,0.2447,0.95985,-0.13712,199.83

> view matrix models
> #3,0.7064,-0.4253,0.56579,157.56,0.3865,-0.43789,-0.81171,108.84,0.59297,0.79207,-0.14495,197.91

> fitmap #3 inMap #2

Fit molecule fold_s1domain_model_1.cif (#3) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms  
average map value = 0.057, steps = 140  
shifted from previous position = 8.64  
rotated from previous position = 40 degrees  
atoms outside contour = 355, contour level = 0.074721  
  
Position of fold_s1domain_model_1.cif (#3) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.87064244 -0.19188813 -0.45294667 134.31464498  
-0.49130252 0.29321200 0.82015154 169.18135869  
-0.02456795 0.93659258 -0.34955793 220.00413042  
Axis 0.21746043 -0.80002225 -0.55917382  
Axis point 82.32214637 0.00000000 66.57043206  
Rotation angle (degrees) 164.47081111  
Shift along axis -229.16128017  
  

> view matrix models
> #3,0.95229,0.22388,0.20741,154.09,-0.28611,0.41832,0.86206,83.875,0.10624,-0.88028,0.46241,224.1

> open Q8TCS8 fromDatabase alphafold_pae format pae

Fetching an AlphaFold database PAE file requires specifying the structure to
associate. For example "open P29474 from alphafold_pae structure #1"  

> open /Users/madhurikanavalli/Downloads/AF-Q8TCS8-F1-model_v6.pdb

AF-Q8TCS8-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for polyribonucleotide
nucleotidyltransferase 1, mitochondrial (Q8TCS8) [more info...]  
  
Chain information for AF-Q8TCS8-F1-model_v6.pdb #7  
---  
Chain | Description | UniProt  
A | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 1-783  
  
Computing secondary structure  

> hide #!3 models

> select subtract #3

1 model selected  

> hide #6 models

> hide #!2 models

> show #!2 models

> hide #1 models

> close #1

> close #6

> close #5

> close #4

> select add #7

6032 atoms, 6129 bonds, 783 residues, 1 model selected  

> view matrix models
> #7,0.93203,-0.33526,0.13754,27.703,-0.3055,-0.5228,0.79584,135.27,-0.19491,-0.78376,-0.58968,172.48

> view matrix models
> #7,0.99383,0.081244,-0.075482,18.858,0.10523,-0.47615,0.87304,113.59,0.034988,-0.8756,-0.48177,159.02

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #7,0.99383,0.081244,-0.075482,17.188,0.10523,-0.47615,0.87304,122.02,0.034988,-0.8756,-0.48177,152.46

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.96007,-0.2796,-0.0089378,326.83,0.13649,-0.44028,-0.88742,273.98,0.24419,-0.85321,0.46087,83.166

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.88144,0.35786,-0.30822,1.7984,0.34471,0.93357,0.098144,71.119,0.32287,-0.019738,-0.94624,110.86

> view matrix models
> #7,-0.099404,0.88065,-0.46322,0.9821,0.94473,0.22969,0.23394,71.545,0.31242,-0.41436,-0.85481,105.94

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.76785,-0.43102,-0.47394,-6.4138,-0.52462,0.84765,0.079073,63.133,0.36766,0.30936,-0.877,107.93

> view matrix models
> #7,-0.33896,-0.93514,-0.10302,5.3628,-0.91127,0.35356,-0.21114,50.667,0.23387,0.022309,-0.97201,103.39

> view matrix models
> #7,0.12187,-0.96241,-0.24272,2.542,-0.96457,-0.05719,-0.25755,47.564,0.23399,0.2655,-0.93528,105.4

> view matrix models
> #7,-0.20108,-0.97283,-0.11478,5.3796,-0.68218,0.22315,-0.6963,35.543,0.70299,-0.061709,-0.70852,113.32

> fitmap #7 inMap #2

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#7) to map
cryosparc_P1_J482_004_volume_map.mrc (#2) using 6032 atoms  
average map value = -5.856e-05, steps = 368  
shifted from previous position = 2.09  
rotated from previous position = 5.84 degrees  
atoms outside contour = 6032, contour level = 0.074721  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#7) relative to
cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.08710074 -0.92938392 0.35869061 59.59075313  
-0.79201574 -0.28300142 -0.54094475 16.28119012  
0.60425532 -0.23697192 -0.76073634 160.17750188  
Axis 0.73385821 -0.59284799 0.33163743  
Axis point 0.00000000 22.84851283 71.47256607  
Rotation angle (degrees) 168.04719174  
Shift along axis 87.19974831  
  

> view matrix models
> #7,-0.17868,-0.97881,-0.10005,6.648,-0.7608,0.20193,-0.61677,36.832,0.62391,-0.034088,-0.78076,112.96

> view matrix models
> #7,-0.20095,-0.96996,0.13707,14.191,-0.86316,0.10916,-0.493,40.09,0.46323,-0.21738,-0.85917,109.21

> view matrix models
> #7,-0.10038,-0.9943,0.035932,11.249,-0.86855,0.069951,-0.49065,40.01,0.48534,-0.080459,-0.87062,109.4

> ui mousemode right "move picked models"

> view matrix models
> #7,-0.10038,-0.9943,0.035932,7.572,-0.86855,0.069951,-0.49065,29.368,0.48534,-0.080459,-0.87062,77.9

> view matrix models
> #2,0.85656,0.43699,0.27448,-91.905,-0.45132,0.89228,-0.012127,31.709,-0.25021,-0.11349,0.96152,-24.5

> view matrix models
> #7,0.10537,-0.99398,0.030033,12.071,-0.94351,-0.10947,-0.31273,46.098,0.31413,0.0046163,-0.94937,108.85

> view matrix models
> #7,-0.56765,-0.71499,-0.40811,-7.3912,-0.38128,0.66768,-0.6394,71.402,0.72966,-0.20735,-0.65162,110.98

> view matrix models
> #2,0.93609,0.26905,0.22662,-77.448,-0.28402,0.95816,0.035632,19.557,-0.20755,-0.097718,0.97333,-57.413

> view matrix models
> #2,0.93609,0.26905,0.22662,-77.709,-0.28402,0.95816,0.035632,24.136,-0.20755,-0.097718,0.97333,-56.529

> view matrix models
> #7,0.039543,-0.98518,0.16692,17.982,-0.87376,-0.11513,-0.47253,24.985,0.48474,-0.12716,-0.86536,114.25

> view matrix models
> #2,0.93609,0.26905,0.22662,-72.357,-0.28402,0.95816,0.035632,7.0311,-0.20755,-0.097718,0.97333,-29.712

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.097094,-0.9571,0.27301,20.96,-0.44484,-0.20365,-0.87215,13.504,0.89033,-0.20613,-0.40599,130.24

> view matrix models
> #7,-0.07236,-0.95607,0.28407,21.412,-0.44804,-0.2233,-0.86568,13.632,0.89108,-0.18992,-0.4122,130.1

> ui mousemode right "move picked models"

> view matrix models
> #7,-0.07236,-0.95607,0.28407,15.841,-0.44804,-0.2233,-0.86568,68.667,0.89108,-0.18992,-0.4122,123.93

> view matrix models
> #7,-0.31735,-0.94146,-0.11376,0.63703,-0.20623,0.18561,-0.96074,85.778,0.92561,-0.28142,-0.25306,128.41

> view matrix models
> #7,0.29795,0.52938,-0.79435,-11.389,0.3903,0.69185,0.60746,91.578,0.87114,-0.49103,-0.00047747,123.65

> view matrix models
> #2,-0.0079881,0.99894,0.04544,-17.486,-0.99199,-0.0021879,-0.12629,318.3,-0.12606,-0.046085,0.99095,-56.337

> view matrix models
> #7,-0.1715,0.44788,-0.87749,-17.133,0.40556,0.84381,0.35143,88.21,0.89784,-0.29561,-0.32636,109.47

> view matrix models
> #7,-0.1715,0.44788,-0.87749,-17.408,0.40556,0.84381,0.35143,90.261,0.89784,-0.29561,-0.32636,108.77

> view matrix models
> #7,-0.19986,0.45505,-0.86775,-15.159,0.30662,0.87018,0.38571,82.163,0.93061,-0.18898,-0.31344,118.36

> view matrix models
> #7,-0.19986,0.45505,-0.86775,-19.12,0.30662,0.87018,0.38571,99.076,0.93061,-0.18898,-0.31344,101

> view matrix models
> #7,-0.19986,0.45505,-0.86775,-20.753,0.30662,0.87018,0.38571,106.14,0.93061,-0.18898,-0.31344,93.903

> view matrix models
> #7,-0.19986,0.45505,-0.86775,-14.691,0.30662,0.87018,0.38571,84.809,0.93061,-0.18898,-0.31344,123.13

> view matrix models
> #7,-0.19986,0.45505,-0.86775,-19.112,0.30662,0.87018,0.38571,85.454,0.93061,-0.18898,-0.31344,93.102

> view matrix models
> #7,-0.44672,-0.85339,-0.26864,-7.3842,-0.29981,0.4257,-0.85375,105.34,0.84294,-0.30085,-0.44603,111.24

> close session

> open
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramerfit_J482_goodone.pdb
> format pdb

Chain information for tetramerfit_J482_goodone.pdb #1  
---  
Chain | Description  
A C | No description available  
B D | No description available  
  

> view matrix models #1,1,0,0,29.011,0,1,0,-2.0292,0,0,1,-1.0087

> view matrix models #1,1,0,0,23.646,0,1,0,-0.29777,0,0,1,-1.2033

> view matrix models #1,1,0,0,15.181,0,1,0,-4.4582,0,0,1,-0.91014

> view matrix models #1,1,0,0,-15.467,0,1,0,-15.673,0,0,1,15.003

> view matrix models #1,1,0,0,-18.434,0,1,0,-4.2218,0,0,1,-10.466

> view matrix models #1,1,0,0,-39.086,0,1,0,-2.3932,0,0,1,-42.474

> view matrix models #1,1,0,0,-7.3595,0,1,0,2.1169,0,0,1,-20.622

> view matrix models #1,1,0,0,56.725,0,1,0,-22.296,0,0,1,-11.337

> view matrix models #1,1,0,0,58.82,0,1,0,-0.298,0,0,1,12.068

> close session

> open /Users/madhurikanavalli/Downloads/cryosparc_P1_J482_004_volume_map.mrc

Opened cryosparc_P1_J482_004_volume_map.mrc as #1, grid size 352,352,352,
pixel 0.846, shown at level 0.0477, step 2, values float32  

> volume #1 level 0.06529

> volume #1 level 0.09016

> volume #1 level 0.06115

> open /Users/madhurikanavalli/Downloads/AF-Q8TCS8-F1-model_v6.pdb

AF-Q8TCS8-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for polyribonucleotide
nucleotidyltransferase 1, mitochondrial (Q8TCS8) [more info...]  
  
Chain information for AF-Q8TCS8-F1-model_v6.pdb #2  
---  
Chain | Description | UniProt  
A | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 1-783  
  
Computing secondary structure  

> tile

2 models tiled  

> select add #2

6032 atoms, 6129 bonds, 783 residues, 1 model selected  

> view matrix models #2,1,0,0,132.15,0,1,0,269.68,0,0,1,174.53

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.42944,0.66337,0.61279,141.41,0.035656,-0.69047,0.72248,301.34,0.90239,-0.28841,-0.32017,144.99

> transparency 50

> view matrix models
> #2,0.63269,0.58288,0.50986,140.27,0.123,-0.72566,0.67697,300.82,0.76458,-0.3656,-0.53081,138.86

> view matrix models
> #2,0.60082,0.75463,0.26374,132.09,0.39851,-0.56876,0.71952,302.55,0.69297,-0.32719,-0.64245,135.08

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.60082,0.75463,0.26374,148.79,0.39851,-0.56876,0.71952,180.76,0.69297,-0.32719,-0.64245,188.93

> view matrix models
> #2,0.6614,0.18966,0.72565,161.37,0.2615,-0.9651,0.0139,190.89,0.70297,0.18057,-0.68792,178.28

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.19924,0.94382,-0.26363,126.11,0.83456,-0.022419,0.55046,202.79,0.51363,-0.32969,-0.79215,177.72

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.19924,0.94382,-0.26363,128.38,0.83456,-0.022419,0.55046,186.45,0.51363,-0.32969,-0.79215,184.65

> view matrix models
> #2,0.58266,0.81137,0.046707,142.97,0.47764,-0.38837,0.78805,177.72,0.65754,-0.43686,-0.61384,190.77

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.57664,0.24616,0.77903,167.09,-0.2162,-0.87356,0.43606,167.17,0.78787,-0.41988,-0.45051,195.95

> view matrix models
> #2,0.76261,0.6462,-0.029199,143.01,0.45171,-0.4997,0.73909,176.95,0.46301,-0.57683,-0.67297,188.94

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.76261,0.6462,-0.029199,142.26,0.45171,-0.4997,0.73909,182.18,0.46301,-0.57683,-0.67297,186.98

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.8634,0.49418,-0.10162,141.85,0.3123,-0.3653,0.87694,184.3,0.39625,-0.78889,-0.46973,193.67

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.72969,0.68377,0.0039503,132.51,0.33003,-0.35725,0.87376,248.15,0.59886,-0.63627,-0.48634,180.84

> view matrix models
> #2,0.066442,0.43084,-0.89998,103.3,0.93501,0.288,0.2069,257.15,0.34834,-0.85524,-0.3837,150.16

> view matrix models
> #2,0.23351,-0.30901,0.92195,156.19,-0.87131,-0.48737,0.057337,254.89,0.43161,-0.81669,-0.38305,176.46

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.80143,0.40414,0.44089,141.31,0.16742,-0.85928,0.48333,275.26,0.57418,-0.31354,-0.75631,163.52

> view matrix models
> #2,0.84875,0.50355,0.16142,133.15,0.28808,-0.6963,0.65741,279.7,0.44344,-0.51147,-0.73604,164.66

> view matrix models
> #2,0.86791,0.39835,0.29673,137.73,0.20619,-0.83241,0.51438,276.16,0.45191,-0.38525,-0.80459,161.95

> view matrix models
> #2,0.86632,0.49881,-0.026064,128.07,0.28331,-0.44774,0.84809,283.3,0.41136,-0.74211,-0.5292,171.77

> view matrix models
> #2,0.49235,0.85007,0.18702,129.46,0.42603,-0.42273,0.79988,282.62,0.75901,-0.31414,-0.57028,169.77

> view matrix models
> #2,0.85019,0.48331,0.20878,134.61,0.064393,-0.48905,0.86988,282.92,0.52253,-0.72611,-0.4469,174.6

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.85019,0.48331,0.20878,150.49,0.064393,-0.48905,0.86988,188.61,0.52253,-0.72611,-0.4469,184.74

> view matrix models
> #2,0.64449,0.16707,0.74614,168.48,-0.5504,-0.576,0.60439,164.48,0.53075,-0.80019,-0.27927,193.65

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.76356,0.63639,0.10946,148.31,0.32497,-0.52519,0.78649,174.28,0.558,-0.56497,-0.60782,183.09

> view matrix models
> #2,0.73909,0.6609,-0.13024,141.34,0.49027,-0.39519,0.77682,174.09,0.46193,-0.63799,-0.6161,182.8

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.73909,0.6609,-0.13024,139.59,0.49027,-0.39519,0.77682,180.83,0.46193,-0.63799,-0.6161,188.6

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.54319,0.83658,-0.071278,138.91,0.55669,-0.29531,0.77646,180.54,0.62852,-0.46144,-0.62613,188.1

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.75355,0.36167,0.54895,167.57,-0.16644,-0.70289,0.69155,141.22,0.63597,-0.61249,-0.46947,186.49

> view matrix models
> #2,-0.30331,-0.83983,0.45021,143.72,-0.74643,-0.084284,-0.66011,224.32,0.59232,-0.53627,-0.60131,183.9

> view matrix models
> #2,0.58684,-0.34812,0.73105,150.57,-0.47667,-0.87836,-0.035635,264.27,0.65453,-0.32756,-0.6814,180.79

> view matrix models
> #2,0.58684,-0.34812,0.73105,148.38,-0.47667,-0.87836,-0.035635,276.44,0.65453,-0.32756,-0.6814,180.97

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.63354,0.76624,0.10724,123.81,0.39183,-0.43726,0.80949,302.01,0.66715,-0.47082,-0.57726,184.9

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.63354,0.76624,0.10724,144.96,0.39183,-0.43726,0.80949,181.31,0.66715,-0.47082,-0.57726,189.07

> view matrix models
> #2,0.71133,0.30401,0.63372,164.61,-0.18947,-0.78531,0.5894,164.41,0.67684,-0.53933,-0.50101,194.83

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 6032 atoms  
average map value = 0.04859, steps = 152  
shifted from previous position = 3.28  
rotated from previous position = 5.39 degrees  
atoms outside contour = 4287, contour level = 0.06115  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.56426932 0.76409521 0.31266369 143.04419452  
0.21814827 -0.50324783 0.83615363 170.83785223  
0.79624833 -0.40360881 -0.45065337 194.48298911  
Axis -0.86191870 -0.33620203 -0.37955810  
Axis point 0.00000000 81.61235096 44.75810236  
Rotation angle (degrees) 134.01255267  
Shift along axis -254.54609246  
  

> view matrix models
> #2,0.3492,0.93478,0.065211,136.26,0.66686,-0.2968,0.68352,191.6,0.6583,-0.1952,-0.72701,180.45

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.89941,-0.31265,0.30546,154.53,-0.35641,-0.92913,0.098419,173.65,0.25305,-0.19739,-0.9471,171.99

> view matrix models
> #2,0.83384,0.55193,-0.008982,139.59,0.4892,-0.73133,0.47523,187.7,0.25573,-0.40066,-0.87981,175.24

> view matrix models
> #2,0.64415,0.75125,0.14382,141.39,0.64873,-0.63619,0.41762,186.39,0.40524,-0.17572,-0.89717,174.12

> ui mousemode right "move picked models"

> view matrix models
> #1,0.87519,0.38044,-0.29884,-2.3734,-0.45145,0.86428,-0.22185,170.72,0.17388,0.32907,0.92816,-69.898

> volume #1 level 0.1131

> volume #1 level 0.07917

> view matrix models
> #2,-0.10638,-0.94919,0.29618,133.6,-0.9431,0.0019433,-0.3325,286.13,0.31503,-0.3147,-0.89539,123

> select #1/A:760-783

Nothing selected  

> select #2/A:760-783

180 atoms, 180 bonds, 24 residues, 1 model selected  

> delete sel

> select #2/1-598

Nothing selected  

> select #2/A:1-598

4596 atoms, 4670 bonds, 598 residues, 1 model selected  

> delete sel

> ui mousemode right "rotate selected models"

> select add #2

1256 atoms, 1277 bonds, 161 residues, 1 model selected  

> view matrix models
> #2,0.6471,0.64962,0.39906,131.95,-0.0059555,-0.5191,0.85469,367.73,0.76238,-0.55545,-0.33205,150

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.6471,0.64962,0.39906,125.43,-0.0059555,-0.5191,0.85469,234.19,0.76238,-0.55545,-0.33205,186.89

> view matrix models
> #2,0.52432,0.60365,0.60057,138.39,0.096076,-0.74273,0.66266,241.7,0.84608,-0.28975,-0.44743,177.45

> view matrix models
> #2,0.58461,0.53787,0.60739,138.89,-0.0034217,-0.74701,0.6648,246.96,0.81131,-0.39073,-0.43487,176.3

> ui mousemode right "move picked models"

> view matrix models
> #1,0.99119,-0.014958,-0.1316,23.999,0.0189,0.99941,0.028756,83.761,0.13109,-0.030989,0.99089,-73.95

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.58461,0.53787,0.60739,147.74,-0.0034217,-0.74701,0.6648,281.09,0.81131,-0.39073,-0.43487,122.35

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 1256 atoms  
average map value = 0.05979, steps = 140  
shifted from previous position = 3.87  
rotated from previous position = 19.7 degrees  
atoms outside contour = 892, contour level = 0.079169  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.69579863 0.56968136 0.43740983 146.46213387  
-0.14760186 -0.48259090 0.86331897 199.16111950  
0.70290675 -0.66525869 -0.25170006 197.09026824  
Axis -0.89429762 -0.15532954 -0.41964808  
Axis point 0.00000000 116.56159785 13.49387603  
Rotation angle (degrees) 121.28170019  
Shift along axis -244.62489409  
  

> view matrix models
> #2,0.64344,0.55251,0.52983,143.2,-0.18754,-0.55726,0.80888,290.18,0.74217,-0.61983,-0.25495,141.57

> view matrix models
> #2,0.31612,0.83453,-0.45126,95.295,0.56826,0.21433,0.79445,277.99,0.75971,-0.50757,-0.40647,132.89

> view matrix models
> #2,-0.86195,-0.25115,-0.44043,128.41,-0.093041,0.93229,-0.34954,173.5,0.49839,-0.2603,-0.82695,98.206

> view matrix models
> #2,0.65233,0.046187,0.75653,156.98,-0.2638,-0.9219,0.28375,231.83,0.71055,-0.38467,-0.5892,137.62

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.81295,-0.58161,0.028996,122.48,-0.56819,-0.78132,0.25828,234.38,-0.12756,-0.22645,-0.96563,130.95

> view matrix models
> #2,-0.96437,-0.16164,-0.20942,136.53,-0.11386,0.96816,-0.22294,185.23,0.23878,-0.19116,-0.95207,125.06

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.96437,-0.16164,-0.20942,138.86,-0.11386,0.96816,-0.22294,195.83,0.23878,-0.19116,-0.95207,110.89

> view matrix models
> #2,0.78818,0.14656,0.59774,147.24,-0.054142,-0.95095,0.30456,271.11,0.61306,-0.27241,-0.74159,120.56

> view matrix models
> #2,0.92372,0.30232,0.23524,127.49,-0.038846,0.68486,-0.72764,196.22,-0.38109,0.663,0.64437,183.01

> view matrix models
> #2,0.92372,0.30232,0.23524,121.11,-0.038846,0.68486,-0.72764,201.1,-0.38109,0.663,0.64437,222.65

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.13548,-0.69196,-0.70912,99.679,-0.31493,-0.64852,0.69299,291.92,-0.93939,0.31721,-0.13006,195.35

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.13548,-0.69196,-0.70912,105.56,-0.31493,-0.64852,0.69299,261.53,-0.93939,0.31721,-0.13006,158.07

> view matrix models
> #2,-0.31376,-0.10292,-0.94391,84.999,-0.37062,-0.90198,0.22155,314.04,-0.87418,0.41934,0.24486,213.94

> view matrix models
> #2,0.23037,-0.936,-0.26616,124.75,-0.098671,-0.29457,0.95052,259,-0.96809,-0.19271,-0.16022,160.32

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.51055,-0.83648,-0.19907,122.5,-0.11184,-0.29416,0.94919,259.15,-0.85254,-0.46235,-0.24374,156.56

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.51055,-0.83648,-0.19907,122.82,-0.11184,-0.29416,0.94919,256.93,-0.85254,-0.46235,-0.24374,154.51

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.4007,-0.62248,-0.67228,111.87,-0.21408,-0.64984,0.7293,250.64,-0.89085,0.43616,0.12713,165.9

> ui mousemode right "translate selected models"

[Repeated 2 time(s)]

> view matrix models
> #2,-0.4007,-0.62248,-0.67228,113.93,-0.21408,-0.64984,0.7293,255.19,-0.89085,0.43616,0.12713,153.24

> ui tool show "Map Filter"

> volume gaussian #1 sDev 0.42

Opened cryosparc_P1_J482_004_volume_map.mrc gaussian as #3, grid size
352,352,352, pixel 0.846, shown at step 1, values float32  

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 1256 atoms  
average map value = 0.04212, steps = 80  
shifted from previous position = 5.77  
rotated from previous position = 6.87 degrees  
atoms outside contour = 1022, contour level = 0.079169  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.14765691 -0.51103760 -0.84678093 101.20040909  
0.33912440 0.77810326 -0.52872480 135.10645661  
0.92908129 -0.36523397 0.05841302 88.77346607  
Axis 0.08275295 -0.89887510 0.43032024  
Axis point -0.71225091 0.00000000 127.79384097  
Rotation angle (degrees) 98.94987464  
Shift along axis -74.86817754  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen  
self.plane_viewer.on_color_changed()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> view matrix models
> #2,-0.45927,-0.66663,-0.58709,119.96,-0.13295,-0.60189,0.78744,265.8,-0.87829,0.4397,0.1878,186.5

> hide #!3 models

> close #3

> view matrix models
> #2,0.77415,0.41998,-0.4736,92.737,-0.24702,-0.48843,-0.83691,197.65,-0.58281,0.76488,-0.27438,166.01

> view matrix models
> #2,0.75644,0.34979,0.55267,145.43,0.10707,0.76736,-0.63222,187.93,-0.64524,0.53741,0.54301,220.16

> view matrix models
> #2,0.70708,-0.70671,-0.024594,127.59,-0.32887,-0.35943,0.8733,284.08,-0.62601,-0.6094,-0.48656,169.56

> view matrix models
> #2,0.70708,-0.70671,-0.024594,129.66,-0.32887,-0.35943,0.8733,293.52,-0.62601,-0.6094,-0.48656,156.99

> view matrix models
> #2,0.99039,-0.12068,-0.067563,115.55,-0.028314,-0.65509,0.75502,280.22,-0.13537,-0.74586,-0.65221,150.64

> show #!1 models

> transparency 0

> transparency 50

> view matrix models
> #2,0.8449,0.48463,0.22644,131.66,0.11966,-0.58382,0.80302,264.44,0.52137,-0.65138,-0.55126,117.9

> view matrix models
> #2,0.38736,0.91086,0.1424,130.54,0.57477,-0.35937,0.73518,271.04,0.72083,-0.20294,-0.66274,108.58

> view matrix models
> #2,-0.38746,-0.87366,-0.29427,135.28,0.3028,-0.42209,0.85449,293.62,-0.87074,0.24197,0.42809,205.05

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.17337,-0.56863,-0.80411,96.434,-0.65603,-0.67565,0.33634,285.56,-0.73455,0.46921,-0.49018,153.04

> view matrix models
> #2,0.86201,-0.50664,0.016077,126.55,-0.38189,-0.62824,0.67785,298.11,-0.33332,-0.59045,-0.73503,143.5

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.86201,-0.50664,0.016077,128.49,-0.38189,-0.62824,0.67785,285.93,-0.33332,-0.59045,-0.73503,131.16

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 1256 atoms  
average map value = 0.06804, steps = 208  
shifted from previous position = 4.34  
rotated from previous position = 49.4 degrees  
atoms outside contour = 775, contour level = 0.079169  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.04261260 0.99909171 -0.00032583 124.39404394  
0.54482783 -0.02351097 -0.83821837 104.44003070  
-0.83746464 0.03554113 -0.54533477 199.64463617  
Axis 0.67601140 0.64767865 -0.35145548  
Axis point 0.00000000 -69.26766377 146.15003188  
Rotation angle (degrees) 139.73972107  
Shift along axis 81.56916779  
  

> save
> /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/S1_KH_AF_Q8TCS8.pdb

> select #2/A:599-680

634 atoms, 645 bonds, 82 residues, 1 model selected  

> select #2/A:599-678

625 atoms, 636 bonds, 80 residues, 1 model selected  

> delete sel

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms  
average map value = 0.08786, steps = 116  
shifted from previous position = 6.49  
rotated from previous position = 8.34 degrees  
atoms outside contour = 299, contour level = 0.079169  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.08642435 0.98758308 -0.13118947 114.63946268  
0.49800827 -0.15687479 -0.85286471 106.34543108  
-0.86285503 0.00837483 -0.50538229 203.22585816  
Axis 0.69930517 0.59409431 -0.39752262  
Axis point 0.00000000 -51.69253347 151.23207638  
Rotation angle (degrees) 141.99121366  
Shift along axis 62.56030846  
  

> select add #2

631 atoms, 640 bonds, 81 residues, 1 model selected  

> view matrix models
> #2,-0.12421,-0.93788,0.32398,174.03,-0.66983,0.32014,0.66996,284.8,-0.73205,-0.13379,-0.66798,133.24

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms  
average map value = 0.06691, steps = 176  
shifted from previous position = 13.3  
rotated from previous position = 44.4 degrees  
atoms outside contour = 409, contour level = 0.079169  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.08570214 0.84446583 0.52870857 166.53390201  
0.80947457 0.25036444 -0.53110145 116.83892504  
-0.58086681 0.47349266 -0.66211680 176.42251434  
Axis 0.67098439 0.74110306 -0.02337122  
Axis point 85.33225300 0.00000000 79.05264705  
Rotation angle (degrees) 131.53099228  
Shift along axis 194.20812316  
  

> undo

> ui tool show "Fit Loops"

> select #2/A:678-750

568 atoms, 576 bonds, 72 residues, 1 model selected  

> help help:user/selection.html

> select #2/A:678-759

631 atoms, 640 bonds, 81 residues, 1 model selected  

> select add #1

631 atoms, 640 bonds, 81 residues, 3 models selected  

> ui tool show "Fit Loops"

> select #2/A:678-759

631 atoms, 640 bonds, 81 residues, 1 model selected  

> view matrix models
> #2,-0.080102,0.99257,0.091628,132.2,0.78592,0.11943,-0.60668,151.24,-0.61311,0.023417,-0.78965,108.42

> view matrix models
> #2,-0.72601,0.14287,0.67268,201.64,0.41779,0.8686,0.26644,223.05,-0.54622,0.47448,-0.6903,110.38

> view matrix models
> #2,0.41003,-0.81571,-0.40804,121.18,-0.77968,-0.54561,0.30724,268.36,-0.47325,0.19216,-0.85971,105.09

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms  
average map value = 0.06322, steps = 88  
shifted from previous position = 3.4  
rotated from previous position = 9.25 degrees  
atoms outside contour = 424, contour level = 0.079169  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.03035950 0.89245803 0.45010791 155.53133934  
0.87362537 0.19510483 -0.44577237 120.58172191  
-0.48565132 0.40675911 -0.77375062 165.41563616  
Axis 0.67339426 0.73913388 -0.01487547  
Axis point 63.44943971 0.00000000 77.49031568  
Rotation angle (degrees) 140.72740844  
Shift along axis 191.39931233  
  

> view matrix models
> #2,-0.2609,0.80697,0.52985,161.6,-0.79532,-0.49076,0.35582,304.63,0.54717,-0.32857,0.76984,238.37

> view matrix models
> #2,-0.2609,0.80697,0.52985,162.1,-0.79532,-0.49076,0.35582,311.26,0.54717,-0.32857,0.76984,235.39

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.79732,-0.18475,-0.57458,82.674,0.32329,0.93464,0.14809,246.3,0.50967,-0.30383,0.80494,238.13

> view matrix models
> #2,-0.26525,0.76742,0.5837,166.72,0.96297,0.1805,0.2003,251.51,0.048357,0.61522,-0.78687,118.67

> view matrix models
> #2,-0.5306,0.57497,0.62279,178.59,0.83975,0.45646,0.29404,255.22,-0.11521,0.67901,-0.72503,125.08

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.5306,0.57497,0.62279,182.25,0.83975,0.45646,0.29404,229.39,-0.11521,0.67901,-0.72503,101.71

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms  
average map value = 0.07811, steps = 376  
shifted from previous position = 14.4  
rotated from previous position = 20.2 degrees  
atoms outside contour = 373, contour level = 0.079169  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.07173609 0.89418681 0.44190955 152.95290020  
0.99703897 0.07659145 0.00687161 107.65452962  
-0.02770198 0.44109399 -0.89703339 138.81763398  
Axis 0.67028894 0.72491753 0.15876812  
Axis point 38.94893660 -0.00000000 55.65097782  
Rotation angle (degrees) 161.10063978  
Shift along axis 202.60310684  
  

> fitmap #2 inMap #1

Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms  
average map value = 0.07811, steps = 60  
shifted from previous position = 0.00204  
rotated from previous position = 0.0118 degrees  
atoms outside contour = 372, contour level = 0.079169  
  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.07176106 0.89413760 0.44200504 152.95957123  
0.99704175 0.07653997 0.00703955 107.66663533  
-0.02753672 0.44120265 -0.89698504 138.81658330  
Axis 0.67028233 0.72490165 0.15886848  
Axis point 38.94180658 0.00000000 55.64258504  
Rotation angle (degrees) 161.10312462  
Shift along axis 202.62739965  
  

> fitmap #2 inMap #1 search 100

Found 87 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (87 of 100).  
  
Average map values and times found:  
0.08675 (1), 0.0858 (1), 0.08496 (1), 0.08402 (1), 0.08091 (1), 0.07993 (1),
0.07989 (1), 0.07882 (1), 0.07649 (1), 0.07503 (1), 0.07278 (1), 0.07178 (1),
0.07137 (1), 0.07135 (1), 0.07125 (1), 0.07038 (1), 0.06968 (1), 0.0696 (1),
0.06958 (1), 0.06919 (1), 0.06882 (1), 0.06881 (1), 0.06872 (1), 0.06856 (1),
0.06817 (1), 0.06804 (1), 0.06775 (1), 0.067 (1), 0.06694 (1), 0.06685 (1),
0.06679 (1), 0.06644 (1), 0.06608 (1), 0.06546 (1), 0.06522 (1), 0.06505 (1),
0.06501 (1), 0.06456 (1), 0.06449 (1), 0.06445 (1), 0.06412 (1), 0.06391 (1),
0.06383 (1), 0.06328 (1), 0.06317 (1), 0.06302 (1), 0.06279 (1), 0.06259 (1),
0.06247 (1), 0.06224 (1), 0.06208 (1), 0.06175 (1), 0.06135 (1), 0.06096 (1),
0.06089 (1), 0.06063 (1), 0.06061 (1), 0.06049 (1), 0.06034 (1), 0.06004 (1),
0.05993 (1), 0.05944 (1), 0.05883 (1), 0.05862 (1), 0.05856 (1), 0.05812 (1),
0.05806 (1), 0.05762 (1), 0.05748 (1), 0.05743 (1), 0.05698 (1), 0.05681 (1),
0.05641 (1), 0.05503 (1), 0.05483 (1), 0.05464 (1), 0.05438 (1), 0.05405 (1),
0.05346 (1), 0.05336 (1), 0.05331 (1), 0.05263 (1), 0.05247 (1), 0.05073 (1),
0.04919 (1), 0.04544 (1), 0.0362 (1)  
  
Best fit found:  
Fit molecule AF-Q8TCS8-F1-model_v6.pdb (#2) to map
cryosparc_P1_J482_004_volume_map.mrc (#1) using 631 atoms  
average map value = 0.08675, steps = 68  
shifted from previous position = 1.68  
rotated from previous position = 1.81 degrees  
atoms outside contour = 358, contour level = 0.079169  
Position of AF-Q8TCS8-F1-model_v6.pdb (#2) relative to
cryosparc_P1_J482_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.70736822 -0.65675968 0.26133708 180.10612296  
0.21398252 -0.15340721 -0.96471646 104.42350305  
0.67367783 0.73833129 0.03201965 146.82400859  
Axis 0.87037715 -0.21073512 0.44501049  
Axis point 0.00000000 47.11093603 95.62601638  
Rotation angle (degrees) 101.94716792  
Shift along axis 200.09277743  
  
Found 87 fits.  

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> hide #12 models

> show #10 models

> hide #2 models

> select subtract #2

Nothing selected  

> select add #10

631 atoms, 640 bonds, 81 residues, 1 model selected  

> view matrix models
> #10,-0.76824,-0.34676,-0.53812,99.406,-0.30813,-0.53651,0.78563,251.71,-0.56113,0.76936,0.30532,130.5

> view matrix models
> #10,0.0083816,-0.32273,-0.94645,48.86,-0.68359,-0.69264,0.23013,270.4,-0.72982,0.64506,-0.22642,136.05

> view matrix models
> #10,0.40111,0.42379,-0.8121,36.805,-0.50188,-0.63997,-0.58186,252.21,-0.76631,0.64097,-0.044006,144.17

> view matrix models
> #10,0.42445,0.50945,-0.74854,38.601,0.14388,-0.85414,-0.49974,187.19,-0.89395,0.10441,-0.43584,131.32

> view matrix models
> #10,0.14263,0.44845,0.88235,158.31,0.50713,0.73245,-0.45424,158.91,-0.84999,0.51225,-0.12295,150.79

> view matrix models
> #10,-0.53518,0.37484,0.75702,165.86,0.57045,0.82133,-0.0034073,164.81,-0.62304,0.43002,-0.65338,103.74

> view matrix models
> #10,-0.3295,0.66242,0.67278,141.81,0.70653,0.64567,-0.2897,186.36,-0.6263,0.37989,-0.68076,156.02

Desktop color scheme is dark  

> close session

> open /Users/madhurikanavalli/Downloads/cryosparc_P1_J275_004_volume_map.mrc

Opened cryosparc_P1_J275_004_volume_map.mrc as #1, grid size 450,450,450,
pixel 0.846, shown at level 0.00835, step 2, values float32  

> volume #1 level 0.03433

> open /Users/madhurikanavalli/Downloads/cryosparc_P1_J482_004_volume_map.mrc

Opened cryosparc_P1_J482_004_volume_map.mrc as #2, grid size 352,352,352,
pixel 0.846, shown at level 0.0477, step 2, values float32  

> tile

2 models tiled  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag  
cb(event)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
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.  
  

> color #2 #7a81ffff models

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.  
  

> tile

2 models tiled  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag  
cb(event)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1777, in <lambda>  
sm.addAction("%d" % step, lambda s=step: self.data_step_cb(s))  
^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1850, in data_step_cb  
self.plane_viewer.update_and_rerender()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 833, in
update_and_rerender  
self.view.drawing.parent.update_drawings()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'update_drawings'  
  
AttributeError: 'NoneType' object has no attribute 'update_drawings'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 833, in
update_and_rerender  
self.view.drawing.parent.update_drawings()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11B0002QZE/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 13822.1.2

Software:

    System Software Overview:

      System Version: macOS 26.0.1 (25A362)
      Kernel Version: Darwin 25.0.0
      Time since boot: 2 days, 4 hours, 34 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
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    ParmEd: 4.2.2
    parso: 0.8.5
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    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
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    pycollada: 0.8
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    Pygments: 2.18.0
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    pynrrd: 1.0.0
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    PyOpenGL-accelerate: 3.1.10
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    pyproject_hooks: 1.2.0
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    PyQt6-Qt6: 6.9.1
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.1
    PyQt6_sip: 13.10.2
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    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
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    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
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    soupsieve: 2.8
    Sphinx: 8.2.3
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    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
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    sphinxcontrib-serializinghtml: 2.0.0
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    tinyarray: 1.2.5
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    traitlets: 5.14.3
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    tzdata: 2025.2
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    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14