Save map fits: m.filename is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.7.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202410250340 (2024-10-25 03:40:02 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.9.dev202410250340 (2024-10-25)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/mansoore.esmaili/Desktop/MST1R/LocalResolution_1/session of
> local resolutionmapchanged_Nov152024.cxs" format session

Opened cryosparc_P1083_J180_004_volume_map_sharp_full.ccp4 as #1, grid size
340,340,340, pixel 0.839, shown at level 0.0452, step 1, values float32  
Opened cryosparc_P1083_J180_004_volume_map_sharp_local_resolution.ccp4 as #2,
grid size 340,340,340, pixel 0.839, shown at level 13.7, step 2, values
float32  
Map values for surface "surface": minimum 3.579, mean 4.685, maximum 11.29  
Log from Fri Nov 15 15:56:37 2024UCSF ChimeraX version: 1.9.dev202410250340
(2024-10-25)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/mansoore.esmaili/Downloads/lowres1078_fit_to2qe3assambly1cif.cxs
> format session

Opened cryosparc_P1050_J361_class_00_00022_volume_sharp.mrc as #1, grid size
128,128,128, pixel 1.97, shown at level 0.0373, step 1, values float32  
Opened 2qe3-assembly1.cif map 5 as #3, grid size 54,54,54, pixel 1.67, shown
at level 0.105, step 1, values float32  
Log from Thu Oct 31 14:41:43 2024 Startup Messages  
---  
warning | QCoreApplication::postEvent: Unexpected null receiver  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9.dev202410250340 (2024-10-25)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Unable to load numpy_formathandler accelerator from OpenGL_accelerate  

> open /Users/mansoore.esmaili/Downloads/2qe3.pdb

2qe3.pdb title:  
Crystal structure of human TL1A extracellular domain [more info...]  
  
Chain information for 2qe3.pdb #1  
---  
Chain | Description | UniProt  
A | TNF superfamily ligand TL1A | Q8NFE9_HUMAN 5-184  
  
Non-standard residues in 2qe3.pdb #1  
---  
CL — chloride ion  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> open
> /Users/mansoore.esmaili/Downloads/cryosparc_P1050_J339_004_volume_map_sharp.mrc

Opened cryosparc_P1050_J339_004_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.839, shown at level 0.0623, step 2, values float32  

> volume #2 step 1

> view clip false

> show target m

Cell requested for row 1 is out of bounds for table with 3 rows! Resizing
table model.  

Cell requested for row 0 is out of bounds for table with 3 rows! Resizing
table model.  

> select add #1

1181 atoms, 1149 bonds, 2 pseudobonds, 200 residues, 3 models selected  

> select subtract #1

Nothing selected  

> ui mousemode right zoom

[Repeated 1 time(s)]

> ui mousemode right "translate selected models"

[Repeated 2 time(s)]

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,11.732,0,1,0,-33.639,0,0,1,13.931

> view matrix models #2,1,0,0,8.9379,0,1,0,-29.9,0,0,1,13.97

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> view matrix models
> #2,0.28477,0.70398,0.65063,-50.41,-0.60284,0.65924,-0.44944,123.96,-0.74531,-0.26424,0.61211,169.92

> view matrix models
> #2,0.28182,0.78753,0.54807,-48.673,-0.65027,0.57679,-0.49443,143.12,-0.70549,-0.21705,0.67466,153.7

> view matrix models
> #2,0.22163,0.29252,0.93022,-26.777,-0.42074,0.88926,-0.1794,49.898,-0.87969,-0.35163,0.32016,225.08

> view matrix models
> #2,0.058323,0.9553,-0.28983,45.014,-0.8898,-0.081884,-0.44894,238.34,-0.45261,0.28408,0.84525,51.966

> view matrix models
> #2,-0.68173,0.71473,-0.15626,144.4,-0.057012,-0.26483,-0.96261,213.11,-0.72938,-0.64733,0.22129,249.78

> select add #1

1181 atoms, 1149 bonds, 2 pseudobonds, 200 residues, 5 models selected  

> select subtract #2

1181 atoms, 1149 bonds, 2 pseudobonds, 200 residues, 3 models selected  

> view matrix models
> #1,0.99869,-0.039329,0.032735,0.17289,0.039648,0.99917,-0.009163,0.29429,-0.032347,0.010449,0.99942,-0.28544

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,99.279,-0.057012,-0.26483,-0.96261,217.16,-0.72938,-0.64733,0.22129,257.64

> view matrix models
> #2,-0.68173,0.71473,-0.15626,24.527,-0.057012,-0.26483,-0.96261,242.12,-0.72938,-0.64733,0.22129,255.64

> select subtract #1

Nothing selected  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,23.775,-0.057012,-0.26483,-0.96261,242.43,-0.72938,-0.64733,0.22129,255.86

> view matrix models
> #1,0.99869,-0.039329,0.032735,-17.908,0.039648,0.99917,-0.009163,26.798,-0.032347,0.010449,0.99942,-3.4116

> ui mousemode right "rotate selected models"

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.000665, steps = 92  
shifted from previous position = 2.4  
rotated from previous position = 4.43 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67017445 -0.10542350 -0.73467822 229.16921311  
0.72059361 -0.32954207 -0.61003843 195.39485902  
-0.17779499 -0.93823660 0.29681817 158.54148193  
Axis -0.31290516 -0.53093421 0.78752729  
Axis point 115.77205515 189.50676524 -0.00000000  
Rotation angle (degrees) 148.36964092  
Shift along axis -50.59430068  
  

> ui mousemode right "move picked models"

> view matrix models
> #1,0.99968,-0.017053,0.018459,-44.613,0.018517,0.99644,-0.082274,54.8,-0.01699,0.08259,0.99644,17.819

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = -0.001195, steps = 92  
shifted from previous position = 4.73  
rotated from previous position = 12.1 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.68727935 -0.18333628 -0.70287617 234.02415421  
0.68010746 -0.50229368 -0.53399897 157.76465508  
-0.25514887 -0.84503779 0.46990444 132.74693043  
Axis -0.30459767 -0.43845554 0.84556313  
Axis point 117.31924324 149.89444440 0.00000000  
Rotation angle (degrees) 149.29798215  
Shift along axis -28.21008993  
  

> view matrix models
> #1,0.9945,-0.10197,0.024079,-13.627,0.10468,0.95692,-0.27084,30.136,0.0045761,0.27187,0.96232,15.382

> view matrix models
> #1,0.9945,-0.10197,0.024079,32.884,0.10468,0.95692,-0.27084,22.266,0.0045761,0.27187,0.96232,33.181

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = -0.002207, steps = 64  
shifted from previous position = 2.53  
rotated from previous position = 6.37 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.73784733 -0.22424913 -0.63662678 166.46417869  
0.63157446 -0.56210982 -0.53399088 209.22042826  
-0.23810718 -0.79608095 0.55638124 161.97284474  
Axis -0.26750249 -0.40674942 0.87349718  
Axis point 75.96776947 167.73527020 0.00000000  
Rotation angle (degrees) 150.66708000  
Shift along axis 11.85295233  
  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,7.3143,-0.057012,-0.26483,-0.96261,236.88,-0.72938,-0.64733,0.22129,248.12

> view matrix models
> #1,0.99162,-0.12448,-0.034592,60.319,0.10401,0.92796,-0.35786,35.389,0.076647,0.35126,0.93313,41.963

> view matrix models
> #2,-0.68173,0.71473,-0.15626,89.513,-0.057012,-0.26483,-0.96261,262.99,-0.72938,-0.64733,0.22129,288.39

> view matrix models
> #1,0.99162,-0.12448,-0.034592,114.28,0.10401,0.92796,-0.35786,47.142,0.076647,0.35126,0.93313,73.753

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = -0.002425, steps = 88  
shifted from previous position = 4.88  
rotated from previous position = 2.87 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.76272710 -0.23377187 -0.60299095 150.13450565  
0.61566506 -0.54792382 -0.56633561 215.06497810  
-0.19799977 -0.80319998 0.56184152 152.39688960  
Axis -0.24409077 -0.41734690 0.87535208  
Axis point 64.08438226 166.31309182 0.00000000  
Rotation angle (degrees) 150.97460024  
Shift along axis 6.99778560  
  

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = -0.002425, steps = 40  
shifted from previous position = 0.00383  
rotated from previous position = 0.03 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.76283900 -0.23355037 -0.60293523 150.13083669  
0.61558635 -0.54760845 -0.56672607 215.06379381  
-0.19781334 -0.80347944 0.56150749 152.40611694  
Axis -0.24403556 -0.41758285 0.87525494  
Axis point 64.08962899 166.33321642 0.00000000  
Rotation angle (degrees) 150.98230900  
Shift along axis 6.94999070  
  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,97.63,-0.057012,-0.26483,-0.96261,267.74,-0.72938,-0.64733,0.22129,290.22

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,146.37,-0.057012,-0.26483,-0.96261,243.07,-0.72938,-0.64733,0.22129,288.14

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.07114, steps = 256  
shifted from previous position = 32.8  
rotated from previous position = 17.2 degrees  
atoms outside contour = 667, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.61786486 -0.42771302 -0.65977616 170.84483335  
0.74291751 -0.59238125 -0.31170184 147.43480786  
-0.25752009 -0.68274888 0.68376705 126.46138422  
Axis -0.28713671 -0.31128798 0.90589862  
Axis point 74.41083400 131.13724478 0.00000000  
Rotation angle (degrees) 139.75062606  
Shift along axis 19.61068624  
  

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.07114, steps = 44  
shifted from previous position = 0.00819  
rotated from previous position = 0.0299 degrees  
atoms outside contour = 668, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.61757834 -0.42814601 -0.65976358 170.84349480  
0.74319171 -0.59221736 -0.31135941 147.43320981  
-0.25741616 -0.68261965 0.68393518 126.46145767  
Axis -0.28713942 -0.31118281 0.90593389  
Axis point 74.38724752 131.15424631 0.00000000  
Rotation angle (degrees) 139.72320850  
Shift along axis 19.63113708  
  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,135.54,-0.057012,-0.26483,-0.96261,249.2,-0.72938,-0.64733,0.22129,288.08

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09051, steps = 116  
shifted from previous position = 3.83  
rotated from previous position = 21.2 degrees  
atoms outside contour = 564, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.40991226 -0.52660519 -0.74475426 163.80520265  
0.91157870 -0.26477063 -0.31451676 152.20219134  
-0.03156290 -0.80782640 0.58857480 133.84436346  
Axis -0.29374238 -0.42467147 0.85636998  
Axis point 56.24713709 161.50683288 0.00000000  
Rotation angle (degrees) 122.89178408  
Shift along axis 1.86783552  
  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,130.96,-0.057012,-0.26483,-0.96261,248.28,-0.72938,-0.64733,0.22129,290.92

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09352, steps = 144  
shifted from previous position = 6.76  
rotated from previous position = 12.3 degrees  
atoms outside contour = 559, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.58748772 -0.50771050 -0.63014937 154.42227727  
0.80870649 -0.39643595 -0.43454845 157.39716013  
-0.02918906 -0.76489776 0.64349003 128.55096743  
Axis -0.22255776 -0.40486955 0.88687580  
Axis point 52.29608107 147.61368795 0.00000000  
Rotation angle (degrees) 132.08380123  
Shift along axis 15.91554911  
  

> select add #2

2 models selected  

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09353, steps = 28  
shifted from previous position = 0.0157  
rotated from previous position = 0.0287 degrees  
atoms outside contour = 559, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.58740844 -0.50794726 -0.63003247 154.43591159  
0.80875721 -0.39670182 -0.43421128 157.40142430  
-0.02937860 -0.76460267 0.64383200 128.53409043  
Axis -0.22256507 -0.40462485 0.88698564  
Axis point 52.29529346 147.59650247 0.00000000  
Rotation angle (degrees) 132.07780349  
Shift along axis 15.94732467  
  

> select subtract #2

Nothing selected  

> vop gaussian #2 sdev 2.52

Opened cryosparc_P1050_J339_004_volume_map_sharp.mrc gaussian as #3, grid size
300,300,300, pixel 0.839, shown at step 1, values float32  

> undo

> fitmap #1 inMap #3

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc gaussian (#3) using 1181 atoms  
average map value = 0.09849, steps = 184  
shifted from previous position = 24.9  
rotated from previous position = 31 degrees  
atoms outside contour = 158, contour level = 0.059631  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc gaussian (#3) coordinates:  
Matrix rotation and translation  
-0.66926527 -0.72246083 -0.17359249 131.45171190  
0.72450851 -0.58269810 -0.36817163 149.02241979  
0.16483757 -0.37217372 0.91340862 127.48865917  
Axis -0.00269315 -0.22774179 0.97371784  
Axis point 27.16452203 119.52050911 0.00000000  
Rotation angle (degrees) 132.01131701  
Shift along axis 89.84533015  
  

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1136, steps = 88  
shifted from previous position = 1.13  
rotated from previous position = 3.16 degrees  
atoms outside contour = 392, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67026005 -0.72368288 -0.16442187 132.19052098  
0.71189623 -0.56438792 -0.41793545 148.86468144  
0.20965501 -0.39717675 0.89347379 128.99628300  
Axis 0.01399153 -0.25213086 0.96759199  
Axis point 25.84689495 121.28571068 0.00000000  
Rotation angle (degrees) 132.11239292  
Shift along axis 89.13193893  
  

> surface dust #3 size 8.39

> volume #!3 style surface

> hide #!3 models

> show #!2 models

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1136, steps = 40  
shifted from previous position = 0.0112  
rotated from previous position = 0.0437 degrees  
atoms outside contour = 392, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67000254 -0.72376972 -0.16508782 132.20263965  
0.71218538 -0.56391759 -0.41807767 148.86962327  
0.20949603 -0.39768623 0.89328443 128.99562472  
Axis 0.01373949 -0.25238979 0.96752810  
Axis point 25.84617588 121.33134926 0.00000000  
Rotation angle (degrees) 132.09160122  
Shift along axis 89.05011603  
  

> surface dust #2 size 8.39

> volume #2 color #b2b2b274

> volume #2 color #b2b2b277

> volume #2 color #b2b2b291

> volume #2 color #fcfcfc91

> volume #2 color #e3fc1691

> volume #2 color #84fcd391

> volume #2 color #43f2fc91

> volume #2 color #f9ecfc91

> volume #2 color #f9ecfc60

> volume #2 color #f9ecfc61

> select subtract #2

Nothing selected  

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1137, steps = 28  
shifted from previous position = 0.0244  
rotated from previous position = 0.061 degrees  
atoms outside contour = 394, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67027982 -0.72374679 -0.16405960 132.19088463  
0.71175774 -0.56438372 -0.41817694 148.85782868  
0.21006165 -0.39706625 0.89342739 129.01250348  
Axis 0.01422931 -0.25217028 0.96757825  
Axis point 25.83113038 121.28108573 0.00000000  
Rotation angle (degrees) 132.11478588  
Shift along axis 89.17315714  
  

> ui mousemode right "rotate selected models"

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1136, steps = 28  
shifted from previous position = 0.0211  
rotated from previous position = 0.0439 degrees  
atoms outside contour = 391, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67020693 -0.72366642 -0.16471062 132.19748221  
0.71186280 -0.56402700 -0.41847927 148.86869645  
0.20993816 -0.39771907 0.89316600 129.00301011  
Axis 0.01399164 -0.25249998 0.96749573  
Axis point 25.83762560 121.32256000 0.00000000  
Rotation angle (degrees) 132.10828932  
Shift along axis 89.07017937  
  

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1137, steps = 28  
shifted from previous position = 0.0233  
rotated from previous position = 0.0644 degrees  
atoms outside contour = 393, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67039900 -0.72370060 -0.16377616 132.18712031  
0.71164641 -0.56462996 -0.41803396 148.85951478  
0.21005850 -0.39680027 0.89354629 129.01198454  
Axis 0.01431437 -0.25201498 0.96761746  
Axis point 25.83458743 121.26015063 0.00000000  
Rotation angle (degrees) 132.12430699  
Shift along axis 89.21159713  
  

> hide #!1 models

> open /Users/mansoore.esmaili/Downloads/2qe3.pdb1

2qe3.pdb1 title:  
Crystal structure of human TL1A extracellular domain [more info...]  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 2qe3.pdb1  
---  
Chain | Description  
4.1/A | No description available  
4.2/A 4.3/A | No description available  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1136, steps = 40  
shifted from previous position = 0.0257  
rotated from previous position = 0.0815 degrees  
atoms outside contour = 391, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67011339 -0.72371099 -0.16489527 132.20230126  
0.71192571 -0.56380928 -0.41866560 148.86953214  
0.21002341 -0.39794661 0.89304461 129.00593754  
Axis 0.01396225 -0.25265266 0.96745630  
Axis point 25.83191820 121.34243509 0.00000000  
Rotation angle (degrees) 132.10095856  
Shift along axis 89.04116444  
  

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,114.29,-0.057012,-0.26483,-0.96261,272.88,-0.72938,-0.64733,0.22129,284.92

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,75.044,-0.057012,-0.26483,-0.96261,222.88,-0.72938,-0.64733,0.22129,303.54

> view matrix models
> #2,-0.68173,0.71473,-0.15626,59.667,-0.057012,-0.26483,-0.96261,207.51,-0.72938,-0.64733,0.22129,309.99

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = -0.002615, steps = 72  
shifted from previous position = 1.7  
rotated from previous position = 4.8 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.64446501 -0.72579555 -0.24059442 94.67560782  
0.74107060 -0.51536781 -0.43036077 202.30835440  
0.18835931 -0.45564991 0.87000226 75.61231564  
Axis -0.01654498 -0.28063556 0.95967179  
Axis point -1.94938048 135.18489285 0.00000000  
Rotation angle (degrees) 130.15932384  
Shift along axis 14.22168262  
  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,10.546,-0.057012,-0.26483,-0.96261,151.47,-0.72938,-0.64733,0.22129,302.74

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,-32.659,-0.057012,-0.26483,-0.96261,108.75,-0.72938,-0.64733,0.22129,245.32

> fitmap #1 inMap #2

Fit molecule 2qe3.pdb (#1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb (#1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.64446501 -0.72579555 -0.24059442 -21.07084872  
0.74107060 -0.51536781 -0.43036077 200.27317162  
0.18835931 -0.45564991 0.87000226 -19.56961912  
Axis -0.01654498 -0.28063556 0.95967179  
Axis point -54.11404488 91.87568121 0.00000000  
Rotation angle (degrees) 130.15932384  
Shift along axis -74.63556746  
  

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.0003961, steps = 96  
shifted from previous position = 2.51  
rotated from previous position = 10.9 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.61759421 0.10433074 -0.77954634 163.74502896  
0.72063624 -0.32197730 -0.61401468 209.92020957  
-0.31505684 -0.94098125 0.12366680 43.57492745  
Axis -0.39010655 -0.55418632 0.73531925  
Axis point 74.34307474 137.20352175 0.00000000  
Rotation angle (degrees) 155.22389819  
Shift along axis -148.17143335  
  

> view matrix models #4.2,1,0,0,1.4158,0,1,0,1.3122,0,0,1,1.8238

> view matrix models #4.3,1,0,0,0.67167,0,1,0,2.5586,0,0,1,2.1424

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.0003961, steps = 48  
shifted from previous position = 0.0164  
rotated from previous position = 0.0738 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.61773092 0.10392111 -0.77949273 163.74525375  
0.72025463 -0.32311715 -0.61386365 209.91246049  
-0.31566086 -0.94063580 0.12474979 43.56153472  
Axis -0.39006983 -0.55367882 0.73572093  
Axis point 74.33283794 137.16134235 0.00000000  
Rotation angle (degrees) 155.23713389  
Shift along axis -148.04703373  
  

> view matrix models #4.3,1,0,0,-4.0071,0,1,0,10.32,0,0,1,4.0961

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.0003958, steps = 40  
shifted from previous position = 0.0172  
rotated from previous position = 0.0436 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.61736146 0.10431037 -0.77973340 163.75663339  
0.72058487 -0.32269337 -0.61369898 209.92227941  
-0.31562997 -0.94073819 0.12405398 43.56246036  
Axis -0.39029024 -0.55386337 0.73546509  
Axis point 74.34785909 137.17894299 0.00000000  
Rotation angle (degrees) 155.23047149  
Shift along axis -148.14220726  
  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,-28.802,-0.057012,-0.26483,-0.96261,112.85,-0.72938,-0.64733,0.22129,250.64

Cell requested for row 3 is out of bounds for table with 7 rows! Resizing
table model.  

> close #4

> open /Users/mansoore.esmaili/Downloads/2qe3.pdb1

2qe3.pdb1 title:  
Crystal structure of human TL1A extracellular domain [more info...]  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 2qe3.pdb1  
---  
Chain | Description  
4.1/A | No description available  
4.2/A 4.3/A | No description available  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,-33.818,-0.057012,-0.26483,-0.96261,105.37,-0.72938,-0.64733,0.22129,242.31

> view matrix models #4.2,1,0,0,-0.0042073,0,1,0,2.2735,0,0,1,1.4969

Cell requested for row 3 is out of bounds for table with 7 rows! Resizing
table model.  

> close #4

> hide #!2 models

> show #!2 models

> color #2 #e6fce961 models

> color #2 #e6fce9ff models

> color #2 #e6fce9e6 models

> color #2 #e6fce9d9 models

> open /Users/mansoore.esmaili/Downloads/2qe3.pdb1

2qe3.pdb1 title:  
Crystal structure of human TL1A extracellular domain [more info...]  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 2qe3.pdb1  
---  
Chain | Description  
4.1/A | No description available  
4.2/A 4.3/A | No description available  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

Cell requested for row 3 is out of bounds for table with 7 rows! Resizing
table model.  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,-20.005,-0.057012,-0.26483,-0.96261,113.8,-0.72938,-0.64733,0.22129,248.83

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,5.6962,-0.057012,-0.26483,-0.96261,146.08,-0.72938,-0.64733,0.22129,256.38

> ui mousemode right "rotate selected models"

> select add #4

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 8 models selected  

> view matrix models
> #4,0.9558,0.28283,-0.08032,-0.51751,-0.26874,0.95121,0.15156,0.50672,0.11927,-0.12328,0.98518,0.074502

> ui mousemode right "move picked models"

> view matrix models
> #4.1,1,5.0132e-16,1.6121e-18,-3.7514,-1.3309e-17,1,-1.8858e-16,-12.912,-1.4197e-17,4.5529e-16,1,6.5415

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.6168,0.72999,0.29441,-0.82088,-0.53875,0.11884,0.83404,-1.6003,0.57385,-0.67305,0.46658,1.9923

> ui mousemode right "move picked models"

> view matrix models
> #4.1,1,7.1725e-16,2.7782e-15,15.573,8.0968e-16,1,-6.5898e-16,-54.345,-3.5836e-16,5.7636e-16,1,-20.008

Cell requested for row 3 is out of bounds for table with 7 rows! Resizing
table model.  

> close #4

> open /Users/mansoore.esmaili/Downloads/2qe3.pdb1

2qe3.pdb1 title:  
Crystal structure of human TL1A extracellular domain [more info...]  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 2qe3.pdb1  
---  
Chain | Description  
4.1/A | No description available  
4.2/A 4.3/A | No description available  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,24.605,-0.057012,-0.26483,-0.96261,143.98,-0.72938,-0.64733,0.22129,247.72

> view matrix models
> #2,-0.68173,0.71473,-0.15626,26.311,-0.057012,-0.26483,-0.96261,145.91,-0.72938,-0.64733,0.22129,246.17

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.0007653, steps = 156  
shifted from previous position = 4.44  
rotated from previous position = 9.04 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67857973 0.03222811 -0.73381939 206.19721057  
0.66819032 -0.38780750 -0.63492286 181.09044911  
-0.30504302 -0.92117680 0.24162380 84.28784576  
Axis -0.34965263 -0.52374052 0.77681330  
Axis point 104.44022928 142.47984915 0.00000000  
Rotation angle (degrees) 155.83659015  
Shift along axis -101.46588492  
  

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,58.07,-0.057012,-0.26483,-0.96261,181.91,-0.72938,-0.64733,0.22129,218.31

> ui mousemode right select

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = -0.00165, steps = 56  
shifted from previous position = 1.95  
rotated from previous position = 4.72 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.70193645 -0.03544274 -0.71135717 210.66923262  
0.67395300 -0.35610296 -0.64728512 149.15102468  
-0.23037484 -0.93377433 0.27384839 132.42976349  
Axis -0.31702024 -0.53224041 0.78499574  
Axis point 112.80600430 149.47911620 0.00000000  
Rotation angle (degrees) 153.13776081  
Shift along axis -42.21381226  
  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,57.836,-0.057012,-0.26483,-0.96261,181.76,-0.72938,-0.64733,0.22129,218.27

> view matrix models
> #2,-0.68173,0.71473,-0.15626,35.797,-0.057012,-0.26483,-0.96261,159.38,-0.72938,-0.64733,0.22129,179.73

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08197, steps = 296  
shifted from previous position = 12.2  
rotated from previous position = 34.4 degrees  
atoms outside contour = 531, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.94424420 0.17366912 -0.27971759 154.61945585  
0.14475641 -0.54407387 -0.82645581 138.50078865  
-0.29571689 -0.82086702 0.48859888 122.35376812  
Axis 0.16676229 0.47739809 -0.86271745  
Axis point 89.83937999 102.34166156 0.00000000  
Rotation angle (degrees) 179.03986279  
Shift along axis -13.65202332  
  

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08197, steps = 48  
shifted from previous position = 0.0202  
rotated from previous position = 0.0293 degrees  
atoms outside contour = 531, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.94427426 0.17375129 -0.27956503 154.60301980  
0.14473302 -0.54364919 -0.82673933 138.51092365  
-0.29563233 -0.82113096 0.48820638 122.36043566  
Axis 0.16671566 0.47762002 -0.86260362  
Axis point 89.83280329 102.36590861 0.00000000  
Rotation angle (degrees) 179.03622989  
Shift along axis -13.61821888  
  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,34.788,-0.057012,-0.26483,-0.96261,157.77,-0.72938,-0.64733,0.22129,175.51

> view matrix models
> #2,-0.68173,0.71473,-0.15626,35.178,-0.057012,-0.26483,-0.96261,156.41,-0.72938,-0.64733,0.22129,168.98

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08326, steps = 136  
shifted from previous position = 3.04  
rotated from previous position = 19.1 degrees  
atoms outside contour = 559, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99689003 0.05733090 -0.05406875 147.33044713  
-0.00080065 -0.69343913 -0.72051477 133.29744739  
-0.07880115 -0.71823070 0.69132846 123.54404422  
Axis 0.03613152 0.39124019 -0.91957905  
Axis point 77.42680438 91.64622894 0.00000000  
Rotation angle (degrees) 178.18871071  
Shift along axis -56.13392252  
  

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08326, steps = 28  
shifted from previous position = 0.0239  
rotated from previous position = 0.102 degrees  
atoms outside contour = 562, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99684633 0.05855630 -0.05355884 147.33494002  
-0.00210885 -0.69422676 -0.71975326 133.28917187  
-0.07932807 -0.71737045 0.69216089 123.54201902  
Axis 0.03612813 0.39071245 -0.91980353  
Axis point 77.48571320 91.54440732 0.00000000  
Rotation angle (degrees) 178.11020097  
Shift along axis -56.23371077  
  

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08325, steps = 28  
shifted from previous position = 0.0174  
rotated from previous position = 0.0498 degrees  
atoms outside contour = 560, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99686076 0.05805390 -0.05383659 147.33063025  
-0.00151013 -0.69378983 -0.72017595 133.30367473  
-0.07916030 -0.71783384 0.69169952 123.54457370  
Axis 0.03616257 0.39100253 -0.91967891  
Axis point 77.46139891 91.59924470 0.00000000  
Rotation angle (degrees) 178.14426333  
Shift along axis -56.17140980  
  

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08326, steps = 40  
shifted from previous position = 0.0117  
rotated from previous position = 0.0326 degrees  
atoms outside contour = 560, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99687759 0.05760107 -0.05401093 147.33284555  
-0.00104839 -0.69360276 -0.72035694 133.29583135  
-0.07895547 -0.71805107 0.69149743 123.54422768  
Axis 0.03615613 0.39113078 -0.91962462  
Axis point 77.44129304 91.62545521 0.00000000  
Rotation angle (degrees) 178.17265853  
Shift along axis -56.15122599  
  

> view matrix models
> #2,-0.68173,0.71473,-0.15626,32.162,-0.057012,-0.26483,-0.96261,155.2,-0.72938,-0.64733,0.22129,171.33

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08892, steps = 80  
shifted from previous position = 2.67  
rotated from previous position = 4.06 degrees  
atoms outside contour = 504, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99393207 0.07065879 -0.08429937 144.90815060  
0.00477895 -0.73792451 -0.67486635 137.52977967  
-0.10989181 -0.67117416 0.73310916 122.17829305  
Axis 0.05216968 0.36161524 -0.93086666  
Axis point 77.37922488 91.09071676 0.00000000  
Rotation angle (degrees) 177.97209142  
Shift along axis -56.43902472  
  

> ui mousemode right "translate selected models"

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08892, steps = 44  
shifted from previous position = 0.0126  
rotated from previous position = 0.102 degrees  
atoms outside contour = 502, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99377759 0.07220840 -0.08480591 144.89645907  
0.00390611 -0.73833046 -0.67442782 137.51416495  
-0.11131414 -0.67056251 0.73345421 122.16471938  
Axis 0.05268395 0.36130623 -0.93095768  
Axis point 77.46092569 91.00608865 0.00000000  
Rotation angle (degrees) 177.89769646  
Shift along axis -56.41174156  
  

> ui mousemode right select

Drag select of 2 cryosparc_P1050_J339_004_volume_map_sharp.mrc  
Drag select of 2 cryosparc_P1050_J339_004_volume_map_sharp.mrc , 1 residues  

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08892, steps = 40  
shifted from previous position = 0.000604  
rotated from previous position = 0.00427 degrees  
atoms outside contour = 502, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99378541 0.07216101 -0.08475469 144.89648671  
0.00390372 -0.73834737 -0.67440932 137.51424321  
-0.11124446 -0.67054900 0.73347714 122.16560047  
Axis 0.05265110 0.36129507 -0.93096387  
Axis point 77.45776196 91.00640277 0.00000000  
Rotation angle (degrees) 177.89909629  
Shift along axis -56.41958319  
  

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.68173,0.71473,-0.15626,28.422,-0.057012,-0.26483,-0.96261,165.48,-0.72938,-0.64733,0.22129,171.14

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08985, steps = 80  
shifted from previous position = 2.92  
rotated from previous position = 0.278 degrees  
atoms outside contour = 512, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99418872 0.06990082 -0.08186976 140.28683479  
0.00396543 -0.73621377 -0.67673745 142.75122108  
-0.10757815 -0.67312939 0.73165824 130.10611330  
Axis 0.05091676 0.36279544 -0.93047673  
Axis point 75.27719061 95.37396260 0.00000000  
Rotation angle (degrees) 177.96952977  
Shift along axis -62.12826809  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.58768,0.80293,-0.09969,2.0379,-0.099509,-0.194,-0.97594,164.16,-0.80295,-0.56362,0.19391,173.5,#4.1,0.59817,-0.5651,-0.5682,21.243,0.20315,0.79281,-0.57462,-4.47,0.77519,0.22829,0.58904,5.6278

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08985, steps = 48  
shifted from previous position = 0.00522  
rotated from previous position = 0.00721 degrees  
atoms outside contour = 513, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99419202 0.06992030 -0.08181308 140.28742568  
0.00390112 -0.73628455 -0.67666080 142.74787706  
-0.10755004 -0.67304993 0.73173546 130.10130183  
Axis 0.05089288 0.36274570 -0.93049743  
Axis point 75.27750984 95.36563880 0.00000000  
Rotation angle (degrees) 177.96699365  
Shift along axis -62.13811724  
  

> ui mousemode right select

Drag select of 2 cryosparc_P1050_J339_004_volume_map_sharp.mrc  

> ui mousemode right "contour level"

> select subtract #2

Nothing selected  

> volume #2 level 0.02263

> volume #2 level 0.03141

> volume #2 level -0.00853

> volume #2 level 0.02258

> volume #2 level -0.03093

> volume #2 level -0.1206

> volume #2 level 0.02917

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08985, steps = 48  
shifted from previous position = 0.000787  
rotated from previous position = 0.00123 degrees  
atoms outside contour = 371, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99418980 0.06992963 -0.08183214 140.28782645  
0.00390731 -0.73628386 -0.67666152 142.74726215  
-0.10757038 -0.67304972 0.73173267 130.10102085  
Axis 0.05090351 0.36274614 -0.93049668  
Axis point 75.27851473 95.36525127 0.00000000  
Rotation angle (degrees) 177.96689538  
Shift along axis -62.13640612  
  

> fitmap #4.3 inMap #2

Fit molecule 2qe3.pdb1 (#4.3) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08877, steps = 76  
shifted from previous position = 2.52  
rotated from previous position = 4.18 degrees  
atoms outside contour = 341, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.3) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.57951746 -0.13007557 -0.80451219 156.11606151  
0.81442357 -0.12824184 -0.56592250 125.29225348  
-0.02955943 -0.98317566 0.18025499 126.56814061  
Axis -0.32319671 -0.60026431 0.73159186  
Axis point 79.64080336 150.94617807 0.00000000  
Rotation angle (degrees) 139.79610551  
Shift along axis -33.06844444  
  

> fitmap #4.2 inMap #2

Fit molecule 2qe3.pdb1 (#4.2) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09354, steps = 64  
shifted from previous position = 2.36  
rotated from previous position = 8.31 degrees  
atoms outside contour = 291, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.2) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.58810759 0.04148338 -0.80771814 159.02069151  
0.79371151 -0.16229441 -0.58624446 128.60375617  
-0.15540755 -0.98587000 0.06252074 126.14814265  
Axis -0.37248162 -0.60800345 0.70113425  
Axis point 92.51618257 148.20402574 0.00000000  
Rotation angle (degrees) 147.55861057  
Shift along axis -48.97702895  
  

> ui mousemode right "contour level"

> select add #4.2

1181 atoms, 1149 bonds, 2 pseudobonds, 200 residues, 2 models selected  

> select add #4.1

2362 atoms, 2298 bonds, 4 pseudobonds, 400 residues, 5 models selected  

> select add #4.3

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 7 models selected  

> ui mousemode right distance

[Repeated 2 time(s)]

> ui mousemode right label

[Repeated 1 time(s)]

> ui mousemode right "move label"

[Repeated 1 time(s)]

> ui mousemode right "color key"

> ui mousemode right "move label"

> ui mousemode right "color key"

> key delete

> ui mousemode right "move label"

> ui mousemode right "translate selected atoms"

> fitmap #4.2 inMap #2

Fit molecule 2qe3.pdb1 (#4.2) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09182, steps = 156  
shifted from previous position = 4.42  
rotated from previous position = 11.8 degrees  
atoms outside contour = 307, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.2) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.48604271 0.14803431 -0.86130617 156.28941470  
0.80838877 -0.29832447 -0.50745454 123.66752917  
-0.33206939 -0.94291482 0.02532916 127.33476305  
Axis -0.45754723 -0.55608016 0.69384825  
Axis point 102.83454416 137.03952988 0.00000000  
Rotation angle (degrees) 151.58439629  
Shift along axis -51.92784552  
  

> fitmap #4.3 inMap #2

Fit molecule 2qe3.pdb1 (#4.3) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09289, steps = 144  
shifted from previous position = 2.43  
rotated from previous position = 25.1 degrees  
atoms outside contour = 339, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.3) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.41718379 -0.42876798 -0.80132123 157.01401321  
0.83496202 0.16735203 -0.52424396 124.24024653  
0.35888176 -0.88777887 0.28818842 119.98650333  
Axis -0.20730342 -0.66159821 0.72063382  
Axis point 52.41024371 179.29616805 0.00000000  
Rotation angle (degrees) 118.73908025  
Shift along axis -28.28033496  
  

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.58768,0.80293,-0.09969,4.5397,-0.099509,-0.194,-0.97594,163.38,-0.80295,-0.56362,0.19391,174.71

> view matrix models
> #2,-0.58768,0.80293,-0.09969,3.1562,-0.099509,-0.194,-0.97594,163.18,-0.80295,-0.56362,0.19391,174.54

> ui mousemode right "rotate selected models"

> view matrix models
> #4.1,0.55744,-0.50814,-0.65655,20.846,0.13498,0.83577,-0.53223,-4.3637,0.81917,0.20807,0.53448,5.4551,#4.2,0.98974,-0.13709,0.04024,-2.8385,0.1307,0.98253,0.1325,2.654,-0.057701,-0.12588,0.99037,1.2677,#4.3,0.83757,0.54327,-0.057836,-1.2992,-0.54608,0.82921,-0.11921,9.5868,-0.016802,0.13143,0.99118,-0.83394

> fitmap #4.3 inMap #2

Fit molecule 2qe3.pdb1 (#4.3) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.08367, steps = 72  
shifted from previous position = 3.65  
rotated from previous position = 13.1 degrees  
atoms outside contour = 327, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.3) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.39690183 -0.55158737 -0.73363500 159.73072206  
0.87325802 0.01920650 -0.48687940 126.54602430  
0.28264709 -0.83389597 0.47405500 123.82602637  
Axis -0.19449224 -0.56959522 0.79858253  
Axis point 47.19188582 168.56720337 0.00000000  
Rotation angle (degrees) 116.86052397  
Shift along axis -4.26109439  
  

> view matrix models
> #4.1,0.72068,-0.31857,-0.61574,20.032,0.094574,0.92504,-0.36791,-4.1094,0.68679,0.20691,0.69678,6.1563,#4.2,0.96745,-0.0012547,0.25307,-2.5936,-0.049895,0.97941,0.1956,6.6362,-0.24811,-0.20186,0.94747,5.58,#4.3,0.78957,0.59916,0.13259,-1.8201,-0.56634,0.79468,-0.21852,5.4689,-0.2363,0.097442,0.96678,3.1653

> fitmap #4.3 inMap #2

Fit molecule 2qe3.pdb1 (#4.3) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09289, steps = 116  
shifted from previous position = 3.98  
rotated from previous position = 12.6 degrees  
atoms outside contour = 336, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.3) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.41692349 -0.42841410 -0.80164591 160.70533095  
0.83522828 0.16734562 -0.52382169 120.74202991  
0.35856452 -0.88795090 0.28805325 120.75658019  
Axis -0.20763461 -0.66157790 0.72055711  
Axis point 55.26982373 179.60349317 0.00000000  
Rotation angle (degrees) 118.73520168  
Shift along axis -26.23623502  
  

> view matrix models
> #4.1,0.80488,-0.19509,-0.56045,18.968,0.036895,0.95904,-0.28086,-4.2759,0.59229,0.20538,0.77911,6.3351,#4.2,0.91983,0.073902,0.38528,-2.3469,-0.15911,0.96797,0.19419,8.7871,-0.35859,-0.23993,0.90213,8.0036,#4.3,0.81271,0.56737,0.13264,-6.7316,-0.56279,0.82333,-0.073507,8.3336,-0.15091,-0.014909,0.98843,3.8026

> fitmap #4.3 inMap #2

Fit molecule 2qe3.pdb1 (#4.3) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09513, steps = 96  
shifted from previous position = 2.8  
rotated from previous position = 16.2 degrees  
atoms outside contour = 315, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.3) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.35783256 -0.13992673 -0.92324231 159.65979439  
0.88387374 0.26816406 -0.38321697 119.26960714  
0.30120270 -0.95315715 0.02771972 122.42930855  
Axis -0.33629239 -0.72248203 0.60409200  
Axis point -10.07501688 0.00000000 163.74572518  
Rotation angle (degrees) 122.07131397  
Shift along axis -65.90395504  
  

> ui mousemode right "translate selected models"

> view matrix models
> #4.1,0.80488,-0.19509,-0.56045,17.533,0.036895,0.95904,-0.28086,-4.4152,0.59229,0.20538,0.77911,6.1025,#4.2,0.91983,0.073902,0.38528,-3.782,-0.15911,0.96797,0.19419,8.6478,-0.35859,-0.23993,0.90213,7.771,#4.3,0.88995,0.39257,0.23211,-8.5471,-0.42982,0.89212,0.13916,4.5275,-0.15244,-0.22361,0.96268,2.6259

> fitmap #4.3 inMap #2

Fit molecule 2qe3.pdb1 (#4.3) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09515, steps = 52  
shifted from previous position = 1.47  
rotated from previous position = 0.0299 degrees  
atoms outside contour = 316, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.3) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.35794934 -0.14035189 -0.92313251 159.66884724  
0.88370390 0.26837129 -0.38346352 119.27921807  
0.30156209 -0.95303631 0.02796618 122.41040184  
Axis -0.33603376 -0.72253931 0.60416741  
Axis point -10.04833343 0.00000000 163.76360772  
Rotation angle (degrees) 122.05992443  
Shift along axis -65.88167117  
  

> select subtract #4.1

2362 atoms, 2298 bonds, 4 pseudobonds, 400 residues, 4 models selected  

> select subtract #4.2

1181 atoms, 1149 bonds, 2 pseudobonds, 200 residues, 2 models selected  

> select subtract #4.3

Nothing selected  

> select add #2

2 models selected  

> color #2 white models

> color #2 #ffffff58 models

> color #2 #ffffff9e models

> view matrix models
> #2,-0.58768,0.80293,-0.09969,2.3463,-0.099509,-0.194,-0.97594,163.62,-0.80295,-0.56362,0.19391,174

> fitmap #4.3 inMap #2

Fit molecule 2qe3.pdb1 (#4.3) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09514, steps = 68  
shifted from previous position = 1.06  
rotated from previous position = 0.0392 degrees  
atoms outside contour = 315, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.3) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.35805705 -0.14085122 -0.92301467 159.66673092  
0.88373819 0.26791387 -0.38370428 119.27099386  
0.30133365 -0.95309134 0.02854715 122.43058240  
Axis -0.33592222 -0.72233079 0.60447870  
Axis point -10.05741404 0.00000000 163.84097781  
Rotation angle (degrees) 122.05938902  
Shift along axis -65.78203390  
  

> fitmap #4.2 inMap #2

Fit molecule 2qe3.pdb1 (#4.2) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09043, steps = 88  
shifted from previous position = 2.78  
rotated from previous position = 11 degrees  
atoms outside contour = 280, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.2) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.06385786 0.06600748 -0.99577366 147.73394560  
0.99545264 0.07488654 -0.05887322 117.75852903  
0.07068397 -0.99500504 -0.07048941 118.13033467  
Axis -0.55185642 -0.62868442 0.54791459  
Axis point -51.85507635 0.00000000 153.42060436  
Rotation angle (degrees) 121.98723845  
Shift along axis -90.83554530  
  

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1026, steps = 132  
shifted from previous position = 4.41  
rotated from previous position = 7.33 degrees  
atoms outside contour = 280, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.91953430 -0.24806218 -0.30483081 139.47710359  
0.38280129 -0.38968629 -0.83762031 136.30023626  
0.08899353 -0.88691023 0.45328843 129.37401203  
Axis -0.06613173 -0.52838970 0.84642243  
Axis point 57.52431776 124.67111294 -0.00000000  
Rotation angle (degrees) 158.11995137  
Shift along axis 28.26156176  
  

> select subtract #2

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #4.1

1181 atoms, 1149 bonds, 2 pseudobonds, 200 residues, 3 models selected  

> view matrix models
> #4.1,0.70276,-0.25431,-0.66442,17.821,0.041356,0.94695,-0.31871,-3.3119,0.71022,0.1965,0.676,9.7816

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1057, steps = 164  
shifted from previous position = 1.14  
rotated from previous position = 20.2 degrees  
atoms outside contour = 281, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.92540612 -0.32223562 -0.19946860 140.76980931  
0.28197196 -0.23377960 -0.93050466 136.59391372  
0.25321005 -0.91733926 0.30720248 128.55448360  
Axis 0.01743559 -0.59950439 0.80018153  
Axis point 50.53245695 133.64675573 0.00000000  
Rotation angle (degrees) 157.81836101  
Shift along axis 23.43267647  
  

> view matrix models
> #4.1,0.72472,0.053785,-0.68694,16.648,-0.15614,0.98383,-0.0877,-2.5478,0.67112,0.17082,0.7214,8.8976

> ui mousemode right "translate selected models"

> view matrix models
> #4.1,0.72472,0.053785,-0.68694,24.449,-0.15614,0.98383,-0.0877,-3.603,0.67112,0.17082,0.7214,8.1172

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1018, steps = 112  
shifted from previous position = 5.96  
rotated from previous position = 14.1 degrees  
atoms outside contour = 260, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.93721466 -0.26428994 -0.22755110 135.82607427  
0.32752964 -0.44287559 -0.83461701 139.94009666  
0.11980405 -0.85674503 0.50163229 125.59931742  
Axis -0.03222922 -0.50591895 0.86197871  
Axis point 54.17241695 120.88569975 0.00000000  
Rotation angle (degrees) 159.92247479  
Shift along axis 33.08802303  
  

> view matrix models
> #4.1,0.80182,-0.11487,-0.58642,32.197,-0.087202,0.94835,-0.305,-4.5326,0.59117,0.29569,0.75039,11.52

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1099, steps = 228  
shifted from previous position = 11.2  
rotated from previous position = 27.2 degrees  
atoms outside contour = 259, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.83132931 -0.55499186 -0.02959094 131.80526161  
0.44457126 -0.63208912 -0.63468081 138.59302866  
0.33353857 -0.54078404 0.77220764 131.74618052  
Axis 0.08794986 -0.34013088 0.93625627  
Axis point 33.69447565 112.39358311 0.00000000  
Rotation angle (degrees) 147.73685679  
Shift along axis 87.80067430  
  

> view matrix models
> #4.1,0.81226,-0.12746,-0.5692,36.871,-0.32904,0.70563,-0.62755,-2.3324,0.48163,0.69703,0.53122,11.592

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1026, steps = 152  
shifted from previous position = 11.1  
rotated from previous position = 12.9 degrees  
atoms outside contour = 239, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.85806988 -0.51322934 0.01765584 130.58787010  
0.44989594 -0.76787083 -0.45603512 142.11276076  
0.24760801 -0.38336671 0.88978663 127.04570501  
Axis 0.07319107 -0.23160606 0.97005242  
Axis point 37.86662773 103.10860820 0.00000000  
Rotation angle (degrees) 150.23594228  
Shift along axis 99.88468262  
  

> view matrix models
> #4.1,0.84082,-0.27672,-0.46524,37.238,-0.24355,0.57418,-0.78166,-2.0399,0.48343,0.77055,0.41539,12.501

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1026, steps = 124  
shifted from previous position = 10.3  
rotated from previous position = 0.134 degrees  
atoms outside contour = 237, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.85798343 -0.51335058 0.01831966 130.60034113  
0.44919080 -0.76709607 -0.45802974 142.11543806  
0.24918277 -0.38475291 0.88874808 127.05450350  
Axis 0.07382693 -0.23259622 0.96976728  
Axis point 37.81975816 103.17307592 0.00000000  
Rotation angle (degrees) 150.24617809  
Shift along axis 99.79960877  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #4.1,0.84574,-0.38807,-0.36623,27.44,0.23106,0.88501,-0.4042,-3.1864,0.48097,0.25722,0.83815,15.574

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1089, steps = 236  
shifted from previous position = 6.55  
rotated from previous position = 17.6 degrees  
atoms outside contour = 233, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.85713544 -0.32665380 -0.39826641 136.70201527  
0.50260137 -0.69962191 -0.50785928 141.35079860  
-0.11274174 -0.63547343 0.76384738 128.66787701  
Axis -0.14399021 -0.32216456 0.93566918  
Axis point 58.38231091 110.88771771 0.00000000  
Rotation angle (degrees) 153.69593398  
Shift along axis 55.16859679  
  

> view matrix models
> #4.1,0.9679,-0.22397,-0.11402,22.356,0.19191,0.95159,-0.24011,-3.5303,0.16227,0.21053,0.96403,11.384

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09959, steps = 120  
shifted from previous position = 3.86  
rotated from previous position = 12.9 degrees  
atoms outside contour = 278, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.75724682 -0.14388187 -0.63708340 132.27553927  
0.64749471 -0.29322569 -0.70339840 137.31059777  
-0.08560295 -0.94515433 0.31520697 130.22554933  
Axis -0.24311467 -0.55457993 0.79582433  
Axis point 63.49538382 135.96465708 0.00000000  
Rotation angle (degrees) 150.18470658  
Shift along axis -4.67116439  
  

> view matrix models
> #4.1,0.99916,0.036697,0.018371,21.675,-0.038827,0.99028,0.13356,-2.8571,-0.013291,-0.13416,0.99087,17.162

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.106, steps = 96  
shifted from previous position = 4.58  
rotated from previous position = 18.6 degrees  
atoms outside contour = 258, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.79481729 -0.08466558 -0.60091365 131.66352216  
0.60586195 -0.05426084 -0.79371725 131.34616130  
0.03459445 -0.99493090 0.09442311 130.40983324  
Axis -0.20964468 -0.66213643 0.71946122  
Axis point 63.93862692 148.30003299 0.00000000  
Rotation angle (degrees) 151.32164428  
Shift along axis -20.74681737  
  

> view matrix models
> #4.1,0.99103,0.13306,-0.012798,17.411,-0.11599,0.90356,0.41247,-1.6173,0.066446,-0.40728,0.91088,21.253

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1004, steps = 92  
shifted from previous position = 2.05  
rotated from previous position = 8.27 degrees  
atoms outside contour = 259, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.55757825 0.07469319 -0.82675717 131.40408103  
0.82977231 0.07915223 -0.55246072 129.00366265  
0.02417462 -0.99406029 -0.10611190 131.14133677  
Axis -0.36186482 -0.69728844 0.61874283  
Axis point -8.29947465 0.00000000 149.90650127  
Rotation angle (degrees) 142.39805805  
Shift along axis -56.36051451  
  

> view matrix models
> #4.1,0.98948,0.10837,-0.095812,15.564,-0.10843,0.99409,0.004592,-2.8839,0.095744,0.0058451,0.99539,19.931

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09824, steps = 80  
shifted from previous position = 2.32  
rotated from previous position = 4.6 degrees  
atoms outside contour = 280, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.64832637 -0.08854684 -0.75619599 130.71406926  
0.76111965 -0.10046258 -0.64078401 127.90701389  
-0.01923000 -0.99099280 0.13252728 131.71885742  
Axis -0.29728947 -0.62560459 0.72127516  
Axis point 66.99154304 148.99203975 0.00000000  
Rotation angle (degrees) 143.91370902  
Shift along axis -23.87359125  
  

> view matrix models
> #4.1,0.86794,-0.0143,-0.49645,15.478,0.22994,0.89757,0.37615,-3.1843,0.44022,-0.44064,0.78233,22.368

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.0977, steps = 184  
shifted from previous position = 3.71  
rotated from previous position = 16.4 degrees  
atoms outside contour = 248, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.81766463 0.08748719 -0.56900839 131.46214047  
0.56787551 -0.03977818 -0.82215273 131.42529729  
-0.09456195 -0.99537113 -0.01715663 134.95048903  
Axis -0.24850257 -0.68065028 0.68917463  
Axis point 75.49453964 148.56727834 0.00000000  
Rotation angle (degrees) 159.60291377  
Shift along axis -29.11889232  
  

> view matrix models
> #4.1,0.96327,-0.042289,-0.26517,17.327,0.19531,0.78803,0.58383,-6.2727,0.18428,-0.61418,0.76735,22.025

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1002, steps = 164  
shifted from previous position = 3.68  
rotated from previous position = 25.3 degrees  
atoms outside contour = 222, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.77144643 0.02028238 -0.63597093 133.19315285  
0.62988503 0.16584800 -0.75877487 127.24206942  
0.09008475 -0.98594273 -0.14071842 136.02931584  
Axis -0.23302302 -0.74476946 0.62531490  
Axis point 18.47587229 0.00000000 143.04164671  
Rotation angle (degrees) 150.82776920  
Shift along axis -40.74192025  
  

> view matrix models
> #4.1,0.99031,0.083697,0.11079,13.205,-0.13833,0.52566,0.83937,-5.458,0.012013,-0.84657,0.53215,24.018

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09517, steps = 116  
shifted from previous position = 3.54  
rotated from previous position = 23.8 degrees  
atoms outside contour = 269, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.50704973 0.26083515 -0.82150204 129.17534997  
0.80241348 0.49084254 -0.33942040 123.97241447  
0.31469537 -0.83128733 -0.45817922 134.16756042  
Axis -0.36397812 -0.84077820 0.40076421  
Axis point -2.31630736 0.00000000 118.30193569  
Rotation angle (degrees) 137.49286526  
Shift along axis -97.48074815  
  

> view matrix models
> #4.1,0.91601,0.27323,-0.29373,12.351,-0.31398,0.94404,-0.10102,-5.8246,0.24969,0.18476,0.95054,23.202

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1009, steps = 68  
shifted from previous position = 2.64  
rotated from previous position = 8.76 degrees  
atoms outside contour = 246, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67790555 -0.44504377 -0.58513256 133.85294402  
0.62429112 0.07180279 -0.77788493 125.36439461  
0.38820699 -0.89262557 0.22916136 136.73177318  
Axis -0.07910266 -0.67102416 0.73720373  
Axis point 36.54955065 164.04648901 0.00000000  
Rotation angle (degrees) 133.50917292  
Shift along axis 6.08851219  
  

> view matrix models
> #4.1,0.75649,-0.045264,-0.65244,12.217,-0.45881,0.67419,-0.57876,-7.0666,0.46606,0.73717,0.48925,19.556

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1053, steps = 172  
shifted from previous position = 6.5  
rotated from previous position = 17.7 degrees  
atoms outside contour = 266, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.72184277 -0.67273766 -0.16237936 130.18567951  
0.48285926 -0.32149655 -0.81454706 129.89048121  
0.49577207 -0.66638128 0.55690757 132.91902911  
Axis 0.11072820 -0.49185395 0.86360810  
Axis point 20.56994105 130.11747789 0.00000000  
Rotation angle (degrees) 138.00608439  
Shift along axis 65.31803020  
  

> view matrix models
> #4.1,0.34488,-0.27358,-0.89789,19.522,-0.66152,0.6078,-0.43928,-3.2617,0.66592,0.74547,0.028645,20.228

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09787, steps = 132  
shifted from previous position = 4.44  
rotated from previous position = 23.5 degrees  
atoms outside contour = 286, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.82970299 -0.49847569 0.25122687 131.61007653  
0.29293023 -0.77192725 -0.56419873 136.38634711  
0.47516822 -0.39452543 0.78648894 133.59039714  
Axis 0.20204041 -0.26666070 0.94237558  
Axis point 31.93953734 99.72499996 0.00000000  
Rotation angle (degrees) 155.17176235  
Shift along axis 116.11400415  
  

> view matrix models
> #4.1,0.41474,-0.6161,-0.66964,23.069,-0.0072681,0.73365,-0.67949,-8.1709,0.90991,0.28668,0.2998,17.819

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1099, steps = 196  
shifted from previous position = 3.89  
rotated from previous position = 39.6 degrees  
atoms outside contour = 259, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.83140769 -0.55487382 -0.02960239 131.79881923  
0.44446867 -0.63211723 -0.63472468 138.58494800  
0.33347992 -0.54087232 0.77217115 131.73622240  
Axis 0.08792693 -0.34015884 0.93624827  
Axis point 33.70125100 112.38478197 0.00000000  
Rotation angle (degrees) 147.74453124  
Shift along axis 87.78557925  
  

> view matrix models
> #4.1,0.37432,-0.67007,-0.64101,26.092,0.23709,0.73745,-0.63243,-6.8861,0.89648,0.08475,0.43491,16.096

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.09555, steps = 116  
shifted from previous position = 7.1  
rotated from previous position = 17.5 degrees  
atoms outside contour = 295, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.98231024 0.08906084 -0.16472634 135.33288064  
0.03334282 -0.78242134 -0.62185619 136.73251008  
-0.18426844 -0.61634814 0.76561095 131.46013609  
Axis 0.09288131 0.32953512 -0.93956355  
Axis point 75.41457363 90.30365634 0.00000000  
Rotation angle (degrees) 178.30087310  
Shift along axis -65.88709292  
  

> view matrix models
> #4.1,0.1753,-0.94512,-0.27571,22.106,0.23401,0.31202,-0.92081,-3.4216,0.9563,0.0969,0.27586,13.262

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1011, steps = 116  
shifted from previous position = 4.89  
rotated from previous position = 16.1 degrees  
atoms outside contour = 283, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.98186956 0.18168298 0.05406909 140.13504128  
-0.18907007 -0.95910715 -0.21063237 140.21690799  
0.01358973 -0.21703636 0.97606892 130.56393541  
Axis -0.01716835 0.10852047 -0.99394595  
Axis point 76.17645751 70.69909264 0.00000000  
Rotation angle (degrees) 169.25107289  
Shift along axis -116.96297738  
  

> view matrix models
> #4.1,0.037501,-0.92795,-0.37081,20.99,0.74378,0.27373,-0.60981,-6.4223,0.66737,-0.25293,0.70046,10.705

> fitmap #4.1 inMap #2

Fit molecule 2qe3.pdb1 (#4.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) using 1181 atoms  
average map value = 0.1044, steps = 80  
shifted from previous position = 3.83  
rotated from previous position = 15.3 degrees  
atoms outside contour = 280, contour level = 0.029167  
  
Position of 2qe3.pdb1 (#4.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.53056206 0.67098345 -0.51796247 137.17314597  
-0.45957811 -0.74115789 -0.48935973 136.78403041  
-0.71224425 -0.02159149 0.70159956 130.90012902  
Axis 0.37758599 0.15682570 -0.91259768  
Axis point 123.04937855 50.24280363 0.00000000  
Rotation angle (degrees) 141.72624572  
Shift along axis -46.21324477  
  

> close #4

> open /Users/mansoore.esmaili/Downloads/2qe3.pdb1

2qe3.pdb1 title:  
Crystal structure of human TL1A extracellular domain [more info...]  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 2qe3.pdb1  
---  
Chain | Description  
4.1/A | No description available  
4.2/A 4.3/A | No description available  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select add #4

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 8 models selected  

> color sel bychain

[Repeated 3 time(s)]

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 2 time(s)]Coulombic values for 2qe3.pdb1_A SES surface #4.1.2:
minimum, -16.63, mean -2.02, maximum 9.84  
Coulombic values for 2qe3.pdb1_A SES surface #4.2.2: minimum, -16.16, mean
-1.81, maximum 10.35  
Coulombic values for 2qe3.pdb1_A SES surface #4.3.2: minimum, -16.13, mean
-1.81, maximum 10.35  
To also show corresponding color key, enter the above coulombic command and
add key true  

> style sel sphere

Changed 3543 atom styles  

> select subtract #4.1

2362 atoms, 2298 bonds, 4 pseudobonds, 400 residues, 8 models selected  

> select subtract #4.2

1181 atoms, 1149 bonds, 2 pseudobonds, 200 residues, 5 models selected  

> select subtract #4.3

2 models selected  

> select add #4

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 8 models selected  

> close

> open
> /Users/mansoore.esmaili/Downloads/cryosparc_P1050_J339_004_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P1050_J339_004_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.839, shown at level 0.0623, step 2, values float32  

> volume #1 step 1

> close #1

> open
> /Users/mansoore.esmaili/Downloads/cryosparc_P1050_J339_004_volume_map_sharp.mrc

Opened cryosparc_P1050_J339_004_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.839, shown at level 0.0623, step 2, values float32  

> volume #1 step 1

> open /Users/mansoore.esmaili/Downloads/2qe3.pdb1

2qe3.pdb1 title:  
Crystal structure of human TL1A extracellular domain [more info...]  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 2qe3.pdb1  
---  
Chain | Description  
2.1/A | No description available  
2.2/A 2.3/A | No description available  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> style sphere

Changed 3543 atom styles  

> select add #2

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 8 models selected  

> style sel sphere

Changed 3543 atom styles  

> style sel sphere

Changed 3543 atom styles  

> select subtract #2

Nothing selected  

> style sphere

Changed 3543 atom styles  

> select add #2

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 8 models selected  

> show sel surfaces

> fitmap #2.1 inMap #1

Fit molecule 2qe3.pdb1 (#2.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 1181 atoms  
average map value = 2.496e-06, steps = 136  
shifted from previous position = 3.15  
rotated from previous position = 6.72 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#2.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99451158 -0.04424902 0.09480900 -1.40688699  
0.03919638 0.99774367 0.05450877 -2.28161575  
-0.09700704 -0.05049344 0.99400204 1.18786187  
Axis -0.44862092 0.81953219 0.35651964  
Axis point 14.03488824 0.00000000 19.50904683  
Rotation angle (degrees) 6.72059751  
Shift along axis -0.81520252  
  

> view matrix models
> #2,0.78518,-0.54745,-0.28948,1.7494,0.61274,0.75451,0.2351,0.80379,0.089709,-0.36197,0.92786,1.7114

> select subtract #2

3 models selected  

> select add #2.1

1181 atoms, 1149 bonds, 2 pseudobonds, 200 residues, 3 models selected  

> select add #2

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 9 models selected  

> select subtract #2

3 models selected  

> ui mousemode right "move picked models"

> view matrix models
> #2.2,1,1.9096e-15,-5.6356e-16,-0.20301,-1.8292e-15,1,-1.5549e-16,1.7694,-1.3028e-15,-6.6921e-16,1,3.9065

> view matrix models #1,1,0,0,0.63745,0,1,0,26.092,0,0,1,-16.868

> volume #1 step 2

> volume #1 step 4

> view matrix models #1,1,0,0,5.3937,0,1,0,9.4529,0,0,1,-15.813

> view matrix models
> #2.3,1,9.9837e-17,2.157e-16,-0.078547,-2.4466e-16,1,3.1357e-16,-0.044546,1.4288e-16,-1.9495e-16,1,0.20963

> ~label #1-2 atoms

> volume hide

> volume show

> volume #1 step 2

> view matrix models #1,1,0,0,26.867,0,1,0,-43.463,0,0,1,-24.382

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 1 maps.  

> fitmap #2.1 inMap #1

Fit molecule 2qe3.pdb1 (#2.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 1181 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#2.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 -0.00000000 -26.86658758  
0.00000000 1.00000000 0.00000000 43.46265577  
0.00000000 -0.00000000 1.00000000 24.38183881  
Axis -0.47505588 -0.77237886 -0.42160741  
Axis point -327586752646398080.00000000 64.00000000
-1209573609137115648.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis -31.08607005  
  

> fitmap #2.1 inMap #1

Fit molecule 2qe3.pdb1 (#2.1) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 1181 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 1181, contour level = 0.062298  
  
Position of 2qe3.pdb1 (#2.1) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 -26.86658758  
-0.00000000 1.00000000 0.00000000 43.46265577  
0.00000000 0.00000000 1.00000000 24.38183881  
Axis 0.04226697 -0.16686546 -0.98507331  
Axis point 681783228351536000.00000000 456792662516916608.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis -32.40588396  
  

> vop gaussian #1 sdev 2.52

Opened cryosparc_P1050_J339_004_volume_map_sharp.mrc gaussian as #3, grid size
300,300,300, pixel 0.839, shown at step 1, values float32  

> view matrix models #3,1,0,0,8.0965,0,1,0,10.972,0,0,1,-21.804

> view matrix models
> #2.2,1,2.679e-15,-4.4033e-16,0.11082,-2.1595e-15,1,4.8988e-16,-17.255,-1.7469e-15,-3.7933e-16,1,-31.215

> open /Users/mansoore.esmaili/Downloads/2qe3-assembly1.cif

Summary of feedback from opening
/Users/mansoore.esmaili/Downloads/2qe3-assembly1.cif  
---  
warning | Unable to fetch template for 'CL': will connect using distance criteria  
  
2qe3-assembly1.cif title:  
Crystal structure of human tl1a extracellular domain [more info...]  
  
Chain information for 2qe3-assembly1.cif #4  
---  
Chain | Description  
A A-2 A-3 | TNF superfamily ligand TL1A  
  
Non-standard residues in 2qe3-assembly1.cif #4  
---  
CL — chloride ion  
  
60 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> hide #!2.3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> view matrix models #4,1,0,0,4.9405,0,1,0,181.49,0,0,1,112.95

> surface #1,4

> view matrix models #4,1,0,0,6.5483,0,1,0,115.45,0,0,1,60.685

> view matrix models #1,1,0,0,24.982,0,1,0,-48.39,0,0,1,-21.713

> view matrix models #4,1,0,0,8.1448,0,1,0,110.74,0,0,1,60.273

> ui mousemode right "rotate selected models"

> volume #1 step 1

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,5.9591,0,1,0,-30.055,0,0,1,36.203

> view matrix models #4,1,0,0,22.817,0,1,0,39.052,0,0,1,150.16

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 2.721e-05, steps = 104  
shifted from previous position = 1.97  
rotated from previous position = 3.38 degrees  
atoms outside contour = 3543, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99827897 0.05837770 -0.00557985 15.84093806  
-0.05840658 0.99827954 -0.00516093 68.33081935  
0.00526897 0.00547795 0.99997111 115.43245499  
Axis 0.09033715 -0.09211974 -0.99164164  
Axis point 994.27459519 -426.70073342 0.00000000  
Rotation angle (degrees) 3.37577565  
Shift along axis -119.33122176  
  

> view matrix models
> #4,0.99828,0.058378,-0.0055798,58.006,-0.058407,0.99828,-0.0051609,58.143,0.005269,0.005478,0.99997,89.208

> view matrix models
> #4,0.99828,0.058378,-0.0055798,162.95,-0.058407,0.99828,-0.0051609,135.04,0.005269,0.005478,0.99997,112.56

> view matrix models
> #4,0.99828,0.058378,-0.0055798,163.26,-0.058407,0.99828,-0.0051609,104.97,0.005269,0.005478,0.99997,166.69

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.06924, steps = 176  
shifted from previous position = 4.31  
rotated from previous position = 12.8 degrees  
atoms outside contour = 1934, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98732973 -0.13676051 -0.08047712 153.64400598  
0.14202680 0.98780445 0.06380251 134.18409652  
0.07076999 -0.07442402 0.99471236 129.93607538  
Axis -0.39951762 -0.43715115 0.80578195  
Axis point -798.58490404 1152.61974618 0.00000000  
Rotation angle (degrees) 9.96181325  
Shift along axis -15.34207583  
  

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.06924, steps = 44  
shifted from previous position = 0.015  
rotated from previous position = 0.0322 degrees  
atoms outside contour = 1933, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98724489 -0.13726080 -0.08066593 153.63344968  
0.14254899 0.98772241 0.06390801 134.19107804  
0.07090348 -0.07459170 0.99469029 129.93923357  
Axis -0.39906837 -0.43672695 0.80623446  
Axis point -795.96349908 1149.18983896 0.00000000  
Rotation angle (degrees) 9.99305462  
Shift along axis -15.15362270  
  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #4,0.98724,-0.13726,-0.080666,162.17,0.14255,0.98772,0.063908,101.68,0.070903,-0.074592,0.99469,160.94

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07105, steps = 72  
shifted from previous position = 3.43  
rotated from previous position = 4.59 degrees  
atoms outside contour = 1894, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97292784 -0.20773347 -0.10128286 154.78285844  
0.21157895 0.97693906 0.02871275 131.84723164  
0.09298258 -0.04936475 0.99444324 121.63412646  
Axis -0.16659130 -0.41449755 0.89467263  
Axis point -586.74274373 844.33317200 0.00000000  
Rotation angle (degrees) 13.55263057  
Shift along axis 28.38689220  
  

> view matrix models
> #4,0.97293,-0.20773,-0.10128,161.82,0.21158,0.97694,0.028713,98.712,0.092983,-0.049365,0.99444,161.51

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07906, steps = 196  
shifted from previous position = 6.38  
rotated from previous position = 26.1 degrees  
atoms outside contour = 1693, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98445192 0.14728975 0.09570871 149.33314797  
-0.16585851 0.95886248 0.23037731 126.61805035  
-0.05783927 -0.24266949 0.96838326 123.68274515  
Axis -0.80488779 0.26126146 -0.53282088  
Axis point 0.00000000 261.82695776 -676.38831603  
Rotation angle (degrees) 17.08912142  
Shift along axis -153.01676026  
  

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07906, steps = 44  
shifted from previous position = 0.00863  
rotated from previous position = 0.0196 degrees  
atoms outside contour = 1695, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98439695 0.14754636 0.09587865 149.33403644  
-0.16615638 0.95878502 0.23048502 126.61018633  
-0.05791979 -0.24281960 0.96834082 123.68256882  
Axis -0.80454825 0.26143473 -0.53324853  
Axis point 0.00000000 261.51325548 -676.10187176  
Rotation angle (degrees) 17.10616062  
Shift along axis -152.99968526  
  

> view matrix models
> #4,0.9844,0.14755,0.095879,152.2,-0.16616,0.95879,0.23049,103.21,-0.05792,-0.24282,0.96834,160.62

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07738, steps = 76  
shifted from previous position = 3.53  
rotated from previous position = 7 degrees  
atoms outside contour = 1724, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98964511 0.14348095 -0.00397238 143.49166401  
-0.13572774 0.94445460 0.29930501 131.44646280  
0.04669630 -0.29566658 0.95414922 123.33142809  
Axis -0.90259587 -0.07686642 -0.42357083  
Axis point 0.00000000 197.06714928 -353.32793087  
Rotation angle (degrees) 19.24383982  
Shift along axis -191.85839756  
  

> view matrix models
> #4,0.98965,0.14348,-0.0039724,160.37,-0.13573,0.94445,0.29931,104.43,0.046696,-0.29567,0.95415,153.08

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07505, steps = 100  
shifted from previous position = 4.87  
rotated from previous position = 10.4 degrees  
atoms outside contour = 1807, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95877718 0.25632563 -0.12265192 150.02102271  
-0.22308326 0.94633351 0.23385199 133.24680026  
0.17601187 -0.19685036 0.96450493 117.53798199  
Axis -0.60635999 -0.42047083 -0.67493100  
Axis point 175.91450044 -21.59760413 0.00000000  
Rotation angle (degrees) 20.80288284  
Shift along axis -226.32316499  
  

> view matrix models
> #4,0.95878,0.25633,-0.12265,156.46,-0.22308,0.94633,0.23385,103.23,0.17601,-0.19685,0.9645,163.67

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07593, steps = 108  
shifted from previous position = 3.23  
rotated from previous position = 6.02 degrees  
atoms outside contour = 1735, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95426423 0.29764097 -0.02810051 148.99322619  
-0.28086066 0.92472108 0.25692064 130.50707237  
0.10245524 -0.23727785 0.96602388 126.96112188  
Axis -0.64017653 -0.16911975 -0.74938143  
Axis point 334.48982957 8.07562294 0.00000000  
Rotation angle (degrees) 22.70497247  
Shift along axis -212.59559620  
  

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07592, steps = 76  
shifted from previous position = 0.0152  
rotated from previous position = 0.023 degrees  
atoms outside contour = 1736, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95428387 0.29760925 -0.02776735 148.99951573  
-0.28088648 0.92465342 0.25713584 130.50737013  
0.10220118 -0.23758111 0.96597626 126.94896643  
Axis -0.64065848 -0.16830924 -0.74915200  
Axis point 335.04783031 8.31660958 0.00000000  
Rotation angle (degrees) 22.71206964  
Shift along axis -212.52747123  
  

> view matrix models
> #4,0.95428,0.29761,-0.027767,154.69,-0.28089,0.92465,0.25714,104.41,0.1022,-0.23758,0.96598,159.95

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07642, steps = 92  
shifted from previous position = 2.33  
rotated from previous position = 9.96 degrees  
atoms outside contour = 1747, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90179670 0.42854633 0.05577413 146.26122002  
-0.43063631 0.88027117 0.19918593 134.79927537  
0.03626404 -0.20364358 0.97837325 122.84361831  
Axis -0.42441992 0.02055577 -0.90523212  
Axis point 346.99537560 -92.91516367 0.00000000  
Rotation angle (degrees) 28.33101913  
Shift along axis -170.50726129  
  

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07643, steps = 28  
shifted from previous position = 0.0193  
rotated from previous position = 0.00974 degrees  
atoms outside contour = 1748, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90179012 0.42857917 0.05562798 146.27209467  
-0.43063576 0.88025370 0.19926431 134.78305507  
0.03643380 -0.20364998 0.97836561 122.84342720  
Axis -0.42448294 0.02022168 -0.90521009  
Axis point 346.82429446 -92.88643564 0.00000000  
Rotation angle (degrees) 28.33293210  
Shift along axis -170.56358046  
  

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #4,0.90179,0.42858,0.055628,155.89,-0.43064,0.88025,0.19926,104.59,0.036434,-0.20365,0.97837,161.2

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07879, steps = 76  
shifted from previous position = 3.75  
rotated from previous position = 9.44 degrees  
atoms outside contour = 1702, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.84618648 0.53258390 -0.01796715 150.21399282  
-0.52775451 0.84222839 0.11012051 132.20796140  
0.07378085 -0.08370024 0.99375583 122.27410148  
Axis -0.17916424 -0.08481012 -0.98015683  
Axis point 270.22407400 -150.86205696 0.00000000  
Rotation angle (degrees) 32.74509178  
Shift along axis -157.97334572  
  

> view matrix models #1,1,0,0,6.4938,0,1,0,-30.179,0,0,1,36.286

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.0788, steps = 44  
shifted from previous position = 0.559  
rotated from previous position = 0.0135 degrees  
atoms outside contour = 1701, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.84608923 0.53273933 -0.01793943 150.21657140  
-0.52790063 0.84211760 0.11026727 132.20330404  
0.07385083 -0.08382571 0.99374006 122.27478653  
Axis -0.17935821 -0.08482190 -0.98012034  
Axis point 270.12631241 -150.73519596 0.00000000  
Rotation angle (degrees) 32.75694402  
Shift along axis -158.00031654  
  

> view matrix models
> #4,0.84609,0.53274,-0.017939,152.84,-0.5279,0.84212,0.11027,101.09,0.073851,-0.083826,0.99374,162.69

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07829, steps = 100  
shifted from previous position = 1.56  
rotated from previous position = 10.3 degrees  
atoms outside contour = 1699, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.87997067 0.46446945 -0.09959797 146.06433831  
-0.43132430 0.86909695 0.24213600 129.55019929  
0.19902506 -0.17011355 0.96511678 125.50919055  
Axis -0.40011561 -0.28983351 -0.86942742  
Axis point 189.48220817 -88.81640327 0.00000000  
Rotation angle (degrees) 31.00835356  
Shift along axis -205.11174237  
  

> view matrix models
> #4,0.87997,0.46447,-0.099598,152.3,-0.43132,0.8691,0.24214,99.058,0.19903,-0.17011,0.96512,161.82

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.0783, steps = 64  
shifted from previous position = 0.399  
rotated from previous position = 0.0213 degrees  
atoms outside contour = 1704, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.88013671 0.46415972 -0.09957472 146.06516601  
-0.43105268 0.86927255 0.24198930 129.53513770  
0.19887926 -0.17006172 0.96515597 125.51213410  
Axis -0.40016911 -0.28984776 -0.86939804  
Axis point 189.54638103 -88.90114159 0.00000000  
Rotation angle (degrees) 30.98716911  
Shift along axis -205.11624098  
  

> view matrix models
> #4,0.88014,0.46416,-0.099575,155.43,-0.43105,0.86927,0.24199,102.94,0.19888,-0.17006,0.96516,161.54

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07774, steps = 96  
shifted from previous position = 3.63  
rotated from previous position = 12.1 degrees  
atoms outside contour = 1681, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.76541435 0.63293280 -0.11634836 146.18069040  
-0.57661551 0.75479578 0.31272653 132.79112844  
0.28575413 -0.17227711 0.94269039 122.78821030  
Axis -0.35562937 -0.29484203 -0.88690243  
Axis point 154.13194640 -61.43392897 0.00000000  
Rotation angle (degrees) 42.99188738  
Shift along axis -200.03971577  
  

> view matrix models
> #4,0.76541,0.63293,-0.11635,151.83,-0.57662,0.7548,0.31273,104.11,0.28575,-0.17228,0.94269,160.05

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07774, steps = 60  
shifted from previous position = 1.98  
rotated from previous position = 0.00803 degrees  
atoms outside contour = 1681, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.76542259 0.63289882 -0.11647889 146.18844717  
-0.57655033 0.75483443 0.31275341 132.79302482  
0.28586354 -0.17223258 0.94266536 122.78647666  
Axis -0.35562255 -0.29502304 -0.88684497  
Axis point 154.08775385 -61.46004614 0.00000000  
Rotation angle (degrees) 42.99096907  
Shift along axis -200.05747975  
  

> view matrix models #1,1,0,0,6.6002,0,1,0,-29.466,0,0,1,36.67

> ui mousemode right "rotate selected models"

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07774, steps = 48  
shifted from previous position = 0.815  
rotated from previous position = 0.00748 degrees  
atoms outside contour = 1679, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.76539657 0.63294734 -0.11638624 146.18811825  
-0.57663312 0.75479612 0.31269323 132.79248199  
0.28576623 -0.17222216 0.94269676 122.78759959  
Axis -0.35556157 -0.29487610 -0.88691829  
Axis point 154.13034816 -61.46247229 0.00000000  
Rotation angle (degrees) 42.99235239  
Shift along axis -200.03877434  
  

> select add #4

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 3 models selected  

> view matrix models
> #4,0.76223,0.58726,-0.27229,153.22,-0.56605,0.80875,0.15971,103.54,0.314,0.032396,0.94887,158.64

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.0787, steps = 164  
shifted from previous position = 3.2  
rotated from previous position = 10.4 degrees  
atoms outside contour = 1714, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.70200365 0.69776669 -0.14252203 145.24245168  
-0.66954964 0.71483167 0.20178941 132.65961687  
0.24268119 -0.04623133 0.96900387 119.28254424  
Axis -0.17199419 -0.26712572 -0.94818872  
Axis point 168.66349436 -93.35055971 0.00000000  
Rotation angle (degrees) 46.13833332  
Shift along axis -173.52001596  
  

> view matrix models
> #4,0.93179,-0.25795,0.25539,152.46,-0.33975,-0.37204,0.8638,102.02,-0.12781,-0.89165,-0.43431,163.34

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08476, steps = 100  
shifted from previous position = 2.41  
rotated from previous position = 16.8 degrees  
atoms outside contour = 1601, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98612408 -0.06923771 0.15088217 143.89050989  
-0.16266567 -0.22148637 0.96150074 132.16447573  
-0.03315376 -0.97270238 -0.22967564 125.50021856  
Axis -0.99435498 0.09461108 -0.04803040  
Axis point 0.00000000 120.12210269 1.70461325  
Rotation angle (degrees) 103.44541925  
Shift along axis -136.60184660  
  

> view matrix models
> #4,0.95884,-0.15189,0.2399,150.61,-0.27728,-0.31888,0.90633,103.27,-0.061166,-0.93555,-0.34787,162.33

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08476, steps = 104  
shifted from previous position = 0.1  
rotated from previous position = 9.71 degrees  
atoms outside contour = 1601, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98615203 -0.06926865 0.15068520 143.89242182  
-0.16248690 -0.22166695 0.96148935 132.15614642  
-0.03319915 -0.97265905 -0.22985256 125.50474247  
Axis -0.99436713 0.09453698 -0.04792453  
Axis point 0.00000000 120.11129642 1.73253936  
Rotation angle (degrees) 103.45512621  
Shift along axis -136.60300839  
  

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08476, steps = 40  
shifted from previous position = 0.00609  
rotated from previous position = 0.0068 degrees  
atoms outside contour = 1598, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98616117 -0.06921388 0.15065052 143.89282941  
-0.16243730 -0.22157388 0.96151918 132.15946617  
-0.03317026 -0.97268415 -0.22975048 125.49968664  
Axis -0.99437040 0.09450193 -0.04792599  
Axis point 0.00000000 120.11317631 1.72427163  
Rotation angle (degrees) 103.44910866  
Shift along axis -136.60814211  
  

> view matrix models
> #4,0.242,0.969,-0.04982,148.28,0.046084,0.03981,0.99814,101.29,0.96918,-0.24385,-0.035021,157.25

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07934, steps = 80  
shifted from previous position = 2.37  
rotated from previous position = 11.8 degrees  
atoms outside contour = 1729, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.27930593 0.92756010 -0.24823467 140.78915781  
0.09766165 0.22974035 0.96833960 129.17046774  
0.95522270 -0.29470600 -0.02641921 119.08321123  
Axis -0.65377647 -0.62293247 -0.42957126  
Axis point 0.00000000 11.01317352 19.24944986  
Rotation angle (degrees) 104.99213597  
Shift along axis -223.66384192  
  

> view matrix models
> #4,0.3752,0.88856,-0.26397,147.44,0.11313,0.23875,0.96447,99.703,0.92002,-0.39173,-0.010943,155.98

> view matrix models
> #4,0.27229,-0.78247,0.56,152.48,-0.72781,0.21321,0.6518,102.75,-0.62941,-0.58505,-0.51143,162.69

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07789, steps = 100  
shifted from previous position = 2.08  
rotated from previous position = 5.31 degrees  
atoms outside contour = 1739, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.30437212 -0.74961472 0.58773751 143.74660940  
-0.67988268 0.26119597 0.68522712 131.63604651  
-0.66717101 -0.60815659 -0.43014929 125.29214554  
Axis -0.71716449 0.69583049 0.03866551  
Axis point -0.00000000 190.66102504 6.71082249  
Rotation angle (degrees) 115.61301535  
Shift along axis -6.64910328  
  

> view matrix models
> #4,0.91679,0.27708,0.28761,145.62,-0.23907,-0.19611,0.95099,101.36,0.3199,-0.94062,-0.11355,158.67

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08187, steps = 64  
shifted from previous position = 2  
rotated from previous position = 2.66 degrees  
atoms outside contour = 1668, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.92222706 0.26175062 0.28457664 140.22539662  
-0.25099420 -0.15456956 0.95556798 132.01293837  
0.29410739 -0.95267773 -0.07685035 123.02787988  
Axis -0.96573319 -0.00482337 -0.25949210  
Axis point 0.00000000 100.84940182 -15.45159649  
Rotation angle (degrees) 98.89339084  
Shift along axis -167.98182856  
  

> volume #3 step 2

> volume #1 step 2

> volume #1 step 4

> view matrix models
> #4,0.78265,0.50988,-0.35705,147.62,0.47228,-0.11276,0.8742,101.02,0.40548,-0.85282,-0.32906,159.71

> view matrix models
> #4,-0.22844,0.85991,-0.45648,148.45,-0.40693,0.34162,0.84717,100.89,0.88443,0.37929,0.27188,154.52

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07806, steps = 152  
shifted from previous position = 5.08  
rotated from previous position = 12.7 degrees  
atoms outside contour = 1579, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.14846528 0.79275681 -0.59118077 140.33562398  
-0.55988049 0.42538934 0.71103990 130.77141663  
0.81516372 0.43655532 0.38069352 112.88386302  
Axis -0.13929864 -0.71370813 -0.68645218  
Axis point 67.89416005 0.00000000 60.62981065  
Rotation angle (degrees) 99.85708566  
Shift along axis -190.37055867  
  

> view matrix models
> #4,-0.13826,0.35314,-0.9253,149.14,-0.58667,0.72352,0.36379,102.22,0.79794,0.59314,0.10715,150.35

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07701, steps = 152  
shifted from previous position = 1.63  
rotated from previous position = 0.676 degrees  
atoms outside contour = 1616, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.13509063 0.35053516 -0.92675543 143.89775547  
-0.57846245 0.73148036 0.36099540 132.55115081  
0.80444498 0.58486031 0.10395528 113.53045597  
Axis 0.11321036 -0.87548251 -0.46980186  
Axis point 60.08618835 0.00000000 100.37828655  
Rotation angle (degrees) 98.61692973  
Shift along axis -153.09231734  
  

> view matrix models
> #4,-0.93014,-0.34204,-0.13361,152.56,-0.14893,0.0188,0.98867,101.44,-0.33566,0.9395,-0.068428,153.45

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07785, steps = 64  
shifted from previous position = 3.03  
rotated from previous position = 5.55 degrees  
atoms outside contour = 1604, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92597956 -0.30483581 -0.22279358 145.31174101  
-0.22941053 -0.01442853 0.97322280 131.10192289  
-0.29988775 0.95229562 -0.05657202 119.57886509  
Axis -0.19048002 0.70171398 0.68652374  
Axis point 90.82304603 0.00000000 -7.73477130  
Rotation angle (degrees) 176.85099970  
Shift along axis 146.41079870  
  

> view matrix models
> #4,-0.17251,-0.86664,-0.46816,153.42,0.25175,-0.49829,0.82965,102.98,-0.95229,0.025267,0.30414,158.92

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08078, steps = 68  
shifted from previous position = 2.37  
rotated from previous position = 6.47 degrees  
atoms outside contour = 1642, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.14778702 -0.83152714 -0.53546393 147.55432990  
0.16359213 -0.55450375 0.81594314 135.02013221  
-0.97539562 0.03298812 0.21797975 122.75263106  
Axis -0.58409627 0.32819568 0.74237400  
Axis point 91.27141280 86.06347261 0.00000000  
Rotation angle (degrees) 137.91535681  
Shift along axis 49.25545217  
  

> view matrix models
> #4,-0.81135,0.58048,-0.068867,150.21,-0.10652,-0.030973,0.99383,103.82,0.57477,0.81368,0.08696,154.57

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07621, steps = 92  
shifted from previous position = 3.37  
rotated from previous position = 6.74 degrees  
atoms outside contour = 1669, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.85163923 0.51869901 -0.07524604 146.44645141  
-0.15303799 -0.10878252 0.98221471 134.73871587  
0.50128834 0.84800808 0.17202411 119.59437823  
Axis -0.14989458 -0.64392780 -0.75025902  
Axis point 62.37215109 -2.33392538 0.00000000  
Rotation angle (degrees) 153.40570506  
Shift along axis -198.44029580  
  

> view matrix models
> #4,-0.73378,0.40961,-0.54202,153.76,-0.46731,0.27478,0.8403,105.07,0.49313,0.8699,-0.010215,156.42

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.07595, steps = 88  
shifted from previous position = 3.77  
rotated from previous position = 8.85 degrees  
atoms outside contour = 1602, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.70005316 0.32657570 -0.63503850 147.66688852  
-0.51095715 0.39215894 0.76494063 130.93482447  
0.49884705 0.85997656 -0.10766592 121.06743995  
Axis 0.06726466 -0.80254304 -0.59279013  
Axis point 73.61950414 0.00000000 53.12645277  
Rotation angle (degrees) 135.05458113  
Shift along axis -166.91565236  
  

> view matrix models
> #4,-0.52467,0.31321,-0.79159,154.01,-0.8285,0.025923,0.55939,103.92,0.19572,0.94933,0.24589,157.87

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08063, steps = 164  
shifted from previous position = 3.38  
rotated from previous position = 17.2 degrees  
atoms outside contour = 1582, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.48878925 0.06049146 -0.87030216 146.28840102  
-0.85298605 0.17615689 0.49130799 130.61408752  
0.18302966 0.98250167 -0.03450523 122.91878603  
Axis 0.33228073 -0.71255368 -0.61794560  
Axis point 88.56590822 -0.00000000 62.55868833  
Rotation angle (degrees) 132.34310728  
Shift along axis -120.41785532  
  

> surface dust #1 size 8.39

> view matrix models
> #4,-0.70726,0.067927,-0.70369,153.49,-0.70694,-0.075131,0.70327,100.59,-0.0050977,0.99486,0.10116,159.96

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08236, steps = 140  
shifted from previous position = 3.55  
rotated from previous position = 18.4 degrees  
atoms outside contour = 1520, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.55890845 0.27521770 -0.78222540 143.47449700  
-0.78568056 0.12592141 0.60568131 128.74632038  
0.26519314 0.95309969 0.14585466 120.97286512  
Axis 0.22695500 -0.68423804 -0.69304382  
Axis point 102.76116308 -54.17549280 0.00000000  
Rotation angle (degrees) 130.05825816  
Shift along axis -139.37037241  
  

> view matrix models
> #4,-0.8624,0.27438,-0.42542,150.76,-0.48195,-0.18788,0.85582,98.614,0.15489,0.94309,0.29427,157.89

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08217, steps = 64  
shifted from previous position = 3.22  
rotated from previous position = 2.03 degrees  
atoms outside contour = 1426, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.85345042 0.30277037 -0.42420808 141.98550121  
-0.48578760 -0.16733154 0.85791058 125.90293906  
0.18876651 0.93825916 0.28989127 119.98039665  
Axis 0.08018767 -0.61174700 -0.78697875  
Axis point 81.88109923 -10.09862584 0.00000000  
Rotation angle (degrees) 149.93359694  
Shift along axis -160.05728027  
  

> view matrix models
> #4,-0.96906,0.21685,-0.11791,148.64,-0.19466,-0.37768,0.90524,96.409,0.15177,0.90019,0.40821,156.68

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08109, steps = 100  
shifted from previous position = 7.72  
rotated from previous position = 7.44 degrees  
atoms outside contour = 1540, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98351796 0.10390829 -0.14797126 134.73857898  
-0.17857923 -0.43006387 0.88496018 124.95626108  
0.02831760 0.89679883 0.44153141 120.61716401  
Axis 0.03553096 -0.52909044 -0.84782124  
Axis point 71.79658072 17.88889706 0.00000000  
Rotation angle (degrees) 170.41002913  
Shift along axis -163.58756572  
  

> view matrix models
> #4,-0.76745,0.25959,-0.58621,141.06,-0.6367,-0.20153,0.74431,96.226,0.075071,0.94446,0.31994,157.23

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08637, steps = 84  
shifted from previous position = 1.56  
rotated from previous position = 10.4 degrees  
atoms outside contour = 1401, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69666839 0.27642788 -0.66199757 133.09526407  
-0.71663513 -0.31057207 0.62448306 127.07315816  
-0.03297343 0.90946832 0.41446367 120.31024023  
Axis 0.23560854 -0.52003902 -0.82100428  
Axis point 95.63051041 -8.30488689 0.00000000  
Rotation angle (degrees) 142.78659035  
Shift along axis -133.49984330  
  

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.69667,0.27643,-0.662,139.53,-0.71664,-0.31057,0.62448,97.592,-0.032973,0.90947,0.41446,157.16

> view matrix models
> #4,-0.69667,0.27643,-0.662,142.55,-0.71664,-0.31057,0.62448,96.66,-0.032973,0.90947,0.41446,155.31

> view matrix models
> #4,-0.69667,0.27643,-0.662,145.04,-0.71664,-0.31057,0.62448,97.027,-0.032973,0.90947,0.41446,153.24

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08459, steps = 200  
shifted from previous position = 3.29  
rotated from previous position = 8.62 degrees  
atoms outside contour = 1448, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.67668746 0.40692240 -0.61360267 136.79035997  
-0.72926674 -0.25575835 0.63463193 127.41341969  
0.10131194 0.87692749 0.46982344 119.10910540  
Axis 0.17762459 -0.52409717 -0.83292956  
Axis point 93.66547020 -12.06648487 0.00000000  
Rotation angle (degrees) 136.99642810  
Shift along axis -141.68917640  
  

> view matrix models
> #4,-0.67669,0.40692,-0.6136,140.68,-0.72927,-0.25576,0.63463,98.851,0.10131,0.87693,0.46982,157.41

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08506, steps = 164  
shifted from previous position = 3.43  
rotated from previous position = 9.75 degrees  
atoms outside contour = 1411, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.56717855 0.43756088 -0.69774563 131.57208421  
-0.80433317 -0.11213194 0.58350200 128.71596644  
0.17707808 0.89216977 0.41554356 118.23377211  
Axis 0.19912421 -0.56435622 -0.80115642  
Axis point 95.01787043 -24.61766303 0.00000000  
Rotation angle (degrees) 129.18921812  
Shift along axis -141.16621465  
  

> view matrix models
> #4,-0.56718,0.43756,-0.69775,139.26,-0.80433,-0.11213,0.5835,97.432,0.17708,0.89217,0.41554,157.02

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08506, steps = 144  
shifted from previous position = 2.98  
rotated from previous position = 0.0281 degrees  
atoms outside contour = 1411, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.56746979 0.43716989 -0.69775392 131.57715685  
-0.80417006 -0.11221067 0.58371165 128.70588546  
0.17688572 0.89235153 0.41523510 118.23293113  
Axis 0.19917732 -0.56443896 -0.80108492  
Axis point 95.01420641 -24.61272881 0.00000000  
Rotation angle (degrees) 129.21429879  
Shift along axis -141.15404977  
  

> view matrix models
> #4,-0.56747,0.43717,-0.69775,141.87,-0.80417,-0.11221,0.58371,95.095,0.17689,0.89235,0.41524,152.81

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.085, steps = 72  
shifted from previous position = 2.33  
rotated from previous position = 9.56 degrees  
atoms outside contour = 1402, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.67121105 0.47120855 -0.57222219 135.48403356  
-0.70655522 -0.17323850 0.68612546 124.94993405  
0.22417727 0.86484156 0.44921445 118.22521924  
Axis 0.12471982 -0.55577977 -0.82192080  
Axis point 87.42812207 -17.07545515 0.00000000  
Rotation angle (degrees) 134.23617060  
Shift along axis -149.71886915  
  

> view matrix models
> #4,-0.67121,0.47121,-0.57222,146.23,-0.70656,-0.17324,0.68613,90.479,0.22418,0.86484,0.44921,157.52

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08514, steps = 116  
shifted from previous position = 5.41  
rotated from previous position = 11.2 degrees  
atoms outside contour = 1431, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.78409908 0.36549430 -0.50159999 136.80159577  
-0.58091464 -0.14771675 0.80044859 123.65490060  
0.21846467 0.91901778 0.32814555 119.93388792  
Axis 0.09921355 -0.60251887 -0.79191394  
Axis point 82.13591357 -15.68092659 -0.00000000  
Rotation angle (degrees) 143.30570432  
Shift along axis -155.90915566  
  

> view matrix models
> #4,-0.7841,0.36549,-0.5016,142.16,-0.58091,-0.14772,0.80045,95.959,0.21846,0.91902,0.32815,158.16

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08514, steps = 100  
shifted from previous position = 2.66  
rotated from previous position = 0.00997 degrees  
atoms outside contour = 1429, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.78417344 0.36554037 -0.50145016 136.80220276  
-0.58079478 -0.14778532 0.80052291 123.65509570  
0.21851646 0.91898843 0.32819326 119.93714600  
Axis 0.09913741 -0.60250126 -0.79193687  
Axis point 82.12832507 -15.67216311 -0.00000000  
Rotation angle (degrees) 143.31026960  
Shift along axis -155.92278206  
  

> view matrix models
> #4,-0.78417,0.36554,-0.50145,141.98,-0.58079,-0.14779,0.80052,98.046,0.21852,0.91899,0.32819,154.79

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08344, steps = 80  
shifted from previous position = 1.37  
rotated from previous position = 5.54 degrees  
atoms outside contour = 1423, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.75668316 0.45136649 -0.47296817 134.83143031  
-0.57932854 -0.12763548 0.80503890 126.64141038  
0.30300006 0.88316334 0.35806911 116.87735046  
Axis 0.06044433 -0.60036117 -0.79744150  
Axis point 78.72447881 -13.90013860 0.00000000  
Rotation angle (degrees) 139.74045003  
Shift along axis -161.08363980  
  

> view matrix models
> #4,-0.75668,0.45137,-0.47297,142.53,-0.57933,-0.12764,0.80504,92.057,0.303,0.88316,0.35807,159.17

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08291, steps = 100  
shifted from previous position = 3.54  
rotated from previous position = 4.04 degrees  
atoms outside contour = 1444, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.74674419 0.44784904 -0.49173606 133.18012559  
-0.57335245 -0.05872551 0.81720149 122.01685466  
0.33710545 0.89217854 0.30062828 120.43744789  
Axis 0.05691438 -0.62916587 -0.77518453  
Axis point 75.79850398 -22.39811510 0.00000000  
Rotation angle (degrees) 138.80050471  
Shift along axis -162.55022325  
  

> select add #1

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 8 models selected  

> select subtract #4

5 models selected  

> view matrix models #1,1,0,0,7.5618,0,1,0,-32.381,0,0,1,38.511

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08674, steps = 120  
shifted from previous position = 4.03  
rotated from previous position = 12.5 degrees  
atoms outside contour = 1420, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.72349927 0.59464760 -0.35063235 129.08636919  
-0.53699130 -0.16560986 0.82717212 124.50085183  
0.43380774 0.78674494 0.43913920 121.45355171  
Axis -0.02934760 -0.56945434 -0.82149892  
Axis point 68.48674962 -9.97149829 0.00000000  
Rotation angle (degrees) 136.46759700  
Shift along axis -174.45988696  
  

> view matrix models #1,1,0,0,5.7191,0,1,0,-30.84,0,0,1,42.951

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08474, steps = 84  
shifted from previous position = 3.15  
rotated from previous position = 4.33 degrees  
atoms outside contour = 1403, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69693997 0.64869065 -0.30573701 131.71296130  
-0.53125059 -0.18064285 0.82773243 125.17869580  
0.48171308 0.73930278 0.47051451 118.94536291  
Axis -0.06221644 -0.55402618 -0.83017113  
Axis point 68.31094867 -7.43824846 0.00000000  
Rotation angle (degrees) 134.71124199  
Shift along axis -176.29199245  
  

> view matrix models #1,1,0,0,4.7706,0,1,0,-30.876,0,0,1,46.872

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08407, steps = 104  
shifted from previous position = 2.96  
rotated from previous position = 15.8 degrees  
atoms outside contour = 1498, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.50102028 0.83088818 -0.24208165 130.76506325  
-0.58132429 -0.11588588 0.80537726 127.22296653  
0.64112460 0.54423828 0.54107665 116.92669592  
Axis -0.15488684 -0.52384759 -0.83761194  
Axis point 64.51750035 -6.37143065 0.00000000  
Rotation angle (degrees) 122.54179934  
Shift along axis -184.83842924  
  

> view matrix models #1,1,0,0,4.5837,0,1,0,-29.474,0,0,1,44.867

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08407, steps = 52  
shifted from previous position = 2.45  
rotated from previous position = 0.0294 degrees  
atoms outside contour = 1495, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.50083780 0.83111605 -0.24167667 130.75717624  
-0.58114986 -0.11598118 0.80548942 127.22744983  
0.64142524 0.54386992 0.54109073 116.93993940  
Axis -0.15516590 -0.52376564 -0.83761154  
Axis point 64.49343096 -6.34862245 0.00000000  
Rotation angle (degrees) 122.53835860  
Shift along axis -184.87666518  
  

> view matrix models #1,1,0,0,3.4641,0,1,0,-26.711,0,0,1,43.967

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.0845, steps = 92  
shifted from previous position = 3.29  
rotated from previous position = 9.43 degrees  
atoms outside contour = 1460, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53372829 0.84003032 -0.09738160 129.54194205  
-0.55791776 -0.26324453 0.78703881 125.28460100  
0.63550129 0.47439581 0.60916888 120.35636169  
Axis -0.19429986 -0.45546850 -0.86878997  
Axis point 62.99161734 4.00559883 0.00000000  
Rotation angle (degrees) 126.43439540  
Shift along axis -186.79756973  
  

> view matrix models #1,1,0,0,1.8023,0,1,0,-25.054,0,0,1,47.446

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08449, steps = 76  
shifted from previous position = 4.2  
rotated from previous position = 0.0188 degrees  
atoms outside contour = 1459, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53384060 0.83998647 -0.09714388 129.53476569  
-0.55790049 -0.26355525 0.78694706 125.30079983  
0.63542211 0.47430091 0.60932535 120.34645058  
Axis -0.19432558 -0.45532724 -0.86885826  
Axis point 62.99861929 4.03924893 0.00000000  
Rotation angle (degrees) 126.44388767  
Shift along axis -186.78879288  
  

> view matrix models #1,1,0,0,-0.49018,0,1,0,-25.047,0,0,1,56.737

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08449, steps = 116  
shifted from previous position = 9.57  
rotated from previous position = 0.0221 degrees  
atoms outside contour = 1462, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53415309 0.83979912 -0.09704599 129.53960332  
-0.55768967 -0.26377034 0.78702442 125.29692212  
0.63534456 0.47451307 0.60924103 120.34568624  
Axis -0.19429638 -0.45534613 -0.86885489  
Axis point 62.99589944 4.04560296 0.00000000  
Rotation angle (degrees) 126.46568164  
Shift along axis -186.78548270  
  

> view matrix models #1,1,0,0,-1.0799,0,1,0,-22.45,0,0,1,54.014

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.08449, steps = 84  
shifted from previous position = 3.8  
rotated from previous position = 0.0144 degrees  
atoms outside contour = 1458, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53401453 0.83986441 -0.09724330 129.53443817  
-0.55784519 -0.26357707 0.78697895 125.29201085  
0.63532451 0.47450490 0.60926830 120.34710462  
Axis -0.19424115 -0.45538122 -0.86884885  
Axis point 62.99761128 4.03061855 0.00000000  
Rotation angle (degrees) 126.45289085  
Shift along axis -186.77999023  
  

> select subtract #1

Nothing selected  

> select add #4

3543 atoms, 3447 bonds, 6 pseudobonds, 600 residues, 3 models selected  

> view matrix models
> #4,-0.53401,0.83986,-0.097243,129.44,-0.55785,-0.26358,0.78698,103.49,0.63532,0.4745,0.60927,169.1

> fitmap #4 inMap #1

Fit molecule 2qe3-assembly1.cif (#4) to map
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) using 3543 atoms  
average map value = 0.0845, steps = 92  
shifted from previous position = 5.4  
rotated from previous position = 0.0175 degrees  
atoms outside contour = 1460, contour level = 0.062298  
  
Position of 2qe3-assembly1.cif (#4) relative to
cryosparc_P1050_J339_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53385325 0.83994394 -0.09744174 129.54431210  
-0.55789444 -0.26328301 0.78704247 125.28111582  
0.63541680 0.47452738 0.60915454 120.35015168  
Axis -0.19423620 -0.45549052 -0.86879266  
Axis point 62.99564651 4.00305909 0.00000000  
Rotation angle (degrees) 126.44072596  
Shift along axis -186.78588370  
  

[deleted to fit within ticket limits]

> show sel cartoons

> hide sel cartoons

> cartoon (#!21 & sel)

> surface hidePatches (#!21 & sel)

> surface style #21 solid

> hide #!20 models

> show #!20 models

> hide sel cartoons

[Repeated 1 time(s)]

> show sel cartoons

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> view matrix models #21,1,0,0,118.63,0,1,0,96.59,0,0,1,-9.1455

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = -0.0001528, steps = 256  
shifted from previous position = 2.02  
rotated from previous position = 1.69 degrees  
atoms outside contour = 37720, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99959925 -0.02054237 -0.01947668 120.63084107  
0.02070374 0.99975268 0.00812009 96.53764283  
0.01930505 -0.00852007 0.99977734 -9.36741048  
Axis -0.28198965 -0.65720802 0.69897028  
Axis point -1307.79394648 4470.04510887 0.00000000  
Rotation angle (degrees) 1.69075230  
Shift along axis -104.00950318  
  

> view matrix models
> #21,0.9996,-0.020542,-0.019477,120.61,0.020704,0.99975,0.0081201,96.162,0.019305,-0.0085201,0.99978,-9.3166

> view matrix models
> #21,0.9996,-0.020542,-0.019477,105.95,0.020704,0.99975,0.0081201,99.342,0.019305,-0.0085201,0.99978,110.75

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002218, steps = 2000  
shifted from previous position = 0.88  
rotated from previous position = 3.49 degrees  
atoms outside contour = 35913, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99836268 0.02347690 -0.05216120 106.47088705  
-0.02160001 0.99910895 0.03625936 99.14257277  
0.05296598 -0.03507331 0.99798019 110.06054465  
Axis -0.52916008 -0.77985460 -0.33438960  
Axis point -988.70579722 0.00000000 342.95731468  
Rotation angle (degrees) 3.86476790  
Shift along axis -170.46003665  
  

> view matrix models
> #21,0.99836,0.023477,-0.052161,108.4,-0.0216,0.99911,0.036259,99.833,0.052966,-0.035073,0.99798,115.55

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002211, steps = 56  
shifted from previous position = 1.15  
rotated from previous position = 0.855 degrees  
atoms outside contour = 35910, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99883648 0.02574401 -0.04077898 107.75488193  
-0.02387289 0.99866877 0.04572504 100.66684169  
0.04190184 -0.04469833 0.99812138 115.99042654  
Axis -0.68403805 -0.62546701 -0.37534379  
Axis point 0.00000000 1069.32005905 294.61218652  
Rotation angle (degrees) 3.78974300  
Shift along axis -180.20851451  
  

> view matrix models
> #21,0.99884,0.025744,-0.040779,109.15,-0.023873,0.99867,0.045725,109.66,0.041902,-0.044698,0.99812,108.55

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 76  
shifted from previous position = 0.804  
rotated from previous position = 3.79 degrees  
atoms outside contour = 22330, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000526 0.00006198 109.19714773  
-0.00000525 1.00000000 -0.00004474 109.19496025  
-0.00006199 0.00004474 1.00000000 109.20286831  
Axis 0.58388450 0.80893336 -0.06859816  
Axis point 1921801.67003418 0.00000000 -399522.73139623  
Rotation angle (degrees) 0.00439033  
Shift along axis 144.59885192  
  

> volume #20 step 1

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 24  
shifted from previous position = 0.0037  
rotated from previous position = 0.000195 degrees  
atoms outside contour = 13191, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000366 0.00006372 109.19539768  
-0.00000366 1.00000000 -0.00004230 109.19416588  
-0.00006372 0.00004230 1.00000000 109.19970419  
Axis 0.55237693 0.83222253 -0.04780577  
Axis point 1823191.78094311 0.00000000 -448205.90934980  
Rotation angle (degrees) 0.00438711  
Shift along axis 145.97048672  
  

> view matrix models
> #21,1,3.6618e-06,6.3723e-05,110.7,-3.6591e-06,1,-4.2295e-05,107.56,-6.3723e-05,4.2295e-05,1,108.58

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 76  
shifted from previous position = 2.31  
rotated from previous position = 0.00663 degrees  
atoms outside contour = 13186, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
1.00000000 -0.00001109 -0.00002046 109.19634521  
0.00001109 1.00000000 0.00003575 109.20354228  
0.00002046 -0.00003575 1.00000000 109.20237641  
Axis -0.83808997 -0.47962705 0.25992900  
Axis point -0.00000000 3894925.16662155 -1505071.90101093  
Rotation angle (degrees) 0.00244375  
Shift along axis -115.50847048  
  

> color zone #20 near sel & #21 distance 3.9

> hide #!21 models

> show #!21 models

> view matrix models
> #21,1,-1.1086e-05,-2.0457e-05,106.51,1.1087e-05,1,3.5746e-05,110.68,2.0457e-05,-3.5746e-05,1,113.13

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.003323, steps = 64  
shifted from previous position = 1.73  
rotated from previous position = 0.255 degrees  
atoms outside contour = 33597, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99999338 -0.00262276 0.00252346 106.46518746  
0.00261622 0.99999321 0.00259364 111.93511670  
-0.00253025 -0.00258702 0.99999345 111.93502472  
Axis -0.57984602 0.56563702 0.58637305  
Axis point -28108.53275273 55524.25435086 0.00000000  
Rotation angle (degrees) 0.25595667  
Shift along axis 67.21691189  
  

> view matrix models
> #21,0.99999,-0.0026228,0.0025235,111.01,0.0026162,0.99999,0.0025936,108.48,-0.0025302,-0.002587,0.99999,107.77

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.003324, steps = 80  
shifted from previous position = 2.58  
rotated from previous position = 0.512 degrees  
atoms outside contour = 33617, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99999329 0.00262520 -0.00255604 111.94066258  
-0.00263173 0.99999327 -0.00255485 106.46032600  
0.00254932 0.00256156 0.99999347 106.45971866  
Axis 0.57246955 -0.57123359 -0.58819282  
Axis point 27712.21654079 -55512.23297750 0.00000000  
Rotation angle (degrees) 0.25603920  
Shift along axis -59.34993565  
  

> color #20 #ffb2b23c models

> color #20 #b7f7ec3c models

> color #20 #5cf7e93c models

> color #20 #41afa53c models

> color #20 #41afa53b models

> view matrix models
> #21,0.99999,0.0026252,-0.002556,111.09,-0.0026317,0.99999,-0.0025548,107.78,0.0025493,0.0025616,0.99999,109.21

> color zone #20 near sel & #21 distance 3.9

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 60  
shifted from previous position = 2.36  
rotated from previous position = 0.253 degrees  
atoms outside contour = 13207, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99999999 0.00010706 0.00000283 109.20156758  
-0.00010706 0.99999999 0.00001072 109.19816974  
-0.00000283 -0.00001072 1.00000000 109.20022648  
Axis -0.09957741 0.02627818 -0.99468276  
Axis point 1048688.46469575 -911510.81604439 0.00000000  
Rotation angle (degrees) 0.00616663  
Shift along axis -116.62406250  
  

> view matrix models
> #21,1,0.00010706,2.8288e-06,106.99,-0.00010706,1,1.0717e-05,110.02,-2.8277e-06,-1.0717e-05,1,109.84

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.80467,0.34575,0.48267,106.99,-0.54766,0.74619,0.3785,110.02,-0.2293,-0.56891,0.78979,109.84

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002768, steps = 108  
shifted from previous position = 2.29  
rotated from previous position = 1.86 degrees  
atoms outside contour = 34027, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.81763137 0.32288251 0.47668210 108.86863952  
-0.53035456 0.74459782 0.40533706 109.32659857  
-0.22406020 -0.58422682 0.78004875 108.73773965  
Axis -0.66742327 0.47262408 -0.57547602  
Axis point 0.00000000 195.62827414 -243.89210196  
Rotation angle (degrees) 47.84496808  
Shift along axis -83.56704182  
  

> view matrix models
> #21,0.99872,-0.043992,-0.024864,108.87,0.045028,0.99807,0.04279,109.33,0.022933,-0.043855,0.99877,108.74

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 68  
shifted from previous position = 0.582  
rotated from previous position = 3.82 degrees  
atoms outside contour = 13208, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
1.00000000 -0.00000116 -0.00000100 109.19947373  
0.00000116 1.00000000 0.00000061 109.20045973  
0.00000100 -0.00000061 1.00000000 109.19978296  
Axis -0.36883181 -0.60658531 0.70428499  
Axis point -78878395.48391864 84963331.33298789 0.00000000  
Rotation angle (degrees) 0.00009410  
Shift along axis -29.60786606  
  

> view matrix models
> #21,0.99912,0.039016,0.015225,109.2,-0.039339,0.99899,0.021555,109.2,-0.014368,-0.022135,0.99965,109.2

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 60  
shifted from previous position = 0.00538  
rotated from previous position = 2.7 degrees  
atoms outside contour = 13188, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00007765 0.00004403 109.19656159  
-0.00007765 1.00000000 0.00005600 109.20332227  
-0.00004403 -0.00005600 1.00000000 109.19628645  
Axis -0.53144343 0.41783239 -0.73687446  
Axis point 1906163.18267532 -770622.43948252 0.00000000  
Rotation angle (degrees) 0.00603743  
Shift along axis -92.86706501  
  

> view matrix models
> #21,0.99738,-0.067958,-0.024968,109.2,0.068875,0.9969,0.037937,109.2,0.022312,-0.039557,0.99897,109.2

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 88  
shifted from previous position = 0.0104  
rotated from previous position = 4.7 degrees  
atoms outside contour = 13195, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99999999 -0.00011845 -0.00001287 109.20348513  
0.00011845 0.99999999 0.00006208 109.19828446  
0.00001286 -0.00006208 1.00000000 109.19043399  
Axis -0.46206573 -0.09575662 0.88166089  
Axis point -950369.83237547 1059885.90338705 0.00000000  
Rotation angle (degrees) 0.00769778  
Shift along axis 35.35328890  
  

> view matrix models
> #21,0.99947,0.010491,-0.030681,109.2,-0.011109,0.99974,-0.020059,109.2,0.030463,0.020389,0.99933,109.19

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 44  
shifted from previous position = 0.00964  
rotated from previous position = 2.18 degrees  
atoms outside contour = 13188, contour level = 0.02405  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99999999 0.00003916 -0.00012888 109.20477687  
-0.00003917 1.00000000 -0.00008088 109.19230958  
0.00012888 0.00008089 0.99999999 109.19788175  
Axis 0.51479682 -0.82028028 -0.24924785  
Axis point -730055.90986701 0.00000000 1089298.26562042  
Rotation angle (degrees) 0.00900219  
Shift along axis -60.56736441  
  

> color #20 #b9907c3b models

> color #21 #41cac6ff

> color #21 #17caa6ff

> color #21 #cac061ff

> color #21 #c773caff

> color #20 #c0be233b models

> color #20 #e6e22a3b models

> view matrix models
> #21,0.81164,-0.54569,-0.20848,109.2,0.58296,0.73377,0.34891,109.19,-0.037419,-0.40473,0.91367,109.2

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.81164,-0.54569,-0.20848,109.98,0.58296,0.73377,0.34891,110.01,-0.037419,-0.40473,0.91367,111.29

> volume #20 step 4

> view matrix models
> #21,0.81164,-0.54569,-0.20848,78.781,0.58296,0.73377,0.34891,85.188,-0.037419,-0.40473,0.91367,67.757

> volume #20 step 8

> volume #20 level 0.008551

> volume #20 step 2

> view matrix models
> #21,0.81164,-0.54569,-0.20848,102.92,0.58296,0.73377,0.34891,93.593,-0.037419,-0.40473,0.91367,118.75

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.001924, steps = 168  
shifted from previous position = 6.11  
rotated from previous position = 3.67 degrees  
atoms outside contour = 31841, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.82817980 -0.50275217 -0.24770642 103.03529538  
0.56015748 0.75707781 0.33623917 98.85815419  
0.01848806 -0.41722110 0.90861694 115.64826481  
Axis -0.56660137 -0.20017798 0.79930699  
Axis point -74.66500525 246.54146638 0.00000000  
Rotation angle (degrees) 41.67423262  
Shift along axis 14.26930193  
  

> view matrix models
> #21,0.82818,-0.50275,-0.24771,100.66,0.56016,0.75708,0.33624,97.902,0.018488,-0.41722,0.90862,110.3

> view matrix models
> #21,0.82818,-0.50275,-0.24771,104.22,0.56016,0.75708,0.33624,98.946,0.018488,-0.41722,0.90862,117.31

> view matrix models
> #21,0.82818,-0.50275,-0.24771,109.9,0.56016,0.75708,0.33624,109.11,0.018488,-0.41722,0.90862,107.06

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002675, steps = 120  
shifted from previous position = 1.99  
rotated from previous position = 1.23 degrees  
atoms outside contour = 29931, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.83851991 -0.48474332 -0.24881372 111.22652953  
0.54440667 0.76419901 0.34586305 107.90212248  
0.02248840 -0.42546890 0.90469359 107.92976922  
Axis -0.58682176 -0.20640398 0.78296719  
Axis point -86.74188537 254.67491292 0.00000000  
Rotation angle (degrees) 41.08754675  
Shift along axis -3.03610645  
  

> view matrix models
> #21,0.83852,-0.48474,-0.24881,109.74,0.54441,0.7642,0.34586,111.37,0.022488,-0.42547,0.90469,110.33

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002727, steps = 92  
shifted from previous position = 1.24  
rotated from previous position = 1.58 degrees  
atoms outside contour = 30058, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.83460337 -0.48578601 -0.25970976 110.61845200  
0.55059972 0.74993460 0.36665795 111.60134062  
0.01664803 -0.44901009 0.89337158 111.18517316  
Axis -0.60531499 -0.20508774 0.76911168  
Axis point -86.70274776 251.83065265 0.00000000  
Rotation angle (degrees) 42.35754541  
Shift along axis -4.33325904  
  

> view matrix models
> #21,0.8346,-0.48579,-0.25971,66.828,0.5506,0.74993,0.36666,194.31,0.016648,-0.44901,0.89337,67.074

> view matrix models
> #21,0.8346,-0.48579,-0.25971,14.306,0.5506,0.74993,0.36666,61.933,0.016648,-0.44901,0.89337,58.382

> view matrix models
> #21,0.8346,-0.48579,-0.25971,25.525,0.5506,0.74993,0.36666,87.098,0.016648,-0.44901,0.89337,60.114

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.81967,-0.45642,-0.34614,25.525,0.53986,0.81756,0.20036,87.098,0.19155,-0.3511,0.91654,60.114

> view matrix models
> #21,0.82395,-0.4586,-0.33285,25.525,0.53951,0.81452,0.21327,87.098,0.17331,-0.3553,0.91854,60.114

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.82395,-0.4586,-0.33285,97.652,0.53951,0.81452,0.21327,104.73,0.17331,-0.3553,0.91854,65.464

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.81787,-0.44907,-0.35976,97.652,0.53883,0.81707,0.20507,104.73,0.20186,-0.36157,0.91023,65.464

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.81787,-0.44907,-0.35976,21.054,0.53883,0.81707,0.20507,68.749,0.20186,-0.36157,0.91023,59.09

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.79618,-0.4885,-0.35702,21.054,0.5717,0.80057,0.17956,68.749,0.19811,-0.34707,0.91668,59.09

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.79618,-0.4885,-0.35702,106.87,0.5717,0.80057,0.17956,110.95,0.19811,-0.34707,0.91668,66.307

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.0004233, steps = 76  
shifted from previous position = 1.45  
rotated from previous position = 0.766 degrees  
atoms outside contour = 35261, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.78999621 -0.49169023 -0.36626042 107.50870447  
0.57646978 0.79910282 0.17063785 111.00505859  
0.20877877 -0.34594132 0.91473276 67.61330588  
Axis -0.39178770 -0.43612538 0.81012163  
Axis point -86.38088573 227.05268226 0.00000000  
Rotation angle (degrees) 41.24338750  
Shift along axis -35.75770967  
  

> view matrix models
> #21,0.79,-0.49169,-0.36626,118.57,0.57647,0.7991,0.17064,116.07,0.20878,-0.34594,0.91473,106.07

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002049, steps = 108  
shifted from previous position = 1.32  
rotated from previous position = 0.756 degrees  
atoms outside contour = 31720, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.79273185 -0.49029866 -0.36219254 119.79227147  
0.57625593 0.79651404 0.18301500 116.01770668  
0.19875943 -0.35379742 0.91395956 105.56074046  
Axis -0.40691279 -0.42521098 0.80846621  
Axis point -95.18167048 273.99316421 0.00000000  
Rotation angle (degrees) 41.27059785  
Shift along axis -12.73471847  
  

> view matrix models
> #21,0.79273,-0.4903,-0.36219,113.66,0.57626,0.79651,0.18302,112.53,0.19876,-0.3538,0.91396,115.53

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002353, steps = 104  
shifted from previous position = 1.53  
rotated from previous position = 1.61 degrees  
atoms outside contour = 30785, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.80037391 -0.47683309 -0.36336181 113.76068186  
0.56895194 0.79517786 0.20972806 111.00487350  
0.18893199 -0.37459627 0.90773473 115.54961638  
Axis -0.44295863 -0.41867724 0.79277804  
Axis point -93.07707514 272.65464992 -0.00000000  
Rotation angle (degrees) 41.26707750  
Shift along axis -5.26129181  
  

> view matrix models
> #21,0.80037,-0.47683,-0.36336,108.41,0.56895,0.79518,0.20973,107,0.18893,-0.3746,0.90773,115.1

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002625, steps = 172  
shifted from previous position = 2.38  
rotated from previous position = 0.692 degrees  
atoms outside contour = 30201, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.80000880 -0.48420766 -0.35430052 107.62625180  
0.57283980 0.79203714 0.21102545 108.24832585  
0.17843903 -0.37177966 0.91101010 113.23980291  
Axis -0.44171902 -0.40377338 0.80115627  
Axis point -93.98525980 260.61198280 0.00000000  
Rotation angle (degrees) 41.27708671  
Shift along axis -0.52557742  
  

> save /Users/mansoore.esmaili/Downloads/apo-strucutres.cxs

> view matrix models
> #21,0.80001,-0.48421,-0.3543,110.21,0.57284,0.79204,0.21103,108.87,0.17844,-0.37178,0.91101,111.45

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.017787,0.19765,-0.98011,110.21,0.74967,-0.65126,-0.11773,108.87,-0.66158,-0.73266,-0.15976,111.45

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002812, steps = 72  
shifted from previous position = 0.578  
rotated from previous position = 0.837 degrees  
atoms outside contour = 29923, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.02745788 0.19716033 -0.97998667 110.00274561  
0.75667923 -0.64471900 -0.10850781 108.70261449  
-0.65320946 -0.73855616 -0.16688975 111.96195647  
Axis -0.69713119 -0.36156999 0.61909228  
Axis point 0.00000000 49.95301658 89.09589150  
Rotation angle (degrees) 153.13521495  
Shift along axis -46.67516513  
  

> view matrix models
> #21,-0.53356,0.80884,-0.24717,110,0.13548,0.37021,0.91902,108.7,0.83484,0.45686,-0.30711,111.96

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002843, steps = 92  
shifted from previous position = 0.982  
rotated from previous position = 2.86 degrees  
atoms outside contour = 29885, contour level = 0.0085515  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.54771418 0.80149370 -0.24003547 109.54951621  
0.09781568 0.34627008 0.93302150 108.45607643  
0.83092796 0.48754987 -0.26805568 111.12686243  
Axis -0.32835515 -0.78940237 -0.51867793  
Axis point 27.71901904 0.00000000 32.48986987  
Rotation angle (degrees) 137.28608620  
Shift along axis -179.22568262  
  

> view matrix models
> #21,-0.35329,0.72687,-0.58894,109.55,0.6554,0.64152,0.39862,108.46,0.66756,-0.24516,-0.70303,111.13

> volume #20 step 4

> volume #20 level 0.0119

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002726, steps = 88  
shifted from previous position = 1.48  
rotated from previous position = 1.63 degrees  
atoms outside contour = 32373, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.35211882 0.73325754 -0.58167492 108.36643969  
0.67572448 0.62918163 0.38409232 109.18422115  
0.64761776 -0.25780585 -0.71702676 110.61374938  
Axis -0.46246748 -0.88566679 -0.04145077  
Axis point 1.90998572 0.00000000 61.48708392  
Rotation angle (degrees) 136.05299237  
Shift along axis -151.40181784  
  

> view matrix models
> #21,-0.35807,0.54363,-0.75912,108.37,0.91293,0.37436,-0.16253,109.18,0.19583,-0.75121,-0.63034,110.61

> view matrix models
> #21,0.48039,0.57826,-0.65942,108.37,0.64361,0.27833,0.71295,109.18,0.59581,-0.76691,-0.23846,110.61

> volume #20 step 2

> view matrix models
> #21,0.12752,0.68592,-0.71642,108.37,0.92412,0.18014,0.33696,109.18,0.36019,-0.70503,-0.6109,110.61

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002786, steps = 76  
shifted from previous position = 1.24  
rotated from previous position = 0.737 degrees  
atoms outside contour = 31677, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.11793145 0.69193384 -0.71226381 108.55481335  
0.92327294 0.18766996 0.33518215 108.02510675  
0.36559439 -0.69714242 -0.61671160 111.00243160  
Axis -0.68352525 -0.71367409 0.15317481  
Axis point -39.49929443 0.00000000 72.45067520  
Rotation angle (degrees) 130.96175346  
Shift along axis -134.29190021  
  

> view matrix models
> #21,0.073553,0.96232,0.26177,108.55,0.082373,0.25572,-0.96324,108.03,-0.99388,0.092412,-0.060461,111

> view matrix models
> #21,0.16993,0.96754,0.18706,108.55,0.54384,0.066225,-0.83657,108.03,-0.82181,0.24389,-0.51493,111

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002809, steps = 112  
shifted from previous position = 1.88  
rotated from previous position = 2.59 degrees  
atoms outside contour = 31689, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.14714557 0.96598376 0.21265829 107.75616212  
0.57329181 0.09191122 -0.81417985 109.66016844  
-0.80603020 0.24171821 -0.54026625 111.47976477  
Axis 0.69520349 0.67070470 -0.25854846  
Axis point 0.00000000 -44.27338088 85.51157625  
Rotation angle (degrees) 130.58721149  
Shift along axis 119.63912928  
  

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.14715,0.96598,0.21266,44.972,0.57329,0.091911,-0.81418,174.04,-0.80603,0.24172,-0.54027,104.06

> ui mousemode right "rotate selected models"

> view matrix models
> #21,-0.60839,0.18991,-0.77058,44.972,0.43899,-0.72836,-0.5261,174.04,-0.66117,-0.65835,0.35976,104.06

> ui mousemode right "translate selected models"

> view matrix models
> #21,-0.60839,0.18991,-0.77058,43.98,0.43899,-0.72836,-0.5261,181.45,-0.66117,-0.65835,0.35976,97.486

> ui mousemode right "rotate selected models"

> view matrix models
> #21,-0.48176,0.33936,-0.80792,43.98,0.55185,-0.59869,-0.58055,181.45,-0.68071,-0.72554,0.10114,97.486

> view matrix models
> #21,-0.39711,0.91554,-0.063978,65.604,-0.89732,-0.40195,-0.18237,108.74,-0.19268,-0.01501,0.98115,149.5

> view matrix models
> #21,-0.36799,0.92693,-0.07339,65.604,-0.91097,-0.37522,-0.17127,108.74,-0.18629,0.0038291,0.98249,149.5

> ui mousemode right "translate selected models"

> view matrix models
> #21,-0.36799,0.92693,-0.07339,61.51,-0.91097,-0.37522,-0.17127,122.17,-0.18629,0.0038291,0.98249,140.58

> view matrix models
> #21,-0.36799,0.92693,-0.07339,36.245,-0.91097,-0.37522,-0.17127,188.79,-0.18629,0.0038291,0.98249,100.69

> view matrix models
> #21,-0.36799,0.92693,-0.07339,89.026,-0.91097,-0.37522,-0.17127,45.514,-0.18629,0.0038291,0.98249,192.71

> view matrix models
> #21,-0.36799,0.92693,-0.07339,190.19,-0.91097,-0.37522,-0.17127,-8.8583,-0.18629,0.0038291,0.98249,143.2

> ui mousemode right "rotate selected models"

> view matrix models
> #21,-0.48086,0.090352,0.87213,190.19,-0.4214,-0.89608,-0.13951,-8.8583,0.76889,-0.4346,0.46896,143.2

> view matrix models
> #21,-0.39862,0.42118,0.81469,190.19,0.65977,-0.48532,0.57372,-8.8583,0.63703,0.7662,-0.084425,143.2

> view matrix models
> #21,-0.37076,0.61803,0.69324,190.19,0.47377,-0.51615,0.71353,-8.8583,0.7988,0.59298,-0.10144,143.2

> view matrix models
> #21,-0.43466,0.76631,0.47312,190.19,0.60317,-0.14241,0.7848,-8.8583,0.66877,0.62649,-0.40032,143.2

> ui mousemode right "translate selected models"

> view matrix models
> #21,-0.43466,0.76631,0.47312,107.87,0.60317,-0.14241,0.7848,108.09,0.66877,0.62649,-0.40032,108.93

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002814, steps = 108  
shifted from previous position = 1.64  
rotated from previous position = 1.86 degrees  
atoms outside contour = 31676, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.45896338 0.75221199 0.47278931 107.96586590  
0.58657509 -0.14313242 0.79714664 109.43288623  
0.66729474 0.64318756 -0.37553628 109.85660738  
Axis -0.51615513 -0.65208867 -0.55530554  
Axis point 10.36161519 0.00000000 8.95857729  
Rotation angle (degrees) 171.42288980  
Shift along axis -188.09106407  
  

> view matrix models
> #21,-0.45896,0.75221,0.47279,78.526,0.58658,-0.14313,0.79715,111.73,0.66729,0.64319,-0.37554,111.01

> view matrix models
> #21,-0.45896,0.75221,0.47279,14.951,0.58658,-0.14313,0.79715,15.77,0.66729,0.64319,-0.37554,78.803

> view matrix models
> #21,-0.45896,0.75221,0.47279,10.354,0.58658,-0.14313,0.79715,33.175,0.66729,0.64319,-0.37554,56.581

> view matrix models
> #21,-0.45896,0.75221,0.47279,4.7671,0.58658,-0.14313,0.79715,43.156,0.66729,0.64319,-0.37554,40.501

> ui mousemode right "rotate selected models"

> view matrix models
> #21,-0.71227,0.60556,0.35492,4.7671,0.49752,0.078879,0.86386,43.156,0.49512,0.79188,-0.35746,40.501

> ui mousemode right "translate selected models"

> view matrix models
> #21,-0.71227,0.60556,0.35492,2.9849,0.49752,0.078879,0.86386,39.264,0.49512,0.79188,-0.35746,42.292

> select subtract #21

24 models selected  

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> view matrix models
> #21,-0.71227,0.60556,0.35492,110.01,0.49752,0.078879,0.86386,102.19,0.49512,0.79188,-0.35746,101.8

> view matrix models
> #21,-0.71227,0.60556,0.35492,48.907,0.49752,0.078879,0.86386,94.43,0.49512,0.79188,-0.35746,40.276

> view matrix models
> #21,-0.71227,0.60556,0.35492,2.7755,0.49752,0.078879,0.86386,42.4,0.49512,0.79188,-0.35746,38.989

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 27 models selected  

> select subtract #21

26 models selected  

> view matrix models #20,1,0,0,1.04,0,1,0,0.74707,0,0,1,0.44562

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.99962,0.020136,0.019072,-3.1994,-0.020128,0.9998,-0.0006111,3.0339,-0.01908,0.00022699,0.99982,2.5243

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 25 models selected  

> view matrix models
> #21,-0.84437,0.46413,0.26764,2.7755,0.37733,0.16053,0.91206,42.4,0.38035,0.8711,-0.31067,38.989

> view matrix models
> #21,-0.75729,0.56066,0.33493,2.7755,0.47231,0.11599,0.87377,42.4,0.45104,0.81988,-0.35265,38.989

> ui mousemode right "translate selected models"

> view matrix models
> #21,-0.75729,0.56066,0.33493,113.98,0.47231,0.11599,0.87377,103.4,0.45104,0.81988,-0.35265,105.1

> view matrix models
> #21,-0.75729,0.56066,0.33493,3.9702,0.47231,0.11599,0.87377,42.77,0.45104,0.81988,-0.35265,51.864

> view matrix models
> #21,-0.75729,0.56066,0.33493,111.45,0.47231,0.11599,0.87377,110.37,0.45104,0.81988,-0.35265,109.86

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002824, steps = 88  
shifted from previous position = 1.46  
rotated from previous position = 1.22 degrees  
atoms outside contour = 31640, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.76885481 0.54125205 0.34045337 109.29492624  
0.47541518 0.12782559 0.87042577 108.79126538  
0.42760108 0.83108774 -0.35559876 109.00487002  
Axis -0.33886043 -0.75069625 -0.56712322  
Axis point 29.96537439 0.00000000 14.33955266  
Rotation angle (degrees) 176.67241971  
Shift along axis -180.52411369  
  

> view matrix models
> #21,-0.75083,0.55947,0.35107,110.48,0.49053,0.1164,0.86361,110.1,0.4423,0.82064,-0.36183,111.33

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002751, steps = 64  
shifted from previous position = 1.15  
rotated from previous position = 1.23 degrees  
atoms outside contour = 31650, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.76172721 0.55463689 0.33488740 109.16277582  
0.48183446 0.13939591 0.86510365 109.39364903  
0.43313646 0.82033328 -0.37342483 109.77058240  
Axis -0.34380348 -0.75448058 -0.55906907  
Axis point 29.47697952 0.00000000 15.36545135  
Rotation angle (degrees) 176.26680784  
Shift along axis -181.43526320  
  

> volume #20 step 1

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002751, steps = 60  
shifted from previous position = 0.00214  
rotated from previous position = 0.00553 degrees  
atoms outside contour = 30555, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.76176691 0.55459024 0.33487434 109.16102246  
0.48183816 0.13947668 0.86508857 109.39427964  
0.43306252 0.82035109 -0.37347146 109.76952585  
Axis -0.34377637 -0.75450776 -0.55904905  
Axis point 29.47885695 0.00000000 15.36699068  
Rotation angle (degrees) 176.26925931  
Shift along axis -181.43236254  
  

> view matrix models
> #21,-0.74351,0.57283,0.34504,110.45,0.49681,0.12778,0.8584,109.96,0.44763,0.80965,-0.3796,109.98

> ui mousemode right "rotate selected models"

> view matrix models
> #21,-0.53974,-0.75311,-0.37618,110.45,0.39779,0.16566,-0.9024,109.96,0.74192,-0.6367,0.21017,109.98

> view matrix models
> #21,-0.46284,-0.79736,-0.3873,110.45,0.54942,0.084836,-0.83123,109.96,0.69564,-0.59752,0.39882,109.98

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002824, steps = 100  
shifted from previous position = 1.05  
rotated from previous position = 2.07 degrees  
atoms outside contour = 30557, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.49129722 -0.76966822 -0.40772279 109.31805237  
0.55827477 0.08103918 -0.82568876 109.82370812  
0.66854791 -0.63327994 0.38987203 110.39718362  
Axis 0.11185780 -0.62569518 0.77200608  
Axis point -0.47949853 138.78502451 0.00000000  
Rotation angle (degrees) 120.67668672  
Shift along axis 28.73920863  
  

> view matrix models
> #21,-0.53422,-0.78332,-0.31783,110.39,0.49792,0.012258,-0.86714,110.57,0.68314,-0.6215,0.38348,110.84

> ui mousemode right "translate selected models"

> view matrix models
> #21,-0.53422,-0.78332,-0.31783,99.679,0.49792,0.012258,-0.86714,81.431,0.68314,-0.6215,0.38348,9.9472

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 27 models selected  

> select subtract #21

26 models selected  

> view matrix models
> #20,0.99962,0.020136,0.019072,-10.811,-0.020128,0.9998,-0.0006111,12.745,-0.01908,0.00022699,0.99982,21.083

> ui mousemode right "rotate selected models"

> view matrix models
> #20,-0.25641,-0.43552,0.86289,83.959,0.54653,-0.80165,-0.2422,173.97,0.79722,0.40949,0.44358,-52.007

> view matrix models
> #20,-0.41887,0.064112,0.90578,42.457,0.13166,-0.98268,0.13044,198.35,0.89845,0.17389,0.40317,-32.921

> view matrix models
> #20,-0.54259,0.45669,0.705,35.022,-0.82731,-0.43587,-0.35437,296.3,0.14545,-0.77553,0.61432,129.93

> volume #20 step 4

> view matrix models
> #20,-0.67553,0.63281,0.37843,65.969,-0.60628,-0.18464,-0.77352,290.5,-0.41962,-0.75197,0.50839,200.63

> view matrix models
> #20,0.62855,0.69633,0.34649,-79.885,0.089348,0.37789,-0.92153,169.27,-0.77262,0.61018,0.17531,126.8

> volume #20 step 2

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 25 models selected  

> view matrix models
> #21,-0.59473,-0.71479,-0.36792,99.679,0.37878,0.15452,-0.9125,81.431,0.7091,-0.68205,0.17885,9.9472

> ui mousemode right "translate selected models"

> view matrix models
> #21,-0.59473,-0.71479,-0.36792,103.8,0.37878,0.15452,-0.9125,118.72,0.7091,-0.68205,0.17885,126.15

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002925, steps = 120  
shifted from previous position = 2.48  
rotated from previous position = 4.46 degrees  
atoms outside contour = 31559, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.87883112 0.12549294 -0.46033399 109.26802828  
0.10969477 -0.88580701 -0.45090242 109.43374215  
-0.46435215 -0.44676331 0.76470885 109.47400692  
Axis 0.24610534 0.23891380 -0.93933613  
Axis point 69.24661868 68.36687531 -0.00000000  
Rotation angle (degrees) 179.51818145  
Shift along axis -49.79621406  
  

> ui mousemode right "translate selected atoms"

[Repeated 1 time(s)]

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002917, steps = 100  
shifted from previous position = 2.81  
rotated from previous position = 1.39 degrees  
atoms outside contour = 31521, contour level = 0.011903  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.88655869 0.10544248 -0.45043931 111.19880591  
0.12313225 -0.88477126 -0.44946442 107.38964790  
-0.44592839 -0.45394020 0.77141828 109.62419876  
Axis -0.23811724 -0.23998662 0.94111987  
Axis point 69.16905517 67.97986227 -0.00000000  
Rotation angle (degrees) 179.46151171  
Shift along axis 50.91908002  
  

> save "/Users/mansoore.esmaili/Downloads/Apoferritin human copy/apo-map
> overlapped.cxs"

No map chosen to save  

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 27 models selected  

> save "/Users/mansoore.esmaili/Downloads/Apoferritin human
> copy/overlapped.pdb"

Chain IDs longer than 2 characters; truncating  

Average map value = 0.001131 for 37720 atoms, 34404 outside contour  
Opened 2iu2-assembly1.cif map 5 as #22, grid size 92,92,92, pixel 1.67, shown
at level 0.138, step 1, values float32  
Correlation = 0.1224, Correlation about mean = 0.004391, Overlap = 60.87  
  
Opened 2iu2-assembly1.cif map 5 as #22, grid size 92,92,92, pixel 1.67, shown
at level 0.138, step 1, values float32  

> fitmap #21 inMap #20 resolution 5

Fit map 2iu2-assembly1.cif map 5 in map emd_20026.map using 138432 points  
correlation = 0.0264, correlation about mean = 0.005959, overlap = 13.4  
steps = 128, shift = 3.31, angle = 1.79 degrees  
  
Position of 2iu2-assembly1.cif map 5 (#22) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.88008316 0.08925007 -0.46635615 111.53456905  
0.15198846 -0.87754559 -0.45476723 109.53279968  
-0.44983679 -0.47111373 0.75874812 106.66497628  
Axis -0.24432618 -0.24690975 0.93773146  
Axis point 68.58522708 69.90378682 0.00000000  
Rotation angle (degrees) 178.08297173  
Shift along axis 45.72757198  
  
Average map value = 0.0003282 for 37720 atoms, 36034 outside contour  

> fitmap #21 inMap #20 resolution 5

Fit map 2iu2-assembly1.cif map 5 in map emd_20026.map using 138432 points  
correlation = 0.0264, correlation about mean = 0.005932, overlap = 13.4  
steps = 80, shift = 0.00741, angle = 0.00369 degrees  
  
Position of 2iu2-assembly1.cif map 5 (#22) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.88008065 0.08921608 -0.46636739 111.53475145  
0.15199554 -0.87757389 -0.45471025 109.53804918  
-0.44983931 -0.47106746 0.75877536 106.66890476  
Axis -0.24432805 -0.24688040 0.93773870  
Axis point 68.58509142 69.90586675 0.00000000  
Rotation angle (degrees) 178.08173107  
Shift along axis 45.73369405  
  
Average map value = 0.000329 for 37720 atoms, 36032 outside contour  

> fitmap #21 inMap #20 resolution 5

Fit map 2iu2-assembly1.cif map 5 in map emd_20026.map using 138432 points  
correlation = 0.02639, correlation about mean = 0.00601, overlap = 13.39  
steps = 80, shift = 0.0132, angle = 0.0202 degrees  
  
Position of 2iu2-assembly1.cif map 5 (#22) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.88009045 0.08943943 -0.46630611 111.53913948  
0.15191711 -0.87742816 -0.45501758 109.53022351  
-0.44984662 -0.47129651 0.75862877 106.66565927  
Axis -0.24432315 -0.24703304 0.93769978  
Axis point 68.59231590 69.90560120 0.00000000  
Rotation angle (degrees) 178.09087610  
Shift along axis 45.71118764  
  
Average map value = 0.0003261 for 37720 atoms, 36035 outside contour  

> fitmap #21 inMap #20 resolution 5

Fit map 2iu2-assembly1.cif map 5 in map emd_20026.map using 138432 points  
correlation = 0.02639, correlation about mean = 0.006022, overlap = 13.39  
steps = 136, shift = 0.00837, angle = 0.0138 degrees  
  
Position of 2iu2-assembly1.cif map 5 (#22) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.88010413 0.08931564 -0.46630400 111.53926546  
0.15191761 -0.87753443 -0.45481245 109.52357245  
-0.44981968 -0.47112211 0.75875306 106.67087757  
Axis -0.24430705 -0.24692338 0.93773286  
Axis point 68.58964357 69.89836987 -0.00000000  
Rotation angle (degrees) 178.08714414  
Shift along axis 45.73502684  
  
Average map value = 0.0003277 for 37720 atoms, 36039 outside contour  

> fitmap #21 inMap #20 resolution 5

Fit map 2iu2-assembly1.cif map 5 in map emd_20026.map using 138432 points  
correlation = 0.0264, correlation about mean = 0.005949, overlap = 13.4  
steps = 80, shift = 0.0147, angle = 0.00862 degrees  
  
Position of 2iu2-assembly1.cif map 5 (#22) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.88005117 0.08924631 -0.46641722 111.54105321  
0.15200249 -0.87756722 -0.45472080 109.53993015  
-0.44989462 -0.47107416 0.75873840 106.66692078  
Axis -0.24435861 -0.24688754 0.93772886  
Axis point 68.59024535 69.90676522 0.00000000  
Rotation angle (degrees) 178.08242243  
Shift along axis 45.72458905  
  
Average map value = 0.0003288 for 37720 atoms, 36031 outside contour  
Opened 2iu2-assembly1.cif map 5 as #22, grid size 92,92,92, pixel 1.67, shown
at level 0.138, step 1, values float32  

> fitmap #21 inMap #20 resolution 5 metric correlation

Fit map 2iu2-assembly1.cif map 5 in map emd_20026.map using 138432 points  
correlation = 0.009695, correlation about mean = 0.001835, overlap = 4.276  
steps = 92, shift = 0.635, angle = 1.08 degrees  
  
Position of 2iu2-assembly1.cif map 5 (#22) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.88485242 0.08706934 -0.45766267 111.31099460  
0.15648702 -0.86975081 -0.46802279 108.77993289  
-0.43880291 -0.48574937 0.75597589 107.01246268  
Axis -0.23927029 -0.25456565 0.93698776  
Axis point 68.12777558 70.13602626 0.00000000  
Rotation angle (degrees) 177.87710657  
Shift along axis 45.94431963  
  
Average map value = 2.064e-05 for 37720 atoms, 36615 outside contour  

> volume #20 step 1

> fitmap #20 #21 search 100 radius 5

Missing required "in_map" argument  

> fitmap #20 #21 search 100 radius 5

Missing required "in_map" argument  

> fitin_map #20 #21 search 100 radius 5

Unknown command: fitin_map #20 #21 search 100 radius 5  

> fit_in_map #20 #21 search 100 radius 5

Unknown command: fit_in_map #20 #21 search 100 radius 5  

> fit_inmap #20 #21 search 100 radius 5

Unknown command: fit_inmap #20 #21 search 100 radius 5  

> fit_map #20 #21 search 100 radius 5

Unknown command: fit_map #20 #21 search 100 radius 5  

> fit_map #20 #21 search100 radius 5

Unknown command: fit_map #20 #21 search100 radius 5  

> fitmap #20 #21 search100 radius 5

Expected a keyword  

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> fitmap #20#21 search 100 radius 5

Missing required "in_map" argument  

> fitmap #20 inMap map #21 search 100 radius 5

Invalid "inMap" argument: invalid density map specifier  
Must specify one map, got 0  

> fitmap #21 inMap #20 search 100 radius 5

Found 0 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (0 of 100).  
  
Found 0 fits.  

Populating font family aliases took 60 ms. Replace uses of missing font family
"Courier" with one that exists to avoid this cost.  

> fitmap #21 inMap #20 search 100 radius 5

Found 0 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (0 of 100).  
  
Found 0 fits.  

> show #!22 models

> volume sel hide

> show #!20 models

> hide #!22 models

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 25 models selected  

> select add #22

37720 atoms, 34680 bonds, 7864 residues, 27 models selected  

> show #!22 models

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 29 models selected  

> close #20

> close #21

> close #22

> open "/Users/mansoore.esmaili/Documents/Apoferritin human/emd_20026.map"

Opened emd_20026.map as #20, grid size 336,336,336, pixel 0.65, shown at level
0.0202, step 2, values float32  

> open /Users/mansoore.esmaili/Downloads/2iu2-assembly1.cif

Summary of feedback from opening
/Users/mansoore.esmaili/Downloads/2iu2-assembly1.cif  
---  
warnings | Unable to fetch template for 'GOL': will connect using distance criteria  
Unable to fetch template for 'ZN': will connect using distance criteria  
notes | Combining 4 symmetry atoms into HOH /A-15:2150 O  
Combining 4 symmetry atoms into ZN /A-15:214 ZN  
Combining 2 symmetry atoms into HOH /A-15:2036 O  
Combining 2 symmetry atoms into HOH /A-22:2036 O  
Combining 2 symmetry atoms into HOH /A-12:2036 O  
Combining 2 symmetry atoms into HOH /A-18:2036 O  
Combining 3 symmetry atoms into HOH /A-19:2152 O  
Combining 3 symmetry atoms into HOH /A-10:2152 O  
Combining 3 symmetry atoms into HOH /A-21:2152 O  
Combining 3 symmetry atoms into HOH /A-14:2152 O  
Combining 3 symmetry atoms into ZN /A-19:211 ZN  
3 messages similar to the above omitted  
Combining 4 symmetry atoms into HOH /A-2:2150 O  
Combining 4 symmetry atoms into ZN /A-2:214 ZN  
Combining 2 symmetry atoms into HOH /A-9:2036 O  
Combining 2 symmetry atoms into HOH /A-3:2036 O  
Combining 4 symmetry atoms into HOH /A-8:2150 O  
Combining 4 symmetry atoms into ZN /A-8:214 ZN  
Combining 4 symmetry atoms into ZN /A-3:214 ZN  
Combining 4 symmetry atoms into HOH /A-3:2150 O  
Combining 2 symmetry atoms into HOH /A-16:2036 O  
Combining 2 symmetry atoms into HOH /A-7:2036 O  
Combining 4 symmetry atoms into ZN /A-7:214 ZN  
Combining 4 symmetry atoms into HOH /A-7:2150 O  
Combining 3 symmetry atoms into ZN /A-6:211 ZN  
Combining 3 symmetry atoms into ZN /A:211 ZN  
Combining 3 symmetry atoms into ZN /A-11:211 ZN  
Combining 3 symmetry atoms into ZN /A-4:211 ZN  
Combining 3 symmetry atoms into HOH /A-6:2152 O  
3 messages similar to the above omitted  
Combining 2 symmetry atoms into HOH /A-2:2036 O  
Combining 2 symmetry atoms into HOH /A-8:2036 O  
Combining 2 symmetry atoms into HOH /A:2036 O  
Combining 2 symmetry atoms into HOH /A-5:2036 O  
Combining 4 symmetry atoms into ZN /A:214 ZN  
Combining 4 symmetry atoms into HOH /A:2150 O  
  
2iu2-assembly1.cif title:  
Recombinant human H ferritin, K86Q, E27D and E107D mutant, soaked with Zn ions
[more info...]  
  
Chain information for 2iu2-assembly1.cif #21  
---  
Chain | Description  
A A-10 A-11 A-12 A-13 A-14 A-15 A-16 A-17 A-18 A-19 A-2 A-20 A-21 A-22 A-23 A-24 A-3 A-4 A-5 A-6 A-7 A-8 A-9 | FERRITIN HEAVY CHAIN  
  
Non-standard residues in 2iu2-assembly1.cif #21  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
ZN — zinc ion  
  

> hide #21 surfaces

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> fitmap #21 inMap #20 search 100 radius 5

Found 0 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (0 of 100).  
  
Found 0 fits.  

> ui tool show "Fit to Segments"

Density map not found or not selected  

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  
Density map not found or not selected  

> surface dust #20 size 6.5

Density map not found or not selected  
[Repeated 1 time(s)]

> ui tool show "Fit in Map"

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.0002941, steps = 88  
shifted from previous position = 1.76  
rotated from previous position = 1.58 degrees  
atoms outside contour = 37071, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99985859 -0.00942021 0.01393045 1.39229258  
0.00972095 0.99971767 -0.02168138 -1.01440302  
-0.01372227 0.02181373 0.99966787 -2.06915755  
Axis 0.79109724 0.50295290 0.34814298  
Axis point 0.00000000 92.10997178 -44.99098250  
Rotation angle (degrees) 1.57528080  
Shift along axis -0.12912079  
  

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.003626, steps = 84  
shifted from previous position = 2.75  
rotated from previous position = 1.7 degrees  
atoms outside contour = 34044, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
1.00000000 -0.00008330 -0.00001540 1.62821784  
0.00008334 0.99999650 0.00264579 0.04418290  
0.00001518 -0.00264579 0.99999650 -0.42348437  
Axis -0.99948788 -0.00577727 0.03147373  
Axis point 0.00000000 -140.52139520 -13.30222561  
Rotation angle (degrees) 0.15167055  
Shift along axis -1.64096789  
  

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.003401, steps = 72  
shifted from previous position = 1.31  
rotated from previous position = 1.44 degrees  
atoms outside contour = 34236, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.99968508 0.00108606 0.02507094 -2.36633565  
-0.00118825 0.99999105 0.00406142 0.23843200  
-0.02506631 -0.00408994 0.99967742 1.83627001  
Axis -0.16031328 0.98605222 -0.04472887  
Axis point 73.02375441 0.00000000 91.89892338  
Rotation angle (degrees) 1.45680044  
Shift along axis 0.53232715  
  

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.99969,0.0010861,0.025071,-41.156,-0.0011882,0.99999,0.0040614,-72.51,-0.025066,-0.0040899,0.99968,-16.052

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> view matrix models
> #20,1,0,0,5.7977,0,1,0,10.628,0,0,1,6.7691,#21,0.99969,0.0010861,0.025071,-35.358,-0.0011882,0.99999,0.0040614,-61.882,-0.025066,-0.0040899,0.99968,-9.2826

> ui mousemode right "rotate selected models"

> view matrix models
> #20,-0.51131,0.73107,0.45177,46.93,0.85924,0.42492,0.28486,-55.865,0.016283,0.53383,-0.84544,152.66,#21,-0.52334,0.72866,0.44177,7.7117,0.85133,0.42469,0.30803,-126.61,0.036836,0.5373,-0.84259,126.85

> view matrix models
> #20,-0.27352,-0.89557,-0.35091,221.02,-0.50153,0.44409,-0.74246,168.27,0.82076,-0.027091,-0.57062,91.782,#21,-0.26358,-0.89443,-0.36129,302.84,-0.48329,0.44658,-0.75299,168.63,0.83484,-0.023866,-0.54997,69.126

> select subtract #21

2 models selected  

> view matrix models
> #20,-0.29022,-0.84341,-0.45215,228.2,-0.48762,0.53688,-0.68847,150.72,0.82341,0.020672,-0.56707,85.89

> ui mousemode right "translate selected models"

> view matrix models
> #20,-0.29022,-0.84341,-0.45215,206.3,-0.48762,0.53688,-0.68847,112.59,0.82341,0.020672,-0.56707,26.647

> view matrix models
> #20,-0.29022,-0.84341,-0.45215,206.77,-0.48762,0.53688,-0.68847,113.16,0.82341,0.020672,-0.56707,32.164

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> view matrix models
> #21,-0.26358,-0.89443,-0.36129,337.37,-0.48329,0.44658,-0.75299,232.74,0.83484,-0.023866,-0.54997,95.694

> select subtract #21

Nothing selected  

> select add #20

2 models selected  

> view matrix models
> #20,-0.29022,-0.84341,-0.45215,210.71,-0.48762,0.53688,-0.68847,120.32,0.82341,0.020672,-0.56707,37.81

> view matrix models
> #20,-0.29022,-0.84341,-0.45215,216.14,-0.48762,0.53688,-0.68847,139.85,0.82341,0.020672,-0.56707,34.052

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.40993,-0.65631,-0.63341,139.04,-0.54597,0.37974,-0.7468,169.75,0.73066,0.65197,-0.20266,-64.552

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> select subtract #21

Nothing selected  

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> view matrix models
> #21,-0.37794,0.92528,-0.031916,123.11,-0.92458,-0.37541,0.064886,275.57,0.048056,0.054032,0.99738,0.94676

> select subtract #21

Nothing selected  

> select add #20

2 models selected  

> view matrix models
> #20,0.36814,-0.65289,-0.66198,146.35,-0.56401,0.40921,-0.71725,165.28,0.73917,0.63741,-0.21759,-62.26

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.36814,-0.65289,-0.66198,171.57,-0.56401,0.40921,-0.71725,279.67,0.73917,0.63741,-0.21759,-9.0002

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> select subtract #21

2 models selected  

> view matrix models
> #20,0.36814,-0.65289,-0.66198,267.86,-0.56401,0.40921,-0.71725,211.82,0.73917,0.63741,-0.21759,-10.923

> view matrix models
> #20,0.36814,-0.65289,-0.66198,284.39,-0.56401,0.40921,-0.71725,231.84,0.73917,0.63741,-0.21759,-2.9546

> view matrix models
> #20,0.36814,-0.65289,-0.66198,275.99,-0.56401,0.40921,-0.71725,237.82,0.73917,0.63741,-0.21759,-1.3433

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002816, steps = 128  
shifted from previous position = 2.45  
rotated from previous position = 4.64 degrees  
atoms outside contour = 34553, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.38560624 0.59303698 0.70683447 -73.59498026  
-0.04077410 -0.75437933 0.65517120 118.78531643  
0.92176206 -0.28145864 -0.26671283 66.76249793  
Axis -0.81363496 -0.18670407 -0.55058128  
Axis point 0.00000000 80.92882392 35.13337018  
Rotation angle (degrees) 144.85948958  
Shift along axis 0.94356564  
  

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002816, steps = 40  
shifted from previous position = 0.00184  
rotated from previous position = 0.000392 degrees  
atoms outside contour = 34555, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.38560021 0.59303923 0.70683587 -73.59608985  
-0.04077562 -0.75437849 0.65517208 118.78587250  
0.92176452 -0.28145616 -0.26670696 66.76238266  
Axis -0.81363288 -0.18670483 -0.55058409  
Axis point 0.00000000 80.92935647 35.13367161  
Rotation angle (degrees) 144.85945543  
Shift along axis 0.94399733  
  

> volume #20 step 1

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002816, steps = 60  
shifted from previous position = 0.0099  
rotated from previous position = 0.00907 degrees  
atoms outside contour = 33138, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.38570515 0.59294507 0.70685761 -73.60701560  
-0.04074376 -0.75444578 0.65509656 118.80105979  
0.92172202 -0.28147416 -0.26683481 66.78967885  
Axis -0.81367351 -0.18666981 -0.55053592  
Axis point 0.00000000 80.93921284 35.14890255  
Rotation angle (degrees) 144.86394549  
Shift along axis 0.94539053  
  

> view matrix models
> #20,0.36814,-0.65289,-0.66198,175.65,-0.56401,0.40921,-0.71725,111.97,0.73917,0.63741,-0.21759,54.719

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.16292,-0.56568,-0.80837,204.52,-0.65538,0.55039,-0.51724,84.69,0.73751,0.61406,-0.28107,64.38

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> view matrix models
> #21,-0.22636,0.93421,-0.2757,131.47,-0.8344,-0.33201,-0.43994,317.95,-0.50253,0.13046,0.85466,71.46

> view matrix models
> #21,-0.45054,0.89201,0.036468,125.59,-0.88643,-0.45183,0.10045,275.74,0.10608,0.012932,0.99427,1.245

> view matrix models
> #21,-0.19407,0.93482,-0.2974,130.28,-0.80968,-0.32381,-0.48945,319.92,-0.55385,0.14581,0.81975,79.402

> view matrix models
> #21,-0.76942,0.61705,-0.16507,211.88,-0.63176,-0.77327,0.054185,286.49,-0.094208,0.14597,0.98479,10.422

> view matrix models
> #21,-0.15191,0.90401,0.39961,50.911,-0.91788,-0.279,0.28224,240.82,0.36664,-0.32392,0.87215,21.444

> view matrix models
> #21,0.4397,0.88484,0.154,15.379,-0.74794,0.26581,0.60822,128.8,0.49724,-0.38262,0.77869,23.676

> view matrix models
> #21,0.90454,0.31403,-0.28843,73.384,0.07301,0.55239,0.83038,-16.165,0.42009,-0.77217,0.47673,106.6

> view matrix models
> #21,0.94001,-0.032127,-0.33964,111.36,0.27647,0.65502,0.70322,-35.013,0.19988,-0.75493,0.6246,112.45

> view matrix models
> #21,0.70536,-0.70861,-0.018431,171.84,0.66523,0.65276,0.36246,-39.38,-0.24481,-0.26793,0.93182,76.108

> view matrix models
> #21,0.71127,-0.70253,0.023443,165.87,0.65683,0.67614,0.33378,-37.69,-0.25034,-0.22201,0.94236,70.742

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.71127,-0.70253,0.023443,66.516,0.65683,0.67614,0.33378,-162.21,-0.25034,-0.22201,0.94236,126.45

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.00267, steps = 88  
shifted from previous position = 0.984  
rotated from previous position = 0.879 degrees  
atoms outside contour = 33272, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.50491483 -0.72093671 0.47466965 187.14256037  
-0.18482640 0.62746028 0.75639461 -21.00915134  
-0.84314899 0.29418337 -0.45006214 220.05913659  
Axis -0.30898658 0.88095712 0.35838785  
Axis point 145.80333704 0.00000000 66.35378409  
Rotation angle (degrees) 131.58713926  
Shift along axis 2.53382061  
  

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> view matrix models
> #21,0.70387,-0.71021,0.013273,67.377,0.6653,0.66568,0.33801,-163.41,-0.2489,-0.22909,0.94105,128.1

> view matrix models
> #21,0.70387,-0.71021,0.013273,151.84,0.6653,0.66568,0.33801,-85.424,-0.2489,-0.22909,0.94105,165.57

> view matrix models
> #21,0.70387,-0.71021,0.013273,149.22,0.6653,0.66568,0.33801,-89.75,-0.2489,-0.22909,0.94105,162.86

> view matrix models
> #21,0.70387,-0.71021,0.013273,147.32,0.6653,0.66568,0.33801,-81.287,-0.2489,-0.22909,0.94105,170.3

> select subtract #21

Nothing selected  

> select add #20

2 models selected  

> view matrix models
> #20,0.16292,-0.56568,-0.80837,181.67,-0.65538,0.55039,-0.51724,76.054,0.73751,0.61406,-0.28107,64.343

> ui mousemode right "rotate selected models"

> view matrix models
> #20,-0.13494,-0.23216,0.96327,-15.69,0.51926,0.81141,0.2683,-166.5,-0.8439,0.53639,0.011054,213.61

> view matrix models
> #20,-0.19115,0.55678,0.80837,-78.788,0.77869,0.58741,-0.22046,-117,-0.59759,0.58733,-0.54583,241.97

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.70387,-0.71021,0.013273,42.503,0.6653,0.66568,0.33801,-172.09,-0.2489,-0.22909,0.94105,128.64

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002744, steps = 96  
shifted from previous position = 1.17  
rotated from previous position = 2.15 degrees  
atoms outside contour = 33203, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.52450102 0.78368220 -0.33277754 5.67184666  
0.64100298 -0.10622294 0.76015253 -34.97377029  
0.56036940 -0.61201217 -0.55805667 171.32167483  
Axis -0.83493296 -0.54346087 -0.08681726  
Axis point 0.00000000 34.35229708 96.43124952  
Rotation angle (degrees) 124.74250609  
Shift along axis -0.60241496  
  

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.002744, steps = 44  
shifted from previous position = 0.00971  
rotated from previous position = 0.00798 degrees  
atoms outside contour = 33211, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.52441002 0.78371053 -0.33285424 5.68046739  
0.64102850 -0.10608852 0.76014978 -34.99193545  
0.56042537 -0.61199921 -0.55801467 171.31600553  
Axis -0.83489331 -0.54352201 -0.08681584  
Axis point 0.00000000 34.34443849 96.43390514  
Rotation angle (degrees) 124.73952826  
Shift along axis -0.59664072  
  

> fitmap #21 inMap #20 search 100 radius 5

Found 100 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
0.003825 (1), 0.003141 (1), 0.003076 (1), 0.003007 (1), 0.002904 (1), 0.002901
(1), 0.002874 (1), 0.002872 (1), 0.002862 (1), 0.002856 (1), 0.002854 (1),
0.002843 (1), 0.002842 (1), 0.002841 (1), 0.002839 (1), 0.002836 (1), 0.002834
(1), 0.002826 (1), 0.002824 (1), 0.002817 (1), 0.002815 (1), 0.002815 (1),
0.002804 (1), 0.0028 (1), 0.002799 (1), 0.002799 (1), 0.002792 (1), 0.002787
(1), 0.002785 (1), 0.00278 (1), 0.002775 (1), 0.002773 (1), 0.00277 (1),
0.00277 (1), 0.002766 (1), 0.002765 (1), 0.002762 (1), 0.00276 (1), 0.002757
(1), 0.002756 (1), 0.002755 (1), 0.002755 (1), 0.002754 (1), 0.002754 (1),
0.002743 (1), 0.00274 (1), 0.002738 (1), 0.002732 (1), 0.002731 (1), 0.002729
(1), 0.002727 (1), 0.002726 (1), 0.002724 (1), 0.002717 (1), 0.00271 (1),
0.00271 (1), 0.002705 (1), 0.002704 (1), 0.002703 (1), 0.002702 (1), 0.002698
(1), 0.002696 (1), 0.002695 (1), 0.002694 (1), 0.002694 (1), 0.002693 (1),
0.002687 (1), 0.002686 (1), 0.002681 (1), 0.00268 (1), 0.002679 (1), 0.002677
(1), 0.002674 (1), 0.002672 (1), 0.002666 (1), 0.002664 (1), 0.00266 (1),
0.002654 (1), 0.00265 (1), 0.002648 (1), 0.002645 (1), 0.002643 (1), 0.002631
(1), 0.002625 (1), 0.002623 (1), 0.002617 (1), 0.002611 (1), 0.002603 (1),
0.0026 (1), 0.002596 (1), 0.002587 (1), 0.002582 (1), 0.002572 (1), 0.002569
(1), 0.002565 (1), 0.002554 (1), 0.002535 (1), 0.002533 (1), 0.002488 (1),
0.002447 (1)  
  
Best fit found:  
Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.003825, steps = 76  
shifted from previous position = 1.64  
rotated from previous position = 0.517 degrees  
atoms outside contour = 32261, contour level = 0.020173  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.00000182 -1.00000001 -0.00000203 209.59479165  
-0.99710140 0.00000164 0.07608457 210.24619342  
-0.07608461 0.00000216 -0.99710137 229.07930330  
Axis -0.70684954 0.70685112 0.02692973  
Axis point 214.28040697 0.00000000 106.45298328  
Rotation angle (degrees) 176.91496727  
Shift along axis 6.62982028  
  
Found 100 fits.  

> select subtract #21

2 models selected  

> select subtract #20

Nothing selected  

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> view matrix models
> #21,-0.61667,0.19115,-0.76367,177.76,-0.56893,-0.77869,0.26451,120.76,-0.5441,0.59759,0.58894,114.32

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> color #21 #1d854dff

> color #21 #1d854d59

> color #21 #1d854d7e

> color #21 #1d854d80

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> view matrix models
> #21,-0.61667,0.19115,-0.76367,183.71,-0.56893,-0.77869,0.26451,121.29,-0.5441,0.59759,0.58894,113.8

> fitmap #21 inMap #20 search 100 radius 5

Found 100 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
0.03218 (1), 0.002965 (1), 0.002935 (1), 0.002921 (1), 0.002901 (1), 0.002901
(1), 0.002897 (1), 0.002884 (1), 0.002873 (1), 0.002872 (1), 0.002872 (1),
0.002869 (1), 0.002859 (1), 0.002857 (1), 0.002853 (1), 0.00285 (1), 0.002839
(1), 0.002839 (1), 0.002838 (1), 0.00283 (1), 0.002829 (1), 0.002829 (1),
0.002823 (1), 0.002821 (1), 0.00282 (1), 0.002815 (1), 0.002811 (1), 0.00281
(1), 0.002808 (1), 0.002807 (1), 0.002805 (1), 0.002804 (1), 0.002803 (1),
0.002801 (1), 0.002801 (1), 0.0028 (1), 0.002792 (1), 0.002791 (1), 0.002789
(1), 0.002788 (1), 0.002788 (1), 0.002784 (1), 0.002781 (1), 0.002778 (1),
0.002775 (1), 0.002765 (1), 0.002754 (1), 0.002748 (1), 0.00274 (1), 0.002739
(1), 0.002738 (1), 0.002738 (1), 0.002731 (1), 0.002731 (1), 0.00273 (1),
0.002729 (1), 0.002728 (1), 0.002728 (1), 0.002727 (1), 0.002726 (1), 0.002722
(1), 0.002721 (1), 0.002714 (1), 0.002711 (1), 0.002709 (1), 0.002705 (1),
0.002699 (1), 0.002698 (1), 0.002698 (1), 0.002697 (1), 0.002696 (1), 0.002696
(1), 0.002695 (1), 0.002693 (1), 0.002693 (1), 0.00269 (1), 0.002688 (1),
0.002682 (1), 0.002682 (1), 0.002679 (1), 0.002679 (1), 0.002673 (1), 0.002666
(1), 0.002659 (1), 0.002659 (1), 0.002645 (1), 0.002644 (1), 0.002631 (1),
0.002626 (1), 0.002619 (1), 0.002603 (1), 0.002599 (1), 0.002597 (1), 0.002597
(1), 0.002568 (1), 0.002563 (1), 0.002563 (1), 0.002556 (1), 0.002542 (1),
0.002528 (1)  
  
Best fit found:  
Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 100  
shifted from previous position = 3.05  
rotated from previous position = 4.92 degrees  
atoms outside contour = 10459, contour level = 0.020173  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.00001947 -1.00000007 0.00001105 213.59999218  
1.00000008 0.00001949 0.00006135 -0.68975262  
-0.00006132 0.00001104 1.00000004 -2.63538111  
Axis -0.00002515 0.00003618 1.00000000  
Axis point 107.14479821 106.45721708 0.00000000  
Rotation angle (degrees) 89.99888267  
Shift along axis -2.64077888  
  
Found 100 fits.  

> fitmap #21 inMap #20 search 100 radius 5

Found 100 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
0.03218 (1), 0.002981 (1), 0.002917 (1), 0.002868 (1), 0.002858 (1), 0.002857
(1), 0.002851 (1), 0.002851 (1), 0.00285 (1), 0.002839 (1), 0.002821 (1),
0.002821 (1), 0.002819 (1), 0.002819 (1), 0.00281 (1), 0.002805 (1), 0.002792
(1), 0.002784 (1), 0.00278 (1), 0.002776 (1), 0.002776 (1), 0.002767 (1),
0.002754 (1), 0.002751 (1), 0.00275 (1), 0.002749 (1), 0.002744 (1), 0.002743
(1), 0.002741 (1), 0.00274 (1), 0.00274 (1), 0.002735 (1), 0.002734 (1),
0.002731 (1), 0.002726 (1), 0.002726 (1), 0.002725 (1), 0.002719 (1), 0.002714
(1), 0.002714 (1), 0.002699 (1), 0.002697 (1), 0.002691 (1), 0.00269 (1),
0.002684 (1), 0.002682 (1), 0.002677 (1), 0.002676 (1), 0.002674 (1), 0.002672
(1), 0.002669 (1), 0.002668 (1), 0.002666 (1), 0.002666 (1), 0.002665 (1),
0.002663 (1), 0.002661 (1), 0.002652 (1), 0.002648 (1), 0.002647 (1), 0.002641
(1), 0.002637 (1), 0.002633 (1), 0.002633 (1), 0.002632 (1), 0.002626 (1),
0.002621 (1), 0.00262 (1), 0.00262 (1), 0.002617 (1), 0.002617 (1), 0.002608
(1), 0.002605 (1), 0.002603 (1), 0.002592 (1), 0.002582 (1), 0.002579 (1),
0.002569 (1), 0.002556 (1), 0.002553 (1), 0.002541 (1), 0.002537 (1), 0.002537
(1), 0.002526 (1), 0.002517 (1), 0.002516 (1), 0.002515 (1), 0.002513 (1),
0.002506 (1), 0.0025 (1), 0.00249 (1), 0.002476 (1), 0.002474 (1), 0.002469
(1), 0.002465 (1), 0.002457 (1), 0.002446 (1), 0.002411 (1), 0.002406 (1),
0.002337 (1)  
  
Best fit found:  
Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 96  
shifted from previous position = 2.21  
rotated from previous position = 4.92 degrees  
atoms outside contour = 10449, contour level = 0.020173  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.00002091 -1.00000011 0.00000713 213.60097747  
1.00000011 0.00002088 0.00006631 -0.68351183  
-0.00006628 0.00000714 1.00000005 -2.63219292  
Axis -0.00002958 0.00003671 1.00000000  
Axis point 107.14216444 106.46097636 0.00000000  
Rotation angle (degrees) 89.99880145  
Shift along axis -2.63853734  
  
Found 100 fits.  

> select subtract #21

Nothing selected  

> hide #!20 models

> show #!20 models

> hide #21 models

> show #21 models

> color #20 #cccc9900 models

> color #20 #cccc9971 models

> color #20 #cccc9970 models

> color #21 #33684780

> color #21 #2d5c3f80

> color #21 #41865c80

> volume #20 style mesh

> ui mousemode right translate

> cootmode_wire #20

Unknown command: cootmode_wire #20  

> volume #20 color #3351d570

> volume #20 color #6974d570

> chimera-trimmings alias: “cootmode #20”

Unknown command: chimera-trimmings alias: “cootmode #20”  

> chimera-trimmings alias: cootmode #20

Unknown command: chimera-trimmings alias: cootmode #20  

> chimera-trimmings alias:

Unknown command: chimera-trimmings alias:  

> cp ./misc/coot_trimmings.py ~/.coot-preferences/

Unknown command: cp ./misc/coot_trimmings.py ~/.coot-preferences/  

> cp ./misc/coot_trimmings.py ~/.coot-preferences

Unknown command: cp ./misc/coot_trimmings.py ~/.coot-preferences  

> fitmap #21 inMap #20

Fit molecule 2iu2-assembly1.cif (#21) to map emd_20026.map (#20) using 37720
atoms  
average map value = 0.03218, steps = 24  
shifted from previous position = 0.0015  
rotated from previous position = 0.000947 degrees  
atoms outside contour = 10453, contour level = 0.020173  
  
Position of 2iu2-assembly1.cif (#21) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
0.00000536 -1.00000011 0.00000514 213.60348546  
1.00000011 0.00000533 0.00007157 -0.68384386  
-0.00007154 0.00000515 1.00000005 -2.63119672  
Axis -0.00003321 0.00003834 1.00000000  
Axis point 107.14357222 106.46040131 0.00000000  
Rotation angle (degrees) 89.99969221  
Shift along axis -2.63831731  
  

> hide #!20 models

> style #21 stick

Changed 37720 atom styles  

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> style sel stick

Changed 37720 atom styles  

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> nucleotides sel tube/slab shape box

> show sel atoms

> nucleotides sel tube/slab shape box

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> hide sel atoms

> style sel stick

Changed 37720 atom styles  

> show sel atoms

> show #!20 models

> select subtract #21

Nothing selected  

> style #21 ball

Changed 37720 atom styles  

> hide #21 atoms

> show #21 atoms

> style #21 stick

Changed 37720 atom styles  

> style #21 sphere

Changed 37720 atom styles  

> style #21 stick

Changed 37720 atom styles  

> show #21 atoms

> hide #21 atoms

> show #21 atoms

> hide #21 atoms

> show #21 atoms

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

53466 atoms, 54410 bonds, 5554 residues, 7 models selected  

> color (#21 & sel) byhetero

> select add #21

57322 atoms, 54530 bonds, 9290 residues, 7 models selected  

> select subtract #21

19602 atoms, 19850 bonds, 1426 residues, 6 models selected  

> select subtract #19

16107 atoms, 16313 bonds, 1193 residues, 5 models selected  

> select subtract #18

13978 atoms, 14169 bonds, 1059 residues, 4 models selected  

> select subtract #17

10483 atoms, 10632 bonds, 826 residues, 3 models selected  

> select subtract #16

8354 atoms, 8488 bonds, 692 residues, 2 models selected  

> select subtract #14

5540 atoms, 5607 bonds, 346 residues, 1 model selected  

> select subtract #13

Nothing selected  

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> select subtract #21

Nothing selected  

> select add #20

2 models selected  

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> save /Users/mansoore.esmaili/Downloads/olivmapwire.pdb

Chain IDs longer than 2 characters; truncating  

> save "/Users/mansoore.esmaili/Documents/full sessionNov262024.cxs"

> save /Users/mansoore.esmaili/Documents/editedsession-nove262024.cxs

> hide #!20 models

> hide #21 models

> show #19 models

> hide #19 models

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> select subtract #21

Nothing selected  

> select add #20

2 models selected  

> show #!20 models

> show #21 models

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> show #19 models

> select subtract #20

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> select subtract #21

Nothing selected  

> hide #!20 models

> hide #21 models

> select add #19

3495 atoms, 3537 bonds, 233 residues, 1 model selected  

> select add #18

5624 atoms, 5681 bonds, 367 residues, 2 models selected  

> select add #17

9119 atoms, 9218 bonds, 600 residues, 3 models selected  

> select add #16

11248 atoms, 11362 bonds, 734 residues, 4 models selected  

> select add #15

11248 atoms, 11362 bonds, 734 residues, 6 models selected  

> select add #14

14062 atoms, 14243 bonds, 1080 residues, 7 models selected  

> select add #13

19602 atoms, 19850 bonds, 1426 residues, 8 models selected  

> close #19

> show #18 models

> select subtract #17

12612 atoms, 12776 bonds, 960 residues, 6 models selected  

> select subtract #16

10483 atoms, 10632 bonds, 826 residues, 5 models selected  

> select subtract #15

10483 atoms, 10632 bonds, 826 residues, 3 models selected  

> select subtract #14

7669 atoms, 7751 bonds, 480 residues, 2 models selected  

> select subtract #13

2129 atoms, 2144 bonds, 134 residues, 1 model selected  

> close #17

> select subtract #18

Nothing selected  

> hide #18 models

> close #18

> close #13-14,16#7-12,15

> close #1-6#1.1-3

> show #!20 models

> show #21 models

> save /Users/mansoore.esmaili/Documents/editedsession-nove262024.cxs

> save /Users/mansoore.esmaili/Documents/final-twomolecules.pdb

Chain IDs longer than 2 characters; truncating  

> save /Users/mansoore.esmaili/Downloads/fittedmoldeandstructuretwoonly.pdb

Chain IDs longer than 2 characters; truncating  

> save
> /Users/mansoore.esmaili/Downloads/CIFfileofmapandcrystalstructureapoferritin.cif
> relModel #21

> cootmode wire #21

Unknown command: cootmode wire #21  

> cootmode_wire #21

Unknown command: cootmode_wire #21  

> select add #20

2 models selected  

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> save /Users/mansoore.esmaili/Downloads/PDFforcoot.cif relModel #21

> save /Users/mansoore.esmaili/Downloads/FORCOOT.pdb

Chain IDs longer than 2 characters; truncating  

> save /Users/mansoore.esmaili/Downloads/PDBforcoot1.pdb

Chain IDs longer than 2 characters; truncating  

> hide #!20 models

> select subtract #21

2 models selected  

> show #!20 models

> select subtract #20

Nothing selected  

> select add #20

2 models selected  

> select add #21

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

Cell requested for row 0 is out of bounds for table with 3 rows! Resizing
table model.  

> ui tool show "Build Structure"

> build start atom forcoot

> hide #!20 models

> hide #21 models

> show #!20 models

> show #21 models

> hide #!20 models

> hide #21 models

> show #!20 models

> show #21 models

> save /Users/mansoore.esmaili/foorcoot.pdb

Chain IDs longer than 2 characters; truncating  

> combine #20 #21

> hide #!20 models

> hide #21 models

> hide #1 models

> hide #2 models

> show #2 models

> select subtract #1

Nothing selected  

> show #1 models

> hide #2 models

> show #2 models

> show #!20 models

> hide #!20 models

> show #21 models

> hide #21 models

> show #21 models

> combine #21 #20

> hide #1 models

> hide #2 models

> hide #3 models

> close #21

> close #2

> show #3 models

> show #!20 models

> select add #3

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> select add #20

37720 atoms, 34680 bonds, 7864 residues, 3 models selected  

> combine #3 #20

> hide #3 models

> hide #!20 models

> hide #2 models

> select subtract #3

2 models selected  

> select subtract #20

Nothing selected  

> select add #2

37720 atoms, 34680 bonds, 7864 residues, 1 model selected  

> show #2 models

> select subtract #2

Nothing selected  

> ui tool show "Fit in Map"

> fitmap #3 inMap #20

Fit molecule copy of 2iu2-assembly1.cif (#3) to map emd_20026.map (#20) using
37720 atoms  
average map value = 0.03218, steps = 24  
shifted from previous position = 0.000934  
rotated from previous position = 0.000831 degrees  
atoms outside contour = 10449, contour level = 0.020173  
  
Position of copy of 2iu2-assembly1.cif (#3) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.00000802 -1.00000011 -0.00000037 213.60477085  
1.00000011 -0.00000805 0.00007070 -0.68278101  
-0.00007066 -0.00000036 1.00000005 -2.63092748  
Axis -0.00003553 0.00003515 1.00000000  
Axis point 107.14368009 106.46013890 0.00000000  
Rotation angle (degrees) 90.00045896  
Shift along axis -2.63854037  
  

> fitmap #3 inMap #20 search 100 radius 5

Found 100 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
0.003625 (1), 0.003062 (1), 0.003002 (1), 0.002994 (1), 0.00298 (1), 0.002934
(1), 0.002918 (1), 0.002904 (1), 0.002904 (1), 0.002897 (1), 0.002897 (1),
0.002892 (1), 0.002884 (1), 0.002877 (1), 0.002876 (1), 0.002869 (1), 0.002859
(1), 0.002859 (1), 0.002857 (1), 0.002855 (1), 0.002849 (1), 0.002849 (1),
0.00284 (1), 0.002839 (1), 0.002836 (1), 0.00283 (1), 0.002826 (1), 0.002822
(1), 0.002822 (1), 0.002822 (1), 0.00282 (1), 0.002818 (1), 0.002817 (1),
0.002817 (1), 0.002815 (1), 0.002812 (1), 0.00281 (1), 0.002809 (1), 0.002807
(1), 0.002804 (1), 0.002802 (1), 0.002799 (1), 0.002797 (1), 0.002794 (1),
0.002784 (1), 0.002784 (1), 0.00278 (1), 0.00278 (1), 0.002778 (1), 0.002777
(1), 0.002775 (1), 0.002774 (1), 0.002772 (1), 0.002771 (1), 0.002769 (1),
0.002767 (1), 0.002758 (1), 0.002757 (1), 0.002757 (1), 0.00275 (1), 0.002747
(1), 0.002747 (1), 0.002746 (1), 0.002744 (1), 0.002732 (1), 0.002731 (1),
0.002725 (1), 0.002721 (1), 0.00272 (1), 0.00272 (1), 0.002714 (1), 0.002711
(1), 0.002708 (1), 0.002706 (1), 0.002705 (1), 0.002701 (1), 0.002699 (1),
0.002699 (1), 0.00269 (1), 0.002687 (1), 0.002686 (1), 0.002676 (1), 0.002675
(1), 0.00267 (1), 0.002667 (1), 0.002666 (1), 0.002662 (1), 0.002661 (1),
0.002661 (1), 0.002656 (1), 0.002649 (1), 0.002638 (1), 0.002638 (1), 0.002637
(1), 0.002631 (1), 0.002628 (1), 0.002628 (1), 0.002592 (1), 0.002577 (1),
0.002544 (1)  
  
Best fit found:  
Fit molecule copy of 2iu2-assembly1.cif (#3) to map emd_20026.map (#20) using
37720 atoms  
average map value = 0.003625, steps = 76  
shifted from previous position = 2.32  
rotated from previous position = 1.18 degrees  
atoms outside contour = 32469, contour level = 0.020173  
Position of copy of 2iu2-assembly1.cif (#3) relative to emd_20026.map (#20)
coordinates:  
Matrix rotation and translation  
-0.00009315 -1.00000013 0.00001192 218.18185034  
-0.99999665 0.00009314 -0.00264340 219.35993481  
0.00264336 -0.00001217 -0.99999657 220.75407089  
Axis 0.70707708 -0.70713586 0.00093744  
Axis point 218.61656243 0.00000000 110.66625558  
Rotation angle (degrees) 179.89339340  
Shift along axis -0.63894528  
  
Found 100 fits.  

> show #!20 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitlist.py", line 243, in save_fits_cb  
save_fits(self.session, lfits)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 322, in save_fits  
dpath, fname = os.path.split(m.filename)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen posixpath>", line 103, in split  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
File "", line 103, in split  
  
See log for complete Python traceback.  
  

> close #2

> close #1

> show #3 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitlist.py", line 243, in save_fits_cb  
save_fits(self.session, lfits)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 322, in save_fits  
dpath, fname = os.path.split(m.filename)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen posixpath>", line 103, in split  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
File "", line 103, in split  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitlist.py", line 243, in save_fits_cb  
save_fits(self.session, lfits)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 322, in save_fits  
dpath, fname = os.path.split(m.filename)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen posixpath>", line 103, in split  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
File "", line 103, in split  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,10
      Model Number: MNW83LL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.1 (23H222)
      Kernel Version: Darwin 23.6.0
      Time since boot: 14 days, 5 hours, 28 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 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: 2.4.1
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.3.4
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9.dev202410250340
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.2.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.0
    coverage: 7.6.4
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.7
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    pluggy: 1.5.0
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    pytest: 8.3.3
    pytest-cov: 5.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13