Destroying status bar: wrapped C/C++ object of type QScreen has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/uijin/Desktop/mask making_2.cxs"

Opened cryosparc_P1_J299_005_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.18, shown at level 0.266, step 1, values float32  
Opened 7cak map 5 as #3, grid size 100,105,126, pixel 1.67, shown at level
0.0991, step 1, values float32  
Log from Fri Nov 12 14:36:53 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/uijin/Desktop/mask making.cxs"

Opened cryosparc_P1_J299_005_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.18, shown at level 0.266, step 1, values float32  
Opened 7cak map 5 as #3, grid size 100,105,126, pixel 1.67, shown at level
0.0991, step 1, values float32  
Log from Fri Nov 12 14:26:29 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/uijin/Downloads/cryosparc_P1_J299_005_volume_map_sharp.mrc

Opened cryosparc_P1_J299_005_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.18, shown at level 0.335, step 1, values float32  

> open 7cak

7cak title:  
SARS-CoV-2 S trimer with three RBD in the open state and complexed with three
H014 Fab [more info...]  
  
Chain information for 7cak #2  
---  
Chain | Description  
A B C | Spike glycoprotein  
D F H | Light chain of H014 Fab  
E G I | Heavy chain of H014 Fab  
  
Non-standard residues in 7cak #2  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> show atoms

> hide cartoons

> hide cartoons

> show cartoons

> hide atoms

> select /D/F/H/E/G/I

5328 atoms, 5466 bonds, 687 residues, 1 model selected  

> delete sel

> ui mousemode right "translate selected atoms"

> select #2

24935 atoms, 25583 bonds, 21 pseudobonds, 3144 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.52921,-0.84839,0.013412,262.55,0.81607,0.51325,0.2657,-107.74,-0.2323,-0.12967,0.96396,78.268

> view matrix models
> #2,-0.39973,-0.91242,0.087801,452.28,0.90026,-0.37276,0.22491,58.043,-0.17248,0.16894,0.97042,5.6285

> view matrix models
> #2,0.022121,-0.99394,0.10764,380.19,0.85562,0.074514,0.51221,-64.99,-0.51713,0.080771,0.85209,110.64

> view matrix models
> #2,0.78664,-0.61384,0.066318,155.75,0.58898,0.7783,0.21762,-107.47,-0.1852,-0.13213,0.97378,67.762

> view matrix models
> #2,0.66459,-0.74267,0.08224,203.79,0.71568,0.66431,0.21565,-110.08,-0.21479,-0.08446,0.973,64.358

> view matrix models
> #2,0.98123,-0.19165,-0.021455,45.23,0.19136,0.95382,0.23154,-64.059,-0.023912,-0.2313,0.97259,55.069

> view matrix models
> #2,0.8955,-0.44293,0.04344,103.03,0.42543,0.8806,0.20871,-93.434,-0.1307,-0.16842,0.97701,63.482

> view matrix models
> #2,0.51607,0.75605,0.40256,-112.89,-0.71402,0.63933,-0.28538,259.06,-0.47313,-0.14015,0.86978,143.16

> view matrix models
> #2,0.59568,0.80316,0.0095849,-79.792,-0.80125,0.59334,0.077164,231.82,0.056288,-0.053645,0.99697,-0.24257

> view matrix models
> #2,0.78391,0.61538,0.082383,-91.297,-0.61609,0.78743,-0.019604,170.05,-0.076936,-0.035387,0.99641,23.17

> ui mousemode right "translate selected atoms"

> ui tool show "Fit in Map"

Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 180  
shifted from previous position = 16.7  
rotated from previous position = 20.6 degrees  
atoms outside contour = 10089, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606831 0.85200396 0.08810649 -74.75068471  
-0.84948113 0.52228145 -0.07485917 255.39913005  
-0.10979669 -0.03621235 0.99329419 13.65814057  
Axis 0.02255574 0.11550377 -0.99305091  
Axis point 188.84383223 195.37423925 0.00000000  
Rotation angle (degrees) 58.94758719  
Shift along axis 14.25027508  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 28  
shifted from previous position = 0.0262  
rotated from previous position = 0.0208 degrees  
atoms outside contour = 10106, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51601928 0.85206602 0.08779289 -74.67805469  
-0.84951328 0.52220430 -0.07503235 255.46066207  
-0.10977834 -0.03586309 0.99330889 13.60727049  
Axis 0.02285976 0.11530552 -0.99306700  
Axis point 188.91961992 195.33338287 0.00000000  
Rotation angle (degrees) 58.95131484  
Shift along axis 14.23596917  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.019  
rotated from previous position = 0.0206 degrees  
atoms outside contour = 10097, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51608611 0.85200248 0.08801647 -74.72668129  
-0.84948741 0.52228562 -0.07475874 255.38269304  
-0.10966437 -0.03618693 0.99330974 13.63005246  
Axis 0.02251226 0.11537552 -0.99306681  
Axis point 188.84468506 195.34213292 0.00000000  
Rotation angle (degrees) 58.94633273  
Shift along axis 14.24709114  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.02  
rotated from previous position = 0.0145 degrees  
atoms outside contour = 10094, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51607627 0.85198560 0.08823727 -74.77637984  
-0.84946523 0.52230452 -0.07487860 255.40525893  
-0.10988222 -0.03631142 0.99328112 13.69295102  
Axis 0.02250941 0.11563074 -0.99303719  
Axis point 188.84063188 195.40429367 0.00000000  
Rotation angle (degrees) 58.94698672  
Shift along axis 14.25191694  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.0116  
rotated from previous position = 0.00628 degrees  
atoms outside contour = 10093, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51608072 0.85199389 0.08813121 -74.74927685  
-0.84946676 0.52229823 -0.07490520 255.41086337  
-0.10984955 -0.03620740 0.99328853 13.67157973  
Axis 0.02258568 0.11555000 -0.99304486  
Axis point 188.86000104 195.38176979 0.00000000  
Rotation angle (degrees) 58.94680070  
Shift along axis 14.24797008  
  
Average map value = 0.5515 for 24935 atoms, 10093 outside contour  
Average map value = 0.5515 for 24935 atoms, 10093 outside contour  
Average map value = 0.5515 for 24935 atoms, 10093 outside contour  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.0124  
rotated from previous position = 0.00825 degrees  
atoms outside contour = 10096, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606893 0.85198619 0.08827450 -74.78189408  
-0.84946474 0.52230212 -0.07490088 255.41046154  
-0.10992048 -0.03633206 0.99327613 13.70441494  
Axis 0.02251025 0.11567420 -0.99303211  
Axis point 188.84096226 195.41246493 0.00000000  
Rotation angle (degrees) 58.94747918  
Shift along axis 14.25211899  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 36  
shifted from previous position = 0.00909  
rotated from previous position = 0.012 degrees  
atoms outside contour = 10088, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606242 0.85201144 0.08806864 -74.74340602  
-0.84948515 0.52227212 -0.07487861 255.40862461  
-0.10979323 -0.03617096 0.99329608 13.65543495  
Axis 0.02259114 0.11547912 -0.99305298  
Axis point 188.85444901 195.37177559 0.00000000  
Rotation angle (degrees) 58.94803306  
Shift along axis 14.24525324  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.0102  
rotated from previous position = 0.00928 degrees  
atoms outside contour = 10095, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51603315 0.85204518 0.08791358 -74.70835360  
-0.84951150 0.52222654 -0.07489760 255.42815819  
-0.10972695 -0.03603396 0.99330839 13.62121039  
Axis 0.02268169 0.11534740 -0.99306622  
Axis point 188.87899628 195.34474937 0.00000000  
Rotation angle (degrees) 58.95012433  
Shift along axis 14.24169786  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.00617  
rotated from previous position = 0.00492 degrees  
atoms outside contour = 10102, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51605514 0.85202727 0.08795802 -74.71355020  
-0.84948787 0.52225571 -0.07496219 255.43521787  
-0.10980641 -0.03603465 0.99329958 13.63758239  
Axis 0.02271932 0.11542143 -0.99305676  
Axis point 188.89080418 195.35743190 0.00000000  
Rotation angle (degrees) 58.94870791  
Shift along axis 14.24236381  
  
Opened 7cak map 5 as #3, grid size 100,105,126, pixel 1.67, shown at level
0.0991, step 1, values float32  
Fit map 7cak map 5 in map cryosparc_P1_J299_005_volume_map_sharp.mrc using
91978 points  
correlation = 0.6998, correlation about mean = 0.3331, overlap = 1.537e+04  
steps = 48, shift = 0.159, angle = 0.095 degrees  
  
Position of 7cak map 5 (#3) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.51662135 0.85153183 0.08941987 -75.04810151  
-0.84902517 0.52298726 -0.07510379 255.28904830  
-0.11071872 -0.03711950 0.99315835 13.82839501  
Axis 0.02217783 0.11685458 -0.99290138  
Axis point 188.76682411 195.66401332 0.00000000  
Rotation angle (degrees) 58.91002618  
Shift along axis 14.43705924  
  
Average map value = 0.5507 for 24935 atoms, 10042 outside contour  
Fit map 7cak map 5 in map cryosparc_P1_J299_005_volume_map_sharp.mrc using
91978 points  
correlation = 0.6998, correlation about mean = 0.3331, overlap = 1.537e+04  
steps = 28, shift = 0.0106, angle = 0.0148 degrees  
  
Position of 7cak map 5 (#3) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.51655421 0.85159157 0.08923870 -75.02407710  
-0.84906014 0.52290642 -0.07527123 255.33350186  
-0.11076383 -0.03688735 0.99316197 13.80651262  
Axis 0.02241000 0.11676921 -0.99290621  
Axis point 188.79881493 195.65874557 0.00000000  
Rotation angle (degrees) 58.91485547  
Shift along axis 14.42522996  
  
Average map value = 0.5507 for 24935 atoms, 10045 outside contour  
Average map value = 0.5507 for 24935 atoms, 10045 outside contour  
Correlation = 0.6998, Correlation about mean = 0.3331, Overlap = 1.537e+04  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.3067, steps = 176  
shifted from previous position = 24.6  
rotated from previous position = 3.44 degrees  
atoms outside contour = 16786, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.56511612 0.81875710 0.10139325 -72.18548737  
-0.81658530 0.57262416 -0.07273249 223.92588168  
-0.11761047 -0.04169393 0.99218415 29.39421373  
Axis 0.01880859 0.13271074 -0.99097634  
Axis point 178.57269723 182.99616124 0.00000000  
Rotation angle (degrees) 55.60033238  
Shift along axis -0.76930809  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.3067, steps = 40  
shifted from previous position = 0.0182  
rotated from previous position = 0.0116 degrees  
atoms outside contour = 16778, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.56507247 0.81876793 0.10154893 -72.20803475  
-0.81661688 0.57259407 -0.07261472 223.91929843  
-0.11760092 -0.04189399 0.99217686 29.40405139  
Axis 0.01861536 0.13279483 -0.99096872  
Axis point 178.53851325 183.01332106 0.00000000  
Rotation angle (degrees) 55.60314601  
Shift along axis -0.74734778  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.3067, steps = 44  
shifted from previous position = 0.0184  
rotated from previous position = 0.0121 degrees  
atoms outside contour = 16792, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.56507354 0.81878497 0.10140545 -72.18758166  
-0.81660980 0.57258465 -0.07276845 223.95487709  
-0.11764491 -0.04168916 0.99218027 29.39426695  
Axis 0.01883259 0.13273427 -0.99097273  
Axis point 178.58607579 183.00902932 0.00000000  
Rotation angle (degrees) 55.60331738  
Shift along axis -0.76190853  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.3067, steps = 44  
shifted from previous position = 0.00613  
rotated from previous position = 0.00131 degrees  
atoms outside contour = 16787, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.56508310 0.81878089 0.10138512 -72.18339990  
-0.81660511 0.57259168 -0.07276583 223.94788524  
-0.11763154 -0.04167287 0.99218254 29.39224841  
Axis 0.01884102 0.13271489 -0.99097516  
Axis point 178.58450105 183.00181529 0.00000000  
Rotation angle (degrees) 55.60266258  
Shift along axis -0.76577756  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.3067, steps = 60  
shifted from previous position = 0.0162  
rotated from previous position = 0.00711 degrees  
atoms outside contour = 16780, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.56507856 0.81877589 0.10145077 -72.19182633  
-0.81661527 0.57259050 -0.07266106 223.91973674  
-0.11758287 -0.04178704 0.99218351 29.39514985  
Axis 0.01870832 0.13272491 -0.99097634  
Axis point 178.54977875 182.99600914 0.00000000  
Rotation angle (degrees) 55.60282769  
Shift along axis -0.76075854  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.3067, steps = 48  
shifted from previous position = 0.0237  
rotated from previous position = 0.00957 degrees  
atoms outside contour = 16787, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.56505023 0.81880428 0.10137944 -72.18065380  
-0.81662333 0.57256007 -0.07281005 223.96946573  
-0.11766300 -0.04164748 0.99217988 29.39187192  
Axis 0.01888268 0.13272681 -0.99097277  
Axis point 178.59670971 183.00691958 0.00000000  
Rotation angle (degrees) 55.60499368  
Shift along axis -0.76275700  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.3067, steps = 44  
shifted from previous position = 0.011  
rotated from previous position = 0.00429 degrees  
atoms outside contour = 16789, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.56509350 0.81877317 0.10138954 -72.18414822  
-0.81659896 0.57260204 -0.07275334 223.94186209  
-0.11762434 -0.04168215 0.99218300 29.39418367  
Axis 0.01882800 0.13271437 -0.99097548  
Axis point 178.58170413 183.00067021 0.00000000  
Rotation angle (degrees) 55.60192579  
Shift along axis -0.76769486  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 108  
shifted from previous position = 10.7  
rotated from previous position = 3.49 degrees  
atoms outside contour = 10090, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51604379 0.85202326 0.08806345 -65.77962354  
-0.84949276 0.52225434 -0.07491625 238.45593899  
-0.10982191 -0.03614920 0.99329370 16.59010803  
Axis 0.02262550 0.11549125 -0.99305078  
Axis point 178.74242823 178.98549382 0.00000000  
Rotation angle (degrees) 58.94932989  
Shift along axis 9.57645786  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.0216  
rotated from previous position = 0.0103 degrees  
atoms outside contour = 10102, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51603975 0.85204368 0.08788943 -65.73671120  
-0.84950218 0.52223273 -0.07496014 238.48007887  
-0.10976805 -0.03597985 0.99330581 16.55348512  
Axis 0.02274984 0.11535770 -0.99306346  
Axis point 178.78250323 178.95584618 0.00000000  
Rotation angle (degrees) 58.94978314  
Shift along axis 9.57635279  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 48  
shifted from previous position = 0.0289  
rotated from previous position = 0.0214 degrees  
atoms outside contour = 10092, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51608337 0.85198249 0.08822575 -65.81485914  
-0.84946919 0.52230784 -0.07481050 238.42695654  
-0.10981823 -0.03633660 0.99328727 16.61579164  
Axis 0.02245509 0.11558734 -0.99304347  
Axis point 178.71060369 179.00724067 0.00000000  
Rotation angle (degrees) 58.94643236  
Shift along axis 9.58105675  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 36  
shifted from previous position = 0.00352  
rotated from previous position = 0.00716 degrees  
atoms outside contour = 10091, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51607243 0.85200080 0.08811287 -65.79434592  
-0.84947788 0.52228637 -0.07486179 238.44110822  
-0.10980246 -0.03621583 0.99329343 16.59592673  
Axis 0.02255531 0.11551119 -0.99305006  
Axis point 178.72985706 178.99359440 0.00000000  
Rotation angle (degrees) 58.94731040  
Shift along axis 9.57801831  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 36  
shifted from previous position = 0.0032  
rotated from previous position = 0.00456 degrees  
atoms outside contour = 10087, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606827 0.85201100 0.08803865 -65.78015325  
-0.84948243 0.52227503 -0.07488924 238.44874368  
-0.10978685 -0.03613932 0.99329794 16.58194858  
Axis 0.02261589 0.11545831 -0.99305483  
Axis point 178.74211787 178.98327131 0.00000000  
Rotation angle (degrees) 58.94767784  
Shift along axis 9.57642864  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 36  
shifted from previous position = 0.00704  
rotated from previous position = 0.00489 degrees  
atoms outside contour = 10094, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51607331 0.85200141 0.08810182 -65.78490232  
-0.84948138 0.52228494 -0.07483196 238.43618005  
-0.10977119 -0.03622208 0.99329665 16.59530446  
Axis 0.02253428 0.11548660 -0.99305340  
Axis point 178.73032949 178.98211664 0.00000000  
Rotation angle (degrees) 58.94722087  
Shift along axis 9.57374574  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 36  
shifted from previous position = 0.0111  
rotated from previous position = 0.00811 degrees  
atoms outside contour = 10098, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51608990 0.85200270 0.08799208 -65.76179126  
-0.84948832 0.52228620 -0.07474434 238.41892784  
-0.10963943 -0.03617344 0.99331298 16.55824593  
Axis 0.02251179 0.11534703 -0.99307013  
Axis point 178.72812105 178.94981847 0.00000000  
Rotation angle (degrees) 58.94607792  
Shift along axis 9.57700104  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 60  
shifted from previous position = 3.8  
rotated from previous position = 0.0139 degrees  
atoms outside contour = 10102, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51605044 0.85203869 0.08787496 -67.69168210  
-0.84949718 0.52224161 -0.07495499 235.41557958  
-0.10975651 -0.03596898 0.99330747 15.36610941  
Axis 0.02275335 0.11534338 -0.99306505  
Axis point 174.98441152 179.11263620 0.00000000  
Rotation angle (degrees) 58.94907298  
Shift along axis 10.35387041  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 36  
shifted from previous position = 0.00793  
rotated from previous position = 0.0106 degrees  
atoms outside contour = 10097, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51607313 0.85200793 0.08803987 -67.72310080  
-0.84948054 0.52227962 -0.07487856 235.38950117  
-0.10977856 -0.03614534 0.99329864 15.39632033  
Axis 0.02260623 0.11545460 -0.99305548  
Axis point 174.95276982 179.13162834 0.00000000  
Rotation angle (degrees) 58.94733846  
Shift along axis 10.35643598  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 36  
shifted from previous position = 0.00411  
rotated from previous position = 0.00413 degrees  
atoms outside contour = 10099, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606195 0.85202086 0.08798022 -67.71229629  
-0.84948720 0.52226330 -0.07491688 235.40294732  
-0.10977958 -0.03607632 0.99330103 15.38617486  
Axis 0.02266868 0.11541937 -0.99305816  
Axis point 174.96678356 179.12722441 0.00000000  
Rotation angle (degrees) 58.94817830  
Shift along axis 10.35574491  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 44  
shifted from previous position = 0.0022  
rotated from previous position = 0.00171 degrees  
atoms outside contour = 10100, contour level = 0.3345  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606024 0.85202226 0.08797670 -67.71275603  
-0.84948522 0.52226228 -0.07494640 235.40938086  
-0.10980292 -0.03605805 0.99329912 15.38789891  
Axis 0.02269653 0.11543075 -0.99305620  
Axis point 174.97218530 179.13122307 0.00000000  
Rotation angle (degrees) 58.94833320  
Shift along axis 10.35558762  
  

> volume #1 level 0.406

Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.00256  
rotated from previous position = 0.0014 degrees  
atoms outside contour = 12101, contour level = 0.40603  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606191 0.85202165 0.08797276 -67.71284388  
-0.84948712 0.52226264 -0.07492243 235.40332122  
-0.10978042 -0.03606712 0.99330127 15.38533088  
Axis 0.02267728 0.11541549 -0.99305841  
Axis point 174.96688344 179.12785247 0.00000000  
Rotation angle (degrees) 58.94819328  
Shift along axis 10.35511327  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 44  
shifted from previous position = 0.0162  
rotated from previous position = 0.001 degrees  
atoms outside contour = 12104, contour level = 0.40603  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606480 0.85201962 0.08797548 -67.72468529  
-0.84948706 0.52226520 -0.07490528 235.38858705  
-0.10976730 -0.03607805 0.99330233 15.38622886  
Axis 0.02266094 0.11540967 -0.99305946  
Axis point 174.94879902 179.13103048 0.00000000  
Rotation angle (degrees) 58.94797614  
Shift along axis 10.35197482  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.00813  
rotated from previous position = 0.0184 degrees  
atoms outside contour = 12107, contour level = 0.40603  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51609738 0.85196857 0.08827819 -67.77911783  
-0.84945724 0.52232753 -0.07480871 235.36283144  
-0.10984480 -0.03637997 0.99328275 15.44383302  
Axis 0.02242897 0.11563464 -0.99303855  
Axis point 174.90973820 179.17415805 0.00000000  
Rotation angle (degrees) 58.94545677  
Shift along axis 10.35955976  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.00436  
rotated from previous position = 0.00411 degrees  
atoms outside contour = 12107, contour level = 0.40603  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51611202 0.85196401 0.08823669 -67.77247473  
-0.84945740 0.52233545 -0.07475159 235.34864457  
-0.10977482 -0.03637312 0.99329073 15.42978760  
Axis 0.02239987 0.11557082 -0.99304664  
Axis point 174.90334017 179.16030990 0.00000000  
Rotation angle (degrees) 58.94443519  
Shift along axis 10.35884233  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.0166  
rotated from previous position = 0.0125 degrees  
atoms outside contour = 12107, contour level = 0.40603  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606124 0.85200381 0.08814937 -67.75356795  
-0.84947305 0.52228227 -0.07494513 235.40606775  
-0.10989239 -0.03620423 0.99328390 15.42622329  
Axis 0.02261052 0.11558397 -0.99304034  
Axis point 174.95105413 179.16982415 0.00000000  
Rotation angle (degrees) 58.94814017  
Shift along axis 10.35836338  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.0154  
rotated from previous position = 0.0117 degrees  
atoms outside contour = 12103, contour level = 0.40603  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51605839 0.85202643 0.08794713 -67.70904985  
-0.84949036 0.52225652 -0.07492828 235.40519859  
-0.10977184 -0.03604287 0.99330310 15.38029964  
Axis 0.02269478 0.11539520 -0.99306037  
Axis point 174.96926796 179.12466626 0.00000000  
Rotation angle (degrees) 58.94845432  
Shift along axis 10.35442212  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 44  
shifted from previous position = 0.00696  
rotated from previous position = 0.00877 degrees  
atoms outside contour = 12105, contour level = 0.40603  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51608717 0.85199776 0.08805602 -67.73070033  
-0.84947676 0.52229345 -0.07482507 235.38720440  
-0.10974187 -0.03618528 0.99330124 15.39359602  
Axis 0.02255194 0.11544385 -0.99305797  
Axis point 174.95003184 179.13767854 0.00000000  
Rotation angle (degrees) 58.94631973  
Shift along axis 10.35981348  
  

> ui mousemode right select

> select clear

> volume #1 level 0.3345

> select /A

8169 atoms, 8375 bonds, 7 pseudobonds, 1038 residues, 2 models selected  

> show chaibn /A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show chain /A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> chain #2.ㅁ

Unknown command: chain #2.ㅁ  

> chain #2.A

Unknown command: chain #2.A  

>

Unknown command: sequence #2.A  

>

Unknown command: sequence #2.  

>

Unknown command: sequence #2.  

> show sequence

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show sequence #2.A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show sequence:#2.A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /C

Alignment identifier is 1  
Drag select of 1 cryosparc_P1_J299_005_volume_map_sharp.mrc , 49 residues  

> select clear

Drag select of 1 cryosparc_P1_J299_005_volume_map_sharp.mrc , 125 residues, 2
pseudobonds  
Drag select of 1 cryosparc_P1_J299_005_volume_map_sharp.mrc , 242 residues, 2
pseudobonds  
Drag select of 1 cryosparc_P1_J299_005_volume_map_sharp.mrc , 309 residues  

> view clip false

> select clear

> sequence chain /A

Alignment identifier is 2/A  

> select /A:361-362

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

> select /A:332-361

244 atoms, 251 bonds, 30 residues, 1 model selected  

> volume #1 level 0.3141

> select /A:364-366

26 atoms, 26 bonds, 3 residues, 1 model selected  

> select /A:364-376

102 atoms, 104 bonds, 13 residues, 1 model selected  

> set transparency

Expected a keyword  

> ui tool show "Volume Viewer"

> transparency #1 90

> transparency #1 80

> select down

102 atoms, 104 bonds, 13 residues, 1 model selected  

> transparency #1 75

> select /A:370-371

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

> select /A:370-381

91 atoms, 93 bonds, 12 residues, 1 model selected  

> select /A:337-338

18 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:338-366

238 atoms, 244 bonds, 29 residues, 1 model selected  

> select /A:334

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

> select /A:334-428

754 atoms, 774 bonds, 95 residues, 1 model selected  

> select /A:381-382

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:381-520

1101 atoms, 1131 bonds, 1 pseudobond, 138 residues, 2 models selected  

> select /A:567-568

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

> select /A:381-568

1469 atoms, 1507 bonds, 1 pseudobond, 186 residues, 2 models selected  

> select /A:474-520

364 atoms, 377 bonds, 47 residues, 1 model selected  

> select /A:381-520

1101 atoms, 1131 bonds, 1 pseudobond, 138 residues, 2 models selected  

> select /A:514-558

336 atoms, 341 bonds, 45 residues, 1 model selected  

> select /A:381-558

1380 atoms, 1414 bonds, 1 pseudobond, 176 residues, 2 models selected  

> select /A:538-540

21 atoms, 20 bonds, 3 residues, 1 model selected  

> select /A:381-540

1245 atoms, 1277 bonds, 1 pseudobond, 158 residues, 2 models selected  

> select /A:529-530

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

> select /A:381-530

1168 atoms, 1200 bonds, 1 pseudobond, 148 residues, 2 models selected  

> select /A:522-524

19 atoms, 18 bonds, 3 residues, 1 model selected  

> select /A:381-524

1127 atoms, 1158 bonds, 1 pseudobond, 142 residues, 2 models selected  

> open "/Users/uijin/OneDrive - 연세대학교 (Yonsei University)/Project/Spike-
> Repebody/A6 Repebody.pdb"

A6 Repebody.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for A6 Repebody.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select clear

Drag select of 265 residues  

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.91289,0.29928,-0.2776,32.899,-0.3195,0.10058,-0.94223,145.5,-0.25407,0.94885,0.18744,95.01

> view matrix models
> #4,0.78172,0.032293,-0.62279,87.395,-0.52177,-0.51309,-0.68154,163.64,-0.34155,0.85773,-0.38424,159.73

> view matrix models
> #4,0.59149,-0.63434,-0.49774,116.33,-0.29459,-0.74465,0.59893,20.715,-0.75057,-0.20763,-0.62733,260.74

> ui mousemode right "translate selected atoms"

> ui mousemode right select

> select clear

> ui mousemode right "translate selected atoms"

> ui mousemode right select

Drag select of 265 residues  

> ui mousemode right "translate selected atoms"

> ui mousemode right select

> select clear

Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2868, steps = 156  
shifted from previous position = 2.97  
rotated from previous position = 22.4 degrees  
atoms outside contour = 1263, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48588935 -0.77580577 -0.40253812 101.43142128  
-0.63331752 -0.62991565 0.44957222 102.66376018  
-0.60234579 0.03649209 -0.79740070 287.78712440  
Axis -0.85972357 0.41584997 0.29655385  
Axis point 0.00000000 95.40812251 155.31275285  
Rotation angle (degrees) 166.09928900  
Shift along axis 40.83411940  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2868, steps = 44  
shifted from previous position = 0.00565  
rotated from previous position = 0.00545 degrees  
atoms outside contour = 1263, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48583527 -0.77585752 -0.40250367 101.42580369  
-0.63338608 -0.62985005 0.44956757 102.67856198  
-0.60231733 0.03652444 -0.79742072 287.79329391  
Axis -0.85970793 0.41589214 0.29654004  
Axis point 0.00000000 95.41618326 155.31421621  
Rotation angle (degrees) 166.10030143  
Shift along axis 40.84887432  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2868, steps = 44  
shifted from previous position = 0.00493  
rotated from previous position = 0.00486 degrees  
atoms outside contour = 1262, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48585498 -0.77582657 -0.40253953 101.43321193  
-0.63340335 -0.62988489 0.44949439 102.69330333  
-0.60228327 0.03658080 -0.79744386 287.79320772  
Axis -0.85971522 0.41588054 0.29653518  
Axis point 0.00000000 95.41788661 155.31589838  
Rotation angle (degrees) 166.10486825  
Shift along axis 40.84527999  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2868, steps = 44  
shifted from previous position = 0.000731  
rotated from previous position = 0.01 degrees  
atoms outside contour = 1262, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48596004 -0.77571906 -0.40261989 101.44057015  
-0.63334299 -0.63001571 0.44939611 102.69089835  
-0.60226199 0.03660794 -0.79745869 287.79528177  
Axis -0.85974779 0.41581096 0.29653833  
Axis point 0.00000000 95.40629421 155.31958530  
Rotation angle (degrees) 166.10971019  
Shift along axis 40.82902717  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2868, steps = 44  
shifted from previous position = 0.00346  
rotated from previous position = 0.00392 degrees  
atoms outside contour = 1263, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48591815 -0.77574566 -0.40261919 101.44319718  
-0.63333585 -0.62998361 0.44945117 102.68107027  
-0.60230329 0.03659668 -0.79742801 287.79758388  
Axis -0.85973463 0.41582528 0.29655642  
Axis point 0.00000000 95.40713615 155.32213808  
Rotation angle (degrees) 166.10721707  
Shift along axis 40.83137690  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2868, steps = 44  
shifted from previous position = 0.0225  
rotated from previous position = 0.0184 degrees  
atoms outside contour = 1258, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48564235 -0.77590865 -0.40263789 101.46354217  
-0.63345790 -0.62977547 0.44957084 102.68668491  
-0.60239738 0.03672351 -0.79735110 287.82705243  
Axis -0.85965288 0.41594992 0.29661861  
Axis point 0.00000000 95.42919923 155.34557415  
Rotation angle (degrees) 166.10611484  
Shift along axis 40.86395177  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2868, steps = 48  
shifted from previous position = 0.00529  
rotated from previous position = 0.0294 degrees  
atoms outside contour = 1259, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48574676 -0.77597219 -0.40238942 101.40491340  
-0.63375935 -0.62969325 0.44926105 102.79014855  
-0.60199598 0.03679095 -0.79765109 287.82107943  
Axis -0.85968805 0.41602865 0.29640615  
Axis point 0.00000000 95.44983075 155.31938193  
Rotation angle (degrees) 166.11964408  
Shift along axis 40.89899365  
  

> ui mousemode right "translate selected atoms"

> select #3

2 models selected  

> select #4

2110 atoms, 2152 bonds, 265 residues, 1 model selected  

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.47362,-0.72698,-0.49718,122.67,-0.54385,-0.68543,0.48416,79.872,-0.69275,0.041084,-0.72001,288.19

> view matrix models
> #4,0.48619,-0.80606,-0.33746,88.228,-0.68936,-0.59112,0.41876,118.76,-0.53703,0.029035,-0.84306,285.51

> view matrix models
> #4,-0.027033,-0.29523,-0.95504,303.46,0.22679,-0.93229,0.28178,-15.408,-0.97357,-0.20898,0.092158,173.93

> view matrix models
> #4,-0.66758,-0.11353,-0.73584,372.37,0.52754,-0.76954,-0.35988,60.924,-0.5254,-0.62843,0.57362,-2.3506

> view matrix models
> #4,-0.95501,-0.25889,-0.14471,303.88,0.24306,-0.40356,-0.88208,216.52,0.16996,-0.87756,0.44832,-99.886

> ui mousemode right "translate selected atoms"

> ui mousemode right rotate

Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 84  
shifted from previous position = 1.46  
rotated from previous position = 8.77 degrees  
atoms outside contour = 1268, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92573265 -0.32850161 -0.18736531 302.51946307  
0.28224003 -0.27037059 -0.92045658 226.84025116  
0.25171339 -0.90497869 0.34300719 -96.89083523  
Axis 0.02057263 -0.58360731 0.81177538  
Axis point 139.58183287 115.48122184 0.00000000  
Rotation angle (degrees) 157.90295401  
Shift along axis -204.81560190  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.00252  
rotated from previous position = 0.00891 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92578542 -0.32839126 -0.18729801 302.52596772  
0.28215852 -0.27046766 -0.92045305 226.84166018  
0.25161068 -0.90498973 0.34305341 -96.88480016  
Axis 0.02056025 -0.58357934 0.81179581  
Axis point 139.58809163 115.47267086 0.00000000  
Rotation angle (degrees) 157.91084612  
Shift along axis -204.81077226  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.00293  
rotated from previous position = 0.011 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92575755 -0.32851461 -0.18721940 302.49755661  
0.28216018 -0.27058745 -0.92041733 226.82797761  
0.25171132 -0.90490916 0.34319211 -96.91638832  
Axis 0.02061673 -0.58351920 0.81183760  
Axis point 139.57569775 115.46201248 0.00000000  
Rotation angle (degrees) 157.90728274  
Shift along axis -204.80233745  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.00244  
rotated from previous position = 0.00891 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92575734 -0.32846844 -0.18730146 302.51629484  
0.28218745 -0.27045477 -0.92044797 226.83906149  
0.25168153 -0.90496558 0.34306516 -96.89459307  
Axis 0.02058205 -0.58357734 0.81179669  
Axis point 139.58252849 115.47421461 -0.00000000  
Rotation angle (degrees) 157.90683027  
Shift along axis -204.81044148  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.00273  
rotated from previous position = 0.0168 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92578324 -0.32848925 -0.18713688 302.48992067  
0.28210599 -0.27072199 -0.92039438 226.82083433  
0.25167759 -0.90487812 0.34329866 -96.92680404  
Axis 0.02063111 -0.58346724 0.81187459  
Axis point 139.57486058 115.45012619 0.00000000  
Rotation angle (degrees) 157.91137117  
Shift along axis -204.79423242  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.00248  
rotated from previous position = 0.013 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92576419 -0.32846825 -0.18726791 302.51186357  
0.28217127 -0.27051680 -0.92043470 226.83425759  
0.25167445 -0.90494711 0.34311907 -96.90116291  
Axis 0.02058998 -0.58355195 0.81181474  
Axis point 139.58149838 115.46862209 0.00000000  
Rotation angle (degrees) 157.90797088  
Shift along axis -204.80665377  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.0028  
rotated from previous position = 0.0144 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92578535 -0.32849098 -0.18712339 302.48768630  
0.28209921 -0.27074349 -0.92039013 226.81940552  
0.25167741 -0.90487106 0.34331741 -96.92947372  
Axis 0.02063518 -0.58345839 0.81188084  
Axis point 139.57419889 115.44815753 0.00000000  
Rotation angle (degrees) 157.91174289  
Shift along axis -204.79298004  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.00304  
rotated from previous position = 0.0157 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92576190 -0.32846577 -0.18728361 302.51446655  
0.28218005 -0.27049556 -0.92043825 226.83528821  
0.25167307 -0.90495436 0.34310097 -96.89849083  
Axis 0.02058470 -0.58356060 0.81180866  
Axis point 139.58229918 115.47049180 0.00000000  
Rotation angle (degrees) 157.90755689  
Shift along axis -204.80800191  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.00327  
rotated from previous position = 0.0172 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92578784 -0.32849202 -0.18710926 302.48552062  
0.28209227 -0.27076766 -0.92038515 226.81769972  
0.25167604 -0.90486345 0.34333846 -96.93225093  
Axis 0.02063905 -0.58344846 0.81188788  
Axis point 139.57359847 115.44598438 -0.00000000  
Rotation angle (degrees) 157.91216876  
Shift along axis -204.79154354  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2883, steps = 44  
shifted from previous position = 0.00348  
rotated from previous position = 0.0185 degrees  
atoms outside contour = 1269, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.92575995 -0.32846313 -0.18729788 302.51689160  
0.28218804 -0.27047686 -0.92044130 226.83615090  
0.25167128 -0.90496091 0.34308501 -96.89608502  
Axis 0.02057972 -0.58356823 0.81180330  
Axis point 139.58306293 115.47212981 0.00000000  
Rotation angle (degrees) 157.90719948  
Shift along axis -204.80921821  
  

> ui mousemode right select

Drag select of 1 cryosparc_P1_J299_005_volume_map_sharp.mrc  
Drag select of 1 cryosparc_P1_J299_005_volume_map_sharp.mrc  

> select clear

> ui mousemode right pivot

> ui mousemode right select

> ui mousemode right select

> ui mousemode right select

Drag select of 1 cryosparc_P1_J299_005_volume_map_sharp.mrc , 223 residues, 3
pseudobonds  

> select clear

> select #2/C:493

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

> select clear

> ui mousemode right zoom

> ui mousemode right pivot

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> select #3

2 models selected  

> select #4

2110 atoms, 2152 bonds, 265 residues, 1 model selected  

> view matrix models
> #4,0.28623,-0.27756,-0.91708,251.97,0.28021,-0.89103,0.35713,-25.924,-0.91627,-0.3592,-0.17726,194.21

> view matrix models
> #4,0.63719,-0.6776,-0.36721,83.073,-0.62044,-0.73364,0.27718,126.6,-0.45722,0.051218,-0.88788,275.02

> view matrix models
> #4,0.67745,-0.69588,-0.23835,55.283,-0.56549,-0.69994,0.43624,95.912,-0.4704,-0.16074,-0.86769,257.23

> view matrix models
> #4,0.77549,-0.63018,-0.038458,14.42,-0.47679,-0.62448,0.61863,59.935,-0.41387,-0.46141,-0.78474,212.63

> view matrix models
> #4,0.72892,-0.65813,-0.18852,42.925,-0.54465,-0.72432,0.42275,93.236,-0.41477,-0.20547,-0.88642,248.9

> view matrix models
> #4,0.79901,-0.59525,0.085218,-6.0466,-0.47336,-0.53523,0.69962,53.368,-0.37084,-0.59934,-0.70942,183.77

Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 288  
shifted from previous position = 4.31  
rotated from previous position = 30.3 degrees  
atoms outside contour = 1259, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49147649 -0.84114854 -0.22565461 67.09401177  
-0.61617264 -0.51896367 0.59245927 89.77012420  
-0.61545280 -0.15213760 -0.77335115 266.53880925  
Axis -0.85581253 0.44801983 0.25857910  
Axis point 0.00000000 96.30475979 134.49871634  
Rotation angle (degrees) 154.21321974  
Shift along axis 51.72026556  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 68  
shifted from previous position = 0.025  
rotated from previous position = 0.0361 degrees  
atoms outside contour = 1256, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49108413 -0.84132009 -0.22586918 67.19003738  
-0.61602091 -0.51873024 0.59282138 89.71165078  
-0.61591771 -0.15198503 -0.77301095 266.57829167  
Axis -0.85568443 0.44811437 0.25883907  
Axis point 0.00000000 96.33217799 134.54686493  
Rotation angle (degrees) 154.20128467  
Shift along axis 51.70848897  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 96  
shifted from previous position = 0.00577  
rotated from previous position = 0.0269 degrees  
atoms outside contour = 1257, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49124805 -0.84130313 -0.22557569 67.11633490  
-0.61625371 -0.51872596 0.59258311 89.78621850  
-0.61555399 -0.15209344 -0.77327929 266.55842495  
Axis -0.85573896 0.44814037 0.25861370  
Axis point 0.00000000 96.33681194 134.51122007  
Rotation angle (degrees) 154.20787768  
Shift along axis 51.73842729  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 100  
shifted from previous position = 0.0695  
rotated from previous position = 0.149 degrees  
atoms outside contour = 1259, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48949412 -0.84258689 -0.22459482 67.15110946  
-0.61803135 -0.51692233 0.59230782 90.16881106  
-0.61516888 -0.15112455 -0.77377556 266.66503110  
Axis -0.85521797 0.44930241 0.25832065  
Axis point 0.00000000 96.58249596 134.54030093  
Rotation angle (degrees) 154.23729564  
Shift along axis 51.96931251  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 64  
shifted from previous position = 0.066  
rotated from previous position = 0.142 degrees  
atoms outside contour = 1257, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49125575 -0.84131496 -0.22551480 67.09778946  
-0.61643121 -0.51873375 0.59239166 89.82842774  
-0.61537010 -0.15200145 -0.77344373 266.55682204  
Axis -0.85574809 0.44817440 0.25852449  
Axis point 0.00000000 96.33907874 134.50334980  
Rotation angle (degrees) 154.21871168  
Shift along axis 51.75146112  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 80  
shifted from previous position = 0.0192  
rotated from previous position = 0.0394 degrees  
atoms outside contour = 1256, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49088882 -0.84149300 -0.22564951 67.17226638  
-0.61621761 -0.51845128 0.59286097 89.75288158  
-0.61587663 -0.15197962 -0.77304474 266.57587704  
Axis -0.85562232 0.44826644 0.25878107  
Axis point 0.00000000 96.36115675 134.53727108  
Rotation angle (degrees) 154.19800304  
Shift along axis 51.74390603  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 64  
shifted from previous position = 0.00531  
rotated from previous position = 0.0294 degrees  
atoms outside contour = 1257, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49122100 -0.84122878 -0.22591165 67.18254590  
-0.61604657 -0.51888755 0.59265701 89.72890342  
-0.61578288 -0.15195347 -0.77312457 266.57838928  
Axis -0.85573204 0.44805345 0.25878715  
Axis point 0.00000000 96.32225746 134.54359487  
Rotation angle (degrees) 154.21011025  
Shift along axis 51.70014958  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 64  
shifted from previous position = 0.0779  
rotated from previous position = 0.201 degrees  
atoms outside contour = 1258, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48904635 -0.84290399 -0.22438032 67.15963652  
-0.61853720 -0.51649985 0.59214833 90.28970473  
-0.61501659 -0.15080041 -0.77395984 266.71355697  
Axis -0.85508889 0.44959864 0.25823256  
Axis point 0.00000000 96.65043375 134.55772739  
Rotation angle (degrees) 154.25111169  
Shift along axis 52.04079427  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 64  
shifted from previous position = 0.0294  
rotated from previous position = 0.0881 degrees  
atoms outside contour = 1258, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48966803 -0.84232561 -0.22519500 67.24103351  
-0.61735820 -0.51733283 0.59265133 90.00363333  
-0.61570616 -0.15117643 -0.77333797 266.67502708  
Axis -0.85526317 0.44901499 0.25867055  
Axis point 0.00000000 96.52933122 134.58286217  
Rotation angle (degrees) 154.22405034  
Shift along axis 51.88517760  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 104  
shifted from previous position = 0.0455  
rotated from previous position = 0.105 degrees  
atoms outside contour = 1258, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49109103 -0.84135997 -0.22570555 67.15700434  
-0.61632555 -0.51869624 0.59253441 89.78490535  
-0.61560736 -0.15188024 -0.77327872 266.57716933  
Axis -0.85569589 0.44818755 0.25867442  
Axis point 0.00000000 96.34224461 134.53223398  
Rotation angle (degrees) 154.21622208  
Shift along axis 51.73119943  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 80  
shifted from previous position = 0.0176  
rotated from previous position = 0.0269 degrees  
atoms outside contour = 1258, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49146213 -0.84116200 -0.22563569 67.09736841  
-0.61630516 -0.51897039 0.59231553 89.80903475  
-0.61533156 -0.15204021 -0.77346677 266.55047415  
Axis -0.85581373 0.44804797 0.25852635  
Axis point 0.00000000 96.31561198 134.50155326  
Rotation angle (degrees) 154.22222338  
Shift along axis 51.72622680  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 104  
shifted from previous position = 0.0203  
rotated from previous position = 0.0455 degrees  
atoms outside contour = 1257, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49082577 -0.84152812 -0.22565569 67.17684269  
-0.61640022 -0.51844492 0.59267667 89.79185487  
-0.61574413 -0.15180677 -0.77318424 266.58893434  
Axis -0.85561102 0.44831617 0.25873229  
Axis point 0.00000000 96.36869222 134.54288642  
Rotation angle (degrees) 154.21091843  
Shift along axis 51.75306072  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 64  
shifted from previous position = 0.018  
rotated from previous position = 0.0274 degrees  
atoms outside contour = 1257, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49123001 -0.84131245 -0.22558022 67.11234316  
-0.61631721 -0.51872888 0.59251452 89.79707077  
-0.61550482 -0.15203194 -0.77333053 266.55563434  
Axis -0.85573638 0.44815560 0.25859584  
Axis point 0.00000000 96.33508657 134.50913763  
Rotation angle (degrees) 154.21263138  
Shift along axis 51.74276392  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 68  
shifted from previous position = 0.00819  
rotated from previous position = 0.0173 degrees  
atoms outside contour = 1258, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49127490 -0.84130974 -0.22549258 67.09455379  
-0.61650363 -0.51875293 0.59229947 89.84871426  
-0.61528225 -0.15196487 -0.77352080 266.55985610  
Axis -0.85575715 0.44818122 0.25848267  
Axis point 0.00000000 96.34183966 134.50196717  
Rotation angle (degrees) 154.22379170  
Shift along axis 51.75296394  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 60  
shifted from previous position = 0.0609  
rotated from previous position = 0.149 degrees  
atoms outside contour = 1256, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48937304 -0.84265613 -0.22459891 67.15866909  
-0.61811327 -0.51683827 0.59229570 90.18538368  
-0.61518291 -0.15102598 -0.77378365 266.67739934  
Axis -0.85518259 0.44936217 0.25833385  
Axis point 0.00000000 96.59423078 134.54838993  
Rotation angle (degrees) 154.24026874  
Shift along axis 51.98477316  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 64  
shifted from previous position = 0.0644  
rotated from previous position = 0.168 degrees  
atoms outside contour = 1257, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49126988 -0.84122211 -0.22583014 67.16441504  
-0.61608484 -0.51888282 0.59262137 89.74004766  
-0.61570559 -0.15200651 -0.77317569 266.57134700  
Axis -0.85574696 0.44805565 0.25873398  
Axis point 0.00000000 96.32179184 134.53391196  
Rotation angle (degrees) 154.20994626  
Shift along axis 51.70385686  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 100  
shifted from previous position = 0.0181  
rotated from previous position = 0.0193 degrees  
atoms outside contour = 1258, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49149485 -0.84104323 -0.22600686 67.15954614  
-0.61591394 -0.51916414 0.59255262 89.70056902  
-0.61569703 -0.15203579 -0.77317675 266.55918554  
Axis -0.85581849 0.44790390 0.25876014  
Axis point 0.00000000 96.28455231 134.53191461  
Rotation angle (degrees) 154.21372739  
Shift along axis 51.67574618  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 72  
shifted from previous position = 0.0701  
rotated from previous position = 0.153 degrees  
atoms outside contour = 1259, contour level = 0.31406  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48955697 -0.84243653 -0.22502146 67.22651006  
-0.61756739 -0.51716395 0.59258077 90.05332162  
-0.61558468 -0.15113613 -0.77344255 266.67864710  
Axis -0.85523094 0.44912486 0.25858636  
Axis point 0.00000000 96.55262802 134.57595223  
Rotation angle (degrees) 154.22713116  
Shift along axis 51.91045567  
  

> volume #1 level 0.2171

Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 84  
shifted from previous position = 0.061  
rotated from previous position = 0.115 degrees  
atoms outside contour = 528, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49112457 -0.84139996 -0.22548339 67.10965366  
-0.61635261 -0.51857613 0.59261139 89.79618664  
-0.61555351 -0.15206873 -0.77328454 266.55421574  
Axis -0.85570012 0.44822338 0.25859834  
Axis point 0.00000000 96.34654590 134.50720726  
Rotation angle (degrees) 154.20648837  
Shift along axis 51.75349002  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 88  
shifted from previous position = 0.0529  
rotated from previous position = 0.125 degrees  
atoms outside contour = 524, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48962727 -0.84247739 -0.22471534 67.15335482  
-0.61782927 -0.51707514 0.59238526 90.12335663  
-0.61526590 -0.15121226 -0.77368128 266.65336139  
Axis -0.85525585 0.44919549 0.25838120  
Axis point 0.00000000 96.55932439 134.53941483  
Rotation angle (degrees) 154.23237765  
Shift along axis 51.94792079  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 100  
shifted from previous position = 0.0239  
rotated from previous position = 0.0698 degrees  
atoms outside contour = 529, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49013050 -0.84201311 -0.22535753 67.21345859  
-0.61689547 -0.51774223 0.59277564 89.89759733  
-0.61580197 -0.15151538 -0.77319533 266.63298881  
Axis -0.85539734 0.44872923 0.25872276  
Axis point 0.00000000 96.46323095 134.56377460  
Rotation angle (degrees) 154.21116017  
Shift along axis 51.82948718  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 120  
shifted from previous position = 0.0306  
rotated from previous position = 0.0786 degrees  
atoms outside contour = 531, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49116947 -0.84127690 -0.22584448 67.17742828  
-0.61615376 -0.51882109 0.59260376 89.75514416  
-0.61571673 -0.15191395 -0.77318501 266.58312619  
Axis -0.85571806 0.44810315 0.25874728  
Axis point 0.00000000 96.33324561 134.54227711  
Rotation angle (degrees) 154.21310775  
Shift along axis 51.71228434  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 80  
shifted from previous position = 0.0219  
rotated from previous position = 0.044 degrees  
atoms outside contour = 530, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49065830 -0.84167931 -0.22545590 67.16829492  
-0.61659934 -0.51820521 0.59267919 89.83881352  
-0.61567823 -0.15178700 -0.77324060 266.58609623  
Axis -0.85555886 0.44845310 0.25866744  
Axis point 0.00000000 96.39903058 134.53356571  
Rotation angle (degrees) 154.20987255  
Shift along axis 51.77920877  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 84  
shifted from previous position = 0.00918  
rotated from previous position = 0.00223 degrees  
atoms outside contour = 530, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49065215 -0.84168270 -0.22545665 67.16294935  
-0.61657831 -0.51819512 0.59270989 89.82902553  
-0.61570419 -0.15180270 -0.77321684 266.59110949  
Axis -0.85555583 0.44845254 0.25867846  
Axis point 0.00000000 96.39581037 134.53662901  
Rotation angle (degrees) 154.20804891  
Shift along axis 51.78377914  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 64  
shifted from previous position = 0.0161  
rotated from previous position = 0.0159 degrees  
atoms outside contour = 530, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49078714 -0.84155207 -0.22565038 67.19210478  
-0.61640999 -0.51840943 0.59269755 89.80225143  
-0.61576514 -0.15179518 -0.77316979 266.60104155  
Axis -0.85559867 0.44833435 0.25874162  
Axis point 0.00000000 96.38192392 134.55008175  
Rotation angle (degrees) 154.21017346  
Shift along axis 51.75274501  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 84  
shifted from previous position = 0.0237  
rotated from previous position = 0.0711 degrees  
atoms outside contour = 529, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49007448 -0.84213466 -0.22502494 67.15630658  
-0.61729347 -0.51755656 0.59252340 90.00137380  
-0.61544763 -0.15147417 -0.77348548 266.62458459  
Axis -0.85538673 0.44887564 0.25850376  
Axis point 0.00000000 96.49085203 134.53619283  
Rotation angle (degrees) 154.22173142  
Shift along axis 51.87826862  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 76  
shifted from previous position = 0.0414  
rotated from previous position = 0.0964 degrees  
atoms outside contour = 528, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49132775 -0.84124281 -0.22562706 67.11087345  
-0.61631547 -0.51884793 0.59241208 89.80382055  
-0.61542854 -0.15201105 -0.77339534 266.55740227  
Axis -0.85576997 0.44810591 0.25857078  
Axis point 0.00000000 96.32711339 134.50903046  
Rotation angle (degrees) 154.21830304  
Shift along axis 51.73410641  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 84  
shifted from previous position = 0.0156  
rotated from previous position = 0.0238 degrees  
atoms outside contour = 530, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49117984 -0.84126930 -0.22585021 67.17656257  
-0.61610700 -0.51882277 0.59265090 89.74256143  
-0.61575525 -0.15195028 -0.77314720 266.57885249  
Axis -0.85571934 0.44809126 0.25876367  
Axis point 0.00000000 96.32975669 134.54099005  
Rotation angle (degrees) 154.21004513  
Shift along axis 51.70949523  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 96  
shifted from previous position = 0.0329  
rotated from previous position = 0.0701 degrees  
atoms outside contour = 531, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49031386 -0.84189659 -0.22539398 67.20189114  
-0.61689691 -0.51793034 0.59260979 89.90936746  
-0.61565455 -0.15151995 -0.77331183 266.63125471  
Axis -0.85545874 0.44864732 0.25866181  
Axis point 0.00000000 96.44895471 134.55860793  
Rotation angle (degrees) 154.21914536  
Shift along axis 51.81647316  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 100  
shifted from previous position = 0.0313  
rotated from previous position = 0.0498 degrees  
atoms outside contour = 527, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49105511 -0.84145280 -0.22543751 67.10987250  
-0.61659739 -0.51854280 0.59238588 89.86190373  
-0.61536375 -0.15188993 -0.77347069 266.57362647  
Axis -0.85568792 0.44829507 0.25851446  
Axis point 0.00000000 96.36563186 134.51176433  
Rotation angle (degrees) 154.22112651  
Shift along axis 51.77267780  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 76  
shifted from previous position = 0.0162  
rotated from previous position = 0.0332 degrees  
atoms outside contour = 530, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49112112 -0.84132241 -0.22578008 67.17182791  
-0.61617192 -0.51873745 0.59265810 89.75621109  
-0.61573713 -0.15194756 -0.77316216 266.57826059  
Axis -0.85570081 0.44813862 0.25874293  
Axis point 0.00000000 96.33907521 134.53801791  
Rotation angle (degrees) 154.20927894  
Shift along axis 51.71947861  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 80  
shifted from previous position = 0.0181  
rotated from previous position = 0.0341 degrees  
atoms outside contour = 531, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49150813 -0.84101640 -0.22607780 67.17331041  
-0.61579916 -0.51919754 0.59264265 89.67819051  
-0.61580122 -0.15207016 -0.77308701 266.55987655  
Axis -0.85581971 0.44786793 0.25881836  
Axis point 0.00000000 96.28172495 134.53716734  
Rotation angle (degrees) 154.20914228  
Shift along axis 51.66633296  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2852, steps = 96  
shifted from previous position = 0.0223  
rotated from previous position = 0.0475 degrees  
atoms outside contour = 530, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49094247 -0.84145401 -0.22567819 67.17403158  
-0.61627722 -0.51853364 0.59272696 89.77327728  
-0.61577421 -0.15191451 -0.77313912 266.58296478  
Axis -0.85564389 0.44824696 0.25874350  
Axis point 0.00000000 96.36008293 134.53938116  
Rotation angle (degrees) 154.20610569  
Shift along axis 51.74015834  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 120  
shifted from previous position = 0.0225  
rotated from previous position = 0.0482 degrees  
atoms outside contour = 527, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49161618 -0.84105496 -0.22569912 67.09403805  
-0.61615300 -0.51911381 0.59234815 89.77174328  
-0.61536088 -0.15214274 -0.77342328 266.53886231  
Axis -0.85585886 0.44795104 0.25854491  
Axis point 0.00000000 96.29356324 134.49753228  
Rotation angle (degrees) 154.21865828  
Shift along axis 51.70258436  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2851, steps = 88  
shifted from previous position = 0.00417  
rotated from previous position = 0.0224 degrees  
atoms outside contour = 527, contour level = 0.2171  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49133486 -0.84125727 -0.22555766 67.09903209  
-0.61626178 -0.51879207 0.59251684 89.78351435  
-0.61547663 -0.15212162 -0.77333533 266.54488117  
Axis -0.85576710 0.44810985 0.25857346  
Axis point 0.00000000 96.32352856 134.50088215  
Rotation angle (degrees) 154.21020445  
Shift along axis 51.73316453  
  

> ui mousemode right select

> select clear

> ui mousemode right distance

> ui mousemode right distance

Window position QRect(0,0 640x480) outside any known screen, using primary
screen  

Window position QRect(0,0 640x480) outside any known screen, using primary
screen  

Window position QRect(0,0 640x480) outside any known screen, using primary
screen  

> ui mousemode right "contour level"

> open 6m0j

Summary of feedback from opening 6m0j fetched from pdb  
---  
notes | Fetching compressed mmCIF 6m0j from
http://files.rcsb.org/download/6m0j.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
  
6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #5  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike protein S1  
  
Non-standard residues in 6m0j #5  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
ZN — zinc ion  
  

> view clip false

> view clip false

> view clip false

> view clip false

> volume #1 level -0.5556

> volume #1 level 0.2656

> view clip false

> view #5 clip false

> ui mousemode right zoom

> show #!5 target m

> show #!5 target m

> view #5 clip false

> view #5 clip false

> view #5 clip false

> view #5 clip false

> view #5 clip false

> view #5 clip false

> view #5 clip false

> view #1 clip false

> ui mousemode right translate

> ui mousemode right rotate

> ui mousemode right select

> ui mousemode right translate

> select /A

15278 atoms, 15597 bonds, 10 pseudobonds, 1977 residues, 5 models selected  

> select #5/A:19-615

4870 atoms, 5010 bonds, 597 residues, 1 model selected  

> select #5/A:19-615

4870 atoms, 5010 bonds, 597 residues, 1 model selected  

> chain /#5.A

Unknown command: chain /#5.A  

> chain #5.A

Unknown command: chain #5.A  

> chain /5.A

Unknown command: chain /5.A  

> chain /#5.A

Unknown command: chain /#5.A  

> chain /A

Unknown command: chain /A  

> select /#5.A

Expected an objects specifier or a keyword  

> select /#A

Expected an objects specifier or a keyword  

> delete sel

> ui mousemode right select

Drag select of 14 atoms, 14 bonds  

> save "/Users/uijin/Desktop/mask making.cxs"

——— End of log from Fri Nov 12 14:26:29 2021 ———

opened ChimeraX session  

> ui mousemode right select

Drag select of 14 atoms, 14 bonds  
Drag select of 38 atoms, 8 residues, 39 bonds  

> select clear

Drag select of 25 atoms, 25 bonds  

> delete sel

Drag select of 18 atoms, 17 bonds  

> delete sel

> ui mousemode right translate

> ui mousemode right select

Drag select of 14 atoms, 14 bonds  

> delete sel

> ui mousemode right translate

> ui mousemode right "translate selected atoms"

> ui mousemode right select

Drag select of 19 atoms, 194 residues, 19 bonds  

> ui mousemode right "translate selected atoms"

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.29186,-0.95246,-0.087442,168.52,0.91804,0.30461,-0.2538,-95.786,0.26837,-0.0062016,0.9633,-40.53

> view matrix models
> #5,-0.7219,-0.68677,0.0849,307.45,0.61916,-0.69583,-0.36396,9.4259,0.30903,-0.21018,0.92754,-34.582

> view matrix models
> #5,-0.78447,-0.60938,0.11517,311.36,0.53772,-0.76087,-0.36324,25.759,0.30898,-0.22302,0.92455,-33.703

> ui mousemode right "translate selected atoms"

> ui tool show "Fit in Map"

Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.0136  
rotated from previous position = 0.00711 degrees  
atoms outside contour = 7910, contour level = 0.26558  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51607187 0.85199471 0.08817501 -67.75522215  
-0.84947457 0.52229247 -0.07485670 235.38170787  
-0.10983065 -0.03627099 0.99328830 15.42500879  
Axis 0.02252014 0.11556393 -0.99304472  
Axis point 174.93068964 179.15882081 0.00000000  
Rotation angle (degrees) 58.94729657  
Shift along axis 10.35805402  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.0108  
rotated from previous position = 0.00121 degrees  
atoms outside contour = 7912, contour level = 0.26558  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51608300 0.85198969 0.08815842 -67.74658365  
-0.84946952 0.52230153 -0.07485089 235.38671682  
-0.10981747 -0.03625862 0.99329021 15.41954303  
Axis 0.02252415 0.11554745 -0.99304655  
Axis point 174.94214008 179.15405929 0.00000000  
Rotation angle (degrees) 58.94655786  
Shift along axis 10.36007720  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 40  
shifted from previous position = 0.00596  
rotated from previous position = 0.00647 degrees  
atoms outside contour = 7910, contour level = 0.26558  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51608195 0.85200118 0.08805348 -67.73205291  
-0.84947275 0.52229040 -0.07489184 235.38951468  
-0.10979742 -0.03614870 0.99329643 15.40075481  
Axis 0.02261216 0.11547426 -0.99305306  
Axis point 174.95123705 179.14093566 0.00000000  
Rotation angle (degrees) 58.94675688  
Shift along axis 10.35609510  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 44  
shifted from previous position = 0.0078  
rotated from previous position = 0.0102 degrees  
atoms outside contour = 7913, contour level = 0.26558  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51607396 0.85198870 0.08822091 -67.76291285  
-0.84947278 0.52229876 -0.07483323 235.37566465  
-0.10983474 -0.03632178 0.99328599 15.43279953  
Axis 0.02247686 0.11559335 -0.99304228  
Axis point 174.92218413 179.16336066 0.00000000  
Rotation angle (degrees) 58.94709375  
Shift along axis 10.35934225  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 44  
shifted from previous position = 0.00338  
rotated from previous position = 0.0103 degrees  
atoms outside contour = 7910, contour level = 0.26558  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51605162 0.85201949 0.08805401 -67.73909826  
-0.84949154 0.52226014 -0.07488966 235.39112118  
-0.10979454 -0.03615421 0.99329655 15.40222517  
Axis 0.02260719 0.11547043 -0.99305362  
Axis point 174.94065294 179.14545595 0.00000000  
Rotation angle (degrees) 58.94877901  
Shift along axis 10.35408906  
  
Fit molecule 7cak (#2) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 24935 atoms  
average map value = 0.5515, steps = 36  
shifted from previous position = 0.00203  
rotated from previous position = 0.000896 degrees  
atoms outside contour = 7909, contour level = 0.26558  
  
Position of 7cak (#2) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.51606411 0.85201195 0.08805377 -67.73831079  
-0.84948466 0.52227232 -0.07488280 235.38628463  
-0.10978909 -0.03615600 0.99329708 15.40138522  
Axis 0.02260234 0.11546813 -0.99305400  
Axis point 174.94020811 179.14324286 0.00000000  
Rotation angle (degrees) 58.94793601  
Shift along axis 10.35416320  
  

> ui mousemode right translate

> ui mousemode right "translate selected atoms"

> ui mousemode right translate

Fit molecule 6m0j (#5) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 1631 atoms  
average map value = 0.3644, steps = 1304  
shifted from previous position = 12.7  
rotated from previous position = 42.3 degrees  
atoms outside contour = 408, contour level = 0.26558  
  
Position of 6m0j (#5) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.22379692 -0.96297754 -0.15029705 210.27324796  
0.95234793 -0.18327356 -0.24381187 -42.66015685  
0.20723988 -0.19769943 0.95810572 -23.00745277  
Axis 0.02366007 -0.18345046 0.98274418  
Axis point 123.41536239 61.75637041 0.00000000  
Rotation angle (degrees) 102.97244220  
Shift along axis -9.80933497  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 1631 atoms  
average map value = 0.3644, steps = 48  
shifted from previous position = 0.035  
rotated from previous position = 0.108 degrees  
atoms outside contour = 408, contour level = 0.26558  
  
Position of 6m0j (#5) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.22201968 -0.96342708 -0.15005173 209.89045647  
0.95266159 -0.18155637 -0.24387123 -42.68600817  
0.20770930 -0.19709274 0.95812906 -23.10025808  
Axis 0.02399188 -0.18348947 0.98272886  
Axis point 123.27504726 61.73984538 0.00000000  
Rotation angle (degrees) 102.86904760  
Shift along axis -9.83318977  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J299_005_volume_map_sharp.mrc (#1)
using 1631 atoms  
average map value = 0.3644, steps = 40  
shifted from previous position = 0.0248  
rotated from previous position = 0.00958 degrees  
atoms outside contour = 407, contour level = 0.26558  
  
Position of 6m0j (#5) relative to cryosparc_P1_J299_005_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.22188588 -0.96344386 -0.15014185 209.87984935  
0.95270382 -0.18141741 -0.24380968 -42.68615771  
0.20765859 -0.19713864 0.95813061 -23.07039670  
Axis 0.02393600 -0.18350378 0.98272755  
Axis point 123.27012765 61.75010117 0.00000000  
Rotation angle (degrees) 102.86098695  
Shift along axis -9.81515860  
  

> show #!3 models

> hide #!3 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> select #4

2110 atoms, 2152 bonds, 265 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.47597,-0.84933,-0.22823,69.077,-0.61997,-0.5081,0.59789,90.276,-0.62376,-0.14308,-0.7684,267.63

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.67031,-0.6726,0.31352,-31.667,-0.15866,0.28282,0.94596,30.378,-0.72492,-0.68383,0.082863,103.49

> view matrix models
> #4,0.67047,-0.67249,0.31341,-31.664,-0.15865,0.2827,0.946,30.362,-0.72478,-0.68399,0.082846,103.46

Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 252  
shifted from previous position = 2.61  
rotated from previous position = 40.5 degrees  
atoms outside contour = 727, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82456594 -0.23732705 0.51358241 -52.44917814  
-0.14503951 0.78875697 0.59734913 124.55542116  
-0.54685881 -0.56704348 0.61596033 -1.37706791  
Axis -0.73807241 0.67218084 0.05849821  
Axis point 0.00000000 26.55957338 -61.43901876  
Rotation angle (degrees) 52.07411558  
Shift along axis 122.35450267  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 48  
shifted from previous position = 0.0265  
rotated from previous position = 0.0374 degrees  
atoms outside contour = 724, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82492415 -0.23696285 0.51317518 -52.41255243  
-0.14502622 0.78876207 0.59734562 124.55173625  
-0.54632184 -0.56718868 0.61630305 -1.54580536  
Axis -0.73841984 0.67181672 0.05829612  
Axis point 0.00000000 26.40305051 -61.63783542  
Rotation angle (degrees) 52.04846970  
Shift along axis 122.28829280  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 40  
shifted from previous position = 0.00404  
rotated from previous position = 0.0124 degrees  
atoms outside contour = 726, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82488586 -0.23704543 0.51319858 -52.41522352  
-0.14509487 0.78864094 0.59748887 124.52819841  
-0.54636142 -0.56732260 0.61614468 -1.52157959  
Axis -0.73847956 0.67175111 0.05829579  
Axis point 0.00000000 26.43342198 -61.60063513  
Rotation angle (degrees) 52.06001418  
Shift along axis 122.27082423  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 44  
shifted from previous position = 0.0219  
rotated from previous position = 0.0213 degrees  
atoms outside contour = 727, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82469683 -0.23706740 0.51349215 -52.43262891  
-0.14518035 0.78875498 0.59731754 124.57953275  
-0.54662401 -0.56715486 0.61606621 -1.43725654  
Axis -0.73820860 0.67205273 0.05825111  
Axis point 0.00000000 26.54717813 -61.52216154  
Rotation angle (degrees) 52.06558852  
Shift along axis 122.34651120  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 48  
shifted from previous position = 0.0253  
rotated from previous position = 0.0259 degrees  
atoms outside contour = 725, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82492281 -0.23704991 0.51313711 -52.41166299  
-0.14507865 0.78860789 0.59753643 124.51531746  
-0.54630993 -0.56736667 0.61614976 -1.53641484  
Axis -0.73854093 0.67168247 0.05830918  
Axis point 0.00000000 26.41250680 -61.61382479  
Rotation angle (degrees) 52.05968817  
Shift along axis 122.25332709  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3019, steps = 28  
shifted from previous position = 0.0305  
rotated from previous position = 0.0459 degrees  
atoms outside contour = 727, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82450325 -0.23758059 0.51356582 -52.45536107  
-0.14499275 0.78858611 0.59758602 124.49811086  
-0.54696571 -0.56717493 0.61574435 -1.33319474  
Axis -0.73814205 0.67208891 0.05867554  
Axis point 0.00000000 26.57295561 -61.36959224  
Rotation angle (degrees) 52.09043956  
Shift along axis 122.31508091  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 48  
shifted from previous position = 0.00245  
rotated from previous position = 0.0362 degrees  
atoms outside contour = 729, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82461964 -0.23711177 0.51359562 -52.44269022  
-0.14507652 0.78890419 0.59714570 124.60678550  
-0.54676801 -0.56692873 0.61614654 -1.40736950  
Axis -0.73801187 0.67226023 0.05834946  
Axis point 0.00000000 26.55916535 -61.49710875  
Rotation angle (degrees) 52.06005460  
Shift along axis 122.38939514  
  

> view matrix models
> #4,0.82102,-0.23808,0.51889,-52.857,-0.14536,0.79176,0.59328,125.49,-0.55208,-0.56252,0.61545,-0.20118

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.12329,0.14238,0.9821,35.977,0.28149,0.95402,-0.10297,189.33,-0.95161,0.26376,-0.1577,244.4

> view matrix models
> #4,-0.30017,0.95384,-0.0093463,282.94,0.94443,0.29855,0.13757,6.1225,0.13401,0.032466,-0.99045,206.4

> view matrix models
> #4,-0.35045,0.93363,0.074259,275.08,0.93528,0.34469,0.080218,20.191,0.049298,0.097565,-0.99401,224.01

> view matrix models
> #4,-0.49775,0.86239,-0.09236,317.15,0.77323,0.48947,0.40314,2.5357,0.39287,0.12925,-0.91046,164.42

> view matrix models
> #4,0.87117,0.073117,0.48551,-30.499,-0.33123,-0.64242,0.69108,25.032,0.36243,-0.76286,-0.53543,39.465

> view matrix models
> #4,0.41581,-0.562,0.71502,-52.047,-0.90494,-0.17748,0.38676,191.09,-0.090457,-0.80787,-0.58238,107.63

> view matrix models
> #4,0.66863,-0.19411,0.71781,-59.794,-0.43086,0.68563,0.58675,158.73,-0.60604,-0.7016,0.3748,35.277

> view matrix models
> #4,0.8086,0.015376,0.58816,-42.582,-0.35177,0.81394,0.46234,177.44,-0.47162,-0.58074,0.66356,-20.724

> view matrix models
> #4,0.83181,0.055354,0.5523,-37.018,-0.34358,0.83282,0.434,182.29,-0.43594,-0.55077,0.71177,-31.187

> view matrix models
> #4,-0.49585,0.78688,0.36736,237.27,-0.33142,0.21954,-0.91759,349.92,-0.80268,-0.57673,0.15193,108.54

> view matrix models
> #4,-0.5398,0.71341,0.44683,225.05,-0.20508,0.40336,-0.89176,342.13,-0.81643,-0.57301,-0.071429,146.61

> view matrix models
> #4,-0.61346,0.6663,0.42393,235.5,-0.20735,0.38207,-0.90057,342.21,-0.76202,-0.64036,-0.096227,137.67

> view matrix models
> #4,-0.61823,0.66078,0.42563,235.48,-0.19957,0.3918,-0.89814,341.47,-0.76024,-0.6402,-0.11035,139.7

> view matrix models
> #4,-0.89791,0.17512,0.40384,240.96,-0.13865,0.75822,-0.63708,319.34,-0.41777,-0.62804,-0.65654,179.79

> view matrix models
> #4,-0.57691,0.65693,-0.4854,375.5,0.79695,0.32246,-0.51078,132.88,-0.17902,-0.68151,-0.70957,150.36

> view matrix models
> #4,-0.55453,0.58454,-0.5923,383.87,0.83092,0.4278,-0.35574,111.35,0.045442,-0.68942,-0.72293,120.11

Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 196  
shifted from previous position = 4.36  
rotated from previous position = 41 degrees  
atoms outside contour = 839, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86734583 0.08681481 -0.49007592 377.27106575  
0.49367421 0.27514449 -0.82497351 221.16397879  
0.06322177 -0.95747517 -0.28150366 25.40522552  
Axis -0.18943707 -0.79104738 0.58168517  
Axis point 143.87616102 0.00000000 132.06698119  
Rotation angle (degrees) 159.52951993  
Shift along axis -231.64246784  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 44  
shifted from previous position = 0.0301  
rotated from previous position = 0.048 degrees  
atoms outside contour = 839, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86769950 0.08680244 -0.48945165 377.22109118  
0.49304566 0.27561921 -0.82519091 221.34138122  
0.06327369 -0.95733975 -0.28195222 25.50611186  
Axis -0.18917009 -0.79122226 0.58153418  
Axis point 143.89321248 0.00000000 132.08522065  
Rotation angle (degrees) 159.55636474  
Shift along axis -231.65650103  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 44  
shifted from previous position = 0.0226  
rotated from previous position = 0.0336 degrees  
atoms outside contour = 840, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86744620 0.08681219 -0.48989870 377.25465291  
0.49349418 0.27530702 -0.82502700 221.21466091  
0.06325015 -0.95742869 -0.28165533 25.43592824  
Axis -0.18935908 -0.79110588 0.58163100  
Axis point 143.88045173 0.00000000 132.07074042  
Rotation angle (degrees) 159.53685445  
Shift along axis -231.64648930  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 48  
shifted from previous position = 0.00679  
rotated from previous position = 0.0123 degrees  
atoms outside contour = 839, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86735372 0.08680986 -0.49006282 377.27160510  
0.49365726 0.27519162 -0.82496793 221.17160526  
0.06324583 -0.95746207 -0.28154279 25.41037409  
Axis -0.18942624 -0.79106275 0.58166779  
Axis point 143.87757243 0.00000000 132.06791118  
Rotation angle (degrees) 159.52951164  
Shift along axis -231.64536572  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 40  
shifted from previous position = 0.0285  
rotated from previous position = 0.0346 degrees  
atoms outside contour = 837, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86761633 0.08679079 -0.48960113 377.23213305  
0.49319165 0.27551188 -0.82513951 221.30561619  
0.06327641 -0.95737170 -0.28184310 25.48556599  
Axis -0.18922768 -0.79118206 0.58157014  
Axis point 143.88787453 0.00000000 132.08591065  
Rotation angle (degrees) 159.54939798  
Shift along axis -231.65415219  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 48  
shifted from previous position = 0.00625  
rotated from previous position = 0.0157 degrees  
atoms outside contour = 840, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86771844 0.08665383 -0.48944440 377.21082601  
0.49299373 0.27567075 -0.82520472 221.35191490  
0.06341836 -0.95733837 -0.28192439 25.48507263  
Axis -0.18910448 -0.79123539 0.58153766  
Axis point 143.89474510 0.00000000 132.08711877  
Rotation angle (degrees) 159.55140931  
Shift along axis -231.65319616  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 40  
shifted from previous position = 0.00759  
rotated from previous position = 0.014 degrees  
atoms outside contour = 838, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86769454 0.08689101 -0.48944472 377.22791742  
0.49306406 0.27561640 -0.82518085 221.33832324  
0.06319820 -0.95733252 -0.28199368 25.52237362  
Axis -0.18920272 -0.79122375 0.58152155  
Axis point 143.89377708 0.00000000 132.08398123  
Rotation angle (degrees) 159.55958963  
Shift along axis -231.65887345  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 44  
shifted from previous position = 0.00273  
rotated from previous position = 0.00717 degrees  
atoms outside contour = 839, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86767303 0.08678484 -0.48950169 377.22615414  
0.49309033 0.27558874 -0.82517439 221.32968422  
0.06328852 -0.95735011 -0.28191368 25.49732166  
Axis -0.18918349 -0.79121022 0.58154622  
Axis point 143.89276098 0.00000000 132.08565026  
Rotation angle (degrees) 159.55353275  
Shift along axis -231.65539672  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 40  
shifted from previous position = 0.0195  
rotated from previous position = 0.0253 degrees  
atoms outside contour = 840, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86746593 0.08678242 -0.48986904 377.25143268  
0.49344964 0.27542802 -0.82501325 221.22962459  
0.06332701 -0.95739659 -0.28174717 25.44545527  
Axis -0.18932598 -0.79114479 0.58158886  
Axis point 143.88300961 0.00000000 132.07115465  
Rotation angle (degrees) 159.53608150  
Shift along axis -231.64937011  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 28  
shifted from previous position = 0.022  
rotated from previous position = 0.0233 degrees  
atoms outside contour = 838, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86765915 0.08676504 -0.48952981 377.22258492  
0.49311266 0.27557153 -0.82516679 221.32468706  
0.06330485 -0.95735686 -0.28188710 25.49325314  
Axis -0.18918713 -0.79120319 0.58155460  
Axis point 143.88934549 0.00000000 132.08718762  
Rotation angle (degrees) 159.55162544  
Shift along axis -231.65273794  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 44  
shifted from previous position = 0.0277  
rotated from previous position = 0.0179 degrees  
atoms outside contour = 839, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86752975 0.08668497 -0.48977326 377.23589637  
0.49333089 0.27543394 -0.82508228 221.26387441  
0.06337794 -0.95740371 -0.28171151 25.42378339  
Axis -0.18925357 -0.79114808 0.58160795  
Axis point 143.88444298 0.00000000 132.07155407  
Rotation angle (degrees) 159.53790348  
Shift along axis -231.65905395  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 28  
shifted from previous position = 0.0284  
rotated from previous position = 0.0383 degrees  
atoms outside contour = 840, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86779952 0.08678731 -0.48927698 377.20556879  
0.49286287 0.27580742 -0.82523722 221.39013514  
0.06332610 -0.95728691 -0.28211979 25.53377252  
Axis -0.18908582 -0.79128850 0.58147146  
Axis point 143.89933388 0.00000000 132.08621006  
Rotation angle (degrees) 159.56287651  
Shift along axis -231.66053214  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 44  
shifted from previous position = 0.0262  
rotated from previous position = 0.0501 degrees  
atoms outside contour = 840, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86742391 0.08678072 -0.48994373 377.25701653  
0.49352618 0.27533782 -0.82499758 221.20743036  
0.06330615 -0.95742268 -0.28166317 25.42978838  
Axis -0.18935972 -0.79111317 0.58162088  
Axis point 143.88037983 0.00000000 132.06978285  
Rotation angle (degrees) 159.53314602  
Shift along axis -231.64689901  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 40  
shifted from previous position = 0.00619  
rotated from previous position = 0.0167 degrees  
atoms outside contour = 839, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86755712 0.08671697 -0.48971911 377.23316355  
0.49328599 0.27546947 -0.82509727 221.27094230  
0.06335273 -0.95739059 -0.28176177 25.44669457  
Axis -0.18924391 -0.79116224 0.58159182  
Axis point 143.88589583 0.00000000 132.07478859  
Rotation angle (degrees) 159.54135387  
Shift along axis -231.65070565  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 44  
shifted from previous position = 0.00556  
rotated from previous position = 0.0192 degrees  
atoms outside contour = 840, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86741070 0.08680216 -0.48996333 377.25977161  
0.49355363 0.27529530 -0.82499535 221.20036008  
0.06327323 -0.95743297 -0.28163560 25.42966646  
Axis -0.18937888 -0.79109940 0.58163337  
Axis point 143.87903507 0.00000000 132.07050731  
Rotation angle (degrees) 159.53328894  
Shift along axis -231.64576431  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.287, steps = 48  
shifted from previous position = 0.00611  
rotated from previous position = 0.00816 degrees  
atoms outside contour = 839, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.86735655 0.08680423 -0.49005881 377.26984837  
0.49365137 0.27519921 -0.82496892 221.17287300  
0.06325300 -0.95746040 -0.28154687 25.41073829  
Axis -0.18942194 -0.79106519 0.58166588  
Axis point 143.87727783 0.00000000 132.06795820  
Rotation angle (degrees) 159.52945515  
Shift along axis -231.64478650  
  

> view matrix models
> #4,0.40982,-0.86822,0.27971,-1.0132,-0.7387,-0.136,0.66017,125.51,-0.53513,-0.47717,-0.69709,213.99

Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2847, steps = 176  
shifted from previous position = 5.83  
rotated from previous position = 21.1 degrees  
atoms outside contour = 874, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.53454421 -0.83977894 0.09504640 8.87879962  
-0.44685408 -0.18538180 0.87518856 45.85110939  
-0.71734505 -0.51029885 -0.47435342 205.39509269  
Axis -0.83792989 0.49132679 0.23763730  
Axis point 0.00000000 85.57897060 99.39257942  
Rotation angle (degrees) 124.23548496  
Shift along axis 63.89760180  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2847, steps = 48  
shifted from previous position = 0.0374  
rotated from previous position = 0.226 degrees  
atoms outside contour = 870, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.53486784 -0.83932846 0.09718094 8.52792838  
-0.44537785 -0.18232579 0.87658193 45.68298853  
-0.71802157 -0.51213772 -0.47133850 204.84238534  
Axis -0.83768926 0.49173812 0.23763486  
Axis point 0.00000000 85.51013397 99.12148929  
Rotation angle (degrees) 124.01419148  
Shift along axis 63.99800386  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2847, steps = 48  
shifted from previous position = 0.00357  
rotated from previous position = 0.00922 degrees  
atoms outside contour = 871, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.53479719 -0.83938857 0.09705050 8.55385154  
-0.44532782 -0.18237791 0.87659650 45.66986954  
-0.71810522 -0.51202064 -0.47133828 204.86684795  
Axis -0.83766921 0.49173443 0.23771315  
Axis point 0.00000000 85.51394569 99.14122300  
Rotation angle (degrees) 124.01842682  
Shift along axis 63.99169280  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.2847, steps = 48  
shifted from previous position = 0.0226  
rotated from previous position = 0.0361 degrees  
atoms outside contour = 871, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.53500261 -0.83922796 0.09730696 8.49740230  
-0.44575097 -0.18255287 0.87634498 45.75623145  
-0.71768955 -0.51222152 -0.47175294 204.88143916  
Axis -0.83776976 0.49171532 0.23739815  
Axis point 0.00000000 85.52510903 99.11699544  
Rotation angle (degrees) 124.03170685  
Shift along axis 64.01864791  
  

> view matrix models
> #4,0.54478,-0.83262,0.099816,7.223,-0.4561,-0.19431,0.86846,47.576,-0.7037,-0.51864,-0.48561,204.63

> view matrix models
> #4,0.56058,-0.82149,0.10438,5.1149,-0.47181,-0.21326,0.85552,50.408,-0.68055,-0.52884,-0.50714,204.01

> view matrix models
> #4,0.39268,-0.89178,-0.22479,76.254,-0.54581,-0.4227,0.72347,65.85,-0.7402,-0.1614,-0.65273,264.28

> view matrix models
> #4,0.5575,-0.76815,0.31486,-24.088,-0.52446,-0.031879,0.85084,72.661,-0.64354,-0.63947,-0.42064,176.33

> view matrix models
> #4,0.57875,-0.20453,0.78944,-59.586,-0.6852,0.40297,0.60673,168.26,-0.44221,-0.89207,0.093077,45.839

> view matrix models
> #4,0.77798,0.010129,0.62821,-45.297,-0.5052,0.60452,0.61589,156.92,-0.37353,-0.79653,0.47542,-17.828

> view matrix models
> #4,0.67526,-0.07316,0.73394,-54.17,-0.42631,0.77331,0.46931,182.34,-0.6019,-0.62979,0.491,24.916

> view matrix models
> #4,0.69861,-0.059261,0.71305,-53.046,-0.44686,0.74218,0.49949,178,-0.55881,-0.66758,0.49201,15.727

> ui mousemode right "translate selected atoms"

Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 100  
shifted from previous position = 3.54  
rotated from previous position = 18.9 degrees  
atoms outside contour = 729, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82458740 -0.23721578 0.51359936 -53.45191810  
-0.14510632 0.78879122 0.59728767 125.46465896  
-0.54680872 -0.56704240 0.61600580 2.65455154  
Axis -0.73806965 0.67219343 0.05838825  
Axis point -0.00000000 32.03712907 -59.24219529  
Rotation angle (degrees) 52.07044088  
Shift along axis 123.94275218  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 36  
shifted from previous position = 0.0221  
rotated from previous position = 0.0359 degrees  
atoms outside contour = 727, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82493046 -0.23686972 0.51320803 -53.41798264  
-0.14507442 0.78881281 0.59726691 125.46214367  
-0.54629951 -0.56715702 0.61635198 2.49513908  
Axis -0.73838855 0.67185861 0.05820955  
Axis point 0.00000000 31.88763296 -59.43268034  
Rotation angle (degrees) 52.04461933  
Shift along axis 123.88128936  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 44  
shifted from previous position = 0.0218  
rotated from previous position = 0.0317 degrees  
atoms outside contour = 727, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82463662 -0.23717712 0.51353818 -53.44517963  
-0.14514066 0.78874119 0.59734540 125.45559900  
-0.54672538 -0.56712816 0.61600083 2.63618441  
Axis -0.73815850 0.67209989 0.05834181  
Axis point 0.00000000 32.02684822 -59.26331561  
Rotation angle (degrees) 52.07065106  
Shift along axis 123.92350793  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 40  
shifted from previous position = 0.00393  
rotated from previous position = 0.0172 degrees  
atoms outside contour = 727, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82466449 -0.23706545 0.51354498 -53.44412865  
-0.14506169 0.78891934 0.59712928 125.49373211  
-0.54670429 -0.56692702 0.61620466 2.61337847  
Axis -0.73804347 0.67222698 0.05833290  
Axis point 0.00000000 32.00210625 -59.30306332  
Rotation angle (degrees) 52.05576369  
Shift along axis 123.95680849  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 48  
shifted from previous position = 0.0238  
rotated from previous position = 0.0338 degrees  
atoms outside contour = 726, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82492767 -0.23701141 0.51314709 -53.41895500  
-0.14505600 0.78867037 0.59745946 125.41692241  
-0.54630861 -0.56729591 0.61621608 2.50279375  
Axis -0.73849606 0.67173234 0.05830297  
Axis point 0.00000000 31.87284119 -59.40558400  
Rotation angle (degrees) 52.05483271  
Shift along axis 123.84221084  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 96  
shifted from previous position = 7.09  
rotated from previous position = 0.0144 degrees  
atoms outside contour = 724, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82483873 -0.23715102 0.51322556 -52.37330055  
-0.14492064 0.78875584 0.59737947 118.54943642  
-0.54647881 -0.56711870 0.61622829 3.94837854  
Axis -0.73833616 0.67189291 0.05847757  
Axis point 0.00000000 31.30605002 -54.03871596  
Rotation angle (degrees) 52.05451533  
Shift along axis 118.55251918  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 44  
shifted from previous position = 0.00585  
rotated from previous position = 0.00812 degrees  
atoms outside contour = 725, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82483720 -0.23713400 0.51323588 -52.37267136  
-0.14501368 0.78868095 0.59745577 118.54353262  
-0.54645643 -0.56722997 0.61614571 3.94525478  
Axis -0.73839706 0.67183246 0.05840320  
Axis point -0.00000000 31.31697603 -54.03612880  
Rotation angle (degrees) 52.06029140  
Shift along axis 118.54363491  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) using 2110 atoms  
average map value = 0.3018, steps = 44  
shifted from previous position = 0.0229  
rotated from previous position = 0.02 degrees  
atoms outside contour = 728, contour level = 0.26558  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J299_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.82464767 -0.23716348 0.51352674 -52.38841186  
-0.14514328 0.78874100 0.59734501 118.58628948  
-0.54670802 -0.56713413 0.61601074 4.03216473  
Axis -0.73816961 0.67208853 0.05833210  
Axis point 0.00000000 31.44142451 -53.95449986  
Rotation angle (degrees) 52.06989666  
Shift along axis 118.60722316  
  

> ui mousemode right translate

> /A

Unknown command: sequence /A  

> sequence chain /A

Chains must have same sequence  

> sequence chain /A

Chains must have same sequence  

> sequence chain /A

Chains must have same sequence  

> sequence chain /A

Chains must have same sequence  

> sel

Unknown command: sequence sel  

> selec

Unknown command: sequence selec  

> sele

Unknown command: sequence sele  

> /A

Unknown command: sequence /A  

> show sequence:#2.A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> sequence chain /A

Chains must have same sequence  

> sequence chain /E

Alignment identifier is 5/E  

> select #4/A

2110 atoms, 2152 bonds, 265 residues, 1 model selected  

> select sequence #4.A

Nothing selected  

> select #5/E:333-339

51 atoms, 52 bonds, 7 residues, 1 model selected  

> select #5/E:333

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

> select #5/E:333-526

1536 atoms, 1583 bonds, 194 residues, 1 model selected  

> save "/Users/uijin/Desktop/mask making_2.cxs"

——— End of log from Fri Nov 12 14:36:53 2021 ———

opened ChimeraX session  

> open /Users/uijin/Downloads/cryosparc_P1_J314_map_locres.mrc format mrc

Opened cryosparc_P1_J314_map_locres.mrc as #6, grid size 256,256,256, pixel
1.18, shown at level 7.24, step 1, values float32  

> hide #!6 models

> show #!6 models

> hide #!5 models

> show #!5 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> hide #!5 models

> open /Users/uijin/Downloads/cryosparc_P1_J299_005_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P1_J299_005_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.18, shown at level 0.335, step 1, values float32  

> ui tool show "Color Zone"

> ui tool show "Surface Color"

> color sample #1.1 map #6 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 0, mean 4.567, maximum 8.633  

> color sample #1.1 map #6 palette
> #ff0000:#ffffff:#0000ff:#808080:#808080:#808080:#808080:#808080

Map values for surface "surface": minimum 0, mean 4.567, maximum 8.633  

> color sample #1.1 map #6 palette
> #0000ff:#0091ff:#00ffda:#00ff48:#48ff00:#daff00:#ff9100:#ff0000

Map values for surface "surface": minimum 0, mean 4.567, maximum 8.633  

> color sample #1.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.567, maximum 8.633  

> hide #!1 models

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 3.02, mean 4.237, maximum 7.878  

> volume #6 level 7.022

> volume #7 level 0.1098

> hide #!7 models

> show #!7 models

> hide #!6 models

> volume #7 level 0.1847

> volume #7 level 0.2222

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.808, maximum 8.642  

> volume #7 level 0.2596

> volume #7 level 0.2034

> color sample #7.1 map #6 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff

Map values for surface "surface": minimum 0, mean 4.904, maximum 8.665  

> hide #!7 models

> show #!5 models

> show #!1 models

> color single #1.1

> show #4 models

> open /Users/uijin/Downloads/cryosparc_P1_J313_003_volume_map_sharp.mrc

Opened cryosparc_P1_J313_003_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 1.18, shown at level 0.114, step 1, values float32  

> volume #8 level 0.1391

> volume #8 level 0.2892

> set transparency #8 80

Expected a keyword  

> set transparency 80

Expected a keyword  

> set #8 transparency 80

Expected a keyword  

> ui tool show "Volume Viewer"

> volume #8 color #b2b2b26a

> ui mousemode right select

> select clear

> ui mousemode right translate

> hide #!1 models

> volume #8 level 0.4518

> ui tool show "Fit in Map"

Fit molecule 6m0j (#5) to map cryosparc_P1_J313_003_volume_map_sharp.mrc (#8)
using 1631 atoms  
average map value = 0.515, steps = 224  
shifted from previous position = 0.621  
rotated from previous position = 1.97 degrees  
atoms outside contour = 702, contour level = 0.45178  
  
Position of 6m0j (#5) relative to cryosparc_P1_J313_003_volume_map_sharp.mrc
(#8) coordinates:  
Matrix rotation and translation  
-0.21233723 -0.96535545 -0.15166329 208.00216779  
0.96117538 -0.17833661 -0.21056579 -46.84617872  
0.17622372 -0.19048598 0.96574339 -17.30530435  
Axis 0.01027449 -0.16777402 0.98577194  
Axis point 123.72559462 60.16186648 0.00000000  
Rotation angle (degrees) 102.26685986  
Shift along axis -7.06239664  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J313_003_volume_map_sharp.mrc (#8)
using 1631 atoms  
average map value = 0.515, steps = 48  
shifted from previous position = 0.0112  
rotated from previous position = 0.0242 degrees  
atoms outside contour = 701, contour level = 0.45178  
  
Position of 6m0j (#5) relative to cryosparc_P1_J313_003_volume_map_sharp.mrc
(#8) coordinates:  
Matrix rotation and translation  
-0.21196206 -0.96546279 -0.15150473 207.91077378  
0.96124286 -0.17799575 -0.21054616 -46.85844772  
0.17630728 -0.19026064 0.96577256 -17.32110224  
Axis 0.01037888 -0.16772175 0.98577974  
Axis point 123.69294959 60.15028628 0.00000000  
Rotation angle (degrees) 102.24501378  
Shift along axis -7.05772897  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J313_003_volume_map_sharp.mrc (#8)
using 1631 atoms  
average map value = 0.515, steps = 44  
shifted from previous position = 0.00382  
rotated from previous position = 0.0312 degrees  
atoms outside contour = 700, contour level = 0.45178  
  
Position of 6m0j (#5) relative to cryosparc_P1_J313_003_volume_map_sharp.mrc
(#8) coordinates:  
Matrix rotation and translation  
-0.21147278 -0.96554213 -0.15168275 207.82794171  
0.96137801 -0.17751846 -0.21033194 -46.88879914  
0.17615786 -0.19030394 0.96579129 -17.29323038  
Axis 0.01024601 -0.16771805 0.98578176  
Axis point 123.67245827 60.14693378 0.00000000  
Rotation angle (degrees) 102.21613133  
Shift along axis -7.05384613  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J313_003_volume_map_sharp.mrc (#8)
using 1631 atoms  
average map value = 0.515, steps = 44  
shifted from previous position = 0.0178  
rotated from previous position = 0.0144 degrees  
atoms outside contour = 699, contour level = 0.45178  
  
Position of 6m0j (#5) relative to cryosparc_P1_J313_003_volume_map_sharp.mrc
(#8) coordinates:  
Matrix rotation and translation  
-0.21124458 -0.96558126 -0.15175166 207.79987600  
0.96144069 -0.17729865 -0.21023082 -46.88983601  
0.17608958 -0.19031034 0.96580248 -17.27561995  
Axis 0.01019048 -0.16770985 0.98578373  
Axis point 123.66257344 60.15659741 0.00000000  
Rotation angle (degrees) 102.20267161  
Shift along axis -7.04855673  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J313_003_volume_map_sharp.mrc (#8)
using 1631 atoms  
average map value = 0.515, steps = 28  
shifted from previous position = 0.0279  
rotated from previous position = 0.0243 degrees  
atoms outside contour = 699, contour level = 0.45178  
  
Position of 6m0j (#5) relative to cryosparc_P1_J313_003_volume_map_sharp.mrc
(#8) coordinates:  
Matrix rotation and translation  
-0.21088284 -0.96563088 -0.15193889 207.72562004  
0.96154295 -0.17693655 -0.21006811 -46.93293074  
0.17596471 -0.19039553 0.96580845 -17.25972696  
Axis 0.01006286 -0.16772822 0.98578191  
Axis point 123.64973302 60.13813839 0.00000000  
Rotation angle (degrees) 102.18128181  
Shift along axis -7.05203639  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 52  
shifted from previous position = 1.43  
rotated from previous position = 4.36 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81390072 -0.18683906 0.55014251 -53.57434671  
-0.17362724 0.82539647 0.53719107 136.35516251  
-0.55445396 -0.53273993 0.63935044 3.94283341  
Axis -0.69572028 0.71826143 0.00859096  
Axis point 43.37797892 0.00000000 -58.97732141  
Rotation angle (degrees) 50.25858349  
Shift along axis 135.24528668  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 48  
shifted from previous position = 0.0124  
rotated from previous position = 0.0281 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81372642 -0.18717121 0.55028744 -53.60479921  
-0.17364845 0.82521528 0.53746252 136.29361168  
-0.55470311 -0.53290402 0.63899748 4.02293979  
Axis -0.69573714 0.71824270 0.00878978  
Axis point 43.41313665 0.00000000 -58.85563808  
Rotation angle (degrees) 50.28497319  
Shift along axis 135.22210204  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 44  
shifted from previous position = 0.0127  
rotated from previous position = 0.025 degrees  
atoms outside contour = 1260, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81373829 -0.18703628 0.55031576 -53.59345337  
-0.17352022 0.82545903 0.53712952 136.35540111  
-0.55472582 -0.53257377 0.63925304 4.00700945  
Axis -0.69549805 0.71847424 0.00878785  
Axis point 43.38126342 0.00000000 -58.89583513  
Rotation angle (degrees) 50.26593284  
Shift along axis 135.27719882  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 48  
shifted from previous position = 0.00248  
rotated from previous position = 0.0281 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81381518 -0.18670298 0.55031523 -53.57984932  
-0.17392777 0.82532079 0.53721013 136.39328655  
-0.55448534 -0.53290486 0.63918575 3.96133264  
Axis -0.69571737 0.71826761 0.00830559  
Axis point 43.47600122 0.00000000 -58.94728717  
Rotation angle (degrees) 50.27072475  
Shift along axis 135.27621315  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4112, steps = 48  
shifted from previous position = 0.0295  
rotated from previous position = 0.0437 degrees  
atoms outside contour = 1260, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81376626 -0.18720034 0.55021860 -53.59488328  
-0.17324357 0.82553823 0.53709710 136.30605982  
-0.55477125 -0.53239333 0.63936391 4.02932788  
Axis -0.69544162 0.71852529 0.00907546  
Axis point 43.32288319 0.00000000 -58.87486217  
Rotation angle (degrees) 50.25780953  
Shift along axis 135.24803161  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4112, steps = 40  
shifted from previous position = 0.00764  
rotated from previous position = 0.0226 degrees  
atoms outside contour = 1261, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81397088 -0.18710996 0.54994662 -53.57782605  
-0.17325433 0.82542432 0.53726867 136.27353504  
-0.55446763 -0.53260168 0.63945375 3.94978986  
Axis -0.69575659 0.71822112 0.00901057  
Axis point 43.27164986 0.00000000 -58.96900409  
Rotation angle (degrees) 50.25108280  
Shift along axis 135.18724649  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 44  
shifted from previous position = 0.0208  
rotated from previous position = 0.0292 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81390407 -0.18682020 0.55014396 -53.57511775  
-0.17374592 0.82529770 0.53730444 136.34627073  
-0.55441187 -0.53289954 0.63925391 3.94113472  
Axis -0.69582559 0.71816049 0.00850064  
Axis point 43.40826359 0.00000000 -58.97353288  
Rotation angle (degrees) 50.26573450  
Shift along axis 135.23094438  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4112, steps = 64  
shifted from previous position = 0.0201  
rotated from previous position = 0.0273 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81379720 -0.18712395 0.55019882 -53.59075980  
-0.17338811 0.82544508 0.53719362 136.30861637  
-0.55468070 -0.53256460 0.63929983 4.01029971  
Axis -0.69556826 0.71840451 0.00893119  
Axis point 43.35041175 0.00000000 -58.89423546  
Rotation angle (degrees) 50.26251453  
Shift along axis 135.23657243  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 40  
shifted from previous position = 0.0227  
rotated from previous position = 0.0232 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81385140 -0.18685234 0.55021096 -53.58040001  
-0.17373209 0.82532904 0.53726077 136.35641187  
-0.55449351 -0.53283973 0.63923295 3.95980282  
Axis -0.69574241 0.71824072 0.00853033  
Axis point 43.41616791 0.00000000 -58.95188240  
Rotation angle (degrees) 50.26730969  
Shift along axis 135.24866246  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 60  
shifted from previous position = 0.00522  
rotated from previous position = 0.0105 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81392160 -0.18683790 0.55011201 -53.57396727  
-0.17361349 0.82539123 0.53720357 136.34819115  
-0.55442762 -0.53274846 0.63936617 3.93750873  
Axis -0.69574576 0.71823665 0.00859929  
Axis point 43.37025983 0.00000000 -58.98257342  
Rotation angle (degrees) 50.25741478  
Shift along axis 135.23798846  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4112, steps = 60  
shifted from previous position = 0.0163  
rotated from previous position = 0.0202 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81380633 -0.18711324 0.55018897 -53.58976438  
-0.17338446 0.82545048 0.53718650 136.31066998  
-0.55466845 -0.53255999 0.63931430 4.00555908  
Axis -0.69557153 0.71840139 0.00892674  
Axis point 43.34647299 0.00000000 -58.90055561  
Rotation angle (degrees) 50.26143458  
Shift along axis 135.23704599  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4112, steps = 40  
shifted from previous position = 0.00268  
rotated from previous position = 0.008 degrees  
atoms outside contour = 1261, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81387785 -0.18713893 0.55007442 -53.58478909  
-0.17332078 0.82541948 0.53725468 136.28605225  
-0.55458341 -0.53259901 0.63935557 3.98440263  
Axis -0.69567200 0.71830337 0.00898525  
Axis point 43.31368079 0.00000000 -58.92652431  
Rotation angle (degrees) 50.25838720  
Shift along axis 135.20796925  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 48  
shifted from previous position = 0.027  
rotated from previous position = 0.0366 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81392503 -0.18673967 0.55014030 -53.57169793  
-0.17388431 0.82522363 0.53737344 136.35457339  
-0.55433771 -0.53304246 0.63919906 3.92508005  
Axis -0.69592277 0.71806799 0.00835781  
Axis point 43.43678133 0.00000000 -58.99032043  
Rotation angle (degrees) 50.26975641  
Shift along axis 135.22642437  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 64  
shifted from previous position = 0.00236  
rotated from previous position = 0.00854 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81386346 -0.18680931 0.55020773 -53.57873257  
-0.17382313 0.82527224 0.53731857 136.35713491  
-0.55444728 -0.53294278 0.63918715 3.95199454  
Axis -0.69581295 0.71817342 0.00844276  
Axis point 43.43637810 0.00000000 -58.95855383  
Rotation angle (degrees) 50.27068261  
Shift along axis 135.24221165  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 60  
shifted from previous position = 0.00746  
rotated from previous position = 0.00798 degrees  
atoms outside contour = 1262, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81387516 -0.18686362 0.55017198 -53.57854516  
-0.17370137 0.82532525 0.53727653 136.34421986  
-0.55446827 -0.53284164 0.63925326 3.95611738  
Axis -0.69576904 0.71821460 0.00855783  
Axis point 43.40557877 0.00000000 -58.95612521  
Rotation angle (degrees) 50.26580946  
Shift along axis 135.23655749  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4112, steps = 60  
shifted from previous position = 0.0158  
rotated from previous position = 0.0276 degrees  
atoms outside contour = 1261, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81380033 -0.18715607 0.55018327 -53.59119649  
-0.17331198 0.82548387 0.53715858 136.30686214  
-0.55469991 -0.53249319 0.63934265 4.01061299  
Axis -0.69553090 0.71843979 0.00900199  
Axis point 43.32888491 0.00000000 -58.89615813  
Rotation angle (degrees) 50.25935782  
Shift along axis 135.23870998  
  
Fit molecule A6 Repebody.pdb (#4) to map
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) using 2110 atoms  
average map value = 0.4113, steps = 40  
shifted from previous position = 0.0166  
rotated from previous position = 0.0198 degrees  
atoms outside contour = 1261, contour level = 0.45178  
  
Position of A6 Repebody.pdb (#4) relative to
cryosparc_P1_J313_003_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.81385942 -0.18704257 0.55013446 -53.58973836  
-0.17353463 0.82532547 0.53733007 136.30663693  
-0.55454358 -0.53277852 0.63924055 3.97043341  
Axis -0.69575220 0.71822820 0.00878245  
Axis point 43.35514259 0.00000000 -58.92968177  
Rotation angle (degrees) 50.26686111  
Shift along axis 135.21931908  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J313_003_volume_map_sharp.mrc (#8)
using 1631 atoms  
average map value = 0.515, steps = 40  
shifted from previous position = 0.00266  
rotated from previous position = 0.0117 degrees  
atoms outside contour = 699, contour level = 0.45178  
  
Position of 6m0j (#5) relative to cryosparc_P1_J313_003_volume_map_sharp.mrc
(#8) coordinates:  
Matrix rotation and translation  
-0.21071014 -0.96568197 -0.15185377 207.68486323  
0.96158378 -0.17679304 -0.21000206 -46.94263802  
0.17594851 -0.19026968 0.96583620 -17.25556097  
Axis 0.01009306 -0.16767003 0.98579151  
Axis point 123.63616049 60.13201062 0.00000000  
Rotation angle (degrees) 102.17120136  
Shift along axis -7.04333636  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J313_003_volume_map_sharp.mrc (#8)
using 1631 atoms  
average map value = 0.515, steps = 40  
shifted from previous position = 0.0229  
rotated from previous position = 0.00501 degrees  
atoms outside contour = 699, contour level = 0.45178  
  
Position of 6m0j (#5) relative to cryosparc_P1_J313_003_volume_map_sharp.mrc
(#8) coordinates:  
Matrix rotation and translation  
-0.21074497 -0.96568535 -0.15178394 207.70090303  
0.96156687 -0.17683153 -0.21004706 -46.91998888  
0.17599918 -0.19021677 0.96583739 -17.25909918  
Axis 0.01014322 -0.16766156 0.98579243  
Axis point 123.63437918 60.14651966 0.00000000  
Rotation angle (degrees) 102.17331517  
Shift along axis -7.04045369  
  
Fit molecule 6m0j (#5) to map cryosparc_P1_J313_003_volume_map_sharp.mrc (#8)
using 1631 atoms  
average map value = 0.515, steps = 36  
shifted from previous position = 0.00559  
rotated from previous position = 0.0305 degrees  
atoms outside contour = 698, contour level = 0.45178  
  
Position of 6m0j (#5) relative to cryosparc_P1_J313_003_volume_map_sharp.mrc
(#8) coordinates:  
Matrix rotation and translation  
-0.21026309 -0.96576313 -0.15195726 207.61694279  
0.96169597 -0.17635832 -0.20985377 -46.94962533  
0.17587011 -0.19026119 0.96585216 -17.23533829  
Axis 0.01002057 -0.16766627 0.98579288  
Axis point 123.61318954 60.14206434 0.00000000  
Rotation angle (degrees) 102.14489337  
Shift along axis -7.03816581  
  
Traceback (most recent call last):  
File
"/private/var/folders/d7/yr3jp9rn6pbc676s_kkn0wq40000gn/T/AppTranslocation/F836A459-A0B1-4297-AF0B-E5865467B5A1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 609, in closeEvent  
sbar.destroy()  
File
"/private/var/folders/d7/yr3jp9rn6pbc676s_kkn0wq40000gn/T/AppTranslocation/F836A459-A0B1-4297-AF0B-E5865467B5A1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/private/var/folders/d7/yr3jp9rn6pbc676s_kkn0wq40000gn/T/AppTranslocation/F836A459-A0B1-4297-AF0B-E5865467B5A1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/private/var/folders/d7/yr3jp9rn6pbc676s_kkn0wq40000gn/T/AppTranslocation/F836A459-A0B1-4297-AF0B-E5865467B5A1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/private/var/folders/d7/yr3jp9rn6pbc676s_kkn0wq40000gn/T/AppTranslocation/F836A459-A0B1-4297-AF0B-E5865467B5A1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/private/var/folders/d7/yr3jp9rn6pbc676s_kkn0wq40000gn/T/AppTranslocation/F836A459-A0B1-4297-AF0B-E5865467B5A1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/private/var/folders/d7/yr3jp9rn6pbc676s_kkn0wq40000gn/T/AppTranslocation/F836A459-A0B1-4297-AF0B-E5865467B5A1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  




OpenGL version: unknown
Could not make opengl context currentHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 4 days 21:52

Graphics/Displays:

    Apple G13G:

      Chipset Model: Apple G13G
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        LS32A600U:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
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    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0