![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Last modified 4 years ago
#5253 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202109060834 (2021-09-06 08:34:57 UTC)
Description
Error happend when I tried to change the alpha channel for transparency.
Log:
UCSF ChimeraX version: 1.3.dev202109060834 (2021-09-06)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\Krios\20210423\csrelion\6221\model\rln121demod_modelfit.cxs format
> session
Opened rlnJ121_4M4_denmod_map.ccp4 as #1, grid size 130,175,176, pixel 0.835,
shown at level 0.162, step 1, values float32
Log from Mon Sep 13 16:42:26 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> E:\\\Krios\\\20210423\\\csrelion\\\6221\\\model\\\rlnJ121_AFmodelfit.cxs
Opened rlnJ121_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
0.835, shown at level 0.00787, step 1, values float32
Log from Sun Aug 1 00:14:47 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\Krios\20210423\csrelion\6221\rlnJ121_rlnJ84_AFmodelfit.cxs format
> session
Opened rlnJ121_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
0.835, shown at level 0.00787, step 1, values float32
Log from Fri Jul 30 02:44:06 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\Krios\20210423\csrelion\6221\rlnJ121_rlnJ84_AFmodelfit.cxs format
> session
Opened rlnJ031_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
0.835, shown at level 0.00933, step 1, values float32
Opened rlnJ121_Refine3D_class001.mrc as #10, grid size 352,352,352, pixel
0.835, shown at level 0.00933, step 1, values float32
Log from Fri Jul 30 02:27:40 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\Krios\20210423\csrelion\6221\rlnJ031_AFmodelfit.cxs format session
Opened rlnJ031_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
0.835, shown at level 0.00933, step 1, values float32
Log from Wed Jul 28 23:41:31 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\Krios\20210423\csrelion\6221\rlnJ031_modelfit.cxs format session
Opened rlnJ031_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
0.835, shown at level 0.00933, step 1, values float32
Log from Sun Jul 25 16:29:33 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\H7N100
> cryoEM\20210423\20210423_6429mics\csJ200_modelfit.cxs" format session
Opened cryosparc_P19_J200_004_volume_map.mrc as #1, grid size 352,352,352,
pixel 0.835, shown at level 0.242, step 2, values float32
Log from Sat Jul 24 18:49:24 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\H7N100
> cryoEM\20210423\20210423_6429mics\csJ200_modelfit.cxs" format session
Opened cryosparc_P19_J200_004_volume_map.mrc as #1, grid size 352,352,352,
pixel 0.835, shown at level 0.228, step 2, values float32
Log from Sat Jul 24 18:31:45 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\H7N100
> cryoEM\20210423\20210423_6429mics\csJ200_modelfit.cxs" format session
Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
size 352,352,352, pixel 0.835, shown at level 0.00981, step 1, values float32
Opened cryosparc_P19_J200_004_volume_map.mrc as #6, grid size 352,352,352,
pixel 0.835, shown at level 0.32, step 2, values float32
Log from Sat Jul 24 17:51:44 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\H7N100
> cryoEM\20210423\20210423_6429mics\cs124_model_fit.cxs" format session
Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
size 352,352,352, pixel 0.835, shown at level 0.00981, step 1, values float32
Log from Sat Jun 19 22:49:00 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\H7N100
> cryoEM\20210423\20210423_6429mics\cs124_model_fit.cxs" format session
Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
size 352,352,352, pixel 0.835, shown at level 0.0103, step 1, values float32
Log from Sat Jun 19 20:21:38 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
> E:\Krios\20210423\csrelion\cryosparc\csJ124\cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc
> format mrc
Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
size 352,352,352, pixel 0.835, shown at level 0.00386, step 2, values float32
> volume #1 step 1
> volume #1 level 0.007122
> volume #1 level 0.008949
> volume #1 level 0.01234
> volume #1 level 0.007774
> close session
> open "E:\temp\EM data\H7N100
> cryoEM\20210423\20210423_6429mics\NU\cryosparc_P19_J124_008_volume_map.mrc"
> format mrc
Opened cryosparc_P19_J124_008_volume_map.mrc as #1, grid size 352,352,352,
pixel 0.835, shown at level 0.106, step 2, values float32
> volume #1 level 0.3358
> open "E:/temp/EM data/4n9f.pdb1"
Summary of feedback from opening E:/temp/EM data/4n9f.pdb1
---
warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C
18 GLN C 32 1 15
Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54
1 19
Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82
1 27
Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107
1 23
Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C
110 5 3
680 messages similar to the above omitted
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (133 )
33 messages similar to the above omitted
4n9f.pdb1 title:
Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
info...]
Chain information for 4n9f.pdb1 #2
---
Chain | Description
U | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
Non-standard residues in 4n9f.pdb1 #2
---
ZN — zinc ion
> volume #1 level 0.1176
> hide #!2 models
> show #!2 models
> select #2
6505 atoms, 6643 bonds, 8 pseudobonds, 800 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,82.069,0,1,0,125.95,0,0,1,150.79
> select /X:1-98
748 atoms, 762 bonds, 1 pseudobond, 95 residues, 2 models selected
> sequence chain #2/X
Alignment identifier is 2/X
> sequence chain #2/Y
Alignment identifier is 2/Y
> sequence chain #2/a
Alignment identifier is 2/a
> sequence chain #2/b
Alignment identifier is 2/b
> select #2
6505 atoms, 6643 bonds, 8 pseudobonds, 800 residues, 3 models selected
> select clear
> style sphere
Changed 6505 atom styles
> hide atoms
> show cartoons
> open "E:/temp/EM data/6p3x chain A.pdb" "E:/temp/EM data/6p40 chain A.pdb"
Summary of feedback from opening E:/temp/EM data/6p3x chain A.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (65 )
Cannot find LINK/SSBOND residue CYS (97 )
Cannot find LINK/SSBOND residue CYS (100 )
Cannot find LINK/SSBOND residue ZN (701 )
Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (65 )
Cannot find LINK/SSBOND residue CYS (97 )
Cannot find LINK/SSBOND residue CYS (100 )
Cannot find LINK/SSBOND residue HIS (257 )
Cannot find LINK/SSBOND residue CYS (287 )
2 messages similar to the above omitted
6p3x chain A.pdb title:
Crystal structure of full length APOBEC3G E/Q (pH 7.0) [more info...]
Chain information for 6p3x chain A.pdb #3
---
Chain | Description
A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G
Non-standard residues in 6p3x chain A.pdb #3
---
ZN — zinc ion
6p40 chain A.pdb title:
Crystal structure of full length APOBEC3G FKL [more info...]
Chain information for 6p40 chain A.pdb #4
---
Chain | Description
A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G
Non-standard residues in 6p40 chain A.pdb #4
---
ZN — zinc ion
> hide #!3 models
> show #!3 models
> select #3
3217 atoms, 3119 bonds, 5 pseudobonds, 558 residues, 3 models selected
> view matrix models #3,1,0,0,-46.848,0,1,0,-21.585,0,0,1,10.858
> view matrix models #3,1,0,0,-48.22,0,1,0,-25.148,0,0,1,12.671
> hide #!3 models
> show #!3 models
> ~select #3
Nothing selected
> sequence chain #2/a
Alignment identifier is 2/a
> select #4/A:7-382
3020 atoms, 3120 bonds, 364 residues, 1 model selected
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:7-382
3020 atoms, 3120 bonds, 364 residues, 1 model selected
> select #4/A:266-269
40 atoms, 43 bonds, 4 residues, 1 model selected
> select #4/A:264-269
56 atoms, 59 bonds, 6 residues, 1 model selected
> select #4/A:264
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:264
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> volume #1 level 0.3448
> hide #!2 models
> hide #!4 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #2/U,X,Y cartoons
> hide #!3 models
> ui tool show "Side View"
> select #2/b:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,89.797,0,1,0,73.59,0,0,1,220.75
> view matrix models #2,1,0,0,105.3,0,1,0,141.33,0,0,1,219.37
> view matrix models #2,1,0,0,89.879,0,1,0,100.16,0,0,1,218.31
> view matrix models #2,1,0,0,95.388,0,1,0,87.113,0,0,1,217.57
> view matrix models
> #2,-0.47392,0.18512,-0.86089,62.626,0.34948,-0.85782,-0.37685,-2.7076,-0.80825,-0.47946,0.34184,168.35
> view matrix models
> #2,-0.47392,0.18512,-0.86089,62.096,0.34948,-0.85782,-0.37685,-2.3394,-0.80825,-0.47946,0.34184,168.14
> view matrix models
> #2,-0.13369,-0.48627,-0.86352,35.836,0.89747,-0.42898,0.10262,36.616,-0.42033,-0.76126,0.49376,164.22
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> select #3/A:282
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models #3,1,0,0,75.338,0,1,0,83.713,0,0,1,32.568
> view matrix models #3,1,0,0,76.767,0,1,0,90.212,0,0,1,41.682
> view matrix models
> #3,0.98757,-0.087,-0.13093,78.712,0.072499,0.99109,-0.11172,89.276,0.13948,0.10084,0.98508,37.502
> view matrix models
> #3,0.99211,-0.12267,-0.02597,78.575,0.11504,0.97286,-0.20077,88.995,0.049894,0.1962,0.97929,38.274
> view matrix models
> #3,0.66084,-0.64639,-0.38141,93.814,0.24387,0.66554,-0.7054,92.343,0.70981,0.37314,0.59745,23.642
> view matrix models
> #3,0.66084,-0.64639,-0.38141,97.595,0.24387,0.66554,-0.7054,96.165,0.70981,0.37314,0.59745,25.082
> view matrix models
> #3,0.56087,-0.72856,-0.39322,96.213,0.21775,0.58805,-0.77896,93.094,0.79875,0.35127,0.48847,21.719
> view matrix models
> #3,0.56087,-0.72856,-0.39322,93.728,0.21775,0.58805,-0.77896,93.041,0.79875,0.35127,0.48847,24.94
> view matrix models
> #3,-0.23024,-0.97284,0.024087,111.85,-0.33671,0.056418,-0.93992,112.29,0.91302,-0.22452,-0.34056,33.414
> view matrix models
> #3,0.031463,-0.9748,0.22087,105.35,0.36203,-0.19486,-0.91157,100.25,0.93163,0.10864,0.34678,25.738
> view matrix models
> #3,-0.031769,-0.97212,0.23232,106.62,0.3211,-0.23005,-0.91868,101.59,0.94651,0.045414,0.31946,26.327
> view matrix models
> #3,-0.031769,-0.97212,0.23232,106.14,0.3211,-0.23005,-0.91868,100.12,0.94651,0.045414,0.31946,24.469
> select #3/A:4-383
3021 atoms, 3119 bonds, 1 pseudobond, 362 residues, 2 models selected
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:148-187
343 atoms, 355 bonds, 40 residues, 1 model selected
> select #3/A:4-8
44 atoms, 43 bonds, 5 residues, 1 model selected
> select #3/A:383
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:208-383
1351 atoms, 1390 bonds, 1 pseudobond, 162 residues, 2 models selected
> select #3/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:194-198
45 atoms, 45 bonds, 5 residues, 1 model selected
> select clear
> hide #3/A:199-379
> show #3/A:199-379
> hide #3/A:199-379
> hide #3/A:199-379 cartoons
> sequence chain #3/A
Alignment identifier is 3/A
> hide #3/A:198-385 cartoons
> ui mousemode right "translate selected models"
> select #3
3217 atoms, 3119 bonds, 5 pseudobonds, 558 residues, 3 models selected
> view matrix models
> #3,-0.031769,-0.97212,0.23232,112.65,0.3211,-0.23005,-0.91868,74.3,0.94651,0.045414,0.31946,101.89
> view matrix models
> #3,-0.031769,-0.97212,0.23232,113.89,0.3211,-0.23005,-0.91868,77.891,0.94651,0.045414,0.31946,100.3
> view matrix models
> #3,-0.031769,-0.97212,0.23232,110.84,0.3211,-0.23005,-0.91868,69.534,0.94651,0.045414,0.31946,89.418
> view matrix models
> #3,0.095623,-0.93742,0.33483,110.26,0.75414,-0.15133,-0.63905,68.081,0.64972,0.31361,0.69247,86.102
> view matrix models
> #3,-0.30817,-0.77321,0.55423,108.61,0.68542,-0.58447,-0.43428,76.789,0.65972,0.24605,0.71009,87.38
> view matrix models
> #3,0.031642,-0.83897,0.54326,109.16,0.68853,-0.3757,-0.6203,72.395,0.72452,0.39368,0.56577,84.119
> view matrix models
> #3,-0.098809,-0.882,0.46078,109.96,0.25251,-0.47011,-0.84571,74.3,0.96254,0.032786,0.26916,89.476
> view matrix models
> #3,-0.5214,-0.63349,0.57169,106.49,0.27011,-0.75805,-0.59364,80.305,0.80943,-0.1551,0.56636,94.084
> select clear
> volume #1 level 0.2431
> select #3/A:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.5214,-0.63349,0.57169,113.84,0.27011,-0.75805,-0.59364,133.83,0.80943,-0.1551,0.56636,94.989
> view matrix models
> #3,-0.5163,-0.64003,0.56902,113.95,0.29417,-0.75654,-0.58404,133.78,0.8043,-0.13416,0.57888,94.649
> view matrix models
> #3,-0.5163,-0.64003,0.56902,80.793,0.29417,-0.75654,-0.58404,209.7,0.8043,-0.13416,0.57888,93.988
> show #!2 models
> view matrix models
> #3,-0.5163,-0.64003,0.56902,39.036,0.29417,-0.75654,-0.58404,186.73,0.8043,-0.13416,0.57888,65.545
> hide #!2 models
> hide #!3 models
> volume #1 level 0.2831
> symclip 15
Unknown command: symclip 15
> ui mousemode right clip
> ui mousemode right clip
> select #1
3 models selected
> select #1
3 models selected
> select clear
> select #1
3 models selected
> select clear
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right zone
> ui mousemode right "contour level"
> volume #1 level 0.2765
> ui mousemode right "move planes"
> volume #1 region 0,0,0,351,351,351
> volume #1 region 0,0,0,351,351,351
> volume #1 region 0,0,0,351,351,351
> select #1
3 models selected
> volume #1 region 0,0,0,351,351,351
> select clear
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #1 region 0,0,0,351,351,351
> select clear
> select #3/A:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> volume #1 region 0,0,0,351,351,351
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.5163,-0.64003,0.56902,44.26,0.29417,-0.75654,-0.58404,143.34,0.8043,-0.13416,0.57888,132.86
> view matrix models
> #3,-0.5163,-0.64003,0.56902,163.71,0.29417,-0.75654,-0.58404,145.93,0.8043,-0.13416,0.57888,121.53
> hide #!1 models
> view matrix models
> #3,-0.5163,-0.64003,0.56902,164.91,0.29417,-0.75654,-0.58404,134.33,0.8043,-0.13416,0.57888,113.77
> view matrix models
> #3,-0.74687,0.63083,-0.21032,139.65,-0.42642,-0.69705,-0.57645,134.6,-0.51025,-0.34084,0.7896,120.64
> view matrix models
> #3,0.30996,0.94419,0.11152,132.83,-0.6873,0.30357,-0.6599,116.39,-0.65692,0.12789,0.74303,112.14
> view matrix models
> #3,0.10196,0.93746,-0.33283,132.06,-0.74126,-0.15153,-0.65389,124.9,-0.66343,0.31338,0.67945,108.55
> view matrix models
> #3,0.018085,0.92014,0.39116,134.62,-0.61282,0.31933,-0.72283,115.78,-0.79002,-0.22664,0.56966,118.43
> view matrix models
> #3,0.8274,0.34339,-0.44441,141.34,-0.54098,0.27477,-0.79489,116.26,-0.15085,0.8981,0.41311,96.036
> view matrix models
> #3,0.28275,0.035649,-0.95853,146.55,-0.95896,0.032369,-0.28168,122.99,0.020985,0.99884,0.043338,92.791
> view matrix models
> #3,-0.11008,-0.54525,0.83101,163.16,0.15298,-0.83542,-0.52788,136.21,0.98208,0.069018,0.17538,108.53
> view matrix models
> #3,0.39195,-0.51294,0.76372,161.43,0.12714,-0.79197,-0.59717,135.26,0.91116,0.33116,-0.2452,102.61
> view matrix models
> #3,0.20589,-0.086388,0.97476,154.52,0.29632,-0.94383,-0.14623,139.04,0.93264,0.31894,-0.16872,103.02
> view matrix models
> #3,-0.29935,-0.35094,0.88726,160.09,0.29859,-0.91765,-0.26222,138.22,0.90622,0.18643,0.37949,107.09
> view matrix models
> #3,-0.55253,-0.53977,0.6351,163.32,0.5311,-0.81526,-0.23084,135.99,0.64238,0.20975,0.73713,108.19
> view matrix models
> #3,-0.40994,0.7637,-0.4987,135.74,-0.87204,-0.16787,0.45975,128.66,0.2674,0.62336,0.73479,101.25
> view matrix models
> #3,0.28939,0.95548,-0.057521,132.17,-0.95602,0.2915,0.032473,119.11,0.047795,0.045593,0.99782,113.08
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view matrix models
> #3,0.28939,0.95548,-0.057521,132.13,-0.95602,0.2915,0.032473,118.95,0.047795,0.045593,0.99782,113.46
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view matrix models
> #3,0.28939,0.95548,-0.057521,133.05,-0.95602,0.2915,0.032473,116.86,0.047795,0.045593,0.99782,113.77
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view matrix models
> #3,0.28939,0.95548,-0.057521,55.181,-0.95602,0.2915,0.032473,122.77,0.047795,0.045593,0.99782,111.92
> view matrix models
> #3,0.28939,0.95548,-0.057521,44.323,-0.95602,0.2915,0.032473,136.59,0.047795,0.045593,0.99782,121.8
> view matrix models
> #3,-0.83724,0.41686,0.35393,57.548,-0.54202,-0.5468,-0.63814,149.35,-0.072488,-0.72611,0.68375,135.35
> view matrix models
> #3,-0.80717,0.35904,0.46858,58.889,-0.58585,-0.58476,-0.56111,150.35,0.072543,-0.72742,0.68234,135.1
> view matrix models
> #3,-0.53163,0.73326,0.4239,51.344,-0.82204,-0.32616,-0.46676,146.29,-0.204,-0.59661,0.77617,133.47
> view matrix models
> #3,-0.54174,0.79862,0.26213,49.69,-0.7492,-0.31742,-0.58133,145.67,-0.38106,-0.51132,0.77029,132.21
> view matrix models
> #3,-0.65111,0.67807,0.341,52.345,-0.72076,-0.41161,-0.55775,147.42,-0.23784,-0.60894,0.75672,133.71
> view matrix models
> #3,-0.65111,0.67807,0.341,54.254,-0.72076,-0.41161,-0.55775,144.43,-0.23784,-0.60894,0.75672,133.12
> view matrix models
> #3,-0.65111,0.67807,0.341,54.317,-0.72076,-0.41161,-0.55775,143.5,-0.23784,-0.60894,0.75672,134.8
> view matrix models
> #3,-0.65111,0.67807,0.341,61.57,-0.72076,-0.41161,-0.55775,127.97,-0.23784,-0.60894,0.75672,133.57
> view matrix models
> #3,-0.65111,0.67807,0.341,60.541,-0.72076,-0.41161,-0.55775,132.03,-0.23784,-0.60894,0.75672,132.11
> view matrix models
> #3,-0.91071,0.39011,0.13573,65.744,-0.3548,-0.57059,-0.74064,133.75,-0.21148,-0.72266,0.65805,133.87
> view matrix models
> #3,-0.89981,0.43223,-0.059307,64.384,-0.20848,-0.54541,-0.81183,132.81,-0.38324,-0.71813,0.58088,133.89
> view matrix models
> #3,-0.92064,0.3857,0.060425,65.627,-0.28693,-0.56352,-0.77467,133.4,-0.26474,-0.73053,0.62947,134.04
> view matrix models
> #3,-0.82793,0.55971,-0.035486,61.967,-0.29928,-0.49444,-0.81606,132.03,-0.4743,-0.66502,0.57687,133.07
> view matrix models
> #3,0.99856,-0.049604,-0.02065,69.84,0.052977,0.84477,0.53251,110.56,-0.00897,-0.53283,0.84617,130.54
> view matrix models
> #3,-0.26273,-0.9556,0.13342,89.348,-0.70163,0.28414,0.65343,122.66,-0.66233,0.078062,-0.74513,115.9
> view matrix models
> #3,-0.87646,-0.43241,0.21177,81.07,-0.2802,0.81575,0.506,111.64,-0.39155,0.38415,-0.83613,109.48
> view matrix models
> #3,-0.83922,0.21291,-0.50038,67.043,-0.042031,0.89202,0.45004,109.63,0.54217,0.39871,-0.73965,107.75
> view matrix models
> #3,-0.83922,0.21291,-0.50038,84.217,-0.042031,0.89202,0.45004,86.62,0.54217,0.39871,-0.73965,84.77
> view matrix models
> #3,-0.83922,0.21291,-0.50038,140.69,-0.042031,0.89202,0.45004,84.619,0.54217,0.39871,-0.73965,95.119
> view matrix models
> #3,-0.83922,0.21291,-0.50038,139.93,-0.042031,0.89202,0.45004,84.666,0.54217,0.39871,-0.73965,94.908
> view matrix models
> #3,-0.83922,0.21291,-0.50038,139.68,-0.042031,0.89202,0.45004,99.584,0.54217,0.39871,-0.73965,100.19
> fitmap #3 inMap #1
Fit molecule 6p3x chain A.pdb (#3) to map
cryosparc_P19_J124_008_volume_map.mrc (#1) using 3217 atoms
average map value = 0.1892, steps = 132
shifted from previous position = 2.04
rotated from previous position = 5.82 degrees
atoms outside contour = 2206, contour level = 0.27648
Position of 6p3x chain A.pdb (#3) relative to
cryosparc_P19_J124_008_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.87034826 0.22874541 -0.43608420 140.10276575
0.03062042 0.90898975 0.41569220 100.13842757
0.49148375 0.34844390 -0.79814193 101.03676319
Axis -0.07072275 -0.97549160 -0.20836129
Axis point 56.79793799 0.00000000 56.80721198
Rotation angle (degrees) 151.61224811
Shift along axis -128.64479799
> volume #1 level 0.4892
> volume #1 level 0.2179
> show #3/A
> hide #3/A
> show #3/A cartoons
> hide #3/A 199-385 cartoon
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #3/A:199-385 cartoons
> hide #!1 models
> show #!1 models
> show #3/A:199-385 cartoons
> hide #3/A:1-199 cartoons
> select #3/A:372
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.87035,0.22875,-0.43608,140.48,0.03062,0.90899,0.41569,99.894,0.49148,0.34844,-0.79814,94.631
> view matrix models
> #3,-0.87341,0.22505,-0.43187,140.58,0.017543,0.90078,0.43393,100.28,0.48667,0.37142,-0.79069,94.653
> view matrix models
> #3,-0.87871,0.21819,-0.42458,140.75,-0.0053811,0.88485,0.46585,100.97,0.47733,0.41164,-0.77635,94.716
> view matrix models
> #3,-0.9775,-0.020504,-0.20992,143.85,-0.094828,0.93173,0.35056,105.13,0.1884,0.36258,-0.91271,107.12
> view matrix models
> #3,-0.87089,-0.4578,0.17879,138.53,-0.41734,0.88099,0.22291,118.77,-0.25956,0.11951,-0.9583,125.75
> view matrix models
> #3,-0.89518,-0.44555,-0.012122,140.96,-0.38279,0.78246,-0.49115,123.69,0.22831,-0.43502,-0.87099,108.79
> view matrix models
> #3,0.21421,0.7278,-0.65147,98.429,0.10868,0.64506,0.75637,95.296,0.97072,-0.23283,0.059085,71.849
> view matrix models
> #3,0.39182,0.65691,-0.64417,91.873,0.69699,0.2451,0.6739,75.182,0.60057,-0.71302,-0.36182,91.599
> view matrix models
> #3,0.39182,0.65691,-0.64417,92.889,0.69699,0.2451,0.6739,80.962,0.60057,-0.71302,-0.36182,98.671
> view matrix models
> #3,0.39182,0.65691,-0.64417,89.219,0.69699,0.2451,0.6739,63.16,0.60057,-0.71302,-0.36182,84.852
> view matrix models
> #3,-0.04909,0.68197,-0.72973,106.71,0.94315,0.2721,0.19084,57.535,0.32871,-0.67888,-0.65656,97.526
> view matrix models
> #3,-0.95366,0.23223,0.1913,135.89,0.11572,0.87001,-0.47925,92.071,-0.27773,-0.43491,-0.85658,121.33
> view matrix models
> #3,-0.61477,-0.52766,0.5862,123.05,-0.73143,0.6595,-0.17344,123,-0.29508,-0.53538,-0.79139,121.91
> view matrix models
> #3,-0.88079,-0.26572,-0.39192,140.05,-0.23914,0.96401,-0.11615,102.31,0.40868,-0.0085789,-0.91264,93.574
> view matrix models
> #3,-0.87594,-0.44788,-0.17929,138.94,-0.39912,0.46401,0.79082,103.27,-0.271,0.76427,-0.5852,113.54
> view matrix models
> #3,-0.81781,-0.48877,0.30379,132.96,-0.13462,0.67571,0.72477,92.726,-0.55952,0.55183,-0.61841,125.82
> view matrix models
> #3,-0.86669,-0.43087,0.25139,135.01,-0.28403,0.84051,0.46138,99.87,-0.41009,0.32847,-0.85084,122.97
> view matrix models
> #3,-0.89763,-0.39751,0.19039,136.54,-0.36182,0.91126,0.19672,104.69,-0.2517,0.1077,-0.9618,118.78
> view matrix models
> #3,-0.84038,0.28985,-0.45798,136.58,0.10384,0.91544,0.38883,85.255,0.53196,0.2792,-0.79942,86.649
> view matrix models
> #3,-0.90227,0.19335,-0.38539,138.79,-0.17087,0.66029,0.73131,94.131,0.39587,0.72569,-0.56272,87.96
> view matrix models
> #3,0.94919,-0.31323,0.030575,66.651,-0.14687,-0.52678,-0.83722,111.25,0.27835,0.79018,-0.54601,92.045
> view matrix models
> #3,-0.67255,0.5638,-0.47939,129.1,0.69424,0.25625,-0.67258,74.183,-0.25635,-0.78516,-0.56375,119.68
> view matrix models
> #3,-0.67255,0.5638,-0.47939,130.89,0.69424,0.25625,-0.67258,77.137,-0.25635,-0.78516,-0.56375,104.71
> view matrix models
> #3,-0.67255,0.5638,-0.47939,128.69,0.69424,0.25625,-0.67258,67.03,-0.25635,-0.78516,-0.56375,98.504
> view matrix models
> #3,-0.67767,0.62545,-0.38675,127.86,0.73489,0.55706,-0.38682,61.81,-0.026494,-0.54635,-0.83714,90.858
> view matrix models
> #3,-0.88356,0.462,-0.076695,133.96,0.068844,0.29012,0.95451,77.609,0.46323,0.83809,-0.28814,61.471
> view matrix models
> #3,-0.67717,0.6242,-0.38963,127.87,0.73508,0.55001,-0.39642,61.912,-0.03314,-0.55485,-0.83129,91.103
> view matrix models
> #3,-0.67717,0.6242,-0.38963,128.06,0.73508,0.55001,-0.39642,64.335,-0.03314,-0.55485,-0.83129,97.544
> view matrix models
> #3,-0.67717,0.6242,-0.38963,128.21,0.73508,0.55001,-0.39642,64.095,-0.03314,-0.55485,-0.83129,94.506
> view matrix models
> #3,-0.67717,0.6242,-0.38963,127.84,0.73508,0.55001,-0.39642,62.771,-0.03314,-0.55485,-0.83129,94.818
> view matrix models
> #3,-0.67868,0.62771,-0.38128,127.82,0.7343,0.57008,-0.36852,62.485,-0.013963,-0.53008,-0.84783,94.108
> view matrix models
> #3,-0.70335,0.44619,-0.55337,130.97,0.51347,-0.21944,-0.82958,78.207,-0.49158,-0.86762,-0.074766,107.62
> view matrix models
> #3,0.056509,0.61704,-0.7849,102.96,0.63751,-0.62732,-0.44727,72.145,-0.76837,-0.4751,-0.42882,119.38
> view matrix models
> #3,0.10522,0.73282,-0.67223,99.66,0.97009,-0.22434,-0.092715,54.718,-0.21875,-0.64237,-0.73451,101.54
> view matrix models
> #3,0.066368,0.81588,-0.5744,99.985,0.95427,0.11627,0.27541,50.817,0.29149,-0.56641,-0.77085,81.929
> view matrix models
> #3,0.093534,0.77836,-0.62082,99.487,0.99456,-0.044318,0.09428,51.459,0.045871,-0.62626,-0.77827,91.673
> view matrix models
> #3,0.093534,0.77836,-0.62082,99.83,0.99456,-0.044318,0.09428,53.316,0.045871,-0.62626,-0.77827,93.706
> view matrix models
> #3,0.093534,0.77836,-0.62082,99.271,0.99456,-0.044318,0.09428,50.013,0.045871,-0.62626,-0.77827,89.344
> view matrix models
> #3,-0.50639,0.29676,-0.80963,125.95,0.85721,0.27513,-0.43531,58.177,0.093569,-0.91446,-0.3937,85.66
> view matrix models
> #3,-0.38444,0.06422,-0.92092,123.21,0.88278,0.31737,-0.34638,56.285,0.27003,-0.94613,-0.1787,77.283
> view matrix models
> #3,-0.3964,0.083027,-0.91431,123.53,0.85411,0.39859,-0.33411,56.925,0.33669,-0.91336,-0.22892,74.99
> view matrix models
> #3,-0.3964,0.083027,-0.91431,123.73,0.85411,0.39859,-0.33411,58.903,0.33669,-0.91336,-0.22892,79.664
> view matrix models
> #3,-0.3964,0.083027,-0.91431,123.1,0.85411,0.39859,-0.33411,57.081,0.33669,-0.91336,-0.22892,81.941
> view matrix models
> #3,-0.43087,0.12332,-0.89395,124.08,0.76033,0.58318,-0.28602,59.467,0.48606,-0.80293,-0.34504,76.669
> view matrix models
> #3,-0.39014,0.073603,-0.91781,122.93,0.86944,0.35758,-0.34091,56.73,0.30309,-0.93098,-0.2035,83.1
> view matrix models
> #3,-0.39014,0.073603,-0.91781,122.87,0.86944,0.35758,-0.34091,56.524,0.30309,-0.93098,-0.2035,83.249
> view matrix models
> #3,-0.39014,0.073603,-0.91781,122.84,0.86944,0.35758,-0.34091,55.815,0.30309,-0.93098,-0.2035,80.871
> view matrix models
> #3,-0.38492,0.06505,-0.92065,122.7,0.88167,0.3209,-0.34595,55.549,0.27293,-0.94488,-0.18087,81.904
> view matrix models
> #3,-0.69031,-0.082931,0.71875,121.72,-0.62592,0.56674,-0.53575,113.82,-0.36291,-0.81971,-0.44313,107.87
> view matrix models
> #3,-0.66236,-0.054639,0.74719,120.29,-0.55495,0.70578,-0.44034,109.7,-0.50329,-0.70632,-0.49781,113.19
> view matrix models
> #3,-0.62269,-0.031018,0.78185,118.36,-0.43965,0.84044,-0.31681,103.65,-0.64727,-0.54102,-0.53697,118.48
> view matrix models
> #3,-0.62269,-0.031018,0.78185,118.43,-0.43965,0.84044,-0.31681,104.09,-0.64727,-0.54102,-0.53697,119.13
> view matrix models
> #3,-0.62269,-0.031018,0.78185,117.31,-0.43965,0.84044,-0.31681,98.49,-0.64727,-0.54102,-0.53697,114.33
> view matrix models
> #3,-0.62269,-0.031018,0.78185,118.13,-0.43965,0.84044,-0.31681,102.97,-0.64727,-0.54102,-0.53697,119.29
> show #3/A cartoons
> view matrix models
> #3,-0.62269,-0.031018,0.78185,123.87,-0.43965,0.84044,-0.31681,117.03,-0.64727,-0.54102,-0.53697,88.45
> select clear
> hide #!3 models
> show #!4 models
> select clear
> select #4/A:69
11 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models #4,1,0,0,5.7691,0,1,0,135.5,0,0,1,82.984
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:131
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1
3 models selected
> select #1
3 models selected
> select clear
> select #4/A:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #4/A:1-193 cartoons
> hide #4/A:1-193
> hide #4/A:1-193
> select :ZN
4 atoms, 4 residues, 3 models selected
> hide (#!4 & sel) target a
> select #4/A:260
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models #4,1,0,0,20.725,0,1,0,110.33,0,0,1,62.54
> view matrix models #4,1,0,0,19.578,0,1,0,113.48,0,0,1,63.698
> view matrix models #4,1,0,0,85.757,0,1,0,76.546,0,0,1,67.665
> view matrix models #4,1,0,0,98.303,0,1,0,115.37,0,0,1,85.361
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> view matrix models #4,1,0,0,98.72,0,1,0,116.97,0,0,1,87.661
> view matrix models #4,1,0,0,96.89,0,1,0,111.5,0,0,1,86.719
> view matrix models
> #4,0.99612,-0.025471,-0.084224,98.951,0.003591,0.96816,-0.25032,116.93,0.087918,0.24905,0.96449,83.431
> view matrix models
> #4,0.99889,0.0046894,0.046765,95.706,-0.010923,0.99093,0.13395,108.93,-0.045713,-0.13432,0.98988,91.799
> view matrix models
> #4,0.99889,0.0046894,0.046765,95.969,-0.010923,0.99093,0.13395,109.15,-0.045713,-0.13432,0.98988,88.592
> view matrix models
> #4,0.90602,-0.21064,0.36709,93.128,-0.31948,0.22848,0.91963,105.93,-0.27759,-0.95049,0.13971,118.34
> view matrix models
> #4,0.87302,-0.30397,0.38136,94.341,-0.41232,-0.042442,0.91005,110.45,-0.26044,-0.95174,-0.16238,124.29
> view matrix models
> #4,0.87302,-0.30397,0.38136,93.661,-0.41232,-0.042442,0.91005,109.04,-0.26044,-0.95174,-0.16238,127.63
> view matrix models
> #4,0.87302,-0.30397,0.38136,86.937,-0.41232,-0.042442,0.91005,93.587,-0.26044,-0.95174,-0.16238,151.61
> view matrix models
> #4,0.87302,-0.30397,0.38136,88.21,-0.41232,-0.042442,0.91005,96.999,-0.26044,-0.95174,-0.16238,149.96
> view matrix models
> #4,0.78223,-0.61264,0.11311,98.415,-0.61582,-0.78784,-0.0084361,126.96,0.094283,-0.063058,-0.99355,152.05
> view matrix models
> #4,0.78223,-0.61264,0.11311,97.973,-0.61582,-0.78784,-0.0084361,125.6,0.094283,-0.063058,-0.99355,151.61
> view matrix models
> #4,0.78223,-0.61264,0.11311,97.064,-0.61582,-0.78784,-0.0084361,122.9,0.094283,-0.063058,-0.99355,151.25
> ui mousemode right pivot
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.61095,0.79166,-0.0041406,134.5,0.77651,0.60026,0.19162,68.465,0.15418,0.11386,-0.98146,148.19
> view matrix models
> #4,-0.64031,0.76478,0.071537,133.92,0.7134,0.55758,0.42447,65.643,0.28474,0.32282,-0.90261,141.37
> view matrix models
> #4,-0.77154,0.54049,0.33556,133.51,0.63507,0.68558,0.3559,68.807,-0.037697,0.48769,-0.8722,149.68
> view matrix models
> #4,-0.6934,0.59994,0.39909,129.43,0.71787,0.62297,0.31077,67.583,-0.062178,0.50198,-0.86264,150.14
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.6934,0.59994,0.39909,128.47,0.71787,0.62297,0.31077,66.378,-0.062178,0.50198,-0.86264,153.68
> view matrix models
> #4,-0.69611,0.69855,0.16569,133.01,0.67568,0.71546,-0.17766,77.619,-0.24265,-0.011719,-0.97004,164.3
> view matrix models
> #4,-0.69611,0.69855,0.16569,132.75,0.67568,0.71546,-0.17766,76.519,-0.24265,-0.011719,-0.97004,161.44
> view matrix models
> #4,-0.69611,0.69855,0.16569,132.15,0.67568,0.71546,-0.17766,75.723,-0.24265,-0.011719,-0.97004,163.48
> view matrix models
> #4,-0.69611,0.69855,0.16569,132.4,0.67568,0.71546,-0.17766,75.933,-0.24265,-0.011719,-0.97004,162.05
> view matrix models
> #4,-0.69491,0.69681,0.17763,132.11,0.67967,0.71713,-0.15418,75.299,-0.23482,0.013587,-0.97194,161.72
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.69061,0.68419,0.23438,130.84,0.69623,0.71667,-0.040611,72.364,-0.19576,0.13513,-0.9713,159.84
> view matrix models
> #4,-0.69061,0.68419,0.23438,130.9,0.69623,0.71667,-0.040611,72.892,-0.19576,0.13513,-0.9713,161.8
> view matrix models
> #4,0.25249,0.29044,0.92298,89.475,0.56016,0.73391,-0.38418,84.313,-0.78897,0.61402,0.022616,156.04
> view matrix models
> #4,0.11226,0.39737,0.91077,93.44,0.24436,0.87737,-0.41292,93.8,-0.96316,0.26891,0.0013931,163.71
> view matrix models
> #4,0.0030587,0.43449,0.90067,96.792,0.018604,0.90049,-0.43447,101.04,-0.99982,0.018085,-0.005329,166.34
> view matrix models
> #4,0.13845,0.38345,0.91312,92.665,0.30069,0.86221,-0.40766,92.048,-0.94362,0.33101,0.0040702,162.72
> view matrix models
> #4,-0.23648,0.42574,0.8734,104.75,0.4576,0.84177,-0.28642,84.767,-0.85714,0.33193,-0.39387,168.59
> view matrix models
> #4,-0.15878,0.35823,0.92003,101.74,0.6332,0.75193,-0.18349,77.685,-0.75753,0.55343,-0.34622,163.31
> view matrix models
> #4,0.16465,0.2773,0.94657,91.728,0.53484,0.78123,-0.3219,83.495,-0.82875,0.55927,-0.019678,158.46
> view matrix models
> #4,-0.0070054,0.38479,0.92298,96.894,0.15943,0.91162,-0.37885,95.48,-0.98718,0.1445,-0.067735,166.6
> view matrix models
> #4,-0.17725,0.40858,0.89534,102.56,-0.177,0.88168,-0.43739,107.18,-0.96812,-0.23601,-0.08396,168.45
> view matrix models
> #4,-0.36608,0.43792,0.82111,109.76,-0.057875,0.86993,-0.48976,104.73,-0.92878,-0.22681,-0.29312,171.67
> view matrix models
> #4,-0.11966,0.36726,0.92239,100.45,0.4429,0.85124,-0.28148,85.059,-0.88855,0.37484,-0.26452,166.54
> view matrix models
> #4,-0.19871,0.40976,0.89029,103.32,0.27422,0.89537,-0.35089,91.461,-0.94091,0.17441,-0.29028,169.79
> view matrix models
> #4,-0.33474,0.49538,0.80159,108.91,0.39486,0.84612,-0.35801,88.194,-0.85559,0.19667,-0.47884,171.1
> view matrix models
> #4,-0.20676,0.39065,0.89702,103.53,0.6821,0.71484,-0.15409,75.763,-0.70142,0.57999,-0.41426,162.91
> view matrix models
> #4,0.10211,0.3253,0.94008,93.517,0.59868,0.73462,-0.31923,81.741,-0.79445,0.59541,-0.11973,159.36
> view matrix models
> #4,0.093505,0.33456,0.93772,93.78,0.5782,0.7485,-0.32471,82.409,-0.81052,0.57256,-0.12346,160.06
> view matrix models
> #4,0.28649,0.39843,0.87131,88.952,0.51049,0.7061,-0.49074,88.265,-0.81075,0.58539,-0.0011093,157.37
> view matrix models
> #4,0.13994,0.49925,0.85508,93.229,0.18455,0.8353,-0.5179,98.106,-0.97281,0.23028,0.024758,163.72
> view matrix models
> #4,0.050554,0.30951,0.94955,94.976,0.20795,0.92667,-0.31312,92.508,-0.97683,0.21329,-0.017514,164.84
> view matrix models
> #4,0.1675,0.23672,0.95703,91.639,0.46344,0.8379,-0.28836,84.651,-0.87016,0.49182,0.03064,159.02
> view matrix models
> #4,0.43084,0.14413,0.89084,85.51,0.32979,0.89374,-0.3041,88.769,-0.84001,0.42481,0.33752,151.9
> view matrix models
> #4,0.43383,0.14176,0.88977,85.454,0.33664,0.89052,-0.30602,88.618,-0.83574,0.4323,0.33861,151.7
> view matrix models
> #4,0.33752,0.19978,0.91987,87.437,0.1243,0.9592,-0.25393,93.62,-0.93307,0.20005,0.29892,156.8
> view matrix models
> #4,0.17935,0.23598,0.95506,91.322,-0.19811,0.95958,-0.1999,102.32,-0.96363,-0.15336,0.21885,161.38
> view matrix models
> #4,0.086618,0.26649,0.95994,93.887,-0.43549,0.87675,-0.2041,110.12,-0.89602,-0.40036,0.192,161.23
> view matrix models
> #4,-0.46043,0.48495,0.74352,114.05,-0.11434,0.79821,-0.59143,109.02,-0.8803,-0.35732,-0.31207,171.31
> view matrix models
> #4,-0.36301,0.43867,0.82207,109.64,0.15881,0.89847,-0.40931,96.223,-0.91815,-0.018032,-0.39582,172.4
> view matrix models
> #4,-0.34973,0.42763,0.83356,109.55,0.20216,0.90323,-0.37855,94.584,-0.91478,0.036122,-0.40233,170.51
> view matrix models
> #4,-0.36553,0.4406,0.81991,110.26,0.15077,0.89726,-0.41495,96.967,-0.91851,-0.028059,-0.39441,170.81
> view matrix models
> #4,-0.36553,0.4406,0.81991,109.89,0.15077,0.89726,-0.41495,94.973,-0.91851,-0.028059,-0.39441,169.61
> view matrix models
> #4,-0.43805,0.47882,0.76082,113.16,-0.057405,0.82972,-0.55523,104.71,-0.89712,-0.28689,-0.33597,169.12
> view matrix models
> #4,-0.38074,0.45129,0.80708,110.57,0.10366,0.88814,-0.44772,97.164,-0.91885,-0.086806,-0.38493,169.74
> view matrix models
> #4,-0.34498,0.42332,0.83773,108.97,0.21812,0.90424,-0.36711,91.851,-0.91291,0.056076,-0.40428,169.19
> view matrix models
> #4,-0.34498,0.42332,0.83773,108.14,0.21812,0.90424,-0.36711,90.672,-0.91291,0.056076,-0.40428,171.13
> view matrix models
> #4,-0.34498,0.42332,0.83773,107.81,0.21812,0.90424,-0.36711,90.512,-0.91291,0.056076,-0.40428,172.34
> view matrix models
> #4,-0.34498,0.42332,0.83773,108.18,0.21812,0.90424,-0.36711,90.174,-0.91291,0.056076,-0.40428,170.24
> view matrix models
> #4,-0.34498,0.42332,0.83773,107.43,0.21812,0.90424,-0.36711,91.108,-0.91291,0.056076,-0.40428,174.8
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.39381,0.45924,0.79625,109.61,0.064769,0.87796,-0.47433,98.236,-0.91691,-0.13522,-0.3755,175.35
> view matrix models
> #4,-0.36317,0.43879,0.82193,108.24,0.1583,0.8984,-0.40966,93.88,-0.91818,-0.018663,-0.39573,175.18
> view matrix models
> #4,0.47736,0.0089756,0.87866,83.674,0.51039,0.81114,-0.28557,80.935,-0.71528,0.58479,0.38262,149.02
> view matrix models
> #4,0.44701,0.080914,0.89086,83.948,0.3352,0.90819,-0.25068,85.014,-0.82935,0.41067,0.37885,153.54
> view matrix models
> #4,0.35353,0.19014,0.91589,85.673,-0.028519,0.98086,-0.19262,94.495,-0.93499,0.041978,0.35219,159.35
> view matrix models
> #4,-0.17059,-0.18686,-0.96746,144.08,0.053662,-0.98216,0.18024,94.725,-0.98388,-0.021169,0.17757,164.93
> view matrix models
> #4,0.010142,-0.032469,-0.99942,138.39,0.76171,-0.64728,0.028758,74.49,-0.64784,-0.76156,0.018168,162.11
> view matrix models
> #4,-0.11495,0.533,0.83827,99.785,0.3937,0.7992,-0.45418,88.178,-0.91202,0.27782,-0.30171,171.36
> view matrix models
> #4,-0.11495,0.533,0.83827,108.87,0.3937,0.7992,-0.45418,111.68,-0.91202,0.27782,-0.30171,142.27
> view matrix models
> #4,-0.11495,0.533,0.83827,110.66,0.3937,0.7992,-0.45418,110.24,-0.91202,0.27782,-0.30171,138.56
> ui mousemode right "translate selected models"
> ui mousemode right pivot
> ui mousemode right pivot
> ui mousemode right "rotate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.11495,0.533,0.83827,126.63,0.3937,0.7992,-0.45418,105.02,-0.91202,0.27782,-0.30171,141.89
> view matrix models
> #4,-0.09163,-0.1402,0.98587,126.44,0.36928,0.91466,0.16439,91.889,-0.92479,0.37913,-0.032039,135.95
> view matrix models
> #4,-0.09163,-0.1402,0.98587,124.88,0.36928,0.91466,0.16439,98.668,-0.92479,0.37913,-0.032039,140.35
> view matrix models
> #4,-0.11884,-0.067344,0.99063,125.21,0.37981,0.91874,0.10802,99.531,-0.9174,0.38909,-0.083606,141.18
> view matrix models
> #4,-0.11884,-0.067344,0.99063,125.17,0.37981,0.91874,0.10802,98.347,-0.9174,0.38909,-0.083606,141.01
> view matrix models
> #4,-0.11884,-0.067344,0.99063,127.78,0.37981,0.91874,0.10802,99.135,-0.9174,0.38909,-0.083606,140.81
> volume #1 level 0.3412
> volume #1 level 0.2395
> volume #1 level 0.3474
> fitmap #4 inMap #1
Fit molecule 6p40 chain A.pdb (#4) to map
cryosparc_P19_J124_008_volume_map.mrc (#1) using 3132 atoms
average map value = 0.3205, steps = 188
shifted from previous position = 1.7
rotated from previous position = 5.56 degrees
atoms outside contour = 1869, contour level = 0.34738
Position of 6p40 chain A.pdb (#4) relative to
cryosparc_P19_J124_008_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.09632366 -0.11183472 0.98904740 126.78830237
0.29836042 0.94473137 0.13588119 100.70294195
-0.94958033 0.30818117 -0.05763293 141.62014053
Axis 0.08662530 0.97466179 0.20622914
Axis point 111.15167207 0.00000000 7.13181171
Rotation angle (degrees) 96.00484764
Shift along axis 138.34058390
> show #4/A cartoons
> view matrix models
> #4,-0.096324,-0.11183,0.98905,121.07,0.29836,0.94473,0.13588,100.4,-0.94958,0.30818,-0.057633,142.76
> undo
> show #4/A:1-193 cartoons
> hide #4/A:1-193 cartoons
> volume #1 level 0.2241
> show #4/A:1-193 cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> delete #4/A:1-193 cartoon
Expected a keyword
> delete #4/A:1-193
> rename #3 "6p3x chain A.pdb" " 6p3x_chainA_CTD.pdb"
Expected a keyword
> rename #3 " 6p3x_chainA_CTD.pdb"
> select clear
> rename #3 6p3x_chainA_CTD.pdb
> show #!3 models
> select #3/A:288
11 atoms, 11 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.62269,-0.031018,0.78185,128.07,-0.43965,0.84044,-0.31681,61.595,-0.64727,-0.54102,-0.53697,151.89
> ui mousemode right clip
> ui mousemode right clip
> ui mousemode right "translate selected models"
> show #!3 target m
> view matrix models
> #3,-0.62269,-0.031018,0.78185,131.03,-0.43965,0.84044,-0.31681,60.039,-0.64727,-0.54102,-0.53697,132.07
> view matrix models
> #3,-0.62269,-0.031018,0.78185,129.23,-0.43965,0.84044,-0.31681,59.154,-0.64727,-0.54102,-0.53697,136.97
> rename #3 " 6p3x.pdb"
> rename #4 6p40_chainA_CTD
> hide #3/A:199-385
> hide #3/A:199-385 cartoons
> volume #1 level 0.3196
> select #3/A:116
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.62269,-0.031018,0.78185,129.1,-0.43965,0.84044,-0.31681,58.399,-0.64727,-0.54102,-0.53697,138.78
> view matrix models
> #3,-0.62269,-0.031018,0.78185,125.16,-0.43965,0.84044,-0.31681,65.885,-0.64727,-0.54102,-0.53697,112.69
> view matrix models
> #3,-0.62269,-0.031018,0.78185,120.4,-0.43965,0.84044,-0.31681,59.375,-0.64727,-0.54102,-0.53697,122.51
> view matrix models
> #3,-0.62269,-0.031018,0.78185,116.51,-0.43965,0.84044,-0.31681,58.895,-0.64727,-0.54102,-0.53697,117.67
> view matrix models
> #3,-0.62269,-0.031018,0.78185,117.5,-0.43965,0.84044,-0.31681,56.8,-0.64727,-0.54102,-0.53697,124.79
> view matrix models
> #3,-0.62269,-0.031018,0.78185,116.88,-0.43965,0.84044,-0.31681,58.941,-0.64727,-0.54102,-0.53697,118.13
> view matrix models
> #3,-0.62269,-0.031018,0.78185,116.85,-0.43965,0.84044,-0.31681,60.267,-0.64727,-0.54102,-0.53697,114.56
> view matrix models
> #3,-0.62269,-0.031018,0.78185,114.59,-0.43965,0.84044,-0.31681,60.432,-0.64727,-0.54102,-0.53697,110.57
> view matrix models
> #3,-0.62269,-0.031018,0.78185,115.67,-0.43965,0.84044,-0.31681,62.117,-0.64727,-0.54102,-0.53697,107.8
> view matrix models
> #3,-0.62269,-0.031018,0.78185,115.31,-0.43965,0.84044,-0.31681,61.555,-0.64727,-0.54102,-0.53697,108.72
> view matrix models
> #3,-0.74354,0.12105,0.65764,112.64,-0.45736,0.62541,-0.63221,64.276,-0.48782,-0.77085,-0.40965,112.64
> view matrix models
> #3,-0.039904,0.73649,0.67528,101.08,0.14733,0.67276,-0.72504,62.087,-0.98828,0.070555,-0.13535,100.29
> view matrix models
> #3,0.031774,0.71254,-0.70091,97.371,0.36556,-0.66096,-0.65536,84.197,-0.93024,-0.2354,-0.28148,104.88
> view matrix models
> #3,0.047739,-0.16245,-0.98556,111.16,0.071032,-0.98364,0.16557,92.515,-0.99633,-0.077911,-0.035419,103.07
> view matrix models
> #3,0.047739,-0.16245,-0.98556,116.06,0.071032,-0.98364,0.16557,94.077,-0.99633,-0.077911,-0.035419,105.58
> view matrix models
> #3,0.047739,-0.16245,-0.98556,116.68,0.071032,-0.98364,0.16557,94.377,-0.99633,-0.077911,-0.035419,105.73
> view matrix models
> #3,0.038372,-0.1578,-0.98672,116.62,0.065639,-0.98492,0.16007,94.393,-0.99711,-0.07091,-0.027435,105.64
> view matrix models
> #3,-0.058566,-0.10478,-0.99277,115.9,0.0057281,-0.9945,0.10462,94.505,-0.99827,0.00044054,0.058843,104.7
> view matrix models
> #3,0.34144,-0.039623,-0.93907,114.22,-0.28516,-0.95638,-0.063331,93.925,-0.8956,0.28941,-0.33785,98.525
> view matrix models
> #3,0.34144,-0.039623,-0.93907,116.1,-0.28516,-0.95638,-0.063331,94.542,-0.8956,0.28941,-0.33785,99.462
> view matrix models
> #3,0.34144,-0.039623,-0.93907,111.26,-0.28516,-0.95638,-0.063331,91.994,-0.8956,0.28941,-0.33785,98.667
> view matrix models
> #3,-0.067599,0.98474,0.16038,98.059,-0.98603,-0.041407,-0.16136,77.71,-0.15226,-0.16904,0.97378,108.74
> view matrix models
> #3,-0.067599,0.98474,0.16038,97.681,-0.98603,-0.041407,-0.16136,77.6,-0.15226,-0.16904,0.97378,108.52
> view matrix models
> #3,0.40881,0.56903,0.7135,105.34,-0.89275,0.087105,0.44205,77.017,0.18939,-0.81769,0.54361,117.5
> fitmap #4 inMap #1
Fit molecule 6p40_chainA_CTD (#4) to map cryosparc_P19_J124_008_volume_map.mrc
(#1) using 1608 atoms
average map value = 0.4261, steps = 36
shifted from previous position = 0.106
rotated from previous position = 1.81 degrees
atoms outside contour = 601, contour level = 0.31964
Position of 6p40_chainA_CTD (#4) relative to
cryosparc_P19_J124_008_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.09424100 -0.08860480 0.99159862 126.65111036
0.32043160 0.94032897 0.11447723 100.39182267
-0.94257213 0.32852798 -0.06022576 141.43387263
Axis 0.10764416 0.97267671 0.20570065
Axis point 109.73439823 0.00000000 8.60764028
Rotation angle (degrees) 96.14637790
Shift along axis 140.37507882
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.3813
> view matrix models
> #3,0.40881,0.56903,0.7135,106.2,-0.89275,0.087105,0.44205,74.378,0.18939,-0.81769,0.54361,117.85
> view matrix models
> #3,0.334,0.6327,0.69867,105.23,-0.8439,-0.12945,0.52065,78.137,0.41986,-0.7635,0.4907,116.36
> view matrix models
> #3,0.20649,-0.15409,-0.96624,113.83,0.86262,-0.43741,0.2541,79.335,-0.46179,-0.88596,0.042602,118.76
> view matrix models
> #3,0.20649,-0.15409,-0.96624,111.32,0.86262,-0.43741,0.2541,79.083,-0.46179,-0.88596,0.042602,129.17
> volume #1 level 0.4676
> view matrix models
> #3,0.20649,-0.15409,-0.96624,116.42,0.86262,-0.43741,0.2541,82.597,-0.46179,-0.88596,0.042602,118.58
> view matrix models
> #3,0.20649,-0.15409,-0.96624,113.39,0.86262,-0.43741,0.2541,80.557,-0.46179,-0.88596,0.042602,127.47
> view matrix models
> #3,0.20649,-0.15409,-0.96624,113.55,0.86262,-0.43741,0.2541,80.8,-0.46179,-0.88596,0.042602,127.42
> view matrix models
> #3,0.49676,0.051122,0.86638,114.86,-0.76231,0.50289,0.40741,68.542,-0.41487,-0.86284,0.28879,127.66
> view matrix models
> #3,0.84462,0.053096,0.53272,113.22,-0.5273,0.25451,0.81067,73.423,-0.092539,-0.96561,0.24296,128.64
> view matrix models
> #3,0.86598,0.19822,0.45911,110.53,-0.49329,0.48931,0.7192,69.167,-0.082086,-0.84929,0.52151,127.48
> view matrix models
> #3,0.82242,0.3781,0.42504,107.51,-0.55986,0.40551,0.72258,70.703,0.10085,-0.83223,0.54518,126.92
> view matrix models
> #3,0.82242,0.3781,0.42504,137.81,-0.55986,0.40551,0.72258,119.93,0.10085,-0.83223,0.54518,153.55
> view matrix models
> #3,0.82242,0.3781,0.42504,101.6,-0.55986,0.40551,0.72258,89.976,0.10085,-0.83223,0.54518,139.26
> view matrix models
> #3,0.82242,0.3781,0.42504,100.23,-0.55986,0.40551,0.72258,90.579,0.10085,-0.83223,0.54518,137.34
> view matrix models
> #3,-0.4899,0.72474,0.48451,97.048,0.77617,0.10956,0.62093,92.744,0.39693,0.68026,-0.6162,108.12
> view matrix models
> #3,-0.4899,0.72474,0.48451,96.413,0.77617,0.10956,0.62093,92.102,0.39693,0.68026,-0.6162,107.97
> view matrix models
> #3,-0.4899,0.72474,0.48451,95.313,0.77617,0.10956,0.62093,93.13,0.39693,0.68026,-0.6162,105.99
> view matrix models
> #3,-0.013619,0.927,0.37483,90.723,0.95968,-0.093139,0.26521,95.152,0.28076,0.36333,-0.88835,110.73
> view matrix models
> #3,0.13875,0.76546,0.62835,93.873,0.82494,-0.44038,0.35431,101.47,0.54792,0.46919,-0.69256,109.02
> view matrix models
> #3,0.13875,0.76546,0.62835,88.769,0.82494,-0.44038,0.35431,96.404,0.54792,0.46919,-0.69256,107.68
> volume #1 level 0.3351
> view matrix models
> #3,0.13875,0.76546,0.62835,143.69,0.82494,-0.44038,0.35431,141,0.54792,0.46919,-0.69256,130.02
> view matrix models
> #3,0.13875,0.76546,0.62835,143.63,0.82494,-0.44038,0.35431,140.5,0.54792,0.46919,-0.69256,130.34
> ui mousemode right pivot
> ui mousemode right "translate selected models"
> fitmap #3 inMap #1
Fit molecule 6p3x.pdb (#3) to map cryosparc_P19_J124_008_volume_map.mrc (#1)
using 3217 atoms
average map value = 0.192, steps = 160
shifted from previous position = 8.69
rotated from previous position = 12.3 degrees
atoms outside contour = 2689, contour level = 0.33505
Position of 6p3x.pdb (#3) relative to cryosparc_P19_J124_008_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.04625472 0.71117713 0.70148951 138.58865988
0.79678835 -0.39727665 0.45530158 139.60943198
0.60248549 0.57999854 -0.54828174 127.24998494
Axis 0.68978239 0.54765757 0.47357305
Axis point 0.00000000 14.22234683 16.45706034
Rotation angle (degrees) 174.81403565
Shift along axis 232.31634352
> view matrix models
> #3,-0.046255,0.71118,0.70149,138.19,0.79679,-0.39728,0.4553,138.87,0.60249,0.58,-0.54828,127.13
> undo
> view matrix models
> #3,-0.046255,0.71118,0.70149,137.86,0.79679,-0.39728,0.4553,139.18,0.60249,0.58,-0.54828,126.2
> undo
> select clear
> volume #1 level 0.2302
> select #3/A:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.046255,0.71118,0.70149,139.4,0.79679,-0.39728,0.4553,129.88,0.60249,0.58,-0.54828,128.94
> volume showOutlineBox true
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 147 tiltedSlabSpacing 0.835 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 147 tiltedSlabSpacing 0.835 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume showOutlineBox false
> volume zone #1 nearAtoms sel & #3 range 5.01
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 orthoplanes xyz positionPlanes 176,176,176 style image region all
> mousemode rightMode "move planes"
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 147 tiltedSlabSpacing 0.835 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume show
> volume showOutlineBox false
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume style surface
> volume showOutlineBox true
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> close session
> open
> E:\Krios\20210423\csrelion\cryosparc\csJ124\cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc
> format mrc
Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
size 352,352,352, pixel 0.835, shown at level 0.00386, step 2, values float32
> volume all step 1
> volume #1 level 0.007905
> open "E:/temp/EM data/4n9f.pdb1"
Summary of feedback from opening E:/temp/EM data/4n9f.pdb1
---
warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C
18 GLN C 32 1 15
Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54
1 19
Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82
1 27
Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107
1 23
Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C
110 5 3
680 messages similar to the above omitted
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (133 )
33 messages similar to the above omitted
4n9f.pdb1 title:
Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
info...]
Chain information for 4n9f.pdb1 #2
---
Chain | Description
U | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
Non-standard residues in 4n9f.pdb1 #2
---
ZN — zinc ion
> open "E:/temp/EM data/6p3x chain A.pdb" "E:/temp/EM data/6p40 chain A.pdb"
Summary of feedback from opening E:/temp/EM data/6p3x chain A.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (65 )
Cannot find LINK/SSBOND residue CYS (97 )
Cannot find LINK/SSBOND residue CYS (100 )
Cannot find LINK/SSBOND residue ZN (701 )
Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (65 )
Cannot find LINK/SSBOND residue CYS (97 )
Cannot find LINK/SSBOND residue CYS (100 )
Cannot find LINK/SSBOND residue HIS (257 )
Cannot find LINK/SSBOND residue CYS (287 )
2 messages similar to the above omitted
6p3x chain A.pdb title:
Crystal structure of full length APOBEC3G E/Q (pH 7.0) [more info...]
Chain information for 6p3x chain A.pdb #3
---
Chain | Description
A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G
Non-standard residues in 6p3x chain A.pdb #3
---
ZN — zinc ion
6p40 chain A.pdb title:
Crystal structure of full length APOBEC3G FKL [more info...]
Chain information for 6p40 chain A.pdb #4
---
Chain | Description
A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G
Non-standard residues in 6p40 chain A.pdb #4
---
ZN — zinc ion
> select #2/X:86@CA
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,23.182,0,1,0,318.2,0,0,1,272.71
> select clear
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #4/A:98
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models #4,1,0,0,3.3218,0,1,0,55.036,0,0,1,117.25
> select clear
> select #3/A:154
12 atoms, 12 bonds, 1 residue, 1 model selected
> view matrix models #3,1,0,0,3.1774,0,1,0,48.702,0,0,1,79.52
> hide #!3 models
> select clear
> select #1
2 models selected
> cofr frontCenter
> select clear
> hide #4/A:1-193
> hide #4/A:1-193 cartoons
> select clear
> select #4/A:309
11 atoms, 11 bonds, 1 residue, 1 model selected
> view matrix models #4,1,0,0,8.4012,0,1,0,90.59,0,0,1,92.374
> view matrix models
> #4,0.93832,0.034798,0.34402,2.7292,-0.095551,-0.93009,0.35469,95.098,0.33232,-0.36568,-0.86939,124.13
> view matrix models
> #4,-0.92778,-0.15222,-0.34068,75.501,-0.34159,0.71389,0.61129,86.331,0.15015,0.68351,-0.71433,120.15
> view matrix models
> #4,-0.95787,-0.27221,-0.091626,71.749,-0.26547,0.71734,0.64417,83.423,-0.10962,0.64135,-0.75938,128.74
> view matrix models
> #4,-0.97672,-0.20543,-0.061796,71.322,-0.21452,0.93416,0.28517,88.543,-0.00085595,0.29179,-0.95648,131.56
> view matrix models
> #4,-0.78905,0.51263,0.33854,53.128,0.60992,0.71962,0.33189,65.541,-0.073484,0.46836,-0.88048,131.04
> view matrix models
> #4,-0.77901,0.52553,0.342,52.677,0.61367,0.75094,0.24391,67.138,-0.12864,0.39988,-0.90749,133.68
> view matrix models
> #4,-0.57834,0.62047,0.52966,42.005,0.79141,0.58428,0.17969,63.989,-0.19798,0.5231,-0.82896,133.44
> view matrix models
> #4,-0.52111,0.67579,0.5213,40.132,0.67297,0.701,-0.23603,75.873,-0.52493,0.22782,-0.82009,144.86
> view matrix models
> #4,-0.29328,0.084526,0.95228,27.259,0.3887,0.92058,0.037999,77.436,-0.87344,0.3813,-0.30285,143.62
> view matrix models
> #4,-0.29328,0.084526,0.95228,26.88,0.3887,0.92058,0.037999,72.988,-0.87344,0.3813,-0.30285,145.32
> view matrix models
> #4,-0.47912,0.040859,0.8768,34.287,0.32978,0.93411,0.13668,72.588,-0.81344,0.35464,-0.46102,147.03
> view matrix models
> #4,-0.47912,0.040859,0.8768,37.591,0.32978,0.93411,0.13668,107.54,-0.81344,0.35464,-0.46102,131.91
> ui tool show "Side View"
> view matrix models
> #4,-0.42449,0.046237,0.90425,35.315,0.32923,0.93822,0.10658,108.18,-0.84346,0.34295,-0.41349,131.87
> view matrix models
> #4,-0.42449,0.046237,0.90425,131.2,0.32923,0.93822,0.10658,80.091,-0.84346,0.34295,-0.41349,136.14
> view matrix models
> #4,-0.4107,-0.002519,0.91177,130.9,0.42693,0.88307,0.19474,75.561,-0.80564,0.46924,-0.3616,133.18
> view matrix models
> #4,-0.41194,0.0028209,0.91121,130.92,0.41666,0.88991,0.18561,76.036,-0.81037,0.45613,-0.36776,133.53
> view matrix models
> #4,-0.43486,0.073605,0.89749,131.51,0.27016,0.96141,0.052051,82.906,-0.85902,0.2651,-0.43796,137.56
> view matrix models
> #4,-0.44093,0.087513,0.89326,131.7,0.23883,0.97079,0.022784,84.413,-0.86518,0.22339,-0.44896,138.22
> view matrix models
> #4,-0.4332,0.06957,0.89861,131.46,0.27907,0.95837,0.060338,82.511,-0.857,0.27692,-0.43458,137.37
> view matrix models
> #4,0.047961,0.10469,0.99335,115.46,0.26646,0.95711,-0.11374,86.467,-0.96265,0.27014,0.018008,130.95
> view matrix models
> #4,0.013533,0.1605,0.98694,116.19,0.091008,0.98274,-0.16106,92.071,-0.99576,0.091999,-0.0013069,133.36
> view matrix models
> #4,-0.38731,0.11385,0.91489,129.06,0.14675,0.98731,-0.060741,88.416,-0.9102,0.11073,-0.3991,139.16
> view matrix models
> #4,-0.32573,-0.075044,0.94248,127.74,0.56086,0.78717,0.25651,70.555,-0.76114,0.61216,-0.21431,127.91
> view matrix models
> #4,-0.32573,-0.075044,0.94248,129.78,0.56086,0.78717,0.25651,89.458,-0.76114,0.61216,-0.21431,137.5
> volume #1 color #b2b2b2b2
> view matrix models
> #4,-0.32573,-0.075044,0.94248,130.48,0.56086,0.78717,0.25651,89.664,-0.76114,0.61216,-0.21431,137.18
> view matrix models
> #4,-0.33148,-0.11998,0.9358,131.05,0.49381,0.82311,0.28045,90.968,-0.80391,0.55507,-0.2136,138.78
> view matrix models
> #4,-0.076631,-0.13944,0.98726,122.54,0.52766,0.83448,0.15882,92.485,-0.846,0.5331,0.0096301,135.41
> view matrix models
> #4,-0.076631,-0.13944,0.98726,122.04,0.52766,0.83448,0.15882,91.943,-0.846,0.5331,0.0096301,136.36
> view matrix models
> #4,-0.076631,-0.13944,0.98726,125.48,0.52766,0.83448,0.15882,91.815,-0.846,0.5331,0.0096301,137.5
> view matrix models
> #4,-0.076631,-0.13944,0.98726,124.45,0.52766,0.83448,0.15882,91.382,-0.846,0.5331,0.0096301,137.94
> view matrix models
> #4,-0.076631,-0.13944,0.98726,125.18,0.52766,0.83448,0.15882,90.093,-0.846,0.5331,0.0096301,136.69
> volume #1 level 0.01813
> view matrix models
> #4,-0.076631,-0.13944,0.98726,124.55,0.52766,0.83448,0.15882,90.864,-0.846,0.5331,0.0096301,137.84
> view matrix models
> #4,-0.076631,-0.13944,0.98726,124.45,0.52766,0.83448,0.15882,89.823,-0.846,0.5331,0.0096301,138.31
> view matrix models
> #4,-0.0017634,-0.070046,0.99754,121.59,0.57882,0.81338,0.058138,90.631,-0.81546,0.5775,0.039109,136.51
> view matrix models
> #4,-0.0017634,-0.070046,0.99754,122.04,0.57882,0.81338,0.058138,90.725,-0.81546,0.5775,0.039109,135.52
> view matrix models
> #4,-0.0065597,-0.1299,0.9915,122.69,0.54877,0.82841,0.11217,90.356,-0.83595,0.54484,0.065853,135.75
> view matrix models
> #4,-0.060324,-0.17404,0.98289,124.74,0.67199,0.72104,0.16892,86.082,-0.7381,0.67068,0.073458,131.91
> view matrix models
> #4,-0.1071,-0.15416,0.98222,126.05,0.66155,0.72643,0.18615,85.995,-0.74222,0.66972,0.024183,133.1
> view matrix models
> #4,-0.1071,-0.15416,0.98222,127.19,0.66155,0.72643,0.18615,85.326,-0.74222,0.66972,0.024183,135.81
> view matrix models
> #4,-0.1071,-0.15416,0.98222,127.19,0.66155,0.72643,0.18615,85.375,-0.74222,0.66972,0.024183,135.68
> view matrix models
> #4,-0.1071,-0.15416,0.98222,126.34,0.66155,0.72643,0.18615,88.774,-0.74222,0.66972,0.024183,135.33
> view matrix models
> #4,-0.1071,-0.15416,0.98222,127.08,0.66155,0.72643,0.18615,85.919,-0.74222,0.66972,0.024183,135.43
> view matrix models
> #4,-0.1071,-0.15416,0.98222,126.73,0.66155,0.72643,0.18615,87.595,-0.74222,0.66972,0.024183,136.79
> view matrix models
> #4,-0.1071,-0.15416,0.98222,127.57,0.66155,0.72643,0.18615,84.49,-0.74222,0.66972,0.024183,134.61
> fitmap #4 inMap #1
Fit molecule 6p40 chain A.pdb (#4) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.01186, steps = 260
shifted from previous position = 11.9
rotated from previous position = 24.6 degrees
atoms outside contour = 2247, contour level = 0.018135
Position of 6p40 chain A.pdb (#4) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.09942338 -0.10883602 0.98907518 126.88557243
0.30042237 0.94433074 0.13411135 100.65968289
-0.94861024 0.31047412 -0.06119178 141.64964253
Axis 0.08870158 0.97455807 0.20583634
Axis point 110.93643823 0.00000000 7.44799256
Rotation angle (degrees) 96.20823350
Shift along axis 138.51030041
> view matrix models
> #4,-0.099423,-0.10884,0.98908,126.85,0.30042,0.94433,0.13411,101.42,-0.94861,0.31047,-0.061192,141.76
> undo
> select clear
> show #4
> hide #4
> show #4/A:1-193
> hide #4/A:1-193
> show #4/A:1-193 cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/A:194-198
45 atoms, 45 bonds, 5 residues, 1 model selected
> select clear
> select #4/A:199
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:199-206
61 atoms, 63 bonds, 8 residues, 1 model selected
> select clear
> select clear
> select #4/A:193-194
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #4/A:177-194
141 atoms, 143 bonds, 18 residues, 1 model selected
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select clear
> select #3/A:117
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models #3,1,0,0,94.733,0,1,0,73.438,0,0,1,123.72
> hide #3/A:199-385 cartoons
> select clear
> select #3/A:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models #3,1,0,0,122.56,0,1,0,72.784,0,0,1,156.89
> view matrix models #3,1,0,0,120.08,0,1,0,71.527,0,0,1,156.42
> view matrix models
> #3,0.99929,0.019054,-0.032561,119.67,-0.019705,0.99961,-0.019792,71.513,0.032171,0.020419,0.99927,156.02
> view matrix models
> #3,0.99898,-0.023678,0.038487,120.59,0.022744,0.99944,0.024531,71.565,-0.039046,-0.023631,0.99896,156.88
> view matrix models
> #3,0.66534,-0.55387,0.50055,131.42,0.73064,0.34547,-0.58892,79.415,0.15326,0.75755,0.63453,142.4
> view matrix models
> #3,0.67981,-0.49603,0.54019,130.54,0.70946,0.25822,-0.65573,80.722,0.18578,0.82902,0.52745,140.84
> view matrix models
> #3,0.55996,-0.6741,0.4817,133.57,0.81742,0.35465,-0.45392,79.489,0.13515,0.64793,0.74961,144.6
> view matrix models
> #3,0.55886,-0.82407,-0.092633,134.43,0.50283,0.42557,-0.75237,78.028,0.65943,0.37389,0.6522,147.93
> hide #!1 models
> view matrix models
> #3,0.55886,-0.82407,-0.092633,135.43,0.50283,0.42557,-0.75237,79.098,0.65943,0.37389,0.6522,147.18
> view matrix models
> #3,0.56984,-0.81981,-0.056499,135.45,0.52692,0.41728,-0.74043,79.226,0.63059,0.39216,0.66975,146.98
> view matrix models
> #3,0.60038,-0.74007,0.30304,135.09,0.73561,0.36241,-0.57231,80.24,0.31373,0.56652,0.76199,144.92
> view matrix models
> #3,0.68204,-0.71948,0.13103,134.1,0.72461,0.64065,-0.25398,76.524,0.09879,0.26817,0.95829,150.88
> view matrix models
> #3,0.67694,-0.61605,-0.40278,130.84,0.41776,0.77213,-0.47885,74.248,0.606,0.15589,0.78004,151.3
> view matrix models
> #3,-0.17444,-0.92344,0.34179,139.72,0.00826,-0.34848,-0.93728,92.439,0.98463,-0.16067,0.068415,153.84
> view matrix models
> #3,0.45934,-0.5859,-0.66763,129.97,-0.77001,0.11206,-0.62812,87.078,0.44283,0.8026,-0.39968,137.38
> view matrix models
> #3,-0.31951,0.45194,-0.83287,113.59,-0.94096,-0.25502,0.22261,95.994,-0.11179,0.85482,0.50674,140.16
> view matrix models
> #3,-0.87927,0.47085,-0.071961,116.51,-0.19122,-0.21057,0.95869,95.975,0.43625,0.85671,0.27519,138.43
> view matrix models
> #3,-0.966,0.11558,-0.23127,122.16,-0.18862,0.2967,0.93616,87.418,0.17681,0.94795,-0.26481,135.83
> view matrix models
> #3,-0.76442,-0.44355,-0.46789,130.45,-0.63899,0.42478,0.64129,85.264,-0.085693,0.7892,-0.60813,137.99
> view matrix models
> #3,-0.83634,-0.28388,-0.46899,127.91,-0.54643,0.36266,0.75491,86.459,-0.04422,0.88763,-0.45843,136.7
> view matrix models
> #3,-0.7931,-0.37058,-0.48338,129.24,-0.60475,0.38451,0.69745,86.036,-0.072593,0.84547,-0.52906,137.25
> view matrix models
> #3,-0.85088,-0.21481,-0.47944,126.75,-0.52412,0.28429,0.8028,87.866,-0.036147,0.93436,-0.35448,136.2
> view matrix models
> #3,-0.77835,-0.39616,-0.48707,129.63,-0.62319,0.39336,0.67594,85.86,-0.07619,0.82966,-0.55305,137.45
> view matrix models
> #3,-0.80722,-0.49661,-0.31903,131.85,-0.52358,0.35291,0.77544,86.638,-0.27251,0.79299,-0.54489,138.46
> view matrix models
> #3,-0.97283,-0.19767,-0.1205,127.73,-0.20952,0.53036,0.82148,83.216,-0.098473,0.82441,-0.55737,137.57
> view matrix models
> #3,-0.97532,-0.0080383,-0.22066,124.27,-0.21962,0.13878,0.96566,90.203,0.022861,0.99029,-0.13712,135.78
> view matrix models
> #3,-0.81753,-0.38891,-0.42472,129.76,-0.54172,0.26912,0.79631,88.134,-0.19539,0.88109,-0.4307,137.17
> view matrix models
> #3,-0.81898,-0.39761,-0.41374,129.94,-0.53429,0.26536,0.80257,88.201,-0.20931,0.87835,-0.42976,137.24
> view matrix models
> #3,-0.78132,-0.40527,-0.47466,129.82,-0.57242,0.1622,0.80375,90.002,-0.24874,0.89969,-0.35872,137.16
> view matrix models
> #3,-0.82732,-0.40498,-0.38927,130.15,-0.5263,0.31663,0.78915,87.29,-0.19633,0.85775,-0.4751,137.43
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select clear
> show #3/A cartoons
> ui tool show Matchmaker
> matchmaker #!3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6p40 chain A.pdb, chain A (#4) with 6p3x chain A.pdb, chain A (#3),
sequence alignment score = 1956
RMSD between 106 pruned atom pairs is 0.426 angstroms; (across all 358 pairs:
6.515)
> select #3/A:376
5 atoms, 4 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.88518,-0.46461,0.024424,168.97,-0.29383,0.59897,0.74492,121.4,-0.36072,0.65221,-0.66671,127.98
> view matrix models
> #3,-0.70511,-0.66071,0.25745,166.46,-0.25322,0.57374,0.77891,120.69,-0.66235,0.48402,-0.57186,136.11
> view matrix models
> #3,-0.70511,-0.66071,0.25745,165.49,-0.25322,0.57374,0.77891,113.59,-0.66235,0.48402,-0.57186,138.21
> view matrix models
> #3,-0.70511,-0.66071,0.25745,131.32,-0.25322,0.57374,0.77891,85.419,-0.66235,0.48402,-0.57186,153.01
> hide #!3 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
> show #!4 models
> hide #4/A:1-193 cartoons
> show #!3 models
> view matrix models
> #3,0.9594,-0.26694,0.091073,91.415,0.18264,0.83403,0.52061,74.006,-0.21493,-0.48284,0.84893,148.86
> view matrix models
> #3,0.77612,0.20602,-0.59599,92.644,0.0035367,0.94369,0.33081,77.368,0.63058,-0.25886,0.73168,128.45
> view matrix models
> #3,0.77612,0.20602,-0.59599,95.405,0.0035367,0.94369,0.33081,77.872,0.63058,-0.25886,0.73168,130.68
> view matrix models
> #3,0.77612,0.20602,-0.59599,97.719,0.0035367,0.94369,0.33081,79.134,0.63058,-0.25886,0.73168,126.83
> view matrix models
> #3,0.77612,0.20602,-0.59599,96.497,0.0035367,0.94369,0.33081,79.681,0.63058,-0.25886,0.73168,120.58
> view matrix models
> #3,-0.63583,-0.69959,0.32603,133.85,-0.22104,0.56977,0.79152,87.032,-0.7395,0.43121,-0.51692,147.21
> view matrix models
> #3,-0.63583,-0.69959,0.32603,134.82,-0.22104,0.56977,0.79152,87.609,-0.7395,0.43121,-0.51692,145.27
> view matrix models
> #3,-0.63583,-0.69959,0.32603,136.68,-0.22104,0.56977,0.79152,88.435,-0.7395,0.43121,-0.51692,143.46
> view matrix models
> #3,-0.63583,-0.69959,0.32603,135.35,-0.22104,0.56977,0.79152,88.032,-0.7395,0.43121,-0.51692,143.47
> view matrix models
> #3,-0.63583,-0.69959,0.32603,132.35,-0.22104,0.56977,0.79152,86.943,-0.7395,0.43121,-0.51692,144.73
> view matrix models
> #3,-0.48926,-0.75569,0.43539,129.39,-0.15961,0.56837,0.80714,85.567,-0.85741,0.3254,-0.3987,148.04
> view matrix models
> #3,-0.46837,-0.76152,0.44802,128.96,-0.15141,0.56876,0.80845,85.38,-0.87046,0.31082,-0.38169,148.42
> select #3/A:119
11 atoms, 11 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.5416,-0.73893,0.40082,130.47,-0.18072,0.568,0.80295,86.045,-0.82098,0.36244,-0.44116,146.99
> view matrix models
> #3,-0.5416,-0.73893,0.40082,130.32,-0.18072,0.568,0.80295,86.013,-0.82098,0.36244,-0.44116,146.91
> view matrix models
> #3,-0.73202,-0.6425,0.22657,134.02,-0.26651,0.57612,0.7727,87.895,-0.62699,0.50525,-0.59296,141.66
> view matrix models
> #3,0.82546,-0.46079,0.32601,97.824,0.18875,0.76965,0.60993,76.455,-0.53196,-0.44194,0.72229,145.33
> view matrix models
> #3,0.82546,-0.46079,0.32601,124.25,0.18875,0.76965,0.60993,83.118,-0.53196,-0.44194,0.72229,154.19
> hide #3/A:199-385 cartoons
> view matrix models
> #3,0.91955,-0.35306,0.17256,121.83,0.21215,0.81564,0.53826,82.098,-0.33079,-0.45835,0.82492,154.38
> view matrix models
> #3,0.91955,-0.35306,0.17256,168.94,0.21215,0.81564,0.53826,102.39,-0.33079,-0.45835,0.82492,144.84
> view matrix models
> #3,0.89087,-0.40558,0.20459,169.97,0.24214,0.80504,0.54156,102.52,-0.38435,-0.43292,0.81539,144.48
> view matrix models
> #3,0.89087,-0.40558,0.20459,160.53,0.24214,0.80504,0.54156,117.67,-0.38435,-0.43292,0.81539,147.01
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view matrix models
> #3,0.89087,-0.40558,0.20459,161.64,0.24214,0.80504,0.54156,118.11,-0.38435,-0.43292,0.81539,147.3
> view matrix models
> #3,0.80641,-0.33719,0.4858,161.46,0.18517,0.92418,0.33408,115.62,-0.56162,-0.17945,0.8077,143.37
> view matrix models
> #3,0.86766,-0.39403,0.30316,161.77,0.18515,0.82203,0.5385,117.92,-0.46139,-0.41111,0.7862,147
> view matrix models
> #3,0.98849,-0.087773,0.12321,155.9,0.041635,0.94086,0.33623,115.62,-0.14543,-0.32723,0.93369,145.43
> view matrix models
> #3,0.90607,-0.4166,-0.074043,160.99,0.42311,0.89343,0.15089,115.17,0.0032922,-0.16804,0.98577,142.64
> view matrix models
> #3,0.98454,-0.052059,0.16725,155.44,-0.051546,0.82644,0.56066,118.36,-0.16741,-0.56061,0.81098,149.02
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #1 level 0.0215
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view matrix models
> #3,0.89875,0.064113,0.43374,154.42,-0.30619,0.79985,0.51622,119.15,-0.31383,-0.59676,0.7385,149.69
> view matrix models
> #3,0.82872,0.27223,0.48899,151.23,-0.54413,0.18756,0.81776,130.71,0.13091,-0.94377,0.30357,153.41
> view matrix models
> #3,0.95773,0.2866,-0.024615,149.27,-0.11147,0.44865,0.88673,125.73,0.26518,-0.8465,0.46164,151.99
> view matrix models
> #3,0.95508,0.17429,0.23968,151.92,-0.29603,0.52312,0.7992,124.58,0.01391,-0.83425,0.55121,152.51
> view matrix models
> #3,0.99829,-0.016907,0.055931,154.5,-0.020196,0.79839,0.60181,118.88,-0.05483,-0.60191,0.79668,149.46
> view matrix models
> #3,0.93814,0.0687,0.33939,154,-0.25549,0.79888,0.54453,119.15,-0.23372,-0.59755,0.76701,149.64
> view matrix models
> #3,0.96983,0.1396,0.19984,152.35,-0.24276,0.62787,0.73949,122.55,-0.022238,-0.7657,0.64282,151.7
> view matrix models
> #3,0.89289,0.18039,0.41257,152.43,-0.44081,0.53717,0.71912,124.38,-0.091894,-0.82396,0.55915,152.56
> view matrix models
> #3,0.94928,0.30337,0.082688,149.31,-0.16976,0.2731,0.94689,128.95,0.26468,-0.9129,0.31075,152.67
> view matrix models
> #3,0.97708,0.0013259,0.21286,154.69,-0.13459,0.77858,0.61295,119.46,-0.16491,-0.62755,0.76091,149.99
> view matrix models
> #3,0.89288,0.036386,0.44882,154.94,-0.27635,0.83122,0.48239,118.47,-0.35551,-0.55475,0.75224,149.1
> view matrix models
> #3,0.94387,0.32975,0.019366,148.7,-0.28568,0.78548,0.54901,119.44,0.16582,-0.52373,0.83559,147.85
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view matrix models
> #3,0.94387,0.32975,0.019366,133.37,-0.28568,0.78548,0.54901,87.89,0.16582,-0.52373,0.83559,181.7
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> volume #1 level 0.01275
> view matrix models
> #3,0.94387,0.32975,0.019366,131.62,-0.28568,0.78548,0.54901,88.751,0.16582,-0.52373,0.83559,187.91
> view matrix models
> #3,0.85311,0.04477,0.5198,138,-0.35735,0.77606,0.51965,88.958,-0.38013,-0.62907,0.67806,190.24
> view matrix models
> #3,0.8728,0.070145,0.483,137.43,-0.35204,0.77593,0.52346,88.961,-0.33806,-0.62691,0.70193,190.19
> view matrix models
> #3,0.8728,0.070145,0.483,121.07,-0.35204,0.77593,0.52346,89.4,-0.33806,-0.62691,0.70193,191.46
> view matrix models
> #3,0.87128,0.46921,0.14396,113.42,-0.48136,0.7597,0.43721,89.664,0.095772,-0.45022,0.88776,188.23
> view matrix models
> #3,0.64021,0.72573,-0.25188,108.41,-0.61212,0.68005,0.40354,91.144,0.46415,-0.10417,0.87961,181.73
> view matrix models
> #3,0.72374,0.67484,-0.14421,109.42,-0.57838,0.70719,0.40665,90.636,0.37641,-0.21091,0.90213,183.74
> view matrix models
> #3,0.9289,0.32778,-0.17235,114.76,-0.37015,0.83633,-0.4044,85.746,0.011585,0.43944,0.8982,173.53
> view matrix models
> #3,0.39928,0.21043,0.89235,120.79,-0.14544,0.97552,-0.16496,83.688,-0.90522,-0.063915,0.42011,182.28
> view matrix models
> #3,0.25804,0.15043,0.95435,122.23,-0.14336,0.98283,-0.11615,83.703,-0.95544,-0.10684,0.27518,182.67
> view matrix models
> #3,0.25804,0.15043,0.95435,119.62,-0.14336,0.98283,-0.11615,85.307,-0.95544,-0.10684,0.27518,176.49
> view matrix models
> #3,0.24804,0.14604,0.95768,119.61,-0.14349,0.98321,-0.11277,85.315,-0.95806,-0.10945,0.26483,176.46
> view matrix models
> #3,0.24804,0.14604,0.95768,117.28,-0.14349,0.98321,-0.11277,87.299,-0.95806,-0.10945,0.26483,169.08
> volume #1 level 0.01369
> view matrix models
> #3,0.24804,0.14604,0.95768,116.92,-0.14349,0.98321,-0.11277,87.528,-0.95806,-0.10945,0.26483,168.2
> view matrix models
> #3,0.35259,0.19101,0.91608,115.86,-0.14391,0.97837,-0.14861,87.506,-0.92465,-0.079434,0.37245,167.95
> view matrix models
> #3,0.58447,0.28257,0.76062,113.44,-0.16131,0.95916,-0.23238,87.618,-0.79522,0.013126,0.60618,166.83
> view matrix models
> #3,0.82913,0.41569,0.37381,109.64,-0.46093,0.12994,0.87787,105.26,0.31636,-0.90017,0.29934,179.16
> view matrix models
> #3,0.82913,0.41569,0.37381,107.02,-0.46093,0.12994,0.87787,105.61,0.31636,-0.90017,0.29934,177.16
> view matrix models
> #3,0.82913,0.41569,0.37381,109.8,-0.46093,0.12994,0.87787,104.71,0.31636,-0.90017,0.29934,181.03
> view matrix models
> #3,0.82913,0.41569,0.37381,109.29,-0.46093,0.12994,0.87787,105.73,0.31636,-0.90017,0.29934,177.44
> view matrix models
> #3,0.84086,0.19339,0.50553,113.36,-0.44581,-0.28222,0.84947,112.52,0.30695,-0.93966,-0.1511,176.82
> view matrix models
> #3,0.29968,0.73315,0.61048,105.64,-0.61974,-0.3369,0.70882,113.35,0.72534,-0.59076,0.35339,171.66
> view matrix models
> #3,0.29968,0.73315,0.61048,110.99,-0.61974,-0.3369,0.70882,115.53,0.72534,-0.59076,0.35339,165.97
> view matrix models
> #3,0.29968,0.73315,0.61048,105.33,-0.61974,-0.3369,0.70882,113.62,0.72534,-0.59076,0.35339,170.68
> hide #!3 models
> show #!2 models
> select #2/U:211@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
217 atoms, 222 bonds, 25 residues, 1 model selected
> select up
2458 atoms, 2503 bonds, 299 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> select up
12854 atoms, 12882 bonds, 1834 residues, 5 models selected
> select down
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> select down
2458 atoms, 2503 bonds, 299 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> view matrix models #2,1,0,0,59.404,0,1,0,307.52,0,0,1,319.68
> select clear
> hide #1/U
> hide #1/U cartoons
> hide #2/U cartoons
> select #2/a:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,69.647,0,1,0,222.66,0,0,1,297.93
> hide #2/X cartoons
> hide #2/Y cartoons
> view matrix models
> #2,0.63553,0.6941,0.33812,131.99,-0.5999,0.16825,0.78219,307.94,0.48602,-0.69995,0.52331,216.77
> view matrix models
> #2,-0.30105,0.51861,0.80026,209.67,-0.92427,-0.36525,-0.111,215.99,0.23472,-0.77307,0.58929,231.06
> view matrix models
> #2,0.24908,0.55945,0.79056,189.87,-0.95292,0.28734,0.096893,252,-0.17295,-0.77747,0.60468,247.11
> view matrix models
> #2,-0.071584,0.59301,0.802,203.19,-0.87919,0.34223,-0.33152,206.13,-0.47107,-0.72884,0.49687,247.59
> view matrix models
> #2,0.40443,0.48698,0.77414,181.13,-0.90753,0.10885,0.40564,278.68,0.11327,-0.86661,0.48597,222.77
> view matrix models
> #2,0.45723,0.078041,0.88592,182.39,-0.88899,0.068384,0.45279,282.07,-0.025246,-0.9946,0.10064,185.16
> view matrix models
> #2,-0.11713,0.061265,0.99123,213.45,-0.99311,-0.01097,-0.11667,225.16,0.0037253,-0.99806,0.062127,180.06
> view matrix models
> #2,0.62351,-0.12203,0.77223,160.56,-0.63913,0.48932,0.59336,296.4,-0.45028,-0.86352,0.22711,216.13
> view matrix models
> #2,0.62569,-0.091668,0.77466,161.36,-0.72631,0.2938,0.62141,298.38,-0.28456,-0.95146,0.11725,197.02
> view matrix models
> #2,0.62003,-0.11241,0.77649,161.32,-0.6613,0.45769,0.59431,296.63,-0.4222,-0.88198,0.20944,212.91
> view matrix models
> #2,0.28047,0.14205,0.94929,196.59,-0.77807,-0.5455,0.31151,250.82,0.56209,-0.82599,-0.042474,152.85
> view matrix models
> #2,-0.076382,0.034955,0.99647,212,-0.99438,0.070847,-0.078707,230.83,-0.073348,-0.99687,0.029347,179.44
> view matrix models
> #2,0.38028,-0.023996,0.92456,187.04,-0.88582,0.27798,0.37156,277.87,-0.26593,-0.96029,0.084455,192.77
> view matrix models
> #2,0.18793,0.047774,0.98102,201.23,-0.96495,-0.17732,0.19348,252.85,0.1832,-0.98299,0.012776,168.85
> view matrix models
> #2,0.18633,-0.058442,0.98075,199.07,-0.71489,0.67669,0.17614,259.75,-0.67395,-0.73395,0.084305,211.99
> view matrix models
> #2,0.31898,0.040541,0.94689,192.87,-0.94768,0.026381,0.31812,269.35,-0.012084,-0.99883,0.046836,179.02
> view matrix models
> #2,0.37461,-0.046868,0.926,186.92,-0.62721,0.72272,0.29032,269.39,-0.68284,-0.68955,0.24134,229.49
> view matrix models
> #2,0.077413,-0.37201,0.925,190.71,-0.659,0.67711,0.32747,273.44,-0.74814,-0.63493,-0.19274,187.98
> view matrix models
> #2,0.084155,-0.40385,0.91095,188.36,-0.55223,0.74206,0.37999,276.41,-0.82943,-0.53503,-0.16057,196.27
> view matrix models
> #2,0.13487,-0.41028,0.90193,185.49,-0.73431,0.56977,0.36899,278.21,-0.66528,-0.71206,-0.22443,180.15
> view matrix models
> #2,0.0035652,-0.33949,0.9406,195.64,-0.58724,0.76063,0.27675,267.35,-0.8094,-0.55335,-0.19665,191.44
> view matrix models
> #2,0.16039,-0.42635,0.89023,183.03,-0.77127,0.5087,0.38258,279.68,-0.61597,-0.74797,-0.24724,175.29
> view matrix models
> #2,-0.024786,-0.32565,0.94517,197.41,-0.68321,0.69573,0.22179,263.74,-0.7298,-0.64025,-0.23973,182.35
> select #2/b:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models
> #2,-0.024786,-0.32565,0.94517,202.54,-0.68321,0.69573,0.22179,252.06,-0.7298,-0.64025,-0.23973,162.76
> view matrix models
> #2,-0.024786,-0.32565,0.94517,163.8,-0.68321,0.69573,0.22179,234.77,-0.7298,-0.64025,-0.23973,176.43
> view matrix models
> #2,-0.024786,-0.32565,0.94517,251.93,-0.68321,0.69573,0.22179,193.59,-0.7298,-0.64025,-0.23973,123.28
> view matrix models
> #2,-0.024786,-0.32565,0.94517,251.62,-0.68321,0.69573,0.22179,192.77,-0.7298,-0.64025,-0.23973,124.12
> hide #!1 models
> show #!1 models
> view matrix models
> #2,-0.024786,-0.32565,0.94517,264.93,-0.68321,0.69573,0.22179,191.85,-0.7298,-0.64025,-0.23973,132.99
> view matrix models
> #2,-0.56467,0.084465,-0.82098,109.7,0.82484,0.02381,-0.56487,42.689,-0.028164,-0.99614,-0.083115,116.83
> view matrix models
> #2,-0.56467,0.084465,-0.82098,103.31,0.82484,0.02381,-0.56487,41.39,-0.028164,-0.99614,-0.083115,117.09
> hide #2 in #1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> fitmap #2 inMap #1
Fit molecule 4n9f.pdb1 (#2) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 6505 atoms
average map value = 0.005801, steps = 528
shifted from previous position = 35.8
rotated from previous position = 55.5 degrees
atoms outside contour = 5780, contour level = 0.013693
Position of 4n9f.pdb1 (#2) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.83838368 -0.45272076 -0.30357325 135.40362195
0.52740414 -0.53306399 -0.66157966 58.16653402
0.13768688 -0.71476339 0.68567896 171.11823917
Axis -0.04941855 -0.41002085 0.91073636
Axis point 54.78447409 90.30072860 0.00000000
Rotation angle (degrees) 147.44596587
Shift along axis 125.30265982
> view matrix models
> #2,-0.83838,-0.45272,-0.30357,135.19,0.5274,-0.53306,-0.66158,55.983,0.13769,-0.71476,0.68568,170.21
> view matrix models
> #2,-0.83838,-0.45272,-0.30357,144.93,0.5274,-0.53306,-0.66158,108.15,0.13769,-0.71476,0.68568,224.17
> volume #1 level 0.01585
> view matrix models
> #2,-0.57032,-0.71352,-0.40697,119.27,0.75514,-0.6504,0.082088,174.63,-0.32326,-0.2605,0.90975,273.2
> view matrix models
> #2,-0.57032,-0.71352,-0.40697,126.62,0.75514,-0.6504,0.082088,164.31,-0.32326,-0.2605,0.90975,259.64
> view matrix models
> #2,-0.57032,-0.71352,-0.40697,125.57,0.75514,-0.6504,0.082088,169.95,-0.32326,-0.2605,0.90975,261.8
> view matrix models
> #2,-0.51547,-0.76229,-0.39142,124.22,0.74656,-0.62373,0.23155,186.29,-0.42065,-0.17287,0.8906,265.1
> view matrix models
> #2,-0.47707,-0.79555,-0.37352,124.02,0.72998,-0.59535,0.33567,198.26,-0.48942,-0.11252,0.86476,266.12
> view matrix models
> #2,-0.63062,-0.63385,-0.44783,125.14,0.44102,-0.76749,0.46526,218.44,-0.63861,0.095902,0.76353,265.26
> view matrix models
> #2,-0.63062,-0.63385,-0.44783,125.07,0.44102,-0.76749,0.46526,223.52,-0.63861,0.095902,0.76353,265.67
> select #2/a:110
14 atoms, 15 bonds, 1 residue, 1 model selected
> view matrix models
> #2,-0.63062,-0.63385,-0.44783,123.28,0.44102,-0.76749,0.46526,216.31,-0.63861,0.095902,0.76353,262.92
> view matrix models
> #2,-0.88894,-0.16449,-0.42747,144.29,-0.38212,-0.24826,0.89014,300.4,-0.25255,0.95463,0.15783,204.11
> view matrix models
> #2,-0.81267,-0.17413,-0.55609,128.05,-0.49778,-0.28868,0.81785,296.21,-0.30294,0.94146,0.14792,204.61
> view matrix models
> #2,-0.21548,-0.16444,-0.96256,64.83,0.96298,0.12772,-0.23739,143.36,0.16198,-0.97808,0.13083,146.66
> view matrix models
> #2,-0.32867,-0.55591,-0.7635,81.416,0.79295,0.27672,-0.54283,120.86,0.51304,-0.78383,0.34986,160.83
> volume #1 level 0.01154
> view matrix models
> #2,-0.32867,-0.55591,-0.7635,65.68,0.79295,0.27672,-0.54283,75.275,0.51304,-0.78383,0.34986,117.92
> view matrix models
> #2,-0.32867,-0.55591,-0.7635,65.672,0.79295,0.27672,-0.54283,74.878,0.51304,-0.78383,0.34986,117.56
> view matrix models
> #2,-0.43232,-0.46318,-0.77366,70.23,-0.87715,0.017105,0.47991,235.06,-0.20905,0.8861,-0.41368,98.673
> view matrix models
> #2,-0.43232,-0.46318,-0.77366,88.54,-0.87715,0.017105,0.47991,293.27,-0.20905,0.8861,-0.41368,153.3
> view matrix models
> #2,-0.48617,-0.54203,-0.68545,98.277,-0.81653,0.0023377,0.5773,300.61,-0.31131,0.84036,-0.44372,152.66
> view matrix models
> #2,-0.39502,-0.4008,-0.82663,83.312,-0.65638,-0.50642,0.5592,282.52,-0.64275,0.76348,-0.06303,202.34
> view matrix models
> #2,-0.53791,-0.37401,-0.7555,96.332,-0.59328,-0.46874,0.65446,290.92,-0.5989,0.80025,0.030248,211.19
> view matrix models
> #2,-0.83199,-0.27019,-0.48455,137.03,-0.3642,-0.39285,0.84441,303.98,-0.4185,0.87901,0.22845,226.91
> view matrix models
> #2,-0.83199,-0.27019,-0.48455,136.47,-0.3642,-0.39285,0.84441,306.7,-0.4185,0.87901,0.22845,229.32
> view matrix models
> #2,-0.83199,-0.27019,-0.48455,133.61,-0.3642,-0.39285,0.84441,304.91,-0.4185,0.87901,0.22845,227.43
> view matrix models
> #2,-0.83199,-0.27019,-0.48455,109.7,-0.3642,-0.39285,0.84441,256.84,-0.4185,0.87901,0.22845,181.48
> view matrix models
> #2,-0.82202,-0.2135,-0.52792,135.97,-0.44663,-0.33341,0.83028,304.85,-0.35327,0.91829,0.17872,218.82
> view matrix models
> #2,-0.82202,-0.2135,-0.52792,147.22,-0.44663,-0.33341,0.83028,300.36,-0.35327,0.91829,0.17872,215.8
> view matrix models
> #2,-0.82202,-0.2135,-0.52792,147.33,-0.44663,-0.33341,0.83028,300.64,-0.35327,0.91829,0.17872,216.06
> view matrix models
> #2,-0.76952,-0.24517,-0.58968,138.41,-0.50021,-0.34264,0.79523,298.73,-0.39701,0.90691,0.14103,213.49
> view matrix models
> #2,-0.76952,-0.24517,-0.58968,98.998,-0.50021,-0.34264,0.79523,257.11,-0.39701,0.90691,0.14103,171.95
> fitmap #2 inMap #1
Fit molecule 4n9f.pdb1 (#2) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 6505 atoms
average map value = 0.008435, steps = 276
shifted from previous position = 3.27
rotated from previous position = 18.4 degrees
atoms outside contour = 4572, contour level = 0.011539
Position of 4n9f.pdb1 (#2) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.86210944 0.04634696 -0.50459814 121.08378739
-0.48309421 -0.37571105 0.79086105 256.46393677
-0.15292909 0.92557721 0.34629399 181.29939549
Axis 0.20734706 -0.54126795 -0.81488417
Axis point 95.38342485 50.06260965 0.00000000
Rotation angle (degrees) 161.04310620
Shift along axis -261.44734942
> volume #1 level 0.0176
> volume #1 level 0.01006
> volume #1 level 0.01383
> volume #1 level 0.00952
> show #2/X cartoons
> show #2/Y cartoons
> show #2/U cartoons
> hide #2/U cartoons
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs" includeMaps true
> show #!3 models
> select #3/A:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.29968,0.73315,0.61048,150.1,-0.61974,-0.3369,0.70882,141.93,0.72534,-0.59076,0.35339,147.45
> fitmap #4 inMap 1
Invalid "inMap" argument: invalid density map specifier
> fitmap #3 inMap 1
Invalid "inMap" argument: invalid density map specifier
> fitmap #3 inMap #1
Fit molecule 6p3x chain A.pdb (#3) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3217 atoms
average map value = 0.008294, steps = 204
shifted from previous position = 17.8
rotated from previous position = 27.3 degrees
atoms outside contour = 2141, contour level = 0.0095201
Position of 6p3x chain A.pdb (#3) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.18841124 0.92270990 0.33631475 135.59194946
-0.29077977 -0.27468104 0.91651374 144.88041801
0.93805561 -0.27047501 0.21655239 137.19934917
Axis -0.65907300 -0.33411534 -0.67378759
Axis point 32.34542504 45.93828833 0.00000000
Rotation angle (degrees) 115.77630371
Shift along axis -230.21498245
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view matrix models
> #3,0.18841,0.92271,0.33631,133.92,-0.29078,-0.27468,0.91651,102.34,0.93806,-0.27048,0.21655,162.62
> rename #4 "6p40_chain A_CTD"
> open "E:/temp/EM data/6p40 chain A.pdb"
Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (65 )
Cannot find LINK/SSBOND residue CYS (97 )
Cannot find LINK/SSBOND residue CYS (100 )
Cannot find LINK/SSBOND residue HIS (257 )
Cannot find LINK/SSBOND residue CYS (287 )
2 messages similar to the above omitted
6p40 chain A.pdb title:
Crystal structure of full length APOBEC3G FKL [more info...]
Chain information for 6p40 chain A.pdb #5
---
Chain | Description
A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G
Non-standard residues in 6p40 chain A.pdb #5
---
ZN — zinc ion
> select clear
> select #5/A:39
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models #5,1,0,0,-88.501,0,1,0,149.38,0,0,1,61.559
> hide #!3 models
> view matrix models #5,1,0,0,-53.472,0,1,0,87.818,0,0,1,38.736
> view matrix models #5,1,0,0,117.04,0,1,0,69.92,0,0,1,98.468
> select #5/A:289
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
107 atoms, 108 bonds, 14 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show #5/A:1-193
> hide sel atoms
> show #5/A:1-193 cartoons
> select clear
> select #5/A:188
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models #5,1,0,0,120.61,0,1,0,52.455,0,0,1,103.79
> view matrix models #5,1,0,0,121.87,0,1,0,49.895,0,0,1,114.31
> view matrix models #5,1,0,0,121.58,0,1,0,50.772,0,0,1,112.56
> view matrix models #5,1,0,0,159.96,0,1,0,97.317,0,0,1,104.95
> view matrix models #5,1,0,0,159.4,0,1,0,62.841,0,0,1,122.43
> view matrix models
> #5,0.97152,0.22564,0.072322,151.43,-0.17689,0.48759,0.85496,46.887,0.15765,-0.84341,0.51362,159.44
> view matrix models
> #5,0.97368,0.21853,0.064723,151.86,-0.17348,0.52642,0.83234,46.688,0.14782,-0.82166,0.55048,157.67
> view matrix models
> #5,0.9991,-0.040619,0.012418,159.98,0.042163,0.98376,-0.17446,69.068,-0.0051298,0.17483,0.98459,118.65
> view matrix models
> #5,0.99892,-0.044347,0.013963,160.02,0.046199,0.98054,-0.1908,69.694,-0.00523,0.19124,0.98153,118.34
> view matrix models
> #5,0.98091,-0.15759,0.11396,159.47,0.19027,0.65644,-0.72999,95.681,0.040227,0.73774,0.67389,115.17
> view matrix models
> #5,0.98091,-0.15759,0.11396,157.5,0.19027,0.65644,-0.72999,94.697,0.040227,0.73774,0.67389,123.69
> view matrix models
> #5,0.98695,-0.13728,0.084164,158,0.15962,0.76517,-0.62373,88.471,0.021228,0.62902,0.7771,122.92
> view matrix models
> #5,0.93368,-0.16911,0.31565,151.04,0.28263,-0.1933,-0.93955,122.61,0.2199,0.96646,-0.13269,145.01
> view matrix models
> #5,0.9063,-0.086496,0.41369,145.74,0.2469,-0.68609,-0.68434,126.21,0.34302,0.72236,-0.60044,166.64
> view matrix models
> #5,0.89568,-0.019391,0.44428,143.03,0.19798,-0.8772,-0.43741,124.15,0.39821,0.47973,-0.78185,178.5
> view matrix models
> #5,0.9057,0.037702,0.42223,142.31,0.1475,-0.96182,-0.23052,119.36,0.39742,0.27106,-0.87669,187.03
> view matrix models
> #5,0.9057,0.037702,0.42223,150.07,0.1475,-0.96182,-0.23052,124.48,0.39742,0.27106,-0.87669,167.41
> view matrix models
> #5,0.9057,0.037702,0.42223,148.7,0.1475,-0.96182,-0.23052,123.6,0.39742,0.27106,-0.87669,167.64
> view matrix models
> #5,0.98917,0.14619,0.012767,159.77,0.13881,-0.96038,0.24168,107.09,0.047592,-0.23729,-0.97027,185.97
> view matrix models
> #5,0.68378,0.6033,-0.41046,165.26,0.72855,-0.59594,0.33775,90.625,-0.040844,-0.52999,-0.84702,189.56
> select clear
> select #5/A:131
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> view matrix models
> #5,0.68378,0.6033,-0.41046,157.53,0.72855,-0.59594,0.33775,98.617,-0.040844,-0.52999,-0.84702,164.56
> view matrix models
> #5,0.68378,0.6033,-0.41046,160.17,0.72855,-0.59594,0.33775,124.83,-0.040844,-0.52999,-0.84702,175.19
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> view matrix models
> #5,0.69838,0.61397,-0.36784,158.31,0.71571,-0.60255,0.35312,124.55,-0.0048345,-0.50988,-0.86023,174.91
> view matrix models
> #5,0.55389,0.83158,-0.041049,142.42,0.70478,-0.49454,-0.50864,152.1,-0.44327,0.2528,-0.86,158.85
> view matrix models
> #5,0.69802,0.52456,-0.48746,164.73,0.27962,-0.82635,-0.48884,162.57,-0.65923,0.20492,-0.72348,156.73
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> view matrix models
> #5,0.70485,0.51455,-0.48828,164.96,0.24989,-0.82434,-0.50795,163.39,-0.66388,0.23602,-0.70962,155.5
> view matrix models
> #5,0.70485,0.51455,-0.48828,158.41,0.24989,-0.82434,-0.50795,161.7,-0.66388,0.23602,-0.70962,156.05
> view matrix models
> #5,0.70485,0.51455,-0.48828,161.57,0.24989,-0.82434,-0.50795,162.61,-0.66388,0.23602,-0.70962,155.57
> view matrix models
> #5,0.70485,0.51455,-0.48828,159.32,0.24989,-0.82434,-0.50795,161.35,-0.66388,0.23602,-0.70962,157.27
> view matrix models
> #5,0.70485,0.51455,-0.48828,157.49,0.24989,-0.82434,-0.50795,164.4,-0.66388,0.23602,-0.70962,156.87
> view matrix models
> #5,0.70485,0.51455,-0.48828,157.54,0.24989,-0.82434,-0.50795,164.4,-0.66388,0.23602,-0.70962,157.08
> view matrix models
> #5,0.70788,0.50687,-0.49192,157.84,0.22349,-0.82139,-0.52475,165.1,-0.67004,0.26152,-0.69473,155.96
> view matrix models
> #5,0.6083,0.7053,-0.36403,149.09,0.42107,-0.67555,-0.60526,162.94,-0.67281,0.2149,-0.70792,157.61
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.008075, steps = 352
shifted from previous position = 12.9
rotated from previous position = 24.1 degrees
atoms outside contour = 2114, contour level = 0.0095201
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.41748274 0.84548911 -0.33295095 137.00714521
0.23756556 -0.45522148 -0.85810024 170.21429376
-0.87708083 0.27914436 -0.39090620 152.53901710
Axis 0.81253034 0.38876600 -0.43434485
Axis point 0.00000000 1.87532898 144.78306158
Rotation angle (degrees) 135.58770064
Shift along axis 111.24145600
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> view matrix models
> #5,0.41748,0.84549,-0.33295,131.07,0.23757,-0.45522,-0.8581,123.16,-0.87708,0.27914,-0.39091,159.19
> view matrix models
> #5,0.41748,0.84549,-0.33295,131.01,0.23757,-0.45522,-0.8581,123.43,-0.87708,0.27914,-0.39091,158.51
> view matrix models
> #5,0.31579,0.77783,-0.54337,140.76,0.48655,-0.6244,-0.61106,117.31,-0.81458,-0.071409,-0.57564,173.3
> view matrix models
> #5,0.31579,0.77783,-0.54337,164.88,0.48655,-0.6244,-0.61106,141.71,-0.81458,-0.071409,-0.57564,149.64
> view matrix models
> #5,0.31579,0.77783,-0.54337,160.31,0.48655,-0.6244,-0.61106,164.23,-0.81458,-0.071409,-0.57564,155.17
> view matrix models
> #5,0.31579,0.77783,-0.54337,160.14,0.48655,-0.6244,-0.61106,166.25,-0.81458,-0.071409,-0.57564,156.08
> view matrix models
> #5,0.31579,0.77783,-0.54337,153.03,0.48655,-0.6244,-0.61106,166.12,-0.81458,-0.071409,-0.57564,160.13
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.007335, steps = 136
shifted from previous position = 4.79
rotated from previous position = 9.96 degrees
atoms outside contour = 2184, contour level = 0.0095201
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.25923642 0.72247825 -0.64095372 154.22993226
0.36269988 -0.68789226 -0.62869153 171.98248373
-0.89512305 -0.06949409 -0.44036950 155.27549570
Axis 0.78554440 0.35704974 -0.50540625
Axis point 0.00000000 26.59582557 143.04088124
Rotation angle (degrees) 159.14955506
Shift along axis 104.08355356
> volume #1 level 0.01921
> volume #1 level 0.009655
> volume #1 level 0.01625
> volume #1 level 0.02015
> select #5/A:62
5 atoms, 4 bonds, 1 residue, 1 model selected
> view matrix models
> #5,0.25924,0.72248,-0.64095,155.49,0.3627,-0.68789,-0.62869,166.89,-0.89512,-0.069494,-0.44037,163.38
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.008412, steps = 216
shifted from previous position = 7.25
rotated from previous position = 16.4 degrees
atoms outside contour = 2746, contour level = 0.020154
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.19089288 0.85074170 -0.48969224 146.01509921
0.22873444 -0.52368461 -0.82063085 170.08786673
-0.95458916 0.04464311 -0.29456159 154.18248482
Axis 0.74423497 0.39986474 -0.53499767
Axis point -0.00000000 1.76589066 158.08835527
Rotation angle (degrees) 144.45672193
Shift along axis 94.19441374
> view matrix models
> #5,0.19089,0.85074,-0.48969,144.77,0.22873,-0.52368,-0.82063,169.05,-0.95459,0.044643,-0.29456,154.26
> volume #1 level 0.007366
> volume #1 level 0.01262
> select #5/A:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models
> #5,0.19089,0.85074,-0.48969,152.57,0.22873,-0.52368,-0.82063,170.02,-0.95459,0.044643,-0.29456,151.95
> view matrix models
> #5,0.32664,0.82557,-0.46016,151.24,0.23382,-0.54232,-0.80698,169.97,-0.91577,0.156,-0.37017,151.56
> view matrix models
> #5,0.32664,0.82557,-0.46016,150.02,0.23382,-0.54232,-0.80698,169.99,-0.91577,0.156,-0.37017,150.8
> view matrix models
> #5,0.16647,0.85352,-0.49376,151.59,0.2275,-0.52048,-0.82301,170.05,-0.95944,0.024671,-0.28082,151.25
> view matrix models
> #5,0.16647,0.85352,-0.49376,150.94,0.2275,-0.52048,-0.82301,170.06,-0.95944,0.024671,-0.28082,150.79
> view matrix models
> #5,0.27639,0.75891,-0.58963,155.91,0.065966,-0.62707,-0.77617,172.18,-0.95878,0.17563,-0.22338,145.01
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.007872, steps = 96
shifted from previous position = 2.82
rotated from previous position = 3.5 degrees
atoms outside contour = 2380, contour level = 0.012616
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.21852516 0.77753426 -0.58965010 156.66875418
0.07582509 -0.61595677 -0.78412233 172.35391397
-0.97288094 0.12664018 -0.19355865 148.00319513
Axis 0.75150384 0.31621795 -0.57900620
Axis point 0.00000000 8.73070883 166.91115477
Rotation angle (degrees) 142.70204722
Shift along axis 86.54380369
> view matrix models
> #5,0.21853,0.77753,-0.58965,156.56,0.075825,-0.61596,-0.78412,169.58,-0.97288,0.12664,-0.19356,149.03
> view matrix models
> #5,0.21853,0.77753,-0.58965,156.37,0.075825,-0.61596,-0.78412,170.18,-0.97288,0.12664,-0.19356,147.36
> view matrix models
> #5,0.21853,0.77753,-0.58965,158.93,0.075825,-0.61596,-0.78412,170.88,-0.97288,0.12664,-0.19356,150.12
> sequence chain #5/A
Alignment identifier is 5/A
> select
> #5/A:13-21,61-80,97-111,130-141,153-165,177-193,198-206,257-270,287-300,319-330,338-350,362-378
1378 atoms, 1409 bonds, 165 residues, 1 model selected
> select #5/A:209
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:209-215
56 atoms, 58 bonds, 7 residues, 1 model selected
> select clear
> select #5/A:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:181-193
101 atoms, 102 bonds, 13 residues, 1 model selected
> select clear
> select #5/A:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:168-172
42 atoms, 43 bonds, 5 residues, 1 model selected
> select #5/A:166
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:166-169
27 atoms, 26 bonds, 4 residues, 1 model selected
> select #5/A:169
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/A:169-172
31 atoms, 32 bonds, 4 residues, 1 model selected
> select clear
> select #5/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:128-130
23 atoms, 23 bonds, 3 residues, 1 model selected
> view matrix models
> #5,0.21766,0.77434,-0.59415,159.18,0.026056,-0.61314,-0.78954,171.34,-0.97568,0.15637,-0.15363,148
> view matrix models
> #5,0.21837,0.77688,-0.59056,158.98,0.065773,-0.61551,-0.78538,170.98,-0.97365,0.13266,-0.18551,149.7
> view matrix models
> #5,0.21939,0.78869,-0.57432,158.11,0.24282,-0.61428,-0.7508,168.54,-0.94494,0.025259,-0.32628,157.11
> view matrix models
> #5,0.21657,0.77132,-0.59847,159.41,-0.021951,-0.60902,-0.79285,171.68,-0.97602,0.18485,-0.11496,145.94
> view matrix models
> #5,-0.84641,-0.51385,-0.13979,182.63,0.52634,-0.76734,-0.36627,156.97,0.08094,-0.38359,0.91995,116.71
> view matrix models
> #5,-0.79818,-0.58833,-0.12953,183.8,0.59014,-0.72043,-0.36429,155.3,0.121,-0.3672,0.92224,115.94
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.006811, steps = 212
shifted from previous position = 2.32
rotated from previous position = 15.4 degrees
atoms outside contour = 2575, contour level = 0.012616
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.91344490 -0.35646563 -0.19634326 182.98057981
0.40658991 -0.82000877 -0.40282785 162.94952277
-0.01740891 -0.44779223 0.89396815 119.88933337
Axis -0.05727630 -0.22792926 0.97199160
Axis point 76.23180173 115.19241865 0.00000000
Rotation angle (degrees) 156.88850348
Shift along axis 68.91001022
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #5/A:25
7 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.91344,-0.35647,-0.19634,220.35,0.40659,-0.82001,-0.40283,182.3,-0.017409,-0.44779,0.89397,132.3
> view matrix models
> #5,-0.91344,-0.35647,-0.19634,220.04,0.40659,-0.82001,-0.40283,182.12,-0.017409,-0.44779,0.89397,132.27
> view matrix models
> #5,-0.92446,-0.37766,-0.05244,215.6,0.37308,-0.86764,-0.32866,180.94,0.078621,-0.3234,0.94299,126.8
> view matrix models
> #5,-0.92446,-0.37766,-0.05244,180.13,0.37308,-0.86764,-0.32866,162.41,0.078621,-0.3234,0.94299,115.58
> select clear
> select #5/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:194-199
52 atoms, 53 bonds, 6 residues, 1 model selected
> select clear
> select#5/A:180-187
Unknown command: select#5/A:180-187
> select #5/A:180-187
63 atoms, 64 bonds, 8 residues, 1 model selected
> select clear
> volume #1 level 0.008713
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.006854, steps = 68
shifted from previous position = 2.25
rotated from previous position = 4.25 degrees
atoms outside contour = 2260, contour level = 0.0087125
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.90182341 -0.43048481 -0.03738136 178.16886471
0.41292410 -0.83307300 -0.36808026 163.32126915
0.12731155 -0.34737906 0.92904228 114.91113636
Axis 0.02408271 -0.19159527 0.98117851
Axis point 66.98569874 113.14885021 0.00000000
Rotation angle (degrees) 154.54552434
Shift along axis 85.74754519
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.01127
> select #5/A:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.71633,-0.66095,0.22367,173.52,0.65037,-0.74856,-0.12912,151.23,0.25277,0.05297,0.96607,102.77
> view matrix models
> #5,-0.17895,-0.9155,-0.36031,196.67,0.98143,-0.14038,-0.13075,133.87,0.069117,-0.37702,0.92362,116.24
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.00625, steps = 256
shifted from previous position = 11
rotated from previous position = 27.1 degrees
atoms outside contour = 2491, contour level = 0.01127
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.56123226 -0.77014359 -0.30314555 189.69568210
0.81739176 -0.57326484 -0.05690462 143.64372797
-0.12995796 -0.27972538 0.95124374 116.84427533
Axis -0.13818992 -0.10740821 0.98456438
Axis point 64.06928898 129.60119454 0.00000000
Rotation angle (degrees) 126.27252740
Shift along axis 73.39816454
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.00625, steps = 48
shifted from previous position = 0.0127
rotated from previous position = 0.0135 degrees
atoms outside contour = 2496, contour level = 0.01127
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.56119768 -0.77009909 -0.30332255 189.70298154
0.81741785 -0.57321429 -0.05703897 143.65469455
-0.12994316 -0.27995141 0.95117927 116.84053865
Axis -0.13824548 -0.10752615 0.98454371
Axis point 64.07064853 129.61715736 0.00000000
Rotation angle (degrees) 126.27179336
Shift along axis 73.36240148
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.00625, steps = 44
shifted from previous position = 0.004
rotated from previous position = 0.00977 degrees
atoms outside contour = 2497, contour level = 0.01127
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.56127529 -0.77002734 -0.30336110 189.70287737
0.81737705 -0.57325723 -0.05719194 143.65878344
-0.12986458 -0.28006082 0.95115779 116.84462389
Axis -0.13822740 -0.10760575 0.98453755
Axis point 64.07146554 129.61834246 0.00000000
Rotation angle (degrees) 126.27684026
Shift along axis 73.35727353
> volume #1 level 0.01706
> show #!3 models
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6p40 chain A.pdb, chain A (#5) with 6p3x chain A.pdb, chain A (#3),
sequence alignment score = 1956
RMSD between 106 pruned atom pairs is 0.426 angstroms; (across all 358 pairs:
6.515)
> select #5/A:182
12 atoms, 12 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.56128,-0.77003,-0.30336,190.74,0.81738,-0.57326,-0.057192,134.16,-0.12986,-0.28006,0.95116,128.02
> undo
> hide #!3 models
> fetch 6p3x
Unknown command: fetch 6p3x
> open 6p3x
Summary of feedback from opening 6p3x fetched from pdb
---
notes | Fetching compressed mmCIF 6p3x from
http://files.rcsb.org/download/6p3x.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
6p3x title:
Crystal Structure of Full Length APOBEC3G E/Q (pH 7.0) [more info...]
Chain information for 6p3x #6
---
Chain | Description
A B | Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
Non-standard residues in 6p3x #6
---
ZN — zinc ion
> view
> select #6/B:130
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models #6,1,0,0,-0.19639,0,1,0,142.78,0,0,1,168.82
> select clear
> select clear
> select #6/A:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models #6,1,0,0,151.35,0,1,0,141.95,0,0,1,145.99
> view matrix models #6,1,0,0,154.76,0,1,0,180.91,0,0,1,176.99
> view matrix models #6,1,0,0,154.86,0,1,0,182.15,0,0,1,178.76
> color #6/B gold
> view matrix models #6,1,0,0,155.98,0,1,0,184.89,0,0,1,182.99
> view matrix models
> #6,0.96108,0.17527,-0.21354,160.93,-0.25433,0.25957,-0.93163,208.12,-0.10786,0.94969,0.29404,198.95
> view matrix models
> #6,0.62669,0.089492,0.77411,146.35,0.77052,0.077228,-0.63272,185.28,-0.11641,0.99299,-0.020557,205.48
> view matrix models
> #6,0.62674,0.77368,0.092815,160.09,0.22412,-0.064901,-0.9724,201.16,-0.7463,0.63024,-0.21408,219.79
> view matrix models
> #6,0.96698,0.17399,-0.18621,160.28,-0.17317,-0.087506,-0.981,207.85,-0.18698,0.98085,-0.054487,207.32
> view matrix models
> #6,0.98262,0.1778,-0.053275,157.32,-0.1344,0.48364,-0.86489,204.76,-0.12801,0.85702,0.49913,195.13
> view matrix models
> #6,-0.30338,-0.49142,0.81637,160.83,0.78149,-0.61851,-0.081895,174.01,0.54518,0.61314,0.57169,182.66
> view matrix models
> #6,-0.30338,-0.49142,0.81637,162.08,0.78149,-0.61851,-0.081895,185.37,0.54518,0.61314,0.57169,185.35
> select clear
> ui tool show Matchmaker
> matchmaker #!6 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6p40_chain A_CTD, chain A (#4) with 6p3x, chain B (#6), sequence
alignment score = 1959
RMSD between 106 pruned atom pairs is 0.428 angstroms; (across all 358 pairs:
6.546)
> select clear
> select #6/A:16
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.46881,0.44031,-0.76573,169.03,0.65573,-0.75431,-0.032276,178.36,-0.59181,-0.48698,-0.64235,208.88
> volume #1 level 0.00804
> view matrix models
> #6,0.46881,0.44031,-0.76573,174.84,0.65573,-0.75431,-0.032276,218.77,-0.59181,-0.48698,-0.64235,197.84
> volume #1 level 0.01383
> hide #6/A cartoons
> select #6/B:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.46881,0.44031,-0.76573,175.93,0.65573,-0.75431,-0.032276,214.1,-0.59181,-0.48698,-0.64235,189.5
> view matrix models
> #6,0.46881,0.44031,-0.76573,175.29,0.65573,-0.75431,-0.032276,215.91,-0.59181,-0.48698,-0.64235,194.35
> view matrix models
> #6,-0.91432,0.40355,0.034181,146.58,0.07184,0.24467,-0.96694,239.89,-0.39857,-0.88164,-0.2527,186.05
> show #6 dartoon
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #6 cartoons
> select clear
> select #6/A:327
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #6,-0.91432,0.40355,0.034181,145.72,0.07184,0.24467,-0.96694,230.05,-0.39857,-0.88164,-0.2527,191.88
> view matrix models
> #6,-0.91432,0.40355,0.034181,145.38,0.07184,0.24467,-0.96694,246.4,-0.39857,-0.88164,-0.2527,195.34
> view matrix models
> #6,-0.018908,0.11509,-0.99317,151.63,0.99684,-0.074488,-0.02761,212.2,-0.077157,-0.99056,-0.11332,187.26
> view matrix models
> #6,0.95621,-0.25437,0.14476,112.59,0.0092494,0.52062,0.85374,210.38,-0.29254,-0.81501,0.50018,178.29
> view matrix models
> #6,0.020962,-0.1268,-0.99171,150.99,0.42869,-0.89497,0.1235,218.57,-0.90321,-0.42773,0.035599,197.68
> view matrix models
> #6,-0.080355,-0.045221,-0.99574,152.72,0.98993,-0.12041,-0.074418,213.27,-0.11653,-0.99169,0.054441,184.49
> view matrix models
> #6,-0.093028,-0.043561,-0.99471,152.91,0.99542,-0.025935,-0.091959,213.52,-0.021792,-0.99871,0.045774,183.12
> view matrix models
> #6,-0.093028,-0.043561,-0.99471,151.84,0.99542,-0.025935,-0.091959,227.53,-0.021792,-0.99871,0.045774,191.87
> select up
108 atoms, 109 bonds, 12 residues, 1 model selected
> select up
3120 atoms, 3119 bonds, 461 residues, 1 model selected
> select up
6240 atoms, 6238 bonds, 922 residues, 1 model selected
> select up
22226 atoms, 22240 bonds, 3232 residues, 7 models selected
> select down
6240 atoms, 6238 bonds, 922 residues, 1 model selected
> select down
3120 atoms, 3119 bonds, 461 residues, 1 model selected
> hide #6/A
> hide #6/A cartoons
> ui tool show Matchmaker
> matchmaker #!6 to #4/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6p40_chain A_CTD, chain A (#4) with 6p3x, chain B (#6), sequence
alignment score = 1959
RMSD between 106 pruned atom pairs is 0.428 angstroms; (across all 358 pairs:
6.546)
> select #6/B:322
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.46881,0.44031,-0.76573,167.18,0.65573,-0.75431,-0.032276,70.283,-0.59181,-0.48698,-0.64235,135.74
> hide #6/B:1-193
> hide #6/B:1-193
> show #6/B:1-193
> hide #6/B:1-193
> hide #6/B:1-193 cartoons
> hide #6/B:1-193
> hide #6/B:1-193
> ui tool show Matchmaker
> matchmaker #!6 to #4/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6p40_chain A_CTD, chain A (#4) with 6p3x, chain B (#6), sequence
alignment score = 1959
RMSD between 106 pruned atom pairs is 0.428 angstroms; (across all 358 pairs:
6.546)
> select #6/B:292
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.46881,0.44031,-0.76573,166.53,0.65573,-0.75431,-0.032276,73.926,-0.59181,-0.48698,-0.64235,140.79
> show #6/B:1-193 cartoons
> select #6/B:194-385
1465 atoms, 1508 bonds, 1 pseudobond, 176 residues, 2 models selected
> matchmaker #!6 & sel to #4/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6p40_chain A_CTD, chain A (#4) with 6p3x, chain B (#6), sequence
alignment score = 907.2
RMSD between 154 pruned atom pairs is 0.838 angstroms; (across all 175 pairs:
2.006)
> hide #!5 models
> select clear
> select clear
> select clear
> select #6/B:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.40407,0.75377,-0.51823,163.96,0.79723,-0.56797,-0.20452,73.917,-0.4485,-0.33051,-0.83043,140.77
> select #6/B:375
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/B:107
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/B:107
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #6
> hide #6
> show #6 cartoons
> view matrix models
> #6,0.40407,0.75377,-0.51823,158.38,0.79723,-0.56797,-0.20452,56.357,-0.4485,-0.33051,-0.83043,153.77
> hide #6/A cartoons
> hide #6/B:194-385
> hide #6/B:194-385 cartoons
> view matrix models
> #6,0.40407,0.75377,-0.51823,193.38,0.79723,-0.56797,-0.20452,50.436,-0.4485,-0.33051,-0.83043,136.69
> view matrix models
> #6,0.40407,0.75377,-0.51823,192.73,0.79723,-0.56797,-0.20452,52.077,-0.4485,-0.33051,-0.83043,133.88
> view matrix models
> #6,-0.83704,-0.18406,0.51526,164.96,0.41673,0.39577,0.81835,67.876,-0.35455,0.89972,-0.25457,158.51
> view matrix models
> #6,0.23853,-0.74948,-0.61756,161.4,-0.078502,-0.64872,0.75697,43.922,-0.96796,-0.13208,-0.21358,133.97
> view matrix models
> #6,0.06261,0.39478,-0.91664,184.12,0.7433,0.59446,0.30679,74.583,0.66602,-0.70055,-0.25622,131.82
> view matrix models
> #6,-0.21911,0.58091,-0.78393,186.08,0.13326,0.81374,0.56575,75.148,0.96656,0.019495,-0.25571,148.17
> view matrix models
> #6,-0.26929,0.41793,-0.86765,182.61,0.24126,0.90148,0.35934,77.873,0.93235,-0.11256,-0.34359,145.43
> view matrix models
> #6,-0.19029,0.42204,-0.88638,183.18,0.38309,0.86322,0.32877,77.953,0.9039,-0.277,-0.32594,141.89
> view matrix models
> #6,-0.048432,0.48139,-0.87517,185.18,0.49222,0.77392,0.39846,76.652,0.86912,-0.41148,-0.27443,138.88
> view matrix models
> #6,-0.048432,0.48139,-0.87517,184.02,0.49222,0.77392,0.39846,132.9,0.86912,-0.41148,-0.27443,115.08
> view matrix models
> #6,-0.014181,0.40152,-0.91574,182.65,0.56514,0.75874,0.32393,133.13,0.82487,-0.51293,-0.23768,112.71
> view matrix models
> #6,-0.014181,0.40152,-0.91574,166.69,0.56514,0.75874,0.32393,142.03,0.82487,-0.51293,-0.23768,135.14
> view matrix models
> #6,-0.014181,0.40152,-0.91574,167.59,0.56514,0.75874,0.32393,145.25,0.82487,-0.51293,-0.23768,136.59
> view matrix models
> #6,-0.014181,0.40152,-0.91574,167.79,0.56514,0.75874,0.32393,144.84,0.82487,-0.51293,-0.23768,137.08
> view matrix models
> #6,-0.014181,0.40152,-0.91574,165.62,0.56514,0.75874,0.32393,145.2,0.82487,-0.51293,-0.23768,132.44
> fitmap #6 inMap #1
Fit molecule 6p3x (#6) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 6240 atoms
average map value = 0.006877, steps = 436
shifted from previous position = 17.5
rotated from previous position = 60.1 degrees
atoms outside contour = 5530, contour level = 0.013827
Position of 6p3x (#6) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.63630890 0.17548253 -0.75121026 157.29176230
-0.20476553 0.90043268 0.38378647 143.43356904
0.74376210 0.39802872 -0.53702056 148.36715853
Axis 0.00923239 -0.96910085 -0.24649200
Axis point 53.68601736 0.00000000 94.58391160
Rotation angle (degrees) 129.52749180
Shift along axis -174.12073126
> close #6
> show #!5 models
> select #5/A:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.56128,-0.77003,-0.30336,193.5,0.81738,-0.57326,-0.057192,145.91,-0.12986,-0.28006,0.95116,111.15
> volume #1 level 0.009116
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.006265, steps = 144
shifted from previous position = 3.59
rotated from previous position = 12.9 degrees
atoms outside contour = 2320, contour level = 0.0091163
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.59613714 -0.79301675 -0.12547889 186.70622449
0.79229949 -0.60634214 0.06790239 141.91647078
-0.12993087 -0.05893772 0.98976983 107.54906835
Axis -0.07975416 0.00279930 0.99681063
Axis point 62.48115333 119.00374256 0.00000000
Rotation angle (degrees) 127.32638969
Shift along axis 92.71272348
> volume #1 level 0.01423
> select #5/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.59614,-0.79302,-0.12548,190.78,0.7923,-0.60634,0.067902,91.76,-0.12993,-0.058938,0.98977,109.27
> volume #1 level 0.01046
> view matrix models
> #5,-0.78424,-0.57498,0.23316,174.06,0.6067,-0.63196,0.48223,79.152,-0.12992,0.51964,0.84445,99.92
> view matrix models
> #5,-0.35342,-0.22121,0.90893,138.65,0.18638,0.93551,0.30015,49.277,-0.91671,0.27549,-0.2894,151.06
> view matrix models
> #5,-0.35704,-0.17674,0.91722,137.27,0.16352,0.95495,0.24766,50.785,-0.91967,0.2384,-0.31205,152.8
> view matrix models
> #5,-0.30187,0.027337,0.95296,130.56,0.13983,0.99005,0.015894,58.186,-0.94304,0.13805,-0.30269,155.13
> view matrix models
> #5,-0.40939,-0.086787,0.90822,135.7,0.039202,0.99287,0.11255,55.415,-0.91152,0.08168,-0.40307,159.84
> view matrix models
> #5,-0.40939,-0.086787,0.90822,117.68,0.039202,0.99287,0.11255,73.962,-0.91152,0.08168,-0.40307,168.78
> view matrix models
> #5,-0.40939,-0.086787,0.90822,115.35,0.039202,0.99287,0.11255,75.533,-0.91152,0.08168,-0.40307,168.21
> view matrix models
> #5,-0.53151,-0.22286,0.81721,122.77,-0.1201,0.97485,0.18773,74.431,-0.83849,0.0016402,-0.54491,174.68
> view matrix models
> #5,-0.47773,0.18904,0.85793,110.7,-0.02516,0.97323,-0.22846,88.4,-0.87815,-0.13073,-0.46018,175.28
> view matrix models
> #5,-0.28874,0.31492,0.90413,104.66,0.16535,0.94657,-0.2769,89.468,-0.94302,0.069546,-0.32538,166.01
> view matrix models
> #5,-0.09215,0.45095,0.88778,100.5,0.27767,0.86785,-0.412,95.4,-0.95625,0.20854,-0.20519,158.42
> view matrix models
> #5,-0.27111,0.31737,0.90872,104.32,0.15757,0.94598,-0.28337,89.762,-0.94956,0.06636,-0.30647,165.47
> view matrix models
> #5,-0.2721,0.29095,0.91723,104.68,0.17015,0.95272,-0.25174,88.401,-0.94711,0.087569,-0.30874,165
> view matrix models
> #5,-0.30824,0.42381,0.85169,103.91,0.086412,0.90405,-0.4186,96.027,-0.94738,-0.055433,-0.31529,168.8
> undo
> undo
> view matrix models
> #5,-0.27111,0.31737,0.90872,119.01,0.15757,0.94598,-0.28337,118.42,-0.94956,0.06636,-0.30647,160.09
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.006707, steps = 112
shifted from previous position = 4.61
rotated from previous position = 11.1 degrees
atoms outside contour = 2360, contour level = 0.010462
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.10076876 0.31808633 0.94269123 118.24747570
0.24406390 0.92646526 -0.28652215 120.01986316
-0.96450945 0.20120441 -0.17099214 153.62669175
Axis 0.24758105 0.96813827 -0.03757546
Axis point 112.69855375 0.00000000 42.85009907
Rotation angle (degrees) 99.94180476
Shift along axis 139.69906284
> select #5/A:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.10077,0.31809,0.94269,120.03,0.24406,0.92647,-0.28652,113.53,-0.96451,0.2012,-0.17099,150.26
> view matrix models
> #5,-0.10077,0.31809,0.94269,120.59,0.24406,0.92647,-0.28652,111.42,-0.96451,0.2012,-0.17099,146.23
> volume #1 level 0.01477
> volume #1 level 0.01127
> volume #1 level 0.007366
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
> volume #1 level 0.004136
> volume #1 level 0.01706
> select #5/A:185
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.10077,0.31809,0.94269,120.47,0.24406,0.92647,-0.28652,112.49,-0.96451,0.2012,-0.17099,148.5
> view matrix models
> #5,-0.10077,0.31809,0.94269,119.53,0.24406,0.92647,-0.28652,114.04,-0.96451,0.2012,-0.17099,147.54
> view matrix models
> #5,-0.84185,0.25362,0.4764,142.5,-0.081321,0.81302,-0.57652,129.24,-0.53354,-0.52409,-0.66382,179.96
> view matrix models
> #5,-0.84185,0.25362,0.4764,141.66,-0.081321,0.81302,-0.57652,129.5,-0.53354,-0.52409,-0.66382,175.96
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.004591, steps = 140
shifted from previous position = 1.4
rotated from previous position = 11.1 degrees
atoms outside contour = 2817, contour level = 0.017058
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.76067899 0.29670371 0.57735118 137.08474958
-0.01672730 0.88017049 -0.47436286 125.07770686
-0.64891269 -0.37049538 -0.66456414 174.66428318
Axis 0.08178920 0.96560685 -0.24680751
Axis point 99.71323475 0.00000000 79.23709352
Rotation angle (degrees) 140.58219770
Shift along axis 88.87948572
> volume #1 level 0.01033
> view matrix models
> #5,-0.76068,0.2967,0.57735,180.18,-0.016727,0.88017,-0.47436,143.29,-0.64891,-0.3705,-0.66456,181.94
> view matrix models
> #5,-0.76068,0.2967,0.57735,180.08,-0.016727,0.88017,-0.47436,143.96,-0.64891,-0.3705,-0.66456,179.49
> view matrix models
> #5,0.52672,0.33056,0.78313,163.29,0.55074,0.56906,-0.61062,152.64,-0.6475,0.75292,0.11768,124.06
> view matrix models
> #5,0.52672,0.33056,0.78313,165.16,0.55074,0.56906,-0.61062,153.5,-0.6475,0.75292,0.11768,123.92
> view matrix models
> #5,0.20088,0.010767,0.97956,168.47,0.84248,0.50834,-0.17836,137.9,-0.49987,0.86109,0.093045,121.08
> view matrix models
> #5,-0.25775,0.32687,0.90924,166.16,0.69108,0.72003,-0.062949,129.61,-0.67526,0.61214,-0.41148,146.15
> view matrix models
> #5,-0.92395,-0.20617,0.32219,204.54,0.23778,0.35021,0.90599,107.98,-0.29962,0.9137,-0.27455,131.28
> view matrix models
> #5,-0.91503,-0.07685,0.396,198.67,0.37356,0.2091,0.90373,110.66,-0.15226,0.97487,-0.16262,124.83
> view matrix models
> #5,-0.77196,0.15355,0.61684,184.22,0.61469,-0.066896,0.78593,120.03,0.16195,0.98587,-0.042746,118.23
> view matrix models
> #5,-0.76738,0.04877,0.63933,186.01,0.63153,-0.11494,0.76678,121.79,0.11088,0.99217,0.057406,114.91
> view matrix models
> #5,-0.56061,0.162,0.81208,175.73,0.70611,-0.41878,0.57099,135.72,0.43258,0.89352,0.12038,112.98
> view matrix models
> #5,-0.50584,0.37836,0.77522,171.25,0.71632,-0.31648,0.62187,131.31,0.48063,0.86988,-0.11094,121.34
> view matrix models
> #5,-0.31628,0.41762,0.8518,166.31,0.66935,-0.53804,0.51233,140.99,0.67226,0.73219,-0.10936,123.42
> view matrix models
> #5,-0.74761,-0.52287,0.40949,208.19,0.58062,-0.81391,0.02078,165.69,0.32242,0.25329,0.91208,101.98
> view matrix models
> #5,-0.74761,-0.52287,0.40949,209.44,0.58062,-0.81391,0.02078,165.15,0.32242,0.25329,0.91208,105.75
> view matrix models
> #5,-0.74761,-0.52287,0.40949,208.8,0.58062,-0.81391,0.02078,164.72,0.32242,0.25329,0.91208,106.27
> view matrix models
> #5,-0.74761,-0.52287,0.40949,209.35,0.58062,-0.81391,0.02078,165.96,0.32242,0.25329,0.91208,102.82
> view matrix models
> #5,-0.75282,-0.5399,0.37653,210.97,0.58348,-0.81213,0.0020877,166.55,0.30467,0.22127,0.9264,103.23
> view matrix models
> #5,-0.15778,0.69822,0.69828,164.77,0.74691,-0.37818,0.54691,135.54,0.64594,0.60784,-0.46184,139.88
> view matrix models
> #5,-0.43256,0.19449,0.88038,172.83,0.62441,-0.63976,0.44813,146.36,0.65039,0.74356,0.15529,114.86
> view matrix models
> #5,-0.65328,-0.27631,0.7049,193.39,0.57177,-0.79034,0.2201,158.96,0.4963,0.54683,0.67429,102.7
> view matrix models
> #5,-0.59307,-0.13962,0.79295,186.66,0.58041,-0.7567,0.30087,155.26,0.55802,0.63867,0.52982,105.19
> view matrix models
> #5,0.061373,0.89554,-0.44073,199.59,0.98595,0.014346,0.16645,137.98,0.15538,-0.44475,-0.88207,184.39
> view matrix models
> #5,0.061373,0.89554,-0.44073,192.12,0.98595,0.014346,0.16645,138.34,0.15538,-0.44475,-0.88207,171.81
> view matrix models
> #5,0.067671,0.91843,-0.38975,189.72,0.98091,0.010136,0.1942,137.51,0.18231,-0.39545,-0.90021,171.03
> view matrix models
> #5,0.076614,0.98664,-0.14379,179.35,0.94907,-0.027962,0.31381,134.49,0.3056,-0.16051,-0.93853,165.67
> view matrix models
> #5,0.076672,0.98634,-0.1458,181.02,0.94938,-0.027543,0.31293,132.59,0.30464,-0.16241,-0.93852,174.75
> view matrix models
> #5,-0.098827,0.94409,0.31454,167.15,0.80354,0.26216,-0.53441,156.03,-0.58699,0.19993,-0.78452,166.37
> view matrix models
> #5,-0.067318,0.93844,0.33881,166.23,0.81437,0.24787,-0.52475,155.97,-0.57643,0.2406,-0.78092,165.16
> view matrix models
> #5,-0.10231,0.92216,0.37304,165.67,0.81522,0.29263,-0.49979,153.97,-0.57005,0.25297,-0.7817,164.83
> view matrix models
> #5,-0.10231,0.92216,0.37304,126.74,0.81522,0.29263,-0.49979,137.17,-0.57005,0.25297,-0.7817,163.56
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.007758, steps = 216
shifted from previous position = 5.75
rotated from previous position = 24.6 degrees
atoms outside contour = 2237, contour level = 0.010328
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.20949377 0.79797570 0.56510810 122.37099314
0.89548867 0.07553260 -0.43862842 137.36608026
-0.39269889 0.59793781 -0.69875459 149.89847569
Axis 0.73271163 0.67703954 0.06892843
Axis point 0.00000000 -26.48206635 71.08787550
Rotation angle (degrees) 134.98033971
Shift along axis 192.99718453
> volume #1 level 0.01585
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> view matrix models
> #5,0.32876,0.53436,-0.7787,175.19,-0.040264,-0.81585,-0.57685,170.8,-0.94355,0.221,-0.24671,147.21
> view matrix models
> #5,0.32876,0.53436,-0.7787,170.76,-0.040264,-0.81585,-0.57685,168.6,-0.94355,0.221,-0.24671,147.46
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.007698, steps = 112
shifted from previous position = 7.71
rotated from previous position = 11 degrees
atoms outside contour = 2581, contour level = 0.015846
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.29606661 0.66020517 -0.69027076 161.56748446
-0.09665033 -0.69825407 -0.70929542 175.51207137
-0.95026485 0.27671358 -0.14292066 140.81901938
Axis 0.77644740 0.20473620 -0.59599709
Axis point 0.00000000 23.32301978 169.24668610
Rotation angle (degrees) 140.58379847
Shift along axis 77.45460288
> volume #1 level 0.01813
> volume #1 level 0.01033
> select #5/A:163
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #5,0.29607,0.66021,-0.69027,205.78,-0.09665,-0.69825,-0.7093,193.68,-0.95026,0.27671,-0.14292,128.24
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view matrix models
> #5,-0.24298,-0.42246,0.87321,181.71,-0.26473,0.89489,0.35929,117.65,-0.93321,-0.14386,-0.32928,145.14
> view matrix models
> #5,0.019077,-0.66066,0.75044,190.17,0.58551,0.61579,0.52723,112.96,-0.81044,0.42934,0.39857,104.52
> view matrix models
> #5,0.97816,-0.1957,0.070001,195.88,0.081862,0.67234,0.7357,107.67,-0.19104,-0.71391,0.67368,119.2
> view matrix models
> #5,0.5483,0.30699,0.7779,161.47,-0.7575,0.57645,0.30643,130.79,-0.35434,-0.75728,0.54861,125.77
> view matrix models
> #5,0.3787,-0.081141,0.92196,167.26,-0.62237,0.71496,0.31857,126,-0.68501,-0.69444,0.22025,137.95
> view matrix models
> #5,0.3787,-0.081141,0.92196,135.28,-0.62237,0.71496,0.31857,134.2,-0.68501,-0.69444,0.22025,158.56
> view matrix models
> #5,0.37867,-0.20133,0.90337,138.93,-0.73192,0.53227,0.42543,135.76,-0.56648,-0.82229,0.054198,166.76
> view matrix models
> #5,-0.78871,0.27266,-0.55099,185.96,0.29502,-0.61845,-0.72834,197.89,-0.53935,-0.737,0.40734,152.08
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
——— End of log from Sat Jun 19 20:21:38 2021 ———
opened ChimeraX session
> select #5/A:51
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.78871,0.27266,-0.55099,211.31,0.29502,-0.61845,-0.72834,206.96,-0.53935,-0.737,0.40734,155.83
Alignment identifier is 5/A
> select #5/A:139
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:139-142
23 atoms, 22 bonds, 4 residues, 1 model selected
> view matrix models
> #5,-0.79062,0.4173,-0.44808,204.11,0.19038,-0.52799,-0.82764,208.89,-0.58196,-0.73965,0.33799,158.62
> view matrix models
> #5,-0.25471,-0.16131,0.95347,165.83,-0.44285,-0.85706,-0.26331,201.64,0.85965,-0.48932,0.14687,149.27
> view matrix models
> #5,-0.39601,-0.15521,0.90503,168.33,-0.45436,-0.82337,-0.34002,203.56,0.79795,-0.54587,0.25554,147.3
> view matrix models
> #5,0.25427,0.65552,-0.71108,200.6,0.62074,-0.67443,-0.39977,194.77,-0.74164,-0.33975,-0.5784,181.76
> view matrix models
> #5,0.25427,0.65552,-0.71108,159.28,0.62074,-0.67443,-0.39977,179.54,-0.74164,-0.33975,-0.5784,184.88
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.006084, steps = 256
shifted from previous position = 13.1
rotated from previous position = 26 degrees
atoms outside contour = 2639, contour level = 0.010328
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.09195956 0.85279380 -0.51408773 144.29948233
0.41346260 -0.50236738 -0.75939168 185.07390883
-0.90586541 -0.14272273 -0.39879582 173.93072966
Axis 0.72335240 0.45955503 -0.51533530
Axis point -0.00000000 11.83623606 159.90257943
Rotation angle (degrees) 154.76970719
Shift along axis 99.79837809
> undo
> view matrix models
> #5,0.27945,0.76318,-0.58264,193.25,0.088547,-0.62471,-0.77582,210.31,-0.95607,0.16521,-0.24215,158.84
> view matrix models
> #5,0.27945,0.76318,-0.58264,160.9,0.088547,-0.62471,-0.77582,204.76,-0.95607,0.16521,-0.24215,163.21
> view matrix models
> #5,0.27945,0.76318,-0.58264,171.93,0.088547,-0.62471,-0.77582,184.46,-0.95607,0.16521,-0.24215,147.99
> ui tool show "Side View"
> view matrix models
> #5,0.27945,0.76318,-0.58264,160.34,0.088547,-0.62471,-0.77582,172.16,-0.95607,0.16521,-0.24215,150.96
> view matrix models
> #5,0.27945,0.76318,-0.58264,156.9,0.088547,-0.62471,-0.77582,171.07,-0.95607,0.16521,-0.24215,150.94
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.007871, steps = 100
shifted from previous position = 3.05
rotated from previous position = 3.71 degrees
atoms outside contour = 2177, contour level = 0.010328
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.21866269 0.77748978 -0.58965778 156.67069320
0.07560909 -0.61596397 -0.78413754 172.35920284
-0.97286685 0.12687812 -0.19347363 147.98205112
Axis 0.75153744 0.31612625 -0.57901267
Axis point 0.00000000 8.73704125 166.91009236
Rotation angle (degrees) 142.69186681
Shift along axis 86.54767614
> volume #1 level 0.01372
> view matrix models
> #5,0.21866,0.77749,-0.58966,193.34,0.075609,-0.61596,-0.78414,178.01,-0.97287,0.12688,-0.19347,139.68
> view matrix models
> #5,0.051209,0.62052,-0.78252,205.15,-0.038798,-0.78172,-0.62242,177.26,-0.99793,0.062234,-0.015956,135.24
> view matrix models
> #5,-0.22924,-0.032527,-0.97283,230.01,0.0014101,-0.99945,0.033085,159.46,-0.97337,0.0062128,0.22916,127.89
> view matrix models
> #5,-0.87987,-0.45529,-0.13616,215.68,0.28678,-0.73719,0.6118,130.72,-0.37892,0.49926,0.7792,92.294
> view matrix models
> #5,-0.91871,-0.22326,-0.32576,216.79,0.29991,-0.93109,-0.20768,164.16,-0.25694,-0.2885,0.92236,106.11
> view matrix models
> #5,-0.87186,0.42245,-0.24779,197.63,-0.059247,-0.5932,-0.80287,179.01,-0.48616,-0.68531,0.54222,130.87
> view matrix models
> #5,-0.87342,0.35865,-0.32942,202.1,0.18031,-0.3902,-0.9029,175.82,-0.45236,-0.84801,0.27614,144.02
> view matrix models
> #5,-0.82254,0.56398,-0.073177,187.65,-0.089511,-0.25545,-0.96267,176.39,-0.56162,-0.78528,0.2606,143.74
> view matrix models
> #5,-0.6434,-0.51526,0.56617,190.97,-0.53633,-0.22433,-0.81365,173.43,0.54625,-0.82715,-0.13201,151.01
> view matrix models
> #5,-0.56036,-0.39071,0.73031,181.56,-0.59803,-0.41919,-0.68312,174.14,0.57303,-0.81953,0.0012407,145.97
> view matrix models
> #5,-0.54929,-0.3678,0.75034,180.21,-0.55528,-0.51035,-0.65666,175.2,0.62445,-0.77735,0.076099,141.95
> view matrix models
> #5,-0.54929,-0.3678,0.75034,184.33,-0.55528,-0.51035,-0.65666,175.92,0.62445,-0.77735,0.076099,140
> view matrix models
> #5,-0.54929,-0.3678,0.75034,183.66,-0.55528,-0.51035,-0.65666,175.85,0.62445,-0.77735,0.076099,140.21
> view matrix models
> #5,-0.54929,-0.3678,0.75034,185,-0.55528,-0.51035,-0.65666,176.2,0.62445,-0.77735,0.076099,139.28
> view matrix models
> #5,-0.55456,-0.37518,0.74276,185.48,-0.51723,-0.54381,-0.66087,176.92,0.65187,-0.75067,0.10752,137.33
> view matrix models
> #5,-0.55203,-0.35721,0.75344,184.64,-0.62488,-0.42104,-0.65746,174.47,0.55207,-0.83374,0.0092136,143.52
> view matrix models
> #5,-0.5969,-0.45916,0.65794,190.84,-0.49613,-0.43323,-0.75244,177.23,0.63053,-0.77555,0.030791,140.78
> view matrix models
> #5,-0.22162,-0.65103,0.72598,190.69,-0.56655,-0.51998,-0.63925,175.91,0.79366,-0.55297,-0.25361,144.08
> view matrix models
> #5,-0.22162,-0.65103,0.72598,166.06,-0.56655,-0.51998,-0.63925,172.93,0.79366,-0.55297,-0.25361,152.31
> view matrix models
> #5,-0.22162,-0.65103,0.72598,192.74,-0.56655,-0.51998,-0.63925,175.86,0.79366,-0.55297,-0.25361,144.14
> view matrix models
> #5,-0.24646,-0.7165,0.65259,197.11,-0.61134,-0.40756,-0.67835,174.73,0.75201,-0.56615,-0.33758,147.69
> view matrix models
> #5,-0.48841,-0.58855,0.64426,195.86,-0.57112,-0.34261,-0.74595,175.2,0.65976,-0.73227,-0.1688,146.55
> view matrix models
> #5,-0.48841,-0.58855,0.64426,166.22,-0.57112,-0.34261,-0.74595,171.47,0.65976,-0.73227,-0.1688,156.83
> view matrix models
> #5,-0.56524,-0.53297,0.62965,165.87,-0.55153,-0.32345,-0.76889,171.66,0.61345,-0.78187,-0.11112,156.36
> view matrix models
> #5,-0.56524,-0.53297,0.62965,167.42,-0.55153,-0.32345,-0.76889,171.77,0.61345,-0.78187,-0.11112,156.05
> view matrix models
> #5,-0.56524,-0.53297,0.62965,166.31,-0.55153,-0.32345,-0.76889,171.58,0.61345,-0.78187,-0.11112,156.57
> view matrix models
> #5,-0.58736,-0.58385,0.56046,170.15,-0.47798,-0.30858,-0.82238,172.58,0.6531,-0.75093,-0.097818,155.06
> view matrix models
> #5,-0.58978,-0.58799,0.55355,203.06,-0.47167,-0.30559,-0.82713,165.23,0.65551,-0.74892,-0.097108,144.7
> volume #1 level 0.01111
> view matrix models
> #5,-0.58978,-0.58799,0.55355,206.52,-0.47167,-0.30559,-0.82713,167.08,0.65551,-0.74892,-0.097108,145.4
> view matrix models
> #5,-0.58978,-0.58799,0.55355,175.26,-0.47167,-0.30559,-0.82713,190.32,0.65551,-0.74892,-0.097108,150.97
> view matrix models
> #5,-0.58978,-0.58799,0.55355,157.71,-0.47167,-0.30559,-0.82713,170.86,0.65551,-0.74892,-0.097108,155.82
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.00804, steps = 100
shifted from previous position = 1.99
rotated from previous position = 5.47 degrees
atoms outside contour = 2420, contour level = 0.011111
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.60212297 -0.51496451 0.61013074 154.30700984
-0.52194834 -0.32438630 -0.78888750 171.96128146
0.60416710 -0.79346400 -0.07346443 158.20465619
Axis -0.44601907 0.58120845 -0.68063480
Axis point 25.72575256 153.30135800 -0.00000000
Rotation angle (degrees) 179.70604949
Shift along axis -76.55811429
> view matrix models
> #5,-0.60212,-0.51496,0.61013,182.8,-0.52195,-0.32439,-0.78889,140.81,0.60417,-0.79346,-0.073464,133.77
> volume #1 level 0.01737
> view matrix models
> #5,-0.60212,-0.51496,0.61013,183.17,-0.52195,-0.32439,-0.78889,140.43,0.60417,-0.79346,-0.073464,133.24
> view matrix models
> #5,-0.59964,-0.51894,0.60922,183.28,-0.52385,-0.32098,-0.78902,140.37,0.605,-0.79226,-0.079374,133.41
> view matrix models
> #5,-0.59964,-0.51894,0.60922,184.25,-0.52385,-0.32098,-0.78902,139.92,0.605,-0.79226,-0.079374,135.73
> view matrix models
> #5,-0.59964,-0.51894,0.60922,183.25,-0.52385,-0.32098,-0.78902,140.42,0.605,-0.79226,-0.079374,133.66
> view matrix models
> #5,0.54088,-0.53741,0.64702,174.65,0.56824,-0.33368,-0.75217,132.03,0.62012,0.7745,0.1249,87.317
> view matrix models
> #5,0.27433,-0.32301,0.90576,162.05,0.74762,-0.52077,-0.41215,123.58,0.60483,0.79023,0.098625,87.948
> view matrix models
> #5,0.22321,0.24656,0.94307,146.88,0.97137,0.024447,-0.2363,102.3,-0.081318,0.96882,-0.23404,99.801
> view matrix models
> #5,-0.67588,0.24399,0.69545,161.72,0.72014,0.41937,0.55274,66.522,-0.15679,0.87441,-0.45916,110.55
> view matrix models
> #5,-0.48067,0.12039,0.8686,157.41,0.87064,0.18366,0.45635,74.756,-0.10458,0.97559,-0.19309,98.356
> view matrix models
> #5,-0.58665,0.070644,0.80676,161.54,0.8073,0.12986,0.57567,72.35,-0.064099,0.98901,-0.13321,95.65
> view matrix models
> #5,-0.1885,-0.64744,0.73844,179.14,0.85289,-0.4807,-0.20374,114.57,0.48688,0.5914,0.64281,74.654
> view matrix models
> #5,-0.1885,-0.64744,0.73844,151.51,0.85289,-0.4807,-0.20374,140.39,0.48688,0.5914,0.64281,97.143
> view matrix models
> #5,-0.1885,-0.64744,0.73844,149.34,0.85289,-0.4807,-0.20374,142.06,0.48688,0.5914,0.64281,96.511
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.008192, steps = 168
shifted from previous position = 6.89
rotated from previous position = 22.3 degrees
atoms outside contour = 2616, contour level = 0.017374
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.41390429 -0.54871105 0.72636041 147.12022631
0.88413707 -0.43230710 0.17723494 131.26223586
0.21675999 0.71556047 0.66406954 95.04677763
Axis 0.33369232 0.31588646 0.88818083
Axis point 34.01823872 74.05297820 0.00000000
Rotation angle (degrees) 126.23304062
Shift along axis 174.97557788
> view matrix models
> #5,-0.4139,-0.54871,0.72636,147.45,0.88414,-0.43231,0.17723,86.937,0.21676,0.71556,0.66407,103.7
> volume #1 level 0.01372
> view matrix models
> #5,-0.4139,-0.54871,0.72636,159.23,0.88414,-0.43231,0.17723,75.791,0.21676,0.71556,0.66407,97.263
> view matrix models
> #5,-0.67084,-0.57587,-0.46729,203.44,0.70632,-0.30409,-0.63925,102.39,0.22603,-0.75889,0.61074,135.85
> view matrix models
> #5,-0.66532,-0.69332,-0.27687,199.67,0.72111,-0.50079,-0.47876,101.58,0.19328,-0.51818,0.83314,122.28
> view matrix models
> #5,0.11618,-0.68541,-0.71883,209.64,0.95915,0.26538,-0.09802,67.514,0.25795,-0.67807,0.68824,130.9
> view matrix models
> #5,-0.77917,-0.48344,-0.39897,199.48,0.4809,-0.052801,-0.87519,105.91,0.40204,-0.87378,0.27363,149.33
> view matrix models
> #5,-0.50272,-0.79611,-0.33686,203.23,0.23704,0.24779,-0.93937,102.32,0.83131,-0.55209,0.06414,145.72
> view matrix models
> #5,-0.50272,-0.79611,-0.33686,172.02,0.23704,0.24779,-0.93937,131.25,0.83131,-0.55209,0.06414,142.69
> view matrix models
> #5,-0.46109,-0.80121,-0.38138,173.42,0.24883,0.2958,-0.92227,129.37,0.85175,-0.52015,0.062972,141.79
> view matrix models
> #5,-0.46109,-0.80121,-0.38138,196.29,0.24883,0.2958,-0.92227,153.15,0.85175,-0.52015,0.062972,141.77
> view matrix models
> #5,-0.46109,-0.80121,-0.38138,202.78,0.24883,0.2958,-0.92227,149.14,0.85175,-0.52015,0.062972,140.77
> view matrix models
> #5,-0.40029,-0.91085,0.10058,188.22,-0.10903,-0.061636,-0.99213,162.93,0.90988,-0.40811,-0.074638,142.4
> view matrix models
> #5,-0.29318,-0.95515,0.041529,190.67,0.12344,-0.080891,-0.98905,161.72,0.94805,-0.28485,0.14162,131.5
> view matrix models
> #5,-0.45769,-0.88484,-0.087,194.53,-0.068445,0.13263,-0.9888,157.69,0.88647,-0.44661,-0.12127,145.16
> view matrix models
> #5,-0.36501,-0.92896,-0.061646,194.12,0.063684,0.041146,-0.99712,159.37,0.92882,-0.36788,0.044142,137.11
> view matrix models
> #5,-0.46929,-0.81868,-0.33096,201.5,0.069808,0.33923,-0.93811,149.82,0.88028,-0.46335,-0.10205,144.94
> view matrix models
> #5,-0.46929,-0.81868,-0.33096,198.11,0.069808,0.33923,-0.93811,151.04,0.88028,-0.46335,-0.10205,142.96
> view matrix models
> #5,-0.46837,-0.81336,-0.34507,201.14,0.084587,0.34748,-0.93386,149.34,0.87947,-0.46658,-0.093949,143.51
> view matrix models
> #5,-0.36182,-0.84593,-0.39178,202.86,0.24505,0.31918,-0.91547,148.31,0.89946,-0.42724,0.091806,135.89
> view matrix models
> #5,-0.36182,-0.84593,-0.39178,201.58,0.24505,0.31918,-0.91547,148.78,0.89946,-0.42724,0.091806,135.17
> volume #1 level 0.0209
> view matrix models
> #5,-0.36182,-0.84593,-0.39178,205.99,0.24505,0.31918,-0.91547,103.69,0.89946,-0.42724,0.091806,129.94
> volume #1 level 0.01476
Alignment identifier is 5/A
> select #5/A:128-129
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/A:128-142
116 atoms, 117 bonds, 15 residues, 1 model selected
> view matrix models
> #5,-0.18064,-0.79002,0.58587,169.13,0.89577,-0.37813,-0.23369,92.796,0.40615,0.48259,0.77598,86.634
> view matrix models
> #5,-0.18064,-0.79002,0.58587,161.76,0.89577,-0.37813,-0.23369,146.31,0.40615,0.48259,0.77598,93.916
> view matrix models
> #5,-0.18064,-0.79002,0.58587,159.72,0.89577,-0.37813,-0.23369,143.8,0.40615,0.48259,0.77598,86.923
> view matrix models
> #5,-0.18064,-0.79002,0.58587,164.86,0.89577,-0.37813,-0.23369,142.62,0.40615,0.48259,0.77598,97.149
> view matrix models
> #5,-0.30802,-0.80217,0.51151,168.63,0.93704,-0.34881,0.017254,132.82,0.16458,0.48462,0.8591,95.829
> view matrix models
> #5,-0.30802,-0.80217,0.51151,167.66,0.93704,-0.34881,0.017254,132.86,0.16458,0.48462,0.8591,93.722
> view matrix models
> #5,-0.24626,-0.79561,0.55349,165.61,0.92495,-0.36352,-0.11101,137.8,0.28953,0.48461,0.82542,94.053
> view matrix models
> #5,-0.26528,-0.88598,0.38034,174.06,0.92316,-0.34722,-0.16496,139.3,0.27821,0.30736,0.91002,95.589
> view matrix models
> #5,0.064059,-0.92103,0.38418,172.56,0.99735,0.045799,-0.056502,125.19,0.034445,0.38678,0.92153,94.86
> view matrix models
> #5,0.2904,-0.93203,0.21677,177.16,0.95685,0.28519,-0.055643,119.47,-0.0099598,0.22357,0.97464,97.374
> view matrix models
> #5,0.55568,-0.81941,0.14068,173.86,0.82786,0.56092,-0.0028418,112.08,-0.076583,0.11804,0.99005,97.376
> view matrix models
> #5,-0.28695,-0.94228,-0.17251,193.61,0.78879,-0.13024,-0.6007,150.53,0.54356,-0.30845,0.78064,111.14
> view matrix models
> #5,-0.28695,-0.94228,-0.17251,193.61,0.78879,-0.13024,-0.6007,152.46,0.54356,-0.30845,0.78064,113.05
> view matrix models
> #5,-0.28695,-0.94228,-0.17251,193.22,0.78879,-0.13024,-0.6007,152.63,0.54356,-0.30845,0.78064,112.35
> view matrix models
> #5,-0.85542,0.45932,0.23932,147.69,-0.10173,0.30407,-0.9472,159.98,-0.50784,-0.83461,-0.21338,167.43
> view matrix models
> #5,-0.82365,0.47168,0.31484,144.52,-0.13324,0.37866,-0.91589,157.24,-0.55123,-0.79632,-0.24904,168.02
> view matrix models
> #5,-0.82365,0.47168,0.31484,156.37,-0.13324,0.37866,-0.91589,200.4,-0.55123,-0.79632,-0.24904,208.01
> select clear
> select #5/A:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.82365,0.47168,0.31484,156.07,-0.13324,0.37866,-0.91589,205.28,-0.55123,-0.79632,-0.24904,207.64
> view matrix models
> #5,-0.82365,0.47168,0.31484,206.01,-0.13324,0.37866,-0.91589,157.7,-0.55123,-0.79632,-0.24904,188.21
> view matrix models
> #5,-0.93818,-0.17988,0.29572,223.71,-0.28239,0.89184,-0.35339,126.22,-0.20017,-0.41506,-0.8875,198.67
> view matrix models
> #5,-0.92591,-0.31421,0.20969,229.99,-0.35263,0.918,-0.18146,120.02,-0.13548,-0.24195,-0.96078,196.48
> view matrix models
> #5,-0.92087,-0.34269,0.1859,233.73,-0.37019,0.91816,-0.14123,119.05,-0.12229,-0.19887,-0.97237,191.96
> view matrix models
> #5,-0.90889,-0.39412,0.13631,236.66,-0.40509,0.91203,-0.064046,116.74,-0.099076,-0.11343,-0.98859,190.24
> view matrix models
> #5,-0.91563,-0.36737,0.16326,235.1,-0.38638,0.91635,-0.10498,117.94,-0.11104,-0.1592,-0.98098,191.19
> view matrix models
> #5,-0.92309,-0.33082,0.19609,233.09,-0.36273,0.91837,-0.15818,119.59,-0.12776,-0.21715,-0.96774,192.29
> view matrix models
> #5,-0.84733,-0.50739,-0.15683,249.34,-0.2825,0.68068,-0.67592,143.1,0.4497,-0.52842,-0.7201,187.46
> view matrix models
> #5,-0.83733,-0.52303,-0.15912,249.74,-0.30095,0.68397,-0.66454,142.75,0.45641,-0.50855,-0.73012,187.27
> view matrix models
> #5,-0.81785,-0.55152,-0.16414,250.49,-0.33534,0.68862,-0.64292,142.11,0.46762,-0.47077,-0.74814,186.88
> view matrix models
> #5,-0.81785,-0.55152,-0.16414,255.9,-0.33534,0.68862,-0.64292,139.4,0.46762,-0.47077,-0.74814,181.88
> view matrix models
> #5,-0.64367,-0.73903,0.19881,247.39,-0.66987,0.41844,-0.61334,148.41,0.37009,-0.52797,-0.76439,185.49
> view matrix models
> #5,-0.64367,-0.73903,0.19881,254.92,-0.66987,0.41844,-0.61334,158.73,0.37009,-0.52797,-0.76439,197.27
> view matrix models
> #5,-0.64367,-0.73903,0.19881,256.6,-0.66987,0.41844,-0.61334,161.58,0.37009,-0.52797,-0.76439,198.7
> view matrix models
> #5,-0.64367,-0.73903,0.19881,257.86,-0.66987,0.41844,-0.61334,163.22,0.37009,-0.52797,-0.76439,200.9
> view matrix models
> #5,-0.86752,-0.45394,-0.20335,266.35,-0.10889,0.57223,-0.81283,162.55,0.48534,-0.683,-0.54585,196.33
> view matrix models
> #5,-0.73731,-0.66525,0.11753,259.5,-0.46679,0.37593,-0.80049,169.45,0.48835,-0.64507,-0.58771,196.83
> view matrix models
> #5,-0.4949,-0.3882,-0.77741,290.91,0.020993,0.88906,-0.45731,154.64,0.8687,-0.24265,-0.43185,189.04
> view matrix models
> #5,-0.6884,-0.67196,0.27307,262.52,-0.56375,0.25881,-0.78435,185.78,0.45638,-0.69389,-0.55699,207.48
> view matrix models
> #5,-0.6884,-0.67196,0.27307,228.93,-0.56375,0.25881,-0.78435,136.55,0.45638,-0.69389,-0.55699,161.78
> view matrix models
> #5,-0.6884,-0.67196,0.27307,180.57,-0.56375,0.25881,-0.78435,160.64,0.45638,-0.69389,-0.55699,175.99
> view matrix models
> #5,-0.6884,-0.67196,0.27307,179.94,-0.56375,0.25881,-0.78435,157.26,0.45638,-0.69389,-0.55699,174.86
> view matrix models
> #5,-0.6884,-0.67196,0.27307,178.82,-0.56375,0.25881,-0.78435,158.2,0.45638,-0.69389,-0.55699,174.43
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.007946, steps = 252
shifted from previous position = 16
rotated from previous position = 18.4 degrees
atoms outside contour = 2833, contour level = 0.014764
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
-0.73613185 -0.56150059 0.37792463 163.17969107
-0.46612986 0.01572531 -0.88457657 172.81062550
0.49074726 -0.82732692 -0.27330809 169.11103321
Axis 0.36134182 -0.71210116 0.60195019
Axis point 121.35607225 0.00000000 161.76119709
Rotation angle (degrees) 175.45637507
Shift along axis 37.70141919
> view matrix models
> #5,-0.73613,-0.5615,0.37792,153.44,-0.46613,0.015725,-0.88458,221.62,0.49075,-0.82733,-0.27331,206.13
> volume #1 level 0.01215
Alignment identifier is 5/A
> select #5/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:128-130
23 atoms, 23 bonds, 3 residues, 1 model selected
> view matrix models
> #5,-0.73613,-0.5615,0.37792,153.34,-0.46613,0.015725,-0.88458,222.2,0.49075,-0.82733,-0.27331,205.61
> view matrix models
> #5,0.92382,-0.35825,0.13494,145.51,-0.20591,-0.76216,-0.61378,230.36,0.32273,0.53924,-0.77786,190.32
> view matrix models
> #5,0.83569,0.094624,0.54099,120.59,0.35363,-0.84638,-0.39823,221.12,0.4202,0.5241,-0.74078,188.74
> view matrix models
> #5,0.79815,-0.024908,0.60194,121.69,0.58073,-0.23408,-0.77971,217.66,0.16032,0.9719,-0.17237,159.43
> view matrix models
> #5,0.80164,0.00036278,0.59781,121.16,0.57363,-0.28199,-0.76905,218.59,0.1683,0.95942,-0.22626,161.41
> view matrix models
> #5,0.81677,0.093314,0.56937,119.73,0.54325,-0.45676,-0.70445,220.89,0.19433,0.88468,-0.42376,170.01
> view matrix models
> #5,0.69987,0.4515,-0.55347,150.91,-0.39802,-0.39689,-0.82708,230.09,-0.5931,0.79914,-0.09807,166.09
> view matrix models
> #5,0.69987,0.4515,-0.55347,174.83,-0.39802,-0.39689,-0.82708,186.07,-0.5931,0.79914,-0.09807,127.65
> view matrix models
> #5,0.69134,0.45659,-0.55998,174.99,-0.40071,-0.40262,-0.823,186.09,-0.60123,0.79336,-0.095389,127.76
> undo
> undo
> view matrix models
> #5,0.65822,0.46463,-0.59234,152.22,-0.42597,-0.41889,-0.80192,229.94,-0.62072,0.78016,-0.077805,166.04
> undo
> view matrix models
> #5,0.69987,0.4515,-0.55347,119.81,-0.39802,-0.39689,-0.82708,195.51,-0.5931,0.79914,-0.09807,148.44
> view matrix models
> #5,0.69987,0.4515,-0.55347,145.74,-0.39802,-0.39689,-0.82708,161.8,-0.5931,0.79914,-0.09807,128.72
> view matrix models
> #5,0.69987,0.4515,-0.55347,147.39,-0.39802,-0.39689,-0.82708,159.48,-0.5931,0.79914,-0.09807,124.24
> view matrix models
> #5,0.69987,0.4515,-0.55347,157.76,-0.39802,-0.39689,-0.82708,174.41,-0.5931,0.79914,-0.09807,125.5
> view matrix models
> #5,0.69987,0.4515,-0.55347,160.43,-0.39802,-0.39689,-0.82708,172.92,-0.5931,0.79914,-0.09807,122.39
> view matrix models
> #5,0.69987,0.4515,-0.55347,161.72,-0.39802,-0.39689,-0.82708,171.32,-0.5931,0.79914,-0.09807,123.37
> view matrix models
> #5,0.69987,0.4515,-0.55347,160.05,-0.39802,-0.39689,-0.82708,170.79,-0.5931,0.79914,-0.09807,123.55
> view matrix models
> #5,0.44433,0.39281,-0.80515,172.06,-0.44994,-0.67932,-0.57972,169.53,-0.77468,0.61985,-0.1251,130.2
> view matrix models
> #5,0.64607,0.41674,-0.63947,164.29,-0.52222,-0.36966,-0.76853,168.9,-0.55666,0.83047,-0.0212,119.82
> view matrix models
> #5,0.64607,0.41674,-0.63947,164.63,-0.52222,-0.36966,-0.76853,169.08,-0.55666,0.83047,-0.0212,119.41
> view matrix models
> #5,0.47215,0.57572,-0.66755,162.83,-0.45627,-0.48834,-0.74387,170.73,-0.75425,0.6558,0.032118,123.24
> view matrix models
> #5,0.39197,0.62529,-0.67481,162.39,-0.42135,-0.53004,-0.73588,171.25,-0.81781,0.57278,0.055707,124.92
> fitmap #5 inMap #1
Fit molecule 6p40 chain A.pdb (#5) to map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms
average map value = 0.01045, steps = 172
shifted from previous position = 2.81
rotated from previous position = 4.77 degrees
atoms outside contour = 1957, contour level = 0.012155
Position of 6p40 chain A.pdb (#5) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.38106123 0.65097517 -0.65652395 160.69008154
-0.47455243 -0.47170869 -0.74316279 171.13004434
-0.79346856 0.59474555 0.12917196 124.77790708
Axis 0.76289349 0.07808767 -0.64179111
Axis point 0.00000000 14.99606145 194.70479613
Rotation angle (degrees) 118.73359625
Shift along axis 55.87121287
> volume #1 level 0.01881
> volume #1 level 0.009023
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
> hide #!1 models
> show #!1 models
Alignment identifier is 5/A
> select #5/A:180
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:180-188
70 atoms, 71 bonds, 9 residues, 1 model selected
> select #5/A:188
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:188-189
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/A:182
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:182-191
75 atoms, 75 bonds, 10 residues, 1 model selected
> select #5/A:181
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:181-189
72 atoms, 73 bonds, 9 residues, 1 model selected
> select
> #5/A:13-21,61-80,97-111,130-141,153-165,177-193,198-206,257-270,287-300,319-330,338-350,362-378
1378 atoms, 1409 bonds, 165 residues, 1 model selected
> select clear
> select #5/A:181-189
72 atoms, 73 bonds, 9 residues, 1 model selected
> select clear
> volume #1 level 0.006543
> volume #1 level 0.007196
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
> volume #1 level 0.009806
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
——— End of log from Sat Jun 19 22:49:00 2021 ———
opened ChimeraX session
> rename #5 6p40_chainA_NTD
> open "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/3DVA/csJ180new/cryosparc_P19_J200_004_volume_map.mrc"
Opened cryosparc_P19_J200_004_volume_map.mrc as #6, grid size 352,352,352,
pixel 0.835, shown at level 0.13, step 2, values float32
> volume #6 level 0.344
> volume #6 level 0.293
> fitmap #6 inMap #1
Fit map cryosparc_P19_J200_004_volume_map.mrc in map
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc using 19817 points
correlation = 0.9007, correlation about mean = 0.5817, overlap = 117.5
steps = 88, shift = 0.812, angle = 1.51 degrees
Position of cryosparc_P19_J200_004_volume_map.mrc (#6) relative to
cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates:
Matrix rotation and translation
0.99974480 -0.01464200 0.01720299 -0.06061973
0.01487128 0.99980127 -0.01327652 0.34545763
-0.01700518 0.01352896 0.99976387 0.04947551
Axis 0.51025532 0.65116893 0.56179938
Axis point -4.55800784 0.00000000 10.03539832
Rotation angle (degrees) 1.50514621
Shift along axis 0.22181505
> hide #!1 models
> volume #6 level 0.293
> volume #6 color #ffffb2b2
> volume #6 color #ffffb264
> copy #5 id #7
Unknown command: copy #5 id #7
> copy #5
Unknown command: copy #5
> select #5
3132 atoms, 3120 bonds, 6 pseudobonds, 476 residues, 2 models selected
> select clear
> help help:user
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> open "E:/temp/EM data/6p40 chain A.pdb"
Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb
---
warnings | Ignored bad PDB record found on line 6811
END
Cannot find LINK/SSBOND residue HIS (65 )
Cannot find LINK/SSBOND residue CYS (97 )
Cannot find LINK/SSBOND residue CYS (100 )
Cannot find LINK/SSBOND residue HIS (257 )
Cannot find LINK/SSBOND residue CYS (287 )
2 messages similar to the above omitted
6p40 chain A.pdb title:
Crystal structure of full length APOBEC3G FKL [more info...]
Chain information for 6p40 chain A.pdb #7
---
Chain | Description
A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G
Non-standard residues in 6p40 chain A.pdb #7
---
ZN — zinc ion
> hide#7:194-383
Unknown command: hide#7:194-383
> hide #7/A:194-383
> select #7/A:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
63 atoms, 63 bonds, 8 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,23.427,0,1,0,167.66,0,0,1,130.65
> view matrix models #7,1,0,0,125.39,0,1,0,137.14,0,0,1,143.37
> hide #7/A:194-383
> show #7/A:194-383
> hide #7/A:194-383
> hide #7/A:194-383 ribbons
> view matrix models #7,1,0,0,142.32,0,1,0,171.65,0,0,1,153.8
> view matrix models
> #7,0.98253,-0.10314,-0.15489,150.13,0.032562,0.91479,-0.40261,186.96,0.18322,0.39054,0.90217,146.32
> view matrix models
> #7,0.99007,-0.071823,-0.12088,148.14,0.031679,0.95154,-0.3059,182.79,0.13699,0.29903,0.94436,147.51
> view matrix models
> #7,0.99007,-0.071823,-0.12088,148.67,0.031679,0.95154,-0.3059,182.98,0.13699,0.29903,0.94436,144.88
> view matrix models
> #7,0.99007,-0.071823,-0.12088,148.47,0.031679,0.95154,-0.3059,182.86,0.13699,0.29903,0.94436,145.8
> view matrix models
> #7,0.44901,-0.078563,-0.89007,178.93,0.18079,0.98351,0.004393,170.35,0.87505,-0.16289,0.45581,167.63
> view matrix models
> #7,0.52621,-0.067611,-0.84766,176.69,0.32593,0.93674,0.12761,166.27,0.78541,-0.34343,0.51496,170.57
> view matrix models
> #7,0.52621,-0.067611,-0.84766,162.8,0.32593,0.93674,0.12761,126.94,0.78541,-0.34343,0.51496,153.79
> view matrix models
> #7,0.52621,-0.067611,-0.84766,166.77,0.32593,0.93674,0.12761,126.16,0.78541,-0.34343,0.51496,149.55
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2345, steps = 236
shifted from previous position = 1.74
rotated from previous position = 19 degrees
atoms outside contour = 2092, contour level = 0.293
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.35218186 -0.21663380 -0.91051509 171.67301016
0.22929453 0.96316760 -0.14047135 135.10072945
0.90740947 -0.15930467 0.38888310 149.00633462
Axis -0.01006101 -0.97115893 0.23822071
Axis point -42.95329208 0.00000000 218.02893609
Rotation angle (degrees) 69.38318884
Shift along axis -97.43508846
> select clear
> volume #6 level 0.327
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> volume #6 level 0.2964
> volume #6 color #ffffffb2
> volume #6 level 0.3677
> select #7/A:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
120 atoms, 124 bonds, 13 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #7,0.28438,-0.48646,-0.82613,176.39,0.28927,0.86508,-0.40982,146.09,0.91403,-0.12242,0.38673,147.92
> view matrix models
> #7,-0.096362,-0.40031,-0.9113,179.91,0.1117,0.90543,-0.40954,146.62,0.98906,-0.14126,-0.042534,162.17
> view matrix models
> #7,0.5124,-0.29638,-0.80598,169.42,0.063802,0.9491,-0.30845,142.61,0.85637,0.10663,0.50523,139.12
> view matrix models
> #7,0.52087,-0.30239,-0.79829,169.24,0.23441,0.94987,-0.20686,137.86,0.82082,-0.079386,0.56564,141.92
> view matrix models
> #7,0.41908,-0.44299,-0.79255,173.24,0.30951,0.89032,-0.33398,142.91,0.85357,-0.10533,0.51022,144.12
> view matrix models
> #7,0.41908,-0.44299,-0.79255,173.39,0.30951,0.89032,-0.33398,145.41,0.85357,-0.10533,0.51022,144.54
> select clear
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.249, steps = 280
shifted from previous position = 9.53
rotated from previous position = 20 degrees
atoms outside contour = 2477, contour level = 0.36771
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.11069634 -0.33205525 -0.93674203 183.71610499
0.37617038 0.88641112 -0.26976134 135.35304582
0.91991422 -0.32251301 0.22303181 160.36037152
Axis -0.02653708 -0.93400324 0.35627760
Axis point -21.73973328 0.00000000 214.66023968
Rotation angle (degrees) 83.68067049
Shift along axis -74.16266437
> volume #6 level 0.4594
> volume #6 level 0.3541
> select #7/A:76
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
196 atoms, 205 bonds, 20 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #7,0.068742,-0.26406,-0.96205,183.76,0.36397,0.90451,-0.22226,133.71,0.92887,-0.33488,0.15829,162.3
> view matrix models
> #7,0.031079,-0.29339,-0.95549,184.52,0.62346,0.75287,-0.2109,135.24,0.78123,-0.58916,0.20632,167.92
> view matrix models
> #7,0.031079,-0.29339,-0.95549,184.04,0.62346,0.75287,-0.2109,142.82,0.78123,-0.58916,0.20632,167.7
> volume #6 level 0.2387
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2497, steps = 232
shifted from previous position = 8.96
rotated from previous position = 16.4 degrees
atoms outside contour = 1696, contour level = 0.23866
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.02771769 -0.38433519 -0.92277743 184.35664167
0.41599719 0.84383230 -0.33895928 139.63658024
0.90894338 -0.37447765 0.18327144 163.47018180
Axis -0.01776586 -0.91620466 0.40031661
Axis point -15.63386294 0.00000000 214.99083409
Rotation angle (degrees) 88.42928496
Shift along axis -65.77111205
> volume #6 level 0.3134
> volume #6 level 0.2692
> select clear
> volume #6 level 0.3847
> select #7/A:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 93 bonds, 9 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #7,0.65743,0.42292,0.62364,109.46,0.5342,0.32211,-0.78158,165.88,-0.53143,0.84699,-0.014156,152.55
> view matrix models
> #7,0.55964,0.47819,0.67686,107.02,0.60022,0.32928,-0.72891,163.36,-0.57143,0.81419,-0.10274,156.74
> select clear
> select #7/A:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
196 atoms, 205 bonds, 20 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #7,0.55964,0.47819,0.67686,107.43,0.60022,0.32928,-0.72891,166.13,-0.57143,0.81419,-0.10274,153.23
> view matrix models
> #7,0.55964,0.47819,0.67686,107.36,0.60022,0.32928,-0.72891,165.75,-0.57143,0.81419,-0.10274,153.65
> view matrix models
> #7,0.50561,0.51628,0.69124,106.37,0.45468,0.52146,-0.72204,162.08,-0.73323,0.67937,0.028911,153.49
> view matrix models
> #7,0.51797,0.5091,0.68741,106.57,0.48979,0.48232,-0.72627,162.86,-0.70129,0.71287,0.00047346,153.42
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2364, steps = 124
shifted from previous position = 2.31
rotated from previous position = 11.4 degrees
atoms outside contour = 2453, contour level = 0.38469
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.44857260 0.38354159 0.80726604 108.04580538
0.57239194 0.57040868 -0.58906825 154.55189612
-0.68640374 0.72631245 0.03633359 151.54672741
Axis 0.65794204 0.74712070 0.09446131
Axis point 77.18156884 0.00000000 82.59535463
Rotation angle (degrees) 88.41514361
Shift along axis 200.87209951
> view matrix models
> #7,0.42827,0.38759,0.81631,124.11,0.58806,0.56636,-0.57743,196.74,-0.68613,0.72734,0.014628,161.73
> select clear
> select #7/A:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 93 bonds, 9 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #7,0.43534,0.38055,0.81588,124.23,0.6,0.55301,-0.57808,196.98,-0.67118,0.74119,0.012417,161.36
> view matrix models
> #7,0.38009,0.42884,0.81953,123.42,0.506,0.64529,-0.57234,195.38,-0.77427,0.63222,0.028278,164.19
> view matrix models
> #7,-0.22079,0.76543,0.60445,126.79,0.84654,0.45819,-0.271,187.28,-0.48439,0.45186,-0.74913,192.27
> view matrix models
> #7,-0.1662,0.70124,0.69328,124.91,0.93579,0.33384,-0.11334,184.23,-0.31092,0.62993,-0.7117,185.68
> view matrix models
> #7,-0.28697,0.80275,0.52273,129.17,0.7343,0.53477,-0.41812,191.29,-0.61518,0.26385,-0.74292,197.32
> view matrix models
> #7,-0.63305,0.66672,-0.39336,166.09,0.66042,0.73025,0.17488,167.22,0.40384,-0.14908,-0.9026,204.53
> view matrix models
> #7,-0.74541,0.37916,-0.54827,179.15,0.40614,0.91052,0.077501,168.01,0.52859,-0.16491,-0.8327,201.62
> view matrix models
> #7,-0.31048,-0.034345,-0.94996,199.25,-0.17309,0.98468,0.020973,172.54,0.93469,0.17094,-0.31167,172.87
> view matrix models
> #7,-0.37231,-0.72632,-0.57779,203.8,-0.45011,0.68574,-0.57198,202.54,0.81166,0.047116,-0.58223,186.12
> view matrix models
> #7,0.029142,-0.76407,-0.64447,204.02,0.26328,0.62785,-0.73246,204.11,0.96428,-0.14833,0.21946,162.7
> view matrix models
> #7,0.10403,-0.77978,-0.61735,202.95,0.40054,0.60101,-0.69163,202.4,0.91035,-0.17532,0.37486,158.52
> view matrix models
> #7,0.1369,-0.65467,-0.74341,204.02,0.40724,0.72132,-0.56022,195.24,0.903,-0.22605,0.36535,160.05
> view matrix models
> #7,0.013518,-0.51091,-0.85953,205.35,0.52104,0.73728,-0.43005,189.74,0.85342,-0.44204,0.27617,168.36
> view matrix models
> #7,0.013518,-0.51091,-0.85953,182.06,0.52104,0.73728,-0.43005,148.32,0.85342,-0.44204,0.27617,160.11
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2497, steps = 292
shifted from previous position = 7.79
rotated from previous position = 10.2 degrees
atoms outside contour = 2494, contour level = 0.38469
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.02761258 -0.38433750 -0.92277962 184.35021900
0.41570108 0.84393749 -0.33906064 139.63415571
0.90908204 -0.37423815 0.18307281 163.46259403
Axis -0.01759532 -0.91627262 0.40016857
Axis point -15.59643119 0.00000000 214.95779979
Rotation angle (degrees) 88.43497503
Shift along axis -65.77406270
> volume #6 level 0.3677
> view matrix models
> #7,0.037158,-0.40303,-0.91443,182.89,0.40396,0.84302,-0.35515,146.16,0.91402,-0.3562,0.19413,160.34
> view matrix models
> #7,0.037158,-0.40303,-0.91443,182.41,0.40396,0.84302,-0.35515,147.49,0.91402,-0.3562,0.19413,159.47
> view matrix models
> #7,-0.0086695,-0.37647,-0.92639,182.47,0.52778,0.78515,-0.32401,147.01,0.84933,-0.49174,0.19189,163.25
> view matrix models
> #7,-0.0086695,-0.37647,-0.92639,182.29,0.52778,0.78515,-0.32401,147.25,0.84933,-0.49174,0.19189,166.13
> volume #6 level 0.2726
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2497, steps = 168
shifted from previous position = 9.74
rotated from previous position = 8.6 degrees
atoms outside contour = 1924, contour level = 0.27262
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.02770771 -0.38437332 -0.92276185 184.35686250
0.41597835 0.84382454 -0.33900170 139.63842874
0.90895231 -0.37445599 0.18327142 163.46955802
Axis -0.01773380 -0.91620111 0.40032616
Axis point -15.62945026 0.00000000 214.99262378
Rotation angle (degrees) 88.42979388
Shift along axis -65.76509213
> hide #!6 models
> show #!6 models
> view matrix models
> #7,0.037247,-0.40307,-0.91441,180.7,0.40424,0.84291,-0.35509,145.9,0.91389,-0.35642,0.19433,159.1
> view matrix models
> #7,-0.38001,-0.71745,-0.58383,179.99,0.21843,0.54372,-0.81034,169.53,0.89882,-0.43546,-0.049911,169.3
> view matrix models
> #7,-0.39338,-0.7212,-0.5702,179.71,0.31648,0.47607,-0.82049,170.7,0.86319,-0.50321,0.040972,168.04
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2343, steps = 184
shifted from previous position = 13.2
rotated from previous position = 18.4 degrees
atoms outside contour = 1986, contour level = 0.27262
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
-0.37048039 -0.60990412 -0.70054353 186.95343362
0.14410655 0.70733837 -0.69203015 155.73990504
0.91759336 -0.35733651 -0.17416382 169.08068153
Axis 0.18427297 -0.89090098 0.41513722
Axis point 43.75085593 0.00000000 190.25039572
Rotation angle (degrees) 114.74956996
Shift along axis -34.10668609
> view matrix models
> #7,-0.54392,-0.36455,-0.75581,184.8,0.19328,0.82206,-0.53559,148.03,0.81657,-0.4374,-0.37668,178.45
> view matrix models
> #7,-0.47167,-0.43877,-0.76486,186.27,0.36152,0.69493,-0.62159,152.59,0.80426,-0.5697,-0.16915,174.58
> view matrix models
> #7,-0.47167,-0.43877,-0.76486,206.68,0.36152,0.69493,-0.62159,193.85,0.80426,-0.5697,-0.16915,191
> select clear
> select #7/A:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 93 bonds, 9 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #7,-0.33051,-0.63484,-0.69838,208.04,0.70878,0.32166,-0.62782,200.5,0.62321,-0.7025,0.34366,177.62
> view matrix models
> #7,-0.33864,-0.61997,-0.70779,208.05,0.68578,0.35242,-0.6368,200.2,0.64423,-0.70103,0.30582,178.74
> view matrix models
> #7,-0.33864,-0.61997,-0.70779,189.47,0.68578,0.35242,-0.6368,163.28,0.64423,-0.70103,0.30582,171.62
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2497, steps = 296
shifted from previous position = 13.9
rotated from previous position = 37.7 degrees
atoms outside contour = 1927, contour level = 0.27262
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.02748432 -0.38482479 -0.92258034 184.35477027
0.41572058 0.84373085 -0.33955065 139.65756235
0.90907701 -0.37420332 0.18316895 163.46015648
Axis -0.01733274 -0.91616745 0.40042075
Axis point -15.56358630 0.00000000 214.99696624
Rotation angle (degrees) 88.44181763
Shift along axis -65.69224826
> volume #6 level 0.3711
> volume #6 level 0.3066
> view matrix models
> #7,0.037029,-0.40352,-0.91422,181.72,0.40398,0.84281,-0.35563,193.07,0.91402,-0.35616,0.19422,174.34
> view matrix models
> #7,0.030372,-0.39477,-0.91828,181.69,0.56667,0.7636,-0.30953,192.33,0.82339,-0.51095,0.2469,176.95
> view matrix models
> #7,0.030372,-0.39477,-0.91828,181.61,0.56667,0.7636,-0.30953,194.05,0.82339,-0.51095,0.2469,176.37
> view matrix models
> #7,0.030372,-0.39477,-0.91828,181.45,0.56667,0.7636,-0.30953,196.51,0.82339,-0.51095,0.2469,177.24
> view matrix models
> #7,0.030372,-0.39477,-0.91828,181.78,0.56667,0.7636,-0.30953,190.8,0.82339,-0.51095,0.2469,176.85
> view matrix models
> #7,0.18912,0.16033,-0.96878,168.66,0.48733,0.84118,0.23435,171.28,0.85249,-0.51644,0.080952,182.31
> view matrix models
> #7,0.18912,0.16033,-0.96878,171.16,0.48733,0.84118,0.23435,133.44,0.85249,-0.51644,0.080952,168.81
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2436, steps = 184
shifted from previous position = 13.7
rotated from previous position = 17.4 degrees
atoms outside contour = 2150, contour level = 0.30658
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.13209677 -0.10027208 -0.98615209 175.96167690
0.45725245 0.88885975 -0.02912962 126.34528907
0.87947179 -0.44707254 0.16326516 164.88201019
Axis -0.20986364 -0.93679448 0.27995241
Axis point -40.57498104 0.00000000 190.91857114
Rotation angle (degrees) 84.71494613
Shift along axis -109.12841075
> close #7
> open "E:/temp/EM data/4n9f.pdb1"
Summary of feedback from opening E:/temp/EM data/4n9f.pdb1
---
warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C
18 GLN C 32 1 15
Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54
1 19
Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82
1 27
Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107
1 23
Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C
110 5 3
680 messages similar to the above omitted
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (133 )
33 messages similar to the above omitted
4n9f.pdb1 title:
Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
info...]
Chain information for 4n9f.pdb1 #7
---
Chain | Description
U | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
Non-standard residues in 4n9f.pdb1 #7
---
ZN — zinc ion
> close #7
> open "E:/temp/EM data/4n9f_color.pdb"
Summary of feedback from opening E:/temp/EM data/4n9f_color.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (133 )
33 messages similar to the above omitted
4n9f_color.pdb title:
Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
info...]
Chain information for 4n9f_color.pdb #7
---
Chain | Description
U | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
Non-standard residues in 4n9f_color.pdb #7
---
ZN — zinc ion
> select #7/X:71@CA
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
84 atoms, 86 bonds, 11 residues, 1 model selected
> select up
748 atoms, 762 bonds, 95 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> view matrix models #7,1,0,0,40.932,0,1,0,105.11,0,0,1,241.13
> select clear
> select #7/Y:72@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
176 atoms, 181 bonds, 21 residues, 1 model selected
> select up
691 atoms, 706 bonds, 87 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> select #7/b:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
69 atoms, 70 bonds, 9 residues, 1 model selected
> select up
1415 atoms, 1456 bonds, 173 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,104.77,0,1,0,252.07,0,0,1,260.9
> view matrix models #7,1,0,0,101.38,0,1,0,277.45,0,0,1,261.55
> view matrix models #7,1,0,0,98.503,0,1,0,298.92,0,0,1,262.08
> view matrix models
> #7,1,-0.00047943,0.002702,98.722,0.00053402,0.99979,-0.020241,297.1,-0.0026918,0.020243,0.99979,263.02
> view matrix models
> #7,1,-0.00047943,0.002702,99.546,0.00053402,0.99979,-0.020241,290.87,-0.0026918,0.020243,0.99979,263.28
> view matrix models
> #7,1,-0.00047943,0.002702,102.91,0.00053402,0.99979,-0.020241,265.08,-0.0026918,0.020243,0.99979,266.2
> hide #7/U ribbons
> view matrix models
> #7,1,-0.00047943,0.002702,95.36,0.00053402,0.99979,-0.020241,234.69,-0.0026918,0.020243,0.99979,286.42
> view matrix models
> #7,0.99957,-0.0081098,0.028278,97.739,0.006271,0.9979,0.064522,242.91,-0.028741,-0.064317,0.99752,285
> view matrix models
> #7,0.99997,-0.0016563,0.007217,95.782,0.0016955,0.99998,-0.0054339,236.13,-0.0072079,0.005446,0.99996,286.23
> view matrix models
> #7,0.054061,0.85267,0.51964,181.24,-0.96557,-0.087976,0.24481,257.3,0.25446,-0.51499,0.81856,252.99
> view matrix models
> #7,-0.52846,0.83564,0.14979,155.39,-0.7971,-0.54911,0.25122,245.54,0.29218,0.013356,0.95627,276.43
> view matrix models
> #7,-0.49167,0.84476,-0.21126,119.26,-0.38105,-0.42688,-0.82011,134.45,-0.78298,-0.32272,0.53178,248.1
Drag select of 6 cryosparc_P19_J200_004_volume_map.mrc
> select clear
> volume #6 level 0.4628
> hide #7/X ribbons
> hide #7/Y ribbons
> volume #6 level 0.3507
> select #7/b:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
69 atoms, 70 bonds, 9 residues, 1 model selected
> select up
1415 atoms, 1456 bonds, 173 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> view matrix models
> #7,-0.38576,0.89051,-0.24121,113.32,-0.0055743,-0.26369,-0.96459,109.45,-0.92258,-0.37075,0.10668,208.06
> view matrix models
> #7,-0.49484,0.84337,-0.20942,119.54,-0.39202,-0.43174,-0.81236,135.55,-0.77553,-0.31989,0.54426,249.18
> view matrix models
> #7,-0.49484,0.84337,-0.20942,107.97,-0.39202,-0.43174,-0.81236,93.276,-0.77553,-0.31989,0.54426,248.93
> view matrix models
> #7,-0.49484,0.84337,-0.20942,120.31,-0.39202,-0.43174,-0.81236,127.41,-0.77553,-0.31989,0.54426,256.56
> view matrix models
> #7,0.2177,-0.81223,-0.54119,26.378,0.65682,-0.28822,0.69679,249.27,-0.72194,-0.50716,0.47074,243.17
> view matrix models
> #7,0.81458,-0.55795,-0.1586,49.953,0.38535,0.31617,0.86691,289.04,-0.43355,-0.76728,0.47255,227.7
> view matrix models
> #7,0.76012,-0.64475,-0.080709,58.175,0.18527,0.096006,0.97799,303.15,-0.62281,-0.75834,0.19243,205.62
> view matrix models
> #7,0.81497,-0.57799,0.041796,70.284,0.074319,0.17577,0.98162,309.13,-0.57471,-0.79689,0.18621,202.47
> view matrix models
> #7,0.81497,-0.57799,0.041796,60.966,0.074319,0.17577,0.98162,280.42,-0.57471,-0.79689,0.18621,187.47
> view matrix models
> #7,0.81497,-0.57799,0.041796,69.447,0.074319,0.17577,0.98162,318.63,-0.57471,-0.79689,0.18621,199.55
> view matrix models
> #7,0.81497,-0.57799,0.041796,69.914,0.074319,0.17577,0.98162,319.19,-0.57471,-0.79689,0.18621,198.13
> view matrix models
> #7,0.83812,-0.54538,-0.010659,64.327,0.2059,0.29821,0.93203,311.88,-0.50513,-0.78335,0.36223,214.16
> close #7
> open "E:/temp/EM data/6p40 chain A.pdb"
Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (65 )
Cannot find LINK/SSBOND residue CYS (97 )
Cannot find LINK/SSBOND residue CYS (100 )
Cannot find LINK/SSBOND residue HIS (257 )
Cannot find LINK/SSBOND residue CYS (287 )
2 messages similar to the above omitted
6p40 chain A.pdb title:
Crystal structure of full length APOBEC3G FKL [more info...]
Chain information for 6p40 chain A.pdb #7
---
Chain | Description
A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G
Non-standard residues in 6p40 chain A.pdb #7
---
ZN — zinc ion
> select #7/A:278
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
61 atoms, 62 bonds, 7 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models #7,1,0,0,27.84,0,1,0,208.38,0,0,1,171.33
> hide #7/A:194-383 ribbons
> select clear
> hide #7/A:194-383
> select #7/A:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
71 atoms, 71 bonds, 9 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> select clear
> select clear
> select #7/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
32 atoms, 31 bonds, 4 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #7,0.88195,0.22764,0.41272,9.6528,0.46369,-0.26198,-0.84638,262.4,-0.084549,0.93784,-0.33661,195
> view matrix models
> #7,0.84182,0.39087,0.37224,7.4449,0.53552,-0.69107,-0.48543,260.02,0.067505,0.60799,-0.79107,216.7
> view matrix models
> #7,0.43262,-0.81756,0.38004,37.778,-0.46907,-0.5641,-0.67953,270.51,0.76994,0.11572,-0.62754,217.59
> view matrix models
> #7,0.17889,-0.93141,0.31698,44.329,0.37505,-0.2333,-0.89717,264.17,0.90958,0.27938,0.30759,181.44
> view matrix models
> #7,0.12334,-0.90243,-0.4128,68.893,0.062283,0.4222,-0.90436,251.37,0.99041,0.085836,0.10828,192.04
> view matrix models
> #7,0.043959,-0.88045,-0.47209,70.961,0.37835,0.45202,-0.80779,245.21,0.92462,-0.1431,0.35299,189.37
> view matrix models
> #7,-0.033221,-0.68775,-0.72518,75.548,0.29226,0.68718,-0.6651,235.69,0.95576,-0.23404,0.17817,197.06
> view matrix models
> #7,-0.033221,-0.68775,-0.72518,106.42,0.29226,0.68718,-0.6651,149.59,0.95576,-0.23404,0.17817,153.32
> view matrix models
> #7,-0.033221,-0.68775,-0.72518,125.13,0.29226,0.68718,-0.6651,139.24,0.95576,-0.23404,0.17817,153.84
> view matrix models
> #7,-0.033221,-0.68775,-0.72518,113.58,0.29226,0.68718,-0.6651,178.51,0.95576,-0.23404,0.17817,165.48
> view matrix models
> #7,-0.17593,-0.56015,-0.80949,114.37,0.25543,0.76818,-0.58708,174.25,0.95069,-0.31005,0.0079297,172.97
> view matrix models
> #7,0.02238,-0.64325,-0.76533,113.5,0.30588,0.73322,-0.60731,175.44,0.95181,-0.2205,0.21316,164.02
> view matrix models
> #7,-0.054078,-0.62609,-0.77787,114.03,0.53473,0.63974,-0.55209,174.25,0.84329,-0.44581,0.30019,167.13
> view matrix models
> #7,-0.054078,-0.62609,-0.77787,126.47,0.53473,0.63974,-0.55209,133.28,0.84329,-0.44581,0.30019,162.64
> view matrix models
> #7,-0.054078,-0.62609,-0.77787,180.8,0.53473,0.63974,-0.55209,126.09,0.84329,-0.44581,0.30019,155.88
> view matrix models
> #7,-0.054078,-0.62609,-0.77787,192.05,0.53473,0.63974,-0.55209,154.14,0.84329,-0.44581,0.30019,158.63
> view matrix models
> #7,-0.054078,-0.62609,-0.77787,185.6,0.53473,0.63974,-0.55209,150.51,0.84329,-0.44581,0.30019,161.19
> view matrix models
> #7,-0.054078,-0.62609,-0.77787,184.64,0.53473,0.63974,-0.55209,156.79,0.84329,-0.44581,0.30019,161.8
> fitmap #7 inMap #6
Fit molecule 6p40 chain A.pdb (#7) to map
cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms
average map value = 0.2604, steps = 220
shifted from previous position = 4.65
rotated from previous position = 13.1 degrees
atoms outside contour = 2160, contour level = 0.35073
Position of 6p40 chain A.pdb (#7) relative to
cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
-0.23563322 -0.47812350 -0.84609391 182.99965221
0.57781013 0.63109532 -0.51754629 153.35681133
0.78141695 -0.61083273 0.12755758 171.71894929
Axis -0.04802910 -0.83793409 0.54365400
Axis point -4.41864203 0.00000000 220.24652341
Rotation angle (degrees) 103.79744558
Shift along axis -43.93651557
> select clear
> volume #6 level 0.3439
> volume #6 level 0.3575
> volume #6 level 0.3202
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/csJ200_modelfit.cxs" includeMaps true
——— End of log from Sat Jul 24 17:51:44 2021 ———
opened ChimeraX session
> open "E:/temp/EM data/4n9f.pdb1"
Summary of feedback from opening E:/temp/EM data/4n9f.pdb1
---
warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C
18 GLN C 32 1 15
Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54
1 19
Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82
1 27
Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107
1 23
Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C
110 5 3
680 messages similar to the above omitted
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue HIS (139 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (114 )
Cannot find LINK/SSBOND residue CYS (133 )
33 messages similar to the above omitted
4n9f.pdb1 title:
Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
info...]
Chain information for 4n9f.pdb1 #8
---
Chain | Description
U | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
Non-standard residues in 4n9f.pdb1 #8
---
ZN — zinc ion
> select #8/b:106@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
109 atoms, 112 bonds, 13 residues, 1 model selected
> select up
1415 atoms, 1456 bonds, 173 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,-11.694,0,1,0,161.04,0,0,1,203.72
> view
> view matrix models #8,1,0,0,118.48,0,1,0,172.5,0,0,1,237.1
> view matrix models #8,1,0,0,107.44,0,1,0,89.501,0,0,1,237.26
> ui tool show "Side View"
> view
> hide sel atoms
> show sel cartoons
> hide 8/X
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide 8/X cartoon
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #8/X ribbons
> hide #8/Y ribbons
> hide #8/U ribbons
> select clear
> select #8/b:16
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
164 atoms, 168 bonds, 18 residues, 1 model selected
> select up
1415 atoms, 1456 bonds, 173 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> view matrix models
> #8,0.48027,-0.41679,0.77177,197.33,-0.8756,-0.17595,0.44986,143.09,-0.051702,-0.89181,-0.44944,70.571
> view matrix models
> #8,-0.98518,-0.1161,0.12629,188.96,-0.1636,0.8574,-0.48796,41.852,-0.051626,-0.50139,-0.86368,35.711
> view matrix models
> #8,-0.89741,0.3287,0.2943,212.41,0.19574,0.89443,-0.40209,38.688,-0.3954,-0.30323,-0.86701,51.72
> view matrix models
> #8,-0.91671,0.058782,0.39521,217.98,-0.1142,0.90931,-0.40014,50.257,-0.38289,-0.41194,-0.82686,53.19
> view matrix models
> #8,-0.74867,0.33257,0.57349,236.1,0.10539,0.91377,-0.39233,43.322,-0.65451,-0.23328,-0.71916,77.724
> volume #1 level 0.005238
> hide #!1 models
> hide #!6 models
> show #!6 models
> volume #1 level 0.007196
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> volume #1 level 0.007196
> hide #!1 models
> close #1
> rename #6 id #1
> volume #1 level 0.1945
> select clear
> select #8/b:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #8/a:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
69 atoms, 68 bonds, 8 residues, 1 model selected
> select up
1193 atoms, 1216 bonds, 146 residues, 1 model selected
> select up
6505 atoms, 6643 bonds, 800 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.74867,0.33257,0.57349,274.97,0.10539,0.91377,-0.39233,38.971,-0.65451,-0.23328,-0.71916,111.31
> view matrix models
> #8,-0.26681,-0.68425,0.67868,247.71,-0.77097,0.57409,0.27571,132.44,-0.57828,-0.44969,-0.68071,108.11
> view matrix models
> #8,-0.29087,-0.68219,0.67083,247.79,-0.68023,0.64051,0.35641,138.93,-0.67282,-0.35265,-0.65035,116.63
> view matrix models
> #8,0.13528,-0.38059,0.9148,264.08,-0.62431,0.6842,0.37697,139.96,-0.76937,-0.62212,-0.14505,166.86
> view matrix models
> #8,0.13528,-0.38059,0.9148,314.02,-0.62431,0.6842,0.37697,146.46,-0.76937,-0.62212,-0.14505,158.28
> volume #1 level 0.2658
> volume #1 level 0.1707
> view matrix models
> #8,0.13528,-0.38059,0.9148,309.2,-0.62431,0.6842,0.37697,149.03,-0.76937,-0.62212,-0.14505,156.1
> view matrix models
> #8,-0.43346,-0.49107,0.75562,310.73,-0.28672,0.87007,0.40097,143.3,-0.85434,-0.042848,-0.51794,132.45
> view matrix models
> #8,-0.13072,-0.3324,0.93403,321.68,0.22178,0.90844,0.35433,121.12,-0.9663,0.25347,-0.045034,191.54
> view matrix models
> #8,0.2495,-0.43115,0.8671,299.14,-0.01578,0.89349,0.44881,139.07,-0.96825,-0.12566,0.21612,210.85
> view matrix models
> #8,-0.43366,-0.11701,0.89345,332.73,0.44798,0.83231,0.32645,108.59,-0.78182,0.54182,-0.30852,163.61
> view matrix models
> #8,0.55081,-0.39483,0.73534,275.49,-0.17308,0.80785,0.56341,154.79,-0.81649,-0.4376,0.37663,215.62
> view matrix models
> #8,0.55081,-0.39483,0.73534,273.22,-0.17308,0.80785,0.56341,157.97,-0.81649,-0.4376,0.37663,224.38
> view matrix models
> #8,0.55081,-0.39483,0.73534,253.76,-0.17308,0.80785,0.56341,168.66,-0.81649,-0.4376,0.37663,217.19
> view matrix models
> #8,0.55081,-0.39483,0.73534,265.48,-0.17308,0.80785,0.56341,160.44,-0.81649,-0.4376,0.37663,212.66
> view matrix models
> #8,0.41258,0.90446,-0.10828,209.82,0.25459,-0.00035871,0.96705,170.32,0.87462,-0.42655,-0.23041,89.664
> view matrix models
> #8,0.37582,0.92057,-0.10632,211.66,0.27933,-0.0031402,0.96019,168.67,0.88359,-0.39055,-0.25833,87.195
> view matrix models
> #8,0.37582,0.92057,-0.10632,207.44,0.27933,-0.0031402,0.96019,171.28,0.88359,-0.39055,-0.25833,87.069
> view matrix models
> #8,0.37416,-0.88109,0.28927,211.32,-0.27862,-0.40433,-0.87114,-6.7854,0.88452,0.24535,-0.39678,85.809
> view matrix models
> #8,0.6983,-0.70618,-0.117,161.28,-0.57269,-0.45312,-0.68316,22.175,0.42942,0.54406,-0.72084,74.641
> view matrix models
> #8,0.75787,-0.61224,0.22539,196.56,-0.65238,-0.71431,0.25328,116.63,0.0059263,-0.33899,-0.94077,48.76
> view matrix models
> #8,0.27392,-0.6316,0.72529,265.21,-0.95443,-0.085655,0.28587,143.75,-0.11843,-0.77055,-0.62628,76.875
> view matrix models
> #8,-0.40747,-0.34167,0.8469,308.1,-0.86931,0.42921,-0.2451,96.333,-0.27975,-0.83609,-0.47191,97.271
> view matrix models
> #8,-0.59201,0.27394,0.75795,318.17,-0.37894,0.73541,-0.56177,52.346,-0.71129,-0.61979,-0.33156,131.67
> view matrix models
> #8,-0.58087,0.41783,0.69857,314.59,-0.24181,0.73089,-0.63823,39.439,-0.77725,-0.53965,-0.32352,136.51
> view matrix models
> #8,-0.57713,-0.13473,0.80546,314.13,-0.71826,0.55309,-0.42213,75.159,-0.38862,-0.82216,-0.41597,107.24
> volume #1 level 0.4119
> volume #1 level 0.327
> view matrix models
> #8,-0.57713,-0.13473,0.80546,270.89,-0.71826,0.55309,-0.42213,126.74,-0.38862,-0.82216,-0.41597,135.24
> view matrix models
> #8,-0.57713,-0.13473,0.80546,270.42,-0.71826,0.55309,-0.42213,127.63,-0.38862,-0.82216,-0.41597,136.19
> view matrix models
> #8,-0.57713,-0.13473,0.80546,269.85,-0.71826,0.55309,-0.42213,124.67,-0.38862,-0.82216,-0.41597,134.75
> view matrix models
> #8,-0.57713,-0.13473,0.80546,308.35,-0.71826,0.55309,-0.42213,98.423,-0.38862,-0.82216,-0.41597,119.25
> view matrix models
> #8,-0.5922,-0.15142,0.79143,307.09,-0.70545,0.57207,-0.41842,98.742,-0.3894,-0.8061,-0.4456,116.54
> view matrix models
> #8,-0.59434,-0.50182,0.62844,283.05,-0.69805,-0.066136,-0.71299,54.802,0.39936,-0.86244,-0.31099,101.17
> view matrix models
> #8,-0.59434,-0.50182,0.62844,248.71,-0.69805,-0.066136,-0.71299,89.425,0.39936,-0.86244,-0.31099,118.52
> view matrix models
> #8,-0.59434,-0.50182,0.62844,254.17,-0.69805,-0.066136,-0.71299,89.272,0.39936,-0.86244,-0.31099,124.78
> view matrix models
> #8,-0.59434,-0.50182,0.62844,253.56,-0.69805,-0.066136,-0.71299,89.346,0.39936,-0.86244,-0.31099,124.28
> view matrix models
> #8,-0.59434,-0.50182,0.62844,244.61,-0.69805,-0.066136,-0.71299,90.188,0.39936,-0.86244,-0.31099,116.1
> view matrix models
> #8,-0.59434,-0.50182,0.62844,247.02,-0.69805,-0.066136,-0.71299,90.018,0.39936,-0.86244,-0.31099,119.69
> volume #1 level 0.2319
> select clear
> fitmap #8 inMap #1
Fit molecule 4n9f.pdb1 (#8) to map cryosparc_P19_J200_004_volume_map.mrc (#1)
using 6505 atoms
average map value = 0.141, steps = 180
shifted from previous position = 6.65
rotated from previous position = 4.42 degrees
atoms outside contour = 5044, contour level = 0.23187
Position of 4n9f.pdb1 (#8) relative to cryosparc_P19_J200_004_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.57344950 -0.53030875 0.62444238 247.88862513
-0.71948550 -0.03851333 -0.69343877 90.36992892
0.39178601 -0.84692935 -0.35946401 112.93105909
Axis -0.45564790 0.69065726 -0.56158485
Axis point 156.75916491 0.00000000 81.17267996
Rotation angle (degrees) 170.30338560
Shift along axis -113.95565643
> select clear
> volume #1 level 0.3643
> volume #1 level 0.2862
> volume #1 level 0.3168
> volume #1 level 0.4153
> volume #1 level 0.3168
> volume #1 level 0.2115
> volume #1 level 0.1775
> volume #1 level 0.293
> volume #1 level 0.3202
> hide #!1 models
> show #!1 models
> select #8/b:43
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #8/b:43
10 atoms, 10 bonds, 1 residue, 1 model selected
> volume #1 level 0.1028
> volume #1 level 0.2489
> volume #1 level 0.2285
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/csJ200_modelfit.cxs"
——— End of log from Sat Jul 24 18:31:45 2021 ———
opened ChimeraX session
> open "E:/temp/EM data/6p40 chain A.pdb"
Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (65 )
Cannot find LINK/SSBOND residue CYS (97 )
Cannot find LINK/SSBOND residue CYS (100 )
Cannot find LINK/SSBOND residue HIS (257 )
Cannot find LINK/SSBOND residue CYS (287 )
2 messages similar to the above omitted
6p40 chain A.pdb title:
Crystal structure of full length APOBEC3G FKL [more info...]
Chain information for 6p40 chain A.pdb #6
---
Chain | Description
A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G
Non-standard residues in 6p40 chain A.pdb #6
---
ZN — zinc ion
> select #6/A:35
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
80 atoms, 81 bonds, 10 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models #6,1,0,0,41.073,0,1,0,83.801,0,0,1,144.45
> hide #6/A:1-193
> hide #6/A:1-193 ribbons
> view matrix models #6,1,0,0,80.795,0,1,0,193.83,0,0,1,176.77
> view matrix models #6,1,0,0,51.372,0,1,0,106.89,0,0,1,173
> view matrix models
> #6,0.7593,0.11912,-0.63974,71.768,-0.0067285,0.98449,0.17533,103.33,0.6507,-0.12882,0.74832,160.21
> view matrix models
> #6,0.1363,0.61605,-0.77583,90.125,-0.98071,-0.026848,-0.19361,146.54,-0.1401,0.78725,0.6005,180.92
> view matrix models
> #6,0.11504,0.78637,-0.60695,86.297,-0.96734,-0.050263,-0.24847,147.43,-0.22589,0.61571,0.7549,181
> view matrix models
> #6,0.74349,-0.64774,0.16631,59.133,0.59394,0.75387,0.28091,86.709,-0.30733,-0.11008,0.94521,183.3
> view matrix models
> #6,-0.0077101,-0.9767,-0.21445,91.527,0.91235,-0.094656,0.39831,79.103,-0.40933,-0.19258,0.89183,187.86
> view matrix models
> #6,0.34197,-0.93971,0.0014996,76.266,0.88262,0.32175,0.34272,78.914,-0.32254,-0.11588,0.93944,183.69
> view matrix models
> #6,0.44403,0.70442,-0.55374,76.055,0.78498,-0.0078494,0.61947,77.775,0.43202,-0.70974,-0.55644,195.88
> view matrix models
> #6,0.70528,0.69667,-0.13126,59.087,0.19973,-0.01762,0.97969,88.01,0.68021,-0.71717,-0.15157,179.67
> view matrix models
> #6,0.29758,0.954,0.036336,66.513,0.27294,-0.12149,0.95433,86.893,0.91485,-0.27407,-0.29654,173.18
> view matrix models
> #6,0.54405,0.83628,-0.068086,61.909,0.22524,-0.067401,0.97197,87.665,0.80825,-0.54414,-0.22504,176.38
> view matrix models
> #6,0.54446,0.83283,-0.099765,62.594,0.28565,-0.072271,0.9556,86.195,0.78865,-0.54878,-0.27725,178.12
> view matrix models
> #6,0.54446,0.83283,-0.099765,105.81,0.28565,-0.072271,0.9556,76.745,0.78865,-0.54878,-0.27725,170.58
> view matrix models
> #6,0.54446,0.83283,-0.099765,121.25,0.28565,-0.072271,0.9556,113.14,0.78865,-0.54878,-0.27725,182.1
> view matrix models
> #6,0.54446,0.83283,-0.099765,114.43,0.28565,-0.072271,0.9556,114.42,0.78865,-0.54878,-0.27725,178.39
> view matrix models
> #6,0.54446,0.83283,-0.099765,115.52,0.28565,-0.072271,0.9556,115.59,0.78865,-0.54878,-0.27725,178.97
> view matrix models
> #6,0.16866,0.98288,0.074226,122.34,0.29028,-0.12149,0.9492,115.86,0.94196,-0.13854,-0.3058,172.66
> view matrix models
> #6,0.16866,0.98288,0.074226,122.91,0.29028,-0.12149,0.9492,115.94,0.94196,-0.13854,-0.3058,171.61
> view matrix models
> #6,0.17729,0.98079,0.081295,122.51,0.42483,-0.15078,0.89263,113.26,0.88774,-0.12372,-0.44341,176.13
> view matrix models
> #6,0.066098,0.99767,-0.016946,127.92,0.087943,0.011092,0.99606,119.87,0.99393,-0.067328,-0.087005,164.94
> view matrix models
> #6,0.32001,0.94531,-0.063146,122.21,0.079418,0.039651,0.99605,119.94,0.94408,-0.32376,-0.062386,167.33
> view matrix models
> #6,0.095422,0.99518,-0.022489,127.27,0.086608,0.014207,0.99614,119.89,0.99166,-0.097002,-0.084835,165.11
> view matrix models
> #6,0.095422,0.99518,-0.022489,127.34,0.086608,0.014207,0.99614,122.08,0.99166,-0.097002,-0.084835,165.89
> view matrix models
> #6,0.095422,0.99518,-0.022489,127.14,0.086608,0.014207,0.99614,122.08,0.99166,-0.097002,-0.084835,168.29
> view matrix models
> #6,0.11732,0.98837,0.096732,124.13,0.57792,-0.14716,0.80271,112.7,0.80761,-0.038271,-0.58847,184.37
> view matrix models
> #6,0.0072566,0.9994,0.033748,128.78,0.40641,-0.033784,0.91307,114.95,0.91366,0.00709,-0.40641,176.98
> view matrix models
> #6,0.010083,0.97108,0.23855,124.47,0.78231,-0.15624,0.60298,110.78,0.62281,0.18054,-0.76126,192.52
> view matrix models
> #6,-0.086288,0.93523,0.34336,125.37,0.34993,-0.29424,0.88937,118.62,0.93279,0.19689,-0.30187,173.12
> view matrix models
> #6,0.33384,0.92294,0.19167,116.22,0.24943,-0.28258,0.92624,120.75,0.90903,-0.2614,-0.32455,176.83
> view matrix models
> #6,0.33384,0.92294,0.19167,114.35,0.24943,-0.28258,0.92624,121.27,0.90903,-0.2614,-0.32455,173.33
> view matrix models
> #6,0.33384,0.92294,0.19167,113.99,0.24943,-0.28258,0.92624,121.19,0.90903,-0.2614,-0.32455,178.66
> view matrix models
> #6,0.34175,0.93482,0.096494,115.71,0.17543,-0.16433,0.97068,121.81,0.92327,-0.3148,-0.22016,176.28
> view matrix models
> #6,0.34175,0.93482,0.096494,64.01,0.17543,-0.16433,0.97068,126.19,0.92327,-0.3148,-0.22016,177.29
> view matrix models
> #6,0.39681,0.9043,0.15741,61.228,0.15191,-0.23382,0.96034,127.61,0.90524,-0.35716,-0.23016,178.1
> view matrix models
> #6,0.39681,0.9043,0.15741,67.331,0.15191,-0.23382,0.96034,141.95,0.90524,-0.35716,-0.23016,181.9
> view matrix models
> #6,0.39681,0.9043,0.15741,106.65,0.15191,-0.23382,0.96034,115.6,0.90524,-0.35716,-0.23016,171.45
> view matrix models
> #6,0.39681,0.9043,0.15741,113.25,0.15191,-0.23382,0.96034,126.56,0.90524,-0.35716,-0.23016,175.72
> fitmap #8 inMap #1
Fit molecule 4n9f.pdb1 (#8) to map cryosparc_P19_J200_004_volume_map.mrc (#1)
using 6505 atoms
average map value = 0.141, steps = 192
shifted from previous position = 0.0165
rotated from previous position = 0.0209 degrees
atoms outside contour = 5023, contour level = 0.22848
Position of 4n9f.pdb1 (#8) relative to cryosparc_P19_J200_004_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.57353384 -0.53052325 0.62418266 247.85205740
-0.71938580 -0.03828804 -0.69355466 90.36110724
0.39184561 -0.84680522 -0.35969141 112.90168214
Axis -0.45562023 0.69074763 -0.56149615
Axis point 156.72789884 0.00000000 81.16431177
Rotation angle (degrees) 170.31810134
Shift along axis -113.90354990
> select clear
> volume #1 level 0.2522
> volume #1 level 0.259
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/csJ200_modelfit.cxs" includeMaps true
> volume #1 level 0.3371
> volume #1 level 0.2726
> volume #1 level 0.2862
> volume #1 level 0.2421
> save "E:/temp/EM data/H7N100
> cryoEM/20210423/20210423_6429mics/csJ200_modelfit.cxs"
——— End of log from Sat Jul 24 18:49:24 2021 ———
opened ChimeraX session
> open E:/Krios/20210423/csrelion/6221/rlnJ031_Refine3D_class001.mrc
Opened rlnJ031_Refine3D_class001.mrc as #9, grid size 352,352,352, pixel
0.835, shown at level 0.00471, step 2, values float32
> hide #!1 models
> volume #9 level 0.007178
> volume #9 step 1
> volume #1 step 1
> volume #9 level 0.008252
> hide #!9 models
> show #!1 models
> hide #!1 models
> show #!9 models
> hide #!9 models
> show #!1 models
> hide #!1 models
> select #7/A:116
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
71 atoms, 71 bonds, 9 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> select add #6/A:342
3095 atoms, 3131 bonds, 429 residues, 2 models selected
> select up
3204 atoms, 3245 bonds, 441 residues, 2 models selected
> select up
6168 atoms, 6240 bonds, 856 residues, 2 models selected
> select add #8/a:37
6178 atoms, 6250 bonds, 857 residues, 3 models selected
> select up
6293 atoms, 6367 bonds, 871 residues, 3 models selected
> select up
7361 atoms, 7456 bonds, 1002 residues, 3 models selected
> select add #8/b:30
7373 atoms, 7468 bonds, 1003 residues, 3 models selected
> select up
7525 atoms, 7624 bonds, 1020 residues, 3 models selected
> select up
8776 atoms, 8912 bonds, 1175 residues, 3 models selected
> view #9 clip false
No displayed objects specified.
> view matrix models
> #7,-0.23059,-0.49775,-0.83611,183.74,0.56382,0.63197,-0.53172,159.08,0.79306,-0.59402,0.13491,174.01,#8,-0.55611,-0.54439,0.62799,248.48,-0.73297,-0.034927,-0.67936,97.841,0.39177,-0.8381,-0.3796,113.25,#6,0.39681,0.9043,0.15741,113.39,0.15191,-0.23382,0.96034,131.53,0.90524,-0.35716,-0.23016,179.04
> view matrix models
> #7,-0.23059,-0.49775,-0.83611,183.73,0.56382,0.63197,-0.53172,158.89,0.79306,-0.59402,0.13491,173.97,#8,-0.55611,-0.54439,0.62799,248.48,-0.73297,-0.034927,-0.67936,97.656,0.39177,-0.8381,-0.3796,113.22,#6,0.39681,0.9043,0.15741,113.38,0.15191,-0.23382,0.96034,131.34,0.90524,-0.35716,-0.23016,179.01
> view matrix models
> #7,-0.73359,-0.65209,0.19137,155.77,-0.10831,-0.16582,-0.98019,173.4,0.67091,-0.73978,0.051021,176.72,#8,0.42817,-0.0079779,0.90367,244.42,-0.82286,-0.41683,0.3862,218.93,0.3736,-0.90895,-0.18504,135.46,#6,-0.16109,0.57887,-0.79935,157,0.31355,0.79798,0.51469,97.784,0.93581,-0.16772,-0.31006,172.83
> show #!9 models
> hide #!9 models
> view matrix models
> #7,-0.74318,-0.64255,0.18661,155.94,-0.47816,0.31494,-0.81987,167.64,0.46803,-0.69853,-0.54129,198.26,#8,0.41959,0.0027859,0.90771,245.34,-0.88835,0.20668,0.41001,227.77,-0.18646,-0.9784,0.089197,193.01,#6,-0.17264,0.58441,-0.79288,156.91,-0.30369,0.73417,0.60726,109.21,0.937,0.34562,0.050735,150.1
> select #9
2 models selected
> ~select #9
Nothing selected
> show #!9 models
> hide #!9 models
> select #6/A:343
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
120 atoms, 125 bonds, 13 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> select up
3132 atoms, 3120 bonds, 476 residues, 1 model selected
> select up
28755 atoms, 28885 bonds, 4062 residues, 11 models selected
> select down
3132 atoms, 3120 bonds, 476 residues, 1 model selected
> select down
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> select add #8/a:65
3090 atoms, 3125 bonds, 429 residues, 2 models selected
> select up
3144 atoms, 3182 bonds, 435 residues, 2 models selected
> select up
4277 atoms, 4336 bonds, 574 residues, 2 models selected
> select add #8/b:148
4285 atoms, 4343 bonds, 575 residues, 2 models selected
> select up
4359 atoms, 4418 bonds, 585 residues, 2 models selected
> select up
5692 atoms, 5792 bonds, 747 residues, 2 models selected
> select add #7/A:186
5701 atoms, 5800 bonds, 748 residues, 3 models selected
> select up
5822 atoms, 5924 bonds, 764 residues, 3 models selected
> select up
8776 atoms, 8912 bonds, 1175 residues, 3 models selected
> show #!9 models
> hide #!9 models
> view matrix models
> #7,-0.73962,-0.64642,0.18735,155.9,-0.35928,0.14384,-0.92208,171.4,0.5691,-0.7493,-0.33864,190.03,#8,0.42198,-0.0018198,0.9066,245.06,-0.90635,-0.024378,0.42182,228.92,0.021334,-0.9997,-0.011936,170.65,#6,-0.16785,0.58318,-0.79481,156.89,-0.079988,0.79553,0.60061,103.44,0.98256,0.16439,-0.086883,156.64
> show #!9 models
> hide #!9 models
> view matrix models
> #7,-0.72164,-0.65983,0.20941,155.07,-0.38105,0.12607,-0.91592,171.41,0.57795,-0.74076,-0.34241,190.06,#8,0.44808,-0.013932,0.89388,242.29,-0.89387,-0.023266,0.44772,231.49,0.01456,-0.99963,-0.022878,169.63,#6,-0.15288,0.56215,-0.81278,157.58,-0.085914,0.81178,0.57761,103.55,0.9845,0.15813,-0.075805,156.55
> view matrix models
> #7,-0.72164,-0.65983,0.20941,155.13,-0.38105,0.12607,-0.91592,170.1,0.57795,-0.74076,-0.34241,196.7,#8,0.44808,-0.013932,0.89388,242.35,-0.89387,-0.023266,0.44772,230.18,0.01456,-0.99963,-0.022878,176.27,#6,-0.15288,0.56215,-0.81278,157.64,-0.085914,0.81178,0.57761,102.24,0.9845,0.15813,-0.075805,163.19
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> view matrix models
> #7,-0.73037,-0.6327,0.25739,153.23,-0.40938,0.10383,-0.90644,170.05,0.54678,-0.76741,-0.33485,196.73,#8,0.48003,0.028515,0.87679,238.92,-0.87667,-0.020624,0.48064,233.39,0.031788,-0.99938,0.015098,180.04,#6,-0.19037,0.5245,-0.82985,159.65,-0.094621,0.83157,0.5473,102.44,0.97714,0.18271,-0.10868,163.24
> view matrix models
> #7,-0.73037,-0.6327,0.25739,153.21,-0.40938,0.10383,-0.90644,171.35,0.54678,-0.76741,-0.33485,193.52,#8,0.48003,0.028515,0.87679,238.91,-0.87667,-0.020624,0.48064,234.69,0.031788,-0.99938,0.015098,176.84,#6,-0.19037,0.5245,-0.82985,159.63,-0.094621,0.83157,0.5473,103.74,0.97714,0.18271,-0.10868,160.03
> show #!9 models
> view matrix models
> #7,-0.73181,-0.63062,0.2584,138.96,-0.41396,0.11013,-0.90361,175.24,0.54137,-0.76824,-0.34165,194.54,#8,0.48004,0.031239,0.87669,224.69,-0.87687,-0.012335,0.48058,238.73,0.025827,-0.99944,0.021471,178.62,#6,-0.19302,0.52391,-0.82962,145.48,-0.10274,0.83008,0.5481,107.91,0.9758,0.19103,-0.1064,160.52
> view matrix models
> #7,-0.73181,-0.63062,0.2584,139.02,-0.41396,0.11013,-0.90361,175.15,0.54137,-0.76824,-0.34165,193.06,#8,0.48004,0.031239,0.87669,224.75,-0.87687,-0.012335,0.48058,238.64,0.025827,-0.99944,0.021471,177.13,#6,-0.19302,0.52391,-0.82962,145.54,-0.10274,0.83008,0.5481,107.82,0.9758,0.19103,-0.1064,159.03
> view matrix models
> #7,-0.73181,-0.63062,0.2584,138.57,-0.41396,0.11013,-0.90361,174.35,0.54137,-0.76824,-0.34165,193.62,#8,0.48004,0.031239,0.87669,224.31,-0.87687,-0.012335,0.48058,237.83,0.025827,-0.99944,0.021471,177.69,#6,-0.19302,0.52391,-0.82962,145.09,-0.10274,0.83008,0.5481,107.02,0.9758,0.19103,-0.1064,159.59
> view matrix models
> #7,-0.69925,-0.67617,0.23203,139.61,-0.33595,0.024317,-0.94157,175.8,0.63102,-0.73634,-0.24416,189.59,#8,0.47604,-0.030484,0.8789,224.53,-0.87335,-0.1337,0.46839,235.79,0.10323,-0.99055,-0.090271,160.89,#6,-0.13306,0.53911,-0.83166,143.66,0.018694,0.84034,0.54174,104.77,0.99093,0.056537,-0.12189,163.67
> view matrix models
> #7,-0.65005,-0.73512,0.19245,140.97,-0.3564,0.071268,-0.93161,175.48,0.67113,-0.67418,-0.30833,191.41,#8,0.46609,-0.11627,0.87707,224.32,-0.88451,-0.08362,0.45896,235.53,0.019975,-0.98969,-0.14182,158.54,#6,-0.048847,0.55807,-0.82835,141.46,-0.028776,0.82821,0.55967,105.77,0.99839,0.051175,-0.024397,161.83
> view matrix models
> #7,-0.66083,-0.71948,0.21367,140.23,-0.35731,0.051227,-0.93258,175.55,0.66003,-0.69262,-0.29093,190.87,#8,0.47851,-0.090925,0.87336,223.46,-0.87702,-0.098431,0.47027,236.42,0.043207,-0.99098,-0.12684,159.21,#6,-0.072677,0.54434,-0.83571,142.46,-0.016326,0.83717,0.5467,105.48,0.99722,0.053377,-0.051956,162.26
> view matrix models
> #7,-0.68238,-0.69099,0.2385,139.34,-0.35188,0.024518,-0.93573,175.67,0.64073,-0.72245,-0.25988,189.94,#8,0.48856,-0.048647,0.87118,222.94,-0.86854,-0.12254,0.48023,237.03,0.083395,-0.99127,-0.10212,160.29,#6,-0.11345,0.5299,-0.84044,143.73,0.0055266,0.84622,0.5328,105,0.99353,0.055802,-0.098932,163.11
> view matrix models
> #7,-0.68238,-0.69099,0.2385,138.27,-0.35188,0.024518,-0.93573,173.06,0.64073,-0.72245,-0.25988,186.59,#8,0.48856,-0.048647,0.87118,221.87,-0.86854,-0.12254,0.48023,234.42,0.083395,-0.99127,-0.10212,156.93,#6,-0.11345,0.5299,-0.84044,142.67,0.0055266,0.84622,0.5328,102.38,0.99353,0.055802,-0.098932,159.76
> select clear
> select #7
3132 atoms, 3120 bonds, 6 pseudobonds, 476 residues, 2 models selected
> fitmap #7 inMap #9
Fit molecule 6p40 chain A.pdb (#7) to map rlnJ031_Refine3D_class001.mrc (#9)
using 3132 atoms
average map value = 0.007227, steps = 220
shifted from previous position = 6.35
rotated from previous position = 14.6 degrees
atoms outside contour = 1860, contour level = 0.0082516
Position of 6p40 chain A.pdb (#7) relative to rlnJ031_Refine3D_class001.mrc
(#9) coordinates:
Matrix rotation and translation
-0.63754336 -0.77040468 0.00388575 150.98929727
-0.23854083 0.19260203 -0.95184176 167.97891696
0.73255494 -0.60776731 -0.30656512 184.29895480
Axis 0.35636252 -0.75469243 0.55085850
Axis point 86.41125727 0.00000000 177.46455404
Rotation angle (degrees) 151.13424529
Shift along axis 28.55715561
> fitmap #6 inMap #9
Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
using 3132 atoms
average map value = 0.007893, steps = 244
shifted from previous position = 12.4
rotated from previous position = 25.4 degrees
atoms outside contour = 1847, contour level = 0.0082516
Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
(#9) coordinates:
Matrix rotation and translation
-0.23850561 0.75894450 -0.60590289 147.84513899
-0.19733010 0.57301885 0.79543084 104.70296891
0.95088164 0.30927759 0.01309438 155.33804486
Axis -0.25714174 -0.82343229 -0.50580371
Axis point 34.73908461 0.00000000 86.93032961
Rotation angle (degrees) 109.03806143
Shift along axis -202.80352043
> volume #9 level 0.01029
> fitmap #8 inMap #9
Fit molecule 4n9f.pdb1 (#8) to map rlnJ031_Refine3D_class001.mrc (#9) using
6505 atoms
average map value = 0.005075, steps = 260
shifted from previous position = 13.2
rotated from previous position = 10.4 degrees
atoms outside contour = 5408, contour level = 0.010292
Position of 4n9f.pdb1 (#8) relative to rlnJ031_Refine3D_class001.mrc (#9)
coordinates:
Matrix rotation and translation
0.36762856 -0.17583896 0.91319761 234.88617723
-0.92969949 -0.09329134 0.35630824 219.37882466
0.02254056 -0.97998845 -0.19777396 145.93826787
Axis -0.75324502 0.50204644 -0.42493684
Axis point 0.00000000 224.70545159 -107.70282102
Rotation angle (degrees) 117.49804676
Shift along axis -128.80303213
> volume #9 level 0.005674
> volume #9 level 0.006855
> select clear
> select clear
> volume #9 level 0.01094
> select #6/A:365
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
128 atoms, 128 bonds, 17 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #6,-0.15913,0.76947,-0.61854,145.82,-0.16885,0.59608,0.78497,104.01,0.97271,0.22935,0.035071,154.63
> view matrix models
> #6,-0.34437,0.75578,-0.55696,149.88,-0.23898,0.50314,0.83051,105.51,0.90791,0.4191,0.0073522,156.17
> view matrix models
> #6,-0.34437,0.75578,-0.55696,150.03,-0.23898,0.50314,0.83051,103.75,0.90791,0.4191,0.0073522,159.51
> view matrix models
> #6,-0.017509,0.76823,-0.63993,142.46,0.281,0.61801,0.73423,90.446,0.95955,-0.16696,-0.22669,166.13
> view matrix models
> #6,-0.017509,0.76823,-0.63993,139.82,0.281,0.61801,0.73423,87.481,0.95955,-0.16696,-0.22669,158.08
> view matrix models
> #6,-0.017509,0.76823,-0.63993,139.68,0.281,0.61801,0.73423,87.056,0.95955,-0.16696,-0.22669,160.29
> view matrix models
> #6,-0.038542,0.7564,-0.65297,140.63,0.27748,0.63586,0.7202,87.365,0.95996,-0.15343,-0.2344,160.37
> view matrix models
> #6,-0.038542,0.7564,-0.65297,139.62,0.27748,0.63586,0.7202,90.803,0.95996,-0.15343,-0.2344,157.35
> fitmap #6 inMap #9
Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
using 3132 atoms
average map value = 0.007728, steps = 148
shifted from previous position = 11.6
rotated from previous position = 8.93 degrees
atoms outside contour = 2321, contour level = 0.010937
Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
(#9) coordinates:
Matrix rotation and translation
-0.13333327 0.73447066 -0.66541347 149.49306113
0.38637171 0.65680662 0.64755074 98.52677917
0.91265499 -0.17075688 -0.37135286 165.66345422
Axis -0.45175903 -0.87119643 -0.19217326
Axis point 1.71948038 0.00000000 95.99345047
Rotation angle (degrees) 115.08357227
Shift along axis -185.20710454
> view matrix models
> #6,-0.00028857,0.81206,-0.58358,143.3,0.38164,0.5395,0.75053,97.115,0.92431,-0.2225,-0.31007,164.28
> view matrix models
> #6,-0.00028857,0.81206,-0.58358,142.98,0.38164,0.5395,0.75053,96.912,0.92431,-0.2225,-0.31007,161.54
> view matrix models
> #6,-0.00028857,0.81206,-0.58358,139.26,0.38164,0.5395,0.75053,93.797,0.92431,-0.2225,-0.31007,170.84
> view matrix models
> #6,-0.00028857,0.81206,-0.58358,141.82,0.38164,0.5395,0.75053,83.721,0.92431,-0.2225,-0.31007,164.84
> fitmap #6 inMap #9
Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
using 3132 atoms
average map value = 0.007729, steps = 164
shifted from previous position = 14
rotated from previous position = 10 degrees
atoms outside contour = 2320, contour level = 0.010937
Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
(#9) coordinates:
Matrix rotation and translation
-0.13324155 0.73448528 -0.66541570 149.49325604
0.38618835 0.65680998 0.64765669 98.51054761
0.91274599 -0.17068101 -0.37116404 165.65156854
Axis -0.45174250 -0.87118399 -0.19226846
Axis point 1.72593886 0.00000000 95.99015392
Rotation angle (degrees) 115.07459222
Shift along axis -185.20284131
> view matrix models
> #6,-0.17574,0.74494,-0.64357,150.26,0.40985,0.64976,0.64018,97.988,0.89507,-0.15126,-0.4195,167.12
> view matrix models
> #6,-0.17574,0.74494,-0.64357,144.84,0.40985,0.64976,0.64018,85.581,0.89507,-0.15126,-0.4195,167.96
> volume #9 level 0.008037
> view matrix models
> #6,-0.17574,0.74494,-0.64357,139.79,0.40985,0.64976,0.64018,85.601,0.89507,-0.15126,-0.4195,166.6
> fitmap #6 inMap #9
Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
using 3132 atoms
average map value = 0.00765, steps = 164
shifted from previous position = 14.1
rotated from previous position = 7.6 degrees
atoms outside contour = 1848, contour level = 0.0080368
Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
(#9) coordinates:
Matrix rotation and translation
-0.16644106 0.79311293 -0.58589185 146.34040774
0.32281416 0.60526380 0.72763091 96.40061293
0.93171261 -0.06802653 -0.35676883 164.39881319
Axis -0.44777830 -0.85407402 -0.26467368
Axis point 7.34850755 0.00000000 88.88324692
Rotation angle (degrees) 117.32085964
Shift along axis -191.37335764
> view matrix models
> #6,-0.16644,0.79311,-0.58589,137.77,0.32281,0.60526,0.72763,85.502,0.93171,-0.068027,-0.35677,162.83
> fitmap #6 inMap #9
Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
using 3132 atoms
average map value = 0.007133, steps = 128
shifted from previous position = 10.7
rotated from previous position = 9.89 degrees
atoms outside contour = 1958, contour level = 0.0080368
Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
(#9) coordinates:
Matrix rotation and translation
-0.06938187 0.79367977 -0.60436626 144.29595832
0.18857598 0.60533831 0.77330759 93.86982414
0.97960464 -0.06031543 -0.19166844 159.27490300
Axis -0.44119751 -0.83832140 -0.32025302
Axis point 6.13740716 0.00000000 86.73688903
Rotation angle (degrees) 109.13869523
Shift along axis -193.36436754
> select clear
> select #6/A:346
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
120 atoms, 125 bonds, 13 residues, 1 model selected
> select up
3084 atoms, 3120 bonds, 428 residues, 1 model selected
> view matrix models
> #6,-0.036012,0.72711,-0.68558,145.51,0.19677,0.67775,0.70847,94.644,0.97979,-0.10939,-0.16748,159.02
> view matrix models
> #6,-0.036012,0.72711,-0.68558,143.58,0.19677,0.67775,0.70847,88.787,0.97979,-0.10939,-0.16748,160.75
> fitmap #6 inMap #9
Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
using 3132 atoms
average map value = 0.007807, steps = 184
shifted from previous position = 10.1
rotated from previous position = 19.3 degrees
atoms outside contour = 1786, contour level = 0.0080368
Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
(#9) coordinates:
Matrix rotation and translation
-0.23597200 0.70831755 -0.66528450 150.71900005
-0.06978088 0.67049968 0.73862088 102.18862974
0.96925117 0.22071798 -0.10879213 157.50216326
Axis -0.27505384 -0.86808805 -0.41324148
Axis point 28.01824000 0.00000000 93.77146687
Rotation angle (degrees) 109.70224977
Shift along axis -195.25099563
> select clear
> volume #9 level 0.0104
> volume #9 level 0.008574
> volume #9 level 0.008681
> hide #!9 models
> select #7/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> volume #9 level 0.009326
> save E:/Krios/20210423/csrelion/6221/rlnJ31_modelfit.cxs includeMaps true
> close #1
> rename #9 id #1
> save E:/Krios/20210423/csrelion/6221/rlnJ31_modelfit.cxs
——— End of log from Sun Jul 25 16:29:33 2021 ———
opened ChimeraX session
> open "E:/temp/EM data/AF-Q9HC16-F1-model_v1.pdb"
AF-Q9HC16-F1-model_v1.pdb title:
Alphafold V2.0 prediction for DNA DC->du-editing enzyme apobec-3G (Q9HC16)
[more info...]
Chain information for AF-Q9HC16-F1-model_v1.pdb #9
---
Chain | Description
A | DNA DC->du-editing enzyme apobec-3G
> matchmaker #9 to #5/A:1-193
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6p40_chainA_NTD, chain A (#5) with AF-Q9HC16-F1-model_v1.pdb, chain
A (#9), sequence alignment score = 755.6
RMSD between 160 pruned atom pairs is 0.752 angstroms; (across all 183 pairs:
2.237)
> hide #!5 models
> hide #!4 models
> open E:/Krios/20210423/csrelion/6221/rlnJ084_Refine3D_class001.mrc
Opened rlnJ084_Refine3D_class001.mrc as #10, grid size 352,352,352, pixel
0.835, shown at level 0.00157, step 2, values float32
> volume #10 step 1
> volume #10 level 0.00933
> matchmaker #10 to #1
No 'to' model specified
> matchmaker #10 in #1
Expected a keyword
> fitmap #10 inMap #1
Fit map rlnJ084_Refine3D_class001.mrc in map rlnJ031_Refine3D_class001.mrc
using 93051 points
correlation = 0.9473, correlation about mean = 0.6361, overlap = 14.9
steps = 140, shift = 7.01, angle = 11.8 degrees
Position of rlnJ084_Refine3D_class001.mrc (#10) relative to
rlnJ031_Refine3D_class001.mrc (#1) coordinates:
Matrix rotation and translation
0.98858759 -0.02714003 -0.14818232 26.98671062
0.00637153 0.99029048 -0.13886748 20.79485999
0.15051241 0.13633852 0.97916180 -34.44632650
Axis 0.67530404 -0.73294100 0.08223110
Axis point 251.38123504 0.00000000 162.07308841
Rotation angle (degrees) 11.75718438
Shift along axis 0.15026983
> volume #10 color #b2ffff82
> hide #!1 models
> show #!1 models
> hide #!10 models
> hide #!1 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> close #10
> show #!1 models
> select clear
> select clear
> select clear
> select #9/A:249
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
115 atoms, 119 bonds, 14 residues, 1 model selected
> select up
3274 atoms, 3384 bonds, 384 residues, 1 model selected
> fitmap #9 inMap #1
Fit molecule AF-Q9HC16-F1-model_v1.pdb (#9) to map
rlnJ031_Refine3D_class001.mrc (#1) using 3274 atoms
average map value = 0.01332, steps = 52
shifted from previous position = 0.735
rotated from previous position = 3.35 degrees
atoms outside contour = 995, contour level = 0.0093255
Position of AF-Q9HC16-F1-model_v1.pdb (#9) relative to
rlnJ031_Refine3D_class001.mrc (#1) coordinates:
Matrix rotation and translation
0.43226595 -0.13718773 0.89124950 148.79592009
-0.53175670 0.75944351 0.37480711 124.16846329
-0.72827259 -0.63594425 0.25533107 124.38743868
Axis -0.51849395 0.83078038 -0.20240549
Axis point 207.24448422 0.00000000 -35.41841460
Rotation angle (degrees) 77.08412019
Shift along axis 0.83023962
> select clear
> save E:/Krios/20210423/csrelion/6221/rlnJ031_AFmodelfit.cxs includeMaps true
——— End of log from Wed Jul 28 23:41:31 2021 ———
opened ChimeraX session
> open E:/Krios/20210423/csrelion/6221/rlnJ121_Refine3D_class001.mrc
Opened rlnJ121_Refine3D_class001.mrc as #10, grid size 352,352,352, pixel
0.835, shown at level 0.00477, step 2, values float32
> volume #10 step 1
> volume #10 level 0.00933
> volume #10 color #b2b2b282
> fitmap #10 inMap #1
Fit map rlnJ121_Refine3D_class001.mrc in map rlnJ031_Refine3D_class001.mrc
using 178013 points
correlation = 0.9817, correlation about mean = 0.8332, overlap = 36.73
steps = 128, shift = 5.04, angle = 10.8 degrees
Position of rlnJ121_Refine3D_class001.mrc (#10) relative to
rlnJ031_Refine3D_class001.mrc (#1) coordinates:
Matrix rotation and translation
0.98878079 0.10250658 -0.10865058 0.98179692
-0.11418749 0.98763897 -0.10738009 32.45406508
0.09630039 0.11858191 0.98826341 -24.88753251
Axis 0.60386561 -0.54771530 -0.57909781
Axis point 0.00000000 249.08271471 259.43129881
Rotation angle (degrees) 10.78337366
Shift along axis -2.77039899
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #9 models
> volume #1 color #ffffb2
> volume #10 color #b2b2b2
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> hide #!1 models
> show #!10 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #9 models
> hide #!4 models
> hide #!5 models
> volume #10 color #b2b2b282
> save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
> includeMaps true
——— End of log from Fri Jul 30 02:27:40 2021 ———
opened ChimeraX session
> close #1
> rename #10 id #1
> volume #1 level 0.009121
> open "E:/temp/EM data/AF-Q9HC16-F1-model_v1.pdb"
AF-Q9HC16-F1-model_v1.pdb title:
Alphafold V2.0 prediction for DNA DC->du-editing enzyme apobec-3G (Q9HC16)
[more info...]
Chain information for AF-Q9HC16-F1-model_v1.pdb #10
---
Chain | Description
A | DNA DC->du-editing enzyme apobec-3G
> ui windowfill toggle
> ui dockable false "Command Line Interface"
> matchmaker #10 to #7/A:1-193
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6p40 chain A.pdb, chain A (#7) with AF-Q9HC16-F1-model_v1.pdb,
chain A (#10), sequence alignment score = 755.6
RMSD between 160 pruned atom pairs is 0.752 angstroms; (across all 183 pairs:
2.237)
> hide #!6 models
> hide #!7 models
> select clear
> select #9/A:383
9 atoms, 8 bonds, 1 residue, 1 model selected
> set bgColor white
> set bgColor black
> set bgColor white
> set bgColor black
> select clear
> select #10/A:356
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
104 atoms, 109 bonds, 13 residues, 1 model selected
> select up
3274 atoms, 3384 bonds, 384 residues, 1 model selected
> fitmap #10 inMap #1
Fit molecule AF-Q9HC16-F1-model_v1.pdb (#10) to map
rlnJ121_Refine3D_class001.mrc (#1) using 3274 atoms
average map value = 0.01149, steps = 80
shifted from previous position = 1.56
rotated from previous position = 4.99 degrees
atoms outside contour = 1264, contour level = 0.0091212
Position of AF-Q9HC16-F1-model_v1.pdb (#10) relative to
rlnJ121_Refine3D_class001.mrc (#1) coordinates:
Matrix rotation and translation
-0.60937906 0.55872142 -0.56257224 133.88403179
-0.28231498 0.51013129 0.81244342 129.07078099
0.74091525 0.65390858 -0.15312790 175.32494140
Axis -0.10166762 -0.83592017 -0.53935254
Axis point 42.23358963 0.00000000 78.11834209
Rotation angle (degrees) 128.76942468
Shift along axis -216.06649290
> select clear
> volume #1 level 0.00766
> volume #1 level 0.007033
> volume #1 level 0.006929
> save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
> save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
> includeMaps true
> show #8/X
> hide #8/X
> hide #8/X cartoons
> hide #8/X ribbons
> show #9-10#!2,8 cartoons
> hide #9-10#!2,8 cartoons
> show #9-10#!2,8 cartoons
> undo
> undo
> undo
> show #8/X ribbons
> show #8/Y ribbons
> select clear
> volume #1 level 0.006511
> volume #1 level 0.006616
> volume #1 level 0.009017
> volume #1 level 0.00672
> save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
> includeMaps true
> volume #1 level 0.008912
> hide #!1 models
> show #!1 models
> volume #1 level 0.006407
> volume #1 level 0.007868
> save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
> includeMaps true
——— End of log from Fri Jul 30 02:44:06 2021 ———
opened ChimeraX session
> save E:/Krios/20210423/csrelion/6221/rlnJ121_AFmodelfit.cxs includeMaps true
> hide #!1 models
> set bgColor white
> set bgColor black
> show #!1 models
> hide #!1 models
> show #!1 models
> save E:/Krios/20210423/csrelion/6221/rlnJ121_AFmodelfit.cxs
——— End of log from Sun Aug 1 00:14:47 2021 ———
opened ChimeraX session
> open E:\Krios\20210423\csrelion\6221\phenix\rlnJ121_4M4_denmod_map.ccp4
> format ccp4
Opened rlnJ121_4M4_denmod_map.ccp4 as #11, grid size 130,175,176, pixel 0.835,
shown at level 0.554, step 1, values float32
> volume #11 level 0.4258
> volume #11 level 0.2021
> fitmap #11 inMap #1
Fit map rlnJ121_4M4_denmod_map.ccp4 in map rlnJ121_Refine3D_class001.mrc using
126338 points
correlation = 0.95, correlation about mean = 0.8475, overlap = 1154
steps = 120, shift = 5.21, angle = 10.8 degrees
Position of rlnJ121_4M4_denmod_map.ccp4 (#11) relative to
rlnJ121_Refine3D_class001.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000352 -0.00002606 0.00495430
0.00000352 1.00000000 0.00000057 -0.00839066
0.00002606 -0.00000057 1.00000000 -0.00986621
Axis -0.02174917 -0.99077855 0.13373422
Axis point 413.98145302 0.00000000 195.87419765
Rotation angle (degrees) 0.00150686
Shift along axis 0.00688608
> transparency #11.1 50
> open E:\Krios\20210423\csrelion\6221\phenix\csJ245-rsr49-coot2iso-
> cootH_real_space_refined_059.pdb format pdb
Chain information for csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb
#12
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide #9-10#!2,8,12 atoms
> hide #!2 models
> show #9-10#!8,12 cartoons
> undo
> undo
> hide #!2 models
> hide #!8 models
> hide #9 models
> hide #10 models
> select #12
14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected
> hide #!12 models
> show #!12 models
> hide #!12 models
> ~select #12
Nothing selected
> close #12
> open E:/Krios/20210423/csrelion/6221/phenix/csJ245-rsr49-coot2iso-
> cootH_real_space_refined_059.pdb
Chain information for csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb
#12
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide #!12 atoms
> show #!12 cartoons
> fitmap #12 inMap #11
Fit molecule csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb (#12) to
map rlnJ121_4M4_denmod_map.ccp4 (#11) using 14932 atoms
average map value = 0.2592, steps = 112
shifted from previous position = 0.508
rotated from previous position = 2.16 degrees
atoms outside contour = 8173, contour level = 0.2021
Position of csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb (#12)
relative to rlnJ121_4M4_denmod_map.ccp4 (#11) coordinates:
Matrix rotation and translation
0.99099463 -0.12004812 0.05931349 10.61047418
0.11207394 0.98603421 0.12319077 -30.88158629
-0.07327395 -0.11543390 0.99060888 23.45307178
Axis -0.66593181 0.37001284 0.64778493
Axis point 0.00000000 200.25653125 263.47205474
Rotation angle (degrees) 10.32118487
Shift along axis -3.29988928
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!12 models
> hide #!2 models
> show #!12 models
> open E:\Krios\20210423\csrelion\6221\phenix\csJ245-rsr49-coot2iso-
> cootH_real_space_refined_059.pdb format pdb
Chain information for csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb
#13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide #!12-13 atoms
> show #!12-13 cartoons
> show #10 models
> show #!2 models
> hide #!2 models
> show #!8 models
> matchmaker #13/A to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-Q9HC16-F1-model_v1.pdb, chain A (#10) with
csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb, chain A (#13),
sequence alignment score = 2080.4
RMSD between 363 pruned atom pairs is 0.887 angstroms; (across all 384 pairs:
1.243)
> hide #10 models
> hide #!8 models
> fitmap #13 inMap #11
Fit molecule csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb (#13) to
map rlnJ121_4M4_denmod_map.ccp4 (#11) using 14932 atoms
average map value = 0.1492, steps = 48
shifted from previous position = 0.353
rotated from previous position = 0.777 degrees
atoms outside contour = 9972, contour level = 0.2021
Position of csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb (#13)
relative to rlnJ121_4M4_denmod_map.ccp4 (#11) coordinates:
Matrix rotation and translation
-0.83671548 0.54748241 -0.01304662 191.68186460
0.54518727 0.83498616 0.07462540 -64.71580391
0.05174984 0.05532738 -0.99712629 285.05416112
Axis -0.28527083 -0.95784627 -0.03392767
Axis point 102.96142073 0.00000000 145.35994655
Rotation angle (degrees) 178.06165540
Shift along axis -2.36467641
> hide #!11 models
> show #!11 models
> select #13/A:2
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
236 atoms, 239 bonds, 13 residues, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:384
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 4 residues, 1 model selected
> select up
6377 atoms, 6485 bonds, 386 residues, 1 model selected
> style sel stick
Changed 6377 atom styles
> show sel atoms
> select clear
> select #12/A:362
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
187 atoms, 192 bonds, 13 residues, 1 model selected
> select up
6377 atoms, 6485 bonds, 386 residues, 1 model selected
> show sel atoms
> hide sel atoms
> style sel stick
Changed 6377 atom styles
> show sel atoms
> select clear
> select #12/B:125
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
146 atoms, 145 bonds, 9 residues, 1 model selected
> select up
2920 atoms, 2966 bonds, 177 residues, 1 model selected
> style sel stick
Changed 2920 atom styles
> show sel atoms
> select clear
> select #13/B:129
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
153 atoms, 155 bonds, 10 residues, 1 model selected
> select up
2920 atoms, 2966 bonds, 177 residues, 1 model selected
> style sel stick
Changed 2920 atom styles
> show sel atoms
> select #11
2 models selected
> select clear
> hide #!12-13 atoms
> save E:/Krios/20210423/csrelion/6221/model/rln121demod_modelfit.cxs
> select #1
2 models selected
> select #2
6505 atoms, 6643 bonds, 8 pseudobonds, 800 residues, 3 models selected
> select #3
3217 atoms, 3119 bonds, 5 pseudobonds, 558 residues, 3 models selected
> select #4
3132 atoms, 3120 bonds, 6 pseudobonds, 476 residues, 2 models selected
> select #1
2 models selected
> show #!1 models
> show #!2 models
> close #1
> close #2
> close #3
> close #4
> close #5
> close #6
> close #7
> close #8
> close #9
> close #10
> rename #11 id #1
> rename #12 id #2
> rename #13 id #3
> select #3/A:384
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 4 residues, 1 model selected
> select up
6377 atoms, 6485 bonds, 386 residues, 1 model selected
> select clear
> undo
> undo
> undo
> open E:\Krios\20210423\csrelion\6221\phenix\csJ245-rsr49-coot2iso-
> cootH_real_space_refined_059.pdb format pdb
Chain information for csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb
#4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide sel atoms
> show sel cartoons
> hide sel atoms
> select #4
14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected
> select #3
14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected
> select #4
14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb, chain A
(#3) with csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb, chain A
(#4), sequence alignment score = 2111
RMSD between 384 pruned atom pairs is 0.000 angstroms; (across all 384 pairs:
0.000)
> close #3
> select clear
> color #4/A #90ee90
> color #4/A yellow
> rename #4 id #3
> select clear
> select #2/A:366
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
271 atoms, 271 bonds, 17 residues, 1 model selected
> select up
6377 atoms, 6485 bonds, 386 residues, 1 model selected
> style sel stick
Changed 6377 atom styles
> show sel atoms
> color sel byhetero
> select clear
> select #3/A:4
16 atoms, 16 bonds, 1 residue, 1 model selected
> select up
236 atoms, 239 bonds, 13 residues, 1 model selected
> select up
6377 atoms, 6485 bonds, 386 residues, 1 model selected
> style sel stick
Changed 6377 atom styles
> color sel byhetero
> style sel stick
Changed 6377 atom styles
> show sel atoms
> color sel byhetero
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide atoms
> show #!1 models
> volume #1 level 0.1622
> save E:/Krios/20210423/csrelion/6221/model/rln121demod_modelfit.cxs
> includeMaps true
——— End of log from Mon Sep 13 16:42:26 2021 ———
opened ChimeraX session
> combine #2-3
Remapping chain ID 'A' in csJ245-rsr49-coot2iso-
cootH_real_space_refined_059.pdb #3 to 'F'
Remapping chain ID 'B' in csJ245-rsr49-coot2iso-
cootH_real_space_refined_059.pdb #3 to 'G'
Remapping chain ID 'C' in csJ245-rsr49-coot2iso-
cootH_real_space_refined_059.pdb #3 to 'H'
Remapping chain ID 'D' in csJ245-rsr49-coot2iso-
cootH_real_space_refined_059.pdb #3 to 'I'
Remapping chain ID 'E' in csJ245-rsr49-coot2iso-
cootH_real_space_refined_059.pdb #3 to 'J'
> molmap #4 10
Opened combination map 10 as #5, grid size 49,61,57, pixel 3.33, shown at
level 0.0733, step 1, values float32
> vop resample #5 onGrid #1
Opened combination map 10 resampled as #6, grid size 130,175,176, pixel 0.835,
shown at step 1, values float32
> close #6
> close #5
> open E:/Krios/20210423/csrelion/6221/rlnJ121_Refine3D_class001.mrc
Opened rlnJ121_Refine3D_class001.mrc as #5, grid size 352,352,352, pixel
0.835, shown at level 0.00477, step 2, values float32
> fitmap #5 inMap #1
Fit map rlnJ121_Refine3D_class001.mrc in map rlnJ121_4M4_denmod_map.ccp4 using
54491 points
correlation = 0.6593, correlation about mean = 0.8018, overlap = 139.2
steps = 128, shift = 6.12, angle = 10.8 degrees
Position of rlnJ121_Refine3D_class001.mrc (#5) relative to
rlnJ121_4M4_denmod_map.ccp4 (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00002222 -0.00006252 0.00533357
-0.00002222 1.00000000 -0.00001759 0.01355785
0.00006252 0.00001759 1.00000000 -0.01231873
Axis 0.25622251 -0.91079331 -0.32373689
Axis point 233.25028850 0.00000000 113.96071060
Rotation angle (degrees) 0.00393308
Shift along axis -0.00699380
> volume #5 level 0.005475
> volume #5 step 1
> volume #5 level 0.006832
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109060834\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 231, in set_model_color
cmd = "color #%s %s%s" % (m.id_string, color_name(rgba), target_string)
File "C:\Program Files\ChimeraX 1.3.dev202109060834\bin\lib\site-
packages\chimerax\core\colors.py", line 779, in color_name
_color_names = {rgba8:name for name, rgba8 in BuiltinColors.items()}
File "C:\Program Files\ChimeraX 1.3.dev202109060834\bin\lib\site-
packages\chimerax\core\colors.py", line 779, in <dictcomp>
_color_names = {rgba8:name for name, rgba8 in BuiltinColors.items()}
TypeError: unhashable type: 'Color'
TypeError: unhashable type: 'Color'
File "C:\Program Files\ChimeraX 1.3.dev202109060834\bin\lib\site-
packages\chimerax\core\colors.py", line 779, in
_color_names = {rgba8:name for name, rgba8 in BuiltinColors.items()}
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109060834\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 237, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
File "C:\Program Files\ChimeraX 1.3.dev202109060834\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 237, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 471.68
OpenGL renderer: NVIDIA GeForce RTX 2060 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 34,261,569,536
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('zh_TW', 'cp950')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.0
chardet: 4.0.0
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.29.1
ChimeraX-AtomicLibrary: 4.1.4
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.3
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: 1.4.1
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202109060834
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.4
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: 1.1
ChimeraX-Hbonds: 2.1.1
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.1
ChimeraX-MDcrds: 2.5
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.1
ChimeraX-ModelPanel: 1.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.1
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: 2.1
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: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.12
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.10.0
Cython: 0.29.23
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 2.11.3
jupyter-client: 6.1.12
jupyter-core: 4.7.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 1.1.1
matplotlib: 3.4.2
matplotlib-inline: 0.1.2
msgpack: 1.0.2
netCDF4: 1.5.6
networkx: 2.6.2
numexpr: 2.7.3
numpy: 1.21.0
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pickleshare: 0.7.5
Pillow: 8.2.0
pip: 21.1.1
pkginfo: 1.7.0
prompt-toolkit: 3.0.20
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.9.0
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
pywin32: 228
pyzmq: 22.2.1
qtconsole: 5.1.0
QtPy: 1.11.0
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.6.3
setuptools: 57.0.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.0.1
sphinx-autodoc-typehints: 1.12.0
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
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.0
urllib3: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.2
wheel-filename: 1.3.0
WMI: 1.5.1
Note:
See TracTickets
for help on using tickets.
