Changes between Initial Version and Version 1 of Ticket #5254


Ignore:
Timestamp:
Sep 20, 2021, 11:40:25 AM (4 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #5254

    • Property Component Unassigned → General Controls
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → 'MultiColorButton' object has no attribute 'delayed_cmd_text'

  • Ticket #5254 – Description

    initial v1  
    2626© 2016-2021 Regents of the University of California. All rights reserved. 
    2727
    28 > open E:\Krios\20210423\csrelion\6221\rlnJ121_rlnJ84_AFmodelfit.cxs format
    29 > session
    30 
    31 Opened rlnJ121_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
    32 0.835, shown at level 0.00787, step 1, values float32 
    33 Log from Fri Jul 30 02:44:06 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    34 © 2016-2021 Regents of the University of California. All rights reserved. 
    35 
    36 > open E:\Krios\20210423\csrelion\6221\rlnJ121_rlnJ84_AFmodelfit.cxs format
    37 > session
    38 
    39 Opened rlnJ031_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
    40 0.835, shown at level 0.00933, step 1, values float32 
    41 Opened rlnJ121_Refine3D_class001.mrc as #10, grid size 352,352,352, pixel
    42 0.835, shown at level 0.00933, step 1, values float32 
    43 Log from Fri Jul 30 02:27:40 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    44 © 2016-2021 Regents of the University of California. All rights reserved. 
    45 
    46 > open E:\Krios\20210423\csrelion\6221\rlnJ031_AFmodelfit.cxs format session
    47 
    48 Opened rlnJ031_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
    49 0.835, shown at level 0.00933, step 1, values float32 
    50 Log from Wed Jul 28 23:41:31 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    51 © 2016-2021 Regents of the University of California. All rights reserved. 
    52 
    53 > open E:\Krios\20210423\csrelion\6221\rlnJ031_modelfit.cxs format session
    54 
    55 Opened rlnJ031_Refine3D_class001.mrc as #1, grid size 352,352,352, pixel
    56 0.835, shown at level 0.00933, step 1, values float32 
    57 Log from Sun Jul 25 16:29:33 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    58 © 2016-2021 Regents of the University of California. All rights reserved. 
    59 
    60 > open "E:\temp\EM data\H7N100
    61 > cryoEM\20210423\20210423_6429mics\csJ200_modelfit.cxs" format session
    62 
    63 Opened cryosparc_P19_J200_004_volume_map.mrc as #1, grid size 352,352,352,
    64 pixel 0.835, shown at level 0.242, step 2, values float32 
    65 Log from Sat Jul 24 18:49:24 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    66 © 2016-2021 Regents of the University of California. All rights reserved. 
    67 
    68 > open "E:\temp\EM data\H7N100
    69 > cryoEM\20210423\20210423_6429mics\csJ200_modelfit.cxs" format session
    70 
    71 Opened cryosparc_P19_J200_004_volume_map.mrc as #1, grid size 352,352,352,
    72 pixel 0.835, shown at level 0.228, step 2, values float32 
    73 Log from Sat Jul 24 18:31:45 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    74 © 2016-2021 Regents of the University of California. All rights reserved. 
    75 
    76 > open "E:\temp\EM data\H7N100
    77 > cryoEM\20210423\20210423_6429mics\csJ200_modelfit.cxs" format session
    78 
    79 Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
    80 size 352,352,352, pixel 0.835, shown at level 0.00981, step 1, values float32 
    81 Opened cryosparc_P19_J200_004_volume_map.mrc as #6, grid size 352,352,352,
    82 pixel 0.835, shown at level 0.32, step 2, values float32 
    83 Log from Sat Jul 24 17:51:44 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    84 © 2016-2021 Regents of the University of California. All rights reserved. 
    85 
    86 > open "E:\temp\EM data\H7N100
    87 > cryoEM\20210423\20210423_6429mics\cs124_model_fit.cxs" format session
    88 
    89 Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
    90 size 352,352,352, pixel 0.835, shown at level 0.00981, step 1, values float32 
    91 Log from Sat Jun 19 22:49:00 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    92 © 2016-2021 Regents of the University of California. All rights reserved. 
    93 
    94 > open "E:\temp\EM data\H7N100
    95 > cryoEM\20210423\20210423_6429mics\cs124_model_fit.cxs" format session
    96 
    97 Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
    98 size 352,352,352, pixel 0.835, shown at level 0.0103, step 1, values float32 
    99 Log from Sat Jun 19 20:21:38 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    100 © 2016-2021 Regents of the University of California. All rights reserved. 
    101 How to cite UCSF ChimeraX 
    102 
    103 > open
    104 > E:\Krios\20210423\csrelion\cryosparc\csJ124\cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc
    105 > format mrc
    106 
    107 Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
    108 size 352,352,352, pixel 0.835, shown at level 0.00386, step 2, values float32 
    109 
    110 > volume #1 step 1
    111 
    112 > volume #1 level 0.007122
    113 
    114 > volume #1 level 0.008949
    115 
    116 > volume #1 level 0.01234
    117 
    118 > volume #1 level 0.007774
    119 
    120 > close session
    121 
    122 > open "E:\temp\EM data\H7N100
    123 > cryoEM\20210423\20210423_6429mics\NU\cryosparc_P19_J124_008_volume_map.mrc"
    124 > format mrc
    125 
    126 Opened cryosparc_P19_J124_008_volume_map.mrc as #1, grid size 352,352,352,
    127 pixel 0.835, shown at level 0.106, step 2, values float32 
    128 
    129 > volume #1 level 0.3358
    130 
    131 > open "E:/temp/EM data/4n9f.pdb1"
    132 
    133 Summary of feedback from opening E:/temp/EM data/4n9f.pdb1 
    134 --- 
    135 warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C
    136 18 GLN C 32 1 15 
    137 Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54
    138 1 19 
    139 Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82
    140 1 27 
    141 Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107
    142 1 23 
    143 Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C
    144 110 5 3 
    145 680 messages similar to the above omitted 
    146 Cannot find LINK/SSBOND residue HIS (139 ) 
    147 Cannot find LINK/SSBOND residue HIS (139 ) 
    148 Cannot find LINK/SSBOND residue CYS (114 ) 
    149 Cannot find LINK/SSBOND residue CYS (114 ) 
    150 Cannot find LINK/SSBOND residue CYS (133 ) 
    151 33 messages similar to the above omitted 
    152  
    153 4n9f.pdb1 title: 
    154 Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
    155 info...] 
    156  
    157 Chain information for 4n9f.pdb1 #2 
    158 --- 
    159 Chain | Description 
    160 U | No description available 
    161 X | No description available 
    162 Y | No description available 
    163 a | No description available 
    164 b | No description available 
    165  
    166 Non-standard residues in 4n9f.pdb1 #2 
    167 --- 
    168 ZN — zinc ion 
    169  
    170 
    171 > volume #1 level 0.1176
    172 
    173 > hide #!2 models
    174 
    175 > show #!2 models
    176 
    177 > select #2
    178 
    179 6505 atoms, 6643 bonds, 8 pseudobonds, 800 residues, 3 models selected 
    180 
    181 > ui mousemode right "translate selected models"
    182 
    183 > view matrix models #2,1,0,0,82.069,0,1,0,125.95,0,0,1,150.79
    184 
    185 > select /X:1-98
    186 
    187 748 atoms, 762 bonds, 1 pseudobond, 95 residues, 2 models selected 
    188 
    189 > sequence chain #2/X
    190 
    191 Alignment identifier is 2/X 
    192 
    193 > sequence chain #2/Y
    194 
    195 Alignment identifier is 2/Y 
    196 
    197 > sequence chain #2/a
    198 
    199 Alignment identifier is 2/a 
    200 
    201 > sequence chain #2/b
    202 
    203 Alignment identifier is 2/b 
    204 
    205 > select #2
    206 
    207 6505 atoms, 6643 bonds, 8 pseudobonds, 800 residues, 3 models selected 
    208 
    209 > select clear
    210 
    211 > style sphere
    212 
    213 Changed 6505 atom styles 
    214 
    215 > hide atoms
    216 
    217 > show cartoons
    218 
    219 > open "E:/temp/EM data/6p3x chain A.pdb" "E:/temp/EM data/6p40 chain A.pdb"
    220 
    221 Summary of feedback from opening E:/temp/EM data/6p3x chain A.pdb 
    222 --- 
    223 warnings | Cannot find LINK/SSBOND residue HIS (65 ) 
    224 Cannot find LINK/SSBOND residue CYS (97 ) 
    225 Cannot find LINK/SSBOND residue CYS (100 ) 
    226 Cannot find LINK/SSBOND residue ZN (701 ) 
    227  
    228 Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb 
    229 --- 
    230 warnings | Cannot find LINK/SSBOND residue HIS (65 ) 
    231 Cannot find LINK/SSBOND residue CYS (97 ) 
    232 Cannot find LINK/SSBOND residue CYS (100 ) 
    233 Cannot find LINK/SSBOND residue HIS (257 ) 
    234 Cannot find LINK/SSBOND residue CYS (287 ) 
    235 2 messages similar to the above omitted 
    236  
    237 6p3x chain A.pdb title: 
    238 Crystal structure of full length APOBEC3G E/Q (pH 7.0) [more info...] 
    239  
    240 Chain information for 6p3x chain A.pdb #3 
    241 --- 
    242 Chain | Description 
    243 A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G 
    244  
    245 Non-standard residues in 6p3x chain A.pdb #3 
    246 --- 
    247 ZN — zinc ion 
    248  
    249 6p40 chain A.pdb title: 
    250 Crystal structure of full length APOBEC3G FKL [more info...] 
    251  
    252 Chain information for 6p40 chain A.pdb #4 
    253 --- 
    254 Chain | Description 
    255 A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G 
    256  
    257 Non-standard residues in 6p40 chain A.pdb #4 
    258 --- 
    259 ZN — zinc ion 
    260  
    261 
    262 > hide #!3 models
    263 
    264 > show #!3 models
    265 
    266 > select #3
    267 
    268 3217 atoms, 3119 bonds, 5 pseudobonds, 558 residues, 3 models selected 
    269 
    270 > view matrix models #3,1,0,0,-46.848,0,1,0,-21.585,0,0,1,10.858
    271 
    272 > view matrix models #3,1,0,0,-48.22,0,1,0,-25.148,0,0,1,12.671
    273 
    274 > hide #!3 models
    275 
    276 > show #!3 models
    277 
    278 > ~select #3
    279 
    280 Nothing selected 
    281 
    282 > sequence chain #2/a
    283 
    284 Alignment identifier is 2/a 
    285 
    286 > select #4/A:7-382
    287 
    288 3020 atoms, 3120 bonds, 364 residues, 1 model selected 
    289 
    290 > sequence chain #4/A
    291 
    292 Alignment identifier is 4/A 
    293 
    294 > select #4/A:7-382
    295 
    296 3020 atoms, 3120 bonds, 364 residues, 1 model selected 
    297 
    298 > select #4/A:266-269
    299 
    300 40 atoms, 43 bonds, 4 residues, 1 model selected 
    301 
    302 > select #4/A:264-269
    303 
    304 56 atoms, 59 bonds, 6 residues, 1 model selected 
    305 
    306 > select #4/A:264
    307 
    308 8 atoms, 7 bonds, 1 residue, 1 model selected 
    309 
    310 > select #4/A:264
    311 
    312 8 atoms, 7 bonds, 1 residue, 1 model selected 
    313 
    314 > select clear
    315 
    316 > volume #1 level 0.3448
    317 
    318 > hide #!2 models
    319 
    320 > hide #!4 models
    321 
    322 > hide #!3 models
    323 
    324 > show #!2 models
    325 
    326 > show #!3 models
    327 
    328 > hide #!1 models
    329 
    330 > show #!1 models
    331 
    332 > hide #2/U,X,Y cartoons
    333 
    334 > hide #!3 models
    335 
    336 > ui tool show "Side View"
    337 
    338 > select #2/b:64
    339 
    340 8 atoms, 7 bonds, 1 residue, 1 model selected 
    341 
    342 > view matrix models #2,1,0,0,89.797,0,1,0,73.59,0,0,1,220.75
    343 
    344 > view matrix models #2,1,0,0,105.3,0,1,0,141.33,0,0,1,219.37
    345 
    346 > view matrix models #2,1,0,0,89.879,0,1,0,100.16,0,0,1,218.31
    347 
    348 > view matrix models #2,1,0,0,95.388,0,1,0,87.113,0,0,1,217.57
    349 
    350 > view matrix models
    351 > #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
    352 
    353 > view matrix models
    354 > #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
    355 
    356 > view matrix models
    357 > #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
    358 
    359 > hide #!2 models
    360 
    361 > show #!3 models
    362 
    363 > hide #!3 models
    364 
    365 > show #!4 models
    366 
    367 > hide #!4 models
    368 
    369 > show #!3 models
    370 
    371 > select #3/A:282
    372 
    373 7 atoms, 6 bonds, 1 residue, 1 model selected 
    374 
    375 > view matrix models #3,1,0,0,75.338,0,1,0,83.713,0,0,1,32.568
    376 
    377 > view matrix models #3,1,0,0,76.767,0,1,0,90.212,0,0,1,41.682
    378 
    379 > view matrix models
    380 > #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
    381 
    382 > view matrix models
    383 > #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
    384 
    385 > view matrix models
    386 > #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
    387 
    388 > view matrix models
    389 > #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
    390 
    391 > view matrix models
    392 > #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
    393 
    394 > view matrix models
    395 > #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
    396 
    397 > view matrix models
    398 > #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
    399 
    400 > view matrix models
    401 > #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
    402 
    403 > view matrix models
    404 > #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
    405 
    406 > view matrix models
    407 > #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
    408 
    409 > select #3/A:4-383
    410 
    411 3021 atoms, 3119 bonds, 1 pseudobond, 362 residues, 2 models selected 
    412 
    413 > sequence chain #3/A
    414 
    415 Alignment identifier is 3/A 
    416 
    417 > select #3/A:148
    418 
    419 7 atoms, 6 bonds, 1 residue, 1 model selected 
    420 
    421 > select #3/A:148-187
    422 
    423 343 atoms, 355 bonds, 40 residues, 1 model selected 
    424 
    425 > select #3/A:4-8
    426 
    427 44 atoms, 43 bonds, 5 residues, 1 model selected 
    428 
    429 > select #3/A:383
    430 
    431 9 atoms, 8 bonds, 1 residue, 1 model selected 
    432 
    433 > select #3/A:208-383
    434 
    435 1351 atoms, 1390 bonds, 1 pseudobond, 162 residues, 2 models selected 
    436 
    437 > select #3/A:194
    438 
    439 11 atoms, 10 bonds, 1 residue, 1 model selected 
    440 
    441 > select #3/A:194-198
    442 
    443 45 atoms, 45 bonds, 5 residues, 1 model selected 
    444 
    445 > select clear
    446 
    447 > hide #3/A:199-379
    448 
    449 > show #3/A:199-379
    450 
    451 > hide #3/A:199-379
    452 
    453 > hide #3/A:199-379 cartoons
    454 
    455 > sequence chain #3/A
    456 
    457 Alignment identifier is 3/A 
    458 
    459 > hide #3/A:198-385 cartoons
    460 
    461 > ui mousemode right "translate selected models"
    462 
    463 > select #3
    464 
    465 3217 atoms, 3119 bonds, 5 pseudobonds, 558 residues, 3 models selected 
    466 
    467 > view matrix models
    468 > #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
    469 
    470 > view matrix models
    471 > #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
    472 
    473 > view matrix models
    474 > #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
    475 
    476 > view matrix models
    477 > #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
    478 
    479 > view matrix models
    480 > #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
    481 
    482 > view matrix models
    483 > #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
    484 
    485 > view matrix models
    486 > #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
    487 
    488 > view matrix models
    489 > #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
    490 
    491 > select clear
    492 
    493 > volume #1 level 0.2431
    494 
    495 > select #3/A:55
    496 
    497 9 atoms, 8 bonds, 1 residue, 1 model selected 
    498 
    499 > view matrix models
    500 > #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
    501 
    502 > view matrix models
    503 > #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
    504 
    505 > view matrix models
    506 > #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
    507 
    508 > show #!2 models
    509 
    510 > view matrix models
    511 > #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
    512 
    513 > hide #!2 models
    514 
    515 > hide #!3 models
    516 
    517 > volume #1 level 0.2831
    518 
    519 > symclip 15
    520 
    521 Unknown command: symclip 15 
    522 
    523 > ui mousemode right clip
    524 
    525 > ui mousemode right clip
    526 
    527 > select #1
    528 
    529 3 models selected 
    530 
    531 > select #1
    532 
    533 3 models selected 
    534 
    535 > select clear
    536 
    537 > select #1
    538 
    539 3 models selected 
    540 
    541 > select clear
    542 
    543 > ui mousemode right "clip rotate"
    544 
    545 > ui mousemode right clip
    546 
    547 > ui mousemode right zone
    548 
    549 > ui mousemode right "contour level"
    550 
    551 > volume #1 level 0.2765
    552 
    553 > ui mousemode right "move planes"
    554 
    555 > volume #1 region 0,0,0,351,351,351
    556 
    557 > volume #1 region 0,0,0,351,351,351
    558 
    559 > volume #1 region 0,0,0,351,351,351
    560 
    561 > select #1
    562 
    563 3 models selected 
    564 
    565 > volume #1 region 0,0,0,351,351,351
    566 
    567 > select clear
    568 
    569 > show #!2 models
    570 
    571 > hide #!2 models
    572 
    573 > show #!3 models
    574 
    575 > volume #1 region 0,0,0,351,351,351
    576 
    577 > select clear
    578 
    579 > select #3/A:118
    580 
    581 8 atoms, 7 bonds, 1 residue, 1 model selected 
    582 
    583 > volume #1 region 0,0,0,351,351,351
    584 
    585 > ui mousemode right "translate selected models"
    586 
    587 > view matrix models
    588 > #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
    589 
    590 > view matrix models
    591 > #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
    592 
    593 > hide #!1 models
    594 
    595 > view matrix models
    596 > #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
    597 
    598 > view matrix models
    599 > #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
    600 
    601 > view matrix models
    602 > #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
    603 
    604 > view matrix models
    605 > #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
    606 
    607 > view matrix models
    608 > #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
    609 
    610 > view matrix models
    611 > #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
    612 
    613 > view matrix models
    614 > #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
    615 
    616 > view matrix models
    617 > #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
    618 
    619 > view matrix models
    620 > #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
    621 
    622 > view matrix models
    623 > #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
    624 
    625 > view matrix models
    626 > #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
    627 
    628 > view matrix models
    629 > #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
    630 
    631 > view matrix models
    632 > #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
    633 
    634 > view matrix models
    635 > #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
    636 
    637 > show #!1 models
    638 
    639 > hide #!1 models
    640 
    641 > show #!1 models
    642 
    643 > hide #!1 models
    644 
    645 > view matrix models
    646 > #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
    647 
    648 > show #!1 models
    649 
    650 > hide #!1 models
    651 
    652 > show #!1 models
    653 
    654 > hide #!1 models
    655 
    656 > view matrix models
    657 > #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
    658 
    659 > show #!1 models
    660 
    661 > hide #!1 models
    662 
    663 > show #!1 models
    664 
    665 > hide #!1 models
    666 
    667 > show #!1 models
    668 
    669 > view matrix models
    670 > #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
    671 
    672 > view matrix models
    673 > #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
    674 
    675 > view matrix models
    676 > #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
    677 
    678 > view matrix models
    679 > #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
    680 
    681 > view matrix models
    682 > #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
    683 
    684 > view matrix models
    685 > #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
    686 
    687 > view matrix models
    688 > #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
    689 
    690 > view matrix models
    691 > #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
    692 
    693 > view matrix models
    694 > #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
    695 
    696 > view matrix models
    697 > #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
    698 
    699 > view matrix models
    700 > #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
    701 
    702 > view matrix models
    703 > #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
    704 
    705 > view matrix models
    706 > #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
    707 
    708 > view matrix models
    709 > #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
    710 
    711 > view matrix models
    712 > #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
    713 
    714 > view matrix models
    715 > #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
    716 
    717 > view matrix models
    718 > #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
    719 
    720 > view matrix models
    721 > #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
    722 
    723 > view matrix models
    724 > #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
    725 
    726 > view matrix models
    727 > #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
    728 
    729 > view matrix models
    730 > #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
    731 
    732 > view matrix models
    733 > #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
    734 
    735 > view matrix models
    736 > #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
    737 
    738 > fitmap #3 inMap #1
    739 
    740 Fit molecule 6p3x chain A.pdb (#3) to map
    741 cryosparc_P19_J124_008_volume_map.mrc (#1) using 3217 atoms 
    742 average map value = 0.1892, steps = 132 
    743 shifted from previous position = 2.04 
    744 rotated from previous position = 5.82 degrees 
    745 atoms outside contour = 2206, contour level = 0.27648 
    746  
    747 Position of 6p3x chain A.pdb (#3) relative to
    748 cryosparc_P19_J124_008_volume_map.mrc (#1) coordinates: 
    749 Matrix rotation and translation 
    750 -0.87034826 0.22874541 -0.43608420 140.10276575 
    751 0.03062042 0.90898975 0.41569220 100.13842757 
    752 0.49148375 0.34844390 -0.79814193 101.03676319 
    753 Axis -0.07072275 -0.97549160 -0.20836129 
    754 Axis point 56.79793799 0.00000000 56.80721198 
    755 Rotation angle (degrees) 151.61224811 
    756 Shift along axis -128.64479799 
    757  
    758 
    759 > volume #1 level 0.4892
    760 
    761 > volume #1 level 0.2179
    762 
    763 > show #3/A
    764 
    765 > hide #3/A
    766 
    767 > show #3/A cartoons
    768 
    769 > hide #3/A 199-385 cartoon
    770 
    771 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    772 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    773 
    774 > hide #3/A:199-385 cartoons
    775 
    776 > hide #!1 models
    777 
    778 > show #!1 models
    779 
    780 > show #3/A:199-385 cartoons
    781 
    782 > hide #3/A:1-199 cartoons
    783 
    784 > select #3/A:372
    785 
    786 4 atoms, 3 bonds, 1 residue, 1 model selected 
    787 
    788 > view matrix models
    789 > #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
    790 
    791 > view matrix models
    792 > #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
    793 
    794 > view matrix models
    795 > #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
    796 
    797 > view matrix models
    798 > #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
    799 
    800 > view matrix models
    801 > #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
    802 
    803 > view matrix models
    804 > #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
    805 
    806 > view matrix models
    807 > #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
    808 
    809 > view matrix models
    810 > #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
    811 
    812 > view matrix models
    813 > #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
    814 
    815 > view matrix models
    816 > #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
    817 
    818 > view matrix models
    819 > #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
    820 
    821 > view matrix models
    822 > #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
    823 
    824 > view matrix models
    825 > #3,-0.61477,-0.52766,0.5862,123.05,-0.73143,0.6595,-0.17344,123,-0.29508,-0.53538,-0.79139,121.91
    826 
    827 > view matrix models
    828 > #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
    829 
    830 > view matrix models
    831 > #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
    832 
    833 > view matrix models
    834 > #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
    835 
    836 > view matrix models
    837 > #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
    838 
    839 > view matrix models
    840 > #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
    841 
    842 > view matrix models
    843 > #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
    844 
    845 > view matrix models
    846 > #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
    847 
    848 > view matrix models
    849 > #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
    850 
    851 > view matrix models
    852 > #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
    853 
    854 > view matrix models
    855 > #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
    856 
    857 > view matrix models
    858 > #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
    859 
    860 > view matrix models
    861 > #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
    862 
    863 > view matrix models
    864 > #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
    865 
    866 > view matrix models
    867 > #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
    868 
    869 > view matrix models
    870 > #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
    871 
    872 > view matrix models
    873 > #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
    874 
    875 > view matrix models
    876 > #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
    877 
    878 > view matrix models
    879 > #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
    880 
    881 > view matrix models
    882 > #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
    883 
    884 > view matrix models
    885 > #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
    886 
    887 > view matrix models
    888 > #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
    889 
    890 > view matrix models
    891 > #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
    892 
    893 > view matrix models
    894 > #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
    895 
    896 > view matrix models
    897 > #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
    898 
    899 > view matrix models
    900 > #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
    901 
    902 > view matrix models
    903 > #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
    904 
    905 > view matrix models
    906 > #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
    907 
    908 > view matrix models
    909 > #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
    910 
    911 > view matrix models
    912 > #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
    913 
    914 > view matrix models
    915 > #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
    916 
    917 > view matrix models
    918 > #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
    919 
    920 > view matrix models
    921 > #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
    922 
    923 > view matrix models
    924 > #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
    925 
    926 > view matrix models
    927 > #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
    928 
    929 > view matrix models
    930 > #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
    931 
    932 > view matrix models
    933 > #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
    934 
    935 > view matrix models
    936 > #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
    937 
    938 > view matrix models
    939 > #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
    940 
    941 > view matrix models
    942 > #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
    943 
    944 > view matrix models
    945 > #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
    946 
    947 > view matrix models
    948 > #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
    949 
    950 > show #3/A cartoons
    951 
    952 > view matrix models
    953 > #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
    954 
    955 > select clear
    956 
    957 > hide #!3 models
    958 
    959 > show #!4 models
    960 
    961 > select clear
    962 
    963 > select #4/A:69
    964 
    965 11 atoms, 10 bonds, 1 residue, 1 model selected 
    966 
    967 > view matrix models #4,1,0,0,5.7691,0,1,0,135.5,0,0,1,82.984
    968 
    969 > sequence chain #4/A
    970 
    971 Alignment identifier is 4/A 
    972 
    973 > select #4/A:131
    974 
    975 12 atoms, 12 bonds, 1 residue, 1 model selected 
    976 
    977 > select #1
    978 
    979 3 models selected 
    980 
    981 > select #1
    982 
    983 3 models selected 
    984 
    985 > select clear
    986 
    987 > select #4/A:196
    988 
    989 8 atoms, 7 bonds, 1 residue, 1 model selected 
    990 
    991 > hide #4/A:1-193 cartoons
    992 
    993 > hide #4/A:1-193
    994 
    995 > hide #4/A:1-193
    996 
    997 > select :ZN
    998 
    999 4 atoms, 4 residues, 3 models selected 
    1000 
    1001 > hide (#!4 & sel) target a
    1002 
    1003 > select #4/A:260
    1004 
    1005 8 atoms, 7 bonds, 1 residue, 1 model selected 
    1006 
    1007 > view matrix models #4,1,0,0,20.725,0,1,0,110.33,0,0,1,62.54
    1008 
    1009 > view matrix models #4,1,0,0,19.578,0,1,0,113.48,0,0,1,63.698
    1010 
    1011 > view matrix models #4,1,0,0,85.757,0,1,0,76.546,0,0,1,67.665
    1012 
    1013 > view matrix models #4,1,0,0,98.303,0,1,0,115.37,0,0,1,85.361
    1014 
    1015 > hide #!1 models
    1016 
    1017 > show #!1 models
    1018 
    1019 > hide #!4 models
    1020 
    1021 > show #!4 models
    1022 
    1023 > hide #!4 models
    1024 
    1025 > show #!4 models
    1026 
    1027 > hide #!4 models
    1028 
    1029 > show #!4 models
    1030 
    1031 > hide #!1 models
    1032 
    1033 > show #!1 models
    1034 
    1035 > view matrix models #4,1,0,0,98.72,0,1,0,116.97,0,0,1,87.661
    1036 
    1037 > view matrix models #4,1,0,0,96.89,0,1,0,111.5,0,0,1,86.719
    1038 
    1039 > view matrix models
    1040 > #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
    1041 
    1042 > view matrix models
    1043 > #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
    1044 
    1045 > view matrix models
    1046 > #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
    1047 
    1048 > view matrix models
    1049 > #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
    1050 
    1051 > view matrix models
    1052 > #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
    1053 
    1054 > view matrix models
    1055 > #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
    1056 
    1057 > view matrix models
    1058 > #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
    1059 
    1060 > view matrix models
    1061 > #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
    1062 
    1063 > view matrix models
    1064 > #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
    1065 
    1066 > view matrix models
    1067 > #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
    1068 
    1069 > view matrix models
    1070 > #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
    1071 
    1072 > ui mousemode right pivot
    1073 
    1074 > ui mousemode right "rotate selected models"
    1075 
    1076 > view matrix models
    1077 > #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
    1078 
    1079 > view matrix models
    1080 > #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
    1081 
    1082 > view matrix models
    1083 > #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
    1084 
    1085 > view matrix models
    1086 > #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
    1087 
    1088 > ui mousemode right "translate selected models"
    1089 
    1090 > view matrix models
    1091 > #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
    1092 
    1093 > view matrix models
    1094 > #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
    1095 
    1096 > view matrix models
    1097 > #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
    1098 
    1099 > view matrix models
    1100 > #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
    1101 
    1102 > view matrix models
    1103 > #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
    1104 
    1105 > view matrix models
    1106 > #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
    1107 
    1108 > ui mousemode right "rotate selected models"
    1109 
    1110 > view matrix models
    1111 > #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
    1112 
    1113 > view matrix models
    1114 > #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
    1115 
    1116 > view matrix models
    1117 > #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
    1118 
    1119 > view matrix models
    1120 > #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
    1121 
    1122 > view matrix models
    1123 > #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
    1124 
    1125 > view matrix models
    1126 > #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
    1127 
    1128 > view matrix models
    1129 > #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
    1130 
    1131 > view matrix models
    1132 > #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
    1133 
    1134 > view matrix models
    1135 > #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
    1136 
    1137 > view matrix models
    1138 > #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
    1139 
    1140 > view matrix models
    1141 > #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
    1142 
    1143 > view matrix models
    1144 > #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
    1145 
    1146 > view matrix models
    1147 > #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
    1148 
    1149 > view matrix models
    1150 > #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
    1151 
    1152 > view matrix models
    1153 > #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
    1154 
    1155 > view matrix models
    1156 > #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
    1157 
    1158 > view matrix models
    1159 > #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
    1160 
    1161 > view matrix models
    1162 > #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
    1163 
    1164 > view matrix models
    1165 > #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
    1166 
    1167 > view matrix models
    1168 > #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
    1169 
    1170 > view matrix models
    1171 > #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
    1172 
    1173 > view matrix models
    1174 > #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
    1175 
    1176 > view matrix models
    1177 > #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
    1178 
    1179 > view matrix models
    1180 > #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
    1181 
    1182 > view matrix models
    1183 > #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
    1184 
    1185 > view matrix models
    1186 > #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
    1187 
    1188 > view matrix models
    1189 > #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
    1190 
    1191 > view matrix models
    1192 > #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
    1193 
    1194 > view matrix models
    1195 > #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
    1196 
    1197 > view matrix models
    1198 > #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
    1199 
    1200 > view matrix models
    1201 > #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
    1202 
    1203 > view matrix models
    1204 > #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
    1205 
    1206 > view matrix models
    1207 > #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
    1208 
    1209 > view matrix models
    1210 > #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
    1211 
    1212 > view matrix models
    1213 > #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
    1214 
    1215 > view matrix models
    1216 > #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
    1217 
    1218 > view matrix models
    1219 > #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
    1220 
    1221 > view matrix models
    1222 > #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
    1223 
    1224 > view matrix models
    1225 > #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
    1226 
    1227 > ui mousemode right "translate selected models"
    1228 
    1229 > view matrix models
    1230 > #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
    1231 
    1232 > view matrix models
    1233 > #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
    1234 
    1235 > view matrix models
    1236 > #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
    1237 
    1238 > view matrix models
    1239 > #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
    1240 
    1241 > view matrix models
    1242 > #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
    1243 
    1244 > view matrix models
    1245 > #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
    1246 
    1247 > view matrix models
    1248 > #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
    1249 
    1250 > view matrix models
    1251 > #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
    1252 
    1253 > view matrix models
    1254 > #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
    1255 
    1256 > view matrix models
    1257 > #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
    1258 
    1259 > ui mousemode right "translate selected models"
    1260 
    1261 > ui mousemode right pivot
    1262 
    1263 > ui mousemode right pivot
    1264 
    1265 > ui mousemode right "rotate selected models"
    1266 
    1267 > ui mousemode right "rotate selected models"
    1268 
    1269 > ui mousemode right "translate selected models"
    1270 
    1271 > view matrix models
    1272 > #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
    1273 
    1274 > view matrix models
    1275 > #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
    1276 
    1277 > view matrix models
    1278 > #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
    1279 
    1280 > view matrix models
    1281 > #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
    1282 
    1283 > view matrix models
    1284 > #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
    1285 
    1286 > view matrix models
    1287 > #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
    1288 
    1289 > volume #1 level 0.3412
    1290 
    1291 > volume #1 level 0.2395
    1292 
    1293 > volume #1 level 0.3474
    1294 
    1295 > fitmap #4 inMap #1
    1296 
    1297 Fit molecule 6p40 chain A.pdb (#4) to map
    1298 cryosparc_P19_J124_008_volume_map.mrc (#1) using 3132 atoms 
    1299 average map value = 0.3205, steps = 188 
    1300 shifted from previous position = 1.7 
    1301 rotated from previous position = 5.56 degrees 
    1302 atoms outside contour = 1869, contour level = 0.34738 
    1303  
    1304 Position of 6p40 chain A.pdb (#4) relative to
    1305 cryosparc_P19_J124_008_volume_map.mrc (#1) coordinates: 
    1306 Matrix rotation and translation 
    1307 -0.09632366 -0.11183472 0.98904740 126.78830237 
    1308 0.29836042 0.94473137 0.13588119 100.70294195 
    1309 -0.94958033 0.30818117 -0.05763293 141.62014053 
    1310 Axis 0.08662530 0.97466179 0.20622914 
    1311 Axis point 111.15167207 0.00000000 7.13181171 
    1312 Rotation angle (degrees) 96.00484764 
    1313 Shift along axis 138.34058390 
    1314  
    1315 
    1316 > show #4/A cartoons
    1317 
    1318 > view matrix models
    1319 > #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
    1320 
    1321 > undo
    1322 
    1323 > show #4/A:1-193 cartoons
    1324 
    1325 > hide #4/A:1-193 cartoons
    1326 
    1327 > volume #1 level 0.2241
    1328 
    1329 > show #4/A:1-193 cartoons
    1330 
    1331 > hide #!1 models
    1332 
    1333 > show #!1 models
    1334 
    1335 > hide #!1 models
    1336 
    1337 > show #!1 models
    1338 
    1339 > hide #!1 models
    1340 
    1341 > show #!1 models
    1342 
    1343 > delete #4/A:1-193 cartoon
    1344 
    1345 Expected a keyword 
    1346 
    1347 > delete #4/A:1-193
    1348 
    1349 > rename #3 "6p3x chain A.pdb" " 6p3x_chainA_CTD.pdb"
    1350 
    1351 Expected a keyword 
    1352 
    1353 > rename #3 " 6p3x_chainA_CTD.pdb"
    1354 
    1355 > select clear
    1356 
    1357 > rename #3 6p3x_chainA_CTD.pdb
    1358 
    1359 > show #!3 models
    1360 
    1361 > select #3/A:288
    1362 
    1363 11 atoms, 11 bonds, 1 residue, 1 model selected 
    1364 
    1365 > view matrix models
    1366 > #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
    1367 
    1368 > ui mousemode right clip
    1369 
    1370 > ui mousemode right clip
    1371 
    1372 > ui mousemode right "translate selected models"
    1373 
    1374 > show #!3 target m
    1375 
    1376 > view matrix models
    1377 > #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
    1378 
    1379 > view matrix models
    1380 > #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
    1381 
    1382 > rename #3 " 6p3x.pdb"
    1383 
    1384 > rename #4 6p40_chainA_CTD
    1385 
    1386 > hide #3/A:199-385
    1387 
    1388 > hide #3/A:199-385 cartoons
    1389 
    1390 > volume #1 level 0.3196
    1391 
    1392 > select #3/A:116
    1393 
    1394 8 atoms, 7 bonds, 1 residue, 1 model selected 
    1395 
    1396 > view matrix models
    1397 > #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
    1398 
    1399 > view matrix models
    1400 > #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
    1401 
    1402 > view matrix models
    1403 > #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
    1404 
    1405 > view matrix models
    1406 > #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
    1407 
    1408 > view matrix models
    1409 > #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
    1410 
    1411 > view matrix models
    1412 > #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
    1413 
    1414 > view matrix models
    1415 > #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
    1416 
    1417 > view matrix models
    1418 > #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
    1419 
    1420 > view matrix models
    1421 > #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
    1422 
    1423 > view matrix models
    1424 > #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
    1425 
    1426 > view matrix models
    1427 > #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
    1428 
    1429 > view matrix models
    1430 > #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
    1431 
    1432 > view matrix models
    1433 > #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
    1434 
    1435 > view matrix models
    1436 > #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
    1437 
    1438 > view matrix models
    1439 > #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
    1440 
    1441 > view matrix models
    1442 > #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
    1443 
    1444 > view matrix models
    1445 > #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
    1446 
    1447 > view matrix models
    1448 > #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
    1449 
    1450 > view matrix models
    1451 > #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
    1452 
    1453 > view matrix models
    1454 > #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
    1455 
    1456 > view matrix models
    1457 > #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
    1458 
    1459 > view matrix models
    1460 > #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
    1461 
    1462 > view matrix models
    1463 > #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
    1464 
    1465 > view matrix models
    1466 > #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
    1467 
    1468 > fitmap #4 inMap #1
    1469 
    1470 Fit molecule 6p40_chainA_CTD (#4) to map cryosparc_P19_J124_008_volume_map.mrc
    1471 (#1) using 1608 atoms 
    1472 average map value = 0.4261, steps = 36 
    1473 shifted from previous position = 0.106 
    1474 rotated from previous position = 1.81 degrees 
    1475 atoms outside contour = 601, contour level = 0.31964 
    1476  
    1477 Position of 6p40_chainA_CTD (#4) relative to
    1478 cryosparc_P19_J124_008_volume_map.mrc (#1) coordinates: 
    1479 Matrix rotation and translation 
    1480 -0.09424100 -0.08860480 0.99159862 126.65111036 
    1481 0.32043160 0.94032897 0.11447723 100.39182267 
    1482 -0.94257213 0.32852798 -0.06022576 141.43387263 
    1483 Axis 0.10764416 0.97267671 0.20570065 
    1484 Axis point 109.73439823 0.00000000 8.60764028 
    1485 Rotation angle (degrees) 96.14637790 
    1486 Shift along axis 140.37507882 
    1487  
    1488 
    1489 > hide #!1 models
    1490 
    1491 > show #!1 models
    1492 
    1493 > hide #!1 models
    1494 
    1495 > show #!1 models
    1496 
    1497 > volume #1 level 0.3813
    1498 
    1499 > view matrix models
    1500 > #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
    1501 
    1502 > view matrix models
    1503 > #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
    1504 
    1505 > view matrix models
    1506 > #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
    1507 
    1508 > view matrix models
    1509 > #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
    1510 
    1511 > volume #1 level 0.4676
    1512 
    1513 > view matrix models
    1514 > #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
    1515 
    1516 > view matrix models
    1517 > #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
    1518 
    1519 > view matrix models
    1520 > #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
    1521 
    1522 > view matrix models
    1523 > #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
    1524 
    1525 > view matrix models
    1526 > #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
    1527 
    1528 > view matrix models
    1529 > #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
    1530 
    1531 > view matrix models
    1532 > #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
    1533 
    1534 > view matrix models
    1535 > #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
    1536 
    1537 > view matrix models
    1538 > #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
    1539 
    1540 > view matrix models
    1541 > #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
    1542 
    1543 > view matrix models
    1544 > #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
    1545 
    1546 > view matrix models
    1547 > #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
    1548 
    1549 > view matrix models
    1550 > #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
    1551 
    1552 > view matrix models
    1553 > #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
    1554 
    1555 > view matrix models
    1556 > #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
    1557 
    1558 > view matrix models
    1559 > #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
    1560 
    1561 > volume #1 level 0.3351
    1562 
    1563 > view matrix models
    1564 > #3,0.13875,0.76546,0.62835,143.69,0.82494,-0.44038,0.35431,141,0.54792,0.46919,-0.69256,130.02
    1565 
    1566 > view matrix models
    1567 > #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
    1568 
    1569 > ui mousemode right pivot
    1570 
    1571 > ui mousemode right "translate selected models"
    1572 
    1573 > fitmap #3 inMap #1
    1574 
    1575 Fit molecule 6p3x.pdb (#3) to map cryosparc_P19_J124_008_volume_map.mrc (#1)
    1576 using 3217 atoms 
    1577 average map value = 0.192, steps = 160 
    1578 shifted from previous position = 8.69 
    1579 rotated from previous position = 12.3 degrees 
    1580 atoms outside contour = 2689, contour level = 0.33505 
    1581  
    1582 Position of 6p3x.pdb (#3) relative to cryosparc_P19_J124_008_volume_map.mrc
    1583 (#1) coordinates: 
    1584 Matrix rotation and translation 
    1585 -0.04625472 0.71117713 0.70148951 138.58865988 
    1586 0.79678835 -0.39727665 0.45530158 139.60943198 
    1587 0.60248549 0.57999854 -0.54828174 127.24998494 
    1588 Axis 0.68978239 0.54765757 0.47357305 
    1589 Axis point 0.00000000 14.22234683 16.45706034 
    1590 Rotation angle (degrees) 174.81403565 
    1591 Shift along axis 232.31634352 
    1592  
    1593 
    1594 > view matrix models
    1595 > #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
    1596 
    1597 > undo
    1598 
    1599 > view matrix models
    1600 > #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
    1601 
    1602 > undo
    1603 
    1604 > select clear
    1605 
    1606 > volume #1 level 0.2302
    1607 
    1608 > select #3/A:57
    1609 
    1610 9 atoms, 8 bonds, 1 residue, 1 model selected 
    1611 
    1612 > view matrix models
    1613 > #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
    1614 
    1615 > volume showOutlineBox true
    1616 
    1617 > volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
    1618 > 0,0,1 tiltedSlabOffset 147 tiltedSlabSpacing 0.835 tiltedSlabPlaneCount 10
    1619 
    1620 > mousemode rightMode "rotate slab"
    1621 
    1622 > volume region all imageMode "full region"
    1623 
    1624 > volume unzone
    1625 
    1626 > mousemode rightMode "crop volume"
    1627 
    1628 > volume planes z style image imageMode "full region"
    1629 
    1630 > mousemode rightMode "move planes"
    1631 
    1632 > volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
    1633 > 0,0,1 tiltedSlabOffset 147 tiltedSlabSpacing 0.835 tiltedSlabPlaneCount 10
    1634 
    1635 > mousemode rightMode "rotate slab"
    1636 
    1637 > volume showOutlineBox false
    1638 
    1639 > volume zone #1 nearAtoms sel & #3 range 5.01
    1640 
    1641 > volume region all imageMode "full region"
    1642 
    1643 > volume unzone
    1644 
    1645 > mousemode rightMode "crop volume"
    1646 
    1647 > volume #1 orthoplanes xyz positionPlanes 176,176,176 style image region all
    1648 
    1649 > mousemode rightMode "move planes"
    1650 
    1651 > volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
    1652 > 0,0,1 tiltedSlabOffset 147 tiltedSlabSpacing 0.835 tiltedSlabPlaneCount 10
    1653 
    1654 > mousemode rightMode "rotate slab"
    1655 
    1656 > volume planes z style image imageMode "full region"
    1657 
    1658 > mousemode rightMode "move planes"
    1659 
    1660 > volume show
    1661 
    1662 > volume showOutlineBox false
    1663 
    1664 > volume region all imageMode "full region"
    1665 
    1666 > volume unzone
    1667 
    1668 > mousemode rightMode "crop volume"
    1669 
    1670 > volume region all imageMode "full region"
    1671 
    1672 > volume unzone
    1673 
    1674 > mousemode rightMode "crop volume"
    1675 
    1676 > volume style surface
    1677 
    1678 > volume showOutlineBox true
    1679 
    1680 > preset "initial styles" "original look"
    1681 
    1682 Preset implemented in Python; no expansion to individual ChimeraX commands
    1683 available. 
    1684 
    1685 > close session
    1686 
    1687 > open
    1688 > E:\Krios\20210423\csrelion\cryosparc\csJ124\cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc
    1689 > format mrc
    1690 
    1691 Opened cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc as #1, grid
    1692 size 352,352,352, pixel 0.835, shown at level 0.00386, step 2, values float32 
    1693 
    1694 > volume all step 1
    1695 
    1696 > volume #1 level 0.007905
    1697 
    1698 > open "E:/temp/EM data/4n9f.pdb1"
    1699 
    1700 Summary of feedback from opening E:/temp/EM data/4n9f.pdb1 
    1701 --- 
    1702 warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C
    1703 18 GLN C 32 1 15 
    1704 Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54
    1705 1 19 
    1706 Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82
    1707 1 27 
    1708 Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107
    1709 1 23 
    1710 Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C
    1711 110 5 3 
    1712 680 messages similar to the above omitted 
    1713 Cannot find LINK/SSBOND residue HIS (139 ) 
    1714 Cannot find LINK/SSBOND residue HIS (139 ) 
    1715 Cannot find LINK/SSBOND residue CYS (114 ) 
    1716 Cannot find LINK/SSBOND residue CYS (114 ) 
    1717 Cannot find LINK/SSBOND residue CYS (133 ) 
    1718 33 messages similar to the above omitted 
    1719  
    1720 4n9f.pdb1 title: 
    1721 Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
    1722 info...] 
    1723  
    1724 Chain information for 4n9f.pdb1 #2 
    1725 --- 
    1726 Chain | Description 
    1727 U | No description available 
    1728 X | No description available 
    1729 Y | No description available 
    1730 a | No description available 
    1731 b | No description available 
    1732  
    1733 Non-standard residues in 4n9f.pdb1 #2 
    1734 --- 
    1735 ZN — zinc ion 
    1736  
    1737 
    1738 > open "E:/temp/EM data/6p3x chain A.pdb" "E:/temp/EM data/6p40 chain A.pdb"
    1739 
    1740 Summary of feedback from opening E:/temp/EM data/6p3x chain A.pdb 
    1741 --- 
    1742 warnings | Cannot find LINK/SSBOND residue HIS (65 ) 
    1743 Cannot find LINK/SSBOND residue CYS (97 ) 
    1744 Cannot find LINK/SSBOND residue CYS (100 ) 
    1745 Cannot find LINK/SSBOND residue ZN (701 ) 
    1746  
    1747 Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb 
    1748 --- 
    1749 warnings | Cannot find LINK/SSBOND residue HIS (65 ) 
    1750 Cannot find LINK/SSBOND residue CYS (97 ) 
    1751 Cannot find LINK/SSBOND residue CYS (100 ) 
    1752 Cannot find LINK/SSBOND residue HIS (257 ) 
    1753 Cannot find LINK/SSBOND residue CYS (287 ) 
    1754 2 messages similar to the above omitted 
    1755  
    1756 6p3x chain A.pdb title: 
    1757 Crystal structure of full length APOBEC3G E/Q (pH 7.0) [more info...] 
    1758  
    1759 Chain information for 6p3x chain A.pdb #3 
    1760 --- 
    1761 Chain | Description 
    1762 A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G 
    1763  
    1764 Non-standard residues in 6p3x chain A.pdb #3 
    1765 --- 
    1766 ZN — zinc ion 
    1767  
    1768 6p40 chain A.pdb title: 
    1769 Crystal structure of full length APOBEC3G FKL [more info...] 
    1770  
    1771 Chain information for 6p40 chain A.pdb #4 
    1772 --- 
    1773 Chain | Description 
    1774 A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G 
    1775  
    1776 Non-standard residues in 6p40 chain A.pdb #4 
    1777 --- 
    1778 ZN — zinc ion 
    1779  
    1780 
    1781 > select #2/X:86@CA
    1782 
    1783 1 atom, 1 residue, 1 model selected 
    1784 
    1785 > ui mousemode right "translate selected models"
    1786 
    1787 > view matrix models #2,1,0,0,23.182,0,1,0,318.2,0,0,1,272.71
    1788 
    1789 > select clear
    1790 
    1791 > hide #!1 models
    1792 
    1793 > show #!1 models
    1794 
    1795 > hide #!2 models
    1796 
    1797 > select #4/A:98
    1798 
    1799 7 atoms, 6 bonds, 1 residue, 1 model selected 
    1800 
    1801 > view matrix models #4,1,0,0,3.3218,0,1,0,55.036,0,0,1,117.25
    1802 
    1803 > select clear
    1804 
    1805 > select #3/A:154
    1806 
    1807 12 atoms, 12 bonds, 1 residue, 1 model selected 
    1808 
    1809 > view matrix models #3,1,0,0,3.1774,0,1,0,48.702,0,0,1,79.52
    1810 
    1811 > hide #!3 models
    1812 
    1813 > select clear
    1814 
    1815 > select #1
    1816 
    1817 2 models selected 
    1818 
    1819 > cofr frontCenter
    1820 
    1821 > select clear
    1822 
    1823 > hide #4/A:1-193
    1824 
    1825 > hide #4/A:1-193 cartoons
    1826 
    1827 > select clear
    1828 
    1829 > select #4/A:309
    1830 
    1831 11 atoms, 11 bonds, 1 residue, 1 model selected 
    1832 
    1833 > view matrix models #4,1,0,0,8.4012,0,1,0,90.59,0,0,1,92.374
    1834 
    1835 > view matrix models
    1836 > #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
    1837 
    1838 > view matrix models
    1839 > #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
    1840 
    1841 > view matrix models
    1842 > #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
    1843 
    1844 > view matrix models
    1845 > #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
    1846 
    1847 > view matrix models
    1848 > #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
    1849 
    1850 > view matrix models
    1851 > #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
    1852 
    1853 > view matrix models
    1854 > #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
    1855 
    1856 > view matrix models
    1857 > #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
    1858 
    1859 > view matrix models
    1860 > #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
    1861 
    1862 > view matrix models
    1863 > #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
    1864 
    1865 > view matrix models
    1866 > #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
    1867 
    1868 > view matrix models
    1869 > #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
    1870 
    1871 > ui tool show "Side View"
    1872 
    1873 > view matrix models
    1874 > #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
    1875 
    1876 > view matrix models
    1877 > #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
    1878 
    1879 > view matrix models
    1880 > #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
    1881 
    1882 > view matrix models
    1883 > #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
    1884 
    1885 > view matrix models
    1886 > #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
    1887 
    1888 > view matrix models
    1889 > #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
    1890 
    1891 > view matrix models
    1892 > #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
    1893 
    1894 > view matrix models
    1895 > #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
    1896 
    1897 > view matrix models
    1898 > #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
    1899 
    1900 > view matrix models
    1901 > #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
    1902 
    1903 > view matrix models
    1904 > #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
    1905 
    1906 > view matrix models
    1907 > #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
    1908 
    1909 > volume #1 color #b2b2b2b2
    1910 
    1911 > view matrix models
    1912 > #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
    1913 
    1914 > view matrix models
    1915 > #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
    1916 
    1917 > view matrix models
    1918 > #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
    1919 
    1920 > view matrix models
    1921 > #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
    1922 
    1923 > view matrix models
    1924 > #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
    1925 
    1926 > view matrix models
    1927 > #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
    1928 
    1929 > view matrix models
    1930 > #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
    1931 
    1932 > volume #1 level 0.01813
    1933 
    1934 > view matrix models
    1935 > #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
    1936 
    1937 > view matrix models
    1938 > #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
    1939 
    1940 > view matrix models
    1941 > #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
    1942 
    1943 > view matrix models
    1944 > #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
    1945 
    1946 > view matrix models
    1947 > #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
    1948 
    1949 > view matrix models
    1950 > #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
    1951 
    1952 > view matrix models
    1953 > #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
    1954 
    1955 > view matrix models
    1956 > #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
    1957 
    1958 > view matrix models
    1959 > #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
    1960 
    1961 > view matrix models
    1962 > #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
    1963 
    1964 > view matrix models
    1965 > #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
    1966 
    1967 > view matrix models
    1968 > #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
    1969 
    1970 > view matrix models
    1971 > #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
    1972 
    1973 > fitmap #4 inMap #1
    1974 
    1975 Fit molecule 6p40 chain A.pdb (#4) to map
    1976 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    1977 average map value = 0.01186, steps = 260 
    1978 shifted from previous position = 11.9 
    1979 rotated from previous position = 24.6 degrees 
    1980 atoms outside contour = 2247, contour level = 0.018135 
    1981  
    1982 Position of 6p40 chain A.pdb (#4) relative to
    1983 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    1984 Matrix rotation and translation 
    1985 -0.09942338 -0.10883602 0.98907518 126.88557243 
    1986 0.30042237 0.94433074 0.13411135 100.65968289 
    1987 -0.94861024 0.31047412 -0.06119178 141.64964253 
    1988 Axis 0.08870158 0.97455807 0.20583634 
    1989 Axis point 110.93643823 0.00000000 7.44799256 
    1990 Rotation angle (degrees) 96.20823350 
    1991 Shift along axis 138.51030041 
    1992  
    1993 
    1994 > view matrix models
    1995 > #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
    1996 
    1997 > undo
    1998 
    1999 > select clear
    2000 
    2001 > show #4
    2002 
    2003 > hide #4
    2004 
    2005 > show #4/A:1-193
    2006 
    2007 > hide #4/A:1-193
    2008 
    2009 > show #4/A:1-193 cartoons
    2010 
    2011 > hide #!1 models
    2012 
    2013 > show #!1 models
    2014 
    2015 > hide #!1 models
    2016 
    2017 > show #!1 models
    2018 
    2019 > hide #!1 models
    2020 
    2021 > show #!1 models
    2022 
    2023 > hide #!1 models
    2024 
    2025 > show #!1 models
    2026 
    2027 > hide #!1 models
    2028 
    2029 > show #!1 models
    2030 
    2031 > hide #!1 models
    2032 
    2033 > show #!1 models
    2034 
    2035 > hide #!1 models
    2036 
    2037 > show #!1 models
    2038 
    2039 > hide #!1 models
    2040 
    2041 > show #!1 models
    2042 
    2043 > hide #!1 models
    2044 
    2045 > show #!1 models
    2046 
    2047 > hide #!1 models
    2048 
    2049 > show #!1 models
    2050 
    2051 > hide #!1 models
    2052 
    2053 > show #!1 models
    2054 
    2055 > hide #!1 models
    2056 
    2057 > show #!1 models
    2058 
    2059 > hide #!1 models
    2060 
    2061 > show #!1 models
    2062 
    2063 > hide #!1 models
    2064 
    2065 > show #!1 models
    2066 
    2067 > hide #!1 models
    2068 
    2069 > show #!1 models
    2070 
    2071 > hide #!1 models
    2072 
    2073 > show #!1 models
    2074 
    2075 > hide #!1 models
    2076 
    2077 > show #!1 models
    2078 
    2079 > hide #!1 models
    2080 
    2081 > sequence chain #4/A
    2082 
    2083 Alignment identifier is 4/A 
    2084 
    2085 > select #4/A:194
    2086 
    2087 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2088 
    2089 > select #4/A:194-198
    2090 
    2091 45 atoms, 45 bonds, 5 residues, 1 model selected 
    2092 
    2093 > select clear
    2094 
    2095 > select #4/A:199
    2096 
    2097 7 atoms, 7 bonds, 1 residue, 1 model selected 
    2098 
    2099 > select #4/A:199-206
    2100 
    2101 61 atoms, 63 bonds, 8 residues, 1 model selected 
    2102 
    2103 > select clear
    2104 
    2105 > select clear
    2106 
    2107 > select #4/A:193-194
    2108 
    2109 19 atoms, 18 bonds, 2 residues, 1 model selected 
    2110 
    2111 > select #4/A:177-194
    2112 
    2113 141 atoms, 143 bonds, 18 residues, 1 model selected 
    2114 
    2115 > show #!1 models
    2116 
    2117 > show #!3 models
    2118 
    2119 > hide #!3 models
    2120 
    2121 > show #!3 models
    2122 
    2123 > select clear
    2124 
    2125 > select #3/A:117
    2126 
    2127 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2128 
    2129 > view matrix models #3,1,0,0,94.733,0,1,0,73.438,0,0,1,123.72
    2130 
    2131 > hide #3/A:199-385 cartoons
    2132 
    2133 > select clear
    2134 
    2135 > select #3/A:99
    2136 
    2137 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2138 
    2139 > view matrix models #3,1,0,0,122.56,0,1,0,72.784,0,0,1,156.89
    2140 
    2141 > view matrix models #3,1,0,0,120.08,0,1,0,71.527,0,0,1,156.42
    2142 
    2143 > view matrix models
    2144 > #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
    2145 
    2146 > view matrix models
    2147 > #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
    2148 
    2149 > view matrix models
    2150 > #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
    2151 
    2152 > view matrix models
    2153 > #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
    2154 
    2155 > view matrix models
    2156 > #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
    2157 
    2158 > view matrix models
    2159 > #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
    2160 
    2161 > hide #!1 models
    2162 
    2163 > view matrix models
    2164 > #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
    2165 
    2166 > view matrix models
    2167 > #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
    2168 
    2169 > view matrix models
    2170 > #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
    2171 
    2172 > view matrix models
    2173 > #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
    2174 
    2175 > view matrix models
    2176 > #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
    2177 
    2178 > view matrix models
    2179 > #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
    2180 
    2181 > view matrix models
    2182 > #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
    2183 
    2184 > view matrix models
    2185 > #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
    2186 
    2187 > view matrix models
    2188 > #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
    2189 
    2190 > view matrix models
    2191 > #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
    2192 
    2193 > view matrix models
    2194 > #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
    2195 
    2196 > view matrix models
    2197 > #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
    2198 
    2199 > view matrix models
    2200 > #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
    2201 
    2202 > view matrix models
    2203 > #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
    2204 
    2205 > view matrix models
    2206 > #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
    2207 
    2208 > view matrix models
    2209 > #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
    2210 
    2211 > view matrix models
    2212 > #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
    2213 
    2214 > view matrix models
    2215 > #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
    2216 
    2217 > view matrix models
    2218 > #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
    2219 
    2220 > view matrix models
    2221 > #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
    2222 
    2223 > view matrix models
    2224 > #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
    2225 
    2226 > view matrix models
    2227 > #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
    2228 
    2229 > show #!1 models
    2230 
    2231 > hide #!3 models
    2232 
    2233 > show #!3 models
    2234 
    2235 > hide #!4 models
    2236 
    2237 > show #!4 models
    2238 
    2239 > hide #!4 models
    2240 
    2241 > show #!4 models
    2242 
    2243 > hide #!4 models
    2244 
    2245 > show #!4 models
    2246 
    2247 > select clear
    2248 
    2249 > show #3/A cartoons
    2250 
    2251 > ui tool show Matchmaker
    2252 
    2253 > matchmaker #!3 to #4
    2254 
    2255 Parameters 
    2256 --- 
    2257 Chain pairing | bb 
    2258 Alignment algorithm | Needleman-Wunsch 
    2259 Similarity matrix | BLOSUM-62 
    2260 SS fraction | 0.3 
    2261 Gap open (HH/SS/other) | 18/18/6 
    2262 Gap extend | 1 
    2263 SS matrix |  |  | H | S | O 
    2264 ---|---|---|--- 
    2265 H | 6 | -9 | -6 
    2266 S |  | 6 | -6 
    2267 O |  |  | 4 
    2268 Iteration cutoff | 2 
    2269  
    2270 Matchmaker 6p40 chain A.pdb, chain A (#4) with 6p3x chain A.pdb, chain A (#3),
    2271 sequence alignment score = 1956 
    2272 RMSD between 106 pruned atom pairs is 0.426 angstroms; (across all 358 pairs:
    2273 6.515) 
    2274  
    2275 
    2276 > select #3/A:376
    2277 
    2278 5 atoms, 4 bonds, 1 residue, 1 model selected 
    2279 
    2280 > view matrix models
    2281 > #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
    2282 
    2283 > view matrix models
    2284 > #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
    2285 
    2286 > view matrix models
    2287 > #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
    2288 
    2289 > view matrix models
    2290 > #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
    2291 
    2292 > hide #!3 models
    2293 
    2294 > show #!3 models
    2295 
    2296 > hide #!3 models
    2297 
    2298 > hide #!4 models
    2299 
    2300 > show #!4 models
    2301 
    2302 > hide #!4 models
    2303 
    2304 > show #!4 models
    2305 
    2306 > hide #!4 models
    2307 
    2308 > show #!4 models
    2309 
    2310 > hide #!4 models
    2311 
    2312 > show #!4 models
    2313 
    2314 > hide #4/A:1-193 cartoons
    2315 
    2316 > show #!3 models
    2317 
    2318 > view matrix models
    2319 > #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
    2320 
    2321 > view matrix models
    2322 > #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
    2323 
    2324 > view matrix models
    2325 > #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
    2326 
    2327 > view matrix models
    2328 > #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
    2329 
    2330 > view matrix models
    2331 > #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
    2332 
    2333 > view matrix models
    2334 > #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
    2335 
    2336 > view matrix models
    2337 > #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
    2338 
    2339 > view matrix models
    2340 > #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
    2341 
    2342 > view matrix models
    2343 > #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
    2344 
    2345 > view matrix models
    2346 > #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
    2347 
    2348 > view matrix models
    2349 > #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
    2350 
    2351 > view matrix models
    2352 > #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
    2353 
    2354 > select #3/A:119
    2355 
    2356 11 atoms, 11 bonds, 1 residue, 1 model selected 
    2357 
    2358 > view matrix models
    2359 > #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
    2360 
    2361 > view matrix models
    2362 > #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
    2363 
    2364 > view matrix models
    2365 > #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
    2366 
    2367 > view matrix models
    2368 > #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
    2369 
    2370 > view matrix models
    2371 > #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
    2372 
    2373 > hide #3/A:199-385 cartoons
    2374 
    2375 > view matrix models
    2376 > #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
    2377 
    2378 > view matrix models
    2379 > #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
    2380 
    2381 > view matrix models
    2382 > #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
    2383 
    2384 > view matrix models
    2385 > #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
    2386 
    2387 > hide #!1 models
    2388 
    2389 > show #!1 models
    2390 
    2391 > hide #!3 models
    2392 
    2393 > show #!3 models
    2394 
    2395 > hide #!3 models
    2396 
    2397 > show #!3 models
    2398 
    2399 > hide #!3 models
    2400 
    2401 > show #!3 models
    2402 
    2403 > hide #!3 models
    2404 
    2405 > show #!3 models
    2406 
    2407 > view matrix models
    2408 > #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
    2409 
    2410 > view matrix models
    2411 > #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
    2412 
    2413 > view matrix models
    2414 > #3,0.86766,-0.39403,0.30316,161.77,0.18515,0.82203,0.5385,117.92,-0.46139,-0.41111,0.7862,147
    2415 
    2416 > view matrix models
    2417 > #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
    2418 
    2419 > view matrix models
    2420 > #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
    2421 
    2422 > view matrix models
    2423 > #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
    2424 
    2425 > hide #!1 models
    2426 
    2427 > show #!1 models
    2428 
    2429 > hide #!1 models
    2430 
    2431 > hide #!3 models
    2432 
    2433 > show #!1 models
    2434 
    2435 > hide #!1 models
    2436 
    2437 > show #!1 models
    2438 
    2439 > show #!3 models
    2440 
    2441 > hide #!3 models
    2442 
    2443 > show #!3 models
    2444 
    2445 > hide #!3 models
    2446 
    2447 > show #!3 models
    2448 
    2449 > hide #!3 models
    2450 
    2451 > show #!3 models
    2452 
    2453 > hide #!3 models
    2454 
    2455 > show #!3 models
    2456 
    2457 > hide #!3 models
    2458 
    2459 > show #!3 models
    2460 
    2461 > volume #1 level 0.0215
    2462 
    2463 > hide #!3 models
    2464 
    2465 > show #!3 models
    2466 
    2467 > hide #!3 models
    2468 
    2469 > show #!3 models
    2470 
    2471 > hide #!3 models
    2472 
    2473 > show #!3 models
    2474 
    2475 > hide #!3 models
    2476 
    2477 > show #!3 models
    2478 
    2479 > hide #!3 models
    2480 
    2481 > show #!3 models
    2482 
    2483 > hide #!3 models
    2484 
    2485 > show #!3 models
    2486 
    2487 > hide #!3 models
    2488 
    2489 > show #!3 models
    2490 
    2491 > hide #!3 models
    2492 
    2493 > show #!3 models
    2494 
    2495 > hide #!3 models
    2496 
    2497 > show #!3 models
    2498 
    2499 > view matrix models
    2500 > #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
    2501 
    2502 > view matrix models
    2503 > #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
    2504 
    2505 > view matrix models
    2506 > #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
    2507 
    2508 > view matrix models
    2509 > #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
    2510 
    2511 > view matrix models
    2512 > #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
    2513 
    2514 > view matrix models
    2515 > #3,0.93814,0.0687,0.33939,154,-0.25549,0.79888,0.54453,119.15,-0.23372,-0.59755,0.76701,149.64
    2516 
    2517 > view matrix models
    2518 > #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
    2519 
    2520 > view matrix models
    2521 > #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
    2522 
    2523 > view matrix models
    2524 > #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
    2525 
    2526 > view matrix models
    2527 > #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
    2528 
    2529 > view matrix models
    2530 > #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
    2531 
    2532 > view matrix models
    2533 > #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
    2534 
    2535 > hide #!1 models
    2536 
    2537 > show #!1 models
    2538 
    2539 > hide #!1 models
    2540 
    2541 > show #!1 models
    2542 
    2543 > hide #!3 models
    2544 
    2545 > show #!3 models
    2546 
    2547 > hide #!3 models
    2548 
    2549 > show #!3 models
    2550 
    2551 > hide #!3 models
    2552 
    2553 > show #!3 models
    2554 
    2555 > hide #!3 models
    2556 
    2557 > show #!3 models
    2558 
    2559 > hide #!3 models
    2560 
    2561 > show #!3 models
    2562 
    2563 > hide #!3 models
    2564 
    2565 > show #!3 models
    2566 
    2567 > hide #!3 models
    2568 
    2569 > show #!3 models
    2570 
    2571 > hide #!3 models
    2572 
    2573 > show #!3 models
    2574 
    2575 > view matrix models
    2576 > #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
    2577 
    2578 > hide #!1 models
    2579 
    2580 > show #!1 models
    2581 
    2582 > hide #!1 models
    2583 
    2584 > show #!1 models
    2585 
    2586 > hide #!1 models
    2587 
    2588 > show #!1 models
    2589 
    2590 > hide #!1 models
    2591 
    2592 > show #!1 models
    2593 
    2594 > hide #!1 models
    2595 
    2596 > show #!1 models
    2597 
    2598 > hide #!1 models
    2599 
    2600 > show #!1 models
    2601 
    2602 > hide #!1 models
    2603 
    2604 > show #!1 models
    2605 
    2606 > hide #!3 models
    2607 
    2608 > show #!3 models
    2609 
    2610 > volume #1 level 0.01275
    2611 
    2612 > view matrix models
    2613 > #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
    2614 
    2615 > view matrix models
    2616 > #3,0.85311,0.04477,0.5198,138,-0.35735,0.77606,0.51965,88.958,-0.38013,-0.62907,0.67806,190.24
    2617 
    2618 > view matrix models
    2619 > #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
    2620 
    2621 > view matrix models
    2622 > #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
    2623 
    2624 > view matrix models
    2625 > #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
    2626 
    2627 > view matrix models
    2628 > #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
    2629 
    2630 > view matrix models
    2631 > #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
    2632 
    2633 > view matrix models
    2634 > #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
    2635 
    2636 > view matrix models
    2637 > #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
    2638 
    2639 > view matrix models
    2640 > #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
    2641 
    2642 > view matrix models
    2643 > #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
    2644 
    2645 > view matrix models
    2646 > #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
    2647 
    2648 > view matrix models
    2649 > #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
    2650 
    2651 > volume #1 level 0.01369
    2652 
    2653 > view matrix models
    2654 > #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
    2655 
    2656 > view matrix models
    2657 > #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
    2658 
    2659 > view matrix models
    2660 > #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
    2661 
    2662 > view matrix models
    2663 > #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
    2664 
    2665 > view matrix models
    2666 > #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
    2667 
    2668 > view matrix models
    2669 > #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
    2670 
    2671 > view matrix models
    2672 > #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
    2673 
    2674 > view matrix models
    2675 > #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
    2676 
    2677 > view matrix models
    2678 > #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
    2679 
    2680 > view matrix models
    2681 > #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
    2682 
    2683 > view matrix models
    2684 > #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
    2685 
    2686 > hide #!3 models
    2687 
    2688 > show #!2 models
    2689 
    2690 > select #2/U:211@CA
    2691 
    2692 1 atom, 1 residue, 1 model selected 
    2693 
    2694 > select up
    2695 
    2696 9 atoms, 8 bonds, 1 residue, 1 model selected 
    2697 
    2698 > select up
    2699 
    2700 217 atoms, 222 bonds, 25 residues, 1 model selected 
    2701 
    2702 > select up
    2703 
    2704 2458 atoms, 2503 bonds, 299 residues, 1 model selected 
    2705 
    2706 > select up
    2707 
    2708 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    2709 
    2710 > select up
    2711 
    2712 12854 atoms, 12882 bonds, 1834 residues, 5 models selected 
    2713 
    2714 > select down
    2715 
    2716 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    2717 
    2718 > select down
    2719 
    2720 2458 atoms, 2503 bonds, 299 residues, 1 model selected 
    2721 
    2722 > select up
    2723 
    2724 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    2725 
    2726 > hide sel atoms
    2727 
    2728 > show sel cartoons
    2729 
    2730 > view matrix models #2,1,0,0,59.404,0,1,0,307.52,0,0,1,319.68
    2731 
    2732 > select clear
    2733 
    2734 > hide #1/U
    2735 
    2736 > hide #1/U cartoons
    2737 
    2738 > hide #2/U cartoons
    2739 
    2740 > select #2/a:11
    2741 
    2742 9 atoms, 8 bonds, 1 residue, 1 model selected 
    2743 
    2744 > view matrix models #2,1,0,0,69.647,0,1,0,222.66,0,0,1,297.93
    2745 
    2746 > hide #2/X cartoons
    2747 
    2748 > hide #2/Y cartoons
    2749 
    2750 > view matrix models
    2751 > #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
    2752 
    2753 > view matrix models
    2754 > #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
    2755 
    2756 > view matrix models
    2757 > #2,0.24908,0.55945,0.79056,189.87,-0.95292,0.28734,0.096893,252,-0.17295,-0.77747,0.60468,247.11
    2758 
    2759 > view matrix models
    2760 > #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
    2761 
    2762 > view matrix models
    2763 > #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
    2764 
    2765 > view matrix models
    2766 > #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
    2767 
    2768 > view matrix models
    2769 > #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
    2770 
    2771 > view matrix models
    2772 > #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
    2773 
    2774 > view matrix models
    2775 > #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
    2776 
    2777 > view matrix models
    2778 > #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
    2779 
    2780 > view matrix models
    2781 > #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
    2782 
    2783 > view matrix models
    2784 > #2,-0.076382,0.034955,0.99647,212,-0.99438,0.070847,-0.078707,230.83,-0.073348,-0.99687,0.029347,179.44
    2785 
    2786 > view matrix models
    2787 > #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
    2788 
    2789 > view matrix models
    2790 > #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
    2791 
    2792 > view matrix models
    2793 > #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
    2794 
    2795 > view matrix models
    2796 > #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
    2797 
    2798 > view matrix models
    2799 > #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
    2800 
    2801 > view matrix models
    2802 > #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
    2803 
    2804 > view matrix models
    2805 > #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
    2806 
    2807 > view matrix models
    2808 > #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
    2809 
    2810 > view matrix models
    2811 > #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
    2812 
    2813 > view matrix models
    2814 > #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
    2815 
    2816 > view matrix models
    2817 > #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
    2818 
    2819 > select #2/b:56
    2820 
    2821 10 atoms, 10 bonds, 1 residue, 1 model selected 
    2822 
    2823 > view matrix models
    2824 > #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
    2825 
    2826 > view matrix models
    2827 > #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
    2828 
    2829 > view matrix models
    2830 > #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
    2831 
    2832 > view matrix models
    2833 > #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
    2834 
    2835 > hide #!1 models
    2836 
    2837 > show #!1 models
    2838 
    2839 > view matrix models
    2840 > #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
    2841 
    2842 > view matrix models
    2843 > #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
    2844 
    2845 > view matrix models
    2846 > #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
    2847 
    2848 > hide #2 in #1
    2849 
    2850 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    2851 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    2852 
    2853 > fitmap #2 inMap #1
    2854 
    2855 Fit molecule 4n9f.pdb1 (#2) to map
    2856 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 6505 atoms 
    2857 average map value = 0.005801, steps = 528 
    2858 shifted from previous position = 35.8 
    2859 rotated from previous position = 55.5 degrees 
    2860 atoms outside contour = 5780, contour level = 0.013693 
    2861  
    2862 Position of 4n9f.pdb1 (#2) relative to
    2863 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    2864 Matrix rotation and translation 
    2865 -0.83838368 -0.45272076 -0.30357325 135.40362195 
    2866 0.52740414 -0.53306399 -0.66157966 58.16653402 
    2867 0.13768688 -0.71476339 0.68567896 171.11823917 
    2868 Axis -0.04941855 -0.41002085 0.91073636 
    2869 Axis point 54.78447409 90.30072860 0.00000000 
    2870 Rotation angle (degrees) 147.44596587 
    2871 Shift along axis 125.30265982 
    2872  
    2873 
    2874 > view matrix models
    2875 > #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
    2876 
    2877 > view matrix models
    2878 > #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
    2879 
    2880 > volume #1 level 0.01585
    2881 
    2882 > view matrix models
    2883 > #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
    2884 
    2885 > view matrix models
    2886 > #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
    2887 
    2888 > view matrix models
    2889 > #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
    2890 
    2891 > view matrix models
    2892 > #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
    2893 
    2894 > view matrix models
    2895 > #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
    2896 
    2897 > view matrix models
    2898 > #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
    2899 
    2900 > view matrix models
    2901 > #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
    2902 
    2903 > select #2/a:110
    2904 
    2905 14 atoms, 15 bonds, 1 residue, 1 model selected 
    2906 
    2907 > view matrix models
    2908 > #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
    2909 
    2910 > view matrix models
    2911 > #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
    2912 
    2913 > view matrix models
    2914 > #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
    2915 
    2916 > view matrix models
    2917 > #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
    2918 
    2919 > view matrix models
    2920 > #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
    2921 
    2922 > volume #1 level 0.01154
    2923 
    2924 > view matrix models
    2925 > #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
    2926 
    2927 > view matrix models
    2928 > #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
    2929 
    2930 > view matrix models
    2931 > #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
    2932 
    2933 > view matrix models
    2934 > #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
    2935 
    2936 > view matrix models
    2937 > #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
    2938 
    2939 > view matrix models
    2940 > #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
    2941 
    2942 > view matrix models
    2943 > #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
    2944 
    2945 > view matrix models
    2946 > #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
    2947 
    2948 > view matrix models
    2949 > #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
    2950 
    2951 > view matrix models
    2952 > #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
    2953 
    2954 > view matrix models
    2955 > #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
    2956 
    2957 > view matrix models
    2958 > #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
    2959 
    2960 > view matrix models
    2961 > #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
    2962 
    2963 > view matrix models
    2964 > #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
    2965 
    2966 > view matrix models
    2967 > #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
    2968 
    2969 > view matrix models
    2970 > #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
    2971 
    2972 > fitmap #2 inMap #1
    2973 
    2974 Fit molecule 4n9f.pdb1 (#2) to map
    2975 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 6505 atoms 
    2976 average map value = 0.008435, steps = 276 
    2977 shifted from previous position = 3.27 
    2978 rotated from previous position = 18.4 degrees 
    2979 atoms outside contour = 4572, contour level = 0.011539 
    2980  
    2981 Position of 4n9f.pdb1 (#2) relative to
    2982 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    2983 Matrix rotation and translation 
    2984 -0.86210944 0.04634696 -0.50459814 121.08378739 
    2985 -0.48309421 -0.37571105 0.79086105 256.46393677 
    2986 -0.15292909 0.92557721 0.34629399 181.29939549 
    2987 Axis 0.20734706 -0.54126795 -0.81488417 
    2988 Axis point 95.38342485 50.06260965 0.00000000 
    2989 Rotation angle (degrees) 161.04310620 
    2990 Shift along axis -261.44734942 
    2991  
    2992 
    2993 > volume #1 level 0.0176
    2994 
    2995 > volume #1 level 0.01006
    2996 
    2997 > volume #1 level 0.01383
    2998 
    2999 > volume #1 level 0.00952
    3000 
    3001 > show #2/X cartoons
    3002 
    3003 > show #2/Y cartoons
    3004 
    3005 > show #2/U cartoons
    3006 
    3007 > hide #2/U cartoons
    3008 
    3009 > save "E:/temp/EM data/H7N100
    3010 > cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs" includeMaps true
    3011 
    3012 > show #!3 models
    3013 
    3014 > select #3/A:89
    3015 
    3016 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3017 
    3018 > view matrix models
    3019 > #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
    3020 
    3021 > fitmap #4 inMap 1
    3022 
    3023 Invalid "inMap" argument: invalid density map specifier 
    3024 
    3025 > fitmap #3 inMap 1
    3026 
    3027 Invalid "inMap" argument: invalid density map specifier 
    3028 
    3029 > fitmap #3 inMap #1
    3030 
    3031 Fit molecule 6p3x chain A.pdb (#3) to map
    3032 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3217 atoms 
    3033 average map value = 0.008294, steps = 204 
    3034 shifted from previous position = 17.8 
    3035 rotated from previous position = 27.3 degrees 
    3036 atoms outside contour = 2141, contour level = 0.0095201 
    3037  
    3038 Position of 6p3x chain A.pdb (#3) relative to
    3039 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3040 Matrix rotation and translation 
    3041 0.18841124 0.92270990 0.33631475 135.59194946 
    3042 -0.29077977 -0.27468104 0.91651374 144.88041801 
    3043 0.93805561 -0.27047501 0.21655239 137.19934917 
    3044 Axis -0.65907300 -0.33411534 -0.67378759 
    3045 Axis point 32.34542504 45.93828833 0.00000000 
    3046 Rotation angle (degrees) 115.77630371 
    3047 Shift along axis -230.21498245 
    3048  
    3049 
    3050 > hide #!3 models
    3051 
    3052 > show #!3 models
    3053 
    3054 > hide #!3 models
    3055 
    3056 > show #!3 models
    3057 
    3058 > view matrix models
    3059 > #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
    3060 
    3061 > rename #4 "6p40_chain A_CTD"
    3062 
    3063 > open "E:/temp/EM data/6p40 chain A.pdb"
    3064 
    3065 Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb 
    3066 --- 
    3067 warnings | Cannot find LINK/SSBOND residue HIS (65 ) 
    3068 Cannot find LINK/SSBOND residue CYS (97 ) 
    3069 Cannot find LINK/SSBOND residue CYS (100 ) 
    3070 Cannot find LINK/SSBOND residue HIS (257 ) 
    3071 Cannot find LINK/SSBOND residue CYS (287 ) 
    3072 2 messages similar to the above omitted 
    3073  
    3074 6p40 chain A.pdb title: 
    3075 Crystal structure of full length APOBEC3G FKL [more info...] 
    3076  
    3077 Chain information for 6p40 chain A.pdb #5 
    3078 --- 
    3079 Chain | Description 
    3080 A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G 
    3081  
    3082 Non-standard residues in 6p40 chain A.pdb #5 
    3083 --- 
    3084 ZN — zinc ion 
    3085  
    3086 
    3087 > select clear
    3088 
    3089 > select #5/A:39
    3090 
    3091 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3092 
    3093 > view matrix models #5,1,0,0,-88.501,0,1,0,149.38,0,0,1,61.559
    3094 
    3095 > hide #!3 models
    3096 
    3097 > view matrix models #5,1,0,0,-53.472,0,1,0,87.818,0,0,1,38.736
    3098 
    3099 > view matrix models #5,1,0,0,117.04,0,1,0,69.92,0,0,1,98.468
    3100 
    3101 > select #5/A:289
    3102 
    3103 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3104 
    3105 > select up
    3106 
    3107 107 atoms, 108 bonds, 14 residues, 1 model selected 
    3108 
    3109 > select up
    3110 
    3111 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    3112 
    3113 > hide sel atoms
    3114 
    3115 > show sel atoms
    3116 
    3117 > hide sel atoms
    3118 
    3119 > hide sel cartoons
    3120 
    3121 > show #5/A:1-193
    3122 
    3123 > hide sel atoms
    3124 
    3125 > show #5/A:1-193 cartoons
    3126 
    3127 > select clear
    3128 
    3129 > select #5/A:188
    3130 
    3131 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3132 
    3133 > view matrix models #5,1,0,0,120.61,0,1,0,52.455,0,0,1,103.79
    3134 
    3135 > view matrix models #5,1,0,0,121.87,0,1,0,49.895,0,0,1,114.31
    3136 
    3137 > view matrix models #5,1,0,0,121.58,0,1,0,50.772,0,0,1,112.56
    3138 
    3139 > view matrix models #5,1,0,0,159.96,0,1,0,97.317,0,0,1,104.95
    3140 
    3141 > view matrix models #5,1,0,0,159.4,0,1,0,62.841,0,0,1,122.43
    3142 
    3143 > view matrix models
    3144 > #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
    3145 
    3146 > view matrix models
    3147 > #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
    3148 
    3149 > view matrix models
    3150 > #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
    3151 
    3152 > view matrix models
    3153 > #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
    3154 
    3155 > view matrix models
    3156 > #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
    3157 
    3158 > view matrix models
    3159 > #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
    3160 
    3161 > view matrix models
    3162 > #5,0.98695,-0.13728,0.084164,158,0.15962,0.76517,-0.62373,88.471,0.021228,0.62902,0.7771,122.92
    3163 
    3164 > view matrix models
    3165 > #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
    3166 
    3167 > view matrix models
    3168 > #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
    3169 
    3170 > view matrix models
    3171 > #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
    3172 
    3173 > view matrix models
    3174 > #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
    3175 
    3176 > view matrix models
    3177 > #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
    3178 
    3179 > view matrix models
    3180 > #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
    3181 
    3182 > view matrix models
    3183 > #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
    3184 
    3185 > view matrix models
    3186 > #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
    3187 
    3188 > select clear
    3189 
    3190 > select #5/A:131
    3191 
    3192 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3193 
    3194 > select #5/A:28
    3195 
    3196 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3197 
    3198 > view matrix models
    3199 > #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
    3200 
    3201 > view matrix models
    3202 > #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
    3203 
    3204 > hide #!1 models
    3205 
    3206 > show #!1 models
    3207 
    3208 > hide #!5 models
    3209 
    3210 > show #!5 models
    3211 
    3212 > hide #!5 models
    3213 
    3214 > show #!5 models
    3215 
    3216 > hide #!5 models
    3217 
    3218 > show #!5 models
    3219 
    3220 > view matrix models
    3221 > #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
    3222 
    3223 > view matrix models
    3224 > #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
    3225 
    3226 > view matrix models
    3227 > #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
    3228 
    3229 > hide #!1 models
    3230 
    3231 > show #!1 models
    3232 
    3233 > hide #!5 models
    3234 
    3235 > show #!5 models
    3236 
    3237 > view matrix models
    3238 > #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
    3239 
    3240 > view matrix models
    3241 > #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
    3242 
    3243 > view matrix models
    3244 > #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
    3245 
    3246 > view matrix models
    3247 > #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
    3248 
    3249 > view matrix models
    3250 > #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
    3251 
    3252 > view matrix models
    3253 > #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
    3254 
    3255 > view matrix models
    3256 > #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
    3257 
    3258 > view matrix models
    3259 > #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
    3260 
    3261 > fitmap #5 inMap #1
    3262 
    3263 Fit molecule 6p40 chain A.pdb (#5) to map
    3264 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3265 average map value = 0.008075, steps = 352 
    3266 shifted from previous position = 12.9 
    3267 rotated from previous position = 24.1 degrees 
    3268 atoms outside contour = 2114, contour level = 0.0095201 
    3269  
    3270 Position of 6p40 chain A.pdb (#5) relative to
    3271 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3272 Matrix rotation and translation 
    3273 0.41748274 0.84548911 -0.33295095 137.00714521 
    3274 0.23756556 -0.45522148 -0.85810024 170.21429376 
    3275 -0.87708083 0.27914436 -0.39090620 152.53901710 
    3276 Axis 0.81253034 0.38876600 -0.43434485 
    3277 Axis point 0.00000000 1.87532898 144.78306158 
    3278 Rotation angle (degrees) 135.58770064 
    3279 Shift along axis 111.24145600 
    3280  
    3281 
    3282 > hide #!5 models
    3283 
    3284 > show #!5 models
    3285 
    3286 > hide #!5 models
    3287 
    3288 > show #!5 models
    3289 
    3290 > view matrix models
    3291 > #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
    3292 
    3293 > view matrix models
    3294 > #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
    3295 
    3296 > view matrix models
    3297 > #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
    3298 
    3299 > view matrix models
    3300 > #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
    3301 
    3302 > view matrix models
    3303 > #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
    3304 
    3305 > view matrix models
    3306 > #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
    3307 
    3308 > view matrix models
    3309 > #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
    3310 
    3311 > fitmap #5 inMap #1
    3312 
    3313 Fit molecule 6p40 chain A.pdb (#5) to map
    3314 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3315 average map value = 0.007335, steps = 136 
    3316 shifted from previous position = 4.79 
    3317 rotated from previous position = 9.96 degrees 
    3318 atoms outside contour = 2184, contour level = 0.0095201 
    3319  
    3320 Position of 6p40 chain A.pdb (#5) relative to
    3321 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3322 Matrix rotation and translation 
    3323 0.25923642 0.72247825 -0.64095372 154.22993226 
    3324 0.36269988 -0.68789226 -0.62869153 171.98248373 
    3325 -0.89512305 -0.06949409 -0.44036950 155.27549570 
    3326 Axis 0.78554440 0.35704974 -0.50540625 
    3327 Axis point 0.00000000 26.59582557 143.04088124 
    3328 Rotation angle (degrees) 159.14955506 
    3329 Shift along axis 104.08355356 
    3330  
    3331 
    3332 > volume #1 level 0.01921
    3333 
    3334 > volume #1 level 0.009655
    3335 
    3336 > volume #1 level 0.01625
    3337 
    3338 > volume #1 level 0.02015
    3339 
    3340 > select #5/A:62
    3341 
    3342 5 atoms, 4 bonds, 1 residue, 1 model selected 
    3343 
    3344 > view matrix models
    3345 > #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
    3346 
    3347 > fitmap #5 inMap #1
    3348 
    3349 Fit molecule 6p40 chain A.pdb (#5) to map
    3350 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3351 average map value = 0.008412, steps = 216 
    3352 shifted from previous position = 7.25 
    3353 rotated from previous position = 16.4 degrees 
    3354 atoms outside contour = 2746, contour level = 0.020154 
    3355  
    3356 Position of 6p40 chain A.pdb (#5) relative to
    3357 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3358 Matrix rotation and translation 
    3359 0.19089288 0.85074170 -0.48969224 146.01509921 
    3360 0.22873444 -0.52368461 -0.82063085 170.08786673 
    3361 -0.95458916 0.04464311 -0.29456159 154.18248482 
    3362 Axis 0.74423497 0.39986474 -0.53499767 
    3363 Axis point -0.00000000 1.76589066 158.08835527 
    3364 Rotation angle (degrees) 144.45672193 
    3365 Shift along axis 94.19441374 
    3366  
    3367 
    3368 > view matrix models
    3369 > #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
    3370 
    3371 > volume #1 level 0.007366
    3372 
    3373 > volume #1 level 0.01262
    3374 
    3375 > select #5/A:15
    3376 
    3377 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3378 
    3379 > view matrix models
    3380 > #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
    3381 
    3382 > view matrix models
    3383 > #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
    3384 
    3385 > view matrix models
    3386 > #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
    3387 
    3388 > view matrix models
    3389 > #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
    3390 
    3391 > view matrix models
    3392 > #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
    3393 
    3394 > view matrix models
    3395 > #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
    3396 
    3397 > fitmap #5 inMap #1
    3398 
    3399 Fit molecule 6p40 chain A.pdb (#5) to map
    3400 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3401 average map value = 0.007872, steps = 96 
    3402 shifted from previous position = 2.82 
    3403 rotated from previous position = 3.5 degrees 
    3404 atoms outside contour = 2380, contour level = 0.012616 
    3405  
    3406 Position of 6p40 chain A.pdb (#5) relative to
    3407 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3408 Matrix rotation and translation 
    3409 0.21852516 0.77753426 -0.58965010 156.66875418 
    3410 0.07582509 -0.61595677 -0.78412233 172.35391397 
    3411 -0.97288094 0.12664018 -0.19355865 148.00319513 
    3412 Axis 0.75150384 0.31621795 -0.57900620 
    3413 Axis point 0.00000000 8.73070883 166.91115477 
    3414 Rotation angle (degrees) 142.70204722 
    3415 Shift along axis 86.54380369 
    3416  
    3417 
    3418 > view matrix models
    3419 > #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
    3420 
    3421 > view matrix models
    3422 > #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
    3423 
    3424 > view matrix models
    3425 > #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
    3426 
    3427 > sequence chain #5/A
    3428 
    3429 Alignment identifier is 5/A 
    3430 
    3431 > select
    3432 > #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
    3433 
    3434 1378 atoms, 1409 bonds, 165 residues, 1 model selected 
    3435 
    3436 > select #5/A:209
    3437 
    3438 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3439 
    3440 > select #5/A:209-215
    3441 
    3442 56 atoms, 58 bonds, 7 residues, 1 model selected 
    3443 
    3444 > select clear
    3445 
    3446 > select #5/A:193
    3447 
    3448 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3449 
    3450 > select #5/A:181-193
    3451 
    3452 101 atoms, 102 bonds, 13 residues, 1 model selected 
    3453 
    3454 > select clear
    3455 
    3456 > select #5/A:168
    3457 
    3458 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3459 
    3460 > select #5/A:168-172
    3461 
    3462 42 atoms, 43 bonds, 5 residues, 1 model selected 
    3463 
    3464 > select #5/A:166
    3465 
    3466 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3467 
    3468 > select #5/A:166-169
    3469 
    3470 27 atoms, 26 bonds, 4 residues, 1 model selected 
    3471 
    3472 > select #5/A:169
    3473 
    3474 4 atoms, 3 bonds, 1 residue, 1 model selected 
    3475 
    3476 > select #5/A:169-172
    3477 
    3478 31 atoms, 32 bonds, 4 residues, 1 model selected 
    3479 
    3480 > select clear
    3481 
    3482 > select #5/A:128
    3483 
    3484 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3485 
    3486 > select #5/A:128-130
    3487 
    3488 23 atoms, 23 bonds, 3 residues, 1 model selected 
    3489 
    3490 > view matrix models
    3491 > #5,0.21766,0.77434,-0.59415,159.18,0.026056,-0.61314,-0.78954,171.34,-0.97568,0.15637,-0.15363,148
    3492 
    3493 > view matrix models
    3494 > #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
    3495 
    3496 > view matrix models
    3497 > #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
    3498 
    3499 > view matrix models
    3500 > #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
    3501 
    3502 > view matrix models
    3503 > #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
    3504 
    3505 > view matrix models
    3506 > #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
    3507 
    3508 > hide #!1 models
    3509 
    3510 > show #!1 models
    3511 
    3512 > hide #!1 models
    3513 
    3514 > show #!1 models
    3515 
    3516 > fitmap #5 inMap #1
    3517 
    3518 Fit molecule 6p40 chain A.pdb (#5) to map
    3519 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3520 average map value = 0.006811, steps = 212 
    3521 shifted from previous position = 2.32 
    3522 rotated from previous position = 15.4 degrees 
    3523 atoms outside contour = 2575, contour level = 0.012616 
    3524  
    3525 Position of 6p40 chain A.pdb (#5) relative to
    3526 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3527 Matrix rotation and translation 
    3528 -0.91344490 -0.35646563 -0.19634326 182.98057981 
    3529 0.40658991 -0.82000877 -0.40282785 162.94952277 
    3530 -0.01740891 -0.44779223 0.89396815 119.88933337 
    3531 Axis -0.05727630 -0.22792926 0.97199160 
    3532 Axis point 76.23180173 115.19241865 0.00000000 
    3533 Rotation angle (degrees) 156.88850348 
    3534 Shift along axis 68.91001022 
    3535  
    3536 
    3537 > hide #!1 models
    3538 
    3539 > show #!1 models
    3540 
    3541 > hide #!1 models
    3542 
    3543 > show #!1 models
    3544 
    3545 > hide #!1 models
    3546 
    3547 > show #!1 models
    3548 
    3549 > hide #!1 models
    3550 
    3551 > show #!1 models
    3552 
    3553 > select #5/A:25
    3554 
    3555 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3556 
    3557 > view matrix models
    3558 > #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
    3559 
    3560 > view matrix models
    3561 > #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
    3562 
    3563 > view matrix models
    3564 > #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
    3565 
    3566 > view matrix models
    3567 > #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
    3568 
    3569 > select clear
    3570 
    3571 > select #5/A:194
    3572 
    3573 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3574 
    3575 > select #5/A:194-199
    3576 
    3577 52 atoms, 53 bonds, 6 residues, 1 model selected 
    3578 
    3579 > select clear
    3580 
    3581 > select#5/A:180-187
    3582 
    3583 Unknown command: select#5/A:180-187 
    3584 
    3585 > select #5/A:180-187
    3586 
    3587 63 atoms, 64 bonds, 8 residues, 1 model selected 
    3588 
    3589 > select clear
    3590 
    3591 > volume #1 level 0.008713
    3592 
    3593 > fitmap #5 inMap #1
    3594 
    3595 Fit molecule 6p40 chain A.pdb (#5) to map
    3596 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3597 average map value = 0.006854, steps = 68 
    3598 shifted from previous position = 2.25 
    3599 rotated from previous position = 4.25 degrees 
    3600 atoms outside contour = 2260, contour level = 0.0087125 
    3601  
    3602 Position of 6p40 chain A.pdb (#5) relative to
    3603 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3604 Matrix rotation and translation 
    3605 -0.90182341 -0.43048481 -0.03738136 178.16886471 
    3606 0.41292410 -0.83307300 -0.36808026 163.32126915 
    3607 0.12731155 -0.34737906 0.92904228 114.91113636 
    3608 Axis 0.02408271 -0.19159527 0.98117851 
    3609 Axis point 66.98569874 113.14885021 0.00000000 
    3610 Rotation angle (degrees) 154.54552434 
    3611 Shift along axis 85.74754519 
    3612  
    3613 
    3614 > hide #!1 models
    3615 
    3616 > show #!1 models
    3617 
    3618 > hide #!1 models
    3619 
    3620 > show #!1 models
    3621 
    3622 > hide #!1 models
    3623 
    3624 > show #!1 models
    3625 
    3626 > hide #!1 models
    3627 
    3628 > show #!1 models
    3629 
    3630 > volume #1 level 0.01127
    3631 
    3632 > select #5/A:191
    3633 
    3634 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3635 
    3636 > view matrix models
    3637 > #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
    3638 
    3639 > view matrix models
    3640 > #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
    3641 
    3642 > fitmap #5 inMap #1
    3643 
    3644 Fit molecule 6p40 chain A.pdb (#5) to map
    3645 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3646 average map value = 0.00625, steps = 256 
    3647 shifted from previous position = 11 
    3648 rotated from previous position = 27.1 degrees 
    3649 atoms outside contour = 2491, contour level = 0.01127 
    3650  
    3651 Position of 6p40 chain A.pdb (#5) relative to
    3652 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3653 Matrix rotation and translation 
    3654 -0.56123226 -0.77014359 -0.30314555 189.69568210 
    3655 0.81739176 -0.57326484 -0.05690462 143.64372797 
    3656 -0.12995796 -0.27972538 0.95124374 116.84427533 
    3657 Axis -0.13818992 -0.10740821 0.98456438 
    3658 Axis point 64.06928898 129.60119454 0.00000000 
    3659 Rotation angle (degrees) 126.27252740 
    3660 Shift along axis 73.39816454 
    3661  
    3662 
    3663 > fitmap #5 inMap #1
    3664 
    3665 Fit molecule 6p40 chain A.pdb (#5) to map
    3666 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3667 average map value = 0.00625, steps = 48 
    3668 shifted from previous position = 0.0127 
    3669 rotated from previous position = 0.0135 degrees 
    3670 atoms outside contour = 2496, contour level = 0.01127 
    3671  
    3672 Position of 6p40 chain A.pdb (#5) relative to
    3673 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3674 Matrix rotation and translation 
    3675 -0.56119768 -0.77009909 -0.30332255 189.70298154 
    3676 0.81741785 -0.57321429 -0.05703897 143.65469455 
    3677 -0.12994316 -0.27995141 0.95117927 116.84053865 
    3678 Axis -0.13824548 -0.10752615 0.98454371 
    3679 Axis point 64.07064853 129.61715736 0.00000000 
    3680 Rotation angle (degrees) 126.27179336 
    3681 Shift along axis 73.36240148 
    3682  
    3683 
    3684 > fitmap #5 inMap #1
    3685 
    3686 Fit molecule 6p40 chain A.pdb (#5) to map
    3687 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    3688 average map value = 0.00625, steps = 44 
    3689 shifted from previous position = 0.004 
    3690 rotated from previous position = 0.00977 degrees 
    3691 atoms outside contour = 2497, contour level = 0.01127 
    3692  
    3693 Position of 6p40 chain A.pdb (#5) relative to
    3694 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    3695 Matrix rotation and translation 
    3696 -0.56127529 -0.77002734 -0.30336110 189.70287737 
    3697 0.81737705 -0.57325723 -0.05719194 143.65878344 
    3698 -0.12986458 -0.28006082 0.95115779 116.84462389 
    3699 Axis -0.13822740 -0.10760575 0.98453755 
    3700 Axis point 64.07146554 129.61834246 0.00000000 
    3701 Rotation angle (degrees) 126.27684026 
    3702 Shift along axis 73.35727353 
    3703  
    3704 
    3705 > volume #1 level 0.01706
    3706 
    3707 > show #!3 models
    3708 
    3709 > hide #!3 models
    3710 
    3711 > show #!3 models
    3712 
    3713 > ui tool show Matchmaker
    3714 
    3715 > matchmaker #!3 to #5
    3716 
    3717 Parameters 
    3718 --- 
    3719 Chain pairing | bb 
    3720 Alignment algorithm | Needleman-Wunsch 
    3721 Similarity matrix | BLOSUM-62 
    3722 SS fraction | 0.3 
    3723 Gap open (HH/SS/other) | 18/18/6 
    3724 Gap extend | 1 
    3725 SS matrix |  |  | H | S | O 
    3726 ---|---|---|--- 
    3727 H | 6 | -9 | -6 
    3728 S |  | 6 | -6 
    3729 O |  |  | 4 
    3730 Iteration cutoff | 2 
    3731  
    3732 Matchmaker 6p40 chain A.pdb, chain A (#5) with 6p3x chain A.pdb, chain A (#3),
    3733 sequence alignment score = 1956 
    3734 RMSD between 106 pruned atom pairs is 0.426 angstroms; (across all 358 pairs:
    3735 6.515) 
    3736  
    3737 
    3738 > select #5/A:182
    3739 
    3740 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3741 
    3742 > view matrix models
    3743 > #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
    3744 
    3745 > undo
    3746 
    3747 > hide #!3 models
    3748 
    3749 > fetch 6p3x
    3750 
    3751 Unknown command: fetch 6p3x 
    3752 
    3753 > open 6p3x
    3754 
    3755 Summary of feedback from opening 6p3x fetched from pdb 
    3756 --- 
    3757 notes | Fetching compressed mmCIF 6p3x from
    3758 http://files.rcsb.org/download/6p3x.cif 
    3759 Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif 
    3760  
    3761 6p3x title: 
    3762 Crystal Structure of Full Length APOBEC3G E/Q (pH 7.0) [more info...] 
    3763  
    3764 Chain information for 6p3x #6 
    3765 --- 
    3766 Chain | Description 
    3767 A B | Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G 
    3768  
    3769 Non-standard residues in 6p3x #6 
    3770 --- 
    3771 ZN — zinc ion 
    3772  
    3773 
    3774 > view
    3775 
    3776 > select #6/B:130
    3777 
    3778 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3779 
    3780 > view matrix models #6,1,0,0,-0.19639,0,1,0,142.78,0,0,1,168.82
    3781 
    3782 > select clear
    3783 
    3784 > select clear
    3785 
    3786 > select #6/A:193
    3787 
    3788 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3789 
    3790 > view matrix models #6,1,0,0,151.35,0,1,0,141.95,0,0,1,145.99
    3791 
    3792 > view matrix models #6,1,0,0,154.76,0,1,0,180.91,0,0,1,176.99
    3793 
    3794 > view matrix models #6,1,0,0,154.86,0,1,0,182.15,0,0,1,178.76
    3795 
    3796 > color #6/B gold
    3797 
    3798 > view matrix models #6,1,0,0,155.98,0,1,0,184.89,0,0,1,182.99
    3799 
    3800 > view matrix models
    3801 > #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
    3802 
    3803 > view matrix models
    3804 > #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
    3805 
    3806 > view matrix models
    3807 > #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
    3808 
    3809 > view matrix models
    3810 > #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
    3811 
    3812 > view matrix models
    3813 > #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
    3814 
    3815 > view matrix models
    3816 > #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
    3817 
    3818 > view matrix models
    3819 > #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
    3820 
    3821 > select clear
    3822 
    3823 > ui tool show Matchmaker
    3824 
    3825 > matchmaker #!6 to #4
    3826 
    3827 Parameters 
    3828 --- 
    3829 Chain pairing | bb 
    3830 Alignment algorithm | Needleman-Wunsch 
    3831 Similarity matrix | BLOSUM-62 
    3832 SS fraction | 0.3 
    3833 Gap open (HH/SS/other) | 18/18/6 
    3834 Gap extend | 1 
    3835 SS matrix |  |  | H | S | O 
    3836 ---|---|---|--- 
    3837 H | 6 | -9 | -6 
    3838 S |  | 6 | -6 
    3839 O |  |  | 4 
    3840 Iteration cutoff | 2 
    3841  
    3842 Matchmaker 6p40_chain A_CTD, chain A (#4) with 6p3x, chain B (#6), sequence
    3843 alignment score = 1959 
    3844 RMSD between 106 pruned atom pairs is 0.428 angstroms; (across all 358 pairs:
    3845 6.546) 
    3846  
    3847 
    3848 > select clear
    3849 
    3850 > select #6/A:16
    3851 
    3852 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3853 
    3854 > view matrix models
    3855 > #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
    3856 
    3857 > volume #1 level 0.00804
    3858 
    3859 > view matrix models
    3860 > #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
    3861 
    3862 > volume #1 level 0.01383
    3863 
    3864 > hide #6/A cartoons
    3865 
    3866 > select #6/B:294
    3867 
    3868 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3869 
    3870 > view matrix models
    3871 > #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
    3872 
    3873 > view matrix models
    3874 > #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
    3875 
    3876 > view matrix models
    3877 > #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
    3878 
    3879 > show #6 dartoon
    3880 
    3881 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    3882 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    3883 
    3884 > show #6 cartoons
    3885 
    3886 > select clear
    3887 
    3888 > select #6/A:327
    3889 
    3890 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3891 
    3892 > view matrix models
    3893 > #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
    3894 
    3895 > view matrix models
    3896 > #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
    3897 
    3898 > view matrix models
    3899 > #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
    3900 
    3901 > view matrix models
    3902 > #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
    3903 
    3904 > view matrix models
    3905 > #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
    3906 
    3907 > view matrix models
    3908 > #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
    3909 
    3910 > view matrix models
    3911 > #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
    3912 
    3913 > view matrix models
    3914 > #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
    3915 
    3916 > select up
    3917 
    3918 108 atoms, 109 bonds, 12 residues, 1 model selected 
    3919 
    3920 > select up
    3921 
    3922 3120 atoms, 3119 bonds, 461 residues, 1 model selected 
    3923 
    3924 > select up
    3925 
    3926 6240 atoms, 6238 bonds, 922 residues, 1 model selected 
    3927 
    3928 > select up
    3929 
    3930 22226 atoms, 22240 bonds, 3232 residues, 7 models selected 
    3931 
    3932 > select down
    3933 
    3934 6240 atoms, 6238 bonds, 922 residues, 1 model selected 
    3935 
    3936 > select down
    3937 
    3938 3120 atoms, 3119 bonds, 461 residues, 1 model selected 
    3939 
    3940 > hide #6/A
    3941 
    3942 > hide #6/A cartoons
    3943 
    3944 > ui tool show Matchmaker
    3945 
    3946 > matchmaker #!6 to #4/A pairing bs
    3947 
    3948 Parameters 
    3949 --- 
    3950 Chain pairing | bs 
    3951 Alignment algorithm | Needleman-Wunsch 
    3952 Similarity matrix | BLOSUM-62 
    3953 SS fraction | 0.3 
    3954 Gap open (HH/SS/other) | 18/18/6 
    3955 Gap extend | 1 
    3956 SS matrix |  |  | H | S | O 
    3957 ---|---|---|--- 
    3958 H | 6 | -9 | -6 
    3959 S |  | 6 | -6 
    3960 O |  |  | 4 
    3961 Iteration cutoff | 2 
    3962  
    3963 Matchmaker 6p40_chain A_CTD, chain A (#4) with 6p3x, chain B (#6), sequence
    3964 alignment score = 1959 
    3965 RMSD between 106 pruned atom pairs is 0.428 angstroms; (across all 358 pairs:
    3966 6.546) 
    3967  
    3968 
    3969 > select #6/B:322
    3970 
    3971 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3972 
    3973 > view matrix models
    3974 > #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
    3975 
    3976 > hide #6/B:1-193
    3977 
    3978 > hide #6/B:1-193
    3979 
    3980 > show #6/B:1-193
    3981 
    3982 > hide #6/B:1-193
    3983 
    3984 > hide #6/B:1-193 cartoons
    3985 
    3986 > hide #6/B:1-193
    3987 
    3988 > hide #6/B:1-193
    3989 
    3990 > ui tool show Matchmaker
    3991 
    3992 > matchmaker #!6 to #4/A pairing bs
    3993 
    3994 Parameters 
    3995 --- 
    3996 Chain pairing | bs 
    3997 Alignment algorithm | Needleman-Wunsch 
    3998 Similarity matrix | BLOSUM-62 
    3999 SS fraction | 0.3 
    4000 Gap open (HH/SS/other) | 18/18/6 
    4001 Gap extend | 1 
    4002 SS matrix |  |  | H | S | O 
    4003 ---|---|---|--- 
    4004 H | 6 | -9 | -6 
    4005 S |  | 6 | -6 
    4006 O |  |  | 4 
    4007 Iteration cutoff | 2 
    4008  
    4009 Matchmaker 6p40_chain A_CTD, chain A (#4) with 6p3x, chain B (#6), sequence
    4010 alignment score = 1959 
    4011 RMSD between 106 pruned atom pairs is 0.428 angstroms; (across all 358 pairs:
    4012 6.546) 
    4013  
    4014 
    4015 > select #6/B:292
    4016 
    4017 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4018 
    4019 > view matrix models
    4020 > #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
    4021 
    4022 > show #6/B:1-193 cartoons
    4023 
    4024 > select #6/B:194-385
    4025 
    4026 1465 atoms, 1508 bonds, 1 pseudobond, 176 residues, 2 models selected 
    4027 
    4028 > matchmaker #!6 & sel to #4/A pairing bs
    4029 
    4030 Parameters 
    4031 --- 
    4032 Chain pairing | bs 
    4033 Alignment algorithm | Needleman-Wunsch 
    4034 Similarity matrix | BLOSUM-62 
    4035 SS fraction | 0.3 
    4036 Gap open (HH/SS/other) | 18/18/6 
    4037 Gap extend | 1 
    4038 SS matrix |  |  | H | S | O 
    4039 ---|---|---|--- 
    4040 H | 6 | -9 | -6 
    4041 S |  | 6 | -6 
    4042 O |  |  | 4 
    4043 Iteration cutoff | 2 
    4044  
    4045 Matchmaker 6p40_chain A_CTD, chain A (#4) with 6p3x, chain B (#6), sequence
    4046 alignment score = 907.2 
    4047 RMSD between 154 pruned atom pairs is 0.838 angstroms; (across all 175 pairs:
    4048 2.006) 
    4049  
    4050 
    4051 > hide #!5 models
    4052 
    4053 > select clear
    4054 
    4055 > select clear
    4056 
    4057 > select clear
    4058 
    4059 > select #6/B:63
    4060 
    4061 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4062 
    4063 > view matrix models
    4064 > #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
    4065 
    4066 > select #6/B:375
    4067 
    4068 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4069 
    4070 > select #6/B:107
    4071 
    4072 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4073 
    4074 > select #6/B:107
    4075 
    4076 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4077 
    4078 > show #6
    4079 
    4080 > hide #6
    4081 
    4082 > show #6 cartoons
    4083 
    4084 > view matrix models
    4085 > #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
    4086 
    4087 > hide #6/A cartoons
    4088 
    4089 > hide #6/B:194-385
    4090 
    4091 > hide #6/B:194-385 cartoons
    4092 
    4093 > view matrix models
    4094 > #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
    4095 
    4096 > view matrix models
    4097 > #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
    4098 
    4099 > view matrix models
    4100 > #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
    4101 
    4102 > view matrix models
    4103 > #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
    4104 
    4105 > view matrix models
    4106 > #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
    4107 
    4108 > view matrix models
    4109 > #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
    4110 
    4111 > view matrix models
    4112 > #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
    4113 
    4114 > view matrix models
    4115 > #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
    4116 
    4117 > view matrix models
    4118 > #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
    4119 
    4120 > view matrix models
    4121 > #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
    4122 
    4123 > view matrix models
    4124 > #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
    4125 
    4126 > view matrix models
    4127 > #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
    4128 
    4129 > view matrix models
    4130 > #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
    4131 
    4132 > view matrix models
    4133 > #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
    4134 
    4135 > view matrix models
    4136 > #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
    4137 
    4138 > fitmap #6 inMap #1
    4139 
    4140 Fit molecule 6p3x (#6) to map
    4141 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 6240 atoms 
    4142 average map value = 0.006877, steps = 436 
    4143 shifted from previous position = 17.5 
    4144 rotated from previous position = 60.1 degrees 
    4145 atoms outside contour = 5530, contour level = 0.013827 
    4146  
    4147 Position of 6p3x (#6) relative to
    4148 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4149 Matrix rotation and translation 
    4150 -0.63630890 0.17548253 -0.75121026 157.29176230 
    4151 -0.20476553 0.90043268 0.38378647 143.43356904 
    4152 0.74376210 0.39802872 -0.53702056 148.36715853 
    4153 Axis 0.00923239 -0.96910085 -0.24649200 
    4154 Axis point 53.68601736 0.00000000 94.58391160 
    4155 Rotation angle (degrees) 129.52749180 
    4156 Shift along axis -174.12073126 
    4157  
    4158 
    4159 > close #6
    4160 
    4161 > show #!5 models
    4162 
    4163 > select #5/A:55
    4164 
    4165 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4166 
    4167 > view matrix models
    4168 > #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
    4169 
    4170 > volume #1 level 0.009116
    4171 
    4172 > fitmap #5 inMap #1
    4173 
    4174 Fit molecule 6p40 chain A.pdb (#5) to map
    4175 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4176 average map value = 0.006265, steps = 144 
    4177 shifted from previous position = 3.59 
    4178 rotated from previous position = 12.9 degrees 
    4179 atoms outside contour = 2320, contour level = 0.0091163 
    4180  
    4181 Position of 6p40 chain A.pdb (#5) relative to
    4182 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4183 Matrix rotation and translation 
    4184 -0.59613714 -0.79301675 -0.12547889 186.70622449 
    4185 0.79229949 -0.60634214 0.06790239 141.91647078 
    4186 -0.12993087 -0.05893772 0.98976983 107.54906835 
    4187 Axis -0.07975416 0.00279930 0.99681063 
    4188 Axis point 62.48115333 119.00374256 0.00000000 
    4189 Rotation angle (degrees) 127.32638969 
    4190 Shift along axis 92.71272348 
    4191  
    4192 
    4193 > volume #1 level 0.01423
    4194 
    4195 > select #5/A:186
    4196 
    4197 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4198 
    4199 > view matrix models
    4200 > #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
    4201 
    4202 > volume #1 level 0.01046
    4203 
    4204 > view matrix models
    4205 > #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
    4206 
    4207 > view matrix models
    4208 > #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
    4209 
    4210 > view matrix models
    4211 > #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
    4212 
    4213 > view matrix models
    4214 > #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
    4215 
    4216 > view matrix models
    4217 > #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
    4218 
    4219 > view matrix models
    4220 > #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
    4221 
    4222 > view matrix models
    4223 > #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
    4224 
    4225 > view matrix models
    4226 > #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
    4227 
    4228 > view matrix models
    4229 > #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
    4230 
    4231 > view matrix models
    4232 > #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
    4233 
    4234 > view matrix models
    4235 > #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
    4236 
    4237 > view matrix models
    4238 > #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
    4239 
    4240 > view matrix models
    4241 > #5,-0.2721,0.29095,0.91723,104.68,0.17015,0.95272,-0.25174,88.401,-0.94711,0.087569,-0.30874,165
    4242 
    4243 > view matrix models
    4244 > #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
    4245 
    4246 > undo
    4247 
    4248 > undo
    4249 
    4250 > view matrix models
    4251 > #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
    4252 
    4253 > fitmap #5 inMap #1
    4254 
    4255 Fit molecule 6p40 chain A.pdb (#5) to map
    4256 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4257 average map value = 0.006707, steps = 112 
    4258 shifted from previous position = 4.61 
    4259 rotated from previous position = 11.1 degrees 
    4260 atoms outside contour = 2360, contour level = 0.010462 
    4261  
    4262 Position of 6p40 chain A.pdb (#5) relative to
    4263 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4264 Matrix rotation and translation 
    4265 -0.10076876 0.31808633 0.94269123 118.24747570 
    4266 0.24406390 0.92646526 -0.28652215 120.01986316 
    4267 -0.96450945 0.20120441 -0.17099214 153.62669175 
    4268 Axis 0.24758105 0.96813827 -0.03757546 
    4269 Axis point 112.69855375 0.00000000 42.85009907 
    4270 Rotation angle (degrees) 99.94180476 
    4271 Shift along axis 139.69906284 
    4272  
    4273 
    4274 > select #5/A:72
    4275 
    4276 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4277 
    4278 > view matrix models
    4279 > #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
    4280 
    4281 > view matrix models
    4282 > #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
    4283 
    4284 > volume #1 level 0.01477
    4285 
    4286 > volume #1 level 0.01127
    4287 
    4288 > volume #1 level 0.007366
    4289 
    4290 > save "E:/temp/EM data/H7N100
    4291 > cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
    4292 
    4293 > volume #1 level 0.004136
    4294 
    4295 > volume #1 level 0.01706
    4296 
    4297 > select #5/A:185
    4298 
    4299 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4300 
    4301 > view matrix models
    4302 > #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
    4303 
    4304 > view matrix models
    4305 > #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
    4306 
    4307 > view matrix models
    4308 > #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
    4309 
    4310 > view matrix models
    4311 > #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
    4312 
    4313 > fitmap #5 inMap #1
    4314 
    4315 Fit molecule 6p40 chain A.pdb (#5) to map
    4316 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4317 average map value = 0.004591, steps = 140 
    4318 shifted from previous position = 1.4 
    4319 rotated from previous position = 11.1 degrees 
    4320 atoms outside contour = 2817, contour level = 0.017058 
    4321  
    4322 Position of 6p40 chain A.pdb (#5) relative to
    4323 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4324 Matrix rotation and translation 
    4325 -0.76067899 0.29670371 0.57735118 137.08474958 
    4326 -0.01672730 0.88017049 -0.47436286 125.07770686 
    4327 -0.64891269 -0.37049538 -0.66456414 174.66428318 
    4328 Axis 0.08178920 0.96560685 -0.24680751 
    4329 Axis point 99.71323475 0.00000000 79.23709352 
    4330 Rotation angle (degrees) 140.58219770 
    4331 Shift along axis 88.87948572 
    4332  
    4333 
    4334 > volume #1 level 0.01033
    4335 
    4336 > view matrix models
    4337 > #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
    4338 
    4339 > view matrix models
    4340 > #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
    4341 
    4342 > view matrix models
    4343 > #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
    4344 
    4345 > view matrix models
    4346 > #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
    4347 
    4348 > view matrix models
    4349 > #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
    4350 
    4351 > view matrix models
    4352 > #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
    4353 
    4354 > view matrix models
    4355 > #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
    4356 
    4357 > view matrix models
    4358 > #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
    4359 
    4360 > view matrix models
    4361 > #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
    4362 
    4363 > view matrix models
    4364 > #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
    4365 
    4366 > view matrix models
    4367 > #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
    4368 
    4369 > view matrix models
    4370 > #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
    4371 
    4372 > view matrix models
    4373 > #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
    4374 
    4375 > view matrix models
    4376 > #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
    4377 
    4378 > view matrix models
    4379 > #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
    4380 
    4381 > view matrix models
    4382 > #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
    4383 
    4384 > view matrix models
    4385 > #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
    4386 
    4387 > view matrix models
    4388 > #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
    4389 
    4390 > view matrix models
    4391 > #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
    4392 
    4393 > view matrix models
    4394 > #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
    4395 
    4396 > view matrix models
    4397 > #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
    4398 
    4399 > view matrix models
    4400 > #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
    4401 
    4402 > view matrix models
    4403 > #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
    4404 
    4405 > view matrix models
    4406 > #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
    4407 
    4408 > view matrix models
    4409 > #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
    4410 
    4411 > view matrix models
    4412 > #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
    4413 
    4414 > view matrix models
    4415 > #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
    4416 
    4417 > view matrix models
    4418 > #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
    4419 
    4420 > view matrix models
    4421 > #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
    4422 
    4423 > view matrix models
    4424 > #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
    4425 
    4426 > view matrix models
    4427 > #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
    4428 
    4429 > fitmap #5 inMap #1
    4430 
    4431 Fit molecule 6p40 chain A.pdb (#5) to map
    4432 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4433 average map value = 0.007758, steps = 216 
    4434 shifted from previous position = 5.75 
    4435 rotated from previous position = 24.6 degrees 
    4436 atoms outside contour = 2237, contour level = 0.010328 
    4437  
    4438 Position of 6p40 chain A.pdb (#5) relative to
    4439 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4440 Matrix rotation and translation 
    4441 0.20949377 0.79797570 0.56510810 122.37099314 
    4442 0.89548867 0.07553260 -0.43862842 137.36608026 
    4443 -0.39269889 0.59793781 -0.69875459 149.89847569 
    4444 Axis 0.73271163 0.67703954 0.06892843 
    4445 Axis point 0.00000000 -26.48206635 71.08787550 
    4446 Rotation angle (degrees) 134.98033971 
    4447 Shift along axis 192.99718453 
    4448  
    4449 
    4450 > volume #1 level 0.01585
    4451 
    4452 > hide #!1 models
    4453 
    4454 > show #!1 models
    4455 
    4456 > hide #!5 models
    4457 
    4458 > show #!5 models
    4459 
    4460 > view matrix models
    4461 > #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
    4462 
    4463 > view matrix models
    4464 > #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
    4465 
    4466 > fitmap #5 inMap #1
    4467 
    4468 Fit molecule 6p40 chain A.pdb (#5) to map
    4469 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4470 average map value = 0.007698, steps = 112 
    4471 shifted from previous position = 7.71 
    4472 rotated from previous position = 11 degrees 
    4473 atoms outside contour = 2581, contour level = 0.015846 
    4474  
    4475 Position of 6p40 chain A.pdb (#5) relative to
    4476 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4477 Matrix rotation and translation 
    4478 0.29606661 0.66020517 -0.69027076 161.56748446 
    4479 -0.09665033 -0.69825407 -0.70929542 175.51207137 
    4480 -0.95026485 0.27671358 -0.14292066 140.81901938 
    4481 Axis 0.77644740 0.20473620 -0.59599709 
    4482 Axis point 0.00000000 23.32301978 169.24668610 
    4483 Rotation angle (degrees) 140.58379847 
    4484 Shift along axis 77.45460288 
    4485  
    4486 
    4487 > volume #1 level 0.01813
    4488 
    4489 > volume #1 level 0.01033
    4490 
    4491 > select #5/A:163
    4492 
    4493 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4494 
    4495 > view matrix models
    4496 > #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
    4497 
    4498 > hide #!1 models
    4499 
    4500 > show #!1 models
    4501 
    4502 > hide #!1 models
    4503 
    4504 > show #!1 models
    4505 
    4506 > hide #!1 models
    4507 
    4508 > show #!1 models
    4509 
    4510 > view matrix models
    4511 > #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
    4512 
    4513 > view matrix models
    4514 > #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
    4515 
    4516 > view matrix models
    4517 > #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
    4518 
    4519 > view matrix models
    4520 > #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
    4521 
    4522 > view matrix models
    4523 > #5,0.3787,-0.081141,0.92196,167.26,-0.62237,0.71496,0.31857,126,-0.68501,-0.69444,0.22025,137.95
    4524 
    4525 > view matrix models
    4526 > #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
    4527 
    4528 > view matrix models
    4529 > #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
    4530 
    4531 > view matrix models
    4532 > #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
    4533 
    4534 > save "E:/temp/EM data/H7N100
    4535 > cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
    4536 
    4537 ——— End of log from Sat Jun 19 20:21:38 2021 ———
    4538 
    4539 opened ChimeraX session 
    4540 
    4541 > select #5/A:51
    4542 
    4543 5 atoms, 4 bonds, 1 residue, 1 model selected 
    4544 
    4545 > ui mousemode right "translate selected models"
    4546 
    4547 > view matrix models
    4548 > #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
    4549 
    4550 Alignment identifier is 5/A 
    4551 
    4552 > select #5/A:139
    4553 
    4554 5 atoms, 4 bonds, 1 residue, 1 model selected 
    4555 
    4556 > select #5/A:139-142
    4557 
    4558 23 atoms, 22 bonds, 4 residues, 1 model selected 
    4559 
    4560 > view matrix models
    4561 > #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
    4562 
    4563 > view matrix models
    4564 > #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
    4565 
    4566 > view matrix models
    4567 > #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
    4568 
    4569 > view matrix models
    4570 > #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
    4571 
    4572 > view matrix models
    4573 > #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
    4574 
    4575 > fitmap #5 inMap #1
    4576 
    4577 Fit molecule 6p40 chain A.pdb (#5) to map
    4578 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4579 average map value = 0.006084, steps = 256 
    4580 shifted from previous position = 13.1 
    4581 rotated from previous position = 26 degrees 
    4582 atoms outside contour = 2639, contour level = 0.010328 
    4583  
    4584 Position of 6p40 chain A.pdb (#5) relative to
    4585 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4586 Matrix rotation and translation 
    4587 0.09195956 0.85279380 -0.51408773 144.29948233 
    4588 0.41346260 -0.50236738 -0.75939168 185.07390883 
    4589 -0.90586541 -0.14272273 -0.39879582 173.93072966 
    4590 Axis 0.72335240 0.45955503 -0.51533530 
    4591 Axis point -0.00000000 11.83623606 159.90257943 
    4592 Rotation angle (degrees) 154.76970719 
    4593 Shift along axis 99.79837809 
    4594  
    4595 
    4596 > undo
    4597 
    4598 > view matrix models
    4599 > #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
    4600 
    4601 > view matrix models
    4602 > #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
    4603 
    4604 > view matrix models
    4605 > #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
    4606 
    4607 > ui tool show "Side View"
    4608 
    4609 > view matrix models
    4610 > #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
    4611 
    4612 > view matrix models
    4613 > #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
    4614 
    4615 > fitmap #5 inMap #1
    4616 
    4617 Fit molecule 6p40 chain A.pdb (#5) to map
    4618 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4619 average map value = 0.007871, steps = 100 
    4620 shifted from previous position = 3.05 
    4621 rotated from previous position = 3.71 degrees 
    4622 atoms outside contour = 2177, contour level = 0.010328 
    4623  
    4624 Position of 6p40 chain A.pdb (#5) relative to
    4625 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4626 Matrix rotation and translation 
    4627 0.21866269 0.77748978 -0.58965778 156.67069320 
    4628 0.07560909 -0.61596397 -0.78413754 172.35920284 
    4629 -0.97286685 0.12687812 -0.19347363 147.98205112 
    4630 Axis 0.75153744 0.31612625 -0.57901267 
    4631 Axis point 0.00000000 8.73704125 166.91009236 
    4632 Rotation angle (degrees) 142.69186681 
    4633 Shift along axis 86.54767614 
    4634  
    4635 
    4636 > volume #1 level 0.01372
    4637 
    4638 > view matrix models
    4639 > #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
    4640 
    4641 > view matrix models
    4642 > #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
    4643 
    4644 > view matrix models
    4645 > #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
    4646 
    4647 > view matrix models
    4648 > #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
    4649 
    4650 > view matrix models
    4651 > #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
    4652 
    4653 > view matrix models
    4654 > #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
    4655 
    4656 > view matrix models
    4657 > #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
    4658 
    4659 > view matrix models
    4660 > #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
    4661 
    4662 > view matrix models
    4663 > #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
    4664 
    4665 > view matrix models
    4666 > #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
    4667 
    4668 > view matrix models
    4669 > #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
    4670 
    4671 > view matrix models
    4672 > #5,-0.54929,-0.3678,0.75034,184.33,-0.55528,-0.51035,-0.65666,175.92,0.62445,-0.77735,0.076099,140
    4673 
    4674 > view matrix models
    4675 > #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
    4676 
    4677 > view matrix models
    4678 > #5,-0.54929,-0.3678,0.75034,185,-0.55528,-0.51035,-0.65666,176.2,0.62445,-0.77735,0.076099,139.28
    4679 
    4680 > view matrix models
    4681 > #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
    4682 
    4683 > view matrix models
    4684 > #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
    4685 
    4686 > view matrix models
    4687 > #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
    4688 
    4689 > view matrix models
    4690 > #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
    4691 
    4692 > view matrix models
    4693 > #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
    4694 
    4695 > view matrix models
    4696 > #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
    4697 
    4698 > view matrix models
    4699 > #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
    4700 
    4701 > view matrix models
    4702 > #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
    4703 
    4704 > view matrix models
    4705 > #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
    4706 
    4707 > view matrix models
    4708 > #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
    4709 
    4710 > view matrix models
    4711 > #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
    4712 
    4713 > view matrix models
    4714 > #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
    4715 
    4716 > view matrix models
    4717 > #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
    4718 
    4719 > view matrix models
    4720 > #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
    4721 
    4722 > volume #1 level 0.01111
    4723 
    4724 > view matrix models
    4725 > #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
    4726 
    4727 > view matrix models
    4728 > #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
    4729 
    4730 > view matrix models
    4731 > #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
    4732 
    4733 > fitmap #5 inMap #1
    4734 
    4735 Fit molecule 6p40 chain A.pdb (#5) to map
    4736 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4737 average map value = 0.00804, steps = 100 
    4738 shifted from previous position = 1.99 
    4739 rotated from previous position = 5.47 degrees 
    4740 atoms outside contour = 2420, contour level = 0.011111 
    4741  
    4742 Position of 6p40 chain A.pdb (#5) relative to
    4743 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4744 Matrix rotation and translation 
    4745 -0.60212297 -0.51496451 0.61013074 154.30700984 
    4746 -0.52194834 -0.32438630 -0.78888750 171.96128146 
    4747 0.60416710 -0.79346400 -0.07346443 158.20465619 
    4748 Axis -0.44601907 0.58120845 -0.68063480 
    4749 Axis point 25.72575256 153.30135800 -0.00000000 
    4750 Rotation angle (degrees) 179.70604949 
    4751 Shift along axis -76.55811429 
    4752  
    4753 
    4754 > view matrix models
    4755 > #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
    4756 
    4757 > volume #1 level 0.01737
    4758 
    4759 > view matrix models
    4760 > #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
    4761 
    4762 > view matrix models
    4763 > #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
    4764 
    4765 > view matrix models
    4766 > #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
    4767 
    4768 > view matrix models
    4769 > #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
    4770 
    4771 > view matrix models
    4772 > #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
    4773 
    4774 > view matrix models
    4775 > #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
    4776 
    4777 > view matrix models
    4778 > #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
    4779 
    4780 > view matrix models
    4781 > #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
    4782 
    4783 > view matrix models
    4784 > #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
    4785 
    4786 > view matrix models
    4787 > #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
    4788 
    4789 > view matrix models
    4790 > #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
    4791 
    4792 > view matrix models
    4793 > #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
    4794 
    4795 > view matrix models
    4796 > #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
    4797 
    4798 > fitmap #5 inMap #1
    4799 
    4800 Fit molecule 6p40 chain A.pdb (#5) to map
    4801 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    4802 average map value = 0.008192, steps = 168 
    4803 shifted from previous position = 6.89 
    4804 rotated from previous position = 22.3 degrees 
    4805 atoms outside contour = 2616, contour level = 0.017374 
    4806  
    4807 Position of 6p40 chain A.pdb (#5) relative to
    4808 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    4809 Matrix rotation and translation 
    4810 -0.41390429 -0.54871105 0.72636041 147.12022631 
    4811 0.88413707 -0.43230710 0.17723494 131.26223586 
    4812 0.21675999 0.71556047 0.66406954 95.04677763 
    4813 Axis 0.33369232 0.31588646 0.88818083 
    4814 Axis point 34.01823872 74.05297820 0.00000000 
    4815 Rotation angle (degrees) 126.23304062 
    4816 Shift along axis 174.97557788 
    4817  
    4818 
    4819 > view matrix models
    4820 > #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
    4821 
    4822 > volume #1 level 0.01372
    4823 
    4824 > view matrix models
    4825 > #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
    4826 
    4827 > view matrix models
    4828 > #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
    4829 
    4830 > view matrix models
    4831 > #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
    4832 
    4833 > view matrix models
    4834 > #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
    4835 
    4836 > view matrix models
    4837 > #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
    4838 
    4839 > view matrix models
    4840 > #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
    4841 
    4842 > view matrix models
    4843 > #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
    4844 
    4845 > view matrix models
    4846 > #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
    4847 
    4848 > view matrix models
    4849 > #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
    4850 
    4851 > view matrix models
    4852 > #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
    4853 
    4854 > view matrix models
    4855 > #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
    4856 
    4857 > view matrix models
    4858 > #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
    4859 
    4860 > view matrix models
    4861 > #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
    4862 
    4863 > view matrix models
    4864 > #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
    4865 
    4866 > view matrix models
    4867 > #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
    4868 
    4869 > view matrix models
    4870 > #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
    4871 
    4872 > view matrix models
    4873 > #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
    4874 
    4875 > view matrix models
    4876 > #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
    4877 
    4878 > view matrix models
    4879 > #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
    4880 
    4881 > volume #1 level 0.0209
    4882 
    4883 > view matrix models
    4884 > #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
    4885 
    4886 > volume #1 level 0.01476
    4887 
    4888 Alignment identifier is 5/A 
    4889 
    4890 > select #5/A:128-129
    4891 
    4892 15 atoms, 15 bonds, 2 residues, 1 model selected 
    4893 
    4894 > select #5/A:128-142
    4895 
    4896 116 atoms, 117 bonds, 15 residues, 1 model selected 
    4897 
    4898 > view matrix models
    4899 > #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
    4900 
    4901 > view matrix models
    4902 > #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
    4903 
    4904 > view matrix models
    4905 > #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
    4906 
    4907 > view matrix models
    4908 > #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
    4909 
    4910 > view matrix models
    4911 > #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
    4912 
    4913 > view matrix models
    4914 > #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
    4915 
    4916 > view matrix models
    4917 > #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
    4918 
    4919 > view matrix models
    4920 > #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
    4921 
    4922 > view matrix models
    4923 > #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
    4924 
    4925 > view matrix models
    4926 > #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
    4927 
    4928 > view matrix models
    4929 > #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
    4930 
    4931 > view matrix models
    4932 > #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
    4933 
    4934 > view matrix models
    4935 > #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
    4936 
    4937 > view matrix models
    4938 > #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
    4939 
    4940 > view matrix models
    4941 > #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
    4942 
    4943 > view matrix models
    4944 > #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
    4945 
    4946 > view matrix models
    4947 > #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
    4948 
    4949 > select clear
    4950 
    4951 > select #5/A:102
    4952 
    4953 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4954 
    4955 > view matrix models
    4956 > #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
    4957 
    4958 > view matrix models
    4959 > #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
    4960 
    4961 > view matrix models
    4962 > #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
    4963 
    4964 > view matrix models
    4965 > #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
    4966 
    4967 > view matrix models
    4968 > #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
    4969 
    4970 > view matrix models
    4971 > #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
    4972 
    4973 > view matrix models
    4974 > #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
    4975 
    4976 > view matrix models
    4977 > #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
    4978 
    4979 > view matrix models
    4980 > #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
    4981 
    4982 > view matrix models
    4983 > #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
    4984 
    4985 > view matrix models
    4986 > #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
    4987 
    4988 > view matrix models
    4989 > #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
    4990 
    4991 > view matrix models
    4992 > #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
    4993 
    4994 > view matrix models
    4995 > #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
    4996 
    4997 > view matrix models
    4998 > #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
    4999 
    5000 > view matrix models
    5001 > #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
    5002 
    5003 > view matrix models
    5004 > #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
    5005 
    5006 > view matrix models
    5007 > #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
    5008 
    5009 > view matrix models
    5010 > #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
    5011 
    5012 > view matrix models
    5013 > #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
    5014 
    5015 > view matrix models
    5016 > #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
    5017 
    5018 > view matrix models
    5019 > #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
    5020 
    5021 > view matrix models
    5022 > #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
    5023 
    5024 > view matrix models
    5025 > #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
    5026 
    5027 > fitmap #5 inMap #1
    5028 
    5029 Fit molecule 6p40 chain A.pdb (#5) to map
    5030 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    5031 average map value = 0.007946, steps = 252 
    5032 shifted from previous position = 16 
    5033 rotated from previous position = 18.4 degrees 
    5034 atoms outside contour = 2833, contour level = 0.014764 
    5035  
    5036 Position of 6p40 chain A.pdb (#5) relative to
    5037 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    5038 Matrix rotation and translation 
    5039 -0.73613185 -0.56150059 0.37792463 163.17969107 
    5040 -0.46612986 0.01572531 -0.88457657 172.81062550 
    5041 0.49074726 -0.82732692 -0.27330809 169.11103321 
    5042 Axis 0.36134182 -0.71210116 0.60195019 
    5043 Axis point 121.35607225 0.00000000 161.76119709 
    5044 Rotation angle (degrees) 175.45637507 
    5045 Shift along axis 37.70141919 
    5046  
    5047 
    5048 > view matrix models
    5049 > #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
    5050 
    5051 > volume #1 level 0.01215
    5052 
    5053 Alignment identifier is 5/A 
    5054 
    5055 > select #5/A:128
    5056 
    5057 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5058 
    5059 > select #5/A:128-130
    5060 
    5061 23 atoms, 23 bonds, 3 residues, 1 model selected 
    5062 
    5063 > view matrix models
    5064 > #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
    5065 
    5066 > view matrix models
    5067 > #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
    5068 
    5069 > view matrix models
    5070 > #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
    5071 
    5072 > view matrix models
    5073 > #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
    5074 
    5075 > view matrix models
    5076 > #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
    5077 
    5078 > view matrix models
    5079 > #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
    5080 
    5081 > view matrix models
    5082 > #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
    5083 
    5084 > view matrix models
    5085 > #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
    5086 
    5087 > view matrix models
    5088 > #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
    5089 
    5090 > undo
    5091 
    5092 > undo
    5093 
    5094 > view matrix models
    5095 > #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
    5096 
    5097 > undo
    5098 
    5099 > view matrix models
    5100 > #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
    5101 
    5102 > view matrix models
    5103 > #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
    5104 
    5105 > view matrix models
    5106 > #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
    5107 
    5108 > view matrix models
    5109 > #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
    5110 
    5111 > view matrix models
    5112 > #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
    5113 
    5114 > view matrix models
    5115 > #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
    5116 
    5117 > view matrix models
    5118 > #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
    5119 
    5120 > view matrix models
    5121 > #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
    5122 
    5123 > view matrix models
    5124 > #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
    5125 
    5126 > view matrix models
    5127 > #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
    5128 
    5129 > view matrix models
    5130 > #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
    5131 
    5132 > view matrix models
    5133 > #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
    5134 
    5135 > fitmap #5 inMap #1
    5136 
    5137 Fit molecule 6p40 chain A.pdb (#5) to map
    5138 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) using 3132 atoms 
    5139 average map value = 0.01045, steps = 172 
    5140 shifted from previous position = 2.81 
    5141 rotated from previous position = 4.77 degrees 
    5142 atoms outside contour = 1957, contour level = 0.012155 
    5143  
    5144 Position of 6p40 chain A.pdb (#5) relative to
    5145 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    5146 Matrix rotation and translation 
    5147 0.38106123 0.65097517 -0.65652395 160.69008154 
    5148 -0.47455243 -0.47170869 -0.74316279 171.13004434 
    5149 -0.79346856 0.59474555 0.12917196 124.77790708 
    5150 Axis 0.76289349 0.07808767 -0.64179111 
    5151 Axis point 0.00000000 14.99606145 194.70479613 
    5152 Rotation angle (degrees) 118.73359625 
    5153 Shift along axis 55.87121287 
    5154  
    5155 
    5156 > volume #1 level 0.01881
    5157 
    5158 > volume #1 level 0.009023
    5159 
    5160 > save "E:/temp/EM data/H7N100
    5161 > cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
    5162 
    5163 > hide #!1 models
    5164 
    5165 > show #!1 models
    5166 
    5167 Alignment identifier is 5/A 
    5168 
    5169 > select #5/A:180
    5170 
    5171 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5172 
    5173 > select #5/A:180-188
    5174 
    5175 70 atoms, 71 bonds, 9 residues, 1 model selected 
    5176 
    5177 > select #5/A:188
    5178 
    5179 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5180 
    5181 > select #5/A:188-189
    5182 
    5183 15 atoms, 14 bonds, 2 residues, 1 model selected 
    5184 
    5185 > select #5/A:182
    5186 
    5187 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5188 
    5189 > select #5/A:182-191
    5190 
    5191 75 atoms, 75 bonds, 10 residues, 1 model selected 
    5192 
    5193 > select #5/A:181
    5194 
    5195 10 atoms, 10 bonds, 1 residue, 1 model selected 
    5196 
    5197 > select #5/A:181-189
    5198 
    5199 72 atoms, 73 bonds, 9 residues, 1 model selected 
    5200 
    5201 > select
    5202 > #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
    5203 
    5204 1378 atoms, 1409 bonds, 165 residues, 1 model selected 
    5205 
    5206 > select clear
    5207 
    5208 > select #5/A:181-189
    5209 
    5210 72 atoms, 73 bonds, 9 residues, 1 model selected 
    5211 
    5212 > select clear
    5213 
    5214 > volume #1 level 0.006543
    5215 
    5216 > volume #1 level 0.007196
    5217 
    5218 > save "E:/temp/EM data/H7N100
    5219 > cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
    5220 
    5221 > volume #1 level 0.009806
    5222 
    5223 > save "E:/temp/EM data/H7N100
    5224 > cryoEM/20210423/20210423_6429mics/cs124_model_fit.cxs"
    5225 
    5226 ——— End of log from Sat Jun 19 22:49:00 2021 ———
    5227 
    5228 opened ChimeraX session 
    5229 
    5230 > rename #5 6p40_chainA_NTD
    5231 
    5232 > open "E:/temp/EM data/H7N100
    5233 > cryoEM/20210423/20210423_6429mics/3DVA/csJ180new/cryosparc_P19_J200_004_volume_map.mrc"
    5234 
    5235 Opened cryosparc_P19_J200_004_volume_map.mrc as #6, grid size 352,352,352,
    5236 pixel 0.835, shown at level 0.13, step 2, values float32 
    5237 
    5238 > volume #6 level 0.344
    5239 
    5240 > volume #6 level 0.293
    5241 
    5242 > fitmap #6 inMap #1
    5243 
    5244 Fit map cryosparc_P19_J200_004_volume_map.mrc in map
    5245 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc using 19817 points 
    5246 correlation = 0.9007, correlation about mean = 0.5817, overlap = 117.5 
    5247 steps = 88, shift = 0.812, angle = 1.51 degrees 
    5248  
    5249 Position of cryosparc_P19_J200_004_volume_map.mrc (#6) relative to
    5250 cryosparc_P19_J124_008_particles_R31_rln_reconstruct.mrc (#1) coordinates: 
    5251 Matrix rotation and translation 
    5252 0.99974480 -0.01464200 0.01720299 -0.06061973 
    5253 0.01487128 0.99980127 -0.01327652 0.34545763 
    5254 -0.01700518 0.01352896 0.99976387 0.04947551 
    5255 Axis 0.51025532 0.65116893 0.56179938 
    5256 Axis point -4.55800784 0.00000000 10.03539832 
    5257 Rotation angle (degrees) 1.50514621 
    5258 Shift along axis 0.22181505 
    5259  
    5260 
    5261 > hide #!1 models
    5262 
    5263 > volume #6 level 0.293
    5264 
    5265 > volume #6 color #ffffb2b2
    5266 
    5267 > volume #6 color #ffffb264
    5268 
    5269 > copy #5 id #7
    5270 
    5271 Unknown command: copy #5 id #7 
    5272 
    5273 > copy #5
    5274 
    5275 Unknown command: copy #5 
    5276 
    5277 > select #5
    5278 
    5279 3132 atoms, 3120 bonds, 6 pseudobonds, 476 residues, 2 models selected 
    5280 
    5281 > select clear
    5282 
    5283 > help help:user
    5284 
    5285 > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
    5286 
    5287 Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html 
    5288 
    5289 > open "E:/temp/EM data/6p40 chain A.pdb"
    5290 
    5291 Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb 
    5292 --- 
    5293 warnings | Ignored bad PDB record found on line 6811 
    5294 END 
    5295  
    5296 Cannot find LINK/SSBOND residue HIS (65 ) 
    5297 Cannot find LINK/SSBOND residue CYS (97 ) 
    5298 Cannot find LINK/SSBOND residue CYS (100 ) 
    5299 Cannot find LINK/SSBOND residue HIS (257 ) 
    5300 Cannot find LINK/SSBOND residue CYS (287 ) 
    5301 2 messages similar to the above omitted 
    5302  
    5303 6p40 chain A.pdb title: 
    5304 Crystal structure of full length APOBEC3G FKL [more info...] 
    5305  
    5306 Chain information for 6p40 chain A.pdb #7 
    5307 --- 
    5308 Chain | Description 
    5309 A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G 
    5310  
    5311 Non-standard residues in 6p40 chain A.pdb #7 
    5312 --- 
    5313 ZN — zinc ion 
    5314  
    5315 
    5316 > hide#7:194-383
    5317 
    5318 Unknown command: hide#7:194-383 
    5319 
    5320 > hide #7/A:194-383
    5321 
    5322 > select #7/A:55
    5323 
    5324 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5325 
    5326 > select up
    5327 
    5328 63 atoms, 63 bonds, 8 residues, 1 model selected 
    5329 
    5330 > select up
    5331 
    5332 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    5333 
    5334 > ui mousemode right "translate selected models"
    5335 
    5336 > view matrix models #7,1,0,0,23.427,0,1,0,167.66,0,0,1,130.65
    5337 
    5338 > view matrix models #7,1,0,0,125.39,0,1,0,137.14,0,0,1,143.37
    5339 
    5340 > hide #7/A:194-383
    5341 
    5342 > show #7/A:194-383
    5343 
    5344 > hide #7/A:194-383
    5345 
    5346 > hide #7/A:194-383 ribbons
    5347 
    5348 > view matrix models #7,1,0,0,142.32,0,1,0,171.65,0,0,1,153.8
    5349 
    5350 > view matrix models
    5351 > #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
    5352 
    5353 > view matrix models
    5354 > #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
    5355 
    5356 > view matrix models
    5357 > #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
    5358 
    5359 > view matrix models
    5360 > #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
    5361 
    5362 > view matrix models
    5363 > #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
    5364 
    5365 > view matrix models
    5366 > #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
    5367 
    5368 > view matrix models
    5369 > #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
    5370 
    5371 > view matrix models
    5372 > #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
    5373 
    5374 > fitmap #7 inMap #6
    5375 
    5376 Fit molecule 6p40 chain A.pdb (#7) to map
    5377 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5378 average map value = 0.2345, steps = 236 
    5379 shifted from previous position = 1.74 
    5380 rotated from previous position = 19 degrees 
    5381 atoms outside contour = 2092, contour level = 0.293 
    5382  
    5383 Position of 6p40 chain A.pdb (#7) relative to
    5384 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5385 Matrix rotation and translation 
    5386 0.35218186 -0.21663380 -0.91051509 171.67301016 
    5387 0.22929453 0.96316760 -0.14047135 135.10072945 
    5388 0.90740947 -0.15930467 0.38888310 149.00633462 
    5389 Axis -0.01006101 -0.97115893 0.23822071 
    5390 Axis point -42.95329208 0.00000000 218.02893609 
    5391 Rotation angle (degrees) 69.38318884 
    5392 Shift along axis -97.43508846 
    5393  
    5394 
    5395 > select clear
    5396 
    5397 > volume #6 level 0.327
    5398 
    5399 > hide #!7 models
    5400 
    5401 > show #!7 models
    5402 
    5403 > hide #!7 models
    5404 
    5405 > show #!7 models
    5406 
    5407 > hide #!7 models
    5408 
    5409 > show #!7 models
    5410 
    5411 > hide #!7 models
    5412 
    5413 > show #!7 models
    5414 
    5415 > hide #!7 models
    5416 
    5417 > show #!7 models
    5418 
    5419 > hide #!7 models
    5420 
    5421 > show #!7 models
    5422 
    5423 > hide #!7 models
    5424 
    5425 > show #!7 models
    5426 
    5427 > hide #!7 models
    5428 
    5429 > show #!7 models
    5430 
    5431 > hide #!7 models
    5432 
    5433 > show #!7 models
    5434 
    5435 > volume #6 level 0.2964
    5436 
    5437 > volume #6 color #ffffffb2
    5438 
    5439 > volume #6 level 0.3677
    5440 
    5441 > select #7/A:162
    5442 
    5443 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5444 
    5445 > select up
    5446 
    5447 120 atoms, 124 bonds, 13 residues, 1 model selected 
    5448 
    5449 > select up
    5450 
    5451 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    5452 
    5453 > view matrix models
    5454 > #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
    5455 
    5456 > view matrix models
    5457 > #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
    5458 
    5459 > view matrix models
    5460 > #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
    5461 
    5462 > view matrix models
    5463 > #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
    5464 
    5465 > view matrix models
    5466 > #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
    5467 
    5468 > view matrix models
    5469 > #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
    5470 
    5471 > select clear
    5472 
    5473 > fitmap #7 inMap #6
    5474 
    5475 Fit molecule 6p40 chain A.pdb (#7) to map
    5476 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5477 average map value = 0.249, steps = 280 
    5478 shifted from previous position = 9.53 
    5479 rotated from previous position = 20 degrees 
    5480 atoms outside contour = 2477, contour level = 0.36771 
    5481  
    5482 Position of 6p40 chain A.pdb (#7) relative to
    5483 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5484 Matrix rotation and translation 
    5485 0.11069634 -0.33205525 -0.93674203 183.71610499 
    5486 0.37617038 0.88641112 -0.26976134 135.35304582 
    5487 0.91991422 -0.32251301 0.22303181 160.36037152 
    5488 Axis -0.02653708 -0.93400324 0.35627760 
    5489 Axis point -21.73973328 0.00000000 214.66023968 
    5490 Rotation angle (degrees) 83.68067049 
    5491 Shift along axis -74.16266437 
    5492  
    5493 
    5494 > volume #6 level 0.4594
    5495 
    5496 > volume #6 level 0.3541
    5497 
    5498 > select #7/A:76
    5499 
    5500 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5501 
    5502 > select up
    5503 
    5504 196 atoms, 205 bonds, 20 residues, 1 model selected 
    5505 
    5506 > select up
    5507 
    5508 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    5509 
    5510 > view matrix models
    5511 > #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
    5512 
    5513 > view matrix models
    5514 > #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
    5515 
    5516 > view matrix models
    5517 > #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
    5518 
    5519 > volume #6 level 0.2387
    5520 
    5521 > fitmap #7 inMap #6
    5522 
    5523 Fit molecule 6p40 chain A.pdb (#7) to map
    5524 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5525 average map value = 0.2497, steps = 232 
    5526 shifted from previous position = 8.96 
    5527 rotated from previous position = 16.4 degrees 
    5528 atoms outside contour = 1696, contour level = 0.23866 
    5529  
    5530 Position of 6p40 chain A.pdb (#7) relative to
    5531 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5532 Matrix rotation and translation 
    5533 0.02771769 -0.38433519 -0.92277743 184.35664167 
    5534 0.41599719 0.84383230 -0.33895928 139.63658024 
    5535 0.90894338 -0.37447765 0.18327144 163.47018180 
    5536 Axis -0.01776586 -0.91620466 0.40031661 
    5537 Axis point -15.63386294 0.00000000 214.99083409 
    5538 Rotation angle (degrees) 88.42928496 
    5539 Shift along axis -65.77111205 
    5540  
    5541 
    5542 > volume #6 level 0.3134
    5543 
    5544 > volume #6 level 0.2692
    5545 
    5546 > select clear
    5547 
    5548 > volume #6 level 0.3847
    5549 
    5550 > select #7/A:89
    5551 
    5552 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5553 
    5554 > select up
    5555 
    5556 88 atoms, 93 bonds, 9 residues, 1 model selected 
    5557 
    5558 > select up
    5559 
    5560 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    5561 
    5562 > view matrix models
    5563 > #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
    5564 
    5565 > view matrix models
    5566 > #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
    5567 
    5568 > select clear
    5569 
    5570 > select #7/A:72
    5571 
    5572 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5573 
    5574 > select up
    5575 
    5576 196 atoms, 205 bonds, 20 residues, 1 model selected 
    5577 
    5578 > select up
    5579 
    5580 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    5581 
    5582 > view matrix models
    5583 > #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
    5584 
    5585 > view matrix models
    5586 > #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
    5587 
    5588 > view matrix models
    5589 > #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
    5590 
    5591 > view matrix models
    5592 > #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
    5593 
    5594 > fitmap #7 inMap #6
    5595 
    5596 Fit molecule 6p40 chain A.pdb (#7) to map
    5597 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5598 average map value = 0.2364, steps = 124 
    5599 shifted from previous position = 2.31 
    5600 rotated from previous position = 11.4 degrees 
    5601 atoms outside contour = 2453, contour level = 0.38469 
    5602  
    5603 Position of 6p40 chain A.pdb (#7) relative to
    5604 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5605 Matrix rotation and translation 
    5606 0.44857260 0.38354159 0.80726604 108.04580538 
    5607 0.57239194 0.57040868 -0.58906825 154.55189612 
    5608 -0.68640374 0.72631245 0.03633359 151.54672741 
    5609 Axis 0.65794204 0.74712070 0.09446131 
    5610 Axis point 77.18156884 0.00000000 82.59535463 
    5611 Rotation angle (degrees) 88.41514361 
    5612 Shift along axis 200.87209951 
    5613  
    5614 
    5615 > view matrix models
    5616 > #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
    5617 
    5618 > select clear
    5619 
    5620 > select #7/A:88
    5621 
    5622 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5623 
    5624 > select up
    5625 
    5626 88 atoms, 93 bonds, 9 residues, 1 model selected 
    5627 
    5628 > select up
    5629 
    5630 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    5631 
    5632 > view matrix models
    5633 > #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
    5634 
    5635 > view matrix models
    5636 > #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
    5637 
    5638 > view matrix models
    5639 > #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
    5640 
    5641 > view matrix models
    5642 > #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
    5643 
    5644 > view matrix models
    5645 > #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
    5646 
    5647 > view matrix models
    5648 > #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
    5649 
    5650 > view matrix models
    5651 > #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
    5652 
    5653 > view matrix models
    5654 > #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
    5655 
    5656 > view matrix models
    5657 > #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
    5658 
    5659 > view matrix models
    5660 > #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
    5661 
    5662 > view matrix models
    5663 > #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
    5664 
    5665 > view matrix models
    5666 > #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
    5667 
    5668 > view matrix models
    5669 > #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
    5670 
    5671 > view matrix models
    5672 > #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
    5673 
    5674 > fitmap #7 inMap #6
    5675 
    5676 Fit molecule 6p40 chain A.pdb (#7) to map
    5677 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5678 average map value = 0.2497, steps = 292 
    5679 shifted from previous position = 7.79 
    5680 rotated from previous position = 10.2 degrees 
    5681 atoms outside contour = 2494, contour level = 0.38469 
    5682  
    5683 Position of 6p40 chain A.pdb (#7) relative to
    5684 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5685 Matrix rotation and translation 
    5686 0.02761258 -0.38433750 -0.92277962 184.35021900 
    5687 0.41570108 0.84393749 -0.33906064 139.63415571 
    5688 0.90908204 -0.37423815 0.18307281 163.46259403 
    5689 Axis -0.01759532 -0.91627262 0.40016857 
    5690 Axis point -15.59643119 0.00000000 214.95779979 
    5691 Rotation angle (degrees) 88.43497503 
    5692 Shift along axis -65.77406270 
    5693  
    5694 
    5695 > volume #6 level 0.3677
    5696 
    5697 > view matrix models
    5698 > #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
    5699 
    5700 > view matrix models
    5701 > #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
    5702 
    5703 > view matrix models
    5704 > #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
    5705 
    5706 > view matrix models
    5707 > #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
    5708 
    5709 > volume #6 level 0.2726
    5710 
    5711 > fitmap #7 inMap #6
    5712 
    5713 Fit molecule 6p40 chain A.pdb (#7) to map
    5714 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5715 average map value = 0.2497, steps = 168 
    5716 shifted from previous position = 9.74 
    5717 rotated from previous position = 8.6 degrees 
    5718 atoms outside contour = 1924, contour level = 0.27262 
    5719  
    5720 Position of 6p40 chain A.pdb (#7) relative to
    5721 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5722 Matrix rotation and translation 
    5723 0.02770771 -0.38437332 -0.92276185 184.35686250 
    5724 0.41597835 0.84382454 -0.33900170 139.63842874 
    5725 0.90895231 -0.37445599 0.18327142 163.46955802 
    5726 Axis -0.01773380 -0.91620111 0.40032616 
    5727 Axis point -15.62945026 0.00000000 214.99262378 
    5728 Rotation angle (degrees) 88.42979388 
    5729 Shift along axis -65.76509213 
    5730  
    5731 
    5732 > hide #!6 models
    5733 
    5734 > show #!6 models
    5735 
    5736 > view matrix models
    5737 > #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
    5738 
    5739 > view matrix models
    5740 > #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
    5741 
    5742 > view matrix models
    5743 > #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
    5744 
    5745 > fitmap #7 inMap #6
    5746 
    5747 Fit molecule 6p40 chain A.pdb (#7) to map
    5748 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5749 average map value = 0.2343, steps = 184 
    5750 shifted from previous position = 13.2 
    5751 rotated from previous position = 18.4 degrees 
    5752 atoms outside contour = 1986, contour level = 0.27262 
    5753  
    5754 Position of 6p40 chain A.pdb (#7) relative to
    5755 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5756 Matrix rotation and translation 
    5757 -0.37048039 -0.60990412 -0.70054353 186.95343362 
    5758 0.14410655 0.70733837 -0.69203015 155.73990504 
    5759 0.91759336 -0.35733651 -0.17416382 169.08068153 
    5760 Axis 0.18427297 -0.89090098 0.41513722 
    5761 Axis point 43.75085593 0.00000000 190.25039572 
    5762 Rotation angle (degrees) 114.74956996 
    5763 Shift along axis -34.10668609 
    5764  
    5765 
    5766 > view matrix models
    5767 > #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
    5768 
    5769 > view matrix models
    5770 > #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
    5771 
    5772 > view matrix models
    5773 > #7,-0.47167,-0.43877,-0.76486,206.68,0.36152,0.69493,-0.62159,193.85,0.80426,-0.5697,-0.16915,191
    5774 
    5775 > select clear
    5776 
    5777 > select #7/A:88
    5778 
    5779 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5780 
    5781 > select up
    5782 
    5783 88 atoms, 93 bonds, 9 residues, 1 model selected 
    5784 
    5785 > select up
    5786 
    5787 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    5788 
    5789 > view matrix models
    5790 > #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
    5791 
    5792 > view matrix models
    5793 > #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
    5794 
    5795 > view matrix models
    5796 > #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
    5797 
    5798 > fitmap #7 inMap #6
    5799 
    5800 Fit molecule 6p40 chain A.pdb (#7) to map
    5801 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5802 average map value = 0.2497, steps = 296 
    5803 shifted from previous position = 13.9 
    5804 rotated from previous position = 37.7 degrees 
    5805 atoms outside contour = 1927, contour level = 0.27262 
    5806  
    5807 Position of 6p40 chain A.pdb (#7) relative to
    5808 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5809 Matrix rotation and translation 
    5810 0.02748432 -0.38482479 -0.92258034 184.35477027 
    5811 0.41572058 0.84373085 -0.33955065 139.65756235 
    5812 0.90907701 -0.37420332 0.18316895 163.46015648 
    5813 Axis -0.01733274 -0.91616745 0.40042075 
    5814 Axis point -15.56358630 0.00000000 214.99696624 
    5815 Rotation angle (degrees) 88.44181763 
    5816 Shift along axis -65.69224826 
    5817  
    5818 
    5819 > volume #6 level 0.3711
    5820 
    5821 > volume #6 level 0.3066
    5822 
    5823 > view matrix models
    5824 > #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
    5825 
    5826 > view matrix models
    5827 > #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
    5828 
    5829 > view matrix models
    5830 > #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
    5831 
    5832 > view matrix models
    5833 > #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
    5834 
    5835 > view matrix models
    5836 > #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
    5837 
    5838 > view matrix models
    5839 > #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
    5840 
    5841 > view matrix models
    5842 > #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
    5843 
    5844 > fitmap #7 inMap #6
    5845 
    5846 Fit molecule 6p40 chain A.pdb (#7) to map
    5847 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    5848 average map value = 0.2436, steps = 184 
    5849 shifted from previous position = 13.7 
    5850 rotated from previous position = 17.4 degrees 
    5851 atoms outside contour = 2150, contour level = 0.30658 
    5852  
    5853 Position of 6p40 chain A.pdb (#7) relative to
    5854 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    5855 Matrix rotation and translation 
    5856 0.13209677 -0.10027208 -0.98615209 175.96167690 
    5857 0.45725245 0.88885975 -0.02912962 126.34528907 
    5858 0.87947179 -0.44707254 0.16326516 164.88201019 
    5859 Axis -0.20986364 -0.93679448 0.27995241 
    5860 Axis point -40.57498104 0.00000000 190.91857114 
    5861 Rotation angle (degrees) 84.71494613 
    5862 Shift along axis -109.12841075 
    5863  
    5864 
    5865 > close #7
    5866 
    5867 > open "E:/temp/EM data/4n9f.pdb1"
    5868 
    5869 Summary of feedback from opening E:/temp/EM data/4n9f.pdb1 
    5870 --- 
    5871 warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C
    5872 18 GLN C 32 1 15 
    5873 Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54
    5874 1 19 
    5875 Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82
    5876 1 27 
    5877 Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107
    5878 1 23 
    5879 Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C
    5880 110 5 3 
    5881 680 messages similar to the above omitted 
    5882 Cannot find LINK/SSBOND residue HIS (139 ) 
    5883 Cannot find LINK/SSBOND residue HIS (139 ) 
    5884 Cannot find LINK/SSBOND residue CYS (114 ) 
    5885 Cannot find LINK/SSBOND residue CYS (114 ) 
    5886 Cannot find LINK/SSBOND residue CYS (133 ) 
    5887 33 messages similar to the above omitted 
    5888  
    5889 4n9f.pdb1 title: 
    5890 Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
    5891 info...] 
    5892  
    5893 Chain information for 4n9f.pdb1 #7 
    5894 --- 
    5895 Chain | Description 
    5896 U | No description available 
    5897 X | No description available 
    5898 Y | No description available 
    5899 a | No description available 
    5900 b | No description available 
    5901  
    5902 Non-standard residues in 4n9f.pdb1 #7 
    5903 --- 
    5904 ZN — zinc ion 
    5905  
    5906 
    5907 > close #7
    5908 
    5909 > open "E:/temp/EM data/4n9f_color.pdb"
    5910 
    5911 Summary of feedback from opening E:/temp/EM data/4n9f_color.pdb 
    5912 --- 
    5913 warnings | Cannot find LINK/SSBOND residue HIS (139 ) 
    5914 Cannot find LINK/SSBOND residue HIS (139 ) 
    5915 Cannot find LINK/SSBOND residue CYS (114 ) 
    5916 Cannot find LINK/SSBOND residue CYS (114 ) 
    5917 Cannot find LINK/SSBOND residue CYS (133 ) 
    5918 33 messages similar to the above omitted 
    5919  
    5920 4n9f_color.pdb title: 
    5921 Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
    5922 info...] 
    5923  
    5924 Chain information for 4n9f_color.pdb #7 
    5925 --- 
    5926 Chain | Description 
    5927 U | No description available 
    5928 X | No description available 
    5929 Y | No description available 
    5930 a | No description available 
    5931 b | No description available 
    5932  
    5933 Non-standard residues in 4n9f_color.pdb #7 
    5934 --- 
    5935 ZN — zinc ion 
    5936  
    5937 
    5938 > select #7/X:71@CA
    5939 
    5940 1 atom, 1 residue, 1 model selected 
    5941 
    5942 > select up
    5943 
    5944 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5945 
    5946 > select up
    5947 
    5948 84 atoms, 86 bonds, 11 residues, 1 model selected 
    5949 
    5950 > select up
    5951 
    5952 748 atoms, 762 bonds, 95 residues, 1 model selected 
    5953 
    5954 > select up
    5955 
    5956 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    5957 
    5958 > view matrix models #7,1,0,0,40.932,0,1,0,105.11,0,0,1,241.13
    5959 
    5960 > select clear
    5961 
    5962 > select #7/Y:72@NZ
    5963 
    5964 1 atom, 1 residue, 1 model selected 
    5965 
    5966 > select up
    5967 
    5968 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5969 
    5970 > select up
    5971 
    5972 176 atoms, 181 bonds, 21 residues, 1 model selected 
    5973 
    5974 > select up
    5975 
    5976 691 atoms, 706 bonds, 87 residues, 1 model selected 
    5977 
    5978 > select up
    5979 
    5980 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    5981 
    5982 > hide sel atoms
    5983 
    5984 > show sel cartoons
    5985 
    5986 > select clear
    5987 
    5988 > select #7/b:56
    5989 
    5990 10 atoms, 10 bonds, 1 residue, 1 model selected 
    5991 
    5992 > select up
    5993 
    5994 69 atoms, 70 bonds, 9 residues, 1 model selected 
    5995 
    5996 > select up
    5997 
    5998 1415 atoms, 1456 bonds, 173 residues, 1 model selected 
    5999 
    6000 > select up
    6001 
    6002 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    6003 
    6004 > ui mousemode right "translate selected models"
    6005 
    6006 > view matrix models #7,1,0,0,104.77,0,1,0,252.07,0,0,1,260.9
    6007 
    6008 > view matrix models #7,1,0,0,101.38,0,1,0,277.45,0,0,1,261.55
    6009 
    6010 > view matrix models #7,1,0,0,98.503,0,1,0,298.92,0,0,1,262.08
    6011 
    6012 > view matrix models
    6013 > #7,1,-0.00047943,0.002702,98.722,0.00053402,0.99979,-0.020241,297.1,-0.0026918,0.020243,0.99979,263.02
    6014 
    6015 > view matrix models
    6016 > #7,1,-0.00047943,0.002702,99.546,0.00053402,0.99979,-0.020241,290.87,-0.0026918,0.020243,0.99979,263.28
    6017 
    6018 > view matrix models
    6019 > #7,1,-0.00047943,0.002702,102.91,0.00053402,0.99979,-0.020241,265.08,-0.0026918,0.020243,0.99979,266.2
    6020 
    6021 > hide #7/U ribbons
    6022 
    6023 > view matrix models
    6024 > #7,1,-0.00047943,0.002702,95.36,0.00053402,0.99979,-0.020241,234.69,-0.0026918,0.020243,0.99979,286.42
    6025 
    6026 > view matrix models
    6027 > #7,0.99957,-0.0081098,0.028278,97.739,0.006271,0.9979,0.064522,242.91,-0.028741,-0.064317,0.99752,285
    6028 
    6029 > view matrix models
    6030 > #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
    6031 
    6032 > view matrix models
    6033 > #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
    6034 
    6035 > view matrix models
    6036 > #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
    6037 
    6038 > view matrix models
    6039 > #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
    6040 
    6041 Drag select of 6 cryosparc_P19_J200_004_volume_map.mrc 
    6042 
    6043 > select clear
    6044 
    6045 > volume #6 level 0.4628
    6046 
    6047 > hide #7/X ribbons
    6048 
    6049 > hide #7/Y ribbons
    6050 
    6051 > volume #6 level 0.3507
    6052 
    6053 > select #7/b:54
    6054 
    6055 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6056 
    6057 > select up
    6058 
    6059 69 atoms, 70 bonds, 9 residues, 1 model selected 
    6060 
    6061 > select up
    6062 
    6063 1415 atoms, 1456 bonds, 173 residues, 1 model selected 
    6064 
    6065 > select up
    6066 
    6067 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    6068 
    6069 > view matrix models
    6070 > #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
    6071 
    6072 > view matrix models
    6073 > #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
    6074 
    6075 > view matrix models
    6076 > #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
    6077 
    6078 > view matrix models
    6079 > #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
    6080 
    6081 > view matrix models
    6082 > #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
    6083 
    6084 > view matrix models
    6085 > #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
    6086 
    6087 > view matrix models
    6088 > #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
    6089 
    6090 > view matrix models
    6091 > #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
    6092 
    6093 > view matrix models
    6094 > #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
    6095 
    6096 > view matrix models
    6097 > #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
    6098 
    6099 > view matrix models
    6100 > #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
    6101 
    6102 > view matrix models
    6103 > #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
    6104 
    6105 > close #7
    6106 
    6107 > open "E:/temp/EM data/6p40 chain A.pdb"
    6108 
    6109 Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb 
    6110 --- 
    6111 warnings | Cannot find LINK/SSBOND residue HIS (65 ) 
    6112 Cannot find LINK/SSBOND residue CYS (97 ) 
    6113 Cannot find LINK/SSBOND residue CYS (100 ) 
    6114 Cannot find LINK/SSBOND residue HIS (257 ) 
    6115 Cannot find LINK/SSBOND residue CYS (287 ) 
    6116 2 messages similar to the above omitted 
    6117  
    6118 6p40 chain A.pdb title: 
    6119 Crystal structure of full length APOBEC3G FKL [more info...] 
    6120  
    6121 Chain information for 6p40 chain A.pdb #7 
    6122 --- 
    6123 Chain | Description 
    6124 A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G 
    6125  
    6126 Non-standard residues in 6p40 chain A.pdb #7 
    6127 --- 
    6128 ZN — zinc ion 
    6129  
    6130 
    6131 > select #7/A:278
    6132 
    6133 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6134 
    6135 > select up
    6136 
    6137 61 atoms, 62 bonds, 7 residues, 1 model selected 
    6138 
    6139 > select up
    6140 
    6141 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    6142 
    6143 > view matrix models #7,1,0,0,27.84,0,1,0,208.38,0,0,1,171.33
    6144 
    6145 > hide #7/A:194-383 ribbons
    6146 
    6147 > select clear
    6148 
    6149 > hide #7/A:194-383
    6150 
    6151 > select #7/A:118
    6152 
    6153 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6154 
    6155 > select up
    6156 
    6157 71 atoms, 71 bonds, 9 residues, 1 model selected 
    6158 
    6159 > select up
    6160 
    6161 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    6162 
    6163 > select clear
    6164 
    6165 > select clear
    6166 
    6167 > select #7/A:149
    6168 
    6169 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6170 
    6171 > select up
    6172 
    6173 32 atoms, 31 bonds, 4 residues, 1 model selected 
    6174 
    6175 > select up
    6176 
    6177 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    6178 
    6179 > view matrix models
    6180 > #7,0.88195,0.22764,0.41272,9.6528,0.46369,-0.26198,-0.84638,262.4,-0.084549,0.93784,-0.33661,195
    6181 
    6182 > view matrix models
    6183 > #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
    6184 
    6185 > view matrix models
    6186 > #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
    6187 
    6188 > view matrix models
    6189 > #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
    6190 
    6191 > view matrix models
    6192 > #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
    6193 
    6194 > view matrix models
    6195 > #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
    6196 
    6197 > view matrix models
    6198 > #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
    6199 
    6200 > view matrix models
    6201 > #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
    6202 
    6203 > view matrix models
    6204 > #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
    6205 
    6206 > view matrix models
    6207 > #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
    6208 
    6209 > view matrix models
    6210 > #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
    6211 
    6212 > view matrix models
    6213 > #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
    6214 
    6215 > view matrix models
    6216 > #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
    6217 
    6218 > view matrix models
    6219 > #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
    6220 
    6221 > view matrix models
    6222 > #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
    6223 
    6224 > view matrix models
    6225 > #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
    6226 
    6227 > view matrix models
    6228 > #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
    6229 
    6230 > view matrix models
    6231 > #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
    6232 
    6233 > fitmap #7 inMap #6
    6234 
    6235 Fit molecule 6p40 chain A.pdb (#7) to map
    6236 cryosparc_P19_J200_004_volume_map.mrc (#6) using 3132 atoms 
    6237 average map value = 0.2604, steps = 220 
    6238 shifted from previous position = 4.65 
    6239 rotated from previous position = 13.1 degrees 
    6240 atoms outside contour = 2160, contour level = 0.35073 
    6241  
    6242 Position of 6p40 chain A.pdb (#7) relative to
    6243 cryosparc_P19_J200_004_volume_map.mrc (#6) coordinates: 
    6244 Matrix rotation and translation 
    6245 -0.23563322 -0.47812350 -0.84609391 182.99965221 
    6246 0.57781013 0.63109532 -0.51754629 153.35681133 
    6247 0.78141695 -0.61083273 0.12755758 171.71894929 
    6248 Axis -0.04802910 -0.83793409 0.54365400 
    6249 Axis point -4.41864203 0.00000000 220.24652341 
    6250 Rotation angle (degrees) 103.79744558 
    6251 Shift along axis -43.93651557 
    6252  
    6253 
    6254 > select clear
    6255 
    6256 > volume #6 level 0.3439
    6257 
    6258 > volume #6 level 0.3575
    6259 
    6260 > volume #6 level 0.3202
    6261 
    6262 > save "E:/temp/EM data/H7N100
    6263 > cryoEM/20210423/20210423_6429mics/csJ200_modelfit.cxs" includeMaps true
    6264 
    6265 ——— End of log from Sat Jul 24 17:51:44 2021 ———
    6266 
    6267 opened ChimeraX session 
    6268 
    6269 > open "E:/temp/EM data/4n9f.pdb1"
    6270 
    6271 Summary of feedback from opening E:/temp/EM data/4n9f.pdb1 
    6272 --- 
    6273 warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C
    6274 18 GLN C 32 1 15 
    6275 Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54
    6276 1 19 
    6277 Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82
    6278 1 27 
    6279 Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107
    6280 1 23 
    6281 Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C
    6282 110 5 3 
    6283 680 messages similar to the above omitted 
    6284 Cannot find LINK/SSBOND residue HIS (139 ) 
    6285 Cannot find LINK/SSBOND residue HIS (139 ) 
    6286 Cannot find LINK/SSBOND residue CYS (114 ) 
    6287 Cannot find LINK/SSBOND residue CYS (114 ) 
    6288 Cannot find LINK/SSBOND residue CYS (133 ) 
    6289 33 messages similar to the above omitted 
    6290  
    6291 4n9f.pdb1 title: 
    6292 Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more
    6293 info...] 
    6294  
    6295 Chain information for 4n9f.pdb1 #8 
    6296 --- 
    6297 Chain | Description 
    6298 U | No description available 
    6299 X | No description available 
    6300 Y | No description available 
    6301 a | No description available 
    6302 b | No description available 
    6303  
    6304 Non-standard residues in 4n9f.pdb1 #8 
    6305 --- 
    6306 ZN — zinc ion 
    6307  
    6308 
    6309 > select #8/b:106@CD2
    6310 
    6311 1 atom, 1 residue, 1 model selected 
    6312 
    6313 > select up
    6314 
    6315 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6316 
    6317 > select up
    6318 
    6319 109 atoms, 112 bonds, 13 residues, 1 model selected 
    6320 
    6321 > select up
    6322 
    6323 1415 atoms, 1456 bonds, 173 residues, 1 model selected 
    6324 
    6325 > select up
    6326 
    6327 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    6328 
    6329 > ui mousemode right translate
    6330 
    6331 > ui mousemode right "translate selected models"
    6332 
    6333 > view matrix models #8,1,0,0,-11.694,0,1,0,161.04,0,0,1,203.72
    6334 
    6335 > view
    6336 
    6337 > view matrix models #8,1,0,0,118.48,0,1,0,172.5,0,0,1,237.1
    6338 
    6339 > view matrix models #8,1,0,0,107.44,0,1,0,89.501,0,0,1,237.26
    6340 
    6341 > ui tool show "Side View"
    6342 
    6343 > view
    6344 
    6345 > hide sel atoms
    6346 
    6347 > show sel cartoons
    6348 
    6349 > hide 8/X
    6350 
    6351 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    6352 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    6353 
    6354 > hide 8/X cartoon
    6355 
    6356 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    6357 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    6358 
    6359 > hide #8/X ribbons
    6360 
    6361 > hide #8/Y ribbons
    6362 
    6363 > hide #8/U ribbons
    6364 
    6365 > select clear
    6366 
    6367 > select #8/b:16
    6368 
    6369 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6370 
    6371 > select up
    6372 
    6373 164 atoms, 168 bonds, 18 residues, 1 model selected 
    6374 
    6375 > select up
    6376 
    6377 1415 atoms, 1456 bonds, 173 residues, 1 model selected 
    6378 
    6379 > select up
    6380 
    6381 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    6382 
    6383 > view matrix models
    6384 > #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
    6385 
    6386 > view matrix models
    6387 > #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
    6388 
    6389 > view matrix models
    6390 > #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
    6391 
    6392 > view matrix models
    6393 > #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
    6394 
    6395 > view matrix models
    6396 > #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
    6397 
    6398 > volume #1 level 0.005238
    6399 
    6400 > hide #!1 models
    6401 
    6402 > hide #!6 models
    6403 
    6404 > show #!6 models
    6405 
    6406 > volume #1 level 0.007196
    6407 
    6408 > hide #!1 models
    6409 
    6410 > show #!1 models
    6411 
    6412 > hide #!6 models
    6413 
    6414 > show #!6 models
    6415 
    6416 > hide #!1 models
    6417 
    6418 > volume #1 level 0.007196
    6419 
    6420 > hide #!1 models
    6421 
    6422 > close #1
    6423 
    6424 > rename #6 id #1
    6425 
    6426 > volume #1 level 0.1945
    6427 
    6428 > select clear
    6429 
    6430 > select #8/b:125
    6431 
    6432 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6433 
    6434 > select clear
    6435 
    6436 > select #8/a:129
    6437 
    6438 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6439 
    6440 > select up
    6441 
    6442 69 atoms, 68 bonds, 8 residues, 1 model selected 
    6443 
    6444 > select up
    6445 
    6446 1193 atoms, 1216 bonds, 146 residues, 1 model selected 
    6447 
    6448 > select up
    6449 
    6450 6505 atoms, 6643 bonds, 800 residues, 1 model selected 
    6451 
    6452 > ui mousemode right "translate selected models"
    6453 
    6454 > ui mousemode right "rotate selected models"
    6455 
    6456 > ui mousemode right "translate selected models"
    6457 
    6458 > view matrix models
    6459 > #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
    6460 
    6461 > view matrix models
    6462 > #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
    6463 
    6464 > view matrix models
    6465 > #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
    6466 
    6467 > view matrix models
    6468 > #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
    6469 
    6470 > view matrix models
    6471 > #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
    6472 
    6473 > volume #1 level 0.2658
    6474 
    6475 > volume #1 level 0.1707
    6476 
    6477 > view matrix models
    6478 > #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
    6479 
    6480 > view matrix models
    6481 > #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
    6482 
    6483 > view matrix models
    6484 > #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
    6485 
    6486 > view matrix models
    6487 > #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
    6488 
    6489 > view matrix models
    6490 > #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
    6491 
    6492 > view matrix models
    6493 > #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
    6494 
    6495 > view matrix models
    6496 > #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
    6497 
    6498 > view matrix models
    6499 > #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
    6500 
    6501 > view matrix models
    6502 > #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
    6503 
    6504 > view matrix models
    6505 > #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
    6506 
    6507 > view matrix models
    6508 > #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
    6509 
    6510 > view matrix models
    6511 > #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
    6512 
    6513 > view matrix models
    6514 > #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
    6515 
    6516 > view matrix models
    6517 > #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
    6518 
    6519 > view matrix models
    6520 > #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
    6521 
    6522 > view matrix models
    6523 > #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
    6524 
    6525 > view matrix models
    6526 > #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
    6527 
    6528 > view matrix models
    6529 > #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
    6530 
    6531 > view matrix models
    6532 > #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
    6533 
    6534 > view matrix models
    6535 > #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
    6536 
    6537 > volume #1 level 0.4119
    6538 
    6539 > volume #1 level 0.327
    6540 
    6541 > view matrix models
    6542 > #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
    6543 
    6544 > view matrix models
    6545 > #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
    6546 
    6547 > view matrix models
    6548 > #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
    6549 
    6550 > view matrix models
    6551 > #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
    6552 
    6553 > view matrix models
    6554 > #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
    6555 
    6556 > view matrix models
    6557 > #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
    6558 
    6559 > view matrix models
    6560 > #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
    6561 
    6562 > view matrix models
    6563 > #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
    6564 
    6565 > view matrix models
    6566 > #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
    6567 
    6568 > view matrix models
    6569 > #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
    6570 
    6571 > view matrix models
    6572 > #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
    6573 
    6574 > volume #1 level 0.2319
    6575 
    6576 > select clear
    6577 
    6578 > fitmap #8 inMap #1
    6579 
    6580 Fit molecule 4n9f.pdb1 (#8) to map cryosparc_P19_J200_004_volume_map.mrc (#1)
    6581 using 6505 atoms 
    6582 average map value = 0.141, steps = 180 
    6583 shifted from previous position = 6.65 
    6584 rotated from previous position = 4.42 degrees 
    6585 atoms outside contour = 5044, contour level = 0.23187 
    6586  
    6587 Position of 4n9f.pdb1 (#8) relative to cryosparc_P19_J200_004_volume_map.mrc
    6588 (#1) coordinates: 
    6589 Matrix rotation and translation 
    6590 -0.57344950 -0.53030875 0.62444238 247.88862513 
    6591 -0.71948550 -0.03851333 -0.69343877 90.36992892 
    6592 0.39178601 -0.84692935 -0.35946401 112.93105909 
    6593 Axis -0.45564790 0.69065726 -0.56158485 
    6594 Axis point 156.75916491 0.00000000 81.17267996 
    6595 Rotation angle (degrees) 170.30338560 
    6596 Shift along axis -113.95565643 
    6597  
    6598 
    6599 > select clear
    6600 
    6601 > volume #1 level 0.3643
    6602 
    6603 > volume #1 level 0.2862
    6604 
    6605 > volume #1 level 0.3168
    6606 
    6607 > volume #1 level 0.4153
    6608 
    6609 > volume #1 level 0.3168
    6610 
    6611 > volume #1 level 0.2115
    6612 
    6613 > volume #1 level 0.1775
    6614 
    6615 > volume #1 level 0.293
    6616 
    6617 > volume #1 level 0.3202
    6618 
    6619 > hide #!1 models
    6620 
    6621 > show #!1 models
    6622 
    6623 > select #8/b:43
    6624 
    6625 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6626 
    6627 > select clear
    6628 
    6629 > hide #!1 models
    6630 
    6631 > show #!1 models
    6632 
    6633 > hide #!1 models
    6634 
    6635 > show #!1 models
    6636 
    6637 > select #8/b:43
    6638 
    6639 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6640 
    6641 > volume #1 level 0.1028
    6642 
    6643 > volume #1 level 0.2489
    6644 
    6645 > volume #1 level 0.2285
    6646 
    6647 > save "E:/temp/EM data/H7N100
    6648 > cryoEM/20210423/20210423_6429mics/csJ200_modelfit.cxs"
    6649 
    6650 ——— End of log from Sat Jul 24 18:31:45 2021 ———
    6651 
    6652 opened ChimeraX session 
    6653 
    6654 > open "E:/temp/EM data/6p40 chain A.pdb"
    6655 
    6656 Summary of feedback from opening E:/temp/EM data/6p40 chain A.pdb 
    6657 --- 
    6658 warnings | Cannot find LINK/SSBOND residue HIS (65 ) 
    6659 Cannot find LINK/SSBOND residue CYS (97 ) 
    6660 Cannot find LINK/SSBOND residue CYS (100 ) 
    6661 Cannot find LINK/SSBOND residue HIS (257 ) 
    6662 Cannot find LINK/SSBOND residue CYS (287 ) 
    6663 2 messages similar to the above omitted 
    6664  
    6665 6p40 chain A.pdb title: 
    6666 Crystal structure of full length APOBEC3G FKL [more info...] 
    6667  
    6668 Chain information for 6p40 chain A.pdb #6 
    6669 --- 
    6670 Chain | Description 
    6671 A | apolipoprotein B MRNA editing enzyme, catalytic peptide- like 3G 
    6672  
    6673 Non-standard residues in 6p40 chain A.pdb #6 
    6674 --- 
    6675 ZN — zinc ion 
    6676  
    6677 
    6678 > select #6/A:35
    6679 
    6680 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6681 
    6682 > select up
    6683 
    6684 80 atoms, 81 bonds, 10 residues, 1 model selected 
    6685 
    6686 > select up
    6687 
    6688 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    6689 
    6690 > view matrix models #6,1,0,0,41.073,0,1,0,83.801,0,0,1,144.45
    6691 
    6692 > hide #6/A:1-193
    6693 
    6694 > hide #6/A:1-193 ribbons
    6695 
    6696 > view matrix models #6,1,0,0,80.795,0,1,0,193.83,0,0,1,176.77
    6697 
    6698 > view matrix models #6,1,0,0,51.372,0,1,0,106.89,0,0,1,173
    6699 
    6700 > view matrix models
    6701 > #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
    6702 
    6703 > view matrix models
    6704 > #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
    6705 
    6706 > view matrix models
    6707 > #6,0.11504,0.78637,-0.60695,86.297,-0.96734,-0.050263,-0.24847,147.43,-0.22589,0.61571,0.7549,181
    6708 
    6709 > view matrix models
    6710 > #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
    6711 
    6712 > view matrix models
    6713 > #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
    6714 
    6715 > view matrix models
    6716 > #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
    6717 
    6718 > view matrix models
    6719 > #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
    6720 
    6721 > view matrix models
    6722 > #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
    6723 
    6724 > view matrix models
    6725 > #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
    6726 
    6727 > view matrix models
    6728 > #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
    6729 
    6730 > view matrix models
    6731 > #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
    6732 
    6733 > view matrix models
    6734 > #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
    6735 
    6736 > view matrix models
    6737 > #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
    6738 
    6739 > view matrix models
    6740 > #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
    6741 
    6742 > view matrix models
    6743 > #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
    6744 
    6745 > view matrix models
    6746 > #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
    6747 
    6748 > view matrix models
    6749 > #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
    6750 
    6751 > view matrix models
    6752 > #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
    6753 
    6754 > view matrix models
    6755 > #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
    6756 
    6757 > view matrix models
    6758 > #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
    6759 
    6760 > view matrix models
    6761 > #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
    6762 
    6763 > view matrix models
    6764 > #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
    6765 
    6766 > view matrix models
    6767 > #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
    6768 
    6769 > view matrix models
    6770 > #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
    6771 
    6772 > view matrix models
    6773 > #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
    6774 
    6775 > view matrix models
    6776 > #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
    6777 
    6778 > view matrix models
    6779 > #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
    6780 
    6781 > view matrix models
    6782 > #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
    6783 
    6784 > view matrix models
    6785 > #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
    6786 
    6787 > view matrix models
    6788 > #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
    6789 
    6790 > view matrix models
    6791 > #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
    6792 
    6793 > view matrix models
    6794 > #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
    6795 
    6796 > view matrix models
    6797 > #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
    6798 
    6799 > view matrix models
    6800 > #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
    6801 
    6802 > view matrix models
    6803 > #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
    6804 
    6805 > view matrix models
    6806 > #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
    6807 
    6808 > fitmap #8 inMap #1
    6809 
    6810 Fit molecule 4n9f.pdb1 (#8) to map cryosparc_P19_J200_004_volume_map.mrc (#1)
    6811 using 6505 atoms 
    6812 average map value = 0.141, steps = 192 
    6813 shifted from previous position = 0.0165 
    6814 rotated from previous position = 0.0209 degrees 
    6815 atoms outside contour = 5023, contour level = 0.22848 
    6816  
    6817 Position of 4n9f.pdb1 (#8) relative to cryosparc_P19_J200_004_volume_map.mrc
    6818 (#1) coordinates: 
    6819 Matrix rotation and translation 
    6820 -0.57353384 -0.53052325 0.62418266 247.85205740 
    6821 -0.71938580 -0.03828804 -0.69355466 90.36110724 
    6822 0.39184561 -0.84680522 -0.35969141 112.90168214 
    6823 Axis -0.45562023 0.69074763 -0.56149615 
    6824 Axis point 156.72789884 0.00000000 81.16431177 
    6825 Rotation angle (degrees) 170.31810134 
    6826 Shift along axis -113.90354990 
    6827  
    6828 
    6829 > select clear
    6830 
    6831 > volume #1 level 0.2522
    6832 
    6833 > volume #1 level 0.259
    6834 
    6835 > save "E:/temp/EM data/H7N100
    6836 > cryoEM/20210423/20210423_6429mics/csJ200_modelfit.cxs" includeMaps true
    6837 
    6838 > volume #1 level 0.3371
    6839 
    6840 > volume #1 level 0.2726
    6841 
    6842 > volume #1 level 0.2862
    6843 
    6844 > volume #1 level 0.2421
    6845 
    6846 > save "E:/temp/EM data/H7N100
    6847 > cryoEM/20210423/20210423_6429mics/csJ200_modelfit.cxs"
    6848 
    6849 ——— End of log from Sat Jul 24 18:49:24 2021 ———
    6850 
    6851 opened ChimeraX session 
    6852 
    6853 > open E:/Krios/20210423/csrelion/6221/rlnJ031_Refine3D_class001.mrc
    6854 
    6855 Opened rlnJ031_Refine3D_class001.mrc as #9, grid size 352,352,352, pixel
    6856 0.835, shown at level 0.00471, step 2, values float32 
    6857 
    6858 > hide #!1 models
    6859 
    6860 > volume #9 level 0.007178
    6861 
    6862 > volume #9 step 1
    6863 
    6864 > volume #1 step 1
    6865 
    6866 > volume #9 level 0.008252
    6867 
    6868 > hide #!9 models
    6869 
    6870 > show #!1 models
    6871 
    6872 > hide #!1 models
    6873 
    6874 > show #!9 models
    6875 
    6876 > hide #!9 models
    6877 
    6878 > show #!1 models
    6879 
    6880 > hide #!1 models
    6881 
    6882 > select #7/A:116
    6883 
    6884 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6885 
    6886 > select up
    6887 
    6888 71 atoms, 71 bonds, 9 residues, 1 model selected 
    6889 
    6890 > select up
    6891 
    6892 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    6893 
    6894 > select add #6/A:342
    6895 
    6896 3095 atoms, 3131 bonds, 429 residues, 2 models selected 
    6897 
    6898 > select up
    6899 
    6900 3204 atoms, 3245 bonds, 441 residues, 2 models selected 
    6901 
    6902 > select up
    6903 
    6904 6168 atoms, 6240 bonds, 856 residues, 2 models selected 
    6905 
    6906 > select add #8/a:37
    6907 
    6908 6178 atoms, 6250 bonds, 857 residues, 3 models selected 
    6909 
    6910 > select up
    6911 
    6912 6293 atoms, 6367 bonds, 871 residues, 3 models selected 
    6913 
    6914 > select up
    6915 
    6916 7361 atoms, 7456 bonds, 1002 residues, 3 models selected 
    6917 
    6918 > select add #8/b:30
    6919 
    6920 7373 atoms, 7468 bonds, 1003 residues, 3 models selected 
    6921 
    6922 > select up
    6923 
    6924 7525 atoms, 7624 bonds, 1020 residues, 3 models selected 
    6925 
    6926 > select up
    6927 
    6928 8776 atoms, 8912 bonds, 1175 residues, 3 models selected 
    6929 
    6930 > view #9 clip false
    6931 
    6932 No displayed objects specified. 
    6933 
    6934 > view matrix models
    6935 > #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
    6936 
    6937 > view matrix models
    6938 > #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
    6939 
    6940 > view matrix models
    6941 > #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
    6942 
    6943 > show #!9 models
    6944 
    6945 > hide #!9 models
    6946 
    6947 > view matrix models
    6948 > #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
    6949 
    6950 > select #9
    6951 
    6952 2 models selected 
    6953 
    6954 > ~select #9
    6955 
    6956 Nothing selected 
    6957 
    6958 > show #!9 models
    6959 
    6960 > hide #!9 models
    6961 
    6962 > select #6/A:343
    6963 
    6964 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6965 
    6966 > select up
    6967 
    6968 120 atoms, 125 bonds, 13 residues, 1 model selected 
    6969 
    6970 > select up
    6971 
    6972 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    6973 
    6974 > select up
    6975 
    6976 3132 atoms, 3120 bonds, 476 residues, 1 model selected 
    6977 
    6978 > select up
    6979 
    6980 28755 atoms, 28885 bonds, 4062 residues, 11 models selected 
    6981 
    6982 > select down
    6983 
    6984 3132 atoms, 3120 bonds, 476 residues, 1 model selected 
    6985 
    6986 > select down
    6987 
    6988 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    6989 
    6990 > select add #8/a:65
    6991 
    6992 3090 atoms, 3125 bonds, 429 residues, 2 models selected 
    6993 
    6994 > select up
    6995 
    6996 3144 atoms, 3182 bonds, 435 residues, 2 models selected 
    6997 
    6998 > select up
    6999 
    7000 4277 atoms, 4336 bonds, 574 residues, 2 models selected 
    7001 
    7002 > select add #8/b:148
    7003 
    7004 4285 atoms, 4343 bonds, 575 residues, 2 models selected 
    7005 
    7006 > select up
    7007 
    7008 4359 atoms, 4418 bonds, 585 residues, 2 models selected 
    7009 
    7010 > select up
    7011 
    7012 5692 atoms, 5792 bonds, 747 residues, 2 models selected 
    7013 
    7014 > select add #7/A:186
    7015 
    7016 5701 atoms, 5800 bonds, 748 residues, 3 models selected 
    7017 
    7018 > select up
    7019 
    7020 5822 atoms, 5924 bonds, 764 residues, 3 models selected 
    7021 
    7022 > select up
    7023 
    7024 8776 atoms, 8912 bonds, 1175 residues, 3 models selected 
    7025 
    7026 > show #!9 models
    7027 
    7028 > hide #!9 models
    7029 
    7030 > view matrix models
    7031 > #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
    7032 
    7033 > show #!9 models
    7034 
    7035 > hide #!9 models
    7036 
    7037 > view matrix models
    7038 > #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
    7039 
    7040 > view matrix models
    7041 > #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
    7042 
    7043 > show #!9 models
    7044 
    7045 > hide #!9 models
    7046 
    7047 > show #!9 models
    7048 
    7049 > hide #!9 models
    7050 
    7051 > show #!9 models
    7052 
    7053 > hide #!9 models
    7054 
    7055 > view matrix models
    7056 > #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
    7057 
    7058 > view matrix models
    7059 > #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
    7060 
    7061 > show #!9 models
    7062 
    7063 > view matrix models
    7064 > #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
    7065 
    7066 > view matrix models
    7067 > #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
    7068 
    7069 > view matrix models
    7070 > #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
    7071 
    7072 > view matrix models
    7073 > #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
    7074 
    7075 > view matrix models
    7076 > #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
    7077 
    7078 > view matrix models
    7079 > #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
    7080 
    7081 > view matrix models
    7082 > #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
    7083 
    7084 > view matrix models
    7085 > #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
    7086 
    7087 > select clear
    7088 
    7089 > select #7
    7090 
    7091 3132 atoms, 3120 bonds, 6 pseudobonds, 476 residues, 2 models selected 
    7092 
    7093 > fitmap #7 inMap #9
    7094 
    7095 Fit molecule 6p40 chain A.pdb (#7) to map rlnJ031_Refine3D_class001.mrc (#9)
    7096 using 3132 atoms 
    7097 average map value = 0.007227, steps = 220 
    7098 shifted from previous position = 6.35 
    7099 rotated from previous position = 14.6 degrees 
    7100 atoms outside contour = 1860, contour level = 0.0082516 
    7101  
    7102 Position of 6p40 chain A.pdb (#7) relative to rlnJ031_Refine3D_class001.mrc
    7103 (#9) coordinates: 
    7104 Matrix rotation and translation 
    7105 -0.63754336 -0.77040468 0.00388575 150.98929727 
    7106 -0.23854083 0.19260203 -0.95184176 167.97891696 
    7107 0.73255494 -0.60776731 -0.30656512 184.29895480 
    7108 Axis 0.35636252 -0.75469243 0.55085850 
    7109 Axis point 86.41125727 0.00000000 177.46455404 
    7110 Rotation angle (degrees) 151.13424529 
    7111 Shift along axis 28.55715561 
    7112  
    7113 
    7114 > fitmap #6 inMap #9
    7115 
    7116 Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
    7117 using 3132 atoms 
    7118 average map value = 0.007893, steps = 244 
    7119 shifted from previous position = 12.4 
    7120 rotated from previous position = 25.4 degrees 
    7121 atoms outside contour = 1847, contour level = 0.0082516 
    7122  
    7123 Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
    7124 (#9) coordinates: 
    7125 Matrix rotation and translation 
    7126 -0.23850561 0.75894450 -0.60590289 147.84513899 
    7127 -0.19733010 0.57301885 0.79543084 104.70296891 
    7128 0.95088164 0.30927759 0.01309438 155.33804486 
    7129 Axis -0.25714174 -0.82343229 -0.50580371 
    7130 Axis point 34.73908461 0.00000000 86.93032961 
    7131 Rotation angle (degrees) 109.03806143 
    7132 Shift along axis -202.80352043 
    7133  
    7134 
    7135 > volume #9 level 0.01029
    7136 
    7137 > fitmap #8 inMap #9
    7138 
    7139 Fit molecule 4n9f.pdb1 (#8) to map rlnJ031_Refine3D_class001.mrc (#9) using
    7140 6505 atoms 
    7141 average map value = 0.005075, steps = 260 
    7142 shifted from previous position = 13.2 
    7143 rotated from previous position = 10.4 degrees 
    7144 atoms outside contour = 5408, contour level = 0.010292 
    7145  
    7146 Position of 4n9f.pdb1 (#8) relative to rlnJ031_Refine3D_class001.mrc (#9)
    7147 coordinates: 
    7148 Matrix rotation and translation 
    7149 0.36762856 -0.17583896 0.91319761 234.88617723 
    7150 -0.92969949 -0.09329134 0.35630824 219.37882466 
    7151 0.02254056 -0.97998845 -0.19777396 145.93826787 
    7152 Axis -0.75324502 0.50204644 -0.42493684 
    7153 Axis point 0.00000000 224.70545159 -107.70282102 
    7154 Rotation angle (degrees) 117.49804676 
    7155 Shift along axis -128.80303213 
    7156  
    7157 
    7158 > volume #9 level 0.005674
    7159 
    7160 > volume #9 level 0.006855
    7161 
    7162 > select clear
    7163 
    7164 > select clear
    7165 
    7166 > volume #9 level 0.01094
    7167 
    7168 > select #6/A:365
    7169 
    7170 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7171 
    7172 > select up
    7173 
    7174 128 atoms, 128 bonds, 17 residues, 1 model selected 
    7175 
    7176 > select up
    7177 
    7178 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    7179 
    7180 > view matrix models
    7181 > #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
    7182 
    7183 > view matrix models
    7184 > #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
    7185 
    7186 > view matrix models
    7187 > #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
    7188 
    7189 > view matrix models
    7190 > #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
    7191 
    7192 > view matrix models
    7193 > #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
    7194 
    7195 > view matrix models
    7196 > #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
    7197 
    7198 > view matrix models
    7199 > #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
    7200 
    7201 > view matrix models
    7202 > #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
    7203 
    7204 > fitmap #6 inMap #9
    7205 
    7206 Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
    7207 using 3132 atoms 
    7208 average map value = 0.007728, steps = 148 
    7209 shifted from previous position = 11.6 
    7210 rotated from previous position = 8.93 degrees 
    7211 atoms outside contour = 2321, contour level = 0.010937 
    7212  
    7213 Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
    7214 (#9) coordinates: 
    7215 Matrix rotation and translation 
    7216 -0.13333327 0.73447066 -0.66541347 149.49306113 
    7217 0.38637171 0.65680662 0.64755074 98.52677917 
    7218 0.91265499 -0.17075688 -0.37135286 165.66345422 
    7219 Axis -0.45175903 -0.87119643 -0.19217326 
    7220 Axis point 1.71948038 0.00000000 95.99345047 
    7221 Rotation angle (degrees) 115.08357227 
    7222 Shift along axis -185.20710454 
    7223  
    7224 
    7225 > view matrix models
    7226 > #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
    7227 
    7228 > view matrix models
    7229 > #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
    7230 
    7231 > view matrix models
    7232 > #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
    7233 
    7234 > view matrix models
    7235 > #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
    7236 
    7237 > fitmap #6 inMap #9
    7238 
    7239 Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
    7240 using 3132 atoms 
    7241 average map value = 0.007729, steps = 164 
    7242 shifted from previous position = 14 
    7243 rotated from previous position = 10 degrees 
    7244 atoms outside contour = 2320, contour level = 0.010937 
    7245  
    7246 Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
    7247 (#9) coordinates: 
    7248 Matrix rotation and translation 
    7249 -0.13324155 0.73448528 -0.66541570 149.49325604 
    7250 0.38618835 0.65680998 0.64765669 98.51054761 
    7251 0.91274599 -0.17068101 -0.37116404 165.65156854 
    7252 Axis -0.45174250 -0.87118399 -0.19226846 
    7253 Axis point 1.72593886 0.00000000 95.99015392 
    7254 Rotation angle (degrees) 115.07459222 
    7255 Shift along axis -185.20284131 
    7256  
    7257 
    7258 > view matrix models
    7259 > #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
    7260 
    7261 > view matrix models
    7262 > #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
    7263 
    7264 > volume #9 level 0.008037
    7265 
    7266 > view matrix models
    7267 > #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
    7268 
    7269 > fitmap #6 inMap #9
    7270 
    7271 Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
    7272 using 3132 atoms 
    7273 average map value = 0.00765, steps = 164 
    7274 shifted from previous position = 14.1 
    7275 rotated from previous position = 7.6 degrees 
    7276 atoms outside contour = 1848, contour level = 0.0080368 
    7277  
    7278 Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
    7279 (#9) coordinates: 
    7280 Matrix rotation and translation 
    7281 -0.16644106 0.79311293 -0.58589185 146.34040774 
    7282 0.32281416 0.60526380 0.72763091 96.40061293 
    7283 0.93171261 -0.06802653 -0.35676883 164.39881319 
    7284 Axis -0.44777830 -0.85407402 -0.26467368 
    7285 Axis point 7.34850755 0.00000000 88.88324692 
    7286 Rotation angle (degrees) 117.32085964 
    7287 Shift along axis -191.37335764 
    7288  
    7289 
    7290 > view matrix models
    7291 > #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
    7292 
    7293 > fitmap #6 inMap #9
    7294 
    7295 Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
    7296 using 3132 atoms 
    7297 average map value = 0.007133, steps = 128 
    7298 shifted from previous position = 10.7 
    7299 rotated from previous position = 9.89 degrees 
    7300 atoms outside contour = 1958, contour level = 0.0080368 
    7301  
    7302 Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
    7303 (#9) coordinates: 
    7304 Matrix rotation and translation 
    7305 -0.06938187 0.79367977 -0.60436626 144.29595832 
    7306 0.18857598 0.60533831 0.77330759 93.86982414 
    7307 0.97960464 -0.06031543 -0.19166844 159.27490300 
    7308 Axis -0.44119751 -0.83832140 -0.32025302 
    7309 Axis point 6.13740716 0.00000000 86.73688903 
    7310 Rotation angle (degrees) 109.13869523 
    7311 Shift along axis -193.36436754 
    7312  
    7313 
    7314 > select clear
    7315 
    7316 > select #6/A:346
    7317 
    7318 14 atoms, 15 bonds, 1 residue, 1 model selected 
    7319 
    7320 > select up
    7321 
    7322 120 atoms, 125 bonds, 13 residues, 1 model selected 
    7323 
    7324 > select up
    7325 
    7326 3084 atoms, 3120 bonds, 428 residues, 1 model selected 
    7327 
    7328 > view matrix models
    7329 > #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
    7330 
    7331 > view matrix models
    7332 > #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
    7333 
    7334 > fitmap #6 inMap #9
    7335 
    7336 Fit molecule 6p40 chain A.pdb (#6) to map rlnJ031_Refine3D_class001.mrc (#9)
    7337 using 3132 atoms 
    7338 average map value = 0.007807, steps = 184 
    7339 shifted from previous position = 10.1 
    7340 rotated from previous position = 19.3 degrees 
    7341 atoms outside contour = 1786, contour level = 0.0080368 
    7342  
    7343 Position of 6p40 chain A.pdb (#6) relative to rlnJ031_Refine3D_class001.mrc
    7344 (#9) coordinates: 
    7345 Matrix rotation and translation 
    7346 -0.23597200 0.70831755 -0.66528450 150.71900005 
    7347 -0.06978088 0.67049968 0.73862088 102.18862974 
    7348 0.96925117 0.22071798 -0.10879213 157.50216326 
    7349 Axis -0.27505384 -0.86808805 -0.41324148 
    7350 Axis point 28.01824000 0.00000000 93.77146687 
    7351 Rotation angle (degrees) 109.70224977 
    7352 Shift along axis -195.25099563 
    7353  
    7354 
    7355 > select clear
    7356 
    7357 > volume #9 level 0.0104
    7358 
    7359 > volume #9 level 0.008574
    7360 
    7361 > volume #9 level 0.008681
    7362 
    7363 > hide #!9 models
    7364 
    7365 > select #7/A:128
    7366 
    7367 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7368 
    7369 > select clear
    7370 
    7371 > show #!9 models
    7372 
    7373 > hide #!9 models
    7374 
    7375 > show #!9 models
    7376 
    7377 > hide #!9 models
    7378 
    7379 > show #!9 models
    7380 
    7381 > volume #9 level 0.009326
    7382 
    7383 > save E:/Krios/20210423/csrelion/6221/rlnJ31_modelfit.cxs includeMaps true
    7384 
    7385 > close #1
    7386 
    7387 > rename #9 id #1
    7388 
    7389 > save E:/Krios/20210423/csrelion/6221/rlnJ31_modelfit.cxs
    7390 
    7391 ——— End of log from Sun Jul 25 16:29:33 2021 ———
    7392 
    7393 opened ChimeraX session 
    7394 
    7395 > open "E:/temp/EM data/AF-Q9HC16-F1-model_v1.pdb"
    7396 
    7397 AF-Q9HC16-F1-model_v1.pdb title: 
    7398 Alphafold V2.0 prediction for DNA DC->du-editing enzyme apobec-3G (Q9HC16)
    7399 [more info...] 
    7400  
    7401 Chain information for AF-Q9HC16-F1-model_v1.pdb #9 
    7402 --- 
    7403 Chain | Description 
    7404 A | DNA DC->du-editing enzyme apobec-3G 
    7405  
    7406 
    7407 > matchmaker #9 to #5/A:1-193
    7408 
    7409 Parameters 
    7410 --- 
    7411 Chain pairing | bb 
    7412 Alignment algorithm | Needleman-Wunsch 
    7413 Similarity matrix | BLOSUM-62 
    7414 SS fraction | 0.3 
    7415 Gap open (HH/SS/other) | 18/18/6 
    7416 Gap extend | 1 
    7417 SS matrix |  |  | H | S | O 
    7418 ---|---|---|--- 
    7419 H | 6 | -9 | -6 
    7420 S |  | 6 | -6 
    7421 O |  |  | 4 
    7422 Iteration cutoff | 2 
    7423  
    7424 Matchmaker 6p40_chainA_NTD, chain A (#5) with AF-Q9HC16-F1-model_v1.pdb, chain
    7425 A (#9), sequence alignment score = 755.6 
    7426 RMSD between 160 pruned atom pairs is 0.752 angstroms; (across all 183 pairs:
    7427 2.237) 
    7428  
    7429 
    7430 > hide #!5 models
    7431 
    7432 > hide #!4 models
    7433 
    7434 > open E:/Krios/20210423/csrelion/6221/rlnJ084_Refine3D_class001.mrc
    7435 
    7436 Opened rlnJ084_Refine3D_class001.mrc as #10, grid size 352,352,352, pixel
    7437 0.835, shown at level 0.00157, step 2, values float32 
    7438 
    7439 > volume #10 step 1
    7440 
    7441 > volume #10 level 0.00933
    7442 
    7443 > matchmaker #10 to #1
    7444 
    7445 No 'to' model specified 
    7446 
    7447 > matchmaker #10 in #1
    7448 
    7449 Expected a keyword 
    7450 
    7451 > fitmap #10 inMap #1
    7452 
    7453 Fit map rlnJ084_Refine3D_class001.mrc in map rlnJ031_Refine3D_class001.mrc
    7454 using 93051 points 
    7455 correlation = 0.9473, correlation about mean = 0.6361, overlap = 14.9 
    7456 steps = 140, shift = 7.01, angle = 11.8 degrees 
    7457  
    7458 Position of rlnJ084_Refine3D_class001.mrc (#10) relative to
    7459 rlnJ031_Refine3D_class001.mrc (#1) coordinates: 
    7460 Matrix rotation and translation 
    7461 0.98858759 -0.02714003 -0.14818232 26.98671062 
    7462 0.00637153 0.99029048 -0.13886748 20.79485999 
    7463 0.15051241 0.13633852 0.97916180 -34.44632650 
    7464 Axis 0.67530404 -0.73294100 0.08223110 
    7465 Axis point 251.38123504 0.00000000 162.07308841 
    7466 Rotation angle (degrees) 11.75718438 
    7467 Shift along axis 0.15026983 
    7468  
    7469 
    7470 > volume #10 color #b2ffff82
    7471 
    7472 > hide #!1 models
    7473 
    7474 > show #!1 models
    7475 
    7476 > hide #!10 models
    7477 
    7478 > hide #!1 models
    7479 
    7480 > show #!10 models
    7481 
    7482 > hide #!10 models
    7483 
    7484 > show #!10 models
    7485 
    7486 > hide #!10 models
    7487 
    7488 > show #!10 models
    7489 
    7490 > close #10
    7491 
    7492 > show #!1 models
    7493 
    7494 > select clear
    7495 
    7496 > select clear
    7497 
    7498 > select clear
    7499 
    7500 > select #9/A:249
    7501 
    7502 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7503 
    7504 > select up
    7505 
    7506 115 atoms, 119 bonds, 14 residues, 1 model selected 
    7507 
    7508 > select up
    7509 
    7510 3274 atoms, 3384 bonds, 384 residues, 1 model selected 
    7511 
    7512 > fitmap #9 inMap #1
    7513 
    7514 Fit molecule AF-Q9HC16-F1-model_v1.pdb (#9) to map
    7515 rlnJ031_Refine3D_class001.mrc (#1) using 3274 atoms 
    7516 average map value = 0.01332, steps = 52 
    7517 shifted from previous position = 0.735 
    7518 rotated from previous position = 3.35 degrees 
    7519 atoms outside contour = 995, contour level = 0.0093255 
    7520  
    7521 Position of AF-Q9HC16-F1-model_v1.pdb (#9) relative to
    7522 rlnJ031_Refine3D_class001.mrc (#1) coordinates: 
    7523 Matrix rotation and translation 
    7524 0.43226595 -0.13718773 0.89124950 148.79592009 
    7525 -0.53175670 0.75944351 0.37480711 124.16846329 
    7526 -0.72827259 -0.63594425 0.25533107 124.38743868 
    7527 Axis -0.51849395 0.83078038 -0.20240549 
    7528 Axis point 207.24448422 0.00000000 -35.41841460 
    7529 Rotation angle (degrees) 77.08412019 
    7530 Shift along axis 0.83023962 
    7531  
    7532 
    7533 > select clear
    7534 
    7535 > save E:/Krios/20210423/csrelion/6221/rlnJ031_AFmodelfit.cxs includeMaps true
    7536 
    7537 ——— End of log from Wed Jul 28 23:41:31 2021 ———
    7538 
    7539 opened ChimeraX session 
    7540 
    7541 > open E:/Krios/20210423/csrelion/6221/rlnJ121_Refine3D_class001.mrc
    7542 
    7543 Opened rlnJ121_Refine3D_class001.mrc as #10, grid size 352,352,352, pixel
    7544 0.835, shown at level 0.00477, step 2, values float32 
    7545 
    7546 > volume #10 step 1
    7547 
    7548 > volume #10 level 0.00933
    7549 
    7550 > volume #10 color #b2b2b282
    7551 
    7552 > fitmap #10 inMap #1
    7553 
    7554 Fit map rlnJ121_Refine3D_class001.mrc in map rlnJ031_Refine3D_class001.mrc
    7555 using 178013 points 
    7556 correlation = 0.9817, correlation about mean = 0.8332, overlap = 36.73 
    7557 steps = 128, shift = 5.04, angle = 10.8 degrees 
    7558  
    7559 Position of rlnJ121_Refine3D_class001.mrc (#10) relative to
    7560 rlnJ031_Refine3D_class001.mrc (#1) coordinates: 
    7561 Matrix rotation and translation 
    7562 0.98878079 0.10250658 -0.10865058 0.98179692 
    7563 -0.11418749 0.98763897 -0.10738009 32.45406508 
    7564 0.09630039 0.11858191 0.98826341 -24.88753251 
    7565 Axis 0.60386561 -0.54771530 -0.57909781 
    7566 Axis point 0.00000000 249.08271471 259.43129881 
    7567 Rotation angle (degrees) 10.78337366 
    7568 Shift along axis -2.77039899 
    7569  
    7570 
    7571 > hide #!1 models
    7572 
    7573 > show #!1 models
    7574 
    7575 > hide #!1 models
    7576 
    7577 > show #!1 models
    7578 
    7579 > hide #!1 models
    7580 
    7581 > show #!1 models
    7582 
    7583 > hide #!1 models
    7584 
    7585 > show #!1 models
    7586 
    7587 > hide #!2 models
    7588 
    7589 > hide #!6 models
    7590 
    7591 > hide #!7 models
    7592 
    7593 > hide #!8 models
    7594 
    7595 > hide #9 models
    7596 
    7597 > volume #1 color #ffffb2
    7598 
    7599 > volume #10 color #b2b2b2
    7600 
    7601 > hide #!10 models
    7602 
    7603 > show #!10 models
    7604 
    7605 > hide #!10 models
    7606 
    7607 > show #!10 models
    7608 
    7609 > hide #!10 models
    7610 
    7611 > show #!10 models
    7612 
    7613 > hide #!1 models
    7614 
    7615 > show #!1 models
    7616 
    7617 > hide #!1 models
    7618 
    7619 > show #!1 models
    7620 
    7621 > hide #!1 models
    7622 
    7623 > show #!1 models
    7624 
    7625 > hide #!1 models
    7626 
    7627 > show #!1 models
    7628 
    7629 > hide #!1 models
    7630 
    7631 > show #!1 models
    7632 
    7633 > hide #!1 models
    7634 
    7635 > show #!1 models
    7636 
    7637 > hide #!1 models
    7638 
    7639 > show #!1 models
    7640 
    7641 > hide #!10 models
    7642 
    7643 > hide #!1 models
    7644 
    7645 > show #!10 models
    7646 
    7647 > show #!1 models
    7648 
    7649 > hide #!1 models
    7650 
    7651 > show #!1 models
    7652 
    7653 > hide #!1 models
    7654 
    7655 > show #!2 models
    7656 
    7657 > show #!3 models
    7658 
    7659 > show #!4 models
    7660 
    7661 > hide #!4 models
    7662 
    7663 > hide #!3 models
    7664 
    7665 > show #!4 models
    7666 
    7667 > show #!5 models
    7668 
    7669 > show #!6 models
    7670 
    7671 > show #!7 models
    7672 
    7673 > show #!8 models
    7674 
    7675 > show #9 models
    7676 
    7677 > hide #!4 models
    7678 
    7679 > hide #!5 models
    7680 
    7681 > volume #10 color #b2b2b282
    7682 
    7683 > save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
    7684 > includeMaps true
    7685 
    7686 ——— End of log from Fri Jul 30 02:27:40 2021 ———
    7687 
    7688 opened ChimeraX session 
    7689 
    7690 > close #1
    7691 
    7692 > rename #10 id #1
    7693 
    7694 > volume #1 level 0.009121
    7695 
    7696 > open "E:/temp/EM data/AF-Q9HC16-F1-model_v1.pdb"
    7697 
    7698 AF-Q9HC16-F1-model_v1.pdb title: 
    7699 Alphafold V2.0 prediction for DNA DC->du-editing enzyme apobec-3G (Q9HC16)
    7700 [more info...] 
    7701  
    7702 Chain information for AF-Q9HC16-F1-model_v1.pdb #10 
    7703 --- 
    7704 Chain | Description 
    7705 A | DNA DC->du-editing enzyme apobec-3G 
    7706  
    7707 
    7708 > ui windowfill toggle
    7709 
    7710 > ui dockable false "Command Line Interface"
    7711 
    7712 > matchmaker #10 to #7/A:1-193
    7713 
    7714 Parameters 
    7715 --- 
    7716 Chain pairing | bb 
    7717 Alignment algorithm | Needleman-Wunsch 
    7718 Similarity matrix | BLOSUM-62 
    7719 SS fraction | 0.3 
    7720 Gap open (HH/SS/other) | 18/18/6 
    7721 Gap extend | 1 
    7722 SS matrix |  |  | H | S | O 
    7723 ---|---|---|--- 
    7724 H | 6 | -9 | -6 
    7725 S |  | 6 | -6 
    7726 O |  |  | 4 
    7727 Iteration cutoff | 2 
    7728  
    7729 Matchmaker 6p40 chain A.pdb, chain A (#7) with AF-Q9HC16-F1-model_v1.pdb,
    7730 chain A (#10), sequence alignment score = 755.6 
    7731 RMSD between 160 pruned atom pairs is 0.752 angstroms; (across all 183 pairs:
    7732 2.237) 
    7733  
    7734 
    7735 > hide #!6 models
    7736 
    7737 > hide #!7 models
    7738 
    7739 > select clear
    7740 
    7741 > select #9/A:383
    7742 
    7743 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7744 
    7745 > set bgColor white
    7746 
    7747 > set bgColor black
    7748 
    7749 > set bgColor white
    7750 
    7751 > set bgColor black
    7752 
    7753 > select clear
    7754 
    7755 > select #10/A:356
    7756 
    7757 6 atoms, 5 bonds, 1 residue, 1 model selected 
    7758 
    7759 > select up
    7760 
    7761 104 atoms, 109 bonds, 13 residues, 1 model selected 
    7762 
    7763 > select up
    7764 
    7765 3274 atoms, 3384 bonds, 384 residues, 1 model selected 
    7766 
    7767 > fitmap #10 inMap #1
    7768 
    7769 Fit molecule AF-Q9HC16-F1-model_v1.pdb (#10) to map
    7770 rlnJ121_Refine3D_class001.mrc (#1) using 3274 atoms 
    7771 average map value = 0.01149, steps = 80 
    7772 shifted from previous position = 1.56 
    7773 rotated from previous position = 4.99 degrees 
    7774 atoms outside contour = 1264, contour level = 0.0091212 
    7775  
    7776 Position of AF-Q9HC16-F1-model_v1.pdb (#10) relative to
    7777 rlnJ121_Refine3D_class001.mrc (#1) coordinates: 
    7778 Matrix rotation and translation 
    7779 -0.60937906 0.55872142 -0.56257224 133.88403179 
    7780 -0.28231498 0.51013129 0.81244342 129.07078099 
    7781 0.74091525 0.65390858 -0.15312790 175.32494140 
    7782 Axis -0.10166762 -0.83592017 -0.53935254 
    7783 Axis point 42.23358963 0.00000000 78.11834209 
    7784 Rotation angle (degrees) 128.76942468 
    7785 Shift along axis -216.06649290 
    7786  
    7787 
    7788 > select clear
    7789 
    7790 > volume #1 level 0.00766
    7791 
    7792 > volume #1 level 0.007033
    7793 
    7794 > volume #1 level 0.006929
    7795 
    7796 > save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
    7797 
    7798 > save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
    7799 > includeMaps true
    7800 
    7801 > show #8/X
    7802 
    7803 > hide #8/X
    7804 
    7805 > hide #8/X cartoons
    7806 
    7807 > hide #8/X ribbons
    7808 
    7809 > show #9-10#!2,8 cartoons
    7810 
    7811 > hide #9-10#!2,8 cartoons
    7812 
    7813 > show #9-10#!2,8 cartoons
    7814 
    7815 > undo
    7816 
    7817 > undo
    7818 
    7819 > undo
    7820 
    7821 > show #8/X ribbons
    7822 
    7823 > show #8/Y ribbons
    7824 
    7825 > select clear
    7826 
    7827 > volume #1 level 0.006511
    7828 
    7829 > volume #1 level 0.006616
    7830 
    7831 > volume #1 level 0.009017
    7832 
    7833 > volume #1 level 0.00672
    7834 
    7835 > save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
    7836 > includeMaps true
    7837 
    7838 > volume #1 level 0.008912
    7839 
    7840 > hide #!1 models
    7841 
    7842 > show #!1 models
    7843 
    7844 > volume #1 level 0.006407
    7845 
    7846 > volume #1 level 0.007868
    7847 
    7848 > save E:/Krios/20210423/csrelion/6221/rlnJ121_rlnJ84_AFmodelfit.cxs
    7849 > includeMaps true
    7850 
    7851 ——— End of log from Fri Jul 30 02:44:06 2021 ———
    7852 
    7853 opened ChimeraX session 
    7854 
    7855 > save E:/Krios/20210423/csrelion/6221/rlnJ121_AFmodelfit.cxs includeMaps true
    7856 
    7857 > hide #!1 models
    7858 
    7859 > set bgColor white
    7860 
    7861 > set bgColor black
    7862 
    7863 > show #!1 models
    7864 
    7865 > hide #!1 models
    7866 
    7867 > show #!1 models
    7868 
    7869 > save E:/Krios/20210423/csrelion/6221/rlnJ121_AFmodelfit.cxs
    7870 
    7871 ——— End of log from Sun Aug 1 00:14:47 2021 ———
    7872 
    7873 opened ChimeraX session 
    7874 
    7875 > open E:\Krios\20210423\csrelion\6221\phenix\rlnJ121_4M4_denmod_map.ccp4
    7876 > format ccp4
    7877 
    7878 Opened rlnJ121_4M4_denmod_map.ccp4 as #11, grid size 130,175,176, pixel 0.835,
    7879 shown at level 0.554, step 1, values float32 
    7880 
    7881 > volume #11 level 0.4258
    7882 
    7883 > volume #11 level 0.2021
    7884 
    7885 > fitmap #11 inMap #1
    7886 
    7887 Fit map rlnJ121_4M4_denmod_map.ccp4 in map rlnJ121_Refine3D_class001.mrc using
    7888 126338 points 
    7889 correlation = 0.95, correlation about mean = 0.8475, overlap = 1154 
    7890 steps = 120, shift = 5.21, angle = 10.8 degrees 
    7891  
    7892 Position of rlnJ121_4M4_denmod_map.ccp4 (#11) relative to
    7893 rlnJ121_Refine3D_class001.mrc (#1) coordinates: 
    7894 Matrix rotation and translation 
    7895 1.00000000 -0.00000352 -0.00002606 0.00495430 
    7896 0.00000352 1.00000000 0.00000057 -0.00839066 
    7897 0.00002606 -0.00000057 1.00000000 -0.00986621 
    7898 Axis -0.02174917 -0.99077855 0.13373422 
    7899 Axis point 413.98145302 0.00000000 195.87419765 
    7900 Rotation angle (degrees) 0.00150686 
    7901 Shift along axis 0.00688608 
    7902  
    7903 
    7904 > transparency #11.1 50
    7905 
    7906 > open E:\Krios\20210423\csrelion\6221\phenix\csJ245-rsr49-coot2iso-
    7907 > cootH_real_space_refined_059.pdb format pdb
    7908 
    7909 Chain information for csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb
    7910 #12 
    7911 --- 
    7912 Chain | Description 
    7913 A | No description available 
    7914 B | No description available 
    7915 C | No description available 
    7916 D | No description available 
    7917 E | No description available 
    7918  
    7919 
    7920 > hide #9-10#!2,8,12 atoms
    7921 
    7922 > hide #!2 models
    7923 
    7924 > show #9-10#!8,12 cartoons
    7925 
    7926 > undo
    7927 
    7928 > undo
    7929 
    7930 > hide #!2 models
    7931 
    7932 > hide #!8 models
    7933 
    7934 > hide #9 models
    7935 
    7936 > hide #10 models
    7937 
    7938 > select #12
    7939 
    7940 14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected 
    7941 
    7942 > hide #!12 models
    7943 
    7944 > show #!12 models
    7945 
    7946 > hide #!12 models
    7947 
    7948 > ~select #12
    7949 
    7950 Nothing selected 
    7951 
    7952 > close #12
    7953 
    7954 > open E:/Krios/20210423/csrelion/6221/phenix/csJ245-rsr49-coot2iso-
    7955 > cootH_real_space_refined_059.pdb
    7956 
    7957 Chain information for csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb
    7958 #12 
    7959 --- 
    7960 Chain | Description 
    7961 A | No description available 
    7962 B | No description available 
    7963 C | No description available 
    7964 D | No description available 
    7965 E | No description available 
    7966  
    7967 
    7968 > hide #!12 atoms
    7969 
    7970 > show #!12 cartoons
    7971 
    7972 > fitmap #12 inMap #11
    7973 
    7974 Fit molecule csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb (#12) to
    7975 map rlnJ121_4M4_denmod_map.ccp4 (#11) using 14932 atoms 
    7976 average map value = 0.2592, steps = 112 
    7977 shifted from previous position = 0.508 
    7978 rotated from previous position = 2.16 degrees 
    7979 atoms outside contour = 8173, contour level = 0.2021 
    7980  
    7981 Position of csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb (#12)
    7982 relative to rlnJ121_4M4_denmod_map.ccp4 (#11) coordinates: 
    7983 Matrix rotation and translation 
    7984 0.99099463 -0.12004812 0.05931349 10.61047418 
    7985 0.11207394 0.98603421 0.12319077 -30.88158629 
    7986 -0.07327395 -0.11543390 0.99060888 23.45307178 
    7987 Axis -0.66593181 0.37001284 0.64778493 
    7988 Axis point 0.00000000 200.25653125 263.47205474 
    7989 Rotation angle (degrees) 10.32118487 
    7990 Shift along axis -3.29988928 
    7991  
    7992 
    7993 > show #!2 models
    7994 
    7995 > hide #!2 models
    7996 
    7997 > show #!2 models
    7998 
    7999 > hide #!2 models
    8000 
    8001 > show #!2 models
    8002 
    8003 > hide #!2 models
    8004 
    8005 > show #!2 models
    8006 
    8007 > hide #!12 models
    8008 
    8009 > hide #!2 models
    8010 
    8011 > show #!12 models
    8012 
    8013 > open E:\Krios\20210423\csrelion\6221\phenix\csJ245-rsr49-coot2iso-
    8014 > cootH_real_space_refined_059.pdb format pdb
    8015 
    8016 Chain information for csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb
    8017 #13 
    8018 --- 
    8019 Chain | Description 
    8020 A | No description available 
    8021 B | No description available 
    8022 C | No description available 
    8023 D | No description available 
    8024 E | No description available 
    8025  
    8026 
    8027 > hide #!12-13 atoms
    8028 
    8029 > show #!12-13 cartoons
    8030 
    8031 > show #10 models
    8032 
    8033 > show #!2 models
    8034 
    8035 > hide #!2 models
    8036 
    8037 > show #!8 models
    8038 
    8039 > matchmaker #13/A to #10
    8040 
    8041 Parameters 
    8042 --- 
    8043 Chain pairing | bb 
    8044 Alignment algorithm | Needleman-Wunsch 
    8045 Similarity matrix | BLOSUM-62 
    8046 SS fraction | 0.3 
    8047 Gap open (HH/SS/other) | 18/18/6 
    8048 Gap extend | 1 
    8049 SS matrix |  |  | H | S | O 
    8050 ---|---|---|--- 
    8051 H | 6 | -9 | -6 
    8052 S |  | 6 | -6 
    8053 O |  |  | 4 
    8054 Iteration cutoff | 2 
    8055  
    8056 Matchmaker AF-Q9HC16-F1-model_v1.pdb, chain A (#10) with
    8057 csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb, chain A (#13),
    8058 sequence alignment score = 2080.4 
    8059 RMSD between 363 pruned atom pairs is 0.887 angstroms; (across all 384 pairs:
    8060 1.243) 
    8061  
    8062 
    8063 > hide #10 models
    8064 
    8065 > hide #!8 models
    8066 
    8067 > fitmap #13 inMap #11
    8068 
    8069 Fit molecule csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb (#13) to
    8070 map rlnJ121_4M4_denmod_map.ccp4 (#11) using 14932 atoms 
    8071 average map value = 0.1492, steps = 48 
    8072 shifted from previous position = 0.353 
    8073 rotated from previous position = 0.777 degrees 
    8074 atoms outside contour = 9972, contour level = 0.2021 
    8075  
    8076 Position of csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb (#13)
    8077 relative to rlnJ121_4M4_denmod_map.ccp4 (#11) coordinates: 
    8078 Matrix rotation and translation 
    8079 -0.83671548 0.54748241 -0.01304662 191.68186460 
    8080 0.54518727 0.83498616 0.07462540 -64.71580391 
    8081 0.05174984 0.05532738 -0.99712629 285.05416112 
    8082 Axis -0.28527083 -0.95784627 -0.03392767 
    8083 Axis point 102.96142073 0.00000000 145.35994655 
    8084 Rotation angle (degrees) 178.06165540 
    8085 Shift along axis -2.36467641 
    8086  
    8087 
    8088 > hide #!11 models
    8089 
    8090 > show #!11 models
    8091 
    8092 > select #13/A:2
    8093 
    8094 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8095 
    8096 > select up
    8097 
    8098 236 atoms, 239 bonds, 13 residues, 1 model selected 
    8099 
    8100 > select down
    8101 
    8102 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8103 
    8104 > select #13/A:384
    8105 
    8106 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8107 
    8108 > select up
    8109 
    8110 61 atoms, 60 bonds, 4 residues, 1 model selected 
    8111 
    8112 > select up
    8113 
    8114 6377 atoms, 6485 bonds, 386 residues, 1 model selected 
    8115 
    8116 > style sel stick
    8117 
    8118 Changed 6377 atom styles 
    8119 
    8120 > show sel atoms
    8121 
    8122 > select clear
    8123 
    8124 > select #12/A:362
    8125 
    8126 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8127 
    8128 > select up
    8129 
    8130 187 atoms, 192 bonds, 13 residues, 1 model selected 
    8131 
    8132 > select up
    8133 
    8134 6377 atoms, 6485 bonds, 386 residues, 1 model selected 
    8135 
    8136 > show sel atoms
    8137 
    8138 > hide sel atoms
    8139 
    8140 > style sel stick
    8141 
    8142 Changed 6377 atom styles 
    8143 
    8144 > show sel atoms
    8145 
    8146 > select clear
    8147 
    8148 > select #12/B:125
    8149 
    8150 19 atoms, 18 bonds, 1 residue, 1 model selected 
    8151 
    8152 > select up
    8153 
    8154 146 atoms, 145 bonds, 9 residues, 1 model selected 
    8155 
    8156 > select up
    8157 
    8158 2920 atoms, 2966 bonds, 177 residues, 1 model selected 
    8159 
    8160 > style sel stick
    8161 
    8162 Changed 2920 atom styles 
    8163 
    8164 > show sel atoms
    8165 
    8166 > select clear
    8167 
    8168 > select #13/B:129
    8169 
    8170 16 atoms, 15 bonds, 1 residue, 1 model selected 
    8171 
    8172 > select up
    8173 
    8174 153 atoms, 155 bonds, 10 residues, 1 model selected 
    8175 
    8176 > select up
    8177 
    8178 2920 atoms, 2966 bonds, 177 residues, 1 model selected 
    8179 
    8180 > style sel stick
    8181 
    8182 Changed 2920 atom styles 
    8183 
    8184 > show sel atoms
    8185 
    8186 > select #11
    8187 
    8188 2 models selected 
    8189 
    8190 > select clear
    8191 
    8192 > hide #!12-13 atoms
    8193 
    8194 > save E:/Krios/20210423/csrelion/6221/model/rln121demod_modelfit.cxs
    8195 
    8196 > select #1
    8197 
    8198 2 models selected 
    8199 
    8200 > select #2
    8201 
    8202 6505 atoms, 6643 bonds, 8 pseudobonds, 800 residues, 3 models selected 
    8203 
    8204 > select #3
    8205 
    8206 3217 atoms, 3119 bonds, 5 pseudobonds, 558 residues, 3 models selected 
    8207 
    8208 > select #4
    8209 
    8210 3132 atoms, 3120 bonds, 6 pseudobonds, 476 residues, 2 models selected 
    8211 
    8212 > select #1
    8213 
    8214 2 models selected 
    8215 
    8216 > show #!1 models
    8217 
    8218 > show #!2 models
    8219 
    8220 > close #1
    8221 
    8222 > close #2
    8223 
    8224 > close #3
    8225 
    8226 > close #4
    8227 
    8228 > close #5
    8229 
    8230 > close #6
    8231 
    8232 > close #7
    8233 
    8234 > close #8
    8235 
    8236 > close #9
    8237 
    8238 > close #10
    8239 
    8240 > rename #11 id #1
    8241 
    8242 > rename #12 id #2
    8243 
    8244 > rename #13 id #3
    8245 
    8246 > select #3/A:384
    8247 
    8248 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8249 
    8250 > select up
    8251 
    8252 61 atoms, 60 bonds, 4 residues, 1 model selected 
    8253 
    8254 > select up
    8255 
    8256 6377 atoms, 6485 bonds, 386 residues, 1 model selected 
    8257 
    8258 > select clear
    8259 
    8260 > undo
    8261 
    8262 > undo
    8263 
    8264 > undo
    8265 
    8266 > open E:\Krios\20210423\csrelion\6221\phenix\csJ245-rsr49-coot2iso-
    8267 > cootH_real_space_refined_059.pdb format pdb
    8268 
    8269 Chain information for csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb
    8270 #4 
    8271 --- 
    8272 Chain | Description 
    8273 A | No description available 
    8274 B | No description available 
    8275 C | No description available 
    8276 D | No description available 
    8277 E | No description available 
    8278  
    8279 
    8280 > hide sel atoms
    8281 
    8282 > show sel cartoons
    8283 
    8284 > hide sel atoms
    8285 
    8286 > select #4
    8287 
    8288 14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected 
    8289 
    8290 > select #3
    8291 
    8292 14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected 
    8293 
    8294 > select #4
    8295 
    8296 14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected 
    8297 
    8298 > hide sel atoms
    8299 
    8300 > show sel cartoons
    8301 
    8302 > matchmaker #4 to #3
    8303 
    8304 Parameters 
    8305 --- 
    8306 Chain pairing | bb 
    8307 Alignment algorithm | Needleman-Wunsch 
    8308 Similarity matrix | BLOSUM-62 
    8309 SS fraction | 0.3 
    8310 Gap open (HH/SS/other) | 18/18/6 
    8311 Gap extend | 1 
    8312 SS matrix |  |  | H | S | O 
    8313 ---|---|---|--- 
    8314 H | 6 | -9 | -6 
    8315 S |  | 6 | -6 
    8316 O |  |  | 4 
    8317 Iteration cutoff | 2 
    8318  
    8319 Matchmaker csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb, chain A
    8320 (#3) with csJ245-rsr49-coot2iso-cootH_real_space_refined_059.pdb, chain A
    8321 (#4), sequence alignment score = 2111 
    8322 RMSD between 384 pruned atom pairs is 0.000 angstroms; (across all 384 pairs:
    8323 0.000) 
    8324  
    8325 
    8326 > close #3
    8327 
    8328 > select clear
    8329 
    8330 > color #4/A #90ee90
    8331 
    8332 > color #4/A yellow
    8333 
    8334 > rename #4 id #3
    8335 
    8336 > select clear
    8337 
    8338 > select #2/A:366
    8339 
    8340 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8341 
    8342 > select up
    8343 
    8344 271 atoms, 271 bonds, 17 residues, 1 model selected 
    8345 
    8346 > select up
    8347 
    8348 6377 atoms, 6485 bonds, 386 residues, 1 model selected 
    8349 
    8350 > style sel stick
    8351 
    8352 Changed 6377 atom styles 
    8353 
    8354 > show sel atoms
    8355 
    8356 > color sel byhetero
    8357 
    8358 > select clear
    8359 
    8360 > select #3/A:4
    8361 
    8362 16 atoms, 16 bonds, 1 residue, 1 model selected 
    8363 
    8364 > select up
    8365 
    8366 236 atoms, 239 bonds, 13 residues, 1 model selected 
    8367 
    8368 > select up
    8369 
    8370 6377 atoms, 6485 bonds, 386 residues, 1 model selected 
    8371 
    8372 > style sel stick
    8373 
    8374 Changed 6377 atom styles 
    8375 
    8376 > color sel byhetero
    8377 
    8378 > style sel stick
    8379 
    8380 Changed 6377 atom styles 
    8381 
    8382 > show sel atoms
    8383 
    8384 > color sel byhetero
     28[deleted voluminous log]
    838529
    838630> select clear