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Opened 3 years ago
Closed 3 years ago
#7078 closed defect (duplicate)
Problem restoring clip caps when volume surface not restored
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/mcarmina/Desktop/ChimeraX_paper/elongation_dimer_APT.cxs
Opened 5.mrc as #2, grid size 150,150,150, pixel 2.12, shown at level 0.014,
step 1, values float32
Opened 844_Zflip.mrc as #3, grid size 500,500,500, pixel 0.83, shown at level
0.00574, step 2, values float32
Log from Mon Apr 25 12:20:22 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/mcarmina/Desktop/ChimeraX_paper/overlap_extra_dimer.cxs
Opened 5.mrc as #2, grid size 150,150,150, pixel 2.12, shown at level 0.0149,
step 1, values float32
Opened 844_Zflip.mrc as #3, grid size 500,500,500, pixel 0.83, shown at level
0.00574, step 2, values float32
Log from Tue Apr 19 14:54:05 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/mcarmina/Desktop/ChimeraX_paper/class5_figureS5_310322.cxs
Opened 5.mrc as #2, grid size 150,150,150, pixel 2.12, shown at level 0.0156,
step 1, values float32
Log from Thu Mar 31 19:02:40 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/mcarmina/Desktop/class5_figureS5_310322.cxs
Opened 5.mrc as #2, grid size 150,150,150, pixel 2.12, shown at level 0.0156,
step 1, values float32
Log from Thu Mar 31 18:57:05 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/mcarmina/Nextcloud3/eBIC/job518/tile_j518.cxs
Opened 6.mrc as #1, grid size 150,150,150, pixel 2.12, shown at level 0.0119,
step 1, values float32
Opened 5.mrc as #2, grid size 150,150,150, pixel 2.12, shown at level 0.014,
step 1, values float32
Opened 4.mrc as #3, grid size 150,150,150, pixel 2.12, shown at level 0.0113,
step 1, values float32
Opened 3.mrc as #4, grid size 150,150,150, pixel 2.12, shown at level 0.0177,
step 1, values float32
Opened 2.mrc as #5, grid size 150,150,150, pixel 2.12, shown at level 0.0103,
step 1, values float32
Opened 1.mrc as #6, grid size 150,150,150, pixel 2.12, shown at level 0.0119,
step 1, values float32
Log from Fri Mar 25 12:26:46 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mcarmina/Nextcloud3/eBIC/job518/6.mrc
Opened 6.mrc as #1, grid size 150,150,150, pixel 2.12, shown at level 0.0313,
step 1, values float32
> open /Users/mcarmina/Nextcloud3/eBIC/job518/5.mrc
Opened 5.mrc as #2, grid size 150,150,150, pixel 2.12, shown at level 0.03,
step 1, values float32
> open /Users/mcarmina/Nextcloud3/eBIC/job518/4.mrc
Opened 4.mrc as #3, grid size 150,150,150, pixel 2.12, shown at level 0.0289,
step 1, values float32
> open /Users/mcarmina/Nextcloud3/eBIC/job518/3.mrc
Opened 3.mrc as #4, grid size 150,150,150, pixel 2.12, shown at level 0.033,
step 1, values float32
> open /Users/mcarmina/Nextcloud3/eBIC/job518/2.mrc
Opened 2.mrc as #5, grid size 150,150,150, pixel 2.12, shown at level 0.0298,
step 1, values float32
> open /Users/mcarmina/Nextcloud3/eBIC/job518/1.mrc
Opened 1.mrc as #6, grid size 150,150,150, pixel 2.12, shown at level 0.0305,
step 1, values float32
> ui tool show "Modeller Comparative"
> volume #1 level 0.01189
> lighting soft
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting full
> lighting soft
> ui tool show AlphaFold
> view clip false
[Repeated 6 time(s)]
> tile
6 models tiled
> volume #2 level 0.01399
> volume #3 level 0.01132
> volume #4 level 0.01772
> volume #5 level 0.01031
> volume #6 level 0.01193
> save /Users/mcarmina/Nextcloud3/eBIC/job518/tile_j518.cxs
——— End of log from Fri Mar 25 12:26:46 2022 ———
opened ChimeraX session
> volume #5 level 0.01031
> ui tool show "Modeller Comparative"
> volume #2 level 0.01009
> volume #2 level 0.01362
> volume #1 level 0.01226
> volume #6 level 0.01847
> volume #3 level 0.01509
> volume #2 level 0.01529
> volume #1 level 0.01468
> volume #6 level 0.01829
> volume #5 level 0.01376
> volume #2 level 0.01473
> volume #2 color #ffffb259
> volume #2 color #ffffb2
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting simple
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
> volume #2 color #ffffb28c
> open /Users/mcarmina/Desktop/5c4x.pdb
5c4x.pdb title:
Crystal structure of A transcribing RNA polymerase II complex reveals A
complete transcription bubble [more info...]
Chain information for 5c4x.pdb #7
---
Chain | Description | UniProt
A | DNA-directed RNA polymerase II subunit RPB1 | RPB1_YEAST
B | DNA-directed RNA polymerase II subunit RPB2 | RPB2_YEAST
C | DNA-directed RNA polymerase II subunit RPB3 | RPB3_YEAST
D | DNA-directed RNA polymerase II subunit RPB4 | RPB4_YEAST
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_YEAST
F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_YEAST
G | DNA-directed RNA polymerase II subunit RPB7 | RPB7_YEAST
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_YEAST
I | DNA-directed RNA polymerase II subunit RPB9 | RPB9_YEAST
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_YEAST
K | DNA-directed RNA polymerase II subunit RPB11 | RPB11_YEAST
L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_YEAST
R | RNA (5'-R(P*up*CP*GP*ap*GP*ap*GP*GP*A)-3') |
S | non-template strand DNA (38-mer) |
U | template strand DNA (40-mer) |
Non-standard residues in 5c4x.pdb #7
---
MG — magnesium ion
ZN — zinc ion
> hide #!2 models
> show #!2 models
> hide #!7 models
> show #!7 models
> select #7
33495 atoms, 34271 bonds, 38 pseudobonds, 4095 residues, 3 models selected
> hide sel atoms
> show sel atoms
> cartoon (#!7 & sel)
> hide sel atoms
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,32.222,0,1,0,-12.875,0,0,1,80.689
> view matrix models #7,1,0,0,99.216,0,1,0,-48,0,0,1,213.63
> view matrix models #7,1,0,0,61.23,0,1,0,-33.697,0,0,1,167.17
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.041221,-0.20036,-0.97886,164.21,-0.97067,0.24028,-0.0083072,111.74,0.23687,0.9498,-0.20439,65.727
> view matrix models
> #7,-0.13111,-0.98931,0.063828,238.24,-0.28631,0.099428,0.95296,65.779,-0.94912,0.10667,-0.29628,236.92
> view matrix models
> #7,0.16604,-0.96389,0.20818,208.63,0.88427,0.23897,0.40119,-71.12,-0.43645,0.11747,0.89202,202.85
> view matrix models
> #7,0.50205,-0.8479,0.17033,166.62,0.79483,0.52999,0.29555,-81.452,-0.34087,-0.012996,0.94002,201.83
> view matrix models
> #7,0.76181,0.21105,-0.61246,62.893,-0.27862,0.96027,-0.015667,-3.0593,0.58482,0.18258,0.79035,92.935
> ui mousemode right "move picked models"
> view matrix models
> #7,0.76181,0.21105,-0.61246,119.25,-0.27862,0.96027,-0.015667,5.7848,0.58482,0.18258,0.79035,228.72
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,93.501,0,1,0,-156.88,0,0,1,162.54
> ui mousemode right "move picked models"
> ui tool show "Selection Inspector"
[Repeated 3 time(s)]
> ui tool show "Fit in Map"
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 128
shifted from previous position = 12.4
rotated from previous position = 23.5 degrees
atoms outside contour = 8371, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76298292 0.08142202 -0.64127021 44.15145231
0.06463340 0.97745498 0.20100814 129.77491888
0.64317926 -0.19481326 0.74051888 79.07008389
Axis -0.29447485 -0.95557761 -0.01249004
Axis point -102.72770633 0.00000000 43.44878371
Rotation angle (degrees) 42.22781585
Shift along axis -137.99908733
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 52
shifted from previous position = 0.0595
rotated from previous position = 0.0694 degrees
atoms outside contour = 8362, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76223318 0.08173952 -0.64212086 44.19244166
0.06474671 0.97739231 0.20127622 129.77230726
0.64405622 -0.19499463 0.73970850 78.92834233
Axis -0.29441808 -0.95559332 -0.01262518
Axis point -102.29580151 0.00000000 43.41902479
Rotation angle (degrees) 42.29694278
Shift along axis -138.01708891
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 48
shifted from previous position = 0.0308
rotated from previous position = 0.0463 degrees
atoms outside contour = 8368, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76273639 0.08150721 -0.64155260 44.15617917
0.06470777 0.97742916 0.20110976 129.76474319
0.64346412 -0.19490717 0.74024665 79.01714484
Axis -0.29448891 -0.95557324 -0.01249252
Axis point -102.59015839 0.00000000 43.42662162
Rotation angle (degrees) 42.25102408
Shift along axis -137.99034483
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 48
shifted from previous position = 0.0328
rotated from previous position = 0.0349 degrees
atoms outside contour = 8368, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76312586 0.08147021 -0.64109398 44.09296664
0.06459122 0.97743907 0.20109905 129.79642510
0.64301389 -0.19487294 0.74064678 79.06932368
Axis -0.29464846 -0.95552317 -0.01255989
Axis point -102.79449404 0.00000000 43.32956698
Rotation angle (degrees) 42.21694837
Shift along axis -138.00851907
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 40
shifted from previous position = 0.0338
rotated from previous position = 0.0113 degrees
atoms outside contour = 8371, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76309057 0.08130039 -0.64115755 44.13765326
0.06468573 0.97746703 0.20093271 129.77730383
0.64304628 -0.19480360 0.74063690 79.06881095
Axis -0.29446893 -0.95558108 -0.01236304
Axis point -102.78393034 0.00000000 43.44504992
Rotation angle (degrees) 42.21768233
Shift along axis -137.98743449
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 44
shifted from previous position = 0.0447
rotated from previous position = 0.0988 degrees
atoms outside contour = 8359, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76204928 0.08185677 -0.64232417 44.20282039
0.06480047 0.97735673 0.20143165 129.76674979
0.64426840 -0.19512375 0.73948964 78.91029479
Axis -0.29452409 -0.95556009 -0.01266782
Axis point -102.21841058 0.00000000 43.39870276
Rotation angle (degrees) 42.31559901
Shift along axis -138.01834376
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 40
shifted from previous position = 0.0385
rotated from previous position = 0.0886 degrees
atoms outside contour = 8368, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76300913 0.08146949 -0.64123301 44.11817009
0.06464151 0.97743515 0.20110194 129.78596593
0.64314736 -0.19489289 0.74052564 79.05690868
Axis -0.29460704 -0.95553647 -0.01251946
Axis point -102.73850811 0.00000000 43.36918035
Rotation angle (degrees) 42.22725649
Shift along axis -138.00249796
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 40
shifted from previous position = 0.0199
rotated from previous position = 0.00984 degrees
atoms outside contour = 8368, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76297544 0.08132873 -0.64129096 44.14843232
0.06471077 0.97746149 0.20095158 129.77361235
0.64318036 -0.19481956 0.74051627 79.05064768
Axis -0.29443659 -0.95559105 -0.01236304
Axis point -102.72186417 0.00000000 43.45561863
Rotation angle (degrees) 42.22796865
Shift along axis -137.98672266
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 28
shifted from previous position = 0.0254
rotated from previous position = 0.0101 degrees
atoms outside contour = 8367, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76296523 0.08149134 -0.64128247 44.11743593
0.06463202 0.97743534 0.20110405 129.78849625
0.64320039 -0.19488278 0.74048223 79.04364074
Axis -0.29458006 -0.95554450 -0.01254188
Axis point -102.70404916 0.00000000 43.36311308
Rotation angle (degrees) 42.23096946
Shift along axis -138.00615666
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02283, steps = 68
shifted from previous position = 0.0308
rotated from previous position = 0.0493 degrees
atoms outside contour = 8373, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.76347045 0.08113227 -0.64072646 44.10448947
0.06464917 0.97749472 0.20080970 129.78540242
0.64259889 -0.19473471 0.74104321 79.12442635
Axis -0.29452285 -0.95556562 -0.01227333
Axis point -102.99443093 0.00000000 43.43138502
Rotation angle (degrees) 42.18297125
Shift along axis -137.97936914
> view matrix models #2,1,0,0,95.536,0,1,0,-162.37,0,0,1,165.9
> view matrix models
> #7,0.76347,0.081132,-0.64073,138.31,0.064649,0.97749,0.20081,-29.033,0.6426,-0.19473,0.74104,242.89
> view matrix models #2,1,0,0,93.526,0,1,0,-159.4,0,0,1,161.18
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.49014,-0.8673,-0.086874,333.15,-0.1799,0.0031333,0.98368,67.972,-0.85288,0.49777,-0.15756,338.99
> ui mousemode right "move picked models"
> ui mousemode right "translate selected atoms"
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 152
shifted from previous position = 25.2
rotated from previous position = 26.2 degrees
atoms outside contour = 9938, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.64005881 -0.63079045 -0.43866631 214.53463381
-0.32691257 -0.29309197 0.89845716 242.68163008
-0.69530776 0.71847096 -0.01861724 158.76611738
Axis -0.41226448 0.58784591 0.69604252
Axis point 142.71093508 76.71245856 0.00000000
Rotation angle (degrees) 167.39139928
Shift along axis 164.72236342
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 28
shifted from previous position = 0.038
rotated from previous position = 0.0144 degrees
atoms outside contour = 9936, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.63992618 -0.63094586 -0.43863631 214.54943215
-0.32699276 -0.29297148 0.89846728 242.66937436
-0.69539213 0.71838363 -0.01883461 158.74461347
Axis -0.41233677 0.58789274 0.69596014
Axis point 142.71952718 76.71382601 0.00000000
Rotation angle (degrees) 167.38670946
Shift along axis 164.67686490
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 44
shifted from previous position = 0.0094
rotated from previous position = 0.00298 degrees
atoms outside contour = 9933, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.63994908 -0.63091354 -0.43864939 214.54523695
-0.32697996 -0.29300245 0.89846184 242.67322902
-0.69537708 0.71839939 -0.01878944 158.75064946
Axis -0.41232493 0.58788063 0.69597738
Axis point 142.71807270 76.71350201 0.00000000
Rotation angle (degrees) 167.38785017
Shift along axis 164.68740134
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 44
shifted from previous position = 0.0372
rotated from previous position = 0.0251 degrees
atoms outside contour = 9938, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.64016942 -0.63060801 -0.43876721 214.52665858
-0.32692811 -0.29321545 0.89841122 242.69257797
-0.69519863 0.71858072 -0.01845593 158.75756695
Axis -0.41221512 0.58780300 0.69610798
Axis point 142.70353516 76.71270324 0.00000000
Rotation angle (degrees) 167.40095318
Shift along axis 164.73670329
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 28
shifted from previous position = 0.0615
rotated from previous position = 0.0293 degrees
atoms outside contour = 9934, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.63991382 -0.63096154 -0.43863180 214.55716346
-0.32699843 -0.29295967 0.89846907 242.66437486
-0.69540084 0.71837468 -0.01885449 158.73396438
Axis -0.41234327 0.58789722 0.69595251
Axis point 142.72059925 76.71603865 0.00000000
Rotation angle (degrees) 167.38614660
Shift along axis 164.66180848
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 40
shifted from previous position = 0.0488
rotated from previous position = 0.0184 degrees
atoms outside contour = 9939, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.64002238 -0.63073804 -0.43879481 214.52801771
-0.32702809 -0.29315702 0.89839390 242.69430043
-0.69528698 0.71849043 -0.01864201 158.75866237
Axis -0.41230044 0.58782543 0.69603852
Axis point 142.71454909 76.71113338 0.00000000
Rotation angle (degrees) 167.39840759
Shift along axis 164.71402897
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 40
shifted from previous position = 0.0208
rotated from previous position = 0.00874 degrees
atoms outside contour = 9932, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.64010059 -0.63071856 -0.43870872 214.54559322
-0.32689870 -0.29316513 0.89843834 242.67589516
-0.69527583 0.71850422 -0.01852591 158.74220286
Axis -0.41224485 0.58781774 0.69607794
Axis point 142.70724130 76.71952728 0.00000000
Rotation angle (degrees) 167.39449794
Shift along axis 164.70082570
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 48
shifted from previous position = 0.0117
rotated from previous position = 0.0177 degrees
atoms outside contour = 9934, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.63995276 -0.63091131 -0.43864723 214.54880573
-0.32698346 -0.29299562 0.89846279 242.67034534
-0.69537205 0.71840413 -0.01879421 158.74306855
Axis -0.41232309 0.58788380 0.69597580
Axis point 142.71759726 76.71443163 0.00000000
Rotation angle (degrees) 167.38806245
Shift along axis 164.67987086
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02219, steps = 44
shifted from previous position = 0.00254
rotated from previous position = 0.00323 degrees
atoms outside contour = 9934, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.63997987 -0.63087116 -0.43866542 214.54717260
-0.32698017 -0.29302388 0.89845477 242.67228846
-0.69534864 0.71842786 -0.01875298 158.74198155
Axis -0.41231005 0.58787362 0.69599211
Axis point 142.71575664 76.71457295 0.00000000
Rotation angle (degrees) 167.38991799
Shift along axis 164.68384896
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.61739,-0.68606,0.38491,223.5,0.4333,0.70496,0.56151,-56.774,-0.65657,-0.17989,0.7325,394.61
> ui mousemode right "move picked models"
> view matrix models
> #7,0.61739,-0.68606,0.38491,265.36,0.4333,0.70496,0.56151,-38.817,-0.65657,-0.17989,0.7325,408.78
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,88.355,0,1,0,-159.69,0,0,1,157.25
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.25296,-0.92353,0.28828,321.58,0.66277,0.38248,0.64377,36.151,-0.70481,0.028215,0.70884,360.21
> view matrix models
> #7,0.49887,-0.50844,-0.70187,-37.712,0.7326,-0.18531,0.65495,159.96,-0.46307,-0.84092,0.28003,427.68
> view matrix models
> #7,0.34076,-0.94014,0.0050243,247.58,0.66063,0.24324,0.71021,83.949,-0.66892,-0.23869,0.70397,415.64
> view matrix models
> #7,0.34523,-0.93846,-0.010495,242.98,0.66093,0.23517,0.71264,86.33,-0.66632,-0.25297,0.70145,417.98
> view matrix models
> #7,0.50473,-0.36339,-0.78307,-90.784,0.75646,-0.25089,0.60401,159.97,-0.41596,-0.89722,0.14826,403.58
> view matrix models
> #7,-0.27913,-0.28946,-0.91559,-81.036,0.46144,-0.87661,0.13646,204.27,-0.84212,-0.3844,0.37826,379.5
> volume #2 color #ffff808c
> view matrix models
> #7,0.086291,-0.86632,-0.49199,125.81,-0.093236,-0.49868,0.86176,344.14,-0.9919,-0.028491,-0.1238,185.78
> view matrix models
> #7,0.17862,-0.88323,-0.4336,137.22,0.061123,-0.42987,0.90082,326.93,-0.98202,-0.18741,-0.022799,245.71
> ui mousemode right "move picked models"
> view matrix models
> #7,0.17862,-0.88323,-0.4336,273.99,0.061123,-0.42987,0.90082,317.55,-0.98202,-0.18741,-0.022799,404.22
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.31138,-0.80173,-0.51016,226.6,0.5179,-0.30695,0.79847,229.91,-0.79676,-0.51284,0.31964,548.44
> ui mousemode right "move picked models"
> view matrix models
> #7,0.31138,-0.80173,-0.51016,233.52,0.5179,-0.30695,0.79847,225.48,-0.79676,-0.51284,0.31964,544.95
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 216
shifted from previous position = 19.2
rotated from previous position = 53.4 degrees
atoms outside contour = 3998, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74210866 -0.59014639 -0.31780804 126.27254541
0.64867064 0.51290189 0.56227934 156.14727526
-0.16882277 -0.62342512 0.76343957 468.51792345
Axis -0.68885572 -0.08655559 0.71971239
Axis point 72.16106070 458.72416056 0.00000000
Rotation angle (degrees) 59.38777458
Shift along axis 236.69917003
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 40
shifted from previous position = 0.04
rotated from previous position = 0.0177 degrees
atoms outside contour = 4001, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74224365 -0.58998243 -0.31779721 126.20183859
0.64850073 0.51286645 0.56250760 156.22534192
-0.16888207 -0.62360942 0.76327592 468.55177990
Axis -0.68908022 -0.08651295 0.71950257
Axis point 72.14978786 458.78062346 0.00000000
Rotation angle (degrees) 59.38990822
Shift along axis 236.64550638
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 40
shifted from previous position = 0.00553
rotated from previous position = 0.00721 degrees
atoms outside contour = 3999, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74219311 -0.59005849 -0.31777403 126.23195430
0.64855843 0.51288385 0.56242521 156.19774057
-0.16888260 -0.62352315 0.76334628 468.54679143
Axis -0.68899105 -0.08650028 0.71958949
Axis point 72.16083360 458.76312677 0.00000000
Rotation angle (degrees) 59.38866942
Shift along axis 236.67751085
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 40
shifted from previous position = 0.0292
rotated from previous position = 0.0114 degrees
atoms outside contour = 3996, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74210638 -0.59015202 -0.31780291 126.27162509
0.64867304 0.51290582 0.56227298 156.14532797
-0.16882357 -0.62341655 0.76344639 468.52180957
Axis -0.68884905 -0.08655240 0.71971915
Axis point 72.16141380 458.72458058 0.00000000
Rotation angle (degrees) 59.38749271
Shift along axis 236.70727840
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 28
shifted from previous position = 0.051
rotated from previous position = 0.0285 degrees
atoms outside contour = 4002, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74230140 -0.58989839 -0.31781834 126.16274281
0.64842462 0.51281413 0.56264302 156.28530488
-0.16892047 -0.62373195 0.76316730 468.56449951
Axis -0.68920564 -0.08649984 0.71938402
Axis point 72.12841827 458.80153291 0.00000000
Rotation angle (degrees) 59.39334299
Shift along axis 236.60708571
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 40
shifted from previous position = 0.0233
rotated from previous position = 0.0111 degrees
atoms outside contour = 4000, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74222558 -0.58999001 -0.31782536 126.20330172
0.64852465 0.51285007 0.56249496 156.22531654
-0.16886965 -0.62361573 0.76327351 468.54744491
Axis -0.68906782 -0.08653542 0.71951175
Axis point 72.14338310 458.77075955 0.00000000
Rotation angle (degrees) 59.39113525
Shift along axis 236.64373749
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 28
shifted from previous position = 0.0505
rotated from previous position = 0.0305 degrees
atoms outside contour = 3996, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74201076 -0.59028142 -0.31778587 126.32643102
0.64878792 0.51293431 0.56211442 156.09040393
-0.16880241 -0.62327059 0.76357024 468.50271764
Axis -0.68868556 -0.08655648 0.71987511
Axis point 72.17712649 458.68682115 0.00000000
Rotation angle (degrees) 59.38560447
Shift along axis 236.75361895
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 28
shifted from previous position = 0.0425
rotated from previous position = 0.0281 degrees
atoms outside contour = 4000, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74224425 -0.59001267 -0.31773967 126.23232496
0.64849755 0.51291213 0.56246963 156.20664116
-0.16889167 -0.62354325 0.76332785 468.54078220
Axis -0.68904298 -0.08647686 0.71954258
Axis point 72.16586731 458.78896995 0.00000000
Rotation angle (degrees) 59.38663926
Shift along axis 236.64728806
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 44
shifted from previous position = 0.00958
rotated from previous position = 0.00289 degrees
atoms outside contour = 3999, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74222508 -0.59001772 -0.31777507 126.22003096
0.64851841 0.51287283 0.56248140 156.21722362
-0.16889579 -0.62357079 0.76330444 468.54840899
Axis -0.68904643 -0.08649260 0.71953738
Axis point 72.15821310 458.77560345 0.00000000
Rotation angle (degrees) 59.38936447
Shift along axis 236.65500129
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 40
shifted from previous position = 0.0289
rotated from previous position = 0.0146 degrees
atoms outside contour = 3996, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74211376 -0.59013888 -0.31781006 126.26589203
0.64866503 0.51290126 0.56228638 156.15026365
-0.16882187 -0.62343274 0.76343355 468.52272019
Axis -0.68886387 -0.08655725 0.71970439
Axis point 72.15860144 458.72688827 0.00000000
Rotation angle (degrees) 59.38782628
Shift along axis 236.70191148
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 28
shifted from previous position = 0.0472
rotated from previous position = 0.0261 degrees
atoms outside contour = 4006, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74230987 -0.58989555 -0.31780384 126.16688330
0.64841943 0.51284526 0.56262064 156.26503300
-0.16890322 -0.62370904 0.76318984 468.56361567
Axis -0.68919404 -0.08650329 0.71939471
Axis point 72.14038978 458.80681995 0.00000000
Rotation angle (degrees) 59.39127491
Shift along axis 236.61128519
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 28
shifted from previous position = 0.0512
rotated from previous position = 0.0307 degrees
atoms outside contour = 3998, contour level = 0.014733
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74205723 -0.59016920 -0.31788578 126.26117600
0.64874281 0.51287277 0.56222263 156.13382422
-0.16877152 -0.62342748 0.76344898 468.51816976
Axis -0.68880730 -0.08662841 0.71974997
Axis point 72.14271486 458.69459733 0.00000000
Rotation angle (degrees) 59.39014304
Shift along axis 236.72069413
> ui mousemode right "move picked models"
> ~select #7
Nothing selected
> volume #2 level 0.0151
> volume #2 level 0.01529
> volume #2 level 0.01566
> volume #2 level 0.01603
> volume #2 level 0.01622
> volume #2 level 0.01641
> volume #2 level 0.01678
> volume #2 level 0.01715
> volume #2 level 0.01789
> volume #2 level 0.01845
> volume #2 level 0.01864
> volume #2 level 0.01882
> select #7
33495 atoms, 34271 bonds, 38 pseudobonds, 4095 residues, 3 models selected
> color (#!7 & sel) cornflower blue
> ~select #7
Nothing selected
> volume #2 level 0.01864
> volume #2 level 0.01845
> volume #2 level 0.01771
> volume #2 level 0.01715
> volume #2 level 0.01659
> volume #2 level 0.01641
> volume #2 level 0.01752
> volume #2 level 0.01789
> volume #2 level 0.01994
> volume #2 level 0.02217
> volume #2 level 0.02421
> volume #2 level 0.02588
> volume #2 level 0.02681
> volume #2 level 0.02793
> volume #2 level 0.02923
> volume #2 level 0.02997
> volume #2 level 0.03016
> volume #2 level 0.02942
> volume #2 level 0.02811
> volume #2 level 0.02663
> volume #2 level 0.02533
> volume #2 level 0.02161
> volume #2 level 0.02068
> volume #2 level 0.01845
> volume #2 level 0.01752
> volume #2 level 0.01678
> volume #2 level 0.01641
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 7/R
> select /R:10
21 atoms, 23 bonds, 1 residue, 1 model selected
> select /R:2-10
197 atoms, 221 bonds, 9 residues, 1 model selected
> select /R:10
21 atoms, 23 bonds, 1 residue, 1 model selected
> select /R:2-10
197 atoms, 221 bonds, 9 residues, 1 model selected
> color sel red
> hide #!7 models
> show #!7 models
> select #7
33495 atoms, 34271 bonds, 38 pseudobonds, 4095 residues, 3 models selected
> ~select #7
Nothing selected
> select #7
33495 atoms, 34271 bonds, 38 pseudobonds, 4095 residues, 3 models selected
> ~select #7
Nothing selected
> hide #!7 models
> open /Users/mcarmina/Desktop/5xon.pdb
5xon.pdb title:
Rna polymerase II elongation complex bound with SPT4/5 and tfiis [more
info...]
Chain information for 5xon.pdb #8
---
Chain | Description | UniProt
A | RNA polymerase II subunit RPB1 | C4R4Y0_KOMPG
B | RNA polymerase II subunit RPB2 | C4QZQ7_KOMPG
C | RNA polymerase II subunit RPB3 | C4R7L2_KOMPG
D | RNA polymerase II subunit RPB4 | C4R2U9_KOMPG
E | RNA polymerase II subunit RPB5 | C4R3P8_KOMPG
F | RNA polymerase II subunit RPB6 | C4R1V1_KOMPG
G | RNA polymerase II subunit RPB7 | C4R9A1_KOMPG
H | RNA polymerase II subunit RPB8 | C4R273_KOMPG
I | RNA polymerase II subunit RPB9 | C4QY79_KOMPG
J | RNA polymerase II subunit RPB10 | C4R009_KOMPG
K | RNA polymerase II subunit RPB11 | C4R3Z5_KOMPG
L | RNA polymerase II subunit RPB12 | C4QWA8_KOMPG
N | DNA (48-mer) |
P | RNA (30-mer) |
T | DNA (48-mer) |
U | general transcription elongation factor tfiis | C4R2R6_KOMPG
V | transcription elongation factor SPT4 | C4R0E6_KOMPG
W | SPT5 | C4R370_KOMPG
Non-standard residues in 5xon.pdb #8
---
MG — magnesium ion
ZN — zinc ion
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> cartoon (#!8 & sel)
> hide sel atoms
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.46694,0.53136,0.70684,28.618,-0.88321,-0.24073,-0.40248,339.92,-0.043703,-0.81222,0.58171,172.07
> view matrix models
> #8,0.3462,-0.87422,-0.34043,251.65,0.81261,0.46077,-0.35687,11.895,0.46884,-0.15309,0.86992,-24.694
> view matrix models
> #8,0.7584,0.24281,0.60488,-83.847,0.60312,-0.61332,-0.50999,204.25,0.24715,0.75159,-0.61158,90.79
> view matrix models
> #8,0.53316,-0.77071,0.34892,116.87,0.66597,0.12799,-0.73492,128.46,0.52175,0.6242,0.5815,-95.108
> view matrix models
> #8,-0.47677,-0.31667,0.82001,127,-0.8333,0.45979,-0.30694,226.74,-0.27983,-0.82965,-0.48309,354.21
> view matrix models
> #8,0.78943,-0.15265,-0.59456,131.31,0.12616,0.98826,-0.086216,-3.4426,0.60074,-0.0069475,0.79942,-52.094
> view matrix models
> #8,0.61504,-0.1489,-0.77431,179.29,-0.094516,0.96101,-0.25987,54.042,0.78281,0.23302,0.57699,-77.608
> color (#!8 & sel) cornflower blue
> select #7/R:10
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #7/R:2-10
197 atoms, 221 bonds, 9 residues, 1 model selected
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/P
Alignment identifier is 8/P
> select #8/P:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #8/P:-5-10
338 atoms, 376 bonds, 16 residues, 1 model selected
> color sel red
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> ~select #8
Nothing selected
> select #8/N:-25
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
889 atoms, 996 bonds, 43 residues, 1 model selected
> select up
38369 atoms, 39283 bonds, 4659 residues, 1 model selected
> select down
889 atoms, 996 bonds, 43 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #8/N:-25
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
889 atoms, 996 bonds, 43 residues, 1 model selected
> color sel gray
> select clear
> select #8/T:26
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
975 atoms, 1092 bonds, 48 residues, 1 model selected
> color sel gray
> select clear
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> ui mousemode right "move picked models"
> view matrix models
> #8,0.61504,-0.1489,-0.77431,265.6,-0.094516,0.96101,-0.25987,-54.932,0.78281,0.23302,0.57699,73.357
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.80866,-0.57509,0.12382,171.35,0.57267,0.81773,0.05793,-169.91,-0.13457,0.024064,0.99061,167.19
> view matrix models
> #8,0.85618,-0.061747,-0.51297,185.2,-0.099322,0.95465,-0.28068,-50.546,0.50704,0.29127,0.81122,70.186
> ui mousemode right "rotate selected models"
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 224
shifted from previous position = 5.44
rotated from previous position = 35 degrees
atoms outside contour = 14735, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68046526 -0.61671805 -0.39575989 176.43037819
0.29172752 0.72342902 -0.62573603 134.29998030
0.67220682 0.31033759 0.67218193 -94.49348241
Axis 0.55525615 -0.63349194 0.53886786
Axis point 253.64155542 0.00000000 294.37390258
Rotation angle (degrees) 57.44981669
Shift along axis -38.03340287
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 40
shifted from previous position = 0.0487
rotated from previous position = 0.109 degrees
atoms outside contour = 14717, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68026764 -0.61733662 -0.39513472 176.50396648
0.29345993 0.72339354 -0.62496650 133.95384021
0.67165254 0.30918829 0.67326476 -94.41912601
Axis 0.55429639 -0.63299608 0.54043638
Axis point 253.46340765 0.00000000 294.88189261
Rotation angle (degrees) 57.42093275
Shift along axis -37.98427575
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 48
shifted from previous position = 0.0145
rotated from previous position = 0.123 degrees
atoms outside contour = 14731, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68020719 -0.61679946 -0.39607652 176.55958855
0.29156895 0.72341539 -0.62582569 134.33240245
0.67253673 0.31020753 0.67191191 -94.48414215
Axis 0.55511837 -0.63374550 0.53871164
Axis point 253.60386611 0.00000000 294.29907078
Rotation angle (degrees) 57.46822575
Shift along axis -38.02079202
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 44
shifted from previous position = 0.0266
rotated from previous position = 0.107 degrees
atoms outside contour = 14727, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68047902 -0.61616718 -0.39659339 176.49736190
0.28987109 0.72343157 -0.62659523 134.67748199
0.67299553 0.31142396 0.67088904 -94.54988891
Axis 0.55614164 -0.63414793 0.53718049
Axis point 253.83723597 0.00000000 293.86702469
Rotation angle (degrees) 57.49319233
Shift along axis -38.03827017
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 40
shifted from previous position = 0.0297
rotated from previous position = 0.115 degrees
atoms outside contour = 14742, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68069169 -0.61549002 -0.39727932 176.44276130
0.28802746 0.72349110 -0.62737619 135.03625605
0.67357177 0.31262241 0.66975240 -94.62503065
Axis 0.55713335 -0.63468909 0.53551114
Axis point 254.03627401 0.00000000 293.34689055
Rotation angle (degrees) 57.52255285
Shift along axis -38.07665022
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 44
shifted from previous position = 0.00619
rotated from previous position = 0.0344 degrees
atoms outside contour = 14739, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68072404 -0.61531885 -0.39748899 176.44743322
0.28748661 0.72348655 -0.62762946 135.14775738
0.67377011 0.31296971 0.66939060 -94.64572842
Axis 0.55741908 -0.63485094 0.53502173
Axis point 254.10374726 0.00000000 293.20390977
Rotation angle (degrees) 57.53389426
Shift along axis -38.08103600
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 44
shifted from previous position = 0.0094
rotated from previous position = 0.0373 degrees
atoms outside contour = 14744, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68069458 -0.61551999 -0.39722794 176.45229410
0.28808083 0.72346643 -0.62738014 135.03313547
0.67354603 0.31262051 0.66977917 -94.62249029
Axis 0.55713562 -0.63464457 0.53556155
Axis point 254.05342869 0.00000000 293.38267195
Rotation angle (degrees) 57.52238343
Shift along axis -38.06635634
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 44
shifted from previous position = 0.0403
rotated from previous position = 0.0178 degrees
atoms outside contour = 14737, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68081726 -0.61537197 -0.39724703 176.37721549
0.28781137 0.72348513 -0.62748224 135.08401285
0.67353723 0.31286854 0.66967219 -94.64182915
Axis 0.55735037 -0.63465891 0.53532105
Axis point 254.08100176 0.00000000 293.29262252
Rotation angle (degrees) 57.52121506
Shift along axis -38.09212864
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 40
shifted from previous position = 0.0623
rotated from previous position = 0.307 degrees
atoms outside contour = 14730, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68034886 -0.61707271 -0.39540701 176.46214802
0.29269663 0.72340015 -0.62531670 134.10964650
0.67190330 0.30969921 0.67277956 -94.45431483
Axis 0.55472378 -0.63321106 0.53974557
Axis point 253.53605259 0.00000000 294.64811820
Rotation angle (degrees) 57.43444103
Shift along axis -38.01325845
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 44
shifted from previous position = 0.0345
rotated from previous position = 0.0396 degrees
atoms outside contour = 14719, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68023495 -0.61731702 -0.39522162 176.52043749
0.29332758 0.72338742 -0.62503572 133.98236373
0.67174346 0.30924175 0.67314949 -94.42228558
Axis 0.55433679 -0.63306461 0.54031465
Axis point 253.46926024 0.00000000 294.83858053
Rotation angle (degrees) 57.42617092
Shift along axis -37.98546348
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 44
shifted from previous position = 0.0605
rotated from previous position = 0.184 degrees
atoms outside contour = 14735, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68065372 -0.61623778 -0.39618371 176.39227323
0.29039902 0.72343654 -0.62634500 134.57081906
0.67259115 0.31127270 0.67136460 -94.54730118
Axis 0.55604131 -0.63382225 0.53766850
Axis point 253.82372938 0.00000000 294.03206361
Rotation angle (degrees) 57.47093192
Shift along axis -38.04769568
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 40
shifted from previous position = 0.0227
rotated from previous position = 0.126 degrees
atoms outside contour = 14729, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68047453 -0.61691920 -0.39543030 176.42163993
0.29239196 0.72341079 -0.62544691 134.17076916
0.67190869 0.30998006 0.67264482 -94.46824183
Axis 0.55496799 -0.63322845 0.53947406
Axis point 253.59718374 0.00000000 294.58619875
Rotation angle (degrees) 57.43438769
Shift along axis -38.01555173
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 48
shifted from previous position = 0.0395
rotated from previous position = 0.081 degrees
atoms outside contour = 14718, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68010628 -0.61745468 -0.39522800 176.55475186
0.29364742 0.72341052 -0.62485877 133.90899041
0.67173400 0.30891270 0.67331000 -94.40362887
Axis 0.55404811 -0.63307597 0.54059737
Axis point 253.37970881 0.00000000 294.88794289
Rotation angle (degrees) 57.42430315
Shift along axis -37.98908970
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 40
shifted from previous position = 0.044
rotated from previous position = 0.235 degrees
atoms outside contour = 14730, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68041711 -0.61620170 -0.39664598 176.50753204
0.28992368 0.72344662 -0.62655353 134.66090238
0.67303547 0.31132069 0.67089691 -94.54916431
Axis 0.55604749 -0.63419345 0.53722422
Axis point 253.79884751 0.00000000 293.85045489
Rotation angle (degrees) 57.49451739
Shift along axis -38.04859346
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 40
shifted from previous position = 0.0434
rotated from previous position = 0.0968 degrees
atoms outside contour = 14737, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68069368 -0.61559837 -0.39710800 176.40866163
0.28837681 0.72348063 -0.62722776 134.96935529
0.67342026 0.31243325 0.66999297 -94.61788941
Axis 0.55698204 -0.63455332 0.53582934
Axis point 253.99036506 0.00000000 293.42695224
Rotation angle (degrees) 57.51467055
Shift along axis -38.08783784
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 48
shifted from previous position = 0.0649
rotated from previous position = 0.163 degrees
atoms outside contour = 14731, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68020696 -0.61662491 -0.39634861 176.57231001
0.29098388 0.72342137 -0.62609103 134.44976627
0.67279031 0.31054042 0.67150415 -94.50302478
Axis 0.55538872 -0.63396087 0.53817933
Axis point 253.65377608 0.00000000 294.12642250
Rotation angle (degrees) 57.48188484
Shift along axis -38.02919663
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 40
shifted from previous position = 0.0393
rotated from previous position = 0.148 degrees
atoms outside contour = 14739, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68060970 -0.61571107 -0.39707722 176.46215191
0.28861497 0.72347461 -0.62712515 134.92093427
0.67340312 0.31222505 0.67010726 -94.60169005
Axis 0.55680291 -0.63453073 0.53604223
Axis point 253.96540931 0.00000000 293.50483490
Rotation angle (degrees) 57.51384592
Shift along axis -38.06733965
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.0201, steps = 40
shifted from previous position = 0.0243
rotated from previous position = 0.0634 degrees
atoms outside contour = 14742, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.68064750 -0.61539430 -0.39750327 176.44940862
0.28761682 0.72348402 -0.62757271 135.12623305
0.67379187 0.31282718 0.66943532 -94.65226590
Axis 0.55729377 -0.63486407 0.53513667
Axis point 254.06100820 -0.00000000 293.20468726
Rotation angle (degrees) 57.53506074
Shift along axis -38.10453296
> view matrix models
> #8,0.61357,-0.40114,-0.68016,284.64,-0.052076,0.83892,-0.54175,-6.1038,0.78792,0.36782,0.49385,64.327
> view matrix models
> #8,-0.1091,-0.16091,-0.98092,391.82,-0.64719,0.7605,-0.052767,16.495,0.75448,0.62909,-0.18711,128.75
> view matrix models
> #8,-0.56969,-0.34485,-0.74601,445.66,-0.78045,0.51151,0.35953,10.24,0.25761,0.78704,-0.56054,226.57
> view matrix models
> #8,-0.79388,-0.53597,0.28722,357.63,0.088439,0.36555,0.92658,-166.19,-0.60161,0.76099,-0.2428,301.57
> view matrix models
> #8,0.24124,-0.75603,0.60846,202.84,0.85679,0.46037,0.23233,-185.76,-0.45576,0.46527,0.75881,182.02
> view matrix models
> #8,0.72145,-0.66751,-0.18423,236.59,0.49816,0.6851,-0.53148,-61.174,0.48099,0.29166,0.82679,69.507
> view matrix models
> #8,0.6314,-0.41781,-0.65328,280.72,-0.0018376,0.84163,-0.54005,-13.467,0.77546,0.34218,0.53064,64.301
> view matrix models
> #8,0.82863,-0.42862,-0.36009,214.83,0.21442,0.8372,-0.5031,-47.138,0.51711,0.33967,0.78564,63.978
> view matrix models
> #8,0.46342,-0.7561,0.46212,193.27,0.77697,0.59746,0.19838,-188.53,-0.4261,0.26712,0.86434,189.71
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,81.172,0,1,0,-150.27,0,0,1,137.23
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 120
shifted from previous position = 10.5
rotated from previous position = 17.7 degrees
atoms outside contour = 10464, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56154326 -0.80215608 0.20301437 138.20164458
0.80732825 0.58491793 0.07805183 -25.42691533
-0.18135649 0.12006976 0.97605998 13.26560799
Axis 0.02538421 0.23220920 0.97233458
Axis point 95.95841156 119.50472994 0.00000000
Rotation angle (degrees) 55.85697971
Shift along axis 10.50238458
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.033
rotated from previous position = 0.0287 degrees
atoms outside contour = 10468, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56176771 -0.80200255 0.20299997 138.13174193
0.80710025 0.58518488 0.07840797 -25.47305627
-0.18167590 0.11979426 0.97603443 13.37687504
Axis 0.02500739 0.23243784 0.97228971
Axis point 95.99053722 119.45352103 0.00000000
Rotation angle (degrees) 55.84085314
Shift along axis 10.53960998
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0392
rotated from previous position = 0.0299 degrees
atoms outside contour = 10465, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56155327 -0.80214559 0.20302813 138.19664139
0.80732544 0.58492637 0.07801770 -25.43107335
-0.18133805 0.12009868 0.97605985 13.25447747
Axis 0.02542249 0.23220812 0.97233384
Axis point 95.95871022 119.50079570 0.00000000
Rotation angle (degrees) 55.85634604
Shift along axis 10.49577778
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0403
rotated from previous position = 0.0289 degrees
atoms outside contour = 10466, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56176296 -0.80199869 0.20302839 138.13032874
0.80710307 0.58518330 0.07839074 -25.46642573
-0.18167808 0.11982782 0.97602990 13.37328759
Axis 0.02503797 0.23245530 0.97228475
Axis point 95.98372351 119.45503247 0.00000000
Rotation angle (degrees) 55.84122907
Shift along axis 10.54134032
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0364
rotated from previous position = 0.0275 degrees
atoms outside contour = 10462, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56159378 -0.80212237 0.20300783 138.17748457
0.80729970 0.58496265 0.07801200 -25.44005919
-0.18132716 0.12007710 0.97606452 13.26395259
Axis 0.02541374 0.23219703 0.97233671
Axis point 95.96049583 119.48417711 0.00000000
Rotation angle (degrees) 55.85352570
Shift along axis 10.50152890
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0175
rotated from previous position = 0.0047 degrees
atoms outside contour = 10461, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56154596 -0.80214864 0.20303631 138.19646531
0.80733858 0.58491463 0.07796967 -25.43072714
-0.18130216 0.12013548 0.97606198 13.24090482
Axis 0.02547356 0.23218977 0.97233688
Axis point 95.95626023 119.50009646 0.00000000
Rotation angle (degrees) 55.85693097
Shift along axis 10.49022168
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0329
rotated from previous position = 0.0217 degrees
atoms outside contour = 10467, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56170996 -0.80208883 0.20281884 138.17177029
0.80720767 0.58506599 0.07818913 -25.46872864
-0.18137702 0.11979731 0.97608964 13.31646971
Axis 0.02514022 0.23213625 0.97235834
Axis point 95.99212632 119.48198480 0.00000000
Rotation angle (degrees) 55.84505705
Shift along axis 10.50983346
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0473
rotated from previous position = 0.0225 degrees
atoms outside contour = 10462, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56147036 -0.80219079 0.20307882 138.21439018
0.80731327 0.58489589 0.07837124 -25.45234507
-0.18164864 0.11994510 0.97602098 13.32931723
Axis 0.02511456 0.23241189 0.97229315
Axis point 95.99405135 119.49035407 0.00000000
Rotation angle (degrees) 55.86161581
Shift along axis 10.51576971
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0378
rotated from previous position = 0.0236 degrees
atoms outside contour = 10466, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56157376 -0.80213502 0.20301324 138.18599537
0.80732147 0.58493827 0.07796949 -25.43804363
-0.18129226 0.12011133 0.97606680 13.24650793
Axis 0.02545967 0.23217520 0.97234072
Axis point 95.95944634 119.49077530 0.00000000
Rotation angle (degrees) 55.85498400
Shift along axis 10.49220541
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 36
shifted from previous position = 0.031
rotated from previous position = 0.0127 degrees
atoms outside contour = 10467, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56165692 -0.80207425 0.20302326 138.17092580
0.80722795 0.58504470 0.07813903 -25.43438098
-0.18145098 0.11999873 0.97605115 13.29580263
Axis 0.02529102 0.23229371 0.97231682
Axis point 95.95907158 119.49271477 0.00000000
Rotation angle (degrees) 55.84896244
Shift along axis 10.51396902
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0371
rotated from previous position = 0.0163 degrees
atoms outside contour = 10459, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56153606 -0.80215665 0.20303205 138.20169392
0.80735383 0.58489893 0.07792951 -25.43309288
-0.18126489 0.12015847 0.97606608 13.22483946
Axis 0.02551149 0.23216263 0.97234237
Axis point 95.95801030 119.50310391 0.00000000
Rotation angle (degrees) 55.85767551
Shift along axis 10.48018843
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0266
rotated from previous position = 0.00607 degrees
atoms outside contour = 10462, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56157976 -0.80214820 0.20294452 138.18905714
0.80732783 0.58493052 0.07796173 -25.43499526
-0.18124529 0.12006102 0.97608171 13.25314147
Axis 0.02543410 0.23210656 0.97235778
Axis point 95.95847514 119.49403204 0.00000000
Rotation angle (degrees) 55.85452836
Shift along axis 10.49788026
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0226
rotated from previous position = 0.00648 degrees
atoms outside contour = 10457, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56152782 -0.80216358 0.20302742 138.20229504
0.80736272 0.58488828 0.07791736 -25.42943455
-0.18125082 0.12016400 0.97606801 13.22512138
Axis 0.02552199 0.23214972 0.97234517
Axis point 95.95480946 119.50335248 0.00000000
Rotation angle (degrees) 55.85826250
Shift along axis 10.48314454
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.027
rotated from previous position = 0.0242 degrees
atoms outside contour = 10470, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56179801 -0.80196593 0.20306081 138.11488827
0.80712747 0.58518873 0.07809843 -25.46330104
-0.18146117 0.12002041 0.97604659 13.29732342
Axis 0.02533156 0.23234927 0.97230249
Axis point 95.96472475 119.45232507 0.00000000
Rotation angle (degrees) 55.83924981
Shift along axis 10.51130687
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 36
shifted from previous position = 0.0312
rotated from previous position = 0.0117 degrees
atoms outside contour = 10470, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56166738 -0.80204436 0.20311238 138.15286755
0.80718717 0.58508583 0.07825228 -25.45213294
-0.18159997 0.11999795 0.97602354 13.32007449
Axis 0.02522237 0.23243985 0.97228368
Axis point 95.97151367 119.46983461 0.00000000
Rotation angle (degrees) 55.84813247
Shift along axis 10.51934342
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0272
rotated from previous position = 0.0194 degrees
atoms outside contour = 10463, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56157176 -0.80214462 0.20298081 138.18507157
0.80732004 0.58493502 0.07800868 -25.43983928
-0.18130481 0.12006301 0.97607041 13.26374739
Axis 0.02540678 0.23216304 0.97234501
Axis point 95.96269936 119.48656993 0.00000000
Rotation angle (degrees) 55.85504082
Shift along axis 10.50158604
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0385
rotated from previous position = 0.0216 degrees
atoms outside contour = 10464, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56173665 -0.80201594 0.20303301 138.14143047
0.80714441 0.58514266 0.07826835 -25.44548885
-0.18157573 0.11991076 0.97603876 13.34326239
Axis 0.02516144 0.23239071 0.97229700
Axis point 95.96517956 119.47182969 0.00000000
Rotation angle (degrees) 55.84323994
Shift along axis 10.53615582
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0211
rotated from previous position = 0.00463 degrees
atoms outside contour = 10471, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56167311 -0.80205321 0.20306160 138.16025396
0.80718725 0.58508383 0.07826645 -25.45352357
-0.18158191 0.11994858 0.97603297 13.32359324
Axis 0.02518411 0.23239951 0.97229431
Axis point 95.97613898 119.47641142 0.00000000
Rotation angle (degrees) 55.84767718
Shift along axis 10.51851117
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0114
rotated from previous position = 0.0159 degrees
atoms outside contour = 10466, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56156056 -0.80214206 0.20302192 138.19973697
0.80731178 0.58493862 0.07806709 -25.42711679
-0.18137625 0.12006259 0.97605719 13.26713485
Axis 0.02537102 0.23222905 0.97233018
Axis point 95.95851711 119.50665579 0.00000000
Rotation angle (degrees) 55.85576124
Shift along axis 10.50138876
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 48
shifted from previous position = 0.023
rotated from previous position = 0.0227 degrees
atoms outside contour = 10463, contour level = 0.016406
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56170591 -0.80202150 0.20309612 138.14807588
0.80714109 0.58513489 0.07836068 -25.45436817
-0.18168556 0.11991157 0.97601822 13.35144563
Axis 0.02510553 0.23248958 0.97227481
Axis point 95.97684384 119.47010995 0.00000000
Rotation angle (degrees) 55.84528453
Shift along axis 10.53167980
> ui mousemode right "rotate selected models"
> ~select #8
Nothing selected
> volume #2 level 0.02119
> volume #2 level 0.0187
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> view matrix models
> #8,-0.51347,-0.70332,-0.49162,447.57,-0.82866,0.25762,0.49694,29.947,-0.22285,0.66255,-0.71509,319.04
> view matrix models
> #8,0.43372,-0.42809,-0.79286,325.28,-0.1154,0.84629,-0.52007,-3.0224,0.89363,0.31706,0.31765,71.068
> view matrix models
> #8,0.33048,-0.85979,-0.38928,340.49,0.94354,0.29099,0.15829,-166.08,-0.022823,-0.41961,0.90742,210.48
> view matrix models
> #8,0.11519,-0.51143,-0.85157,387.42,-0.93692,0.22887,-0.26419,154.16,0.33001,0.82829,-0.4528,186.08
> view matrix models
> #8,-0.19213,0.020425,-0.98116,376.08,-0.89182,0.41362,0.18325,61.312,0.40957,0.91022,-0.061255,110.04
> view matrix models
> #8,-0.48309,-0.62811,-0.61,449.93,-0.37635,-0.48009,0.79239,26.08,-0.79056,0.61237,-0.0044601,303.38
> view matrix models
> #8,0.44666,-0.87354,0.19343,245.67,0.82132,0.48608,0.2986,-195.07,-0.35486,0.025493,0.93457,192.22
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 92
shifted from previous position = 1.57
rotated from previous position = 13.9 degrees
atoms outside contour = 12161, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56166047 -0.80205262 0.20309874 138.14876215
0.80722629 0.58505500 0.07807881 -25.43913349
-0.18144723 0.12009285 0.97604024 13.28320748
Axis 0.02538430 0.23233733 0.97230397
Axis point 95.95246665 119.47118354 0.00000000
Rotation angle (degrees) 55.84885992
Shift along axis 10.51166419
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0222
rotated from previous position = 0.0138 degrees
atoms outside contour = 12161, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56151794 -0.80216397 0.20305310 138.20542465
0.80735703 0.58488937 0.07796791 -25.42410994
-0.18130663 0.12015596 0.97605860 13.23697999
Axis 0.02548641 0.23219723 0.97233476
Axis point 95.95319097 119.50715223 0.00000000
Rotation angle (degrees) 55.85889125
Shift along axis 10.48972765
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0391
rotated from previous position = 0.0217 degrees
atoms outside contour = 12164, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56170315 -0.80203852 0.20303638 138.13969973
0.80717704 0.58510385 0.07822169 -25.45829627
-0.18153416 0.11994892 0.97604177 13.32903789
Axis 0.02521198 0.23236104 0.97230278
Axis point 95.97270938 119.45780219 0.00000000
Rotation angle (degrees) 55.84563780
Shift along axis 10.52711916
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0365
rotated from previous position = 0.0218 degrees
atoms outside contour = 12165, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56155195 -0.80214556 0.20303177 138.19329603
0.80734125 0.58491555 0.07793492 -25.43157071
-0.18127157 0.12015141 0.97606567 13.23340481
Axis 0.02550429 0.23216957 0.97234090
Axis point 95.95465540 119.49788010 0.00000000
Rotation angle (degrees) 55.85656318
Shift along axis 10.48746558
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0214
rotated from previous position = 0.00667 degrees
atoms outside contour = 12159, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56159890 -0.80212969 0.20296457 138.17883393
0.80730300 0.58495892 0.07800549 -25.44391494
-0.18129644 0.12004611 0.97607401 13.26533781
Axis 0.02539907 0.23215338 0.97234752
Axis point 95.96440043 119.48344430 0.00000000
Rotation angle (degrees) 55.85314774
Shift along axis 10.50124131
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 24
shifted from previous position = 0.017
rotated from previous position = 0.00653 degrees
atoms outside contour = 12161, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56160010 -0.80210688 0.20305141 138.16493018
0.80727843 0.58498427 0.07806974 -25.43777317
-0.18140213 0.12007504 0.97605081 13.28696158
Axis 0.02537777 0.23227002 0.97232022
Axis point 95.95692815 119.47351365 0.00000000
Rotation angle (degrees) 55.85303215
Shift along axis 10.51706704
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 36
shifted from previous position = 0.0151
rotated from previous position = 0.0117 degrees
atoms outside contour = 12164, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56167953 -0.80205738 0.20302722 138.15268106
0.80719449 0.58507905 0.07822722 -25.44705207
-0.18152968 0.11994382 0.97604324 13.32926387
Axis 0.02520507 0.23234833 0.97230600
Axis point 95.96776696 119.47106239 0.00000000
Rotation angle (degrees) 55.84726380
Shift along axis 10.52969067
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0317
rotated from previous position = 0.0151 degrees
atoms outside contour = 12162, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56158009 -0.80213150 0.20300948 138.18533736
0.80730679 0.58495093 0.07802618 -25.44055725
-0.18133783 0.12007297 0.97606302 13.26153534
Axis 0.02540240 0.23220192 0.97233584
Axis point 95.96366359 119.48950855 0.00000000
Rotation angle (degrees) 55.85445595
Shift along axis 10.49755961
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0135
rotated from previous position = 0.00699 degrees
atoms outside contour = 12159, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56158637 -0.80212810 0.20300554 138.17865836
0.80732506 0.58494173 0.07790605 -25.43727821
-0.18123702 0.12014048 0.97607343 13.23541666
Axis 0.02551585 0.23213935 0.97234781
Axis point 95.95423025 119.48634420 0.00000000
Rotation angle (degrees) 55.85419687
Shift along axis 10.49018042
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.035
rotated from previous position = 0.00867 degrees
atoms outside contour = 12165, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56152605 -0.80216159 0.20304007 138.20434382
0.80733831 0.58490474 0.07804632 -25.42304342
-0.18136484 0.12009698 0.97605504 13.26209622
Axis 0.02540361 0.23222643 0.97232996
Axis point 95.95546580 119.50657510 0.00000000
Rotation angle (degrees) 55.85820174
Shift along axis 10.50212018
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0236
rotated from previous position = 0.0282 degrees
atoms outside contour = 12173, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56161654 -0.80207871 0.20311718 138.16504234
0.80718119 0.58506355 0.07847991 -25.46660347
-0.18178350 0.11987674 0.97600423 13.37395352
Axis 0.02501066 0.23254484 0.97226404
Axis point 95.99605468 119.46263969 0.00000000
Rotation angle (degrees) 55.85133072
Shift along axis 10.53648627
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.011
rotated from previous position = 0.0103 degrees
atoms outside contour = 12165, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56171016 -0.80203121 0.20304588 138.14713009
0.80714929 0.58512679 0.07833647 -25.45735290
-0.18163586 0.11988594 0.97603059 13.35224860
Axis 0.02510476 0.23243002 0.97228907
Axis point 95.97880296 119.46687706 0.00000000
Rotation angle (degrees) 55.84498834
Shift along axis 10.53334266
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0145
rotated from previous position = 0.00458 degrees
atoms outside contour = 12169, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56168624 -0.80203787 0.20308571 138.15549469
0.80717231 0.58510293 0.07827745 -25.44141004
-0.18160751 0.11995779 0.97602704 13.33130066
Axis 0.02518331 0.23243206 0.97228655
Axis point 95.96504159 119.48011916 0.00000000
Rotation angle (degrees) 55.84676530
Shift along axis 10.52765735
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0258
rotated from previous position = 0.00639 degrees
atoms outside contour = 12167, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56174411 -0.80201421 0.20301909 138.13553846
0.80712963 0.58515497 0.07832853 -25.46439231
-0.18161820 0.11986213 0.97603680 13.35624020
Axis 0.02509588 0.23240967 0.97229416
Axis point 95.98114592 119.45781443 0.00000000
Rotation angle (degrees) 55.84262244
Shift along axis 10.53465603
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0335
rotated from previous position = 0.0252 degrees
atoms outside contour = 12164, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56152458 -0.80216308 0.20303824 138.20556163
0.80734076 0.58490217 0.07804021 -25.42339132
-0.18135847 0.12009954 0.97605591 13.25951906
Axis 0.02540882 0.23222117 0.97233107
Axis point 95.95588341 119.50745358 0.00000000
Rotation angle (degrees) 55.85831118
Shift along axis 10.50043281
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0418
rotated from previous position = 0.0229 degrees
atoms outside contour = 12165, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56177155 -0.80199426 0.20302198 138.11931215
0.80712625 0.58517187 0.07823700 -25.47629218
-0.18154836 0.11991304 0.97604354 13.33486126
Axis 0.02518247 0.23237408 0.97230043
Axis point 95.98225313 119.44243966 0.00000000
Rotation angle (degrees) 55.84085398
Shift along axis 10.52364729
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 36
shifted from previous position = 0.0436
rotated from previous position = 0.0151 degrees
atoms outside contour = 12167, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56161131 -0.80209827 0.20305441 138.18458247
0.80726414 0.58499989 0.07810043 -25.43892718
-0.18143101 0.12005645 0.97604773 13.27345186
Axis 0.02534824 0.23229154 0.97231585
Axis point 95.96509678 119.49711680 0.00000000
Rotation angle (degrees) 55.85220999
Shift along axis 10.49947604
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0279
rotated from previous position = 0.00387 degrees
atoms outside contour = 12158, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56160823 -0.80211604 0.20299273 138.17576393
0.80727033 0.58498817 0.07812419 -25.45618800
-0.18141300 0.11999481 0.97605866 13.29035985
Axis 0.02529660 0.23224302 0.97232878
Axis point 95.97809717 119.47647390 0.00000000
Rotation angle (degrees) 55.85234376
Shift along axis 10.50595455
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.036
rotated from previous position = 0.015 degrees
atoms outside contour = 12165, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56164581 -0.80204798 0.20315762 138.15631782
0.80718957 0.58507734 0.07829077 -25.44927577
-0.18165586 0.12001502 0.97601101 13.32557412
Axis 0.02520899 0.23249690 0.97227038
Axis point 95.97118726 119.47128513 0.00000000
Rotation angle (degrees) 55.84960586
Shift along axis 10.52196481
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0398
rotated from previous position = 0.0156 degrees
atoms outside contour = 12160, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56158958 -0.80212791 0.20299742 138.17868985
0.80728408 0.58496976 0.07811998 -25.45910636
-0.18140955 0.12000521 0.97605802 13.28599356
Axis 0.02530504 0.23224019 0.97232924
Axis point 95.98079186 119.47465235 0.00000000
Rotation angle (degrees) 55.85364873
Shift along axis 10.50234943
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0206
rotated from previous position = 0.0025 degrees
atoms outside contour = 12164, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56159594 -0.80212003 0.20301096 138.18813655
0.80728530 0.58497360 0.07807855 -25.43994673
-0.18138440 0.12003916 0.97605852 13.27075493
Axis 0.02535069 0.23223419 0.97232948
Axis point 95.96613294 119.49589398 0.00000000
Rotation angle (degrees) 55.85327846
Shift along axis 10.49868576
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0372
rotated from previous position = 0.0262 degrees
atoms outside contour = 12163, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56176875 -0.80199418 0.20303004 138.13102140
0.80709129 0.58519426 0.07842997 -25.47012771
-0.18171238 0.11980426 0.97602638 13.38027316
Axis 0.02500017 0.23247830 0.97228022
Axis point 95.98847362 119.45515560 0.00000000
Rotation angle (degrees) 55.84077008
Shift along axis 10.54142143
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0377
rotated from previous position = 0.0295 degrees
atoms outside contour = 12159, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56160019 -0.80212001 0.20299926 138.17598678
0.80729555 0.58496791 0.07801526 -25.44232465
-0.18132564 0.12006700 0.97606602 13.26560113
Axis 0.02540581 0.23219219 0.97233807
Axis point 95.96216999 119.48261054 0.00000000
Rotation angle (degrees) 55.85306867
Shift along axis 10.50161314
> select clear
> show #!7 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
> select #8/W:412
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 2 residues, 1 model selected
> select up
2667 atoms, 2713 bonds, 329 residues, 1 model selected
> hide sel atoms
[Repeated 8 time(s)]
> cartoon hide sel
> select #8/V:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
59 atoms, 58 bonds, 8 residues, 1 model selected
> select up
793 atoms, 808 bonds, 103 residues, 1 model selected
> cartoon hide sel
> select #8/U:124
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
104 atoms, 104 bonds, 14 residues, 1 model selected
> select up
1240 atoms, 1255 bonds, 156 residues, 1 model selected
> cartoon hide sel
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 36
shifted from previous position = 0.0281
rotated from previous position = 0.0191 degrees
atoms outside contour = 12166, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56171113 -0.80203532 0.20302693 138.14458931
0.80716156 0.58511735 0.07828053 -25.45712098
-0.18157831 0.11990448 0.97603902 13.34160376
Axis 0.02514977 0.23238380 0.97229896
Axis point 95.97575055 119.46437842 0.00000000
Rotation angle (degrees) 55.84498967
Shift along axis 10.53050944
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0311
rotated from previous position = 0.0193 degrees
atoms outside contour = 12164, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56156173 -0.80214029 0.20302552 138.19625658
0.80731521 0.58493730 0.07804122 -25.43201070
-0.18135719 0.12008062 0.97605848 13.25995887
Axis 0.02539755 0.23221983 0.97233169
Axis point 95.96036031 119.50149751 0.00000000
Rotation angle (degrees) 55.85572041
Shift along axis 10.49710790
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 48
shifted from previous position = 0.0246
rotated from previous position = 0.0172 degrees
atoms outside contour = 12160, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56174175 -0.80198849 0.20312721 138.11946802
0.80715106 0.58515012 0.07814372 -25.46838212
-0.18153026 0.12005774 0.97602912 13.30037287
Axis 0.02532558 0.23242044 0.97228563
Axis point 95.97070086 119.44478272 0.00000000
Rotation angle (degrees) 55.84313813
Shift along axis 10.51034486
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.022
rotated from previous position = 0.0147 degrees
atoms outside contour = 12165, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56159331 -0.80212196 0.20301058 138.18909505
0.80728779 0.58497054 0.07807576 -25.43826003
-0.18138147 0.12004113 0.97605882 13.27043816
Axis 0.02535351 0.23223168 0.97233001
Axis point 95.96494250 119.49708272 0.00000000
Rotation angle (degrees) 55.85346458
Shift along axis 10.49925383
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0156
rotated from previous position = 0.00301 degrees
atoms outside contour = 12159, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56158502 -0.80212956 0.20300349 138.18258126
0.80730356 0.58495507 0.07802858 -25.44346279
-0.18133693 0.12006575 0.97606407 13.26383222
Axis 0.02539670 0.23219873 0.97233675
Axis point 95.96543406 119.48603296 0.00000000
Rotation angle (degrees) 55.85410549
Shift along axis 10.49835360
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0184
rotated from previous position = 0.00551 degrees
atoms outside contour = 12162, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56153349 -0.80215530 0.20304434 138.20122601
0.80734544 0.58490433 0.07797567 -25.42725400
-0.18131010 0.12014096 0.97605980 13.24056492
Axis 0.02547299 0.23219706 0.97233515
Axis point 95.95497975 119.50424060 0.00000000
Rotation angle (degrees) 55.85779367
Shift along axis 10.49053163
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0311
rotated from previous position = 0.0228 degrees
atoms outside contour = 12166, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56169696 -0.80203707 0.20305921 138.15068173
0.80716960 0.58510776 0.07826934 -25.45134971
-0.18158641 0.11993956 0.97603321 13.33210021
Axis 0.02517742 0.23240537 0.97229308
Axis point 95.97190176 119.47190166 0.00000000
Rotation angle (degrees) 55.84601345
Shift along axis 10.52595631
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 28
shifted from previous position = 0.0349
rotated from previous position = 0.0138 degrees
atoms outside contour = 12158, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56159210 -0.80212564 0.20299943 138.17926890
0.80728302 0.58497198 0.07811431 -25.45922983
-0.18140645 0.12000960 0.97605806 13.28266132
Axis 0.02531117 0.23223998 0.97232913
Axis point 95.98075638 119.47602900 0.00000000
Rotation angle (degrees) 55.85348362
Shift along axis 10.49994641
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0295
rotated from previous position = 0.00685 degrees
atoms outside contour = 12164, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56152867 -0.80216060 0.20303671 138.20457688
0.80733749 0.58490633 0.07804294 -25.42393399
-0.18136041 0.12009579 0.97605601 13.26052329
Axis 0.02540500 0.23222221 0.97233093
Axis point 95.95617037 119.50696822 0.00000000
Rotation angle (degrees) 55.85802211
Shift along axis 10.50070150
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0404
rotated from previous position = 0.0217 degrees
atoms outside contour = 12164, contour level = 0.018702
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56176339 -0.80199825 0.20302878 138.12085775
0.80713285 0.58516391 0.07822857 -25.47495709
-0.18154427 0.11992525 0.97604280 13.33178597
Axis 0.02519477 0.23237412 0.97230010
Axis point 95.98114792 119.44326928 0.00000000
Rotation angle (degrees) 55.84143775
Shift along axis 10.52269916
> show #!7 models
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 96
shifted from previous position = 23.3
rotated from previous position = 0.00677 degrees
atoms outside contour = 6394, contour level = 0.018702
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74206596 -0.59021137 -0.31778710 126.29739157
0.64872172 0.51292648 0.56219796 156.11793510
-0.16881420 -0.62334336 0.76350822 468.51349423
Axis -0.68877291 -0.08654991 0.71979233
Axis point 72.17017933 458.70955402 0.00000000
Rotation angle (degrees) 59.38609224
Shift along axis 236.73020332
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 36
shifted from previous position = 0.003
rotated from previous position = 0.00195 degrees
atoms outside contour = 6396, contour level = 0.018702
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74205193 -0.59023473 -0.31777645 126.30872701
0.64873588 0.51292848 0.56217980 156.11077328
-0.16882145 -0.62331960 0.76352602 468.51314346
Axis -0.68874992 -0.08653969 0.71981556
Axis point 72.17790176 458.70555692 0.00000000
Rotation angle (degrees) 59.38590017
Shift along axis 236.73814572
Fit molecule 5c4x.pdb (#7) to map 5.mrc (#2) using 33495 atoms
average map value = 0.02747, steps = 28
shifted from previous position = 0.0585
rotated from previous position = 0.0338 degrees
atoms outside contour = 6391, contour level = 0.018702
Position of 5c4x.pdb (#7) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.74230058 -0.58990930 -0.31780001 126.17213297
0.64843042 0.51284949 0.56260412 156.25889146
-0.16890182 -0.62369256 0.76320361 468.56280336
Axis -0.68917693 -0.08650213 0.71941124
Axis point 72.14272023 458.80350188 0.00000000
Rotation angle (degrees) 59.39098482
Shift along axis 236.61769841
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> volume #2 level 0.01755
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0202
rotated from previous position = 0.0074 degrees
atoms outside contour = 11251, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56177382 -0.80199744 0.20300312 138.12602858
0.80710606 0.58518455 0.07835037 -25.47228655
-0.18163107 0.11982986 0.97603837 13.36477049
Axis 0.02506381 0.23241360 0.97229405
Axis point 95.98578989 119.44983950 0.00000000
Rotation angle (degrees) 55.84051560
Shift along axis 10.53634527
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0329
rotated from previous position = 0.0259 degrees
atoms outside contour = 11266, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56150767 -0.80218202 0.20301018 138.21198409
0.80734446 0.58488813 0.07810716 -25.42391471
-0.18139439 0.12004137 0.97605639 13.27932514
Axis 0.02533291 0.23222302 0.97233261
Axis point 95.96121531 119.50841582 0.00000000
Rotation angle (degrees) 55.85936597
Shift along axis 10.50921501
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0124
rotated from previous position = 0.0061 degrees
atoms outside contour = 11261, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56159567 -0.80212461 0.20299361 138.19221227
0.80728748 0.58497033 0.07808053 -25.43470199
-0.18137554 0.12002451 0.97606197 13.27288112
Axis 0.02534064 0.23221835 0.97233353
Axis point 95.96340218 119.50180807 0.00000000
Rotation angle (degrees) 55.85328138
Shift along axis 10.50114203
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0312
rotated from previous position = 0.015 degrees
atoms outside contour = 11248, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56173166 -0.80201642 0.20304480 138.12856014
0.80715395 0.58513489 0.07822790 -25.46945990
-0.18154864 0.11994532 0.97603952 13.32971370
Axis 0.02520664 0.23238034 0.97229831
Axis point 95.97866292 119.44754263 0.00000000
Rotation angle (degrees) 55.84365452
Shift along axis 10.52361321
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 48
shifted from previous position = 0.0189
rotated from previous position = 0.0207 degrees
atoms outside contour = 11246, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56157464 -0.80214579 0.20296807 138.18534631
0.80732335 0.58493309 0.07798864 -25.44342051
-0.18128098 0.12006441 0.97607463 13.25761090
Axis 0.02541979 0.23214145 0.97234982
Axis point 95.96506578 119.48575597 0.00000000
Rotation angle (degrees) 55.85486021
Shift along axis 10.49720562
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0236
rotated from previous position = 0.00482 degrees
atoms outside contour = 11252, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56154173 -0.80215059 0.20304014 138.19789764
0.80734174 0.58491069 0.07796626 -25.42970584
-0.18130101 0.12014146 0.97606143 13.23912739
Axis 0.02547914 0.23219057 0.97233654
Axis point 95.95565737 119.50136104 0.00000000
Rotation angle (degrees) 55.85723183
Shift along axis 10.48951303
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0248
rotated from previous position = 0.00523 degrees
atoms outside contour = 11247, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56159701 -0.80212939 0.20297100 138.17877169
0.80731380 0.58495141 0.07795012 -25.44207349
-0.18125423 0.12008472 0.97607710 13.24943095
Axis 0.02545578 0.23213116 0.97235134
Axis point 95.96046390 119.48480305 0.00000000
Rotation angle (degrees) 55.85336652
Shift along axis 10.49465288
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0247
rotated from previous position = 0.00531 degrees
atoms outside contour = 11255, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56156126 -0.80214061 0.20302556 138.19428657
0.80731955 0.58493419 0.07801971 -25.43317604
-0.18133935 0.12009365 0.97606019 13.25518025
Axis 0.02541841 0.23220890 0.97233375
Axis point 95.95982003 119.49901764 0.00000000
Rotation angle (degrees) 55.85578492
Shift along axis 10.49532827
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.022
rotated from previous position = 0.0173 degrees
atoms outside contour = 11256, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56170052 -0.80203481 0.20305830 138.14853250
0.80717587 0.58510539 0.07822232 -25.45115986
-0.18154751 0.11996623 0.97603716 13.32038224
Axis 0.02522200 0.23238181 0.97229756
Axis point 95.96919265 119.47102464 0.00000000
Rotation angle (degrees) 55.84583509
Shift along axis 10.52137060
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.00921
rotated from previous position = 0.00273 degrees
atoms outside contour = 11252, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56171379 -0.80203014 0.20304003 138.14210374
0.80716154 0.58512004 0.07826067 -25.45755723
-0.18157019 0.11992600 0.97603789 13.33546515
Axis 0.02517481 0.23238720 0.97229749
Axis point 95.97437064 119.46288108 0.00000000
Rotation angle (degrees) 55.84484381
Shift along axis 10.52773045
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0291
rotated from previous position = 0.0181 degrees
atoms outside contour = 11261, contour level = 0.017554
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56155366 -0.80214461 0.20303080 138.20114966
0.80731694 0.58493245 0.07805978 -25.42621964
-0.18137452 0.12007545 0.97605590 13.26368852
Axis 0.02538306 0.23223202 0.97232916
Axis point 95.95774667 119.50752080 0.00000000
Rotation angle (degrees) 55.85625715
Shift along axis 10.49985707
> color sel light sea green
> ui tool show "Color Actions"
> set bgColor white
> volume #2 color #ffff6d8c
> volume #2 color #ffff6d45
> volume #2 color #ffff6d0a
> volume #2 color #ffff6d
> volume #2 color #ffff6d90
> volume #2 color #ffff6d65
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> save /Users/mcarmina/Desktop/cl5_fitted.cxs
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> volume #2 color #ffff6d65
> volume #2 color #ffff6d78
> volume #2 color #ffff6d96
> volume #2 color #ffff6d
> volume #2 color #ffff6de2
> lighting soft
> lighting simple
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting full
> volume #2 color #ffff6da8
> volume #2 color #ffff6db9
> lighting simple
> volume #2 color #ffff6d61
> volume #2 color #ffff6d76
> save /Users/mcarmina/Desktop/cl5_fitted.cxs
> volume #2 level 0.01545
> save /Users/mcarmina/Desktop/cl5_fitted.cxs
> volume #1 level 0.01238
> volume #5 level 0.01145
> volume #5 level 0.01269
> select #5
2 models selected
> view matrix models
> #5,0.68775,0.38613,0.61474,99.7,0.6626,0.012063,-0.74888,-63.556,-0.29658,0.92237,-0.24755,-206.63
> view matrix models
> #5,0.6904,0.37956,0.61586,100.22,0.65945,0.019818,-0.75149,-63.974,-0.29744,0.92496,-0.23662,-208.51
> view matrix models
> #5,0.6839,0.39566,0.61297,98.972,0.66717,0.00082818,-0.74491,-62.977,-0.29524,0.91839,-0.26341,-203.87
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.6839,0.39566,0.61297,9.2379,0.66717,0.00082818,-0.74491,10.781,-0.29524,0.91839,-0.26341,114.65
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.45428,-0.66824,-0.58914,391.47,-0.63764,-0.70573,0.3088,165.64,-0.62213,0.23538,-0.7467,344.63
> view matrix models
> #5,-0.40773,-0.86567,-0.29045,507.69,-0.20647,-0.22245,0.95283,-70.583,-0.88945,0.44847,-0.088033,253.61
> view matrix models
> #5,-0.35811,-0.88416,-0.30004,504.75,-0.20059,-0.24099,0.94957,-67.953,-0.91188,0.40024,-0.091055,265.23
> view matrix models
> #5,-0.41229,-0.28158,-0.86645,496.93,-0.91104,0.13221,0.39054,57.589,0.0045822,0.95039,-0.31104,72.028
> view matrix models
> #5,0.41526,0.21625,-0.88363,295.9,-0.2911,0.95185,0.09614,-124.87,0.86187,0.2173,0.45821,-47.146
> view matrix models
> #5,0.19461,0.24012,-0.95104,334.45,-0.50993,0.85302,0.11102,-78.564,0.83791,0.46336,0.28845,-59.018
> view matrix models
> #5,0.21321,0.044118,-0.97601,367.28,-0.33506,0.9417,-0.030627,-98.276,0.91776,0.33355,0.21556,-39.064
> view matrix models
> #5,0.32718,-0.13425,-0.93538,373.59,-0.063571,0.98449,-0.16353,-126.07,0.94282,0.11297,0.31357,-21.07
> view matrix models
> #5,0.33132,-0.14096,-0.93293,373.72,-0.067943,0.98265,-0.1726,-123.8,0.94107,0.12057,0.31599,-22.403
> view matrix models
> #5,0.69515,0.52175,-0.49452,148.12,-0.5007,0.84502,0.18771,-89.78,0.51581,0.11712,0.84866,-36.435
> ui mousemode right "move picked models"
> view matrix models
> #5,0.69515,0.52175,-0.49452,79.451,-0.5007,0.84502,0.18771,-81.664,0.51581,0.11712,0.84866,26.988
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99991,0.013147,0.0031863,44.892,-0.012954,0.86272,0.50551,-202.9,0.0038968,-0.50551,0.86281,202.12
> view matrix models
> #5,0.96516,0.22345,0.13619,-3.5954,-0.26152,0.80567,0.5315,-160.63,0.0090393,-0.5486,0.83604,212.28
> view matrix models
> #5,0.95459,0.28707,0.079654,-4.1806,-0.28897,0.82722,0.48187,-152.86,0.072437,-0.48301,0.87262,186.9
> view matrix models
> #5,0.93909,0.25831,0.22668,-18.587,-0.31908,0.90035,0.29589,-133.28,-0.12766,-0.3502,0.92793,186.79
> ui mousemode right "move picked models"
> view matrix models
> #5,0.93909,0.25831,0.22668,-0.11445,-0.31908,0.90035,0.29589,-147.37,-0.12766,-0.3502,0.92793,229.97
Fit map 2.mrc in map 5.mrc using 113329 points
correlation = 0.9835, correlation about mean = 0.8679, overlap = 80.14
steps = 128, shift = 20.9, angle = 26.4 degrees
Position of 2.mrc (#5) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.99987585 0.01461841 -0.00588206 -1.93045174
-0.01444812 0.99950295 0.02801985 -1.71853983
0.00628874 -0.02793139 0.99959007 4.11651572
Axis -0.87131459 -0.18953283 -0.45264577
Axis point 0.00000000 148.79554294 62.99554028
Rotation angle (degrees) 1.83993283
Shift along axis 0.14442704
Fit map 2.mrc in map 5.mrc using 113329 points
correlation = 0.9835, correlation about mean = 0.8679, overlap = 80.14
steps = 40, shift = 0.00533, angle = 0.0102 degrees
Position of 2.mrc (#5) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.99987804 0.01445206 -0.00592059 -1.89610690
-0.01428108 0.99950679 0.02796844 -1.74024229
0.00632188 -0.02788048 0.99959128 4.10116817
Axis -0.87279142 -0.19132188 -0.44903348
Axis point 0.00000000 148.51840505 63.83998387
Rotation angle (degrees) 1.83345852
Shift along axis 0.14629046
Fit map 2.mrc in map 5.mrc using 113329 points
correlation = 0.9835, correlation about mean = 0.8679, overlap = 80.14
steps = 24, shift = 0.00907, angle = 0.00731 degrees
Position of 2.mrc (#5) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.99987886 0.01438464 -0.00594568 -1.87501111
-0.01421366 0.99951071 0.02786262 -1.73853034
0.00634356 -0.02777473 0.99959408 4.07245134
Axis -0.87270623 -0.19276438 -0.44858191
Axis point 0.00000000 148.02495669 63.99536188
Rotation angle (degrees) 1.82668896
Shift along axis 0.14463261
Fit map 2.mrc in map 5.mrc using 113329 points
correlation = 0.9835, correlation about mean = 0.868, overlap = 80.13
steps = 28, shift = 0.0635, angle = 0.0354 degrees
Position of 2.mrc (#5) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.99987421 0.01473449 -0.00587170 -1.98608933
-0.01456225 0.99949145 0.02836896 -1.73529561
0.00628671 -0.02827989 0.99958028 4.21760100
Axis -0.87253144 -0.18726935 -0.45124171
Axis point 0.00000000 150.67403332 62.84843097
Rotation angle (degrees) 1.86028285
Shift along axis 0.15473557
Fit map 2.mrc in map 5.mrc using 113329 points
correlation = 0.9835, correlation about mean = 0.8679, overlap = 80.14
steps = 28, shift = 0.0646, angle = 0.0364 degrees
Position of 2.mrc (#5) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.99987878 0.01438679 -0.00595419 -1.87411678
-0.01421571 0.99951126 0.02784161 -1.73662675
0.00635183 -0.02775359 0.99959462 4.06664966
Axis -0.87247823 -0.19312342 -0.44887089
Axis point 0.00000000 147.93957724 63.96566741
Rotation angle (degrees) 1.82578140
Shift along axis 0.14510873
Fit map 2.mrc in map 5.mrc using 113329 points
correlation = 0.9835, correlation about mean = 0.8679, overlap = 80.14
steps = 24, shift = 0.00141, angle = 0.00218 degrees
Position of 2.mrc (#5) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.99987866 0.01439404 -0.00595786 -1.87531763
-0.01422309 0.99951219 0.02780456 -1.73182555
0.00635517 -0.02771645 0.99959563 4.05966431
Axis -0.87209121 -0.19340577 -0.44950098
Axis point 0.00000000 147.90029859 63.86790579
Rotation angle (degrees) 1.82415403
Shift along axis 0.14556997
Fit map 2.mrc in map 5.mrc using 113329 points
correlation = 0.9835, correlation about mean = 0.868, overlap = 80.14
steps = 28, shift = 0.0607, angle = 0.031 degrees
Position of 2.mrc (#5) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.99987512 0.01466663 -0.00588610 -1.96964236
-0.01449465 0.99949530 0.02826755 -1.73229433
0.00629772 -0.02817871 0.99958307 4.19465853
Axis -0.87254355 -0.18833695 -0.45077371
Axis point 0.00000000 150.39158835 62.94110546
Rotation angle (degrees) 1.85360193
Shift along axis 0.15401197
> volume #5 color #ffb2ff85
> select #1
2 models selected
> view matrix models #1,1,0,0,101.95,0,1,0,-110.64,0,0,1,149.14
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
> view matrix models #1,1,0,0,95.848,0,1,0,-143.35,0,0,1,156.53
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
> view matrix models #1,1,0,0,79.715,0,1,0,-140.13,0,0,1,133.76
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99295,0.11524,0.027768,57.587,-0.11676,0.99127,0.06119,-129.95,-0.020474,-0.064,0.99774,147.82
> view matrix models
> #1,0.96847,0.14522,0.20242,30.314,-0.13907,0.98929,-0.044343,-110.46,-0.20669,0.014794,0.97829,166.17
> ui mousemode right "move picked models"
> view matrix models
> #1,0.96847,0.14522,0.20242,35.846,-0.13907,0.98929,-0.044343,-114.8,-0.20669,0.014794,0.97829,160.49
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 5.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 223.79056821
0.00000000 1.00000000 0.00000000 -189.85220871
0.00000000 0.00000000 1.00000000 -275.15564845
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -275.15564845
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
Fit map 1.mrc in map 2.mrc using 74716 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 1.mrc (#6) relative to 2.mrc (#5) coordinates:
Matrix rotation and translation
0.99987511 -0.01449465 0.00629772 226.69947785
0.01466663 0.99949529 -0.02817871 -176.84209677
-0.00588610 0.02826755 0.99958306 -285.88037188
Axis 0.87254355 0.18833695 0.45077371
Axis point 0.00000000 10582.71186726 -6703.43089663
Rotation angle (degrees) 1.85360194
Shift along axis 35.63190895
> volume #1 color #b2b2b280
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.01286
> volume #4 level 0.01517
> volume #4 level 0.02223
> volume #4 level 0.02341
> volume #3 level 0.01324
> volume #3 level 0.01269
> volume #5 level 0.01838
> volume #3 level 0.01361
> volume #1 level 0.01257
> volume #5 level 0.015
> close #4
> close #1
> close #6
> close #5
> close #3
> volume #2 color #ffb26d76
> volume #2 color #ffb2ff76
> volume #2 color #ffb2ff1a
> volume #2 color #ffb2ff7d
> lighting full
> lighting soft
> lighting simple
> volume #2 color #bfbfbf
> volume #2 color #bfbfbf67
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> volume #2 color grey
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> volume #2 color #80808073
> volume #2 color #80808053
> volume #2 color #95959553
> volume #2 level 0.01601
> volume #2 level 0.01563
> volume #2 color #95959573
> save /Users/mcarmina/Desktop/class5_figureS5_310322.cxs
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> select #8/T:-21
19 atoms, 20 bonds, 1 residue, 1 model selected
> select down
19 atoms, 20 bonds, 1 residue, 1 model selected
> select down
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
975 atoms, 1092 bonds, 48 residues, 1 model selected
> color sel yellow
> ui tool show "Color Actions"
> set bgColor khaki
[Repeated 1 time(s)]
> set bgColor white
No target buttons for the coloring action are checked
> ui tool show "Color Actions"
No target buttons for the coloring action are checked
> color sel bychain
No target buttons for the coloring action are checked
[Repeated 2 time(s)]
> color sel beige target a
[Repeated 3 time(s)]
> color sel khaki target a
[Repeated 5 time(s)]
> color sel pale goldenrod target ac
[Repeated 3 time(s)]
> color sel khaki target ac
[Repeated 2 time(s)]
> select clear
> select #8/N:22
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
889 atoms, 996 bonds, 43 residues, 1 model selected
> color sel light goldenrod yellow target ac
> select clear
> save /Users/mcarmina/Desktop/class5_figureS5_310322.cxs
> save /Users/mcarmina/Desktop/image1.png supersample 3
> turn y 90
[Repeated 2 time(s)]
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting shadows false
> lighting flat
[Repeated 2 time(s)]
> undo
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 2 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting shadows false
> save /Users/mcarmina/Desktop/class5_figureS5_310322.cxs
——— End of log from Thu Mar 31 18:57:05 2022 ———
opened ChimeraX session
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> ui tool show "Side View"
> save /Users/mcarmina/Desktop/image1.png supersample 3
> turn y -90
> ui tool show "Model Panel"
> ui tool show "Volume Viewer"
> volume #2 color #95959599
> lighting soft
> lighting simple
> lighting full
> volume #2 color #959595ae
> volume #2 color #95959580
> lighting simple
> lighting full
> lighting soft
> volume #2 color #959595a3
> volume #2 color #95959575
> save /Users/mcarmina/Desktop/image2.png supersample 3
> turn y -90
> save /Users/mcarmina/Desktop/image3.png supersample 3
> save /Users/mcarmina/Desktop/class5_figureS5_310322.cxs
——— End of log from Thu Mar 31 19:02:40 2022 ———
opened ChimeraX session
> open
> /Users/mcarmina/Desktop/dimer_flexi_fitting_210921/cryoEM_dimer_placed_280921.pdb
Summary of feedback from opening
/Users/mcarmina/Desktop/dimer_flexi_fitting_210921/cryoEM_dimer_placed_280921.pdb
---
warnings | Cannot find LINK/SSBOND residue ZN (1802 )
Cannot find LINK/SSBOND residue ZN (1802 )
Cannot find LINK/SSBOND residue ZN (1801 )
Cannot find LINK/SSBOND residue ZN (1801 )
Cannot find LINK/SSBOND residue ZN (1801 )
21 messages similar to the above omitted
Chain information for cryoEM_dimer_placed_280921.pdb
---
Chain | Description
1.1/A 1.2/A | No description available
1.1/B 1.2/B | No description available
1.1/C 1.2/C | No description available
1.1/D 1.2/D | No description available
1.1/E 1.2/E | No description available
1.1/F 1.2/F | No description available
1.1/G 1.2/G | No description available
1.1/H 1.2/H | No description available
1.1/I 1.2/I | No description available
1.1/J 1.2/J | No description available
1.1/K 1.2/K | No description available
1.1/L 1.2/L | No description available
1.1/R 1.2/R | No description available
1.1/S 1.2/S | No description available
1.1/U 1.2/U | No description available
> select #1.1
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> surface hidePatches (#!1.2 & sel)
> hide (#!1.2 & sel) target a
> hide sel atoms
[Repeated 3 time(s)]
> select #1.1
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> hide sel atoms
> cartoon (#!1.1 & sel)
> select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> cartoon (#!1.2 & sel)
> color (#!1.2 & sel) hot pink
> select #1.1
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> color (#!1.1 & sel) hot pink
> select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.1
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select add #1.2/S:39
33590 atoms, 34382 bonds, 12 pseudobonds, 4085 residues, 3 models selected
> select up
34351 atoms, 35237 bonds, 12 pseudobonds, 4122 residues, 3 models selected
> select up
67136 atoms, 68716 bonds, 12 pseudobonds, 8168 residues, 3 models selected
> create, sel dimer
Unknown command: create, sel dimer
> name sel dimer
"sel" is reserved and cannot be redefined
> name sel, dimer
"dimer": invalid atom specifier
> name dimer sel
> ui mousemode right "rotate selected models"
> view matrix models
> #1.1,0.36988,0.23959,0.89766,-115.97,0.90798,0.11152,-0.4039,71.947,-0.19688,0.96445,-0.17629,119.6,#1.2,0.36988,0.23959,0.89766,-115.97,0.90798,0.11152,-0.4039,71.947,-0.19688,0.96445,-0.17629,119.6
> view matrix models
> #1.1,0.30642,0.94361,-0.1253,-7.6513,0.31954,0.022032,0.94732,-92.585,0.89666,-0.33031,-0.29477,167.28,#1.2,0.30642,0.94361,-0.1253,-7.6513,0.31954,0.022032,0.94732,-92.585,0.89666,-0.33031,-0.29477,167.28
> view matrix models
> #1.1,0.86983,0.36526,-0.33164,31.072,-0.12819,0.81645,0.563,-64.247,0.47641,-0.4472,0.757,41.595,#1.2,0.86983,0.36526,-0.33164,31.072,-0.12819,0.81645,0.563,-64.247,0.47641,-0.4472,0.757,41.595
> view matrix models
> #1.1,0.92153,0.26906,-0.27997,27.337,-0.12616,0.88936,0.43946,-50.739,0.36723,-0.36965,0.85352,27.123,#1.2,0.92153,0.26906,-0.27997,27.337,-0.12616,0.88936,0.43946,-50.739,0.36723,-0.36965,0.85352,27.123
> view matrix models
> #1.1,0.46793,0.8375,-0.28219,13.82,0.1315,0.24977,0.95933,-99.597,0.87393,-0.48601,0.0067463,134.8,#1.2,0.46793,0.8375,-0.28219,13.82,0.1315,0.24977,0.95933,-99.597,0.87393,-0.48601,0.0067463,134.8
> view matrix models
> #1.1,0.57483,0.74209,-0.34479,23.617,0.032232,0.4005,0.91573,-97.752,0.81764,-0.5375,0.2063,111.73,#1.2,0.57483,0.74209,-0.34479,23.617,0.032232,0.4005,0.91573,-97.752,0.81764,-0.5375,0.2063,111.73
> view matrix models
> #1.1,0.7112,0.59228,-0.37867,31.14,-0.06633,0.59279,0.80262,-88.38,0.69985,-0.54571,0.46088,80.977,#1.2,0.7112,0.59228,-0.37867,31.14,-0.06633,0.59279,0.80262,-88.38,0.69985,-0.54571,0.46088,80.977
> view matrix models
> #1.1,0.97793,0.1283,-0.16492,16.566,-0.088105,0.96888,0.23134,-26.917,0.18947,-0.2117,0.95879,10.163,#1.2,0.97793,0.1283,-0.16492,16.566,-0.088105,0.96888,0.23134,-26.917,0.18947,-0.2117,0.95879,10.163
> view matrix models
> #1.1,0.99863,0.028534,-0.043917,4.3276,-0.026035,0.99806,0.056469,-5.8243,0.045444,-0.055248,0.99744,0.67821,#1.2,0.99863,0.028534,-0.043917,4.3276,-0.026035,0.99806,0.056469,-5.8243,0.045444,-0.055248,0.99744,0.67821
> view matrix models
> #1.1,0.57438,0.74253,-0.34459,23.045,0.032611,0.39987,0.91599,-97.1,0.81794,-0.53737,0.20546,111.83,#1.2,0.57438,0.74253,-0.34459,23.045,0.032611,0.39987,0.91599,-97.1,0.81794,-0.53737,0.20546,111.83
> view matrix models
> #1.1,0.36714,0.90969,-0.19408,0.93276,0.24286,0.10766,0.96407,-96.265,0.8979,-0.40109,-0.1814,155.73,#1.2,0.36714,0.90969,-0.19408,0.93276,0.24286,0.10766,0.96407,-96.265,0.8979,-0.40109,-0.1814,155.73
> ui mousemode right "translate selected models"
> view matrix models
> #1.1,0.36714,0.90969,-0.19408,140.93,0.24286,0.10766,0.96407,-279.88,0.8979,-0.40109,-0.1814,169.81,#1.2,0.36714,0.90969,-0.19408,140.93,0.24286,0.10766,0.96407,-279.88,0.8979,-0.40109,-0.1814,169.81
> view matrix models
> #1.1,0.36714,0.90969,-0.19408,135.95,0.24286,0.10766,0.96407,-316.19,0.8979,-0.40109,-0.1814,239.45,#1.2,0.36714,0.90969,-0.19408,135.95,0.24286,0.10766,0.96407,-316.19,0.8979,-0.40109,-0.1814,239.45
> view matrix models
> #1.1,0.36714,0.90969,-0.19408,110.48,0.24286,0.10766,0.96407,-266.58,0.8979,-0.40109,-0.1814,210.37,#1.2,0.36714,0.90969,-0.19408,110.48,0.24286,0.10766,0.96407,-266.58,0.8979,-0.40109,-0.1814,210.37
> view matrix models
> #1.1,0.36714,0.90969,-0.19408,105.76,0.24286,0.10766,0.96407,-260.53,0.8979,-0.40109,-0.1814,210.13,#1.2,0.36714,0.90969,-0.19408,105.76,0.24286,0.10766,0.96407,-260.53,0.8979,-0.40109,-0.1814,210.13
> view matrix models
> #1.1,0.36714,0.90969,-0.19408,96.275,0.24286,0.10766,0.96407,-257.01,0.8979,-0.40109,-0.1814,223.77,#1.2,0.36714,0.90969,-0.19408,96.275,0.24286,0.10766,0.96407,-257.01,0.8979,-0.40109,-0.1814,223.77
> view matrix models
> #1.1,0.36714,0.90969,-0.19408,93.484,0.24286,0.10766,0.96407,-259.26,0.8979,-0.40109,-0.1814,233.16,#1.2,0.36714,0.90969,-0.19408,93.484,0.24286,0.10766,0.96407,-259.26,0.8979,-0.40109,-0.1814,233.16
> select clear
> ui mousemode right "rotate selected models"
> select dimer
Nothing selected
> select dimer
Nothing selected
> select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.1
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> ~select #8
Nothing selected
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> ~select #8
Nothing selected
> select #1
67136 atoms, 68716 bonds, 24 pseudobonds, 8168 residues, 5 models selected
> ~select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 3 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!1.1 models
> show #!1.1 models
> ~select #1.1
1 model selected
> select #1.1
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.1
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.1
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select #1.2
33568 atoms, 34358 bonds, 12 pseudobonds, 4084 residues, 2 models selected
> select add #1.1/H:126
33577 atoms, 34366 bonds, 12 pseudobonds, 4085 residues, 3 models selected
> select up
33624 atoms, 34413 bonds, 12 pseudobonds, 4091 residues, 3 models selected
> select up
34650 atoms, 35457 bonds, 12 pseudobonds, 4219 residues, 3 models selected
> select up
67136 atoms, 68716 bonds, 12 pseudobonds, 8168 residues, 3 models selected
> view matrix models
> #1.1,-0.085245,0.99499,0.052267,118.11,-0.58848,-0.092609,0.80319,-4.8687,0.80401,0.037711,0.59342,-8.402,#1.2,-0.085245,0.99499,0.052267,118.11,-0.58848,-0.092609,0.80319,-4.8687,0.80401,0.037711,0.59342,-8.402
> view matrix models
> #1.1,-0.70652,0.56485,-0.42635,443.14,-0.57512,-0.80934,-0.11919,341.91,-0.41239,0.16099,0.89667,157.69,#1.2,-0.70652,0.56485,-0.42635,443.14,-0.57512,-0.80934,-0.11919,341.91,-0.41239,0.16099,0.89667,157.69
> view matrix models
> #1.1,-0.5535,0.25703,-0.79219,554.23,-0.039165,-0.95817,-0.28352,293.78,-0.83192,-0.1259,0.54042,385.35,#1.2,-0.5535,0.25703,-0.79219,554.23,-0.039165,-0.95817,-0.28352,293.78,-0.83192,-0.1259,0.54042,385.35
> view matrix models
> #1.1,-0.6744,0.51243,-0.5316,470.35,-0.64398,-0.76042,0.083981,300.75,-0.3612,0.39898,0.84282,112.4,#1.2,-0.6744,0.51243,-0.5316,470.35,-0.64398,-0.76042,0.083981,300.75,-0.3612,0.39898,0.84282,112.4
> view matrix models
> #1.1,-0.58519,0.6614,-0.46915,408.19,-0.78454,-0.31547,0.53383,142.5,0.20507,0.68046,0.70351,-31.777,#1.2,-0.58519,0.6614,-0.46915,408.19,-0.78454,-0.31547,0.53383,142.5,0.20507,0.68046,0.70351,-31.777
> view matrix models
> #1.1,-0.68158,0.54345,-0.49001,456.28,-0.73164,-0.5176,0.44362,190.76,-0.012537,0.66087,0.7504,7.7811,#1.2,-0.68158,0.54345,-0.49001,456.28,-0.73164,-0.5176,0.44362,190.76,-0.012537,0.66087,0.7504,7.7811
> ui mousemode right "translate selected models"
> view matrix models
> #1.1,-0.68158,0.54345,-0.49001,391.32,-0.73164,-0.5176,0.44362,122.54,-0.012537,0.66087,0.7504,-50.423,#1.2,-0.68158,0.54345,-0.49001,391.32,-0.73164,-0.5176,0.44362,122.54,-0.012537,0.66087,0.7504,-50.423
> view matrix models
> #1.1,-0.68158,0.54345,-0.49001,391.06,-0.73164,-0.5176,0.44362,123.54,-0.012537,0.66087,0.7504,-49.485,#1.2,-0.68158,0.54345,-0.49001,391.06,-0.73164,-0.5176,0.44362,123.54,-0.012537,0.66087,0.7504,-49.485
> view matrix models
> #1.1,-0.68158,0.54345,-0.49001,403.75,-0.73164,-0.5176,0.44362,135.54,-0.012537,0.66087,0.7504,-39.34,#1.2,-0.68158,0.54345,-0.49001,403.75,-0.73164,-0.5176,0.44362,135.54,-0.012537,0.66087,0.7504,-39.34
> view matrix models
> #1.1,-0.68158,0.54345,-0.49001,408.58,-0.73164,-0.5176,0.44362,140.31,-0.012537,0.66087,0.7504,-35.293,#1.2,-0.68158,0.54345,-0.49001,408.58,-0.73164,-0.5176,0.44362,140.31,-0.012537,0.66087,0.7504,-35.293
> view matrix models
> #1.1,-0.68158,0.54345,-0.49001,411.25,-0.73164,-0.5176,0.44362,143.02,-0.012537,0.66087,0.7504,-32.989,#1.2,-0.68158,0.54345,-0.49001,411.25,-0.73164,-0.5176,0.44362,143.02,-0.012537,0.66087,0.7504,-32.989
> view matrix models
> #1.1,-0.68158,0.54345,-0.49001,414.84,-0.73164,-0.5176,0.44362,146.24,-0.012537,0.66087,0.7504,-30.278,#1.2,-0.68158,0.54345,-0.49001,414.84,-0.73164,-0.5176,0.44362,146.24,-0.012537,0.66087,0.7504,-30.278
> ui mousemode right "rotate selected models"
> view matrix models
> #1.1,-0.55445,0.70005,-0.45001,348.38,-0.80897,-0.32644,0.48888,115.5,0.19534,0.63511,0.74732,-68.924,#1.2,-0.55445,0.70005,-0.45001,348.38,-0.80897,-0.32644,0.48888,115.5,0.19534,0.63511,0.74732,-68.924
> view matrix models
> #1.1,-0.65096,0.59078,-0.47669,396.14,-0.75289,-0.58272,0.30595,194.55,-0.097026,0.55805,0.82411,-9.0664,#1.2,-0.65096,0.59078,-0.47669,396.14,-0.75289,-0.58272,0.30595,194.55,-0.097026,0.55805,0.82411,-9.0664
> view matrix models
> #1.1,-0.88698,0.37598,0.26815,319.84,-0.24539,-0.87562,0.41603,117.96,0.39122,0.30321,0.86892,-74.161,#1.2,-0.88698,0.37598,0.26815,319.84,-0.24539,-0.87562,0.41603,117.96,0.39122,0.30321,0.86892,-74.161
> view matrix models
> #1.1,-0.85695,0.2927,0.42423,294.36,-0.12562,-0.91689,0.37885,109.05,0.49986,0.27137,0.8225,-80.462,#1.2,-0.85695,0.2927,0.42423,294.36,-0.12562,-0.91689,0.37885,109.05,0.49986,0.27137,0.8225,-80.462
> view matrix models
> #1.1,-0.77903,0.17701,0.60148,260.23,0.0178,-0.95269,0.30343,102.87,0.62674,0.24708,0.73902,-83.566,#1.2,-0.77903,0.17701,0.60148,260.23,0.0178,-0.95269,0.30343,102.87,0.62674,0.24708,0.73902,-83.566
> view matrix models
> #1.1,-0.64696,0.042947,0.76131,222.03,0.15756,-0.96934,0.18857,102.42,0.74607,0.24195,0.62036,-81.044,#1.2,-0.64696,0.042947,0.76131,222.03,0.15756,-0.96934,0.18857,102.42,0.74607,0.24195,0.62036,-81.044
> view matrix models
> #1.1,-0.79813,-0.53602,-0.27507,603.7,0.56054,-0.49329,-0.66518,117.54,0.22086,-0.68509,0.69417,195.86,#1.2,-0.79813,-0.53602,-0.27507,603.7,0.56054,-0.49329,-0.66518,117.54,0.22086,-0.68509,0.69417,195.86
> view matrix models
> #1.1,-0.68719,-0.40815,-0.60098,628.81,0.69308,-0.12042,-0.71073,26.739,0.21772,-0.90494,0.36563,313.83,#1.2,-0.68719,-0.40815,-0.60098,628.81,0.69308,-0.12042,-0.71073,26.739,0.21772,-0.90494,0.36563,313.83
> hide #!1.1 models
> hide #!1.2 models
> open /Users/mcarmina/Desktop/dimer_flexi_fitting_210921/844_Zflip.mrc
Opened 844_Zflip.mrc as #3, grid size 500,500,500, pixel 0.83, shown at level
0.00777, step 2, values float32
> view matrix models
> #1.1,0.26077,0.48199,0.83647,-74.506,0.027159,0.86245,-0.50542,38.336,-0.96502,0.15452,0.21181,540.29,#1.2,0.26077,0.48199,0.83647,-74.506,0.027159,0.86245,-0.50542,38.336,-0.96502,0.15452,0.21181,540.29
> view matrix models
> #1.1,0.41901,0.34133,0.84138,-103.55,0.11106,0.90043,-0.42059,-10.555,-0.90116,0.26968,0.33938,477.41,#1.2,0.41901,0.34133,0.84138,-103.55,0.11106,0.90043,-0.42059,-10.555,-0.90116,0.26968,0.33938,477.41
> ui tool show "Side View"
> volume #2 level 0.0244
> volume #2 level 0.02198
> volume #3 level 0.007557
> volume #3 level 0.007134
> volume #3 color #b2b27c
> volume #3 color #b28b7c
> volume #3 color #b2aa7c
> volume #3 color #caaa7c
> volume #3 color #caaaa7
> volume #3 color #caaaa7cd
> volume #3 color #caaaa7e6
> volume #3 color #caaaa783
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> select #3
3 models selected
> view matrix models
> #3,0.088768,-0.90762,0.41031,280.56,0.95006,0.20088,0.23882,-99.084,-0.29918,0.36862,0.88012,18.239
> view matrix models
> #3,0.57197,-0.78524,0.23716,192.51,0.6949,0.31023,-0.64875,134.46,0.43585,0.53587,0.7231,-136.03
> view matrix models
> #3,0.49874,-0.82164,0.27598,206.53,0.73233,0.22914,-0.64124,140.77,0.46362,0.52192,0.716,-137.59
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.49874,-0.82164,0.27598,333.45,0.73233,0.22914,-0.64124,-19.501,0.46362,0.52192,0.716,-81.325
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.77278,-0.58962,-0.23484,674.43,-0.15488,0.53403,-0.83116,152.57,0.61548,-0.60594,-0.50401,384.51
> view matrix models
> #3,-0.87986,-0.43536,-0.19057,656.84,-0.16686,0.65847,-0.73388,108.6,0.44498,-0.61391,-0.652,455.92
> view matrix models
> #3,-0.63521,-0.69901,0.32847,539.28,-0.70397,0.34907,-0.61853,258.09,0.3177,-0.62413,-0.71381,499.06
> view matrix models
> #3,-0.19703,-0.77833,0.59614,400.94,-0.93203,-0.039933,-0.36018,325.03,0.30414,-0.62659,-0.71755,503.28
> ui mousemode right "rotate selected models"
> ui tool show "Fit in Map"
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1553, overlap = 25.42
steps = 348, shift = 105, angle = 32.7 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56820111 -0.72847347 0.38271906 346.12122124
-0.59892190 0.04716132 -0.79941749 435.62753908
0.56430491 -0.68344875 -0.46309582 259.86341316
Axis 0.46127781 -0.72227670 0.51530491
Axis point 300.34010423 0.00000000 300.87415943
Rotation angle (degrees) 172.77859875
Shift along axis -21.07668948
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 124, shift = 0.0478, angle = 0.0244 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56810812 -0.72839930 0.38299818 346.00630016
-0.59890998 0.04675684 -0.79945019 435.75544836
0.56441119 -0.68355558 -0.46280853 259.79137795
Axis 0.46133359 -0.72213814 0.51544915
Axis point 300.37535208 0.00000000 300.94453498
Rotation angle (degrees) 172.78411742
Shift along axis -21.14205446
> ~select #3
Nothing selected
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 88, shift = 0.0158, angle = 0.00297 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56810629 -0.72837905 0.38303940 345.98590441
-0.59891530 0.04671639 -0.79944857 435.75282501
0.56440738 -0.68357992 -0.46277721 259.79869679
Axis 0.46133615 -0.72212469 0.51546570
Axis point 300.37002492 0.00000000 300.95081052
Rotation angle (degrees) 172.78578264
Shift along axis -21.13474903
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.73, correlation about mean = 0.1552, overlap = 25.42
steps = 136, shift = 0.0109, angle = 0.00447 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56814495 -0.72834484 0.38304711 345.98990092
-0.59887202 0.04669030 -0.79948251 435.76443895
0.56441439 -0.68361816 -0.46271219 259.78389224
Axis 0.46131506 -0.72211560 0.51549731
Axis point 300.37127633 0.00000000 300.95972324
Rotation angle (degrees) 172.78571961
Shift along axis -21.14404780
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 68, shift = 0.0356, angle = 0.0155 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56816352 -0.72841418 0.38288769 346.05447967
-0.59891137 0.04692965 -0.79943902 435.68346434
0.56435394 -0.68352788 -0.46291923 259.83402065
Axis 0.46130201 -0.72219764 0.51539404
Axis point 300.35311760 0.00000000 300.91392485
Rotation angle (degrees) 172.78258601
Shift along axis -21.09703728
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 68, shift = 0.0288, angle = 0.0167 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56810865 -0.72835309 0.38308527 345.97584407
-0.59890615 0.04665709 -0.79945889 435.76669274
0.56441471 -0.68361164 -0.46272142 259.78921526
Axis 0.46133612 -0.72210456 0.51549392
Axis point 300.37547410 0.00000000 300.96104048
Rotation angle (degrees) 172.78712168
Shift along axis -21.13820328
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 80, shift = 0.00646, angle = 0.00387 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56816141 -0.72832940 0.38305207 345.98402610
-0.59886658 0.04669308 -0.79948642 435.75781180
0.56440359 -0.68363442 -0.46270132 259.79392067
Axis 0.46130671 -0.72211680 0.51550311
Axis point 300.36422155 0.00000000 300.96207858
Rotation angle (degrees) 172.78636162
Shift along axis -21.13871045
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 96, shift = 0.0122, angle = 0.0109 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56811555 -0.72841571 0.38295595 346.01371591
-0.59891495 0.04681589 -0.79944301 435.73613372
0.56439843 -0.68353406 -0.46285588 259.79838559
Axis 0.46132864 -0.72215831 0.51542533
Axis point 300.36604746 0.00000000 300.93152085
Rotation angle (degrees) 172.78314164
Shift along axis -21.13776614
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 100, shift = 0.009, angle = 0.00472 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56805906 -0.72846685 0.38294247 346.02080967
-0.59894532 0.04681662 -0.79942021 435.73994257
0.56442306 -0.68347950 -0.46290640 259.78786968
Axis 0.46135793 -0.72215800 0.51539953
Axis point 300.37764881 -0.00000000 300.92357046
Rotation angle (degrees) 172.78161440
Shift along axis -21.13909638
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 100, shift = 0.0357, angle = 0.00877 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56817886 -0.72838748 0.38291571 346.04648884
-0.59886469 0.04685618 -0.79947830 435.69890803
0.56438803 -0.68356137 -0.46282822 259.81186213
Axis 0.46129320 -0.72217192 0.51543797
Axis point 300.35588285 0.00000000 300.92855678
Rotation angle (degrees) 172.78208493
Shift along axis -21.10372981
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 124, shift = 0.0302, angle = 0.0117 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56806751 -0.72838879 0.38307839 345.97470806
-0.59894484 0.04667448 -0.79942888 435.76703974
0.56441507 -0.68357241 -0.46277895 259.78899882
Axis 0.46135829 -0.72211052 0.51546573
Axis point 300.38024335 0.00000000 300.95166686
Rotation angle (degrees) 172.78689241
Shift along axis -21.14134013
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1553, overlap = 25.42
steps = 124, shift = 0.0254, angle = 0.0224 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56808352 -0.72853550 0.38277554 346.07197675
-0.59891694 0.04698747 -0.79943145 435.67911392
0.56442855 -0.68339460 -0.46302504 259.79402203
Axis 0.46133869 -0.72221508 0.51533678
Axis point 300.35786040 0.00000000 300.88789795
Rotation angle (degrees) 172.77529411
Shift along axis -21.11621717
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.73, correlation about mean = 0.1552, overlap = 25.42
steps = 200, shift = 0.0367, angle = 0.0161 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56797880 -0.72852640 0.38294823 346.01272920
-0.59892067 0.04670823 -0.79944502 435.77398152
0.56452998 -0.68342344 -0.46285879 259.74073608
Axis 0.46139743 -0.72211871 0.51541923
Axis point 300.39770416 0.00000000 300.93700337
Rotation angle (degrees) 172.77717471
Shift along axis -21.15579394
Fit map 844_Zflip.mrc in map 5.mrc using 191193 points
correlation = 0.7299, correlation about mean = 0.1552, overlap = 25.42
steps = 88, shift = 0.0454, angle = 0.0132 degrees
Position of 844_Zflip.mrc (#3) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
-0.56809995 -0.72836994 0.38306614 346.01225108
-0.59891970 0.04668666 -0.79944701 435.75077226
0.56440910 -0.68359167 -0.46275778 259.79521628
Axis 0.46134045 -0.72211468 0.51547587
Axis point 300.38768170 0.00000000 300.95257747
Rotation angle (degrees) 172.78668301
Shift along axis -21.11441817
> volume #3 color #caaaa78c
> volume #2 level 0.01526
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!8 models
> show #!8 models
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.005365, steps = 356
shifted from previous position = 13.1
rotated from previous position = 27.5 degrees
atoms outside contour = 24948, contour level = 0.0071341
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.82940322 -0.22942094 0.50936848 275.84883228
-0.55863732 0.33438266 -0.75902078 362.55710434
0.00381126 -0.91408663 -0.40550116 351.29870529
Axis -0.24893778 0.81160548 -0.52851350
Axis point 230.16472335 0.00000000 265.58008385
Rotation angle (degrees) 161.85306004
Shift along axis 39.91802943
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.005365, steps = 40
shifted from previous position = 0.00799
rotated from previous position = 0.00401 degrees
atoms outside contour = 24948, contour level = 0.0071341
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.82943753 -0.22942953 0.50930873 275.85908057
-0.55858615 0.33438860 -0.75905582 362.54757953
0.00384278 -0.91408230 -0.40551062 351.29758290
Axis -0.24892071 0.81160940 -0.52851553
Axis point 230.15665974 0.00000000 265.58108754
Rotation angle (degrees) 161.85654077
Shift along axis 39.91375647
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.005365, steps = 40
shifted from previous position = 0.00676
rotated from previous position = 0.00722 degrees
atoms outside contour = 24952, contour level = 0.0071341
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.82941544 -0.22942909 0.50934491 275.85586668
-0.55861950 0.33448798 -0.75898749 362.52847802
0.00376404 -0.91404605 -0.40559306 351.31031022
Axis -0.24892461 0.81163869 -0.52846871
Axis point 230.15834383 0.00000000 265.56206195
Rotation angle (degrees) 161.85294993
Shift along axis 39.91831758
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.005365, steps = 44
shifted from previous position = 0.0108
rotated from previous position = 0.00618 degrees
atoms outside contour = 24949, contour level = 0.0071341
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.82940214 -0.22943950 0.50936187 275.85132501
-0.55863882 0.33438647 -0.75901800 362.55992690
0.00382498 -0.91408057 -0.40551467 351.29769844
Axis -0.24894305 0.81160715 -0.52850846
Axis point 230.16580511 0.00000000 265.58009469
Rotation angle (degrees) 161.85385363
Shift along axis 39.92115593
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.005365, steps = 44
shifted from previous position = 0.00347
rotated from previous position = 0.00456 degrees
atoms outside contour = 24951, contour level = 0.0071341
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.82940805 -0.22942142 0.50936039 275.84879685
-0.55862984 0.33431822 -0.75905467 362.57149652
0.00385492 -0.91411008 -0.40544788 351.29121715
Axis -0.24894052 0.81158599 -0.52854214
Axis point 230.16598010 0.00000000 265.59194881
Rotation angle (degrees) 161.85453139
Shift along axis 39.91579128
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.005365, steps = 44
shifted from previous position = 0.00613
rotated from previous position = 0.00259 degrees
atoms outside contour = 24949, contour level = 0.0071341
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.82940968 -0.22946078 0.50934002 275.85309411
-0.55862714 0.33431120 -0.75905975 362.57108083
0.00389636 -0.91410277 -0.40546397 351.29081706
Axis -0.24895080 0.81158511 -0.52853866
Axis point 230.16557377 0.00000000 265.59413282
Rotation angle (degrees) 161.85680679
Shift along axis 39.91266249
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.005365, steps = 48
shifted from previous position = 0.014
rotated from previous position = 0.0125 degrees
atoms outside contour = 24948, contour level = 0.0071341
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.82941705 -0.22948975 0.50931497 275.86084747
-0.55861681 0.33451019 -0.75897968 362.51735111
0.00380699 -0.91402269 -0.40564529 351.31451223
Axis -0.24893823 0.81164741 -0.52844890
Axis point 230.15522245 0.00000000 265.55934167
Rotation angle (degrees) 161.85585937
Shift along axis 39.91218894
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> view matrix models
> #8,0.63837,-0.49892,0.58614,111.54,0.4114,0.86475,0.28801,-175.96,-0.65056,0.057281,0.75729,251.96
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> view matrix models
> #8,0.63837,-0.49892,0.58614,-31.87,0.4114,0.86475,0.28801,-284.04,-0.65056,0.057281,0.75729,171.79
> volume #3 level 0.006077
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.64667,-0.38904,0.6561,-56.722,0.34682,0.91606,0.20136,-269.84,-0.67936,0.097338,0.72732,174.72
> view matrix models
> #8,0.63846,-0.49816,0.58669,-32.055,0.41094,0.86517,0.28742,-283.95,-0.65077,0.057587,0.75709,171.8
> view matrix models
> #8,0.56845,-0.75041,0.33726,44.21,0.58188,0.65651,0.48001,-307.14,-0.58162,-0.076618,0.80984,172.27
> view matrix models
> #8,0.59632,0.069229,0.79976,-128.34,0.11529,0.97856,-0.17067,-194.91,-0.79443,0.19398,0.57555,199
> view matrix models
> #8,0.43239,-0.90137,0.023865,125.35,0.72608,0.36375,0.58352,-303.63,-0.53465,-0.23498,0.81175,185.87
> view matrix models
> #8,0.55851,-0.76922,0.31044,51.675,0.59672,0.63254,0.49378,-308,-0.57619,-0.090534,0.81229,172.97
> volume #3 level 0.005865
> view matrix models
> #8,0.21793,-0.81686,0.53409,72.524,0.67598,-0.26838,-0.68631,-39.752,0.70396,0.5106,0.49369,-31.782
> view matrix models
> #8,0.1355,-0.80023,0.58419,74.54,0.0056206,-0.589,-0.80811,108.34,0.99076,0.11278,-0.075309,59.416
> view matrix models
> #8,0.17073,-0.9521,-0.2537,205.64,0.67465,-0.074702,0.73434,-261.77,-0.71812,-0.29654,0.62958,243.75
> view matrix models
> #8,0.15999,-0.95743,-0.24028,205.9,0.64362,-0.08338,0.76079,-260.16,-0.74843,-0.27637,0.60288,248.97
> view matrix models
> #8,0.1421,-0.93033,-0.33808,218.45,0.84155,-0.066277,0.53609,-257.76,-0.52115,-0.36069,0.7735,205.39
> view matrix models
> #8,0.31966,-0.56556,-0.76024,206.72,0.89474,0.44425,0.045725,-261.84,0.31188,-0.69483,0.64803,153.25
> view matrix models
> #8,0.44546,-0.36891,-0.81577,172.42,0.87759,0.36029,0.31628,-286.44,0.17724,-0.85679,0.48425,214.8
> view matrix models
> #8,0.30587,-0.44335,-0.84255,204.44,0.79348,0.60776,-0.031754,-258.28,0.52614,-0.65883,0.53769,135.15
> view matrix models
> #8,-0.38395,-0.56052,-0.73375,297.15,-0.69217,0.70067,-0.17306,-50.406,0.61113,0.44144,-0.65701,149.5
> view matrix models
> #8,-0.24568,-0.60795,-0.755,287.53,-0.96898,0.13256,0.20858,6.2525,-0.026725,0.78283,-0.62166,186.97
> view matrix models
> #8,-0.39868,-0.48548,-0.77805,295.73,-0.90124,0.36443,0.23441,-36.025,0.16974,0.79467,-0.58283,153.6
> view matrix models
> #8,-0.50404,-0.60421,-0.61715,302.68,-0.86342,0.33494,0.37726,-57.218,-0.021237,0.72301,-0.69051,203.42
> view matrix models
> #8,-0.5003,-0.57998,-0.6429,302.67,-0.86484,0.37057,0.33872,-56.21,0.041793,0.72547,-0.68698,194.13
> ui mousemode right "move picked models"
> view matrix models
> #8,-0.5003,-0.57998,-0.6429,428.23,-0.86484,0.37057,0.33872,31.588,0.041793,0.72547,-0.68698,302.5
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.007303, steps = 640
shifted from previous position = 57.1
rotated from previous position = 43 degrees
atoms outside contour = 11582, contour level = 0.0058651
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.39460890 0.52179081 -0.75631885 174.90313195
0.85865698 0.08360782 0.50568553 27.02129049
0.32709621 -0.84896655 -0.41504691 302.49206122
Axis -0.76663215 -0.61313220 0.19064115
Axis point 0.00000000 69.22776462 184.76212010
Rotation angle (degrees) 117.93146593
Shift along axis -92.98655264
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.007303, steps = 48
shifted from previous position = 0.0054
rotated from previous position = 0.00721 degrees
atoms outside contour = 11584, contour level = 0.0058651
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.39456859 0.52182743 -0.75631462 174.90326326
0.85863152 0.08371935 0.50571031 27.00277282
0.32721165 -0.84893305 -0.41502443 302.47263031
Axis -0.76660567 -0.61317790 0.19060066
Axis point 0.00000000 69.21370049 184.75891423
Rotation angle (degrees) 117.92842794
Shift along axis -92.98785235
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.007303, steps = 44
shifted from previous position = 0.00316
rotated from previous position = 0.00623 degrees
atoms outside contour = 11583, contour level = 0.0058651
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.39466483 0.52179515 -0.75628667 174.88930795
0.85860318 0.08364747 0.50577031 27.00607307
0.32716994 -0.84895998 -0.41500224 302.47722801
Axis -0.76664415 -0.61312992 0.19060023
Axis point 0.00000000 69.22884632 184.75409252
Rotation angle (degrees) 117.92691802
Shift along axis -92.98386585
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.007303, steps = 44
shifted from previous position = 0.00369
rotated from previous position = 0.00637 degrees
atoms outside contour = 11582, contour level = 0.0058651
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.39461324 0.52179464 -0.75631394 174.90121654
0.85865705 0.08359753 0.50568711 27.02050221
0.32709078 -0.84896521 -0.41505394 302.49534558
Axis -0.76663527 -0.61312874 0.19063977
Axis point 0.00000000 69.22837185 184.76290429
Rotation angle (degrees) 117.93188648
Shift along axis -92.98484435
> select clear
> show #!2 models
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 116, shift = 4.69, angle = 8.89 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60506862 -0.66918176 0.43137890 343.92412730
-0.66091848 0.12005524 -0.74079250 398.02216674
0.44393552 -0.73333658 -0.51491627 322.32348213
Axis 0.44435490 -0.74834493 0.49247191
Axis point 289.24708453 0.00000000 293.07411656
Rotation angle (degrees) 179.51930611
Shift along axis 13.70176323
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 44, shift = 0.00589, angle = 0.00562 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60508445 -0.66919974 0.43132881 343.93942189
-0.66092692 0.12014496 -0.74077042 398.00480362
0.44390138 -0.73330548 -0.51498999 322.33808275
Axis 0.44434596 -0.74837489 0.49243446
Axis point 289.24137253 -0.00000000 293.06167127
Rotation angle (degrees) 179.51871455
Shift along axis 13.70166925
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 44, shift = 0.0144, angle = 0.00842 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60516770 -0.66909122 0.43138035 343.93082156
-0.66090174 0.12015322 -0.74079155 398.00665211
0.44382538 -0.73340314 -0.51491642 322.36802721
Axis 0.44429943 -0.74837776 0.49247208
Axis point 289.23371238 0.00000000 293.07710132
Rotation angle (degrees) 179.52359914
Shift along axis 13.70619579
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 40, shift = 0.0162, angle = 0.00655 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60509268 -0.66916417 0.43137244 343.92722273
-0.66091337 0.12008484 -0.74079226 398.01691260
0.44391034 -0.73334779 -0.51492202 322.33323638
Axis 0.44434141 -0.74835484 0.49246903
Axis point 289.24323696 -0.00000000 293.07333711
Rotation angle (degrees) 179.52002911
Shift along axis 13.70236453
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 40, shift = 0.00226, angle = 0.00227 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60507772 -0.66919075 0.43135218 343.93158114
-0.66090551 0.12007509 -0.74080085 398.01820632
0.44394243 -0.73332512 -0.51492663 322.32354982
Axis 0.44434970 -0.74835153 0.49246658
Axis point 289.24485616 0.00000000 293.07281364
Rotation angle (degrees) 179.51802296
Shift along axis 13.70193611
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 44, shift = 0.00401, angle = 0.00521 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60511195 -0.66916611 0.43134240 343.93552581
-0.66092116 0.12015572 -0.74077381 398.00246924
0.44387247 -0.73333441 -0.51497372 322.34479833
Axis 0.44433059 -0.74837852 0.49244280
Axis point 289.23705545 -0.00000000 293.06262159
Rotation angle (degrees) 179.52034408
Shift along axis 13.70095280
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 44, shift = 0.00456, angle = 0.00687 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60514896 -0.66912290 0.43135751 343.93051806
-0.66086362 0.12009146 -0.74083557 398.01423236
0.44390769 -0.73338436 -0.51487222 322.33010240
Axis 0.44430972 -0.74835703 0.49249429
Axis point 289.23446044 0.00000000 293.07815271
Rotation angle (degrees) 179.51956046
Shift along axis 13.70065545
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 40, shift = 0.0163, angle = 0.00482 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60515278 -0.66911006 0.43137207 343.93248486
-0.66090398 0.12014694 -0.74079056 398.00735828
0.44384238 -0.73338698 -0.51492478 322.36176809
Axis 0.44430777 -0.74837564 0.49246778
Axis point 289.23553483 0.00000000 293.07534934
Rotation angle (degrees) 179.52262970
Shift along axis 13.70564879
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 40, shift = 0.000572, angle = 0.00112 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60514704 -0.66912228 0.43136116 343.93490510
-0.66089829 0.12014224 -0.74079641 398.00796541
0.44385869 -0.73337661 -0.51492551 322.35772608
Axis 0.44431093 -0.74837404 0.49246735
Axis point 289.23610838 0.00000000 293.07575520
Rotation angle (degrees) 179.52158703
Shift along axis 13.70586258
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 36, shift = 0.0143, angle = 0.00791 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60507147 -0.66921295 0.43132652 343.93935677
-0.66089168 0.12007262 -0.74081359 398.01902235
0.44397154 -0.73330527 -0.51492980 322.31738660
Axis 0.44435308 -0.74835066 0.49246485
Axis point 289.24617980 0.00000000 293.07384724
Rotation angle (degrees) 179.51592540
Shift along axis 13.70269675
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8135, correlation about mean = 0.1795, overlap = 15.89
steps = 36, shift = 0.0167, angle = 0.00683 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.60513335 -0.66913399 0.43136220 343.93590963
-0.66090103 0.12012804 -0.74079626 398.00837777
0.44387326 -0.73336825 -0.51492485 322.35666317
Axis 0.44431860 -0.74836929 0.49246766
Axis point 289.23856676 0.00000000 293.07730217
Rotation angle (degrees) 179.52106598
Shift along axis 13.71010442
> hide #!3 models
> select #2
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.054157,-0.98165,-0.18281,424.32,-0.7428,-0.082748,0.66438,44.06,-0.66732,0.17177,-0.72469,455.34
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.054157,-0.98165,-0.18281,429.18,-0.7428,-0.082748,0.66438,61.376,-0.66732,0.17177,-0.72469,424.09
> ui mousemode right "rotate selected models"
> select clear
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 136
shifted from previous position = 9.91
rotated from previous position = 28.2 degrees
atoms outside contour = 9685, contour level = 0.015262
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56149717 -0.80219022 0.20300687 138.21486511
0.80736418 0.58486927 0.07804473 -25.42117781
-0.18133918 0.12007857 0.97606210 13.26291242
Axis 0.02539286 0.23218541 0.97234003
Axis point 95.95741971 119.51100903 0.00000000
Rotation angle (degrees) 55.86018533
Shift along axis 10.50330463
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0248
rotated from previous position = 0.0062 degrees
atoms outside contour = 9690, contour level = 0.015262
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56158437 -0.80212916 0.20300692 138.18270645
0.80730820 0.58495200 0.07800377 -25.44100424
-0.18131839 0.12008344 0.97606536 13.25728055
Axis 0.02542235 0.23218936 0.97233832
Axis point 95.96238617 119.48756465 0.00000000
Rotation angle (degrees) 55.85419055
Shift along axis 10.49636074
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0293
rotated from previous position = 0.0246 degrees
atoms outside contour = 9690, contour level = 0.015262
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56178718 -0.80198533 0.20301406 138.11770700
0.80710499 0.58519335 0.07829584 -25.47649174
-0.18159458 0.11986805 0.97604049 13.35131314
Axis 0.02512009 0.23240047 0.97229574
Axis point 95.98441115 119.44307483 0.00000000
Rotation angle (degrees) 55.83967572
Shift along axis 10.53020489
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 36
shifted from previous position = 0.0129
rotated from previous position = 0.00886 degrees
atoms outside contour = 9683, contour level = 0.015262
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56168888 -0.80205120 0.20302581 138.14640970
0.80718866 0.58508768 0.07822306 -25.45309196
-0.18152679 0.11994310 0.97604388 13.32956758
Axis 0.02520734 0.23234750 0.97230614
Axis point 95.97061806 119.46372502 0.00000000
Rotation angle (degrees) 55.84661964
Shift along axis 10.52876171
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 40
shifted from previous position = 0.0324
rotated from previous position = 0.0178 degrees
atoms outside contour = 9684, contour level = 0.015262
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56151033 -0.80217437 0.20303309 138.21041273
0.80735025 0.58488794 0.07804895 -25.42148130
-0.18136046 0.12009351 0.97605630 13.26147478
Axis 0.02539961 0.23221658 0.97233241
Axis point 95.95615486 119.51004622 0.00000000
Rotation angle (degrees) 55.85928402
Shift along axis 10.50176229
Fit molecule 5xon.pdb (#8) to map 5.mrc (#2) using 38369 atoms
average map value = 0.02328, steps = 44
shifted from previous position = 0.0206
rotated from previous position = 0.00471 degrees
atoms outside contour = 9686, contour level = 0.015262
Position of 5xon.pdb (#8) relative to 5.mrc (#2) coordinates:
Matrix rotation and translation
0.56152453 -0.80215997 0.20305071 138.20583507
0.80735239 0.58489567 0.07796887 -25.42806067
-0.18130698 0.12015203 0.97605904 13.23309126
Axis 0.02548359 0.23219727 0.97233483
Axis point 95.95641608 119.50748412 0.00000000
Rotation angle (degrees) 55.85843057
Shift along axis 10.48465054
> show #!3 models
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.007303, steps = 288
shifted from previous position = 9.91
rotated from previous position = 28.2 degrees
atoms outside contour = 11584, contour level = 0.0058651
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.39460906 0.52178979 -0.75631947 174.90315755
0.85866097 0.08359786 0.50568040 27.02310623
0.32708554 -0.84896816 -0.41505204 302.49391599
Axis -0.76663359 -0.61312926 0.19064484
Axis point 0.00000000 69.22854277 184.76243657
Rotation angle (degrees) 117.93194977
Shift along axis -92.98638772
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.007303, steps = 48
shifted from previous position = 0.017
rotated from previous position = 0.00606 degrees
atoms outside contour = 11581, contour level = 0.0058651
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.39463961 0.52180298 -0.75629442 174.88980798
0.85861337 0.08365955 0.50575101 26.99481635
0.32717361 -0.84895397 -0.41501163 302.47451882
Axis -0.76663501 -0.61314053 0.19060285
Axis point 0.00000000 69.21908439 184.75618270
Rotation angle (degrees) 117.92764864
Shift along axis -92.97575967
Fit molecule 5xon.pdb (#8) to map 844_Zflip.mrc (#3) using 38369 atoms
average map value = 0.007303, steps = 44
shifted from previous position = 0.00256
rotated from previous position = 0.00462 degrees
atoms outside contour = 11585, contour level = 0.0058651
Position of 5xon.pdb (#8) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.39467665 0.52180517 -0.75627358 174.88138225
0.85857420 0.08369545 0.50581157 26.98926179
0.32723173 -0.84894909 -0.41497580 302.45979940
Axis -0.76664151 -0.61314162 0.19057323
Axis point 0.00000000 69.22120547 184.74789068
Rotation angle (degrees) 117.92412210
Shift along axis -92.97882551
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8981, correlation about mean = 0.5652, overlap = 18.79
steps = 288, shift = 8.42, angle = 28.8 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.35798229 0.55747128 -0.74904904 250.13371370
0.51895731 0.78568620 0.33672024 -28.65096601
0.77622938 -0.26818459 -0.57056554 197.11100172
Axis -0.36855214 -0.92931087 -0.02346552
Axis point 75.82711932 0.00000000 161.93101132
Rotation angle (degrees) 124.85006026
Shift along axis -70.18697523
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8981, correlation about mean = 0.5651, overlap = 18.79
steps = 28, shift = 0.0184, angle = 0.00613 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.35805669 0.55746935 -0.74901492 250.13294723
0.51889349 0.78572067 0.33673816 -28.66273844
0.77623773 -0.26808761 -0.57059975 197.08495459
Axis -0.36851557 -0.92932440 -0.02350396
Axis point 75.84023190 0.00000000 161.91627157
Rotation angle (degrees) 124.85264874
Shift along axis -70.17318086
Fit map 5.mrc in map 844_Zflip.mrc using 104567 points
correlation = 0.8981, correlation about mean = 0.5651, overlap = 18.79
steps = 24, shift = 0.000676, angle = 0.00833 degrees
Position of 5.mrc (#2) relative to 844_Zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.35818766 0.55744258 -0.74897222 250.14936961
0.51883738 0.78577241 0.33670388 -28.65987701
0.77621481 -0.26799161 -0.57067603 197.08149119
Axis -0.36846050 -0.92934574 -0.02352339
Axis point 75.85583995 0.00000000 161.91197128
Rotation angle (degrees) 124.85807755
Shift along axis -70.17125253
> volume #3 level 0.004892
> save /Users/mcarmina/Desktop/ChimeraX_paper/overlap_extra_dimer.cxs
> volume #2 level 0.01563
[Repeated 1 time(s)]
> volume #3 level 0.005738
> save /Users/mcarmina/Desktop/ChimeraX_paper/overlap_extra_dimer.cxs
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!8 models
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 60
shifted from previous position = 17.1
rotated from previous position = 6.99 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 5.mrc (#2) using
33568 atoms
average map value = -1e-09, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 33568, contour level = 0.015635
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 5.mrc (#2)
coordinates:
Matrix rotation and translation
0.81223412 -0.58104650 0.05158009 -96.46959404
-0.31626274 -0.51294075 -0.79804100 484.05518445
0.49015649 0.63188333 -0.60039144 42.40531561
Axis 0.94140342 -0.28874068 0.17432275
Axis point 0.00000000 207.36184154 132.68071226
Rotation angle (degrees) 130.58301303
Shift along axis -223.19101724
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 844_Zflip.mrc (#3)
using 33568 atoms
average map value = 0.0002756, steps = 700
shifted from previous position = 45
rotated from previous position = 23.8 degrees
atoms outside contour = 33568, contour level = 0.0057382
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 844_Zflip.mrc
(#3) coordinates:
Matrix rotation and translation
-0.93654999 -0.33833217 -0.09168003 542.94818229
0.32763055 -0.75189899 -0.57210659 331.68350397
0.12462796 -0.56584369 0.81503907 -59.27907601
Axis 0.00894395 -0.30890593 0.95105054
Axis point 244.74944830 207.94889808 0.00000000
Rotation angle (degrees) 159.50537279
Shift along axis -153.98029893
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 844_Zflip.mrc (#3)
using 33568 atoms
average map value = 0.0002756, steps = 60
shifted from previous position = 0.0265
rotated from previous position = 0.0279 degrees
atoms outside contour = 33568, contour level = 0.0057382
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 844_Zflip.mrc
(#3) coordinates:
Matrix rotation and translation
-0.93645361 -0.33863764 -0.09153655 542.95743453
0.32784051 -0.75202932 -0.57181494 331.61042133
0.12479991 -0.56548765 0.81525983 -59.44999742
Axis 0.00902946 -0.30872633 0.95110805
Axis point 244.74401564 207.92923597 0.00000000
Rotation angle (degrees) 159.49009293
Shift along axis -154.01762773
> show #!3 models
> hide #!2 models
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 844_Zflip.mrc (#3)
using 33568 atoms
average map value = 0.0002756, steps = 64
shifted from previous position = 0.0156
rotated from previous position = 0.0133 degrees
atoms outside contour = 33568, contour level = 0.0057382
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 844_Zflip.mrc
(#3) coordinates:
Matrix rotation and translation
-0.93650475 -0.33847378 -0.09161943 542.95665348
0.32773724 -0.75198561 -0.57193160 331.64964518
0.12468738 -0.56564386 0.81516868 -59.37533550
Axis 0.00897641 -0.30880016 0.95108458
Axis point 244.74895109 207.93805243 0.00000000
Rotation angle (degrees) 159.49815445
Shift along axis -154.01062987
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 844_Zflip.mrc (#3)
using 33568 atoms
average map value = 0.0002756, steps = 60
shifted from previous position = 0.0144
rotated from previous position = 0.0123 degrees
atoms outside contour = 33568, contour level = 0.0057382
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 844_Zflip.mrc
(#3) coordinates:
Matrix rotation and translation
-0.93645793 -0.33862322 -0.09154576 542.95854575
0.32783343 -0.75202929 -0.57181904 331.61196035
0.12478613 -0.56549633 0.81525592 -59.44249505
Axis 0.00902321 -0.30872946 0.95110709
Axis point 244.74504669 207.92945294 0.00000000
Rotation angle (degrees) 159.49076256
Shift along axis -154.01532978
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 844_Zflip.mrc (#3)
using 33568 atoms
average map value = 0.0002756, steps = 56
shifted from previous position = 0.0159
rotated from previous position = 0.0169 degrees
atoms outside contour = 33568, contour level = 0.0057382
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 844_Zflip.mrc
(#3) coordinates:
Matrix rotation and translation
-0.93650881 -0.33846077 -0.09162598 542.95531372
0.32771812 -0.75193263 -0.57201221 331.65686033
0.12470715 -0.56572206 0.81511139 -59.34551965
Axis 0.00898012 -0.30884762 0.95106914
Axis point 244.74836294 207.94385175 0.00000000
Rotation angle (degrees) 159.49883983
Shift along axis -153.99731797
Fit molecule cryoEM_dimer_placed_280921.pdb (#1.1) to map 844_Zflip.mrc (#3)
using 33568 atoms
average map value = 0.0002756, steps = 60
shifted from previous position = 0.0301
rotated from previous position = 0.0293 degrees
atoms outside contour = 33568, contour level = 0.0057382
Position of cryoEM_dimer_placed_280921.pdb (#1.1) relative to 844_Zflip.mrc
(#3) coordinates:
Matrix rotation and translation
-0.93638723 -0.33884014 -0.09146626 542.96665972
0.32797187 -0.75201119 -0.57176346 331.56580786
0.12495278 -0.56539045 0.81530383 -59.50804502
Axis 0.00909024 -0.30869287 0.95111833
Axis point 244.74064820 207.92696013 0.00000000
Rotation angle (degrees) 159.47958752
Shift along axis -154.01549528
> show #!2 models
> volume #2 level 0.01582
> volume #2 level 0.01601
> volume #2 level 0.01638
> volume #2 level 0.01657
> volume #2 level 0.01675
> volume #2 level 0.01731
> volume #2 level 0.01769
> volume #2 level 0.01787
> volume #2 level 0.01843
> volume #2 level 0.01937
> volume #2 level 0.01657
> volume #2 level 0.01508
> volume #2 level 0.01433
> volume #2 level 0.01228
> volume #2 level 0.01097
> volume #2 level 0.01079
> volume #2 level 0.01023
> volume #2 level 0.01004
> volume #2 level 0.01023
> volume #2 level 0.01041
> volume #2 level 0.0106
> volume #2 level 0.01079
> volume #2 level 0.01097
> volume #2 level 0.01265
> volume #2 level 0.01246
> volume #2 level 0.0119
> volume #2 level 0.01153
> volume #2 level 0.01116
> volume #2 level 0.02589
> volume #2 level 0.01582
> volume #2 level 0.01489
> save /Users/mcarmina/Desktop/ChimeraX_paper/overlap_extra_dimer.cxs
——— End of log from Tue Apr 19 14:54:05 2022 ———
opened ChimeraX session
> hide #!3 models
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> ~select #8
Nothing selected
> select #8.1
38 pseudobonds, 1 model selected
> ~select #8.1
Nothing selected
> select #8.2
19 pseudobonds, 1 model selected
> ~select #8.2
Nothing selected
> select #8.1
38 pseudobonds, 1 model selected
> ~select #8.1
Nothing selected
> select #8
38369 atoms, 39283 bonds, 57 pseudobonds, 4659 residues, 3 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/U
Alignment identifier is 8/U
> sequence chain #8/V
Alignment identifier is 8/V
> ui tool show "Show Sequence Viewer"
> sequence chain #8/W
Alignment identifier is 8/W
> select #8/W:760-809
397 atoms, 408 bonds, 50 residues, 1 model selected
> select #8/W:213-809
2667 atoms, 2713 bonds, 5 pseudobonds, 329 residues, 2 models selected
> show sel atoms
> color (#!8 & sel) hot pink
> select #8/V:110
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/V:9-110
792 atoms, 808 bonds, 102 residues, 1 model selected
> show sel atoms
> color sel cyan
> select #8/U:285
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/U:123-285
1239 atoms, 1255 bonds, 2 pseudobonds, 155 residues, 2 models selected
> show sel atoms
> select clear
> select #3
2 models selected
> ~select #3
Nothing selected
> select #3
2 models selected
> show #!3 models
> ~select #3
Nothing selected
> volume #2 level 0.02328
> volume #2 level 0.009107
> volume #2 level 0.01396
> save /Users/mcarmina/Desktop/ChimeraX_paper/elongation_dimer_APT.cxs
——— End of log from Mon Apr 25 12:20:22 2022 ———
opened ChimeraX session
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> lighting soft
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
[Repeated 2 time(s)]
> lighting soft
> lighting simple
> volume style surface
> volume style mesh
> volume style surface
> lighting flat
> lighting full
> lighting simple
> lighting soft
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> set bgColor gray
> set bgColor white
> graphics silhouettes false
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting full
> lighting soft
> volume #3 color #caaaa7f8
> volume #3 color #caaaa7d0
> volume #3 color #caaaa79b
[Repeated 2 time(s)]
> volume #3 color #caaaa75a
[Repeated 1 time(s)]
> volume #3 color #caaaa700
> volume #3 color #caaaa799
> volume #3 color black
> volume #2 color #959595
[Repeated 1 time(s)]
> volume #2 color #95959581
> volume #2 color #95959533
> volume #2 color #959595
[Repeated 1 time(s)]
> volume #2 level 0.01918
> volume #2 level 0.01489
> open /Users/mcarmina/Desktop/ChimeraX_paper/cl5_fitted.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
> open /Users/mcarmina/Desktop/ChimeraX_paper/class5_figureS5_310322.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Users/mcarmina/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File
"/Users/mcarmina/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/cap.py", line 231, in restore_snapshot
c = ClipCap(data['clip_plane_name'], data['clip_cap_owner'])
File
"/Users/mcarmina/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/cap.py", line 210, in __init__
Surface.__init__(self, 'cap ' + plane_name, drawing.session)
AttributeError: 'NoneType' object has no attribute 'session'
Exception ignored in: <function Drawing.__del__ at 0x7ff4934c64c0>
Traceback (most recent call last):
File
"/Users/mcarmina/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1183, in __del__
if not self.was_deleted:
AttributeError: 'ClipCap' object has no attribute 'was_deleted'
opened ChimeraX session
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Users/mcarmina/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File
"/Users/mcarmina/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 119, in restore_snapshot
ti.set_state_from_snapshot(session, data)
File
"/Users/mcarmina/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/log/tool.py", line 499, in set_state_from_snapshot
if self.settings.session_restore_clears and session.restore_options['clear
log']:
KeyError: 'clear log'
opened ChimeraX session
OpenGL version: 4.1 ATI-4.6.20
OpenGL renderer: AMD Radeon R9 M290X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac15,1
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.5 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
System Firmware Version: 432.40.8.0.1
SMC Version (system): 2.22f16
Software:
System Software Overview:
System Version: macOS 11.6.1 (20G224)
Kernel Version: Darwin 20.6.0
Time since boot: 46 days 15:01
Graphics/Displays:
AMD Radeon R9 M290X:
Chipset Model: AMD Radeon R9 M290X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x6810
Revision ID: 0x0000
ROM Revision: 113-C408A0-730
VBIOS Version: 113-C408A0-017
EFI Driver Version: 01.00.730
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem restoring clip caps when volume surface not restored |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #6265