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Opened 21 months ago
Last modified 21 months ago
#14525 assigned defect
expand_alias: cmd.word_info is None
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | pett, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.7-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> "/Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs
> copy.cxs"
Opened 2A1.4_G115_class6 as #1, grid size 140,140,140, pixel 3.19, shown at
level 0.0529, step 1, values float32
Opened 2A1.11_G115_class8 as #5, grid size 140,140,140, pixel 3.19, shown at
level 0.04, step 1, values float32
Opened 2A1.9_G115_66_class1 as #9, grid size 288,288,288, pixel 1.07, shown at
level 0.00655, step 2, values float32
Not registering illegal selector name "2A1.4_1"
Not registering illegal selector name "4_1"
Not registering illegal selector name "2a14 1"
Log from Sun Jan 28 01:14:40 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
Opened 2A1.4_G115_class6 as #1, grid size 140,140,140, pixel 3.19, shown at
level 0.0529, step 1, values float32
Opened 2A1.11_G115_class8 as #5, grid size 140,140,140, pixel 3.19, shown at
level 0.04, step 1, values float32
Opened 2A1.9_G115_66_class1 as #9, grid size 288,288,288, pixel 1.07, shown at
level 0.00655, step 2, values float32
Not registering illegal selector name "2A1.4_1"
Not registering illegal selector name "4_1"
Not registering illegal selector name "2a14 1"
Log from Sat Jan 27 23:12:17 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
Opened 2A1.4_G115_class6 as #1, grid size 140,140,140, pixel 3.19, shown at
level 0.0529, step 1, values float32
Opened 2A1.11_G115_class8 as #5, grid size 140,140,140, pixel 3.19, shown at
level 0.04, step 1, values float32
Opened 2A1.9_G115_66_class1 as #9, grid size 288,288,288, pixel 1.07, shown at
level 0.00655, step 2, values float32
Not registering illegal selector name "2A1.4_1"
Not registering illegal selector name "4_1"
Not registering illegal selector name "2a14 1"
Log from Sat Jan 27 14:24:11 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
Opened 2A1.4_G115_class6 as #1, grid size 140,140,140, pixel 3.19, shown at
level 0.0978, step 1, values float32
Opened 2A1.11_G115_class8 as #5, grid size 140,140,140, pixel 3.19, shown at
level 0.041, step 1, values float32
Opened 2A1.9_G115_66_class1 as #9, grid size 288,288,288, pixel 1.07, shown at
level 0.00633, step 2, values float32
Not registering illegal selector name "2A1.4_1"
Not registering illegal selector name "4_1"
Not registering illegal selector name "2a14 1"
Log from Sat Jan 27 13:09:37 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
Opened 2A1.4_G115_class6 as #1, grid size 140,140,140, pixel 3.19, shown at
level 0.0978, step 1, values float32
Opened 2A1.11_G115_class8 as #5, grid size 140,140,140, pixel 3.19, shown at
level 0.041, step 1, values float32
Opened 2A1.9_G115_66_class1 as #9, grid size 288,288,288, pixel 1.07, shown at
level 0.00633, step 2, values float32
Not registering illegal selector name "2A1.4_1"
Not registering illegal selector name "4_1"
Not registering illegal selector name "2a14 1"
Log from Sat Jan 27 12:55:13 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
Opened 2A1.4_G115_class6 as #1, grid size 140,140,140, pixel 3.19, shown at
level 0.0532, step 1, values float32
Opened 2A1.11_G115_class8 as #5, grid size 140,140,140, pixel 3.19, shown at
level 0.041, step 1, values float32
Not registering illegal selector name "2A1.4_1"
Not registering illegal selector name "4_1"
Not registering illegal selector name "2a14 1"
Log from Sat Jan 27 12:39:58 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
Opened run_it200_class006.mrc as #1, grid size 140,140,140, pixel 3.19, shown
at level 0.0532, step 1, values float32
Log from Fri Jan 26 20:18:41 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/amritaramesh/Desktop/41_3D/41_G115/41_G115_b420_r140/run_it200_class006.mrc
Opened run_it200_class006.mrc as #1, grid size 140,140,140, pixel 3.19, shown
at level 0.00799, step 1, values float32
> volume #1 level 0.03182
> open
> /Users/amritaramesh/Desktop/41_3D/41_G115/41_G115_b420_r140/run_it200_class006.mrc
Opened run_it200_class006.mrc as #2, grid size 140,140,140, pixel 3.19, shown
at level 0.00799, step 1, values float32
> close #2
> open
> /Users/amritaramesh/Desktop/DEsktop/Adams_Lab/Useful_crystal_structures/8dfw-
> BTN2A1+G115.cif
8dfw-BTN2A1+G115.cif title:
Crystal Structure of Human BTN2A1 in Complex With Vgamma9-Vdelta2 T Cell
Receptor [more info...]
Chain information for 8dfw-BTN2A1+G115.cif #2
---
Chain | Description | UniProt
A B | Butyrophilin subfamily 2 member A1 | BT2A1_HUMAN 1-217
D | T cell receptor delta variable chain |
G | T cell receptor gamma variable chain |
Non-standard residues in 8dfw-BTN2A1+G115.cif #2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> delete #2/D
> delete #2/G
> open /Users/amritaramesh/Downloads/7pij.pdb
7pij.pdb title:
Structure of staphylococcus capitis divalent metal ion transporter (DMT) by
nabfab-fiducial assisted cryo-em [more info...]
Chain information for 7pij.pdb #3
---
Chain | Description
B | divalent metal cation transporter MNTH
H | nabfab HC
K | ANTI-fab nanobody
L | nabfab LC
N | DMTNB16_4
> open /Users/amritaramesh/Downloads/7pij.pdb
7pij.pdb title:
Structure of staphylococcus capitis divalent metal ion transporter (DMT) by
nabfab-fiducial assisted cryo-em [more info...]
Chain information for 7pij.pdb #4
---
Chain | Description
B | divalent metal cation transporter MNTH
H | nabfab HC
K | ANTI-fab nanobody
L | nabfab LC
N | DMTNB16_4
> delete #3/B
> delete #4/B
> delete #3/N
> delete #4/N
> ui mousemode right select
> select #3/K:75@O
1 atom, 1 residue, 1 model selected
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,55.546,0,1,0,73.977,0,0,1,121.87
> view matrix models #3,1,0,0,12.633,0,1,0,47.834,0,0,1,115.79
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.69354,-0.64375,0.3234,169.17,0.70249,0.50477,-0.50172,81.936,0.15974,0.57515,0.8023,-13.57
> color #1 #b2b2b270 models
> set bgColor white
> view matrix models
> #3,0.73921,-0.64862,0.18131,178.91,0.65572,0.63173,-0.41346,52.827,0.15364,0.42452,0.89229,8.8611
> view matrix models
> #3,0.70872,-0.63692,0.3034,167.27,0.69453,0.55439,-0.45856,67.542,0.12387,0.53571,0.83527,-2.3426
> view matrix models
> #3,0.67744,-0.72763,-0.10785,242.88,0.62328,0.64567,-0.44117,59.381,0.39064,0.23164,0.89092,5.3777
> view matrix models
> #3,0.54748,-0.8066,-0.22284,298.51,0.6983,0.5871,-0.4095,53.825,0.46113,0.068582,0.88468,27.697
> view matrix models
> #3,0.4144,-0.89461,-0.16718,335.81,0.8129,0.44644,-0.37402,57.881,0.40924,0.019096,0.91223,44.777
> view matrix models
> #3,0.41437,-0.90652,-0.080741,327.81,0.78529,0.40097,-0.47175,84.799,0.46002,0.13207,0.87803,15.119
> view matrix models
> #3,0.49728,-0.8666,-0.041402,298.72,0.71539,0.43658,-0.54554,99.448,0.49084,0.24167,0.83706,-9.1999
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.49728,-0.8666,-0.041402,294.14,0.71539,0.43658,-0.54554,96.731,0.49084,0.24167,0.83706,-11.434
> view matrix models
> #3,0.49728,-0.8666,-0.041402,290.33,0.71539,0.43658,-0.54554,94.21,0.49084,0.24167,0.83706,-9.9587
> view matrix models
> #3,0.49728,-0.8666,-0.041402,295.1,0.71539,0.43658,-0.54554,92.656,0.49084,0.24167,0.83706,-7.1362
> view matrix models
> #3,0.49728,-0.8666,-0.041402,297.15,0.71539,0.43658,-0.54554,89.923,0.49084,0.24167,0.83706,-7.0141
> view matrix models
> #3,0.49728,-0.8666,-0.041402,296.71,0.71539,0.43658,-0.54554,89.272,0.49084,0.24167,0.83706,-7.0852
> fitmap #3 inMap #1
Fit molecule 7pij.pdb (#3) to map run_it200_class006.mrc (#1) using 4191 atoms
average map value = 0.09621, steps = 108
shifted from previous position = 26.7
rotated from previous position = 22.1 degrees
atoms outside contour = 795, contour level = 0.031819
Position of 7pij.pdb (#3) relative to run_it200_class006.mrc (#1) coordinates:
Matrix rotation and translation
0.71384287 -0.68170699 0.16032444 211.46086235
0.58160894 0.44958778 -0.67793942 110.93507064
0.39007613 0.57718836 0.71742192 -46.10918500
Axis 0.69901062 -0.12795420 0.70357080
Axis point -12.61308723 211.74184584 0.00000000
Rotation angle (degrees) 63.86891685
Shift along axis 101.17770409
> fitmap #3 inMap #1
Fit molecule 7pij.pdb (#3) to map run_it200_class006.mrc (#1) using 4191 atoms
average map value = 0.09621, steps = 44
shifted from previous position = 0.00785
rotated from previous position = 0.0394 degrees
atoms outside contour = 793, contour level = 0.031819
Position of 7pij.pdb (#3) relative to run_it200_class006.mrc (#1) coordinates:
Matrix rotation and translation
0.71372692 -0.68187895 0.16010926 211.54359227
0.58136643 0.44923132 -0.67838359 111.10903054
0.39064940 0.57726278 0.71705002 -46.19378696
Axis 0.69913826 -0.12836371 0.70336936
Axis point -12.72610364 211.87441531 0.00000000
Rotation angle (degrees) 63.89585521
Shift along axis 101.14455591
> view matrix models
> #3,0.71373,-0.68188,0.16011,193.67,0.58137,0.44923,-0.67838,134.7,0.39065,0.57726,0.71705,-52.113
> fitmap #3 inMap #1
Fit molecule 7pij.pdb (#3) to map run_it200_class006.mrc (#1) using 4191 atoms
average map value = 0.09621, steps = 104
shifted from previous position = 30.2
rotated from previous position = 0.0575 degrees
atoms outside contour = 796, contour level = 0.031819
Position of 7pij.pdb (#3) relative to run_it200_class006.mrc (#1) coordinates:
Matrix rotation and translation
0.71375671 -0.68165612 0.16092326 211.36769591
0.58146462 0.44862079 -0.67870338 111.24412808
0.39044879 0.57800028 0.71656502 -46.21185111
Axis 0.69952371 -0.12776167 0.70309568
Axis point -12.83081460 211.66357121 0.00000000
Rotation angle (degrees) 63.92984968
Shift along axis 101.15262810
> view matrix models
> #3,0.71376,-0.68166,0.16092,198.03,0.58146,0.44862,-0.6787,124.3,0.39045,0.578,0.71657,-56.663
> view matrix models
> #3,0.71376,-0.68166,0.16092,197.68,0.58146,0.44862,-0.6787,123.01,0.39045,0.578,0.71657,-48.625
> undo
[Repeated 3 time(s)]
> view matrix models
> #3,0.49728,-0.8666,-0.041402,296.36,0.71539,0.43658,-0.54554,90.418,0.49084,0.24167,0.83706,-7.6393
> undo
> select subtract #3
Nothing selected
> select add #4
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> view matrix models #4,1,0,0,36.876,0,1,0,-9.2612,0,0,1,43.057
> view matrix models #4,1,0,0,43.349,0,1,0,5.5839,0,0,1,35.349
> view matrix models #4,1,0,0,38.984,0,1,0,7.6958,0,0,1,30.245
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.87011,0.37685,0.31764,-55.909,-0.43471,0.28311,0.85491,139.29,0.23225,-0.88195,0.41016,247.18
> view matrix models
> #4,0.61842,-0.1522,0.77096,49.789,-0.62145,-0.6952,0.36125,444.61,0.48099,-0.70252,-0.52451,275.74
> view matrix models
> #4,0.027894,0.35932,0.9328,32.483,-0.91357,-0.36958,0.16969,453.69,0.40571,-0.85691,0.31796,220.17
> view matrix models
> #4,0.39232,0.18785,0.90044,4.0241,-0.79906,-0.41528,0.43479,409.36,0.45561,-0.89008,-0.012819,258.22
> view matrix models
> #4,0.42395,0.42743,0.79848,-40.842,-0.82627,-0.17847,0.53425,351.64,0.37086,-0.88626,0.27751,238.01
> view matrix models
> #4,0.46283,0.43748,0.77097,-47.011,-0.81486,-0.13243,0.56432,335.94,0.34898,-0.88942,0.2952,240.68
> view matrix models
> #4,0.46882,0.059346,0.8813,19.377,-0.72506,-0.54399,0.42234,424.41,0.50448,-0.83699,-0.212,261.91
> view matrix models
> #4,0.086373,0.12134,0.98885,65.519,-0.82702,-0.5447,0.13908,478.52,0.5555,-0.8298,0.053305,218.27
> view matrix models
> #4,0.22238,0.014924,0.97485,64.222,-0.90594,-0.36635,0.21227,446.35,0.3603,-0.93036,-0.067947,291.67
> view matrix models
> #4,0.37181,-0.36423,0.85387,131.87,-0.90652,-0.34059,0.24945,436.39,0.19996,-0.8668,-0.45681,355.98
> view matrix models
> #4,0.42532,-0.30171,0.85327,108.4,-0.77912,0.35767,0.51483,230.22,-0.46052,-0.88376,-0.082947,439.26
> view matrix models
> #4,0.46929,-0.2504,0.8468,89.856,-0.80783,0.26553,0.52621,254.01,-0.35661,-0.93102,-0.07767,429.02
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.46929,-0.2504,0.8468,86.909,-0.80783,0.26553,0.52621,242.1,-0.35661,-0.93102,-0.07767,426.2
> view matrix models
> #4,0.46929,-0.2504,0.8468,90.45,-0.80783,0.26553,0.52621,239.63,-0.35661,-0.93102,-0.07767,420.2
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.51148,-0.12493,0.85016,55.157,-0.76869,0.37568,0.51767,209.64,-0.38407,-0.91829,0.096119,401.45
> view matrix models
> #4,0.57438,0.048432,0.81715,10.117,-0.71826,0.50867,0.47472,176.84,-0.39267,-0.8596,0.32696,362.31
> view matrix models
> #4,0.36063,0.22456,0.90527,2.177,-0.88673,0.38353,0.25811,262.07,-0.28924,-0.89581,0.33744,349.16
> volume #1 level 0.08009
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.36063,0.22456,0.90527,-0.32982,-0.88673,0.38353,0.25811,267.3,-0.28924,-0.89581,0.33744,349.09
> save /Users/amritaramesh/Desktop/41_3D/2A1.4_nanobody_.cxs
> volume #1 level 0.03426
> volume #1 level 0.0306
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select subtract #4
Nothing selected
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> view matrix models
> #3,0.49728,-0.8666,-0.041402,300.81,0.71539,0.43658,-0.54554,92.913,0.49084,0.24167,0.83706,-10.024
> view matrix models
> #3,0.49728,-0.8666,-0.041402,304.54,0.71539,0.43658,-0.54554,87.399,0.49084,0.24167,0.83706,-6.0669
> undo
> view matrix models
> #3,0.49728,-0.8666,-0.041402,299.73,0.71539,0.43658,-0.54554,91.673,0.49084,0.24167,0.83706,-7.988
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.51368,-0.85739,-0.031777,293.47,0.7027,0.44168,-0.55779,94.487,0.49228,0.2642,0.82937,-12.149
> view matrix models
> #3,0.55257,-0.83117,-0.061735,284.14,0.69182,0.49871,-0.52218,79.982,0.46481,0.24583,0.8506,-5.5964
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.54144,-0.83986,-0.038434,285.26,0.6861,0.46781,-0.55715,91.959,0.48591,0.2753,0.82952,-13.335
> view matrix models
> #3,0.55334,-0.83279,-0.01648,278.81,0.67935,0.46267,-0.56958,95.861,0.48196,0.30398,0.82177,-17.784
> view matrix models
> #3,0.45733,-0.88627,0.073271,297.51,0.78799,0.36567,-0.49534,86.958,0.41222,0.28427,0.8656,-5.6849
> view matrix models
> #3,0.41692,-0.90869,0.021462,316.31,0.80522,0.35829,-0.4725,82.479,0.42167,0.21428,0.88107,5.6267
> view matrix models
> #3,0.42205,-0.90635,-0.020246,319.94,0.81435,0.38883,-0.43087,69.117,0.39839,0.16536,0.90219,17.942
> view matrix models
> #3,0.37257,-0.91921,-0.12745,345.18,0.71199,0.37123,-0.59604,112.49,0.59519,0.13132,0.79278,1.2604
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.42205,-0.90635,-0.020246,319.79,0.81435,0.38883,-0.43087,69.239,0.39839,0.16536,0.90219,16.575
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.47317,-0.88029,-0.034549,306.26,0.77726,0.43561,-0.454,69.082,0.4147,0.18797,0.89033,10.086
> view matrix models
> #3,0.47816,-0.87822,0.0091949,299.52,0.7791,0.41931,-0.46603,73.693,0.40542,0.23,0.88472,3.5278
> undo
> view matrix models
> #3,0.52063,-0.85233,-0.049751,293.12,0.73827,0.47869,-0.4752,69.842,0.42885,0.21068,0.87847,3.9867
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.52063,-0.85233,-0.049751,293.7,0.73827,0.47869,-0.4752,68.284,0.42885,0.21068,0.87847,3.9241
> view matrix models
> #3,0.52063,-0.85233,-0.049751,291.67,0.73827,0.47869,-0.4752,70.34,0.42885,0.21068,0.87847,4.2269
> view matrix models
> #3,0.52063,-0.85233,-0.049751,292.83,0.73827,0.47869,-0.4752,69.052,0.42885,0.21068,0.87847,4.7314
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.50801,-0.85695,-0.086968,300.76,0.75298,0.49085,-0.43828,59.143,0.41827,0.15716,0.89462,16.228
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.50801,-0.85695,-0.086968,300.71,0.75298,0.49085,-0.43828,59.033,0.41827,0.15716,0.89462,16.359
> view matrix models
> #3,0.50801,-0.85695,-0.086968,300.2,0.75298,0.49085,-0.43828,59.856,0.41827,0.15716,0.89462,16.211
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.49734,-0.86549,-0.05985,300.74,0.75579,0.4661,-0.45993,67.271,0.42596,0.1835,0.88594,10.17
> volume #1 level 0.09965
> volume #1 level 0.02449
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.49734,-0.86549,-0.05985,300.91,0.75579,0.4661,-0.45993,67.839,0.42596,0.1835,0.88594,11.27
> view matrix models
> #3,0.49734,-0.86549,-0.05985,301.61,0.75579,0.4661,-0.45993,69.091,0.42596,0.1835,0.88594,10.214
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.52392,-0.84675,-0.092327,296.52,0.7399,0.50613,-0.44314,61.479,0.42196,0.16386,0.89168,14.48
> view matrix models
> #3,0.53299,-0.83978,-0.10343,294.66,0.73411,0.51975,-0.43697,58.907,0.42072,0.15697,0.89351,15.968
> view matrix models
> #3,0.53403,-0.84125,-0.084349,292.45,0.71884,0.5043,-0.47848,70.185,0.44506,0.19489,0.87404,5.6046
> view matrix models
> #3,0.50507,-0.86307,-0.0021032,292.57,0.74053,0.43461,-0.51256,85.162,0.44329,0.25733,0.85865,-5.5542
> view matrix models
> #3,0.54005,-0.8393,-0.062614,288.23,0.71648,0.4975,-0.48902,73.376,0.44159,0.21924,0.87002,1.5395
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.54005,-0.8393,-0.062614,285.41,0.71648,0.4975,-0.48902,71.395,0.44159,0.21924,0.87002,3.5032
> view matrix models
> #3,0.54005,-0.8393,-0.062614,285.77,0.71648,0.4975,-0.48902,70.899,0.44159,0.21924,0.87002,3.603
> view matrix models
> #3,0.54005,-0.8393,-0.062614,286.44,0.71648,0.4975,-0.48902,71.471,0.44159,0.21924,0.87002,3.3546
> volume #1 level 0.01838
> ui mousemode right select
> select clear
> hide #2 models
> show #2 models
Drag select of 240 atoms, 433 residues, 238 bonds
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,261.66,0,1,0,196.7,0,0,1,281.92
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.164,-0.8814,-0.44298,314.55,-0.56051,-0.28627,0.77709,257.78,-0.81174,0.37574,-0.44709,277.77
> view matrix models
> #2,-0.31432,-0.85287,-0.41691,318.5,-0.41857,-0.26967,0.86722,254,-0.85206,0.4471,-0.27222,278.79
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.31432,-0.85287,-0.41691,265.85,-0.41857,-0.26967,0.86722,254.55,-0.85206,0.4471,-0.27222,233.49
> view matrix models
> #2,-0.31432,-0.85287,-0.41691,263.51,-0.41857,-0.26967,0.86722,251.3,-0.85206,0.4471,-0.27222,235.29
> view matrix models
> #2,-0.31432,-0.85287,-0.41691,265.25,-0.41857,-0.26967,0.86722,252.97,-0.85206,0.4471,-0.27222,235.49
> volume #1 level 0.04771
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.29969,-0.74712,-0.5933,260.02,-0.59396,-0.34054,0.72886,258.64,-0.74659,0.57083,-0.3417,228.25
> view matrix models
> #2,-0.18429,-0.90807,-0.37609,263.39,-0.29244,-0.31466,0.90303,250.89,-0.93836,0.2764,-0.20757,243.2
> view matrix models
> #2,0.14039,-0.8522,-0.50403,250.98,-0.15147,-0.52156,0.83966,251.88,-0.97844,-0.041534,-0.2023,253.36
> view matrix models
> #2,0.080547,-0.7624,-0.64207,249.06,-0.57826,-0.56042,0.59291,263.25,-0.81187,0.32353,-0.48601,235.94
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.080547,-0.7624,-0.64207,246,-0.57826,-0.56042,0.59291,264.16,-0.81187,0.32353,-0.48601,227.11
> view matrix models
> #2,0.080547,-0.7624,-0.64207,243.96,-0.57826,-0.56042,0.59291,252.02,-0.81187,0.32353,-0.48601,231.46
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.14747,-0.65939,-0.73719,238.49,-0.40017,-0.72139,0.56521,250.77,-0.9045,0.21166,-0.37025,238.09
> view matrix models
> #2,0.23395,-0.63405,-0.73705,235.03,-0.54194,-0.71444,0.44258,253.82,-0.8072,0.29589,-0.51076,231.24
> view matrix models
> #2,0.21937,-0.78624,-0.57767,240.72,-0.44529,-0.60751,0.65776,250.18,-0.8681,0.11295,-0.48337,237.9
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.21937,-0.78624,-0.57767,246.34,-0.44529,-0.60751,0.65776,253.86,-0.8681,0.11295,-0.48337,240.83
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.32871,-0.61538,-0.71642,237.47,-0.12582,-0.78035,0.61256,248.46,-0.93601,-0.11121,-0.33393,249.94
> view matrix models
> #2,0.29484,-0.66241,-0.68868,239.92,-0.18279,-0.74651,0.63977,249.53,-0.9379,-0.062748,-0.34119,248.7
> view matrix models
> #2,0.052408,-0.7927,-0.60736,251.2,-0.044533,-0.60944,0.79158,243.27,-0.99763,-0.014437,-0.067241,251.7
> fitmap #2 inMap #1
Fit molecule 8dfw-BTN2A1+G115.cif (#2) to map run_it200_class006.mrc (#1)
using 3669 atoms
average map value = 0.1, steps = 84
shifted from previous position = 7.65
rotated from previous position = 12.9 degrees
atoms outside contour = 516, contour level = 0.047706
Position of 8dfw-BTN2A1+G115.cif (#2) relative to run_it200_class006.mrc (#1)
coordinates:
Matrix rotation and translation
0.25564784 -0.70952236 -0.65667512 237.94011458
-0.02227299 -0.68338876 0.72971482 246.73022667
-0.96651337 -0.17192390 -0.19051005 247.67301931
Axis -0.76717463 0.26363115 0.58475781
Axis point -0.00000000 213.29600404 163.81148714
Rotation angle (degrees) 144.01057665
Shift along axis 27.33288510
> select add #2
3669 atoms, 3657 bonds, 547 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #4
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #4 inMap #1
Fit molecule 7pij.pdb (#4) to map run_it200_class006.mrc (#1) using 4191 atoms
average map value = 0.08187, steps = 84
shifted from previous position = 8.01
rotated from previous position = 36.1 degrees
atoms outside contour = 521, contour level = 0.047706
Position of 7pij.pdb (#4) relative to run_it200_class006.mrc (#1) coordinates:
Matrix rotation and translation
-0.05318163 -0.12728076 0.99043996 149.15070989
-0.99549449 0.08472889 -0.04256458 388.44007483
-0.07850123 -0.98824118 -0.13121332 392.63101741
Axis -0.56608725 0.63987412 -0.51971755
Axis point 403.00807196 0.00000000 300.77310109
Rotation angle (degrees) 123.35555888
Shift along axis -39.93679336
> select subtract #4
Nothing selected
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #3 inMap #1
Fit molecule 7pij.pdb (#3) to map run_it200_class006.mrc (#1) using 4191 atoms
average map value = 0.09622, steps = 104
shifted from previous position = 27.7
rotated from previous position = 22.9 degrees
atoms outside contour = 1044, contour level = 0.047706
Position of 7pij.pdb (#3) relative to run_it200_class006.mrc (#1) coordinates:
Matrix rotation and translation
0.71366284 -0.68181625 0.16066095 211.43942158
0.58126498 0.44841525 -0.67901015 111.36099564
0.39091734 0.57797090 0.71633322 -46.26025458
Axis 0.69957695 -0.12814996 0.70297203
Axis point -12.91764698 211.77509763 0.00000000
Rotation angle (degrees) 63.94679013
Shift along axis 101.12757415
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.71366,-0.68182,0.16066,189.8,0.58126,0.44842,-0.67901,141.94,0.39092,0.57797,0.71633,-41.191
> volume #1 level 0.1003
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.67854,-0.72285,0.13066,208.91,0.57166,0.40795,-0.71189,156.44,0.46128,0.55774,0.69003,-46.994
> view matrix models
> #3,0.4889,-0.83167,0.26326,252.01,0.77474,0.27524,-0.56924,128.91,0.40095,0.48226,0.77889,-30.235
> view matrix models
> #3,0.57787,-0.76721,0.27831,219.48,0.79168,0.44412,-0.41952,71.228,0.19826,0.46276,0.86403,1.9972
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.57787,-0.76721,0.27831,212.65,0.79168,0.44412,-0.41952,68.555,0.19826,0.46276,0.86403,0.93992
> view matrix models
> #3,0.57787,-0.76721,0.27831,210.27,0.79168,0.44412,-0.41952,71.849,0.19826,0.46276,0.86403,0.1591
> volume #1 level 0.04282
> view matrix models
> #3,0.57787,-0.76721,0.27831,212.73,0.79168,0.44412,-0.41952,70.424,0.19826,0.46276,0.86403,1.1357
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.64672,-0.70379,0.29399,184.17,0.73203,0.46447,-0.49841,87.022,0.21422,0.53754,0.81557,-11.992
> view matrix models
> #3,0.48019,-0.84582,-0.2324,310.5,0.43252,0.45881,-0.77616,179,0.76312,0.27219,0.58615,-31.261
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.52173,-0.77627,-0.35386,302.56,0.39773,0.58827,-0.7041,149.06,0.75473,0.22661,0.61566,-23.511
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.52173,-0.77627,-0.35386,308.49,0.39773,0.58827,-0.7041,155.1,0.75473,0.22661,0.61566,-26.556
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.62704,-0.77887,-0.013924,247.53,0.5757,0.47537,-0.66528,140.77,0.52478,0.40914,0.74646,-38.011
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.62704,-0.77887,-0.013924,246.75,0.5757,0.47537,-0.66528,135.73,0.52478,0.40914,0.74646,-33.936
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.62704,-0.77887,-0.013924,243.75,0.5757,0.47537,-0.66528,134.56,0.52478,0.40914,0.74646,-32.604
> view matrix models
> #3,0.62704,-0.77887,-0.013924,243.65,0.5757,0.47537,-0.66528,135.46,0.52478,0.40914,0.74646,-32.22
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.61858,-0.78467,0.040769,239.82,0.58797,0.42784,-0.68647,145.9,0.52121,0.44861,0.72601,-37.498
> view matrix models
> #3,0.56455,-0.82341,0.057295,256.35,0.65366,0.40362,-0.64017,132.97,0.50399,0.39886,0.76609,-28.472
> view matrix models
> #3,0.62183,-0.78215,0.039602,238.8,0.58373,0.42918,-0.68925,146.76,0.5221,0.45172,0.72344,-38.019
> view matrix models
> #3,0.63738,-0.7698,0.033914,233.9,0.63188,0.49698,-0.59476,111.55,0.44099,0.40052,0.80319,-21.406
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.62183,-0.78215,0.039602,237.03,0.58373,0.42918,-0.68925,145.4,0.5221,0.45172,0.72344,-37.297
> view matrix models
> #3,0.62183,-0.78215,0.039602,224.72,0.58373,0.42918,-0.68925,165.31,0.5221,0.45172,0.72344,-34.694
> undo
> view matrix models
> #3,0.62183,-0.78215,0.039602,235.52,0.58373,0.42918,-0.68925,146.65,0.5221,0.45172,0.72344,-37.052
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.61879,-0.78252,0.069023,232.59,0.60478,0.41848,-0.67758,143.52,0.50134,0.46102,0.7322,-36.177
> view matrix models
> #3,0.55182,-0.83344,0.029437,261.04,0.6597,0.41464,-0.62679,127.72,0.51019,0.3653,0.77863,-23.023
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.55182,-0.83344,0.029437,259.27,0.6597,0.41464,-0.62679,127.8,0.51019,0.3653,0.77863,-25.856
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.57227,-0.81877,0.046098,250.21,0.66608,0.43129,-0.60855,120.8,0.47838,0.37896,0.79218,-24.402
> undo
> view matrix models
> #3,0.57226,-0.81641,-0.077375,264.8,0.63632,0.50157,-0.58611,108.65,0.51732,0.28617,0.80653,-13.667
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.57226,-0.81641,-0.077375,264.21,0.63632,0.50157,-0.58611,111.53,0.51732,0.28617,0.80653,-15.634
> view matrix models
> #3,0.57226,-0.81641,-0.077375,264.91,0.63632,0.50157,-0.58611,110.35,0.51732,0.28617,0.80653,-15.231
> volume #1 level 0.0471
> volume #1 level 0.01654
> volume #1 level 0.02387
> volume #1 level 0.03793
> volume #1 level 0.05687
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.58489,-0.80845,-0.065694,259.39,0.63964,0.50952,-0.57554,106.72,0.49877,0.2946,0.81513,-14.569
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.57226,-0.81641,-0.077375,268.95,0.63632,0.50157,-0.58611,112.97,0.51732,0.28617,0.80653,-18.493
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.47301,-0.88017,-0.039475,296.81,0.73489,0.41886,-0.53337,105.55,0.486,0.22328,0.84496,-3.7738
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.47301,-0.88017,-0.039475,293.89,0.73489,0.41886,-0.53337,102.15,0.486,0.22328,0.84496,-6.541
> view matrix models
> #3,0.47301,-0.88017,-0.039475,295.12,0.73489,0.41886,-0.53337,100.16,0.486,0.22328,0.84496,-5.2171
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.41845,-0.90202,-0.10612,318.29,0.73081,0.40377,-0.55036,106.24,0.53928,0.15275,0.82816,1.8359
> view matrix models
> #3,0.36659,-0.92655,-0.084349,330.73,0.79686,0.35948,-0.48558,95.284,0.48024,0.11079,0.87011,16.899
> view matrix models
> #3,0.47192,-0.88161,0.0069837,289.96,0.8137,0.43249,-0.38839,64.575,0.33939,0.18897,0.92147,20.6
> view matrix models
> #3,0.53669,-0.83984,-0.08151,279.53,0.76359,0.52451,-0.3766,52.93,0.35904,0.13988,0.92278,27.23
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.53669,-0.83984,-0.08151,281.25,0.76359,0.52451,-0.3766,51.946,0.35904,0.13988,0.92278,27.078
> view matrix models
> #3,0.53669,-0.83984,-0.08151,280.37,0.76359,0.52451,-0.3766,53.283,0.35904,0.13988,0.92278,28.047
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.58012,-0.8133,-0.044824,261.96,0.72872,0.5428,-0.41754,60.981,0.36391,0.20956,0.90755,14.056
> volume #1 level 0.05321
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.58012,-0.8133,-0.044824,259.78,0.72872,0.5428,-0.41754,62.206,0.36391,0.20956,0.90755,14.889
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.58209,-0.81183,-0.045832,259.21,0.72752,0.54516,-0.41655,61.809,0.36316,0.20913,0.90796,15.075
> view matrix models
> #3,0.6207,-0.78132,-0.065376,247.74,0.70244,0.59119,-0.39633,54.235,0.34831,0.20008,0.91578,18.875
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.6207,-0.78132,-0.065376,249.7,0.70244,0.59119,-0.39633,55.065,0.34831,0.20008,0.91578,18.207
> view matrix models
> #3,0.6207,-0.78132,-0.065376,250.35,0.70244,0.59119,-0.39633,55.576,0.34831,0.20008,0.91578,18.561
> view matrix models
> #3,0.6207,-0.78132,-0.065376,246.54,0.70244,0.59119,-0.39633,41.499,0.34831,0.20008,0.91578,-9.4531
> undo
> save /Users/amritaramesh/Desktop/41_3D/2A1.4_nanobody_.cxs
> color #1 #b2b2b280 models
> color #1 #b2b2b2f2 models
> color #1 #9ec7eaf2 models
> color #1 #9ec7ea7b models
> color #1 #9ec7ea72 models
> view matrix models
> #3,0.6207,-0.78132,-0.065376,250.3,0.70244,0.59119,-0.39633,55.611,0.34831,0.20008,0.91578,18.516
> undo
[Repeated 1 time(s)]
> redo
> ui mousemode right select
> save /Users/amritaramesh/Desktop/41_3D/2A1.4_nanobody_.cxs
> color #2 silver
> select clear
> color #3/K khaki
> color #4/K khaki
> color #4/H #9EC7EA
> color #3/H #9EC7EA
> color #1 #9ec7ea73 models
> color #3 #8397eeff
> color #3 #4780eeff
> color #3 #4082eeff
> color #3/L #9EC7EA
> color #4/L #9EC7EA
> color #4/H #4082EE
> color #3/H #4082EE
> color #3/K khaki
> save /Users/amritaramesh/Desktop/41_3D/2A1.4_nanobody_.cxs
——— End of log from Fri Jan 26 20:18:41 2024 ———
opened ChimeraX session
> ui mousemode right select
Drag select of 28 atoms, 29 bonds
> delete atoms sel
> delete bonds sel
> select clear
> show cartoons
> hide #!3 models
> hide #2 models
> select add #4
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #4 inMap #1
Fit molecule 7pij.pdb (#4) to map run_it200_class006.mrc (#1) using 4191 atoms
average map value = 0.08187, steps = 44
shifted from previous position = 0.0381
rotated from previous position = 0.102 degrees
atoms outside contour = 698, contour level = 0.053206
Position of 7pij.pdb (#4) relative to run_it200_class006.mrc (#1) coordinates:
Matrix rotation and translation
-0.05267744 -0.12897092 0.99024825 149.41613977
-0.99554519 0.08443295 -0.04196259 388.42072771
-0.07819763 -0.98804736 -0.13284409 392.74940200
Axis -0.56664951 0.63993666 -0.51902736
Axis point 403.16971732 0.00000000 300.55993829
Rotation angle (degrees) 123.40436161
Shift along axis -39.94960529
> name frozen 2A1.4_1 sel
Not registering illegal selector name "2A1.4_1"
> name frozen 4_1 sel
Not registering illegal selector name "4_1"
> name frozen "2a14 1" sel
Not registering illegal selector name "2a14 1"
> rename #3 2A1.4_1
> rename #4 2A1.4_2
> select clear
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/48AR_3D/48AR_G115/run_it200_class008*.mrc
Opened run_it200_class008*.mrc as #5, grid size 140,140,140, pixel 3.19, shown
at level 0.00287, step 1, values float32
> volume #5 level 0.04102
> select add #5
2 models selected
> rename #1 2A1.4_G115_class6
> rename #5 2A1.11_G115_class8
> color #5 #7d1518ff models
> color #5 #7d151847 models
> color #5 #7d15184d models
> hide #!1 models
> hide #!4 models
> show #!1 models
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-18.266,0,1,0,9.2292,0,0,1,-10.363
> view matrix models #5,1,0,0,-34.792,0,1,0,-3.1249,0,0,1,1.1906
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.95135,0.14798,-0.27024,-4.5523,-0.17103,0.9832,-0.063725,53.784,0.25627,0.10684,0.96068,-76.566
> view matrix models
> #5,0.95221,0.19862,-0.23206,-23.306,-0.22587,0.9693,-0.097174,76.409,0.20564,0.14495,0.96783,-74.265
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95221,0.19862,-0.23206,-16.15,-0.22587,0.9693,-0.097174,96.851,0.20564,0.14495,0.96783,-76.06
> view matrix models
> #5,0.95221,0.19862,-0.23206,-5.6159,-0.22587,0.9693,-0.097174,94.582,0.20564,0.14495,0.96783,-80.149
> view matrix models
> #5,0.95221,0.19862,-0.23206,-7.2329,-0.22587,0.9693,-0.097174,95.039,0.20564,0.14495,0.96783,-80.167
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.96713,0.23443,-0.098493,-44.242,-0.24466,0.96343,-0.10929,103.16,0.069269,0.1298,0.98912,-48.143
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.96713,0.23443,-0.098493,-43.225,-0.24466,0.96343,-0.10929,103.38,0.069269,0.1298,0.98912,-45.524
> fitmap #5 inMap #1
Fit map 2A1.11_G115_class8 in map 2A1.4_G115_class6 using 9249 points
correlation = 0.9077, correlation about mean = 0.5788, overlap = 71.25
steps = 60, shift = 6.91, angle = 5.88 degrees
Position of 2A1.11_G115_class8 (#5) relative to 2A1.4_G115_class6 (#1)
coordinates:
Matrix rotation and translation
0.96728799 0.22429156 -0.11852101 -36.39378202
-0.24507584 0.94687007 -0.20826644 122.42683025
0.06551159 0.23050026 0.97086449 -58.35301076
Axis 0.65649370 -0.27535416 -0.70227923
Axis point 442.25812700 178.10786203 0.00000000
Rotation angle (degrees) 19.52233821
Shift along axis -16.62291831
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/7pij_Fab-
> nanobody.pdb
7pij_Fab-nanobody.pdb title:
Structure of staphylococcus capitis divalent metal ion transporter (DMT) by
nabfab-fiducial assisted cryo-em [more info...]
Chain information for 7pij_Fab-nanobody.pdb #6
---
Chain | Description
B | divalent metal cation transporter MNTH
H | nabfab HC
K | ANTI-fab nanobody
L | nabfab LC
N | DMTNB16_4
> rename #6 2A1.11_1
> delete #6/B
> delete #6/N
> select add #6
4191 atoms, 4287 bonds, 558 residues, 3 models selected
> select subtract #5
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> hide #!1 models
> view matrix models #6,1,0,0,52.31,0,1,0,-1.1691,0,0,1,12.801
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.18266,-0.98126,0.061342,410.1,0.88569,0.19131,0.42302,-47.664,-0.42683,-0.022938,0.90404,110.42
> view matrix models
> #6,-0.21018,-0.97697,0.036817,486.71,-0.64956,0.1114,-0.7521,404.32,0.73068,-0.18199,-0.65802,115.73
> view matrix models
> #6,-0.23977,-0.72443,0.6463,363.76,-0.68674,0.59712,0.41454,164.78,-0.68622,-0.34445,-0.64067,417.24
> view matrix models
> #6,0.44881,-0.55944,0.69685,191.59,-0.83706,0.0098583,0.54702,302.92,-0.3129,-0.82881,-0.46386,428.57
> view matrix models
> #6,0.41307,-0.55113,0.725,193.15,-0.88801,-0.067164,0.45489,340.34,-0.20201,-0.83171,-0.51715,414.66
> view matrix models
> #6,0.3812,-0.25893,0.88749,116.75,-0.91468,0.033854,0.40275,330.14,-0.13433,-0.9653,-0.22393,394.61
> view matrix models
> #6,0.60949,-0.34471,0.71393,113.02,-0.76605,-0.024133,0.64233,285.08,-0.20419,-0.9384,-0.27878,408.81
> view matrix models
> #6,0.4948,-0.51436,0.70043,172.77,-0.67635,0.27815,0.68204,198.46,-0.54564,-0.81121,-0.21026,437.97
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.4948,-0.51436,0.70043,173.98,-0.67635,0.27815,0.68204,202.09,-0.54564,-0.81121,-0.21026,449.08
> view matrix models
> #6,0.4948,-0.51436,0.70043,163.69,-0.67635,0.27815,0.68204,189.92,-0.54564,-0.81121,-0.21026,455.14
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.12404,-0.39074,0.91211,181.69,-0.90458,0.33329,0.2658,272.27,-0.40786,-0.85804,-0.31211,451.47
> view matrix models
> #6,0.28149,-0.30018,0.9114,132.5,-0.84231,0.37768,0.38454,236.44,-0.45965,-0.87593,-0.14653,444.9
> view matrix models
> #6,0.24794,-0.1437,0.95806,99.643,-0.86919,0.40374,0.2855,248.05,-0.42783,-0.90352,-0.024797,429.9
> view matrix models
> #6,0.15504,-0.31487,0.93639,156.59,-0.89577,0.35491,0.26766,265.74,-0.41661,-0.88028,-0.22703,447.5
> view matrix models
> #6,-0.16871,-0.38463,0.90752,236.48,-0.95321,0.298,-0.050908,327.75,-0.25086,-0.87365,-0.41691,437.83
> view matrix models
> #6,-0.074226,-0.34111,0.93709,205.62,-0.99576,0.07654,-0.051013,383.28,-0.054324,-0.9369,-0.34534,405.35
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.074226,-0.34111,0.93709,202.59,-0.99576,0.07654,-0.051013,388.67,-0.054324,-0.9369,-0.34534,402.11
> view matrix models
> #6,-0.074226,-0.34111,0.93709,204.85,-0.99576,0.07654,-0.051013,389.05,-0.054324,-0.9369,-0.34534,403.35
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.069576,-0.13081,0.98896,152.58,-0.99111,0.12178,-0.05362,378.79,-0.11342,-0.9839,-0.13812,399.31
> view matrix models
> #6,-0.065836,-0.06832,0.99549,137.68,-0.9893,0.13463,-0.056187,376.01,-0.13019,-0.98854,-0.076452,395.95
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.065836,-0.06832,0.99549,139.68,-0.9893,0.13463,-0.056187,376.66,-0.13019,-0.98854,-0.076452,391.92
> fitmap #6 inMap #5
Fit molecule 2A1.11_1 (#6) to map 2A1.11_G115_class8 (#5) using 4191 atoms
average map value = 0.08724, steps = 52
shifted from previous position = 3.59
rotated from previous position = 4.63 degrees
atoms outside contour = 173, contour level = 0.041018
Position of 2A1.11_1 (#6) relative to 2A1.11_G115_class8 (#5) coordinates:
Matrix rotation and translation
0.18396642 -0.18238705 0.96586299 139.68312442
-0.96997818 -0.19269312 0.14836337 400.16393079
0.15905560 -0.96415991 -0.21236052 353.78881475
Axis -0.70236595 0.50935927 -0.49722752
Axis point 0.00000000 362.36248139 -25.14882868
Rotation angle (degrees) 127.62881998
Shift along axis -70.19499965
> rename #2 BTN2A1_2A1.4
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/7pij_Fab-
> nanobody.pdb
7pij_Fab-nanobody.pdb title:
Structure of staphylococcus capitis divalent metal ion transporter (DMT) by
nabfab-fiducial assisted cryo-em [more info...]
Chain information for 7pij_Fab-nanobody.pdb #7
---
Chain | Description
B | divalent metal cation transporter MNTH
H | nabfab HC
K | ANTI-fab nanobody
L | nabfab LC
N | DMTNB16_4
> rename #7 2A1.11_2
> delete #7/B
> delete #7/N
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> select subtract #6
Nothing selected
> select add #7
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> view matrix models #7,1,0,0,80.171,0,1,0,34.807,0,0,1,75.322
> view matrix models #7,1,0,0,49.649,0,1,0,24.345,0,0,1,75.513
> view matrix models #7,1,0,0,30.802,0,1,0,30.358,0,0,1,71.012
> view matrix models #7,1,0,0,12.124,0,1,0,42.864,0,0,1,109.91
> view matrix models #7,1,0,0,20.605,0,1,0,49.969,0,0,1,113.61
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99332,0.11432,-0.015764,-0.6901,-0.098273,0.76635,-0.63486,196.23,-0.060496,0.63217,0.77246,17.471
> view matrix models
> #7,0.97022,-0.18702,-0.15394,85.127,-0.051592,0.46138,-0.8857,283.35,0.23667,0.86727,0.43799,-48.408
> view matrix models
> #7,0.54359,-0.76136,0.35333,227.13,0.82886,0.4206,-0.36889,61.895,0.13225,0.49339,0.85969,-0.028417
> view matrix models
> #7,0.32114,-0.86991,0.37434,290.02,0.94694,0.28957,-0.13945,39.527,0.012913,0.39926,0.91675,35.807
> view matrix models
> #7,0.48299,-0.7958,0.36527,244.55,0.86973,0.3877,-0.30537,53.425,0.10139,0.46518,0.87939,9.4634
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.48299,-0.7958,0.36527,237.74,0.86973,0.3877,-0.30537,52.893,0.10139,0.46518,0.87939,5.0258
> view matrix models
> #7,0.48299,-0.7958,0.36527,231.57,0.86973,0.3877,-0.30537,52.653,0.10139,0.46518,0.87939,20.185
> view matrix models
> #7,0.48299,-0.7958,0.36527,228.57,0.86973,0.3877,-0.30537,50.432,0.10139,0.46518,0.87939,15.697
> view matrix models
> #7,0.48299,-0.7958,0.36527,227.86,0.86973,0.3877,-0.30537,50.228,0.10139,0.46518,0.87939,16.357
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.42886,-0.89522,-0.12109,318.86,0.81644,0.44146,-0.3722,56.99,0.38666,0.060762,0.92022,43.877
> view matrix models
> #7,0.37979,-0.91963,-0.10017,330.84,0.86025,0.39092,-0.32734,54.023,0.34019,0.038152,0.93958,55.171
> view matrix models
> #7,0.21657,-0.90487,0.36648,301.63,0.76501,-0.075921,-0.63953,210.24,0.60652,0.41886,0.67579,-44.684
> view matrix models
> #7,0.31836,-0.94734,0.034585,331.97,0.8509,0.26948,-0.45094,96.913,0.41787,0.17299,0.89188,17.376
> view matrix models
> #7,0.39051,-0.92058,0.0060118,316.04,0.79708,0.33484,-0.50254,99.428,0.46061,0.20104,0.86453,6.5996
> view matrix models
> #7,0.3483,-0.93726,0.01485,326.54,0.82599,0.29938,-0.47761,98.492,0.4432,0.17862,0.87845,13.007
> view matrix models
> #7,0.43004,-0.90246,0.025306,302.3,0.78688,0.36093,-0.50055,95.533,0.44259,0.23517,0.86534,2.6087
> view matrix models
> #7,0.65912,-0.75174,-0.021169,232.22,0.58312,0.52865,-0.61685,112.47,0.4749,0.39424,0.7868,-28
> view matrix models
> #7,0.33305,-0.94222,-0.035969,336.7,0.79265,0.30043,-0.53052,111.06,0.51067,0.14818,0.84691,10.578
> view matrix models
> #7,0.34865,-0.93393,-0.078878,337.21,0.81022,0.34264,-0.47555,91.968,0.47115,0.10189,0.87615,24.419
> view matrix models
> #7,0.35094,-0.93582,-0.032959,331.57,0.77776,0.31091,-0.54628,113.56,0.52146,0.16608,0.83696,5.9129
> view matrix models
> #7,0.38603,-0.91887,0.081612,307.28,0.82036,0.30149,-0.48592,100.13,0.42189,0.25453,0.87018,1.796
> fitmap #7 inMap #5
Fit molecule 2A1.11_2 (#7) to map 2A1.11_G115_class8 (#5) using 4191 atoms
average map value = 0.1086, steps = 48
shifted from previous position = 3.15
rotated from previous position = 8.16 degrees
atoms outside contour = 53, contour level = 0.041018
Position of 2A1.11_2 (#7) relative to 2A1.11_G115_class8 (#5) coordinates:
Matrix rotation and translation
0.32733098 -0.90965002 0.25571720 312.02442815
0.93524309 0.27328148 -0.22502801 41.26480533
0.13481396 0.31281638 0.94019738 27.64818728
Axis 0.27932809 0.06279079 0.95814046
Axis point 128.59281323 212.23017891 0.00000000
Rotation angle (degrees) 74.31163668
Shift along axis 116.23908412
> color #7/K khaki
> color #6/K khaki
> color #6/K light pink
> color #7/K light pink
> color #2/K light blue
> show #2 models
> hide #2 models
> color #3/K light blue
> color #4/K light blue
> color #6/H #FD1518
> color #7/H #FD1518
> color #6 #ff3c36ff
> color #5 #7d1518ff models
> color #5 #7d15184a models
> color #5 #7d15184f models
> color #5 #7d15184c models
> color #5 #7d15184d models
> color #6 #fd1518ff
> color #6 #7d1518ff
> color #6 #913f47ff
> color #6 #91585fff
> color #7/L #91585F
> color #6/L #91585F
> color #6/H #7D1518
> color #7/H #7D1518
> hide #!5 models
> color #6 #ffacb5ff
> undo
[Repeated 6 time(s)]
> color #6/H #7D1518
> color #7/H #7D1518
> color #7 #915565ff
> color #7 #915566ff
> color #7 #915a69ff
> color #7 #914d5eff
> color #7/H #7D1518
> color #6/H #7D1518
> color #7/L #914D5E
> color 67/L #914D5E
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #7/L #914D5E
> color #6/L #914D5E
> color #6/K #FFACB5
> color #7/K #FFACB5
> open /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/8dfw-
> BTN2A1+G115.cif
Summary of feedback from opening
/Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/8dfw-
BTN2A1+G115.cif
---
notes | Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
Fetching CCD BMA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif
8dfw-BTN2A1+G115.cif title:
Crystal Structure of Human BTN2A1 in Complex With Vgamma9-Vdelta2 T Cell
Receptor [more info...]
Chain information for 8dfw-BTN2A1+G115.cif #8
---
Chain | Description | UniProt
A B | Butyrophilin subfamily 2 member A1 | BT2A1_HUMAN 1-217
D | T cell receptor delta variable chain |
G | T cell receptor gamma variable chain |
Non-standard residues in 8dfw-BTN2A1+G115.cif #8
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> color #8 silver
> view matrix models
> #7,0.41002,-0.90501,0.11329,297.62,0.75592,0.26768,-0.59744,130.59,0.51036,0.3306,0.79387,-23.38
> undo
> ui mousemode right rotate
> ui mousemode right select
> select subtract #7
Nothing selected
> select add #8
7171 atoms, 7174 bonds, 1046 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,182.2,0,1,0,50.408,0,0,1,308.98
> show #!5 models
> view matrix models #8,1,0,0,181.05,0,1,0,153.04,0,0,1,224.01
> view matrix models #8,1,0,0,263.57,0,1,0,178.25,0,0,1,275.65
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.013837,0.75199,-0.65903,246.11,0.95941,-0.17569,-0.22062,205.31,-0.28169,-0.63533,-0.71903,289.98
> view matrix models
> #8,-0.54467,0.43217,-0.71872,263.12,0.59593,0.80244,0.030897,177.93,0.59009,-0.41148,-0.69461,271.87
> view matrix models
> #8,-0.64303,0.30881,-0.70082,268.64,0.54366,0.82859,-0.13372,176.64,0.53939,-0.46699,-0.70069,274.35
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.64303,0.30881,-0.70082,250.66,0.54366,0.82859,-0.13372,189.55,0.53939,-0.46699,-0.70069,197.7
> view matrix models
> #8,-0.64303,0.30881,-0.70082,253.84,0.54366,0.82859,-0.13372,188.05,0.53939,-0.46699,-0.70069,202.79
> view matrix models
> #8,-0.64303,0.30881,-0.70082,250.24,0.54366,0.82859,-0.13372,191.65,0.53939,-0.46699,-0.70069,201.03
> view matrix models
> #8,-0.64303,0.30881,-0.70082,250.73,0.54366,0.82859,-0.13372,190.93,0.53939,-0.46699,-0.70069,200.79
> view matrix models
> #8,-0.64303,0.30881,-0.70082,249.75,0.54366,0.82859,-0.13372,188.8,0.53939,-0.46699,-0.70069,205.35
> view matrix models
> #8,-0.64303,0.30881,-0.70082,245.93,0.54366,0.82859,-0.13372,181.79,0.53939,-0.46699,-0.70069,199.63
> view matrix models
> #8,-0.64303,0.30881,-0.70082,244.2,0.54366,0.82859,-0.13372,182.62,0.53939,-0.46699,-0.70069,200.27
> view matrix models
> #8,-0.64303,0.30881,-0.70082,251.32,0.54366,0.82859,-0.13372,186.53,0.53939,-0.46699,-0.70069,199.08
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.43399,0.53582,-0.72425,240.88,0.59075,0.77621,0.22027,189.97,0.6802,-0.33225,-0.6534,193.06
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.43399,0.53582,-0.72425,241.44,0.59075,0.77621,0.22027,201.77,0.6802,-0.33225,-0.6534,201.6
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.48376,0.4995,-0.71866,243.32,0.49179,0.83438,0.24888,201.16,0.72396,-0.23303,-0.64929,197.71
> delete #8/D
> delete #8/G
> ui mousemode right select
> select clear
Drag select of 28 atoms, 29 bonds
> delete atoms sel
> delete bonds sel
> select add #8
3641 atoms, 3628 bonds, 545 residues, 1 model selected
> fitmap #8 inMap #5
Fit molecule 8dfw-BTN2A1+G115.cif (#8) to map 2A1.11_G115_class8 (#5) using
3641 atoms
average map value = 0.106, steps = 76
shifted from previous position = 7.71
rotated from previous position = 27.3 degrees
atoms outside contour = 71, contour level = 0.041018
Position of 8dfw-BTN2A1+G115.cif (#8) relative to 2A1.11_G115_class8 (#5)
coordinates:
Matrix rotation and translation
-0.78345267 -0.09791028 -0.61369006 283.65260191
0.21278753 0.88555435 -0.41293456 191.07901295
0.58388645 -0.45410027 -0.67295583 197.23545104
Axis -0.03325425 -0.96741931 0.25098611
Axis point 96.69215453 0.00000000 173.36450916
Rotation angle (degrees) 141.76019459
Shift along axis -144.78282434
Drag select of 5 2A1.11_G115_class8 , 6 residues
> select clear
> show #2 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!4 models
> hide #!5 models
> select clear
> hide #!6 models
> hide #!7 models
> hide #8 models
> hide #!1 models
> hide #2 models
> hide #!4 models
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
——— End of log from Sat Jan 27 12:39:58 2024 ———
opened ChimeraX session
> show #!5 models
> show #!1 models
> select add #1
2 models selected
> fitmap #1 inMap #5
Fit map 2A1.4_G115_class6 in map 2A1.11_G115_class8 using 7377 points
correlation = 0.9413, correlation about mean = 0.5966, overlap = 66.9
steps = 48, shift = 0.581, angle = 0.232 degrees
Position of 2A1.4_G115_class6 (#1) relative to 2A1.11_G115_class8 (#5)
coordinates:
Matrix rotation and translation
0.96724291 -0.24619695 0.06187253 70.53107633
0.22598258 0.94611584 0.23194113 -95.11276506
-0.11564178 -0.21036130 0.97076006 77.69493323
Axis -0.65927502 0.26459441 0.70380839
Axis point 444.36829226 181.87949263 0.00000000
Rotation angle (degrees) 19.59966597
Shift along axis -16.98333627
> hide #!5 models
> show #2 models
> select subtract #1
Nothing selected
> select add #2
3641 atoms, 3628 bonds, 545 residues, 1 model selected
> fitmap #2 inMap #1
Fit molecule BTN2A1_2A1.4 (#2) to map 2A1.4_G115_class6 (#1) using 3641 atoms
average map value = 0.1009, steps = 48
shifted from previous position = 0.452
rotated from previous position = 0.248 degrees
atoms outside contour = 613, contour level = 0.053206
Position of BTN2A1_2A1.4 (#2) relative to 2A1.4_G115_class6 (#1) coordinates:
Matrix rotation and translation
0.25578585 -0.71125829 -0.65474060 237.95674001
-0.02283521 -0.68152733 0.73143630 246.77354009
-0.96646374 -0.17213992 -0.19056677 247.67778486
Axis -0.76708032 0.26463367 0.58442862
Axis point 0.00000000 213.60431506 163.63881633
Rotation angle (degrees) 143.91597467
Shift along axis 27.52264034
> show #!4 models
> hide #2 models
> fitmap #4 inMap #1
Fit molecule 2A1.4_2 (#4) to map 2A1.4_G115_class6 (#1) using 4191 atoms
average map value = 0.08187, steps = 48
shifted from previous position = 0.806
rotated from previous position = 0.293 degrees
atoms outside contour = 694, contour level = 0.053206
Position of 2A1.4_2 (#4) relative to 2A1.4_G115_class6 (#1) coordinates:
Matrix rotation and translation
-0.05309596 -0.12749872 0.99041653 149.19268270
-0.99550496 0.08465269 -0.04247120 388.46362857
-0.07842639 -0.98821961 -0.13142032 392.63255275
Axis -0.56617432 0.63986511 -0.51963380
Axis point 403.05192728 0.00000000 300.74917100
Rotation angle (degrees) 123.36233409
Shift along axis -39.92988730
> hide #!4 models
> show #!3 models
> volume #1 level 0.09781
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/2A1.9/20240127_dimer_Cryo/run_it200_class001****.mrc
Opened run_it200_class001****.mrc as #9, grid size 288,288,288, pixel 1.07,
shown at level 0.00633, step 2, values float32
> rename #9 2A1.9_G115_66_class1
> color #9 #7d1518ff models
> color #9 #f89a1fff models
> color #9 #f89a1f4d models
> select subtract #2
Nothing selected
> select add #9
2 models selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,28.53,0,1,0,31.167,0,0,1,52.589
> view matrix models #9,1,0,0,80.952,0,1,0,27.47,0,0,1,43.283
> show #!5 models
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.29551,0.7156,-0.63292,176.81,-0.94104,0.33225,-0.063727,254.4,0.16468,0.61444,0.77159,-26.734
> view matrix models
> #9,0.35143,0.89207,0.28409,0.8897,-0.86677,0.42471,-0.26139,262.96,-0.35384,-0.15438,0.92248,123.82
> view matrix models
> #9,0.29542,0.93152,0.21214,14.3,-0.94683,0.3151,-0.065068,257.73,-0.12746,-0.18164,0.97507,89.05
> view matrix models
> #9,0.027443,0.99867,0.043564,67.43,-0.99753,0.024539,0.065849,283.61,0.064692,-0.045263,0.99688,41.325
> view matrix models
> #9,0.22843,0.97332,-0.021702,54.336,-0.96461,0.22929,0.1302,241.1,0.1317,-0.0088074,0.99125,28.282
> view matrix models
> #9,0.28727,0.93554,0.20553,15.879,-0.95612,0.26716,0.12028,236.35,0.057618,-0.23106,0.97123,71.702
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.28727,0.93554,0.20553,14.672,-0.95612,0.26716,0.12028,275.64,0.057618,-0.23106,0.97123,42.577
> view matrix models
> #9,0.28727,0.93554,0.20553,5.4049,-0.95612,0.26716,0.12028,288.75,0.057618,-0.23106,0.97123,61.777
> view matrix models
> #9,0.28727,0.93554,0.20553,9.0782,-0.95612,0.26716,0.12028,290.41,0.057618,-0.23106,0.97123,63.612
> view matrix models
> #9,0.28727,0.93554,0.20553,13.643,-0.95612,0.26716,0.12028,294.76,0.057618,-0.23106,0.97123,61.685
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.10139,0.98834,0.11363,72.777,-0.94501,-0.059982,-0.32149,407.53,-0.31093,-0.13997,0.94007,103.34
> view matrix models
> #9,0.12691,0.99123,0.03689,53.982,-0.99132,0.12804,-0.029794,342.1,-0.034256,-0.032789,0.99888,42.498
> view matrix models
> #9,0.28833,0.94349,0.16338,19.048,-0.95613,0.29292,-0.0042069,310.84,-0.051826,-0.155,0.98655,63.487
> view matrix models
> #9,-0.010554,0.99801,0.062146,67.431,-0.92646,0.013625,-0.37615,403.6,-0.37624,-0.061546,0.92447,103.79
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.010554,0.99801,0.062146,69.179,-0.92646,0.013625,-0.37615,437.15,-0.37624,-0.061546,0.92447,108.31
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.1979,0.97542,0.096917,38.966,-0.96871,0.20973,-0.13274,377.67,-0.1498,-0.067615,0.9864,69.157
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.1979,0.97542,0.096917,36.357,-0.96871,0.20973,-0.13274,360.24,-0.1498,-0.067615,0.9864,64.455
> view matrix models
> #9,0.1979,0.97542,0.096917,37.699,-0.96871,0.20973,-0.13274,359.7,-0.1498,-0.067615,0.9864,63.262
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.17226,0.9822,0.074892,43.662,-0.96913,0.1826,-0.16566,368.64,-0.17639,-0.044043,0.98333,64.072
> ui mousemode right select
> hide #!3 models
> hide #!1 models
> select add #5
4 models selected
> select subtract #9
2 models selected
> fitmap #5 inMap #9
Fit map 2A1.11_G115_class8 in map 2A1.9_G115_66_class1 using 9249 points
correlation = 0.9806, correlation about mean = 0.8387, overlap = 11.82
steps = 68, shift = 4.21, angle = 3.75 degrees
Position of 2A1.11_G115_class8 (#5) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.34899711 -0.93709908 -0.00680632 264.96341781
0.90954926 0.34046796 -0.23833110 -104.78533592
0.22565719 0.07698619 0.97116011 -96.44897170
Axis 0.16703400 -0.12314361 0.97823070
Axis point 219.50171646 136.88925195 0.00000000
Rotation angle (degrees) 70.71225047
Shift along axis -37.18780199
> select subtract #5
Nothing selected
> select add #1
2 models selected
> fitmap #5 inMap #9
Fit map 2A1.11_G115_class8 in map 2A1.9_G115_66_class1 using 9249 points
correlation = 0.9806, correlation about mean = 0.8387, overlap = 11.82
steps = 36, shift = 0.011, angle = 0.00943 degrees
Position of 2A1.11_G115_class8 (#5) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.34898544 -0.93710270 -0.00690607 264.98481586
0.90951566 0.34046911 -0.23845765 -104.74392482
0.22581061 0.07693707 0.97112834 -96.47602146
Axis 0.16707370 -0.12327675 0.97820715
Axis point 219.49075336 136.91823786 0.00000000
Rotation angle (degrees) 70.71353415
Shift along axis -37.18904762
> hide #!5 models
> show #!1 models
> fitmap #1 inMap #9
Fit map 2A1.4_G115_class6 in map 2A1.9_G115_66_class1 using 2997 points
correlation = 0.9511, correlation about mean = 0.2655, overlap = 6.236
steps = 68, shift = 3.23, angle = 2.96 degrees
Position of 2A1.4_G115_class6 (#1) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.13521676 -0.96964067 -0.20374836 377.27168752
0.98470848 0.15430856 -0.08085840 -94.75703619
0.10984371 -0.18969933 0.97567850 -8.55864109
Axis -0.05490531 -0.15819297 0.98588051
Axis point 244.61031300 170.12406382 0.00000000
Rotation angle (degrees) 82.38002766
Shift along axis -14.16211979
> select subtract #1
Nothing selected
> rename #8 BTN2A1_2A1.11
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/7pij_Fab-
> nanobody.pdb
7pij_Fab-nanobody.pdb title:
Structure of staphylococcus capitis divalent metal ion transporter (DMT) by
nabfab-fiducial assisted cryo-em [more info...]
Chain information for 7pij_Fab-nanobody.pdb #10
---
Chain | Description
B | divalent metal cation transporter MNTH
H | nabfab HC
K | ANTI-fab nanobody
L | nabfab LC
N | DMTNB16_4
> delete #10/B
> delete #10/N
> select add #10
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide sel surfaces
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,50.739,0,1,0,-16.11,0,0,1,24.33
> view matrix models #10,1,0,0,54.38,0,1,0,13.856,0,0,1,29.719
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.1264,0.27795,0.95224,92.208,-0.9737,0.14867,-0.17264,402.06,-0.18955,-0.94902,0.25185,360.39
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.1264,0.27795,0.95224,90.123,-0.9737,0.14867,-0.17264,386.23,-0.18955,-0.94902,0.25185,353.64
> view matrix models
> #10,-0.1264,0.27795,0.95224,87.567,-0.9737,0.14867,-0.17264,385.05,-0.18955,-0.94902,0.25185,354.37
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.031164,-0.088628,0.99558,142.73,-0.99896,0.035872,-0.028076,396.34,-0.033225,-0.99542,-0.089654,376.38
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.031164,-0.088628,0.99558,139.16,-0.99896,0.035872,-0.028076,394.38,-0.033225,-0.99542,-0.089654,378.21
> view matrix models
> #10,-0.031164,-0.088628,0.99558,136.14,-0.99896,0.035872,-0.028076,396.88,-0.033225,-0.99542,-0.089654,377.13
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.055809,-0.10039,0.99338,143.6,-0.99506,0.087451,-0.047065,387.41,-0.082147,-0.9911,-0.10477,387.33
> view matrix models
> #10,-0.073887,-0.10805,0.9914,148.92,-0.99038,0.1246,-0.060231,380.17,-0.11702,-0.98631,-0.11622,394.32
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.073887,-0.10805,0.9914,150,-0.99038,0.1246,-0.060231,377.27,-0.11702,-0.98631,-0.11622,394.95
> hide #!1 models
> fitmap #10 inMap #9
Fit molecule 7pij_Fab-nanobody.pdb (#10) to map 2A1.9_G115_66_class1 (#9)
using 4191 atoms
average map value = 0.01388, steps = 68
shifted from previous position = 2.77
rotated from previous position = 7.42 degrees
atoms outside contour = 194, contour level = 0.0063268
Position of 7pij_Fab-nanobody.pdb (#10) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.96801783 0.13838173 0.20926532 -67.53318703
-0.21520619 0.02929166 0.97612924 71.32401292
0.12894873 -0.98994570 0.05813545 303.82724756
Axis -0.98341544 0.04017374 -0.17686194
Axis point 0.00000000 194.53858245 121.02970549
Rotation angle (degrees) 88.41141586
Shift along axis 15.54305522
> rename #10 2A1.9_1
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/7pij_Fab-
> nanobody.pdb
7pij_Fab-nanobody.pdb title:
Structure of staphylococcus capitis divalent metal ion transporter (DMT) by
nabfab-fiducial assisted cryo-em [more info...]
Chain information for 7pij_Fab-nanobody.pdb #11
---
Chain | Description
B | divalent metal cation transporter MNTH
H | nabfab HC
K | ANTI-fab nanobody
L | nabfab LC
N | DMTNB16_4
> rename #11 2A1.9_2
> delete#11/B
Unknown command: delete#11/B
> delete #11/B
> delete #11/N
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> select add #11
8382 atoms, 8574 bonds, 1116 residues, 2 models selected
> select subtract #10
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> view matrix models #11,1,0,0,7.7312,0,1,0,59.828,0,0,1,8.8874
> view matrix models #11,1,0,0,-12.368,0,1,0,49.06,0,0,1,107.2
> view matrix models #11,1,0,0,5.4653,0,1,0,49.348,0,0,1,101.51
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.080057,-0.63655,0.76707,222.65,0.87947,0.40732,0.24623,-20.638,-0.46918,0.6549,0.59244,100.03
> view matrix models
> #11,0.069963,-0.64667,0.75955,227.65,0.88284,0.39464,0.25467,-19.593,-0.46444,0.65274,0.59851,98.852
> view matrix models
> #11,0.43541,-0.76308,0.47763,217.7,0.88786,0.45167,-0.087764,9.0763,-0.14876,0.46228,0.87417,46.078
> view matrix models
> #11,0.21545,-0.89087,0.39991,296.3,0.97572,0.21288,-0.051451,39.123,-0.039296,0.40129,0.91511,33.372
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.21545,-0.89087,0.39991,282.96,0.97572,0.21288,-0.051451,35.198,-0.039296,0.40129,0.91511,36.035
> view matrix models
> #11,0.21545,-0.89087,0.39991,282.83,0.97572,0.21288,-0.051451,38.818,-0.039296,0.40129,0.91511,37.633
> view matrix models
> #11,0.21545,-0.89087,0.39991,283.45,0.97572,0.21288,-0.051451,37.444,-0.039296,0.40129,0.91511,36.839
> view matrix models
> #11,0.21545,-0.89087,0.39991,287.07,0.97572,0.21288,-0.051451,36.407,-0.039296,0.40129,0.91511,47.666
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.61894,-0.71597,0.32294,182.45,0.75705,0.43428,-0.48813,83.822,0.20924,0.54661,0.81082,-17.878
> view matrix models
> #11,0.31569,-0.8415,0.43842,252.77,0.91536,0.14839,-0.37429,101.12,0.24991,0.51947,0.81713,-20.551
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.31569,-0.8415,0.43842,254.16,0.91536,0.14839,-0.37429,101.06,0.24991,0.51947,0.81713,-19.941
> view matrix models
> #11,0.31569,-0.8415,0.43842,252.28,0.91536,0.14839,-0.37429,95.212,0.24991,0.51947,0.81713,-22.085
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.49766,-0.8543,0.15004,255.73,0.82501,0.41282,-0.38593,57.133,0.26776,0.31585,0.91024,6.7707
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.49766,-0.8543,0.15004,256.99,0.82501,0.41282,-0.38593,60.045,0.26776,0.31585,0.91024,4.1222
> fitmap #11 inMap #9
Fit molecule 2A1.9_2 (#11) to map 2A1.9_G115_66_class1 (#9) using 4191 atoms
average map value = 0.01348, steps = 60
shifted from previous position = 3.06
rotated from previous position = 5.41 degrees
atoms outside contour = 231, contour level = 0.0063268
Position of 2A1.9_2 (#11) relative to 2A1.9_G115_66_class1 (#9) coordinates:
Matrix rotation and translation
-0.76173404 -0.56576201 0.31571284 328.60416103
0.59763057 -0.80175492 0.00517267 171.89129408
0.25019782 0.19261985 0.94884069 -5.86419145
Axis 0.15882440 0.05551102 0.98574507
Axis point 136.82102818 139.06097292 0.00000000
Rotation angle (degrees) 143.83531021
Shift along axis 55.95162184
> color #10 #f89a1fff
> color #10 #fbe388ff
> color #10 #fbde8dff
> color #10 #fbc878ff
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
——— End of log from Sat Jan 27 12:55:13 2024 ———
opened ChimeraX session
> color #10 #f7bd75ff
> color #11 #f7bd75ff
> color #11/H F89A1F
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #11/H #F89A1F
> color #10/H #F89A1F
> open /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/8dfw-
> BTN2A1+G115.cif
8dfw-BTN2A1+G115.cif title:
Crystal Structure of Human BTN2A1 in Complex With Vgamma9-Vdelta2 T Cell
Receptor [more info...]
Chain information for 8dfw-BTN2A1+G115.cif #12
---
Chain | Description | UniProt
A B | Butyrophilin subfamily 2 member A1 | BT2A1_HUMAN 1-217
D | T cell receptor delta variable chain |
G | T cell receptor gamma variable chain |
Non-standard residues in 8dfw-BTN2A1+G115.cif #12
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> rename #12 BTN2A1_2A1.9
> delete #12/D
> delete #12/G
> select add #12
7860 atoms, 7944 bonds, 1105 residues, 2 models selected
> select subtract #11
3669 atoms, 3657 bonds, 547 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,18.729,0,1,0,231.74,0,0,1,35.261
> view matrix models #12,1,0,0,182.53,0,1,0,337.09,0,0,1,96.583
> view matrix models #12,1,0,0,278.02,0,1,0,208,0,0,1,274.08
> view matrix models #12,1,0,0,270.27,0,1,0,199.35,0,0,1,263.4
> view matrix models #12,1,0,0,261.92,0,1,0,217.39,0,0,1,274.51
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.19962,-0.67625,-0.70911,309.89,-0.95556,-0.025873,0.29367,277.05,-0.21694,0.73622,-0.64103,243.93
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.19962,-0.67625,-0.70911,251.31,-0.95556,-0.025873,0.29367,252.42,-0.21694,0.73622,-0.64103,193.8
> view matrix models
> #12,-0.19962,-0.67625,-0.70911,250.51,-0.95556,-0.025873,0.29367,235.22,-0.21694,0.73622,-0.64103,201.93
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.62977,-0.66119,-0.40769,266,-0.72501,0.31194,0.61405,222.57,-0.27883,0.68229,-0.67582,204.86
> view matrix models
> #12,0.046067,-0.18849,-0.98099,227.39,-0.80759,-0.58502,0.074481,243.23,-0.58794,0.78881,-0.17917,216.36
> view matrix models
> #12,-0.46889,-0.60483,-0.64368,256.95,-0.75287,-0.10739,0.64935,235.3,-0.46187,0.78908,-0.405,210.47
> view matrix models
> #12,0.2918,-0.90377,-0.31314,245.6,-0.52773,-0.42517,0.73535,238.12,-0.79772,-0.04932,-0.60101,241.62
> view matrix models
> #12,0.22848,-0.87227,-0.43237,245.43,-0.21962,-0.47885,0.84998,231.69,-0.94845,-0.099251,-0.30098,250.3
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.22848,-0.87227,-0.43237,256.75,-0.21962,-0.47885,0.84998,243.03,-0.94845,-0.099251,-0.30098,241.47
> view matrix models
> #12,0.22848,-0.87227,-0.43237,247.22,-0.21962,-0.47885,0.84998,244.34,-0.94845,-0.099251,-0.30098,240.02
> view matrix models
> #12,0.22848,-0.87227,-0.43237,251.74,-0.21962,-0.47885,0.84998,248.72,-0.94845,-0.099251,-0.30098,237.45
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.33243,-0.73521,-0.59072,243.49,0.041791,-0.61425,0.78801,244.29,-0.9422,-0.28665,-0.17347,243.6
> view matrix models
> #12,-0.070282,-0.66109,-0.74701,251.76,0.011715,-0.74936,0.66206,247.48,-0.99746,0.03778,0.060411,239.03
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.070282,-0.66109,-0.74701,245.43,0.011715,-0.74936,0.66206,241.5,-0.99746,0.03778,0.060411,248.62
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.079874,-0.7064,-0.70329,247.28,-0.085997,-0.69803,0.71089,243.48,-0.99309,0.11726,-0.004994,245.85
> view matrix models
> #12,-0.07662,-0.63444,-0.76917,244.72,-0.20769,-0.74436,0.63466,247.44,-0.97519,0.20838,-0.074733,242.35
> view matrix models
> #12,0.11206,-0.7046,-0.70071,241.71,-0.26763,-0.70049,0.66158,248.3,-0.95698,0.1134,-0.26707,242.45
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.11206,-0.7046,-0.70071,247.16,-0.26763,-0.70049,0.66158,247.1,-0.95698,0.1134,-0.26707,240.8
> view matrix models
> #12,0.11206,-0.7046,-0.70071,244.72,-0.26763,-0.70049,0.66158,240.61,-0.95698,0.1134,-0.26707,239.3
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.24891,-0.58358,-0.77296,236.97,-0.034309,-0.8029,0.59513,235.73,-0.96792,-0.12162,-0.21987,246.01
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.24891,-0.58358,-0.77296,240.31,-0.034309,-0.8029,0.59513,239.6,-0.96792,-0.12162,-0.21987,244.4
> hide #!10 models
> hide #!11 models
> hide #12 models
> show #12 models
> fitmap #12 inMap #9
Fit molecule BTN2A1_2A1.9 (#12) to map 2A1.9_G115_66_class1 (#9) using 3669
atoms
average map value = 0.01603, steps = 88
shifted from previous position = 5.29
rotated from previous position = 9.57 degrees
atoms outside contour = 73, contour level = 0.0063268
Position of BTN2A1_2A1.9 (#12) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.20946877 0.58314227 -0.78489995 124.18646371
0.25562216 -0.80745050 -0.53167753 162.88707753
-0.94381150 -0.08926798 -0.31819975 214.04728314
Axis 0.77218810 0.27736655 -0.57165840
Axis point 0.00000000 37.84996767 167.93041250
Rotation angle (degrees) 163.35356839
Shift along axis 18.71280894
> ui mousemode right select
> select clear
Drag select of 28 atoms, 29 bonds
> delete atoms sel
> delete bonds sel
> color #12 silver
> color #12 #f89a1fff
> color #12 #f7bd75ff
> color #12 #faf6c0ff
> color #12 #faf9c7ff
> color #12 #fae1c1ff
> color #12 #faebc4ff
> color #12 #fadfb9ff
> color #10/K FADFB9
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #10/K #FADFB9
> color #11/K #FADFB9
> show #!10 models
> show #!11 models
> color #12 silver
> hide #!10 models
> hide #!11 models
> hide #12 models
> show #!5 models
> select add #5
2 models selected
> fitmap #5 inMap #9
Fit map 2A1.11_G115_class8 in map 2A1.9_G115_66_class1 using 9249 points
correlation = 0.9806, correlation about mean = 0.8387, overlap = 11.82
steps = 48, shift = 0.000932, angle = 0.00449 degrees
Position of 2A1.11_G115_class8 (#5) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.34892203 -0.93712626 -0.00691321 265.00729459
0.90954674 0.34041213 -0.23842042 -104.74632767
0.22578338 0.07690224 0.97113743 -96.46434922
Axis 0.16703209 -0.12326357 0.97821591
Axis point 219.49442641 136.91933463 0.00000000
Rotation angle (degrees) 70.71691187
Shift along axis -37.18683335
> hide #!5 models
> select subtract #5
Nothing selected
> show #!1 models
> select add #1
2 models selected
> fitmap #1 inMap #9
Fit map 2A1.4_G115_class6 in map 2A1.9_G115_66_class1 using 2997 points
correlation = 0.9511, correlation about mean = 0.2652, overlap = 6.236
steps = 44, shift = 0.0135, angle = 0.00809 degrees
Position of 2A1.4_G115_class6 (#1) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.13522757 -0.96961620 -0.20385761 377.28532870
0.98469596 0.15434729 -0.08093685 -94.75508876
0.10994255 -0.18979287 0.97564917 -8.54339682
Axis -0.05491300 -0.15829817 0.98586320
Axis point 244.61687731 170.14038694 0.00000000
Rotation angle (degrees) 82.37944319
Shift along axis -14.14093222
> hide #!9 models
> select subtract #1
Nothing selected
> show #2 models
> select add #2
3641 atoms, 3628 bonds, 545 residues, 1 model selected
> fitmap #2 inMap #1
Fit molecule BTN2A1_2A1.4 (#2) to map 2A1.4_G115_class6 (#1) using 3641 atoms
average map value = 0.1009, steps = 48
shifted from previous position = 2.53
rotated from previous position = 2.98 degrees
atoms outside contour = 1943, contour level = 0.097814
Position of BTN2A1_2A1.4 (#2) relative to 2A1.4_G115_class6 (#1) coordinates:
Matrix rotation and translation
0.25598831 -0.71116283 -0.65476516 237.94878907
-0.02289498 -0.68160432 0.73136268 246.77369917
-0.96640872 -0.17222946 -0.19076479 247.67725568
Axis -0.76715868 0.26458846 0.58434622
Axis point 0.00000000 213.58752970 163.62120594
Rotation angle (degrees) 143.91950372
Shift along axis 27.47826330
> select subtract #2
Nothing selected
> show #!3 models
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> select subtract #3
Nothing selected
> show #!4 models
> hide #!3 models
> select add #4
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #4 inMap #1
Fit molecule 2A1.4_2 (#4) to map 2A1.4_G115_class6 (#1) using 4191 atoms
average map value = 0.08187, steps = 56
shifted from previous position = 3.46
rotated from previous position = 2.96 degrees
atoms outside contour = 2930, contour level = 0.097814
Position of 2A1.4_2 (#4) relative to 2A1.4_G115_class6 (#1) coordinates:
Matrix rotation and translation
-0.05291622 -0.12768588 0.99040203 149.19273374
-0.99551151 0.08467501 -0.04227264 388.42393267
-0.07846468 -0.98819353 -0.13159345 392.65695268
Axis -0.56627112 0.63987206 -0.51951975
Axis point 403.07453509 -0.00000000 300.71121274
Rotation angle (degrees) 123.36134179
Shift along axis -39.93495666
> select subtract #4
Nothing selected
> hide #!4 models
> hide #2 models
> hide #!1 models
> show #!5 models
> show #!6 models
> select add #6
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #6 inMap #5
Fit molecule 2A1.11_1 (#6) to map 2A1.11_G115_class8 (#5) using 4191 atoms
average map value = 0.08724, steps = 48
shifted from previous position = 2.57
rotated from previous position = 3.77 degrees
atoms outside contour = 172, contour level = 0.041018
Position of 2A1.11_1 (#6) relative to 2A1.11_G115_class8 (#5) coordinates:
Matrix rotation and translation
0.18393587 -0.18208737 0.96592535 139.61625346
-0.96997890 -0.19267115 0.14838717 400.14979702
0.15908652 -0.96422094 -0.21206005 353.74995761
Axis -0.70231975 0.50930678 -0.49734653
Axis point 0.00000000 362.34648975 -25.19853924
Rotation angle (degrees) 127.61826225
Shift along axis -70.19256455
> select subtract #6
Nothing selected
> show #!7 models
> select add #7
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #7 inMap #5
Fit molecule 2A1.11_2 (#7) to map 2A1.11_G115_class8 (#5) using 4191 atoms
average map value = 0.1086, steps = 72
shifted from previous position = 7.73
rotated from previous position = 3.74 degrees
atoms outside contour = 53, contour level = 0.041018
Position of 2A1.11_2 (#7) relative to 2A1.11_G115_class8 (#5) coordinates:
Matrix rotation and translation
0.32750043 -0.90950752 0.25600693 311.92360186
0.93517510 0.27334437 -0.22523407 41.29344341
0.13487403 0.31317556 0.94006918 27.58861785
Axis 0.27962590 0.06291101 0.95804570
Axis point 128.53318271 212.17893174 0.00000000
Rotation angle (degrees) 74.30853762
Shift along axis 116.25088619
> select subtract #7
Nothing selected
> hide #!7 models
> show #8 models
> select add #8
3641 atoms, 3628 bonds, 545 residues, 1 model selected
> show #!7 models
> fitmap #8 inMap #5
Fit molecule BTN2A1_2A1.11 (#8) to map 2A1.11_G115_class8 (#5) using 3641
atoms
average map value = 0.106, steps = 56
shifted from previous position = 3.58
rotated from previous position = 3.75 degrees
atoms outside contour = 71, contour level = 0.041018
Position of BTN2A1_2A1.11 (#8) relative to 2A1.11_G115_class8 (#5)
coordinates:
Matrix rotation and translation
-0.78357415 -0.09745801 -0.61360695 283.63941942
0.21299629 0.88563265 -0.41265893 191.07324538
0.58364727 -0.45404487 -0.67320065 197.25739163
Axis -0.03344203 -0.96744465 0.25086348
Axis point 96.68010374 0.00000000 173.33422924
Rotation angle (degrees) 141.77352678
Shift along axis -144.85359112
> select subtract #8
Nothing selected
> hide #8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!9 models
> hide #!9 models
> show #8 models
> show #!5 models
> select add #5
2 models selected
> fitmap #8 inMap #5
Fit molecule BTN2A1_2A1.11 (#8) to map 2A1.11_G115_class8 (#5) using 3641
atoms
average map value = 0.106, steps = 48
shifted from previous position = 0.0561
rotated from previous position = 0.0719 degrees
atoms outside contour = 71, contour level = 0.041018
Position of BTN2A1_2A1.11 (#8) relative to 2A1.11_G115_class8 (#5)
coordinates:
Matrix rotation and translation
-0.78431352 -0.09693176 -0.61274508 283.64477768
0.21301059 0.88558816 -0.41274701 191.02697847
0.58264808 -0.45424426 -0.67393127 197.30138755
Axis -0.03358421 -0.96744581 0.25084000
Axis point 96.74560168 0.00000000 173.24635064
Rotation angle (degrees) 141.84369878
Shift along axis -144.84315446
> hide #!5 models
> select subtract #5
Nothing selected
> hide #8 models
> show #!9 models
> select add #10
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> show #!10 models
> fitmap #10 inMap #9
Fit molecule 2A1.9_1 (#10) to map 2A1.9_G115_66_class1 (#9) using 4191 atoms
average map value = 0.01388, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.0235 degrees
atoms outside contour = 194, contour level = 0.0063268
Position of 2A1.9_1 (#10) relative to 2A1.9_G115_66_class1 (#9) coordinates:
Matrix rotation and translation
0.96803753 0.13831842 0.20921605 -67.51641804
-0.21510188 0.02890104 0.97616387 71.36890787
0.12897488 -0.98996603 0.05772984 303.88591205
Axis -0.98343241 0.04013558 -0.17677620
Axis point 0.00000000 194.52758660 121.04569622
Rotation angle (degrees) 88.43367042
Shift along axis 15.54246930
> select subtract #10
Nothing selected
> hide #!10 models
> show #!11 models
> show #12 models
> select add #12
3641 atoms, 3628 bonds, 545 residues, 1 model selected
> select add #11
7832 atoms, 7915 bonds, 1103 residues, 2 models selected
> select subtract #11
3641 atoms, 3628 bonds, 545 residues, 1 model selected
> fitmap #12 inMap #9
Fit molecule BTN2A1_2A1.9 (#12) to map 2A1.9_G115_66_class1 (#9) using 3641
atoms
average map value = 0.01616, steps = 28
shifted from previous position = 0.029
rotated from previous position = 0.0873 degrees
atoms outside contour = 47, contour level = 0.0063268
Position of BTN2A1_2A1.9 (#12) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.21003485 0.58195568 -0.78562901 124.17563739
0.25554732 -0.80829627 -0.53042690 162.90707850
-0.94370595 -0.08935725 -0.31848760 214.06316203
Axis 0.77241312 0.27682862 -0.57161516
Axis point 0.00000000 37.99350762 167.86586802
Rotation angle (degrees) 163.41041955
Shift along axis 18.65048415
> select add #11
7832 atoms, 7915 bonds, 1103 residues, 2 models selected
> select subtract #12
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> hide #!11 models
> hide #12 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 1 maps.
> show #!11 models
> fitmap #11 inMap #9
Fit molecule 2A1.9_2 (#11) to map 2A1.9_G115_66_class1 (#9) using 4191 atoms
average map value = 0.01348, steps = 44
shifted from previous position = 0.0239
rotated from previous position = 0.0395 degrees
atoms outside contour = 232, contour level = 0.0063268
Position of 2A1.9_2 (#11) relative to 2A1.9_G115_66_class1 (#9) coordinates:
Matrix rotation and translation
-0.76152257 -0.56611249 0.31559472 328.64387432
0.59780476 -0.80162894 0.00453006 171.92905110
0.25042534 0.19211377 0.94888327 -5.81329961
Axis 0.15887012 0.05519386 0.98575551
Axis point 136.81293717 139.11146501 0.00000000
Rotation angle (degrees) 143.81686493
Shift along axis 55.97062834
> select subtract #11
Nothing selected
> hide #!11 models
> show #!10 models
> select add #10
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #10 inMap #9
Fit molecule 2A1.9_1 (#10) to map 2A1.9_G115_66_class1 (#9) using 4191 atoms
average map value = 0.01388, steps = 28
shifted from previous position = 0.0191
rotated from previous position = 0.0321 degrees
atoms outside contour = 194, contour level = 0.0063268
Position of 2A1.9_1 (#10) relative to 2A1.9_G115_66_class1 (#9) coordinates:
Matrix rotation and translation
0.96801392 0.13828735 0.20934578 -67.53101045
-0.21529846 0.02942022 0.97610502 71.31347705
0.12882398 -0.98995508 0.05825224 303.83702585
Axis -0.98341132 0.04027651 -0.17686147
Axis point 0.00000000 194.55523470 121.03619264
Rotation angle (degrees) 88.40449636
Shift along axis 15.54595396
> hide #!10 models
> select subtract #10
Nothing selected
> show #12 models
> select add #12
3641 atoms, 3628 bonds, 545 residues, 1 model selected
> fitmap #12 inMap #9
Fit molecule BTN2A1_2A1.9 (#12) to map 2A1.9_G115_66_class1 (#9) using 3641
atoms
average map value = 0.01616, steps = 28
shifted from previous position = 0.00537
rotated from previous position = 0.0195 degrees
atoms outside contour = 46, contour level = 0.0063268
Position of BTN2A1_2A1.9 (#12) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.20982181 0.58188295 -0.78573980 124.17617608
0.25531776 -0.80835349 -0.53045026 162.91270201
-0.94381547 -0.08931329 -0.31817525 214.07326082
Axis 0.77233989 0.27675791 -0.57174833
Axis point 0.00000000 37.99397847 167.89347267
Rotation angle (degrees) 163.40619574
Shift along axis 18.59756341
> select subtract #12
Nothing selected
> hide #12 models
> hide #!9 models
> show #!9 models
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/2A1.9_2A1ecto_CDJ_Contacts.pdb
Chain information for 2A1.9_2A1ecto_CDJ_Contacts.pdb #13
---
Chain | Description
C | No description available
D | No description available
J | No description available
Drag select of 73 atoms, 644 residues, 70 bonds
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,241.76,0,1,0,204.31,0,0,1,203.19
> view matrix models #13,1,0,0,283.38,0,1,0,184.69,0,0,1,202.92
> view matrix models #13,1,0,0,301.39,0,1,0,194.62,0,0,1,185.07
> view matrix models #13,1,0,0,298.03,0,1,0,209.84,0,0,1,198.37
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.24887,0.61749,0.74617,252.61,-0.96688,-0.11329,-0.22872,238.56,-0.0567,-0.77838,0.62523,228.68
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.24887,0.61749,0.74617,260.06,-0.96688,-0.11329,-0.22872,206.38,-0.0567,-0.77838,0.62523,203.56
> view matrix models
> #13,-0.24887,0.61749,0.74617,248.57,-0.96688,-0.11329,-0.22872,188.34,-0.0567,-0.77838,0.62523,200.48
> view matrix models
> #13,-0.24887,0.61749,0.74617,239.99,-0.96688,-0.11329,-0.22872,198.84,-0.0567,-0.77838,0.62523,210.52
> view matrix models
> #13,-0.24887,0.61749,0.74617,236.36,-0.96688,-0.11329,-0.22872,197.9,-0.0567,-0.77838,0.62523,209.78
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.12615,0.98762,0.093181,219.63,-0.72308,-0.15585,0.67296,208.56,0.67915,0.017518,0.73379,189.79
> view matrix models
> #13,0.13471,0.41834,0.89824,252.58,-0.97999,0.19029,0.058342,186.13,-0.14652,-0.88813,0.43561,211.89
> view matrix models
> #13,-0.055686,0.64066,0.7658,238.99,-0.99453,0.032305,-0.099344,191.82,-0.088385,-0.76714,0.63536,208.77
> view matrix models
> #13,-0.34565,0.489,0.80088,240.34,-0.93784,-0.20865,-0.27736,202.26,0.031471,-0.84696,0.53072,213.85
> view matrix models
> #13,-0.5507,0.28442,0.78475,245.25,-0.82345,-0.33896,-0.45501,209.03,0.13658,-0.89678,0.42087,217.35
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.5507,0.28442,0.78475,243.15,-0.82345,-0.33896,-0.45501,203.6,0.13658,-0.89678,0.42087,223.19
> view matrix models
> #13,-0.5507,0.28442,0.78475,235.82,-0.82345,-0.33896,-0.45501,203.86,0.13658,-0.89678,0.42087,216.77
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.49436,0.34505,0.79784,234.32,-0.83818,-0.43244,-0.33233,208.17,0.23035,-0.83303,0.503,216.16
> view matrix models
> #13,-0.45416,0.41942,0.78602,231.83,-0.88645,-0.30099,-0.35158,201.6,0.089123,-0.85644,0.50849,214.62
> view matrix models
> #13,-0.46363,-0.034383,0.88536,251.48,-0.77467,-0.46926,-0.42389,210.45,0.43004,-0.88239,0.19093,220.38
> view matrix models
> #13,-0.37394,-0.23543,0.89707,261.75,-0.7413,-0.50539,-0.44164,212.51,0.55735,-0.83015,0.014456,219.61
> view matrix models
> #13,-0.36891,0.61282,0.69882,224.71,-0.92946,-0.24423,-0.2765,198.76,0.0012279,-0.75154,0.65969,209.28
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.36891,0.61282,0.69882,225.91,-0.92946,-0.24423,-0.2765,198.7,0.0012279,-0.75154,0.65969,214.08
> fitmap #13 inMap #9
Fit molecule 2A1.9_2A1ecto_CDJ_Contacts.pdb (#13) to map 2A1.9_G115_66_class1
(#9) using 4909 atoms
average map value = 0.01596, steps = 140
shifted from previous position = 2.6
rotated from previous position = 15.1 degrees
atoms outside contour = 37, contour level = 0.0063268
Position of 2A1.9_2A1ecto_CDJ_Contacts.pdb (#13) relative to
2A1.9_G115_66_class1 (#9) coordinates:
Matrix rotation and translation
0.69677836 0.63013071 0.34268820 162.87904665
-0.66196712 0.38092463 0.64551991 148.61010123
0.27622355 -0.67663263 0.68254585 190.12888951
Axis -0.71472699 0.03592935 -0.69848007
Axis point 0.00000000 99.05307311 -148.79646939
Rotation angle (degrees) 67.65861032
Shift along axis -243.87582654
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/2A1.9_2A1ecto_CDJ_Contacts.pdb
Chain information for 2A1.9_2A1ecto_CDJ_Contacts.pdb #14
---
Chain | Description
C | No description available
D | No description available
J | No description available
> select add #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> select add #14
9818 atoms, 10040 bonds, 1294 residues, 2 models selected
> select subtract #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,290.92,0,1,0,231.95,0,0,1,214.06
> view matrix models #14,1,0,0,308.24,0,1,0,219.33,0,0,1,215.48
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.49217,-0.86474,0.099943,318.4,0.30524,-0.27896,-0.9105,274.95,0.81523,-0.41761,0.40125,245.21
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.49217,-0.86474,0.099943,269.32,0.30524,-0.27896,-0.9105,273.09,0.81523,-0.41761,0.40125,274.89
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.43507,-0.90018,0.019671,271.48,0.62131,-0.31596,-0.71704,281.37,0.65168,-0.29974,0.69676,268.33
> view matrix models
> #14,0.085779,-0.83181,0.54839,280.64,0.98021,0.16903,0.10307,271.25,-0.17843,0.5287,0.82985,218.55
> view matrix models
> #14,0.77722,0.026962,0.62865,257.02,0.19606,0.93897,-0.28267,222.26,-0.5979,0.34295,0.7245,218.31
> view matrix models
> #14,0.6309,-0.68822,0.3582,283.52,0.75759,0.44686,-0.47579,252.52,0.16738,0.57155,0.80331,222.9
> view matrix models
> #14,0.8023,-0.41976,0.42439,275.52,0.58583,0.69008,-0.42495,239.28,-0.11449,0.58957,0.79957,216.97
> view matrix models
> #14,0.79763,-0.28612,0.53097,270.26,0.58836,0.56287,-0.58053,243.98,-0.13277,0.77544,0.6173,207.83
> view matrix models
> #14,0.53049,-0.79257,0.30068,285.85,0.54111,0.043577,-0.83982,263.99,0.65251,0.60822,0.45199,228.45
> view matrix models
> #14,0.35247,-0.89235,0.28191,286.77,0.44058,-0.10754,-0.89125,268.35,0.82563,0.43834,0.35524,238.37
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.35247,-0.89235,0.28191,260.66,0.44058,-0.10754,-0.89125,246.05,0.82563,0.43834,0.35524,249.12
> view matrix models
> #14,0.35247,-0.89235,0.28191,262.03,0.44058,-0.10754,-0.89125,247.49,0.82563,0.43834,0.35524,248.45
> view matrix models
> #14,0.35247,-0.89235,0.28191,254.78,0.44058,-0.10754,-0.89125,239.75,0.82563,0.43834,0.35524,239.87
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.77058,-0.55863,0.30682,248.29,0.54791,0.33471,-0.76666,223.47,0.32558,0.75888,0.56399,218.11
> view matrix models
> #14,0.87946,-0.039919,0.47429,228.98,0.35418,0.72058,-0.59609,204.32,-0.31797,0.69222,0.64786,209.64
> view matrix models
> #14,0.85094,0.057658,0.52209,224.54,0.2956,0.76906,-0.56672,201.33,-0.43419,0.63657,0.63738,209.85
> view matrix models
> #14,0.74482,0.20699,0.63435,216.79,0.2221,0.81956,-0.5282,198.03,-0.62922,0.5343,0.56445,210.3
> view matrix models
> #14,0.72108,-0.11258,0.68364,230.22,0.27697,0.95128,-0.13548,195.34,-0.63508,0.28704,0.71713,221.47
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.72108,-0.11258,0.68364,232.13,0.27697,0.95128,-0.13548,207.77,-0.63508,0.28704,0.71713,226.62
> view matrix models
> #14,0.72108,-0.11258,0.68364,241.48,0.27697,0.95128,-0.13548,196.1,-0.63508,0.28704,0.71713,195.53
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.9535,-0.23813,0.18474,248.63,0.19126,0.95182,0.23972,196.35,-0.23292,-0.19324,0.9531,224.48
> view matrix models
> #14,0.87434,-0.097736,0.47537,242.62,-0.20356,0.81533,0.54203,196.45,-0.44056,-0.57069,0.69298,235.51
> view matrix models
> #14,0.24729,-0.17516,0.95298,236.83,0.12592,0.98099,0.14763,193.47,-0.96072,0.083494,0.26465,196.06
> view matrix models
> #14,0.2433,-0.86695,0.43498,263.71,0.52657,-0.25856,-0.80986,248.92,0.81457,0.42609,0.3936,214.43
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.2433,-0.86695,0.43498,258.67,0.52657,-0.25856,-0.80986,257.79,0.81457,0.42609,0.3936,246.03
> view matrix models
> #14,0.2433,-0.86695,0.43498,249.25,0.52657,-0.25856,-0.80986,243.96,0.81457,0.42609,0.3936,240.36
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.52154,-0.6026,0.60404,243.87,0.78309,0.056978,-0.61929,236.11,0.33877,0.79601,0.50161,216.45
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.52154,-0.6026,0.60404,248.86,0.78309,0.056978,-0.61929,244.7,0.33877,0.79601,0.50161,227.29
> view matrix models
> #14,0.52154,-0.6026,0.60404,250.91,0.78309,0.056978,-0.61929,245.8,0.33877,0.79601,0.50161,226.44
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.73262,-0.18538,0.6549,237.22,0.36447,0.91947,-0.14745,203.72,-0.57482,0.34672,0.74119,230.12
> view matrix models
> #14,0.1167,-0.92445,0.36301,256.08,0.60159,-0.22502,-0.76645,253.79,0.79023,0.30783,0.52988,255.61
> fitmap #14 inMap #9
Fit molecule 2A1.9_2A1ecto_CDJ_Contacts.pdb (#14) to map 2A1.9_G115_66_class1
(#9) using 4909 atoms
average map value = 0.0156, steps = 248
shifted from previous position = 4.54
rotated from previous position = 67.3 degrees
atoms outside contour = 36, contour level = 0.0063268
Position of 2A1.9_2A1ecto_CDJ_Contacts.pdb (#14) relative to
2A1.9_G115_66_class1 (#9) coordinates:
Matrix rotation and translation
-0.68342714 -0.62841682 0.37150994 137.57501486
0.67388932 -0.34738673 0.65207026 169.45177105
-0.28071429 0.69599910 0.66089691 181.73787551
Axis 0.03014680 0.44759831 0.89372642
Axis point 50.97887590 70.72960411 0.00000000
Rotation angle (degrees) 133.23234227
Shift along axis 242.41771504
> select subtract #14
Nothing selected
> hide #!14 models
> hide #!9 models
> show #!11 models
> select add #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> select subtract #13
Nothing selected
> select add #11
4191 atoms, 4287 bonds, 558 residues, 1 model selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> select subtract #11
Nothing selected
> hide #!11 models
> color #13/C C0C0C0
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #13/C #C0C0C0
> color #14/C #C0C0C0
> show #!14 models
> color #14/J #F89A1F
> color #13/J #F89A1F
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
[Repeated 1 time(s)]
——— End of log from Sat Jan 27 13:09:37 2024 ———
opened ChimeraX session
> color #13/D #F7BD75
> color #14/D #F7BD75
> show #!9 models
> show #!5 models
> show #!1 models
> show #!10 models
> show #!11 models
> hide #!11 models
> hide #!10 models
> hide #!1 models
> hide #!5 models
> hide #!9 models
> hide #!13 models
> hide #!14 models
> show #!13 models
> show #12 models
> show #!11 models
> show #!10 models
> hide #!10 models
> hide #!11 models
> hide #12 models
> hide #!13 models
> show #!13 models
> show #!14 models
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
> show #2 models
> show #!3 models
> show #!4 models
> show #!6 models
> show #!7 models
> show #8 models
> hide #!13 models
> hide #!14 models
> hide #!7 models
> hide #!6 models
> hide #8 models
> hide #2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!3 models
> volume #1 level 0.06195
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.6207,-0.78132,-0.065376,254.03,0.70244,0.59119,-0.39633,42.388,0.34831,0.20008,0.91578,8.6487
> show #2 models
> show #!4 models
> view matrix models
> #3,0.6207,-0.78132,-0.065376,250.87,0.70244,0.59119,-0.39633,46.44,0.34831,0.20008,0.91578,13.554
> view matrix models
> #3,0.6207,-0.78132,-0.065376,249.57,0.70244,0.59119,-0.39633,48.904,0.34831,0.20008,0.91578,15.192
> view matrix models
> #3,0.6207,-0.78132,-0.065376,250.62,0.70244,0.59119,-0.39633,51.515,0.34831,0.20008,0.91578,15.138
> view matrix models
> #3,0.6207,-0.78132,-0.065376,255.35,0.70244,0.59119,-0.39633,42.973,0.34831,0.20008,0.91578,19.898
> undo
> view matrix models
> #3,0.6207,-0.78132,-0.065376,251.35,0.70244,0.59119,-0.39633,51.675,0.34831,0.20008,0.91578,15.64
> view matrix models
> #3,0.6207,-0.78132,-0.065376,249.01,0.70244,0.59119,-0.39633,53.269,0.34831,0.20008,0.91578,14.375
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> volume #1 level 0.1142
> view matrix models
> #3,0.6207,-0.78132,-0.065376,247.04,0.70244,0.59119,-0.39633,53.655,0.34831,0.20008,0.91578,11.716
> view matrix models
> #3,0.6207,-0.78132,-0.065376,248.86,0.70244,0.59119,-0.39633,53.584,0.34831,0.20008,0.91578,12.599
> select subtract #3
Nothing selected
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #!3 models
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> show #!7 models
> show #!3 models
> volume #1 level 0.04434
> view matrix models
> #3,0.6207,-0.78132,-0.065376,252.36,0.70244,0.59119,-0.39633,50.023,0.34831,0.20008,0.91578,13.641
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.21078,-0.95579,0.20503,334.47,0.86482,0.084548,-0.49492,139.79,0.45571,0.28163,0.8444,-15.486
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!7 models
> hide #!4 models
> hide #2 models
> hide #!1 models
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
> select add #1
2 models selected
> select add #4
4191 atoms, 4287 bonds, 558 residues, 3 models selected
> select subtract #4
2 models selected
> select add #2
3641 atoms, 3628 bonds, 545 residues, 3 models selected
> select add #3
7832 atoms, 7915 bonds, 1103 residues, 4 models selected
> show #!1 models
> select subtract #1
7832 atoms, 7915 bonds, 1103 residues, 2 models selected
> select subtract #2
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> select subtract #3
Nothing selected
> show #!3 models
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> view matrix models
> #3,0.35626,-0.92538,-0.12943,341.22,0.79987,0.37364,-0.46969,87.104,0.483,0.063806,0.87329,22.468
> view matrix models
> #3,0.38057,-0.91557,-0.13001,334.58,0.77764,0.39293,-0.4908,89.769,0.50044,0.085681,0.86152,15.91
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.38057,-0.91557,-0.13001,332.79,0.77764,0.39293,-0.4908,90.122,0.50044,0.085681,0.86152,17.157
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.3584,-0.93265,-0.041282,329.81,0.77228,0.32104,-0.5482,113.55,0.52453,0.1646,0.83533,-1.1179
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.3584,-0.93265,-0.041282,329.56,0.77228,0.32104,-0.5482,112.74,0.52453,0.1646,0.83533,-0.17803
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.2871,-0.95663,-0.049263,349.21,0.80684,0.26922,-0.52585,114.55,0.51631,0.11122,0.84915,11.126
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.2871,-0.95663,-0.049263,351.31,0.80684,0.26922,-0.52585,111.37,0.51631,0.11122,0.84915,9.6469
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.34783,-0.9357,0.058975,322.08,0.86798,0.2976,-0.39756,78.018,0.35444,0.18947,0.91568,15.468
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.34783,-0.9357,0.058975,322.17,0.86798,0.2976,-0.39756,75.697,0.35444,0.18947,0.91568,16.965
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.37018,-0.92842,0.031526,319.73,0.86615,0.33269,-0.37297,65.524,0.33579,0.16537,0.92731,24.246
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.37018,-0.92842,0.031526,321.91,0.86615,0.33269,-0.37297,63.183,0.33579,0.16537,0.92731,23.517
> view matrix models
> #3,0.37018,-0.92842,0.031526,319.51,0.86615,0.33269,-0.37297,67.169,0.33579,0.16537,0.92731,23.603
> view matrix models
> #3,0.37018,-0.92842,0.031526,319.34,0.86615,0.33269,-0.37297,66.874,0.33579,0.16537,0.92731,23.339
> show #2 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!7 models
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!7 models
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
> hide #2 models
> show #!5 models
> show #!9 models
> color #9 #f89a1fff models
> hide #!5 models
> show #!5 models
> color #5 #7d1518ff models
> color #1 #9ec7eaff models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> save /Users/amritaramesh/Desktop/image1.png supersample 3
> undo
> show #12 models
> color #1 #9ec7ea52 models
> color #5 #7d15184e models
> color #9 #f89a1f4c models
> show #!10 models
> show #!11 models
> hide #!1 models
> hide #!5 models
> hide #!9 models
> show #!9 models
> show #!5 models
> show #!1 models
> volume #1 level 0.05453
> volume #1 level 0.04
> volume #5 level 0.04
> volume #9 level 0.04
> volume #9 level 0.01597
> volume #9 level 0.002533
> volume #9 level 0.006547
> volume #1 level 0.05359
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!9 models
> show #!9 models
> color #1 #9ec7ea08 models
> color #1 #9ec7eaff models
> color #5 #7d1518ff models
> color #9 #f89a1fff models
> hide #!10 models
> hide #!11 models
> hide #12 models
> volume #1 level 0.05291
> save /Users/amritaramesh/Desktop/image1.png supersample 3
> hide #!9 models
> hide #!5 models
> color #1 #9ec7ea4d models
> show #2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color #4/K aliceblue
> color #4/K lavender
> color #4/K azure
> color #4/K lavender
> color #1 #9ec7ea33 models
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting soft
> color #1 #9ec7ea00 models
> color #1 #9ec7ea1a models
> color #1 #9ec7ea00 models
> color #1 #9ec7ea4d models
> save /Users/amritaramesh/Desktop/image2.png supersample 3
> hide #2 models
> hide #!4 models
> color #1 #9ec7eaff models
> show #!5 models
> show #!9 models
> save /Users/amritaramesh/Desktop/image3.png supersample 3
> hide #!5 models
> hide #!9 models
> show #2 models
> show #!3 models
> show #!4 models
> color #1 #9ec7ea4d models
> save /Users/amritaramesh/Desktop/image4.png supersample 3
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #2 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #8 models
> color #5 #7d15184d models
> lighting soft
[Repeated 1 time(s)]
> save /Users/amritaramesh/Desktop/image5.png supersample 3
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #8 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!13 models
> show #!14 models
> show #!10 models
> show #!11 models
> color #9 #f89a1f4d models
> hide #10/H,L
> hide #10/H
> hide #11/H
> hide cartoons #11/H
Expected ',' or a keyword
> hide #11/H cartoons
> hide #11/L cartoons
> hide #10/L cartoons
> hide #10/H cartoons
> save /Users/amritaramesh/Desktop/image6.png supersample 3
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/41_3D/2A1.4_BTN2A1_model.pdb
> models #2-4
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/48AR_3D/2A1.11_BTN2A1_model.pdb
> models #6-8
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/2A1.9/2A1.9_BTN2A1.pdb
> models #10-14
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
——— End of log from Sat Jan 27 14:24:11 2024 ———
opened ChimeraX session
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/2A1.9_2A1ecto_CDJ_Contacts.pdb
Chain information for 2A1.9_2A1ecto_CDJ_Contacts.pdb #15
---
Chain | Description
C | No description available
D | No description available
J | No description available
> hide #!14 models
> hide #!13 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> select add #15
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> show #!9 models
> hide #!9 models
> show #!9 models
> ui mousemode right select
Drag select of 168 residues
Drag select of 12 residues
> select clear
Drag select of 73 atoms, 644 residues, 70 bonds
Drag select of 24 residues
Drag select of 73 atoms, 644 residues, 70 bonds
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,377.94,0,1,0,37.811,0,0,1,112.1
> view matrix models #15,1,0,0,266.9,0,1,0,95.795,0,0,1,229.42
> view matrix models #15,1,0,0,234.98,0,1,0,197.74,0,0,1,237.21
> view matrix models #15,1,0,0,267.02,0,1,0,192.69,0,0,1,249.48
> view matrix models #15,1,0,0,295.24,0,1,0,195.62,0,0,1,195.26
> hide #!9 models
> show #!1 models
> view matrix models #15,1,0,0,282.16,0,1,0,201.09,0,0,1,191.82
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.85569,0.29036,0.42835,269.25,-0.47655,0.76481,0.43356,204.55,-0.20172,-0.57512,0.79281,211.64
> view matrix models
> #15,0.27742,0.83871,0.46861,235.53,-0.95464,0.18572,0.23274,219.54,0.10817,-0.51192,0.85219,214.89
> view matrix models
> #15,0.57472,0.74079,0.34775,244.53,-0.81563,0.55312,0.16972,206.11,-0.066615,-0.38118,0.9221,206.47
> view matrix models
> #15,0.068182,0.84605,0.52872,231.7,-0.93932,-0.12414,0.31978,233.45,0.33619,-0.51844,0.78625,219
> view matrix models
> #15,-0.26009,0.59752,0.7585,237.44,-0.95798,-0.061281,-0.28022,227.5,-0.12095,-0.79951,0.58835,221.68
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.26009,0.59752,0.7585,237.82,-0.95798,-0.061281,-0.28022,204.46,-0.12095,-0.79951,0.58835,202.73
> view matrix models
> #15,-0.26009,0.59752,0.7585,237.04,-0.95798,-0.061281,-0.28022,194.41,-0.12095,-0.79951,0.58835,213.5
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.58337,0.34494,0.73532,241.81,-0.77749,-0.49903,-0.38272,215.86,0.23493,-0.79498,0.5593,219.65
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.58337,0.34494,0.73532,229.47,-0.77749,-0.49903,-0.38272,211.28,0.23493,-0.79498,0.5593,217.78
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.3107,0.60284,0.73488,223.44,-0.94718,-0.13175,-0.29239,192.98,-0.079449,-0.78691,0.61193,211.96
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.3107,0.60284,0.73488,226.48,-0.94718,-0.13175,-0.29239,194.52,-0.079449,-0.78691,0.61193,219.98
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.3606,0.46806,0.80678,231.67,-0.92311,-0.30296,-0.23683,202.53,0.13357,-0.83014,0.54131,225.35
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.3606,0.46806,0.80678,226.89,-0.92311,-0.30296,-0.23683,204.82,0.13357,-0.83014,0.54131,217.58
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.58629,0.37619,0.71746,226.26,-0.78096,-0.49786,-0.37713,215.03,0.21533,-0.78142,0.58568,217.21
> view matrix models
> #15,-0.49615,0.27403,0.82386,232.78,-0.83031,-0.42714,-0.35796,211.21,0.25382,-0.86166,0.43946,220.62
> view matrix models
> #15,-0.48724,0.27852,0.82766,232.77,-0.83259,-0.43408,-0.34406,211.53,0.26344,-0.85674,0.44339,220.6
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.48724,0.27852,0.82766,233.01,-0.83259,-0.43408,-0.34406,204.87,0.26344,-0.85674,0.44339,220.94
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.50684,0.39307,0.76721,227.47,-0.75907,-0.62532,-0.18109,215.15,0.40857,-0.67415,0.6153,216.64
> view matrix models
> #15,-0.50683,0.33786,0.79308,229.95,-0.76694,-0.5968,-0.23589,213.53,0.39361,-0.7278,0.56159,218.39
> view matrix models
> #15,-0.5809,0.51589,0.62961,220.21,-0.74951,-0.64071,-0.16654,216.05,0.31748,-0.56864,0.75885,211.19
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.5809,0.51589,0.62961,221.12,-0.74951,-0.64071,-0.16654,218.21,0.31748,-0.56864,0.75885,217.6
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.49455,0.56258,0.66251,220.87,-0.86377,-0.40276,-0.30279,205.32,0.096488,-0.72201,0.68513,219.75
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.49455,0.56258,0.66251,228.44,-0.86377,-0.40276,-0.30279,202.64,0.096488,-0.72201,0.68513,214.23
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.62747,0.38039,0.6794,233.87,-0.77469,-0.3927,-0.49562,202.89,0.078277,-0.83731,0.54109,218.11
> view matrix models
> #15,-0.64934,0.28553,0.70486,237.64,-0.71021,-0.55911,-0.42778,211.49,0.27195,-0.77838,0.56584,219.25
> fitmap #15 inMap #1
Fit molecule 2A1.9_2A1ecto_CDJ_Contacts.pdb (#15) to map 2A1.4_G115_class6
(#1) using 4909 atoms
average map value = 0.08778, steps = 76
shifted from previous position = 5.89
rotated from previous position = 12.7 degrees
atoms outside contour = 515, contour level = 0.052908
Position of 2A1.9_2A1ecto_CDJ_Contacts.pdb (#15) relative to 2A1.4_G115_class6
(#1) coordinates:
Matrix rotation and translation
-0.53450677 0.41432126 0.73664130 229.33776967
-0.82144275 -0.45972517 -0.33746791 210.89643410
0.19883242 -0.78548753 0.58606741 217.17794457
Axis -0.31545417 0.37867549 -0.87011122
Axis point 142.25592344 111.49579766 0.00000000
Rotation angle (degrees) 134.75544928
Shift along axis -181.45321069
> delete #15/C
> fitmap #15 inMap #1
Fit molecule 2A1.9_2A1ecto_CDJ_Contacts.pdb (#15) to map 2A1.4_G115_class6
(#1) using 3217 atoms
average map value = 0.09092, steps = 48
shifted from previous position = 1.12
rotated from previous position = 9.08 degrees
atoms outside contour = 198, contour level = 0.052908
Position of 2A1.9_2A1ecto_CDJ_Contacts.pdb (#15) relative to 2A1.4_G115_class6
(#1) coordinates:
Matrix rotation and translation
-0.47326183 0.34569673 0.81025738 235.63999506
-0.86563495 -0.35310524 -0.35495469 203.97318461
0.16339945 -0.86937361 0.46635840 217.11653082
Axis -0.35080008 0.44111483 -0.82604904
Axis point 145.64870922 113.65127051 0.00000000
Rotation angle (degrees) 132.84398139
Shift along axis -172.03583403
> show #2 models
> color #15/D 9ec7ea
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #15/D #9ec7ea
> color #15/J #94082EE
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #15/J #4082EE
> save
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/2A1.4_2A1.9aln.pdb
> models #2,15
> rename #15 2A1.4_2A1.9aln
> rename #14 2A1.11_2A1.9aln
> show #!14 models
> hide #!14 models
> show #!14 models
> rename #14 2A1.9_me
> rename #14 2A1.9_me2
> rename #1432A1.9_me1
Missing or invalid "models" argument: invalid models specifier
> rename #14 2A1.9_me1
> show #!13 models
> hide #!13 models
> rename #14 2A1.9_me2
> rename #13 2A1.9_me1
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
——— End of log from Sat Jan 27 23:12:17 2024 ———
opened ChimeraX session
> hide #!14 models
> select add #15
3217 atoms, 3292 bonds, 429 residues, 1 model selected
> select subtract #15
Nothing selected
> show #!5 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> hide #!9 models
> hide #!5 models
> save /Users/amritaramesh/Desktop/2A1.4_model_map.cxs
> hide #!1 models
> hide #2 models
> hide #!15 models
> show #!1 models
> show #2 models
> hide #!1 models
> hide #2 models
> show #!1 models
> show #2 models
> show #!15 models
> save /Users/amritaramesh/Desktop/2A1.4_model_map.png width 864 height 597
> supersample 3
> show #12 models
> hide #12 models
> hide #!15 models
> hide #!1 models
> hide #2 models
> show #!5 models
> show #8 models
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/2A1.9_2A1ecto_CDJ_Contacts.pdb
Chain information for 2A1.9_2A1ecto_CDJ_Contacts.pdb #16
---
Chain | Description
C | No description available
D | No description available
J | No description available
> rename #16 2A1.11_2A1.9aln
> delete #16/C
> ui mousemode right select
Drag select of 429 residues
> ui mousemode right "translate selected models"
> view matrix models #16,1,0,0,124.57,0,1,0,-43.146,0,0,1,224.6
> view matrix models #16,1,0,0,274,0,1,0,87.11,0,0,1,127.35
> view matrix models #16,1,0,0,226.02,0,1,0,108.2,0,0,1,168.09
> view matrix models #16,1,0,0,247.12,0,1,0,146.41,0,0,1,190.79
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.92725,-0.34224,0.15191,270.85,0.21374,0.8169,0.53571,176.83,-0.30744,-0.46427,0.83063,208.32
> view matrix models
> #16,0.046935,-0.80205,-0.59541,261.61,0.9988,0.029258,0.039321,220.78,-0.014117,-0.59654,0.80246,219.91
> view matrix models
> #16,0.22202,-0.6969,-0.68194,255.52,0.93619,0.34782,-0.050648,198.21,0.27249,-0.62718,0.72965,224.03
> view matrix models
> #16,-0.8838,-0.42027,0.20561,248.63,-0.028181,-0.39084,-0.92003,200.47,0.46702,-0.81891,0.33358,226.45
> view matrix models
> #16,0.0995,0.46927,0.87743,231.75,-0.35431,0.84072,-0.40945,137.88,-0.92982,-0.27014,0.24992,169.47
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.0995,0.46927,0.87743,241.35,-0.35431,0.84072,-0.40945,136.23,-0.92982,-0.27014,0.24992,143.09
> view matrix models
> #16,0.0995,0.46927,0.87743,247.88,-0.35431,0.84072,-0.40945,166.17,-0.92982,-0.27014,0.24992,156.88
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.71854,-0.028001,0.69492,258.95,-0.62802,-0.40317,-0.66561,227.77,0.29881,-0.9147,0.27211,215.03
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.71854,-0.028001,0.69492,256.88,-0.62802,-0.40317,-0.66561,201.29,0.29881,-0.9147,0.27211,206.98
> view matrix models
> #16,-0.71854,-0.028001,0.69492,243.74,-0.62802,-0.40317,-0.66561,204.01,0.29881,-0.9147,0.27211,215.27
> view matrix models
> #16,-0.71854,-0.028001,0.69492,242.97,-0.62802,-0.40317,-0.66561,196.4,0.29881,-0.9147,0.27211,215.78
> fitmap #16 inMap #5
Fit molecule 2A1.11_2A1.9aln (#16) to map 2A1.11_G115_class8 (#5) using 3217
atoms
average map value = 0.09528, steps = 76
shifted from previous position = 9.56
rotated from previous position = 30.2 degrees
atoms outside contour = 39, contour level = 0.04
Position of 2A1.11_2A1.9aln (#16) relative to 2A1.11_G115_class8 (#5)
coordinates:
Matrix rotation and translation
-0.25394382 0.38580708 0.88694161 261.67009496
-0.87547507 -0.48150264 -0.04121394 202.42278369
0.41116411 -0.78696130 0.46003910 218.46074924
Axis -0.48407439 0.30883342 -0.81871479
Axis point 145.95375220 101.04166547 0.00000000
Rotation angle (degrees) 129.62080126
Shift along axis -243.00991783
> color #16/D #914d5e
> color #16/J #7D1518
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
> select add #16
3217 atoms, 3292 bonds, 429 residues, 1 model selected
> hide #!16 models
> select subtract #16
Nothing selected
> show #!7 models
> show #!6 models
> show #!1 models
> show #2 models
> show #!3 models
> hide #!3 models
> hide #2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!15 models
> hide #3/H
> hide #3/L
> info #3
2 models
#3, 2A1.4_1, hidden
4191 atoms, 4287 bonds, 558 residues, 3 chains (H,L,K)
0 missing structure
#3.1, missing structure, shown, 0 pseudobonds
> show #!3 models
> hide #!3 models
> hide #4/H
> hide #4/L
> hide #4/L cartoons
> hide #4/H cartoons
> hide #!5 models
> hide #!6 models
> hide #!7 models
> save /Users/amritaramesh/Desktop/2A1.4_model_map.png width 864 height 597
> supersample 3
> hide #!4 models
> hide #!1 models
> hide #!15 models
> show #!16 models
> hide #8 models
> show #8 models
> hide #8 models
> show #!1 models
> show #2 models
> hide #!16 models
> show #!15 models
> show #!4 models
> save /Users/amritaramesh/Desktop/2A1.4_model_map.png width 864 height 597
> supersample 3
> hide #!1 models
> hide #2 models
> hide #!4 models
> show #!5 models
> hide #!15 models
> show #!16 models
> show #8 models
> show #!6 models
> hide #6/H cartoons
> hide #6/L cartoons
> show #!7 models
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/2A1.9_2A1ecto_CDJ_Contacts.pdb
Chain information for 2A1.9_2A1ecto_CDJ_Contacts.pdb #17
---
Chain | Description
C | No description available
D | No description available
J | No description available
> rename #17 2A1.11_2A1.9aln
> rename #17 2A1.11_2A1.9aln2
> delete #17/C
> ui mousemode right select
Drag select of 429 residues
> ui mousemode right "translate selected models"
> view matrix models #17,1,0,0,86.367,0,1,0,31.499,0,0,1,360.14
> view matrix models #17,1,0,0,198.63,0,1,0,212.79,0,0,1,286.31
> fitmap #17 inMap #5
Fit molecule 2A1.11_2A1.9aln2 (#17) to map 2A1.11_G115_class8 (#5) using 3217
atoms
average map value = 0.1157, steps = 140
shifted from previous position = 20.4
rotated from previous position = 73.3 degrees
atoms outside contour = 3, contour level = 0.04
Position of 2A1.11_2A1.9aln2 (#17) relative to 2A1.11_G115_class8 (#5)
coordinates:
Matrix rotation and translation
0.34516203 -0.43380226 0.83227326 271.10172482
0.86199304 0.49730154 -0.09828111 234.41245726
-0.37125620 0.75133667 0.54558413 208.89207701
Axis 0.43303799 0.61342170 0.66044827
Axis point 76.68564522 110.73351116 0.00000000
Rotation angle (degrees) 78.81229476
Shift along axis 399.15344488
> view matrix models
> #17,0.54934,-0.45429,0.70132,250.34,0.82656,0.41854,-0.37632,234.96,-0.12257,0.78641,0.60542,214.62
> fitmap #17 inMap #5
Fit molecule 2A1.11_2A1.9aln2 (#17) to map 2A1.11_G115_class8 (#5) using 3217
atoms
average map value = 0.1157, steps = 56
shifted from previous position = 0.174
rotated from previous position = 0.112 degrees
atoms outside contour = 3, contour level = 0.04
Position of 2A1.11_2A1.9aln2 (#17) relative to 2A1.11_G115_class8 (#5)
coordinates:
Matrix rotation and translation
0.34666385 -0.43365838 0.83172386 271.14077988
0.86108807 0.49875362 -0.09885423 234.34128715
-0.37195632 0.75045669 0.54631791 208.92228814
Axis 0.43304337 0.61372779 0.66016031
Axis point 76.86931351 110.83800020 0.00000000
Rotation angle (degrees) 78.70458385
Shift along axis 399.15968002
> ui mousemode right select
> color #17/D #914d5e
> color #17/J #7D1518
> select clear
[Repeated 1 time(s)]
> hide #!17 models
> show #!17 models
> color #17/D #914d5e
> show #!1 models
> hide #!1 models
> save /Users/amritaramesh/Desktop/2A1.11_model_map.png width 864 height 597
> supersample 3
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #7/H cartoons
> hide #7/L cartoons
> save /Users/amritaramesh/Desktop/2A1.11_model_map.png width 864 height 597
> supersample 3
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #8 models
> show #!1 models
> show #2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!17 models
> hide #!16 models
> show #!15 models
> save /Users/amritaramesh/Desktop/2A1.4_model_map.png width 864 height 597
> supersample 3
> hide #!15 models
> hide #2 models
> hide #!1 models
> hide #!4 models
> show #!9 models
> show #!13 models
> show #!14 models
> show #!10 models
> show #!11 models
> save /Users/amritaramesh/Desktop/2A1.9_model_map.png width 864 height 597
> supersample 3
> hide #!13 models
> hide #!14 models
> hide #!11 models
> hide #!10 models
> show #!5 models
> show #!1 models
> transparency #1,5,9 0
> save /Users/amritaramesh/Desktop/Aligned_maps.png width 864 height 597
> supersample 3
> select clear
> save /Users/amritaramesh/Desktop/aligned_maps_top.png width 864 height 597
> supersample 3
> transparency #1,5,9 50
> hide #!5 models
> hide #!9 models
> save
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/Comparison/Compare_Fabs.cxs
——— End of log from Sun Jan 28 01:14:40 2024 ———
opened ChimeraX session
> close #15-17
> close #12#10-11
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/48AR_3D/run_class001.mrc
Opened run_class001.mrc as #10, grid size 140,140,140, pixel 3.19, shown at
level 0.00348, step 1, values float32
> alias #10 2A1.11_map_2
> name #10 2A1.11_map_2
"2A1.11_map_2": invalid atom specifier
> select add #10
2 models selected
> name sel 2A1.11_map_2
"sel" is reserved and cannot be redefined
> volume #10 level 0.0769
> ui mousemode right "translate selected models"
> hide #!1 models
> show #!9 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.96703,-0.036483,0.25204,-46.809,-0.25432,-0.086542,0.96324,77.288,-0.01333,-0.99558,-0.092967,515.06
> view matrix models
> #10,0.8658,0.49519,0.071941,-111.77,0.065925,-0.2554,0.96458,54.558,0.49602,-0.8304,-0.25377,413.48
> view matrix models
> #10,0.71358,0.68315,-0.15527,-71.256,-0.20228,0.4131,0.88794,-36.157,0.67074,-0.6022,0.43297,153.65
> view matrix models
> #10,0.82784,0.56089,0.0092821,-104.77,-0.14642,0.20007,0.96878,-15.307,0.54152,-0.80335,0.24776,274.02
> view matrix models
> #10,0.83542,0.38933,-0.38794,33.603,0.28257,0.30116,0.91074,-110.71,0.47142,-0.87047,0.14158,330.5
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.83542,0.38933,-0.38794,51.486,0.28257,0.30116,0.91074,-112.31,0.47142,-0.87047,0.14158,335.99
> view matrix models
> #10,0.83542,0.38933,-0.38794,57.444,0.28257,0.30116,0.91074,-130.98,0.47142,-0.87047,0.14158,286.47
> view matrix models
> #10,0.83542,0.38933,-0.38794,61.041,0.28257,0.30116,0.91074,-117.08,0.47142,-0.87047,0.14158,282.74
> flip #10
Unknown command: flip #10
> volume flip #10
Opened run_class001.mrc z flip as #11, grid size 140,140,140, pixel 3.19,
shown at step 1, values float32
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.83542,0.38933,-0.38794,61.041,0.28257,0.30116,0.91074,-117.08,0.47142,-0.87047,0.14158,282.74
[Repeated 2 time(s)]
> close #10
> select add #11
2 models selected
> view matrix models
> #11,0.61679,0.43721,-0.65454,145.32,0.0034076,0.83006,0.55766,-120.92,0.78712,-0.34619,0.51049,19.649
> view matrix models
> #11,0.97077,-0.013053,0.23966,8.4656,-0.044127,0.97179,0.23167,-81.738,-0.23592,-0.23548,0.94281,110.39
> view matrix models
> #11,0.92038,-0.39005,0.027636,152.11,0.36815,0.84055,-0.39741,-7.52,0.13178,0.37594,0.91722,-106.45
> view matrix models
> #11,0.93486,-0.35405,0.0261,140.77,0.3383,0.86614,-0.3679,-13.651,0.10765,0.35276,0.9295,-98.44
> view matrix models
> #11,0.87061,-0.49124,0.026803,186.79,0.43042,0.73419,-0.52508,31.211,0.23826,0.46868,0.85063,-137.04
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.87061,-0.49124,0.026803,147.66,0.43042,0.73419,-0.52508,43.066,0.23826,0.46868,0.85063,-120.64
> view matrix models
> #11,0.87061,-0.49124,0.026803,148.29,0.43042,0.73419,-0.52508,42.887,0.23826,0.46868,0.85063,-121.09
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.82078,-0.55465,-0.13669,205.86,0.43819,0.76483,-0.47225,23.463,0.36648,0.32772,0.8708,-116.16
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.82078,-0.55465,-0.13669,217.68,0.43819,0.76483,-0.47225,20.767,0.36648,0.32772,0.8708,-134.06
> view matrix models
> #11,0.82078,-0.55465,-0.13669,221.78,0.43819,0.76483,-0.47225,42.884,0.36648,0.32772,0.8708,-126.12
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.82727,-0.54382,-0.14099,218.71,0.42251,0.76765,-0.48187,47.206,0.37028,0.33907,0.86483,-128.47
> view matrix models
> #11,0.77314,-0.59942,-0.20724,256.05,0.46751,0.75943,-0.45244,34.478,0.42859,0.25291,0.86738,-119.55
> view matrix models
> #11,0.66213,-0.71552,-0.22275,309.41,0.65694,0.69723,-0.28688,-20.594,0.36057,0.043625,0.93171,-67.756
> view matrix models
> #11,0.64782,-0.70147,-0.29709,323.49,0.61015,0.71128,-0.34899,-2.4889,0.45612,0.044811,0.88879,-78.537
> view matrix models
> #11,0.80575,-0.41693,-0.42064,247.2,0.42745,0.90099,-0.074245,-66.628,0.40995,-0.11998,0.90418,-32.269
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.80575,-0.41693,-0.42064,254.77,0.42745,0.90099,-0.074245,-53.653,0.40995,-0.11998,0.90418,-37.897
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.91354,-0.36987,-0.16922,172.35,0.32858,0.9163,-0.22897,-7.2611,0.23975,0.15357,0.95861,-81.502
> fitmap #11 inMap #9
Fit map run_class001.mrc z flip in map 2A1.9_G115_66_class1 using 5613 points
correlation = 0.977, correlation about mean = 0.6188, overlap = 10.04
steps = 124, shift = 2.94, angle = 15.1 degrees
Position of run_class001.mrc z flip (#11) relative to 2A1.9_G115_66_class1
(#9) coordinates:
Matrix rotation and translation
0.01074439 -0.99804102 0.06163364 365.33784131
0.91733091 -0.01469384 -0.39785437 53.60356511
0.39798061 0.06081314 0.91537599 -110.17272757
Axis 0.22955899 -0.16833865 0.95862650
Axis point 171.69836565 202.94570540 0.00000000
Rotation angle (degrees) 92.53827279
Shift along axis -30.77146392
> close #11
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/48AR_3D/2A1.11_refine.mrc
Opened 2A1.11_refine.mrc as #10, grid size 140,140,140, pixel 3.19, shown at
level 0.00348, step 1, values float32
> volume #10 level 0.08542
> volume flip #10
Opened 2A1.11_refine.mrc z flip as #11, grid size 140,140,140, pixel 3.19,
shown at step 1, values float32
> close #10
> select add #11
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,14.459,0,1,0,-2.2028,0,0,1,-16.597
> view matrix models #11,1,0,0,27.904,0,1,0,-7.9021,0,0,1,0.25731
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.91526,-0.38766,-0.10963,160.75,0.34285,0.89242,-0.29331,8.0911,0.21154,0.23087,0.94971,-88.034
> fitmap #11 inMap #9
Fit map 2A1.11_refine.mrc z flip in map 2A1.9_G115_66_class1 using 4872 points
correlation = 0.979, correlation about mean = 0.5833, overlap = 9.347
steps = 132, shift = 3.82, angle = 16.9 degrees
Position of 2A1.11_refine.mrc z flip (#11) relative to 2A1.9_G115_66_class1
(#9) coordinates:
Matrix rotation and translation
0.01181941 -0.99805242 0.06125089 365.17153756
0.91725382 -0.01356729 -0.39807204 53.44248242
0.39812777 0.06088759 0.91530704 -110.23713764
Axis 0.22969445 -0.16859598 0.95854883
Axis point 171.69082376 202.97990505 0.00000000
Rotation angle (degrees) 92.47711924
Shift along axis -30.79999188
> select subtract #11
Nothing selected
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/41_3D/2A1.4_refine.mrc
Opened 2A1.4_refine.mrc as #10, grid size 140,140,140, pixel 3.19, shown at
level 0.00836, step 1, values float32
> volume #10 level 0.06507
> hide #!11 models
> fitmap #9 inMap #10
Fit map 2A1.9_G115_66_class1 in map 2A1.4_refine.mrc using 29244 points
correlation = 0.9152, correlation about mean = 0.5807, overlap = 34.11
steps = 56, shift = 3.51, angle = 4.07 degrees
Position of 2A1.9_G115_66_class1 (#9) relative to 2A1.4_refine.mrc (#10)
coordinates:
Matrix rotation and translation
0.11267576 0.98751077 0.11012107 45.55461675
-0.97378221 0.13178622 -0.18542006 382.37878778
-0.19761674 -0.08634159 0.97646954 77.09163709
Axis 0.04984428 0.15481639 -0.98668507
Axis point 242.50324368 171.03292978 0.00000000
Rotation angle (degrees) 83.65783484
Shift along axis -14.59602567
> volume #10 level 0.04674
> fitmap #9 inMap #10
Fit map 2A1.9_G115_66_class1 in map 2A1.4_refine.mrc using 29244 points
correlation = 0.9152, correlation about mean = 0.5807, overlap = 34.11
steps = 40, shift = 0.00224, angle = 0.00623 degrees
Position of 2A1.9_G115_66_class1 (#9) relative to 2A1.4_refine.mrc (#10)
coordinates:
Matrix rotation and translation
0.11269697 0.98750015 0.11019459 45.54165848
-0.97379329 0.13181485 -0.18534149 382.36370922
-0.19755003 -0.08641933 0.97647616 77.09068338
Axis 0.04976581 0.15482031 -0.98668842
Axis point 242.49103261 171.03265038 0.00000000
Rotation angle (degrees) 83.65620714
Shift along axis -14.60039947
> fitmap #9 inMap #10
Fit map 2A1.9_G115_66_class1 in map 2A1.4_refine.mrc using 29244 points
correlation = 0.9152, correlation about mean = 0.5807, overlap = 34.11
steps = 40, shift = 0.00497, angle = 0.00893 degrees
Position of 2A1.9_G115_66_class1 (#9) relative to 2A1.4_refine.mrc (#10)
coordinates:
Matrix rotation and translation
0.11283574 0.98747703 0.11025970 45.51197497
-0.97377953 0.13196183 -0.18530920 382.33407982
-0.19753865 -0.08645914 0.97647493 77.09952714
Axis 0.04973033 0.15484981 -0.98668558
Axis point 242.49092235 171.03281532 0.00000000
Rotation angle (degrees) 83.64800595
Shift along axis -14.60530738
> color #10 #9ec7eaff models
> color #10 #9ec7ea4d models
> color #11 #7d1518ff models
> color #11 #7d15184d models
> open
> /Users/amritaramesh/Desktop/Adams_Lab/a-BTN2A1_mAb_paper/Structure_Figures/2A1.9/2A1.9_refine.mrc
Opened 2A1.9_refine.mrc as #12, grid size 288,288,288, pixel 1.07, shown at
level 0.00627, step 2, values float32
> select add #12
2 models selected
> hide #!10 models
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,39.479,0,1,0,90.107,0,0,1,37.953
> view matrix models #12,1,0,0,44.347,0,1,0,73.941,0,0,1,80.564
> view matrix models #12,1,0,0,47.905,0,1,0,77.327,0,0,1,79.754
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.87103,0.32846,-0.36526,68.805,-0.42421,0.87788,-0.22219,191.39,0.24768,0.34849,0.904,2.7165
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.87103,0.32846,-0.36526,87.167,-0.42421,0.87788,-0.22219,207.58,0.24768,0.34849,0.904,-2.1574
> fitmap #12 inMap #9
Fit map 2A1.9_refine.mrc in map 2A1.9_G115_66_class1 using 29851 points
correlation = 0.9897, correlation about mean = 0.9048, overlap = 5.753
steps = 88, shift = 2.21, angle = 6.84 degrees
Position of 2A1.9_refine.mrc (#12) relative to 2A1.9_G115_66_class1 (#9)
coordinates:
Matrix rotation and translation
0.35692008 -0.93413474 0.00058036 214.77274056
0.83776660 0.31982418 -0.44256030 24.58222135
0.41322534 0.15844486 0.89673856 -35.63249931
Axis 0.31367439 -0.21536614 0.92478419
Axis point 91.02335312 157.47468498 0.00000000
Rotation angle (degrees) 73.33703090
Shift along axis 29.12215845
> hide #!9 models
> color #12 #f89a1fff models
> color #12 #f89a1f4d models
> hide #!1 target m
> select subtract #12
Nothing selected
> select add #11
2 models selected
> show #!11 models
> hide #!11 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 1 maps.
> show #!11 models
> fitmap #11 inMap #12
Fit map 2A1.11_refine.mrc z flip in map 2A1.9_refine.mrc using 4872 points
correlation = 0.9895, correlation about mean = 0.7433, overlap = 9.818
steps = 72, shift = 3.38, angle = 3.92 degrees
Position of 2A1.11_refine.mrc z flip (#11) relative to 2A1.9_refine.mrc (#12)
coordinates:
Matrix rotation and translation
0.93565241 -0.34603672 0.06937695 47.52095928
0.34921943 0.93617275 -0.04032831 -143.29358667
-0.05099373 0.06196106 0.99677503 -79.37641827
Axis 0.14346839 0.16882876 0.97514803
Axis point 383.74468642 105.26504903 0.00000000
Rotation angle (degrees) 20.88463680
Shift along axis -94.77807973
> hide #!11 models
> show #!10 models
> select add #10
4 models selected
> select subtract #11
2 models selected
> fitmap #10 inMap #12
Fit map 2A1.4_refine.mrc in map 2A1.9_refine.mrc using 8388 points
correlation = 0.9386, correlation about mean = 0.6225, overlap = 10.59
steps = 48, shift = 0.569, angle = 0.747 degrees
Position of 2A1.4_refine.mrc (#10) relative to 2A1.9_refine.mrc (#12)
coordinates:
Matrix rotation and translation
0.91397339 -0.31970855 0.24987814 -21.38414329
0.23452061 0.91873654 0.31768419 -190.24730958
-0.33113853 -0.23175333 0.91467900 73.62335495
Axis -0.56471294 0.59717006 0.56963780
Axis point 246.25582248 0.00000000 305.04075979
Rotation angle (degrees) 29.10915927
Shift along axis -59.59544879
> hide #!12 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #4 cartoons
> select add #4
4191 atoms, 4287 bonds, 558 residues, 3 models selected
> select subtract #10
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #4 inMap #10
Fit molecule 2A1.4_2 (#4) to map 2A1.4_refine.mrc (#10) using 4191 atoms
average map value = 0.08782, steps = 56
shifted from previous position = 4.85
rotated from previous position = 3.86 degrees
atoms outside contour = 373, contour level = 0.046738
Position of 2A1.4_2 (#4) relative to 2A1.4_refine.mrc (#10) coordinates:
Matrix rotation and translation
-0.08604332 -0.12088802 0.98893005 153.06759663
-0.99310748 0.08969988 -0.07544176 391.52845730
-0.07958690 -0.98860509 -0.12777287 391.87809092
Axis -0.55202869 0.64594360 -0.52727716
Axis point 396.19060345 0.00000000 301.65078346
Rotation angle (degrees) 124.19825295
Shift along axis -38.22077026
> show #!3 models
> select add #3
8382 atoms, 8574 bonds, 1116 residues, 2 models selected
> select subtract #4
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> hide #!4 models
> fitmap #3 inMap #10
Fit molecule 2A1.4_1 (#3) to map 2A1.4_refine.mrc (#10) using 4191 atoms
average map value = 0.09424, steps = 120
shifted from previous position = 31.4
rotated from previous position = 31.7 degrees
atoms outside contour = 1054, contour level = 0.046738
Position of 2A1.4_1 (#3) relative to 2A1.4_refine.mrc (#10) coordinates:
Matrix rotation and translation
0.71797067 -0.67922634 0.15221596 209.55355379
0.57029765 0.44862095 -0.68811324 115.78109972
0.39909737 0.58085353 0.70945787 -47.79128573
Axis 0.70579484 -0.13731456 0.69498083
Axis point 0.00000000 210.23696383 19.51141134
Rotation angle (degrees) 64.02208007
Shift along axis 98.78935840
> undo
> redo
> undo
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select subtract #3
Nothing selected
> select add #5
2 models selected
> select add #4
4191 atoms, 4287 bonds, 558 residues, 3 models selected
> select subtract #5
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> fitmap #4 inMap #10
Fit molecule 2A1.4_2 (#4) to map 2A1.4_refine.mrc (#10) using 4191 atoms
average map value = 0.08782, steps = 40
shifted from previous position = 0.0262
rotated from previous position = 0.0308 degrees
atoms outside contour = 373, contour level = 0.046738
Position of 2A1.4_2 (#4) relative to 2A1.4_refine.mrc (#10) coordinates:
Matrix rotation and translation
-0.08572317 -0.12131876 0.98890510 153.08777067
-0.99313640 0.08967613 -0.07508850 391.47455310
-0.07957154 -0.98855448 -0.12817340 391.91567502
Axis -0.55223527 0.64594686 -0.52705679
Axis point 396.24379262 0.00000000 301.58155525
Rotation angle (degrees) 124.20185928
Shift along axis -38.23052370
> select subtract #4
Nothing selected
> show #2 models
> select add #2
3641 atoms, 3628 bonds, 545 residues, 1 model selected
> fitmap #2 inMap #10
Fit molecule BTN2A1_2A1.4 (#2) to map 2A1.4_refine.mrc (#10) using 3641 atoms
average map value = 0.1031, steps = 52
shifted from previous position = 2.57
rotated from previous position = 3.3 degrees
atoms outside contour = 370, contour level = 0.046738
Position of BTN2A1_2A1.4 (#2) relative to 2A1.4_refine.mrc (#10) coordinates:
Matrix rotation and translation
0.24842344 -0.72053938 -0.64738612 237.51117951
-0.02222331 -0.67240115 0.73985324 247.06177709
-0.96839657 -0.16940982 -0.18305298 247.34666185
Axis -0.76372202 0.26962796 0.58654023
Axis point 0.00000000 215.06604155 163.25524083
Rotation angle (degrees) 143.46711652
Shift along axis 30.30101291
> hide #2 models
> select subtract #2
Nothing selected
> hide #!4 models
> show #!6 models
> show #!7 models
> show #6 cartoons
> show #7 cartoons
> show #8 models
> hide #8 models
> hide #!7 models
> show #!11 models
> hide #!10 models
> fitmap #6 inMap #11
Fit molecule 2A1.11_1 (#6) to map 2A1.11_refine.mrc z flip (#11) using 4191
atoms
average map value = 0.09794, steps = 56
shifted from previous position = 5.1
rotated from previous position = 3.61 degrees
atoms outside contour = 1392, contour level = 0.085422
Position of 2A1.11_1 (#6) relative to 2A1.11_refine.mrc z flip (#11)
coordinates:
Matrix rotation and translation
-0.10368061 -0.39925930 0.91095683 177.42318813
-0.96810614 -0.16951881 -0.18448272 448.67204191
0.22808076 -0.90103018 -0.36894957 355.39046860
Axis -0.62764631 0.59815249 -0.49827072
Axis point 0.00000000 395.12519678 -7.76306784
Rotation angle (degrees) 145.19249958
Shift along axis -20.06537628
> show #!7 models
> hide #!6 models
> fitmap #7 inMap #11
Fit molecule 2A1.11_2 (#7) to map 2A1.11_refine.mrc z flip (#11) using 4191
atoms
average map value = 0.09879, steps = 68
shifted from previous position = 6.55
rotated from previous position = 4 degrees
atoms outside contour = 1402, contour level = 0.085422
Position of 2A1.11_2 (#7) relative to 2A1.11_refine.mrc z flip (#11)
coordinates:
Matrix rotation and translation
0.63799218 -0.70299629 0.31426454 168.86837498
0.76906361 0.60227763 -0.21401596 30.29333783
-0.03882207 0.37822993 0.92489728 53.98123696
Axis 0.36433757 0.21721166 0.90558116
Axis point 68.32682157 144.39598725 0.00000000
Rotation angle (degrees) 54.36753906
Shift along axis 116.98954993
> hide #!7 models
> show #8 models
> fitmap #8 inMap #11
Fit molecule BTN2A1_2A1.11 (#8) to map 2A1.11_refine.mrc z flip (#11) using
3641 atoms
average map value = 0.1159, steps = 52
shifted from previous position = 2.14
rotated from previous position = 2.56 degrees
atoms outside contour = 659, contour level = 0.085422
Position of BTN2A1_2A1.11 (#8) relative to 2A1.11_refine.mrc z flip (#11)
coordinates:
Matrix rotation and translation
-0.57550116 0.10832723 -0.81059461 219.95994584
0.49272561 0.83701519 -0.23796436 196.97778299
0.65270198 -0.53634949 -0.53507882 202.15069534
Axis -0.19349434 -0.94890656 0.24927151
Axis point 28.63860195 0.00000000 172.94469122
Rotation angle (degrees) 129.55230710
Shift along axis -179.08410627
> hide #8 models
> hide #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> hide #!14 models
> select add #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> fitmap #13 inMap #12
Fit molecule 2A1.9_me1 (#13) to map 2A1.9_refine.mrc (#12) using 4909 atoms
average map value = 0.01596, steps = 68
shifted from previous position = 3.84
rotated from previous position = 4.08 degrees
atoms outside contour = 21, contour level = 0.0062718
Position of 2A1.9_me1 (#13) relative to 2A1.9_refine.mrc (#12) coordinates:
Matrix rotation and translation
-0.18945348 0.26668317 0.94498014 177.88156550
-0.81325815 -0.58190188 0.00117341 124.82104784
0.55019865 -0.76829050 0.32712560 147.53085884
Axis -0.55615334 0.28534028 -0.78056030
Axis point 81.60451547 69.14468077 0.00000000
Rotation angle (degrees) 136.22936633
Shift along axis -178.46968610
> select subtract #13
Nothing selected
> hide #!13 models
> show #!14 models
> select add #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> select add #14
9818 atoms, 10040 bonds, 1294 residues, 2 models selected
> select subtract #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> select add #13
9818 atoms, 10040 bonds, 1294 residues, 2 models selected
> fitmap #14 inMap #12
Fit molecule 2A1.9_me2 (#14) to map 2A1.9_refine.mrc (#12) using 4909 atoms
average map value = 0.01681, steps = 72
shifted from previous position = 5.29
rotated from previous position = 3.88 degrees
atoms outside contour = 22, contour level = 0.0062718
Position of 2A1.9_me2 (#14) relative to 2A1.9_refine.mrc (#12) coordinates:
Matrix rotation and translation
0.22673947 -0.25462416 0.94008284 185.93259163
0.82263031 0.56680169 -0.04489111 153.25720253
-0.52141018 0.78351922 0.33797786 131.40961965
Axis 0.41510366 0.73233165 0.53979562
Axis point 42.87597729 0.00000000 -47.55511524
Rotation angle (degrees) 86.22953677
Shift along axis 260.35073564
> select subtract #14
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> select subtract #13
Nothing selected
> select add #14
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> fitmap #14 inMap #12
Fit molecule 2A1.9_me2 (#14) to map 2A1.9_refine.mrc (#12) using 4909 atoms
average map value = 0.01681, steps = 28
shifted from previous position = 0.0261
rotated from previous position = 0.0165 degrees
atoms outside contour = 23, contour level = 0.0062718
Position of 2A1.9_me2 (#14) relative to 2A1.9_refine.mrc (#12) coordinates:
Matrix rotation and translation
0.22663064 -0.25445821 0.94015401 185.92053424
0.82273253 0.56664793 -0.04495878 153.24794143
-0.52129620 0.78368433 0.33777083 131.42102536
Axis 0.41521388 0.73229886 0.53975534
Axis point 42.87454294 0.00000000 -47.50237903
Rotation angle (degrees) 86.24301951
Shift along axis 260.35527750
> select subtract #14
Nothing selected
> hide #!14 models
> volume #9 level 0.006772
> hide #!9 models
> select add #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> show #!13 models
> show #!14 models
> select add #14
9818 atoms, 10040 bonds, 1294 residues, 2 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> hide #!14 models
> fitmap #13 inMap #12
Fit molecule 2A1.9_me1 (#13) to map 2A1.9_refine.mrc (#12) using 4909 atoms
average map value = 0.01596, steps = 36
shifted from previous position = 0.0176
rotated from previous position = 0.0184 degrees
atoms outside contour = 22, contour level = 0.0062718
Position of 2A1.9_me1 (#13) relative to 2A1.9_refine.mrc (#12) coordinates:
Matrix rotation and translation
-0.18941696 0.26644202 0.94505548 177.88749438
-0.81312995 -0.58208110 0.00113249 124.82005416
0.55040068 -0.76823840 0.32690802 147.54158749
Axis -0.55623735 0.28532629 -0.78050555
Axis point 81.57878962 69.15818632 0.00000000
Rotation angle (degrees) 136.24428799
Shift along axis -178.49025353
> select subtract #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> select add #13
9818 atoms, 10040 bonds, 1294 residues, 2 models selected
> select subtract #14
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> fitmap #13 inMap #12
Fit molecule 2A1.9_me1 (#13) to map 2A1.9_refine.mrc (#12) using 4909 atoms
average map value = 0.01596, steps = 28
shifted from previous position = 0.022
rotated from previous position = 0.0159 degrees
atoms outside contour = 21, contour level = 0.0062718
Position of 2A1.9_me1 (#13) relative to 2A1.9_refine.mrc (#12) coordinates:
Matrix rotation and translation
-0.18931160 0.26659265 0.94503411 177.88956117
-0.81327683 -0.58187566 0.00122857 124.82400583
0.55021988 -0.76834177 0.32696944 147.52762719
Axis -0.55622526 0.28536138 -0.78050134
Axis point 81.60479552 69.14942792 0.00000000
Rotation angle (degrees) 136.22887151
Shift along axis -178.47222791
> select add #14
9818 atoms, 10040 bonds, 1294 residues, 2 models selected
> show #!14 models
> hide #!13 models
> select subtract #13
4909 atoms, 5020 bonds, 647 residues, 1 model selected
> fitmap #14 inMap #12
Fit molecule 2A1.9_me2 (#14) to map 2A1.9_refine.mrc (#12) using 4909 atoms
average map value = 0.01681, steps = 24
shifted from previous position = 0.00338
rotated from previous position = 0.0202 degrees
atoms outside contour = 23, contour level = 0.0062718
Position of 2A1.9_me2 (#14) relative to 2A1.9_refine.mrc (#12) coordinates:
Matrix rotation and translation
0.22646514 -0.25432828 0.94022904 185.91410696
0.82260491 0.56684539 -0.04480454 153.23976856
-0.52156944 0.78358370 0.33758241 131.41944408
Axis 0.41508403 0.73246960 0.53962351
Axis point 42.93304597 0.00000000 -47.48298200
Rotation angle (degrees) 86.24751118
Shift along axis 260.33047024
> select subtract #14
Nothing selected
> hide #!14 models
> close #9
> close #1
> close #5
> show #!10 models
> show #!11 models
> volume #10 level 0.1012
> hide #!12 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> volume #11 level 0.05511
> volume #10 level 0.07252
> volume #12 level 0.009012
> volume #11 level 0.06127
> transparency #10-12 0
> save /Users/amritaramesh/Desktop/aligned_maps.png width 864 height 597
> supersample 3
> hide #!11 models
> hide #!12 models
> transparency #10 70
> transparency #10 50
> show #2 models
> show #!3 models
> show #!4 models
> select add #4
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> view matrix models
> #3,0.71207,-0.68612,0.14896,184.42,0.57685,0.45078,-0.68121,138.75,0.40024,0.57099,0.71678,-48.975
> view matrix models
> #3,0.71207,-0.68612,0.14896,181.67,0.57685,0.45078,-0.68121,144.53,0.40024,0.57099,0.71678,-39.236
> select subtract #3
Nothing selected
> select add #3
4191 atoms, 4287 bonds, 558 residues, 1 model selected
> hide #!3 models
> volume #10 level 0.0645
> volume #11 level 0.05511
> volume #12 level 0.008297
> color #10 #9ec7eaff models
> save /Users/amritaramesh/Desktop/aligned_maps.png width 864 height 597
> supersample 3
> hide #!11 models
> hide #!12 models
> transparency #2,4,10 50
> save /Users/amritaramesh/Desktop/2A1.4_side.png width 864 height 597
> supersample 3
> hide #2 models
> select subtract #3
Nothing selected
> hide #!4 models
> show #!6 models
> show #!7 models
> show #8 models
> show #!11 models
> hide #!10 models
> color #11 #7d151880 models
> undo
> color #11 #7d15184d models
> save /Users/amritaramesh/Desktop/2A1.11_side.png width 864 height 597
> supersample 3
> hide #!11 models
> hide #8 models
> hide #!7 models
> hide #!6 models
> show #!10 models
> color #10 #9ec7ea4d models
> show #2 models
> show #!3 models
> show #!4 models
> hide #!3 models
> save /Users/amritaramesh/Desktop/2A1.4_side.png width 864 height 597
> supersample 3
> hide #2 models
> hide #!4 models
> hide #!10 models
> show #!12 models
> show #!13 models
> show #!14 models
> color #12 #f89a1f4d models
> volume #12 level 0.01211
> volume #12 level 0.01175
> open
> /Users/amritaramesh/Desktop/Adams_Lab/Useful_crystal_structures/7pij_Fab-
> nanobody.pdb
7pij_Fab-nanobody.pdb title:
Structure of staphylococcus capitis divalent metal ion transporter (DMT) by
nabfab-fiducial assisted cryo-em [more info...]
Chain information for 7pij_Fab-nanobody.pdb #1
---
Chain | Description
B | divalent metal cation transporter MNTH
H | nabfab HC
K | ANTI-fab nanobody
L | nabfab LC
N | DMTNB16_4
> select add #1
8186 atoms, 8352 bonds, 1084 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> view matrix models #1,1,0,0,17.701,0,1,0,-12.575,0,0,1,11.95
> view matrix models #1,1,0,0,17.972,0,1,0,-4.5043,0,0,1,37.194
> view matrix models #1,1,0,0,25.541,0,1,0,-14.394,0,0,1,28.617
> fitmap #1 inMap #12
Fit molecule 7pij_Fab-nanobody.pdb (#1) to map 2A1.9_refine.mrc (#12) using
8186 atoms
average map value = 0.005842, steps = 948
shifted from previous position = 61
rotated from previous position = 82.4 degrees
atoms outside contour = 5938, contour level = 0.011751
Position of 7pij_Fab-nanobody.pdb (#1) relative to 2A1.9_refine.mrc (#12)
coordinates:
Matrix rotation and translation
0.69279909 -0.18894694 -0.69593712 162.08956444
-0.23143697 0.85575522 -0.46273096 29.22058348
0.68298342 0.48164516 0.54913713 -217.67102305
Axis 0.56486983 -0.82478855 -0.02541502
Axis point 333.46196457 0.00000000 26.46709939
Rotation angle (degrees) 56.71213948
Shift along axis 72.99081440
> delete #1/B
> fitmap #1 inMap #12
Fit molecule 7pij_Fab-nanobody.pdb (#1) to map 2A1.9_refine.mrc (#12) using
5122 atoms
average map value = 0.009347, steps = 40
shifted from previous position = 0.0506
rotated from previous position = 0.417 degrees
atoms outside contour = 2868, contour level = 0.011751
Position of 7pij_Fab-nanobody.pdb (#1) relative to 2A1.9_refine.mrc (#12)
coordinates:
Matrix rotation and translation
0.69450781 -0.18187435 -0.69611825 160.26856435
-0.23542268 0.85681710 -0.45873807 29.22507873
0.67987871 0.48247920 0.55224882 -217.65213322
Axis 0.56428898 -0.82495290 -0.03210389
Axis point 332.93339492 0.00000000 24.69211085
Rotation angle (degrees) 56.51031426
Shift along axis 73.31595046
> select subtract #1
Nothing selected
> hide #!1 models
> volume #12 level 0.01276
> volume #12 level 0.01395
> save /Users/amritaramesh/Desktop/2A1.9_side.png width 864 height 597
> supersample 3
> hide #!12 models
> hide #!13 models
> hide #!14 models
> show #!11 models
> show #!6 models
> show #!7 models
> show #8 models
> volume #11 level 0.075
> volume #11 level 0.07263
> volume #11 level 0.07121
> save /Users/amritaramesh/Desktop/2A1.11_side.png width 864 height 597
> supersample 3
> hide #!6 models
> hide #!7 models
> hide #8 models
> hide #!11 models
> show #!10 models
> show #2 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #2 models
> hide #!4 models
> show #2 models
> hide #!3 models
> show #!4 models
> volume #10 level 0.06908
> volume #10 level 0.06507
> volume #10 level 0.06851
> volume #10 level 0.06335
> save /Users/amritaramesh/Desktop/2A1.4_side.png width 864 height 597
> supersample 3
> save /Users/amritaramesh/Desktop/2A1.4_top.png width 864 height 597
> supersample 3
> hide #!10 models
> hide #2 models
> hide #!4 models
> show #!11 models
> show #8 models
> show #!7 models
> show #!6 models
> save /Users/amritaramesh/Desktop/2A1.11_top.png width 864 height 597
> supersample 3
> hide #!11 models
> hide #8 models
> hide #!7 models
> hide #!6 models
> show #!12 models
> show #!13 models
> show #!14 models
> save /Users/amritaramesh/Desktop/2A1.9_top.png width 864 height 597
> supersample 3
> hide #!13 models
> hide #!14 models
> show #!11 models
> show #!10 models
> volume #11 level 0.05416
> volume #12 level 0.008118
> transparency #10-12 0
> save /Users/amritaramesh/Desktop/aligned_maps_top.png width 864 height 597
> supersample 3
> hide #!10 models
> hide #!11 models
> hide #!12 models
> show #2 models
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/H #4/H #6/H #7/H #1/H
Alignment identifier is 1
> select #2/A
1759 atoms, 1739 bonds, 275 residues, 1 model selected
> select #3/A
Nothing selected
> select #3/H
1683 atoms, 1729 bonds, 226 residues, 1 model selected
> select #4/H
1683 atoms, 1729 bonds, 226 residues, 1 model selected
> ui mousemode right select
> select clear
> select #4/H
1683 atoms, 1729 bonds, 226 residues, 1 model selected
> show #4/H:196,140
> show #4/H:196,140 atoms
> select clear
> show #4/H:22,92 atoms
> style #2#!4 stick
Changed 7832 atom styles
> color #4/H:22,92 yellow
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B #8/A #8/B
Alignment identifier is 2
> color #2/C:97
> show #2/C:97, 23
> show #2/C:97, 23 atoms
> color #2/C:97, 23 yellow
> color #2/C:191,137 yellow
> show #2/C:191,137 atoms
> show #2/A:191,137 atoms
> color #2/A:191,137 yellow
> hide #2 models
> show #2 models
> select #2/B:96
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:23
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/B:96
17 atoms, 15 bonds, 2 residues, 1 model selected
> select subtract #2/B:96
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/B:97
12 atoms, 10 bonds, 2 residues, 1 model selected
> color sel yellow
> show sel atoms
> show #8 models
> hide #8 models
> select #2/A:104
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:104
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:104@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #2/B:104@CA
1 atom, 1 residue, 1 model selected
> select add #2/B:23@CB
2 atoms, 2 residues, 1 model selected
> select add #4/H:92@CB
3 atoms, 3 residues, 2 models selected
> ui tool show Angles/Torsions
> hide #2 models
> hide #!4 models
> show #8 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select add #8/A:97
9 atoms, 5 bonds, 4 residues, 3 models selected
> select add #8/A:23
15 atoms, 10 bonds, 5 residues, 3 models selected
> show sel & #8 atoms
> select clear
> select #8/B:104@CA
1 atom, 1 residue, 1 model selected
> select #8/A:104@CA
1 atom, 1 residue, 1 model selected
> select add #8/A:23@CB
2 atoms, 2 residues, 1 model selected
> save /Users/amritaramesh/Desktop/aligned.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 410, in take_snapshot
aliases[name] = expand_alias(name)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3512, in expand_alias
if not cmd.word_info.is_alias():
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'is_alias'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'user_aliases' ->
<chimerax.core.session.UserAliases object at 0x1331ec610>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'user_aliases' ->
<chimerax.core.session.UserAliases object at 0x1331ec610>: Error while saving
session data for 'user_aliases' -> <chimerax.core.session.UserAliases object
at 0x1331ec610>
ValueError: error processing: 'user_aliases' -> : Error while saving session
data for 'user_aliases' ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 410, in take_snapshot
aliases[name] = expand_alias(name)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3512, in expand_alias
if not cmd.word_info.is_alias():
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'is_alias'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'user_aliases' ->
<chimerax.core.session.UserAliases object at 0x1331ec610>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'user_aliases' ->
<chimerax.core.session.UserAliases object at 0x1331ec610>: Error while saving
session data for 'user_aliases' -> <chimerax.core.session.UserAliases object
at 0x1331ec610>
ValueError: error processing: 'user_aliases' -> : Error while saving session
data for 'user_aliases' ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /Users/amritaramesh/Desktop/New_models.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 410, in take_snapshot
aliases[name] = expand_alias(name)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3512, in expand_alias
if not cmd.word_info.is_alias():
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'is_alias'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'user_aliases' ->
<chimerax.core.session.UserAliases object at 0x1331ec610>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'user_aliases' ->
<chimerax.core.session.UserAliases object at 0x1331ec610>: Error while saving
session data for 'user_aliases' -> <chimerax.core.session.UserAliases object
at 0x1331ec610>
ValueError: error processing: 'user_aliases' -> : Error while saving session
data for 'user_aliases' ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 410, in take_snapshot
aliases[name] = expand_alias(name)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3512, in expand_alias
if not cmd.word_info.is_alias():
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'is_alias'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'user_aliases' ->
<chimerax.core.session.UserAliases object at 0x1331ec610>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'user_aliases' ->
<chimerax.core.session.UserAliases object at 0x1331ec610>: Error while saving
session data for 'user_aliases' -> <chimerax.core.session.UserAliases object
at 0x1331ec610>
ValueError: error processing: 'user_aliases' -> : Error while saving session
data for 'user_aliases' ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir7,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.8 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 481.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 12.7 (21G816)
Kernel Version: Darwin 21.6.0
Time since boot: 1 day 5:05
Graphics/Displays:
Intel HD Graphics 6000:
Chipset Model: Intel HD Graphics 6000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1626
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
B277:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (1)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Command Line |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → expand_alias: cmd.word_info is None |
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