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Opened 21 months ago
Last modified 21 months ago
#14542 assigned defect
Log does not scroll to bottom after new command
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Logging | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-13.6.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Log is not auto-scrolling.
When I asked about this in December on the mailing list, Tom requested I open a bug when I saw this.
Unfortunately I do not know exactly when this started happening, or how to reproduce.
I have had ChimeraX running for a while (a few hours), including on an external monitor earlier and now on my laptop. I've also moved (Log, Models) windows around. But again, I'm not sure when the scrolling behavior changed. Sorry this is not more descriptive and likely very difficult to reproduce.
In case it helps, I'm attaching a screenshot I just took, after issuing the "view matrix" command. As you can see, the log window has not scrolled down - it's still got the save command at the bottom.
If you can think of a diagnostic test I can run, please let me know. For my part, I'll try to pay more attention to the scrolling behavior after a ChimeraX restart to see if I can notice when this starts to happen.
Log:
> set bgColor white
> lighting soft
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729_real_space_refined_000.cif
Summary of feedback from opening
/Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729_real_space_refined_000.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 162
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "21": invalid chain "H", near line 116
Invalid residue range for struct_conf "22": invalid chain "H", near line 117
Invalid residue range for struct_conf "23": invalid chain "I", near line 118
Invalid residue range for struct_conf "24": invalid chain "I", near line 119
Invalid residue range for struct_conf "25": invalid chain "L", near line 120
5 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for STR7729_real_space_refined_000.cif #1
---
Chain | Description
C | No description available
D | No description available
H | No description available
I | No description available
L | No description available
M | No description available
> open
> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #2, grid size
300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
> lighting soft
> volume #2 step 1
> volume #2 level 0.29
> ~show
> ribbon
> dssp
> volume #2 color #b2b2b2ab
> save
> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729_mod03.pdb
> models #1
> close
> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
> close
> cd /Users/rohoua/work/Genentech/CD20
Current working directory is: /Users/rohoua/work/Genentech/CD20
> open pdb:6vja name CD20_RTX id 101.1
CD20_RTX title:
Structure of CD20 in complex with rituximab Fab [more info...]
Chain information for CD20_RTX #1
---
Chain | Description | UniProt
C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
H I | Rituximab Fab heavy chain |
L M | Rituximab Fab light chain |
Non-standard residues in CD20_RTX #1
---
Y01 — cholesterol hemisuccinate
> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7668 version_2 2023.12.13
CD20_2H7v16 title:
Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
resolution. [more info...]
Chain information for CD20_2H7v16 #1
---
Chain | Description
C D | No description available
H I | No description available
L M | No description available
Non-standard residues in CD20_2H7v16 #1
---
Y01 — (Y01)
> open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
shown at level 0.0054, step 2, values float32
> volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
> view matrix models
> #102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92
> open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
> 102.10
Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
Fab.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7487 version_1 2023.05.24
2H7v16_XRay title:
Structure of 2H7 Fab at 2.45 A resolution. [more info...]
Chain information for 2H7v16_XRay #1
---
Chain | Description
A B X Y | No description available
Non-standard residues in 2H7v16_XRay #1
---
CL — (CL)
> matchmaker #102.10/A,B to #102.1/H,L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
sequence alignment score = 1228.2
RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
0.804)
> open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
> 103.1
Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7717 version_2 2023.12.15
CD20_2H7v166_D56A title:
Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
info...]
Chain information for CD20_2H7v166_D56A #1
---
Chain | Description
C D | No description available
H I | No description available
L | No description available
M | No description available
Non-standard residues in CD20_2H7v166_D56A #1
---
Y01 — (Y01)
> open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32
> volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
> view matrix models
> #103.2,0.00937853,0.99467855,-0.10259937,-18.50914227,-0.99948588,0.00617870,-0.03146112,352.75851684,-0.03065977,0.10284168,0.99422511,-49.28949280
> open CD20_2H7v166_S92A_D56A/STR7729_alito6vja.pdb name
> CD20_2H7v166_S92A_D56A id 104.1
Summary of feedback from opening CD20_2H7v166_S92A_D56A/STR7729_alito6vja.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7729 version_1 2024.01.12
CD20_2H7v166_S92A_D56A title:
Structure of ABP1AB10781 and Hs_CD20.M1-P297 at 4.5 A resolution. [more
info...]
Chain information for CD20_2H7v166_S92A_D56A #1
---
Chain | Description
C | No description available
D | No description available
H I | No description available
L | No description available
M | No description available
> open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
> id 104.2
Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
> volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
> view matrix models
> #104.2,-0.00249470,0.97079708,0.23988915,-104.32503408,0.99657176,0.02225139,-0.07968446,-45.21631074,-0.08269530,0.23886796,-0.96752446,330.43463437
> rename #101 CD20_RTX
> rename #102 CD20_2H7v16
> rename #103 CD20_2H7v166_D56A
> rename #104 CD20_2H7v166_S92A_D56A
> dssp
> name CD20_RTX #101.1
> name CD20_2H7v16 #102.1
> name CD20_2H7v166_D56A #103.1
> name CD20_2H7v166_S92A_D56A #104.1
> name CD20 /C,D
> name CD20_Monomer /C
> name CD20_H1 /C,D:46-71
> name CD20_ECL1 /C,D:72-79
> name CD20_H2 /C,D:80-105
> name CD20_ICL1 /C,D:106-112
> name CD20_H3 /C,D:113-141
> name CD20_ECL2 /C,D:142-187
> name CD20_ECL2SS /C,D:167,183
> name CD20_H4 /C,D:188-end
> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
> name RTX CD20_RTX & /H,L,I,M
> name RTX_H RTX & /H,I
> name RTX_L RTX & /L,M
> name RTX_Epitope CD20_RTX & /C,D:168-175
> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
> name H7v16 CD20_2H7v16 & /H,L,I,M
> name H7v16_H H7v16 & /H,I
> name H7v16_L H7v16 & /L,M
> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
> name H7v166_D56A_H H7v166_D56A & /H,I
> name H7v166_D56A_L H7v166_D56A & /L,M
> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
> /H,I:119-end)
> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
> & /H,I:1-111)
> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
> (H7v166_S92A_D56A & /H,I:119-end)
> lighting soft
> set bgColor white
> camera ortho
> style stick
Changed 44407 atom styles
> color byhetero
> open CD20_2H7_mutants_color.cxc
> color CD20 burlywood
> color modify CD20_H1 hue - 20
> color modify CD20_H2 hue - 10
> color modify CD20_H3 hue + 0
> color modify CD20_H4 hue + 10
> color modify CD20_ECL1 hue +10
> color modify CD20_ECL2 hue + 40
> color modify CD20 saturation + 80
> color CD20_ECL2 rgb(127,165,90)
> color CD20_H4 rgb(176,215,142)
> color RTX plum
> color modify RTX_H hue - 40
> color H7v16 slate blue
> color modify H7v16_H hue - 40
> color H7v166_D56A dodger blue
> color modify H7v166_D56A_H hue - 40
> color H7v166_S92A_D56A purple
> color modify H7v166_S92A_D56A_H hue - 40
executed CD20_2H7_mutants_color.cxc
> hide
> ribbon
> show CD20_ECL2SS
> style CD20_ECL2SS stick
Changed 96 atom styles
> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
radius 1, and length 140
> marker #1.1 position 155,155,70
> marker #1.1 position 155,155,210
> select
> #101.1/C,D:73,74,75,76,77,78,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,184,185,186,187,188
440 atoms, 446 bonds, 54 residues, 1 model selected
> define plane sel name membrane_plane
Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
> rename ##name=membrane_plane id 10
> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
> combine CD20_RTX name RTX_Va modelId 1001
> select zone (RTX_V & /H,L) 0.1 #1001
Selected 1711 atoms
> delete #1001 & ~sel
> combine #1001 name RTX_Va_copy modelId 1002
> combine CD20_RTX name RTX_Vb modelId 1003
> select zone (RTX_V & /I,M) 0.1 #1003
Selected 1711 atoms
> delete #1003 & ~sel
> combine #1003 name RTX_Vb_copy modelId 1004
> combine CD20_RTX name RTX_Ca modelId 1005
> select zone (RTX_C & /H,L) 0.1 #1005
Selected 1503 atoms
> delete #1005 & ~sel
> combine #1005 name RTX_Ca_copy modelId 1006
> combine CD20_RTX name RTX_Cb modelId 1007
> select zone (RTX_C & /I,M) 0.1 #1007
Selected 1503 atoms
> delete #1007 & ~sel
> combine #1007 name RTX_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
alignment score = 198.7
RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
4.421)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
Matrix rotation and translation
0.65377294 -0.06463426 0.75392530 -36.97668460
0.02426941 -0.99404163 -0.10626495 318.59247232
0.75630149 0.08777047 -0.64830888 90.28955685
Axis 0.90906034 -0.01113250 0.41651574
Axis point 0.00000000 156.41772375 62.99337678
Rotation angle (degrees) 173.87355102
Shift along axis 0.44625393
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
0.65062, and length 52.0496
> rename #2 Va_rotation_axis id #101.3.1.1
> rename #3 Va_rotation_slabs id #101.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
alignment score = 214.3
RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
4.448)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
Matrix rotation and translation
0.65527690 -0.06129532 -0.75289778 163.48223927
0.03113398 -0.99366393 0.10799385 290.56686667
-0.75474688 -0.09420658 -0.64921665 352.74817189
Axis -0.90945183 0.00831685 0.41572611
Axis point 0.00000000 156.83903630 204.83255489
Rotation angle (degrees) 173.61745932
Shift along axis 0.38400661
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
0.648586, and length 51.8869
> rename #2 Vb_rotation_axis id #101.3.1.2
> rename #3 Vb_rotation_slabs id #101.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
alignment score = 238.2
RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
3.308)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
Matrix rotation and translation
0.37780344 0.24165354 0.89379423 -73.66252391
0.01279825 -0.96661035 0.25593093 273.63534365
0.92579737 -0.08525258 -0.36828146 68.27322422
Axis -0.82796624 -0.07766353 -0.55537400
Axis point 0.00000000 144.62953182 41.62502778
Rotation angle (degrees) 168.10978391
Shift along axis 1.82142171
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
0.539289, and length 43.1431
> rename #2 Ca_rotation_axis id #101.3.1.3
> rename #3 Ca_rotation_slabs id #101.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
alignment score = 238.2
RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
3.487)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
Matrix rotation and translation
0.37961795 0.24211100 -0.89290116 191.06761259
0.01296287 -0.96644625 -0.25654164 332.12351027
-0.92505253 0.08581325 -0.37001879 328.82641259
Axis 0.82850834 0.07780721 -0.55454483
Axis point 0.00000000 136.30341759 249.27961172
Rotation angle (degrees) 168.07628341
Shift along axis 1.79372450
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
0.53918, and length 43.1344
> rename #2 Cb_rotation_axis id #101.3.1.4
> rename #3 Cb_rotation_slabs id #101.3.2.4
> rename #101.3 geometry
> rename #101.3.1 rotation_axes
> rename #101.3.2 rotation_slabs
executed CD20_RTX_define_pseudo_symmetries.cxc
> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
> select zone (H7v16_V & /H,L) 0.1 #1001
Selected 1754 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v16_Va_copy modelId 1002
> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
> select zone (H7v16_V & /I,M) 0.1 #1003
Selected 1710 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v16_Vb_copy modelId 1004
> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
> select zone (H7v16_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v16_Ca_copy modelId 1006
> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
> select zone (H7v16_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v16_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
sequence alignment score = 387.9
RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
5.340)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
Matrix rotation and translation
0.58985298 0.00233427 0.80750728 -45.05678546
0.12316682 -0.98855531 -0.08711100 297.16136614
0.79806228 0.15084078 -0.58338980 65.44859378
Axis 0.89106916 0.03536916 0.45248731
Axis point 0.00000000 147.01172040 55.34624717
Rotation angle (degrees) 172.32693090
Shift along axis -0.02370559
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
0.589874, and length 47.1899
> rename #2 Va_rotation_axis id #102.3.1.1
> rename #3 Va_rotation_slabs id #102.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
sequence alignment score = 378.3
RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
4.620)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
Matrix rotation and translation
0.62864598 0.45103819 -0.63353672 71.77949524
0.53321619 -0.84298968 -0.07105560 212.64664720
-0.56611370 -0.29314322 -0.77044294 368.84403487
Axis -0.90200560 -0.27383758 0.33376470
Axis point -0.00000000 108.05935567 190.41757658
Rotation angle (degrees) 172.92851049
Shift along axis 0.13096924
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
0.594923, and length 47.5938
> rename #2 Vb_rotation_axis id #102.3.1.2
> rename #3 Vb_rotation_slabs id #102.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
sequence alignment score = 403.6
RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
3.184)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
Matrix rotation and translation
-0.62547004 0.41276667 0.66212605 49.05674876
0.08546501 -0.80725952 0.58397585 200.07354667
0.77555333 0.42184801 0.46963954 -95.83522576
Axis -0.42390521 -0.29657098 -0.85577452
Axis point 59.57688139 113.83169245 0.00000000
Rotation angle (degrees) 168.97535276
Shift along axis 1.88192618
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
0.550437, and length 44.0349
> rename #2 Ca_rotation_axis id #102.3.1.3
> rename #3 Ca_rotation_slabs id #102.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
sequence alignment score = 396
RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
3.551)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
Matrix rotation and translation
-0.62894249 0.48033740 -0.61131606 312.62038315
0.14842286 -0.69766113 -0.70088487 336.12735996
-0.76315267 -0.53154955 0.36749568 311.24709675
Axis 0.42085200 0.37736216 -0.82491296
Axis point 256.37284203 220.04020388 0.00000000
Rotation angle (degrees) 168.39393838
Shift along axis 1.65689588
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
0.534846, and length 42.7877
> rename #2 Cb_rotation_axis id #102.3.1.4
> rename #3 Cb_rotation_slabs id #102.3.2.4
> rename #102.3 geometry
> rename #102.3.1 rotation_axes
> rename #102.3.2 rotation_slabs
executed CD20_2H7v16_define_pseudo_symmetries.cxc
> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
Selected 1654 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
Selected 1678 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
L (#1002), sequence alignment score = 547.6
RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
2.607)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
coordinates:
Matrix rotation and translation
0.73992366 -0.12116101 0.66168949 -29.70332856
-0.06116680 -0.99168902 -0.11318795 332.06337928
0.66990417 0.04327702 -0.74118520 123.44534698
Axis 0.93259437 -0.04896279 0.35758970
Axis point 0.00000000 162.47254458 74.89799404
Rotation angle (degrees) 175.18797763
Shift along axis 0.18287681
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
0.599212, and length 47.937
> rename #2 Va_rotation_axis id #103.3.1.1
> rename #3 Va_rotation_slabs id #103.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
M (#1004), sequence alignment score = 376.5
RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
3.886)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
coordinates:
Matrix rotation and translation
0.72982969 -0.01372193 -0.68349128 135.94952936
0.06485007 -0.99390027 0.08920045 287.47713002
-0.68054617 -0.10942560 -0.72448806 354.00628960
Axis -0.92979963 -0.01378652 0.36780781
Axis point 0.00000000 152.92822789 195.61279282
Rotation angle (degrees) 173.86847166
Shift along axis -0.16285394
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
0.597156, and length 47.7725
> rename #2 Vb_rotation_axis id #103.3.1.2
> rename #3 Vb_rotation_slabs id #103.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
L (#1006), sequence alignment score = 554.5
RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
3.119)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
coordinates:
Matrix rotation and translation
-0.33391401 0.38072466 0.86229355 -12.40856576
0.05205532 -0.90595556 0.42016042 245.78035810
0.94116506 0.18518442 0.28269251 -52.33839393
Axis -0.57081123 -0.19159720 -0.79841408
Axis point 28.53870248 129.91224226 0.00000000
Rotation angle (degrees) 168.12212217
Shift along axis 1.77983022
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
0.56909, and length 45.5272
> rename #2 Ca_rotation_axis id #103.3.1.3
> rename #3 Ca_rotation_slabs id #103.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
M (#1008), sequence alignment score = 416.6
RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
3.361)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
coordinates:
Matrix rotation and translation
-0.50667380 0.40781938 -0.75958213 323.22163731
0.08178140 -0.85433688 -0.51324487 330.95129120
-0.85825023 -0.32216741 0.39951808 287.19953324
Axis 0.48922423 0.25262440 -0.83476977
Axis point 265.28291179 189.90297685 0.00000000
Rotation angle (degrees) 168.73855860
Shift along axis 1.98873850
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
0.553583, and length 44.2867
> rename #2 Cb_rotation_axis id #103.3.1.4
> rename #3 Cb_rotation_slabs id #103.3.2.4
> rename #103.3 geometry
> rename #103.3.1 rotation_axes
> rename #103.3.2 rotation_slabs
executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
> open
> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
Selected 1734 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
Selected 1678 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
2H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 381.4
RMSD between 68 pruned atom pairs is 1.006 angstroms; (across all 103 pairs:
3.728)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
#1001 coordinates:
Matrix rotation and translation
0.71569156 -0.03206360 0.69768010 -44.96691323
0.04686485 -0.99448942 -0.09377893 313.22701875
0.69684236 0.09981346 -0.71024503 107.14739664
Axis 0.92598883 0.00400704 0.37752965
Axis point 0.00000000 153.67931126 71.60444720
Rotation angle (degrees) 173.99975082
Shift along axis 0.06757359
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [136.48132211 154.26990862
127.24847182] with direction [0.92598883 0.00400704 0.37752965], radius
0.603729, and length 48.2983
> rename #2 Va_rotation_axis id #104.3.1.1
> rename #3 Va_rotation_slabs id #104.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
2H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 348.3
RMSD between 69 pruned atom pairs is 1.043 angstroms; (across all 94 pairs:
4.124)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
#1003 coordinates:
Matrix rotation and translation
0.73259686 -0.07112185 -0.67693686 143.43240534
0.01935436 -0.99194728 0.12516391 289.93644026
-0.68038757 -0.10479637 -0.72532095 353.04193759
Axis -0.93047520 0.01396239 0.36608873
Axis point 0.00000000 157.81290376 195.07385462
Rotation angle (degrees) 172.90173563
Shift along axis -0.16741650
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [172.87152644 155.21885305
127.05880479] with direction [-0.9304752 0.01396239 0.36608873], radius
0.606168, and length 48.4934
> rename #2 Vb_rotation_axis id #104.3.1.2
> rename #3 Vb_rotation_slabs id #104.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
2H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 396.1
RMSD between 52 pruned atom pairs is 0.923 angstroms; (across all 98 pairs:
3.306)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
#1005 coordinates:
Matrix rotation and translation
-0.43925296 0.41144710 0.79860386 4.35549593
0.03727237 -0.87984204 0.47380244 231.94081966
0.89758989 0.23788498 0.37113761 -66.19774762
Axis -0.52046834 -0.21837763 -0.82548405
Axis point 39.20275524 124.36112361 0.00000000
Rotation angle (degrees) 166.90068945
Shift along axis 1.72760165
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [105.62839077 152.23193079
105.353773 ] with direction [-0.52046834 -0.21837763 -0.82548405], radius
0.559049, and length 44.7239
> rename #2 Ca_rotation_axis id #104.3.1.3
> rename #3 Ca_rotation_slabs id #104.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
2H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 364.8
RMSD between 58 pruned atom pairs is 1.017 angstroms; (across all 98 pairs:
3.237)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
#1007 coordinates:
Matrix rotation and translation
-0.44280624 0.37609436 -0.81392608 322.15113366
0.04984109 -0.89604575 -0.44115517 333.30838934
-0.89523098 -0.23591322 0.37802969 283.50270597
Axis 0.52101945 0.20639753 -0.82821422
Axis point 270.23926430 182.69476034 0.00000000
Rotation angle (degrees) 168.64064548
Shift along axis 1.84005980
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [203.87494881 156.40508754
105.49293398] with direction [ 0.52101945 0.20639753 -0.82821422], radius
0.566399, and length 45.312
> rename #2 Cb_rotation_axis id #104.3.1.4
> rename #3 Cb_rotation_slabs id #104.3.2.4
> rename #104.3 geometry
> rename #104.3.1 rotation_axes
> rename #104.3.2 rotation_slabs
executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
> open CD20_2H7_mutants_define_domain_centroids.cxc
> define centroid RTX_C & /L name centroid_RTX_C_L
Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
> rename ##name=centroid_RTX_C_L id 101.3.3.1
> define centroid RTX_C & /M name centroid_RTX_C_M
Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
> rename ##name=centroid_RTX_C_M id 101.3.3.2
> define centroid RTX_C & /H name centroid_RTX_C_H
Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
> rename ##name=centroid_RTX_C_H id 101.3.3.3
> define centroid RTX_C & /I name centroid_RTX_C_I
Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
> rename ##name=centroid_RTX_C_I id 101.3.3.4
> define centroid RTX_V & /L name centroid_RTX_V_L
Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
> rename ##name=centroid_RTX_V_L id 101.3.3.5
> define centroid RTX_V & /M name centroid_RTX_V_M
Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
> rename ##name=centroid_RTX_V_M id 101.3.3.6
> define centroid RTX_V & /H name centroid_RTX_V_H
Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
> rename ##name=centroid_RTX_V_H id 101.3.3.7
> define centroid RTX_V & /I name centroid_RTX_V_I
Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
> rename ##name=centroid_RTX_V_I id 101.3.3.8
> rename #101.3.3 centroids
> define centroid H7v16_C & /L name centroid_2H7v16_C_L
Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
104.71732873]
> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
> define centroid H7v16_C & /M name centroid_2H7v16_C_M
Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
109.46892346]
> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
> define centroid H7v16_C & /H name centroid_2H7v16_C_H
Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
100.10963479]
> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
> define centroid H7v16_C & /I name centroid_2H7v16_C_I
Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
103.22787118]
> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
> define centroid H7v16_V & /L name centroid_2H7v16_V_L
Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
124.64938243]
> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
> define centroid H7v16_V & /M name centroid_2H7v16_V_M
Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
126.48898691]
> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
> define centroid H7v16_V & /H name centroid_2H7v16_V_H
Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
126.96669027]
> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
> define centroid H7v16_V & /I name centroid_2H7v16_V_I
Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
126.76187738]
> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
> rename #102.3.3 centroids
> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
111.74271267]
> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
109.3226675 ]
> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
105.03944622]
> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
103.22947676]
> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
127.91858459]
> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
127.2169787 ]
> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
127.54490507]
> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
127.29650809]
> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
> rename #103.3.3 centroids
> define centroid CD20 & /C name centroid_CD20_C
Centroid 'centroid_CD20_C' placed at [144.85124361 155.47295008 168.48352542]
> rename ##name=centroid_CD20_C id 101.3.3.9
> define centroid CD20 & /D name centroid_CD20_D
Centroid 'centroid_CD20_D' placed at [165.21151856 155.17682163 168.76082258]
> rename ##name=centroid_CD20_D id 101.3.3.10
executed CD20_2H7_mutants_define_domain_centroids.cxc
> turn x 90
> view
> hide #101 models
> hide #!102.2 models
> ~ribbon #102.10/X,Y
executed CD20_2H7_mutants_setup.cxc
> hide #!104 models
> hide #!103 models
> show #!102.2 models
> show #!101 models
> show #101.1 models
> show #!101.3 models
> show #!101.3.1 models
> show #!101.3.2 models
> show #!101.3.3 models
> hide #!102.2 models
> hide #!101.3 models
> hide #!102.3 models
> hide #!102.10 models
> hide #!102 models
> show #!101.3 models
> hide #!101.3.1 models
> show #!101.3.1 models
> show #!101.3.1.1 models
> show #!101.3.1.2 models
> show #!101.3.1.3 models
> show #!101.3.1.4 models
> show #101.3.3.1 models
> show #101.3.3.2 models
> show #101.3.3.3 models
> show #101.3.3.4 models
> show #101.3.3.5 models
> show #101.3.3.6 models
> show #101.3.3.7 models
> show #101.3.3.8 models
> show #101.3.3.9 models
> show #101.3.3.10 models
> show #!102 models
> hide #!102 models
> hide #101.1 models
> show #!102 models
> hide #!102.1 models
> show #!102.3 models
> hide #!102.3.2 models
> close
> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
> close
> cd /Users/rohoua/work/Genentech/CD20
Current working directory is: /Users/rohoua/work/Genentech/CD20
> open pdb:6vja name CD20_RTX id 101.1
CD20_RTX title:
Structure of CD20 in complex with rituximab Fab [more info...]
Chain information for CD20_RTX #1
---
Chain | Description | UniProt
C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
H I | Rituximab Fab heavy chain |
L M | Rituximab Fab light chain |
Non-standard residues in CD20_RTX #1
---
Y01 — cholesterol hemisuccinate
> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7668 version_2 2023.12.13
CD20_2H7v16 title:
Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
resolution. [more info...]
Chain information for CD20_2H7v16 #1
---
Chain | Description
C D | No description available
H I | No description available
L M | No description available
Non-standard residues in CD20_2H7v16 #1
---
Y01 — (Y01)
> open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
shown at level 0.0054, step 2, values float32
> volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
> view matrix models
> #102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92
> open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
> 102.10
Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
Fab.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7487 version_1 2023.05.24
2H7v16_XRay title:
Structure of 2H7 Fab at 2.45 A resolution. [more info...]
Chain information for 2H7v16_XRay #1
---
Chain | Description
A B X Y | No description available
Non-standard residues in 2H7v16_XRay #1
---
CL — (CL)
> matchmaker #102.10/A,B to #102.1/H,L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
sequence alignment score = 1228.2
RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
0.804)
> open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
> 103.1
Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7717 version_2 2023.12.15
CD20_2H7v166_D56A title:
Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
info...]
Chain information for CD20_2H7v166_D56A #1
---
Chain | Description
C D | No description available
H I | No description available
L | No description available
M | No description available
Non-standard residues in CD20_2H7v166_D56A #1
---
Y01 — (Y01)
> open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32
> volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
> view matrix models
> #103.2,0.00937853,0.99467855,-0.10259937,-18.50914227,-0.99948588,0.00617870,-0.03146112,352.75851684,-0.03065977,0.10284168,0.99422511,-49.28949280
> open CD20_2H7v166_S92A_D56A/STR7729_alito6vja.pdb name
> CD20_2H7v166_S92A_D56A id 104.1
Summary of feedback from opening CD20_2H7v166_S92A_D56A/STR7729_alito6vja.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7729 version_1 2024.01.12
CD20_2H7v166_S92A_D56A title:
Structure of ABP1AB10781 and Hs_CD20.M1-P297 at 4.5 A resolution. [more
info...]
Chain information for CD20_2H7v166_S92A_D56A #1
---
Chain | Description
C | No description available
D | No description available
H I | No description available
L | No description available
M | No description available
> open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
> id 104.2
Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
> volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
> view matrix models
> #104.2,-0.00249470,0.97079708,0.23988915,-104.32503408,0.99657176,0.02225139,-0.07968446,-45.21631074,-0.08269530,0.23886796,-0.96752446,330.43463437
> rename #101 CD20_RTX
> rename #102 CD20_2H7v16
> rename #103 CD20_2H7v166_D56A
> rename #104 CD20_2H7v166_S92A_D56A
> dssp
> name CD20_RTX #101.1
> name CD20_2H7v16 #102.1
> name CD20_2H7v166_D56A #103.1
> name CD20_2H7v166_S92A_D56A #104.1
> name CD20 /C,D
> name CD20_Monomer /C
> name CD20_H1 /C,D:46-71
> name CD20_ECL1 /C,D:72-79
> name CD20_H2 /C,D:80-105
> name CD20_ICL1 /C,D:106-112
> name CD20_H3 /C,D:113-141
> name CD20_ECL2 /C,D:142-187
> name CD20_ECL2SS /C,D:167,183
> name CD20_H4 /C,D:188-end
> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
> name RTX CD20_RTX & /H,L,I,M
> name RTX_H RTX & /H,I
> name RTX_L RTX & /L,M
> name RTX_Epitope CD20_RTX & /C,D:168-175
> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
> name H7v16 CD20_2H7v16 & /H,L,I,M
> name H7v16_H H7v16 & /H,I
> name H7v16_L H7v16 & /L,M
> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
> name H7v166_D56A_H H7v166_D56A & /H,I
> name H7v166_D56A_L H7v166_D56A & /L,M
> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
> /H,I:119-end)
> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
> & /H,I:1-111)
> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
> (H7v166_S92A_D56A & /H,I:119-end)
> lighting soft
> set bgColor white
> camera ortho
> style stick
Changed 44407 atom styles
> color byhetero
> open CD20_2H7_mutants_color.cxc
> color CD20 burlywood
> color modify CD20_H1 hue - 20
> color modify CD20_H2 hue - 10
> color modify CD20_H3 hue + 0
> color modify CD20_H4 hue + 10
> color modify CD20_ECL1 hue +10
> color modify CD20_ECL2 hue + 40
> color modify CD20 saturation + 80
> color CD20_ECL2 rgb(127,165,90)
> color CD20_H4 rgb(176,215,142)
> color RTX plum
> color modify RTX_H hue - 40
> color H7v16 slate blue
> color modify H7v16_H hue - 40
> color H7v166_D56A dodger blue
> color modify H7v166_D56A_H hue - 40
> color H7v166_S92A_D56A purple
> color modify H7v166_S92A_D56A_H hue - 40
executed CD20_2H7_mutants_color.cxc
> hide
> ribbon
> show CD20_ECL2SS
> style CD20_ECL2SS stick
Changed 96 atom styles
> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
radius 1, and length 140
> marker #1.1 position 155,155,70
> marker #1.1 position 155,155,210
> select
> #101.1/C,D:73,74,75,76,77,78,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,184,185,186,187,188
440 atoms, 446 bonds, 54 residues, 1 model selected
> define plane sel name membrane_plane
Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
> rename ##name=membrane_plane id 10
> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
> combine CD20_RTX name RTX_Va modelId 1001
> select zone (RTX_V & /H,L) 0.1 #1001
Selected 1711 atoms
> delete #1001 & ~sel
> combine #1001 name RTX_Va_copy modelId 1002
> combine CD20_RTX name RTX_Vb modelId 1003
> select zone (RTX_V & /I,M) 0.1 #1003
Selected 1711 atoms
> delete #1003 & ~sel
> combine #1003 name RTX_Vb_copy modelId 1004
> combine CD20_RTX name RTX_Ca modelId 1005
> select zone (RTX_C & /H,L) 0.1 #1005
Selected 1503 atoms
> delete #1005 & ~sel
> combine #1005 name RTX_Ca_copy modelId 1006
> combine CD20_RTX name RTX_Cb modelId 1007
> select zone (RTX_C & /I,M) 0.1 #1007
Selected 1503 atoms
> delete #1007 & ~sel
> combine #1007 name RTX_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
alignment score = 198.7
RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
4.421)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
Matrix rotation and translation
0.65377294 -0.06463426 0.75392530 -36.97668460
0.02426941 -0.99404163 -0.10626495 318.59247232
0.75630149 0.08777047 -0.64830888 90.28955685
Axis 0.90906034 -0.01113250 0.41651574
Axis point 0.00000000 156.41772375 62.99337678
Rotation angle (degrees) 173.87355102
Shift along axis 0.44625393
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
0.65062, and length 52.0496
> rename #2 Va_rotation_axis id #101.3.1.1
> rename #3 Va_rotation_slabs id #101.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
alignment score = 214.3
RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
4.448)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
Matrix rotation and translation
0.65527690 -0.06129532 -0.75289778 163.48223927
0.03113398 -0.99366393 0.10799385 290.56686667
-0.75474688 -0.09420658 -0.64921665 352.74817189
Axis -0.90945183 0.00831685 0.41572611
Axis point 0.00000000 156.83903630 204.83255489
Rotation angle (degrees) 173.61745932
Shift along axis 0.38400661
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
0.648586, and length 51.8869
> rename #2 Vb_rotation_axis id #101.3.1.2
> rename #3 Vb_rotation_slabs id #101.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
alignment score = 238.2
RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
3.308)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
Matrix rotation and translation
0.37780344 0.24165354 0.89379423 -73.66252391
0.01279825 -0.96661035 0.25593093 273.63534365
0.92579737 -0.08525258 -0.36828146 68.27322422
Axis -0.82796624 -0.07766353 -0.55537400
Axis point 0.00000000 144.62953182 41.62502778
Rotation angle (degrees) 168.10978391
Shift along axis 1.82142171
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
0.539289, and length 43.1431
> rename #2 Ca_rotation_axis id #101.3.1.3
> rename #3 Ca_rotation_slabs id #101.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
alignment score = 238.2
RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
3.487)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
Matrix rotation and translation
0.37961795 0.24211100 -0.89290116 191.06761259
0.01296287 -0.96644625 -0.25654164 332.12351027
-0.92505253 0.08581325 -0.37001879 328.82641259
Axis 0.82850834 0.07780721 -0.55454483
Axis point 0.00000000 136.30341759 249.27961172
Rotation angle (degrees) 168.07628341
Shift along axis 1.79372450
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
0.53918, and length 43.1344
> rename #2 Cb_rotation_axis id #101.3.1.4
> rename #3 Cb_rotation_slabs id #101.3.2.4
> rename #101.3 geometry
> rename #101.3.1 rotation_axes
> rename #101.3.2 rotation_slabs
executed CD20_RTX_define_pseudo_symmetries.cxc
> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
> select zone (H7v16_V & /H,L) 0.1 #1001
Selected 1754 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v16_Va_copy modelId 1002
> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
> select zone (H7v16_V & /I,M) 0.1 #1003
Selected 1710 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v16_Vb_copy modelId 1004
> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
> select zone (H7v16_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v16_Ca_copy modelId 1006
> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
> select zone (H7v16_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v16_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
sequence alignment score = 387.9
RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
5.340)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
Matrix rotation and translation
0.58985298 0.00233427 0.80750728 -45.05678546
0.12316682 -0.98855531 -0.08711100 297.16136614
0.79806228 0.15084078 -0.58338980 65.44859378
Axis 0.89106916 0.03536916 0.45248731
Axis point 0.00000000 147.01172040 55.34624717
Rotation angle (degrees) 172.32693090
Shift along axis -0.02370559
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
0.589874, and length 47.1899
> rename #2 Va_rotation_axis id #102.3.1.1
> rename #3 Va_rotation_slabs id #102.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
sequence alignment score = 378.3
RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
4.620)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
Matrix rotation and translation
0.62864598 0.45103819 -0.63353672 71.77949524
0.53321619 -0.84298968 -0.07105560 212.64664720
-0.56611370 -0.29314322 -0.77044294 368.84403487
Axis -0.90200560 -0.27383758 0.33376470
Axis point -0.00000000 108.05935567 190.41757658
Rotation angle (degrees) 172.92851049
Shift along axis 0.13096924
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
0.594923, and length 47.5938
> rename #2 Vb_rotation_axis id #102.3.1.2
> rename #3 Vb_rotation_slabs id #102.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
sequence alignment score = 403.6
RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
3.184)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
Matrix rotation and translation
-0.62547004 0.41276667 0.66212605 49.05674876
0.08546501 -0.80725952 0.58397585 200.07354667
0.77555333 0.42184801 0.46963954 -95.83522576
Axis -0.42390521 -0.29657098 -0.85577452
Axis point 59.57688139 113.83169245 0.00000000
Rotation angle (degrees) 168.97535276
Shift along axis 1.88192618
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
0.550437, and length 44.0349
> rename #2 Ca_rotation_axis id #102.3.1.3
> rename #3 Ca_rotation_slabs id #102.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
sequence alignment score = 396
RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
3.551)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
Matrix rotation and translation
-0.62894249 0.48033740 -0.61131606 312.62038315
0.14842286 -0.69766113 -0.70088487 336.12735996
-0.76315267 -0.53154955 0.36749568 311.24709675
Axis 0.42085200 0.37736216 -0.82491296
Axis point 256.37284203 220.04020388 0.00000000
Rotation angle (degrees) 168.39393838
Shift along axis 1.65689588
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
0.534846, and length 42.7877
> rename #2 Cb_rotation_axis id #102.3.1.4
> rename #3 Cb_rotation_slabs id #102.3.2.4
> rename #102.3 geometry
> rename #102.3.1 rotation_axes
> rename #102.3.2 rotation_slabs
executed CD20_2H7v16_define_pseudo_symmetries.cxc
> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
Selected 1654 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
Selected 1678 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
L (#1002), sequence alignment score = 547.6
RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
2.607)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
coordinates:
Matrix rotation and translation
0.73992366 -0.12116101 0.66168949 -29.70332856
-0.06116680 -0.99168902 -0.11318795 332.06337928
0.66990417 0.04327702 -0.74118520 123.44534698
Axis 0.93259437 -0.04896279 0.35758970
Axis point 0.00000000 162.47254458 74.89799404
Rotation angle (degrees) 175.18797763
Shift along axis 0.18287681
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
0.599212, and length 47.937
> rename #2 Va_rotation_axis id #103.3.1.1
> rename #3 Va_rotation_slabs id #103.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
M (#1004), sequence alignment score = 376.5
RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
3.886)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
coordinates:
Matrix rotation and translation
0.72982969 -0.01372193 -0.68349128 135.94952936
0.06485007 -0.99390027 0.08920045 287.47713002
-0.68054617 -0.10942560 -0.72448806 354.00628960
Axis -0.92979963 -0.01378652 0.36780781
Axis point 0.00000000 152.92822789 195.61279282
Rotation angle (degrees) 173.86847166
Shift along axis -0.16285394
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
0.597156, and length 47.7725
> rename #2 Vb_rotation_axis id #103.3.1.2
> rename #3 Vb_rotation_slabs id #103.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
L (#1006), sequence alignment score = 554.5
RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
3.119)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
coordinates:
Matrix rotation and translation
-0.33391401 0.38072466 0.86229355 -12.40856576
0.05205532 -0.90595556 0.42016042 245.78035810
0.94116506 0.18518442 0.28269251 -52.33839393
Axis -0.57081123 -0.19159720 -0.79841408
Axis point 28.53870248 129.91224226 0.00000000
Rotation angle (degrees) 168.12212217
Shift along axis 1.77983022
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
0.56909, and length 45.5272
> rename #2 Ca_rotation_axis id #103.3.1.3
> rename #3 Ca_rotation_slabs id #103.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
M (#1008), sequence alignment score = 416.6
RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
3.361)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
coordinates:
Matrix rotation and translation
-0.50667380 0.40781938 -0.75958213 323.22163731
0.08178140 -0.85433688 -0.51324487 330.95129120
-0.85825023 -0.32216741 0.39951808 287.19953324
Axis 0.48922423 0.25262440 -0.83476977
Axis point 265.28291179 189.90297685 0.00000000
Rotation angle (degrees) 168.73855860
Shift along axis 1.98873850
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
0.553583, and length 44.2867
> rename #2 Cb_rotation_axis id #103.3.1.4
> rename #3 Cb_rotation_slabs id #103.3.2.4
> rename #103.3 geometry
> rename #103.3.1 rotation_axes
> rename #103.3.2 rotation_slabs
executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
> open
> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
Selected 1734 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
Selected 1678 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
2H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 381.4
RMSD between 68 pruned atom pairs is 1.006 angstroms; (across all 103 pairs:
3.728)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
#1001 coordinates:
Matrix rotation and translation
0.71569156 -0.03206360 0.69768010 -44.96691323
0.04686485 -0.99448942 -0.09377893 313.22701875
0.69684236 0.09981346 -0.71024503 107.14739664
Axis 0.92598883 0.00400704 0.37752965
Axis point 0.00000000 153.67931126 71.60444720
Rotation angle (degrees) 173.99975082
Shift along axis 0.06757359
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [136.48132211 154.26990862
127.24847182] with direction [0.92598883 0.00400704 0.37752965], radius
0.603729, and length 48.2983
> rename #2 Va_rotation_axis id #104.3.1.1
> rename #3 Va_rotation_slabs id #104.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
2H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 348.3
RMSD between 69 pruned atom pairs is 1.043 angstroms; (across all 94 pairs:
4.124)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
#1003 coordinates:
Matrix rotation and translation
0.73259686 -0.07112185 -0.67693686 143.43240534
0.01935436 -0.99194728 0.12516391 289.93644026
-0.68038757 -0.10479637 -0.72532095 353.04193759
Axis -0.93047520 0.01396239 0.36608873
Axis point 0.00000000 157.81290376 195.07385462
Rotation angle (degrees) 172.90173563
Shift along axis -0.16741650
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [172.87152644 155.21885305
127.05880479] with direction [-0.9304752 0.01396239 0.36608873], radius
0.606168, and length 48.4934
> rename #2 Vb_rotation_axis id #104.3.1.2
> rename #3 Vb_rotation_slabs id #104.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
2H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 396.1
RMSD between 52 pruned atom pairs is 0.923 angstroms; (across all 98 pairs:
3.306)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
#1005 coordinates:
Matrix rotation and translation
-0.43925296 0.41144710 0.79860386 4.35549593
0.03727237 -0.87984204 0.47380244 231.94081966
0.89758989 0.23788498 0.37113761 -66.19774762
Axis -0.52046834 -0.21837763 -0.82548405
Axis point 39.20275524 124.36112361 0.00000000
Rotation angle (degrees) 166.90068945
Shift along axis 1.72760165
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [105.62839077 152.23193079
105.353773 ] with direction [-0.52046834 -0.21837763 -0.82548405], radius
0.559049, and length 44.7239
> rename #2 Ca_rotation_axis id #104.3.1.3
> rename #3 Ca_rotation_slabs id #104.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
2H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 364.8
RMSD between 58 pruned atom pairs is 1.017 angstroms; (across all 98 pairs:
3.237)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
#1007 coordinates:
Matrix rotation and translation
-0.44280624 0.37609436 -0.81392608 322.15113366
0.04984109 -0.89604575 -0.44115517 333.30838934
-0.89523098 -0.23591322 0.37802969 283.50270597
Axis 0.52101945 0.20639753 -0.82821422
Axis point 270.23926430 182.69476034 0.00000000
Rotation angle (degrees) 168.64064548
Shift along axis 1.84005980
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [203.87494881 156.40508754
105.49293398] with direction [ 0.52101945 0.20639753 -0.82821422], radius
0.566399, and length 45.312
> rename #2 Cb_rotation_axis id #104.3.1.4
> rename #3 Cb_rotation_slabs id #104.3.2.4
> rename #104.3 geometry
> rename #104.3.1 rotation_axes
> rename #104.3.2 rotation_slabs
executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
> open CD20_2H7_mutants_define_domain_centroids.cxc
> define centroid RTX_C & /L name centroid_RTX_C_L
Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
> rename ##name=centroid_RTX_C_L id 101.3.3.1
> define centroid RTX_C & /M name centroid_RTX_C_M
Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
> rename ##name=centroid_RTX_C_M id 101.3.3.2
> define centroid RTX_C & /H name centroid_RTX_C_H
Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
> rename ##name=centroid_RTX_C_H id 101.3.3.3
> define centroid RTX_C & /I name centroid_RTX_C_I
Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
> rename ##name=centroid_RTX_C_I id 101.3.3.4
> define centroid RTX_V & /L name centroid_RTX_V_L
Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
> rename ##name=centroid_RTX_V_L id 101.3.3.5
> define centroid RTX_V & /M name centroid_RTX_V_M
Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
> rename ##name=centroid_RTX_V_M id 101.3.3.6
> define centroid RTX_V & /H name centroid_RTX_V_H
Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
> rename ##name=centroid_RTX_V_H id 101.3.3.7
> define centroid RTX_V & /I name centroid_RTX_V_I
Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
> rename ##name=centroid_RTX_V_I id 101.3.3.8
> rename #101.3.3 centroids
> define centroid H7v16_C & /L name centroid_2H7v16_C_L
Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
104.71732873]
> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
> define centroid H7v16_C & /M name centroid_2H7v16_C_M
Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
109.46892346]
> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
> define centroid H7v16_C & /H name centroid_2H7v16_C_H
Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
100.10963479]
> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
> define centroid H7v16_C & /I name centroid_2H7v16_C_I
Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
103.22787118]
> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
> define centroid H7v16_V & /L name centroid_2H7v16_V_L
Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
124.64938243]
> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
> define centroid H7v16_V & /M name centroid_2H7v16_V_M
Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
126.48898691]
> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
> define centroid H7v16_V & /H name centroid_2H7v16_V_H
Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
126.96669027]
> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
> define centroid H7v16_V & /I name centroid_2H7v16_V_I
Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
126.76187738]
> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
> rename #102.3.3 centroids
> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
111.74271267]
> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
109.3226675 ]
> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
105.03944622]
> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
103.22947676]
> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
127.91858459]
> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
127.2169787 ]
> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
127.54490507]
> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
127.29650809]
> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
> rename #103.3.3 centroids
> define centroid CD20 & /C name centroid_CD20_C
Centroid 'centroid_CD20_C' placed at [144.85124361 155.47295008 168.48352542]
> rename ##name=centroid_CD20_C id 101.3.3.9
> define centroid CD20 & /D name centroid_CD20_D
Centroid 'centroid_CD20_D' placed at [165.21151856 155.17682163 168.76082258]
> rename ##name=centroid_CD20_D id 101.3.3.10
executed CD20_2H7_mutants_define_domain_centroids.cxc
> turn x 90
> view
> hide #101 models
> hide #!102.2 models
> ~ribbon #102.10/X,Y
executed CD20_2H7_mutants_setup.cxc
> hide #!102 models
> hide #!103 models
> hide #!102.1 models
> show #!102.1 models
> hide #!102 models
> hide #!104.2 models
> hide #!104.3 models
> open /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729v2.pdb
Summary of feedback from opening
/Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729v2.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7729 version_2 2024.01.29
STR7729v2.pdb title:
Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
resolution. [more info...]
Chain information for STR7729v2.pdb #2
---
Chain | Description
C D | No description available
H | No description available
I | No description available
L M | No description available
> matchmaker #2 to #104.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CD20_2H7v166_S92A_D56A, chain I (#104.1) with STR7729v2.pdb, chain
I (#2), sequence alignment score = 2027.6
RMSD between 229 pruned atom pairs is 0.178 angstroms; (across all 229 pairs:
0.178)
> save
> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb
> models #2
> close
> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
> close
> cd /Users/rohoua/work/Genentech/CD20
Current working directory is: /Users/rohoua/work/Genentech/CD20
> open pdb:6vja name CD20_RTX id 101.1
CD20_RTX title:
Structure of CD20 in complex with rituximab Fab [more info...]
Chain information for CD20_RTX #1
---
Chain | Description | UniProt
C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
H I | Rituximab Fab heavy chain |
L M | Rituximab Fab light chain |
Non-standard residues in CD20_RTX #1
---
Y01 — cholesterol hemisuccinate
> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
**** Deleted thousands of lines here. Full text is attached as description.txt *****
> name CD20_2H7v166_S92A_D56A #104.1
> name CD20_2H7v166 #105.1
> name CD20 /C,D
> name CD20_Monomer /C
> name CD20_H1 /C,D:46-71
> name CD20_ECL1 /C,D:72-79
> name CD20_H2 /C,D:80-105
> name CD20_ICL1 /C,D:106-112
> name CD20_H3 /C,D:113-141
> name CD20_ECL2 /C,D:142-187
> name CD20_ECL2SS /C,D:167,183
> name CD20_H4 /C,D:188-end
> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
> name RTX CD20_RTX & /H,L,I,M
> name RTX_H RTX & /H,I
> name RTX_L RTX & /L,M
> name RTX_Epitope CD20_RTX & /C,D:168-175
> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
> name H7v16 CD20_2H7v16 & /H,L,I,M
> name H7v16_H H7v16 & /H,I
> name H7v16_L H7v16 & /L,M
> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
> name H7v166_D56A_H H7v166_D56A & /H,I
> name H7v166_D56A_L H7v166_D56A & /L,M
> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
> /H,I:119-end)
> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
> & /H,I:1-111)
> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
> (H7v166_S92A_D56A & /H,I:119-end)
> name H7v166 CD20_2H7v166 & /H,L,I,M
> name H7v166_H H7v166 & /H,I
> name H7v166_L H7v166 & /L,M
> name H7v166_Epitope CD20_2H7v166 & /C,D:168-175
> name H7v166_V (H7v166 & /L,M:1-107) | (H7v166 & /H,I:1-111)
> name H7v166_C (H7v166 & /L,M:112-end) | (H7v166 & /H,I:119-end)
> lighting soft
> set bgColor white
> camera ortho
> style stick
Changed 53407 atom styles
> color byhetero
> open CD20_2H7_mutants_color.cxc
> color CD20 burlywood
> color modify CD20_H1 hue - 20
> color modify CD20_H2 hue - 10
> color modify CD20_H3 hue + 0
> color modify CD20_H4 hue + 10
> color modify CD20_ECL1 hue +10
> color modify CD20_ECL2 hue + 40
> color modify CD20 saturation + 80
> color CD20_ECL2 rgb(127,165,90)
> color CD20_H4 rgb(176,215,142)
> color RTX plum
> color modify RTX_H hue - 40
> color H7v16 slate blue
> color modify H7v16_H hue - 40
> color H7v166_D56A dodger blue
> color modify H7v166_D56A_H hue - 40
> color H7v166_S92A_D56A purple
> color modify H7v166_S92A_D56A_H hue - 40
executed CD20_2H7_mutants_color.cxc
> hide
> ribbon
> show CD20_ECL2SS
> style CD20_ECL2SS stick
Changed 120 atom styles
> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
radius 1, and length 140
> marker #1.1 position 155,155,70
> marker #1.1 position 155,155,210
> select
> #101.1/C,D:73,74,75,76,77,78,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,184,185,186,187,188
440 atoms, 446 bonds, 54 residues, 1 model selected
> define plane sel name membrane_plane
Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
> rename ##name=membrane_plane id 10
> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
> combine CD20_RTX name RTX_Va modelId 1001
> select zone (RTX_V & /H,L) 0.1 #1001
Selected 1711 atoms
> delete #1001 & ~sel
> combine #1001 name RTX_Va_copy modelId 1002
> combine CD20_RTX name RTX_Vb modelId 1003
> select zone (RTX_V & /I,M) 0.1 #1003
Selected 1711 atoms
> delete #1003 & ~sel
> combine #1003 name RTX_Vb_copy modelId 1004
> combine CD20_RTX name RTX_Ca modelId 1005
> select zone (RTX_C & /H,L) 0.1 #1005
Selected 1503 atoms
> delete #1005 & ~sel
> combine #1005 name RTX_Ca_copy modelId 1006
> combine CD20_RTX name RTX_Cb modelId 1007
> select zone (RTX_C & /I,M) 0.1 #1007
Selected 1503 atoms
> delete #1007 & ~sel
> combine #1007 name RTX_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
alignment score = 198.7
RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
4.421)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
Matrix rotation and translation
0.65377294 -0.06463426 0.75392530 -36.97668460
0.02426941 -0.99404163 -0.10626495 318.59247232
0.75630149 0.08777047 -0.64830888 90.28955685
Axis 0.90906034 -0.01113250 0.41651574
Axis point 0.00000000 156.41772375 62.99337678
Rotation angle (degrees) 173.87355102
Shift along axis 0.44625393
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
0.65062, and length 52.0496
> rename #2 Va_rotation_axis id #101.3.1.1
> rename #3 Va_rotation_slabs id #101.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
alignment score = 214.3
RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
4.448)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
Matrix rotation and translation
0.65527690 -0.06129532 -0.75289778 163.48223927
0.03113398 -0.99366393 0.10799385 290.56686667
-0.75474688 -0.09420658 -0.64921665 352.74817189
Axis -0.90945183 0.00831685 0.41572611
Axis point 0.00000000 156.83903630 204.83255489
Rotation angle (degrees) 173.61745932
Shift along axis 0.38400661
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
0.648586, and length 51.8869
> rename #2 Vb_rotation_axis id #101.3.1.2
> rename #3 Vb_rotation_slabs id #101.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
alignment score = 238.2
RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
3.308)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
Matrix rotation and translation
0.37780344 0.24165354 0.89379423 -73.66252391
0.01279825 -0.96661035 0.25593093 273.63534365
0.92579737 -0.08525258 -0.36828146 68.27322422
Axis -0.82796624 -0.07766353 -0.55537400
Axis point 0.00000000 144.62953182 41.62502778
Rotation angle (degrees) 168.10978391
Shift along axis 1.82142171
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
0.539289, and length 43.1431
> rename #2 Ca_rotation_axis id #101.3.1.3
> rename #3 Ca_rotation_slabs id #101.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
alignment score = 238.2
RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
3.487)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
Matrix rotation and translation
0.37961795 0.24211100 -0.89290116 191.06761259
0.01296287 -0.96644625 -0.25654164 332.12351027
-0.92505253 0.08581325 -0.37001879 328.82641259
Axis 0.82850834 0.07780721 -0.55454483
Axis point 0.00000000 136.30341759 249.27961172
Rotation angle (degrees) 168.07628341
Shift along axis 1.79372450
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
0.53918, and length 43.1344
> rename #2 Cb_rotation_axis id #101.3.1.4
> rename #3 Cb_rotation_slabs id #101.3.2.4
> rename #101.3 geometry
> rename #101.3.1 rotation_axes
> rename #101.3.2 rotation_slabs
executed CD20_RTX_define_pseudo_symmetries.cxc
> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
> select zone (H7v16_V & /H,L) 0.1 #1001
Selected 1754 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v16_Va_copy modelId 1002
> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
> select zone (H7v16_V & /I,M) 0.1 #1003
Selected 1710 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v16_Vb_copy modelId 1004
> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
> select zone (H7v16_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v16_Ca_copy modelId 1006
> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
> select zone (H7v16_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v16_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
sequence alignment score = 387.9
RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
5.340)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
Matrix rotation and translation
0.58985298 0.00233427 0.80750728 -45.05678546
0.12316682 -0.98855531 -0.08711100 297.16136614
0.79806228 0.15084078 -0.58338980 65.44859378
Axis 0.89106916 0.03536916 0.45248731
Axis point 0.00000000 147.01172040 55.34624717
Rotation angle (degrees) 172.32693090
Shift along axis -0.02370559
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
0.589874, and length 47.1899
> rename #2 Va_rotation_axis id #102.3.1.1
> rename #3 Va_rotation_slabs id #102.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
sequence alignment score = 378.3
RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
4.620)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
Matrix rotation and translation
0.62864598 0.45103819 -0.63353672 71.77949524
0.53321619 -0.84298968 -0.07105560 212.64664720
-0.56611370 -0.29314322 -0.77044294 368.84403487
Axis -0.90200560 -0.27383758 0.33376470
Axis point -0.00000000 108.05935567 190.41757658
Rotation angle (degrees) 172.92851049
Shift along axis 0.13096924
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
0.594923, and length 47.5938
> rename #2 Vb_rotation_axis id #102.3.1.2
> rename #3 Vb_rotation_slabs id #102.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
sequence alignment score = 403.6
RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
3.184)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
Matrix rotation and translation
-0.62547004 0.41276667 0.66212605 49.05674876
0.08546501 -0.80725952 0.58397585 200.07354667
0.77555333 0.42184801 0.46963954 -95.83522576
Axis -0.42390521 -0.29657098 -0.85577452
Axis point 59.57688139 113.83169245 0.00000000
Rotation angle (degrees) 168.97535276
Shift along axis 1.88192618
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
0.550437, and length 44.0349
> rename #2 Ca_rotation_axis id #102.3.1.3
> rename #3 Ca_rotation_slabs id #102.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
sequence alignment score = 396
RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
3.551)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
Matrix rotation and translation
-0.62894249 0.48033740 -0.61131606 312.62038315
0.14842286 -0.69766113 -0.70088487 336.12735996
-0.76315267 -0.53154955 0.36749568 311.24709675
Axis 0.42085200 0.37736216 -0.82491296
Axis point 256.37284203 220.04020388 0.00000000
Rotation angle (degrees) 168.39393838
Shift along axis 1.65689588
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
0.534846, and length 42.7877
> rename #2 Cb_rotation_axis id #102.3.1.4
> rename #3 Cb_rotation_slabs id #102.3.2.4
> rename #102.3 geometry
> rename #102.3.1 rotation_axes
> rename #102.3.2 rotation_slabs
executed CD20_2H7v16_define_pseudo_symmetries.cxc
> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
Selected 1654 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
Selected 1678 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
L (#1002), sequence alignment score = 547.6
RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
2.607)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
coordinates:
Matrix rotation and translation
0.73992366 -0.12116101 0.66168949 -29.70332856
-0.06116680 -0.99168902 -0.11318795 332.06337928
0.66990417 0.04327702 -0.74118520 123.44534698
Axis 0.93259437 -0.04896279 0.35758970
Axis point 0.00000000 162.47254458 74.89799404
Rotation angle (degrees) 175.18797763
Shift along axis 0.18287681
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
0.599212, and length 47.937
> rename #2 Va_rotation_axis id #103.3.1.1
> rename #3 Va_rotation_slabs id #103.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
M (#1004), sequence alignment score = 376.5
RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
3.886)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
coordinates:
Matrix rotation and translation
0.72982969 -0.01372193 -0.68349128 135.94952936
0.06485007 -0.99390027 0.08920045 287.47713002
-0.68054617 -0.10942560 -0.72448806 354.00628960
Axis -0.92979963 -0.01378652 0.36780781
Axis point 0.00000000 152.92822789 195.61279282
Rotation angle (degrees) 173.86847166
Shift along axis -0.16285394
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
0.597156, and length 47.7725
> rename #2 Vb_rotation_axis id #103.3.1.2
> rename #3 Vb_rotation_slabs id #103.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
L (#1006), sequence alignment score = 554.5
RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
3.119)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
coordinates:
Matrix rotation and translation
-0.33391401 0.38072466 0.86229355 -12.40856576
0.05205532 -0.90595556 0.42016042 245.78035810
0.94116506 0.18518442 0.28269251 -52.33839393
Axis -0.57081123 -0.19159720 -0.79841408
Axis point 28.53870248 129.91224226 0.00000000
Rotation angle (degrees) 168.12212217
Shift along axis 1.77983022
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
0.56909, and length 45.5272
> rename #2 Ca_rotation_axis id #103.3.1.3
> rename #3 Ca_rotation_slabs id #103.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
M (#1008), sequence alignment score = 416.6
RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
3.361)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
coordinates:
Matrix rotation and translation
-0.50667380 0.40781938 -0.75958213 323.22163731
0.08178140 -0.85433688 -0.51324487 330.95129120
-0.85825023 -0.32216741 0.39951808 287.19953324
Axis 0.48922423 0.25262440 -0.83476977
Axis point 265.28291179 189.90297685 0.00000000
Rotation angle (degrees) 168.73855860
Shift along axis 1.98873850
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
0.553583, and length 44.2867
> rename #2 Cb_rotation_axis id #103.3.1.4
> rename #3 Cb_rotation_slabs id #103.3.2.4
> rename #103.3 geometry
> rename #103.3.1 rotation_axes
> rename #103.3.2 rotation_slabs
executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
> open
> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
Selected 1653 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
Selected 1678 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
Selected 1461 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
2H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 221.1
RMSD between 66 pruned atom pairs is 1.048 angstroms; (across all 87 pairs:
3.054)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
#1001 coordinates:
Matrix rotation and translation
0.71841270 -0.03882790 0.69453263 -43.77242719
0.04474713 -0.99379351 -0.10184377 314.28607160
0.69417640 0.10424420 -0.71221645 107.06747282
Axis 0.92669760 0.00160183 0.37580447
Axis point 0.00000000 153.96110044 71.86641580
Rotation angle (degrees) 173.61580296
Shift along axis 0.17606353
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [136.49236761 154.19703207
127.21828189] with direction [0.9266976 0.00160183 0.37580447], radius
0.603625, and length 48.29
> rename #2 Va_rotation_axis id #104.3.1.1
> rename #3 Va_rotation_slabs id #104.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
2H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 228.5
RMSD between 66 pruned atom pairs is 1.088 angstroms; (across all 92 pairs:
3.936)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
#1003 coordinates:
Matrix rotation and translation
0.73661563 -0.07135580 -0.67253682 142.18618798
0.02298296 -0.99120309 0.13033888 288.51761976
-0.67592100 -0.11146654 -0.72849572 353.55093768
Axis -0.93153019 0.01303723 0.36343024
Axis point 0.00000000 157.62360929 194.41945478
Rotation angle (degrees) 172.54257925
Shift along axis -0.19815617
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [172.8655548 155.20426996
126.97712173] with direction [-0.93153019 0.01303723 0.36343024], radius
0.60681, and length 48.5448
> rename #2 Vb_rotation_axis id #104.3.1.2
> rename #3 Vb_rotation_slabs id #104.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
2H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 229.8
RMSD between 50 pruned atom pairs is 0.885 angstroms; (across all 82 pairs:
3.058)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
#1005 coordinates:
Matrix rotation and translation
-0.43223566 0.39105435 0.81255697 5.34243089
0.04124481 -0.89156204 0.45101662 236.01875124
0.90081696 0.22845922 0.36923594 -64.79879197
Axis -0.52502754 -0.20821113 -0.82522373
Axis point 38.63388899 125.78498588 0.00000000
Rotation angle (degrees) 167.76344751
Shift along axis 1.52684600
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [105.63109625 152.35419104
105.30435297] with direction [-0.52502754 -0.20821113 -0.82522373], radius
0.532467, and length 42.5974
> rename #2 Ca_rotation_axis id #104.3.1.3
> rename #3 Ca_rotation_slabs id #104.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
2H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 226.4
RMSD between 57 pruned atom pairs is 0.983 angstroms; (across all 98 pairs:
3.247)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
#1007 coordinates:
Matrix rotation and translation
-0.44691350 0.37987962 -0.80991345 321.97311814
0.04334425 -0.89510032 -0.44375297 334.72634524
-0.89352650 -0.23342428 0.38356682 282.18198422
Axis 0.51860284 0.20616286 -0.82978790
Axis point 269.80743377 182.59879005 0.00000000
Rotation angle (degrees) 168.30019456
Shift along axis 1.83311720
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [203.87433587 156.38806637
105.49592574] with direction [ 0.51860284 0.20616286 -0.8297879 ], radius
0.566216, and length 45.2973
> rename #2 Cb_rotation_axis id #104.3.1.4
> rename #3 Cb_rotation_slabs id #104.3.2.4
> rename #104.3 geometry
> rename #104.3.1 rotation_axes
> rename #104.3.2 rotation_slabs
executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
> open CD20_2H7v166/CD20_2H7v166_define_pseudo_symmetries.cxc
> combine CD20_2H7v166 name 2H7_v166_Va modelId 1001
> select zone (H7v166_V & /H,L) 0.1 #1001
Selected 1657 atoms
> delete #1001 & ~sel
> combine #1001 name 2H7_v166_Va_copy modelId 1002
> combine CD20_2H7v166 name 2H7_v166_Vb modelId 1003
> select zone (H7v166_V & /I,M) 0.1 #1003
Selected 1682 atoms
> delete #1003 & ~sel
> combine #1003 name 2H7_v166_Vb_copy modelId 1004
> combine CD20_2H7v166 name 2H7_v166_Ca modelId 1005
> select zone (H7v166_C & /H,L) 0.1 #1005
Selected 1550 atoms
> delete #1005 & ~sel
> combine #1005 name 2H7_v166_Ca_copy modelId 1006
> combine CD20_2H7v166 name 2H7_v166_Cb modelId 1007
> select zone (H7v166_C & /I,M) 0.1 #1007
Selected 1550 atoms
> delete #1007 & ~sel
> combine #1007 name 2H7_v166_Ca_copy modelId 1008
> matchmaker #1002/L to #1001/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_Va, chain H (#1001) with 2H7_v166_Va_copy, chain L
(#1002), sequence alignment score = 377
RMSD between 66 pruned atom pairs is 1.022 angstroms; (across all 90 pairs:
2.960)
> wait 1
> measure rotation #1002 toModel #1001 showSlabs true
Position of 2H7_v166_Va_copy #1002 relative to 2H7_v166_Va #1001 coordinates:
Matrix rotation and translation
0.74036052 -0.11371993 0.66252101 -31.23158610
-0.02845388 -0.99000464 -0.13813468 329.18077129
0.67160754 0.08341817 -0.73619612 115.46673824
Axis 0.93258730 -0.03824813 0.35891226
Axis point 0.00000000 160.25696876 74.26207800
Rotation angle (degrees) 173.17807255
Shift along axis -0.27430151
> close #1001 #1002
> define axis #2 name axis_Va
Axis 'rotation axis #2/axis_Va' centered at [135.68943718 154.69194858
126.48303609] with direction [ 0.9325873 -0.03824813 0.35891226], radius
0.590651, and length 47.2521
> rename #2 Va_rotation_axis id #105.3.1.1
> rename #3 Va_rotation_slabs id #105.3.2.1
> matchmaker #1004/M to #1003/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_Vb, chain I (#1003) with 2H7_v166_Vb_copy, chain M
(#1004), sequence alignment score = 358.4
RMSD between 69 pruned atom pairs is 0.979 angstroms; (across all 95 pairs:
4.646)
> wait 1
> measure rotation #1004 toModel #1003 showSlabs true
Position of 2H7_v166_Vb_copy #1004 relative to 2H7_v166_Vb #1003 coordinates:
Matrix rotation and translation
0.75743859 0.04690774 -0.65121920 117.86722740
0.12590076 -0.98918973 0.07518427 279.29903150
-0.64065262 -0.13893646 -0.75515620 355.61680478
Axis -0.93718783 -0.04624900 0.34574559
Axis point 0.00000000 147.61804807 191.01165258
Rotation angle (degrees) 173.44045283
Shift along axis -0.42808976
> close #1004 #1003
> define axis #2 name axis_Vb
Axis 'rotation axis #2/axis_Vb' centered at [173.55590691 156.18280566
126.98373076] with direction [-0.93718783 -0.046249 0.34574559], radius
0.594071, and length 47.5257
> rename #2 Vb_rotation_axis id #105.3.1.2
> rename #3 Vb_rotation_slabs id #105.3.2.2
> matchmaker #1006/L to #1005/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_Ca, chain H (#1005) with 2H7_v166_Ca_copy, chain L
(#1006), sequence alignment score = 399.2
RMSD between 58 pruned atom pairs is 1.052 angstroms; (across all 98 pairs:
3.123)
> wait 1
> measure rotation #1006 toModel #1005 showSlabs true
Position of 2H7_v166_Ca_copy #1006 relative to 2H7_v166_Ca #1005 coordinates:
Matrix rotation and translation
-0.36716667 0.38456866 0.84693305 -6.67078745
0.04496994 -0.90212482 0.42912530 243.63516386
0.92906746 0.19564703 0.31393613 -56.48454371
Axis -0.55560865 -0.19545541 -0.80814369
Axis point 32.11829117 129.02332751 0.00000000
Rotation angle (degrees) 167.87118034
Shift along axis 1.73416361
> close #1006 #1005
> define axis #2 name axis_Ca
Axis 'rotation axis #2/axis_Ca' centered at [104.82226786 154.59957746
105.74936185] with direction [-0.55560865 -0.19545541 -0.80814369], radius
0.570192, and length 45.6153
> rename #2 Ca_rotation_axis id #105.3.1.3
> rename #3 Ca_rotation_slabs id #105.3.2.3
> matchmaker #1008/M to #1007/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2H7_v166_Cb, chain I (#1007) with 2H7_v166_Ca_copy, chain M
(#1008), sequence alignment score = 402
RMSD between 56 pruned atom pairs is 0.960 angstroms; (across all 98 pairs:
3.231)
> wait 1
> measure rotation #1008 toModel #1007 showSlabs true
Position of 2H7_v166_Ca_copy #1008 relative to 2H7_v166_Cb #1007 coordinates:
Matrix rotation and translation
-0.45572784 0.44991832 -0.76804013 308.16221430
0.12623181 -0.82146310 -0.55611502 324.81402868
-0.88112296 -0.35038819 0.31756960 307.00257135
Axis 0.51450327 0.28280942 -0.80950925
Axis point 271.86890530 196.87368907 0.00000000
Rotation angle (degrees) 168.46727340
Shift along axis 1.88951223
> close #1008 #1007
> define axis #2 name axis_Cb
Axis 'rotation axis #2/axis_Cb' centered at [204.54770711 159.86893059
105.92183993] with direction [ 0.51450327 0.28280942 -0.80950925], radius
0.553089, and length 44.2472
> rename #2 Cb_rotation_axis id #105.3.1.4
> rename #3 Cb_rotation_slabs id #105.3.2.4
> rename #105.3 geometry
> rename #105.3.1 rotation_axes
> rename #105.3.2 rotation_slabs
executed CD20_2H7v166_define_pseudo_symmetries.cxc
> open CD20_2H7_mutants_define_domain_centroids.cxc
> define centroid RTX_C & /L name centroid_RTX_C_L
Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
> rename ##name=centroid_RTX_C_L id 101.3.3.1
> define centroid RTX_C & /M name centroid_RTX_C_M
Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
> rename ##name=centroid_RTX_C_M id 101.3.3.2
> define centroid RTX_C & /H name centroid_RTX_C_H
Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
> rename ##name=centroid_RTX_C_H id 101.3.3.3
> define centroid RTX_C & /I name centroid_RTX_C_I
Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
> rename ##name=centroid_RTX_C_I id 101.3.3.4
> define centroid RTX_V & /L name centroid_RTX_V_L
Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
> rename ##name=centroid_RTX_V_L id 101.3.3.5
> define centroid RTX_V & /M name centroid_RTX_V_M
Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
> rename ##name=centroid_RTX_V_M id 101.3.3.6
> define centroid RTX_V & /H name centroid_RTX_V_H
Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
> rename ##name=centroid_RTX_V_H id 101.3.3.7
> define centroid RTX_V & /I name centroid_RTX_V_I
Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
> rename ##name=centroid_RTX_V_I id 101.3.3.8
> rename #101.3.3 centroids
> define centroid H7v16_C & /L name centroid_2H7v16_C_L
Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
104.71732873]
> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
> define centroid H7v16_C & /M name centroid_2H7v16_C_M
Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
109.46892346]
> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
> define centroid H7v16_C & /H name centroid_2H7v16_C_H
Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
100.10963479]
> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
> define centroid H7v16_C & /I name centroid_2H7v16_C_I
Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
103.22787118]
> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
> define centroid H7v16_V & /L name centroid_2H7v16_V_L
Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
124.64938243]
> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
> define centroid H7v16_V & /M name centroid_2H7v16_V_M
Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
126.48898691]
> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
> define centroid H7v16_V & /H name centroid_2H7v16_V_H
Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
126.96669027]
> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
> define centroid H7v16_V & /I name centroid_2H7v16_V_I
Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
126.76187738]
> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
> rename #102.3.3 centroids
> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
111.74271267]
> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
109.3226675 ]
> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
105.03944622]
> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
103.22947676]
> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
127.91858459]
> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
127.2169787 ]
> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
127.54490507]
> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
127.29650809]
> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
> rename #103.3.3 centroids
> define centroid CD20 & /C name centroid_CD20_C
Centroid 'centroid_CD20_C' placed at [144.71880576 155.32713058 168.44437979]
> rename ##name=centroid_CD20_C id 101.3.3.9
> define centroid CD20 & /D name centroid_CD20_D
Centroid 'centroid_CD20_D' placed at [165.28259991 155.13681165 168.62706115]
> rename ##name=centroid_CD20_D id 101.3.3.10
executed CD20_2H7_mutants_define_domain_centroids.cxc
> turn x 90
> view
> hide #101 models
> hide #!102.2 models
> ~ribbon #102.10/X,Y
executed CD20_2H7_mutants_setup.cxc
> show #!102.2 models
> show #!101 models
> show #101.1 models
> show #!101.3 models
> hide #!101 models
> hide #!102 models
> hide #!103 models
> hide #!104 models
> hide #!105 models
> show #!101 models
> show #!102 models
> hide #!102 models
> show #!102 models
> hide #!102.10 models
> hide #!102.2 models
> hide #!102 models
> show #!102 models
> hide #!102.3 models
> hide #!102 models
> show #!102 models
> hide #!102 models
> show #!102 models
> hide #!102 models
> show #!102 models
> hide #!102 models
> show #!102 models
> hide #!102 models
> show #!102 models
> hide #!102 models
> show #!102 models
> hide #!102 models
> show #!102 models
> hide #!102 models
> open /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A/STR7731.pdb
Summary of feedback from opening
/Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A/STR7731.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7731 version_1 2024.01.12
STR7731.pdb title:
Structure of 2H7v166 LC.S92A Fab and Hs_CD20.M1-P297 at 4.5 A resolut ion.
[more info...]
Chain information for STR7731.pdb #2
---
Chain | Description
C | No description available
D | No description available
H I | No description available
L | No description available
M | No description available
> select ~sel & ##selected
Nothing selected
> matchmaker #2/C,D to #101/C,D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CD20_RTX, chain D (#101.1) with STR7731.pdb, chain D (#2), sequence
alignment score = 1147.4
RMSD between 149 pruned atom pairs is 0.818 angstroms; (across all 158 pairs:
1.025)
> view matrix
view matrix camera
0.97626,0.15017,0.1561,198.03,-0.2019,0.36983,0.9069,440.11,0.078453,-0.91688,0.39137,230.3
view matrix models
#101,1,0,0,0,0,1,0,0,0,0,1,0,#101.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.9,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.10,1,0,0,0,0,1,0,0,0,0,1,0,#102,1,0,0,0,0,1,0,0,0,0,1,0,#102.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92,#102.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.10,0.76603,0.10593,0.63402,98.602,-0.63362,-0.041732,0.77252,142.28,0.10829,-0.9935,0.035152,135.31,#102.10.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#103,1,0,0,0,0,1,0,0,0,0,1,0,#103.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.2,0.0093785,0.99468,-0.1026,-18.509,-0.99949,0.0061787,-0.031461,352.76,-0.03066,0.10284,0.99423,-49.289,#103.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#104,1,0,0,0,0,1,0,0,0,0,1,0,#104.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.2,-0.0024947,0.9708,0.23989,-104.33,0.99657,0.022251,-0.079684,-45.216,-0.082695,0.23887,-0.96752,330.43,#104.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3,1,0,0,0,0,1,0,0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> save
> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A/STR7731_alito6vja.pdb
> models #2
> view matrix
view matrix camera
0.97626,0.15017,0.1561,198.03,-0.2019,0.36983,0.9069,440.11,0.078453,-0.91688,0.39137,230.3
view matrix models
#101,1,0,0,0,0,1,0,0,0,0,1,0,#101.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.9,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.10,1,0,0,0,0,1,0,0,0,0,1,0,#102,1,0,0,0,0,1,0,0,0,0,1,0,#102.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92,#102.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.10,0.76603,0.10593,0.63402,98.602,-0.63362,-0.041732,0.77252,142.28,0.10829,-0.9935,0.035152,135.31,#102.10.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#103,1,0,0,0,0,1,0,0,0,0,1,0,#103.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.2,0.0093785,0.99468,-0.1026,-18.509,-0.99949,0.0061787,-0.031461,352.76,-0.03066,0.10284,0.99423,-49.289,#103.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#104,1,0,0,0,0,1,0,0,0,0,1,0,#104.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.2,-0.0024947,0.9708,0.23989,-104.33,0.99657,0.022251,-0.079684,-45.216,-0.082695,0.23887,-0.96752,330.43,#104.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3,1,0,0,0,0,1,0,0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OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
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 Pro
Model Identifier: Mac14,7
Model Number: Z16T0006PLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.1 (22G313)
Kernel Version: Darwin 22.6.0
Time since boot: 26 days, 21 hours, 57 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
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: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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-Clipper: 0.22.2
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: 1.7.1
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-ISOLDE: 1.7rc1
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: 2.6.1
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: 1.5.14
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: 1.0.4
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: 1.12.4
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: 1.33.3
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: 0.2.1
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: 4.47.2
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
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: 10.2.0
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: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
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: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Attachments (2)
Change History (11)
by , 21 months ago
| Attachment: | Screenshot 2024-02-05 at 6.22.14 PM.jpg added |
|---|
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Logging |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Log does not scroll to bottom after new command |
by , 21 months ago
| Attachment: | description.txt added |
|---|
This is the full log that had to be truncated because Trac has a 256K limit.
comment:2 by , 21 months ago
I've got a theory. The Log is an html pane and Qt in the past had a weird limit where you could not put more than 1 Mbyte in a Qt pane using a string. So our code switches at 1 Mbyte to using a temporary file to put the html that appears in the Log. Maybe when you reach 1 Mbyte that in the Log that is when the automatic scrolling to the end stops working.
We should test if the Qt 1 Mbyte limit still applies. A few years ago that was because Qt encoded the entire html contents in a URL that it sent to a separate Qt Chromium process and the URL had a limit of 1 Mbyte (or maybe 2 Mbytes). Maybe Qt has improved.
comment:3 by , 21 months ago
I confirm that the problem happens once the Log html reaches the 1000000 character limit where it switches to saving the log contents to a file.
Also I see Qt 6.6.1 still has the 2 MB QWebEngineView.setHtml(html) limit.
comment:4 by , 21 months ago
The ChimeraX Log panel code adds an "onload" javascript method to the Log web page but apparently it does not get called when the web page loads from the same temporary file URL over and over. Tests show it does get called it I change the temporary file every time we add to the log. Don't want to contantly make new temporary files. Could switch back and forth between two. There has to be a better way.
I saw online a suggestion that you can simply run some javascript instead of using the temporary file trick
view.page.runJavaScript(jscript)
that will simply replace the html content. I guess I could also run some more javascript that scrolls to the bottom. But this whole direction may make the log updates synchronous instead of loading from a file which is probably handled asynchronously by the separate Chromium process. So I am reluctant to tamper with this code since the performance of constantly adding to a million character html page is horrifying. Already we know from Tristan that Log updates start bogging down ISOLDE every time a new message is logged pausing for 1/4 second.
comment:5 by , 21 months ago
Once loading from a temporary file it scrolls to (near) the top of the page whenever a new command is executed. That it doesn't execute the onload method after repeatedly loading from the same file seems like a bug.
While onload and also onpageshow don't work when repeatedly loading the temp file, a timer that scrolls to the bottom works, although it is not a good solution
<script>setTimeout(function() { window.scrollTo(0, document.body.scrollHeight); }, 1000)</script>
comment:6 by , 21 months ago
Yes, not a great solution since we suppress scrolling when clicking on cxcmd links in the log (so that you stay in the chain table or whatever interface element is presenting the command link).
comment:7 by , 21 months ago
Other than switching between two temporary files I didn't find anything that made the onload function that scrolls to the bottom work.
comment:8 by , 21 months ago
Here is another way to scroll to the bottom. We could add an option to our HtmlView.setHtml(html, url=None, scroll_to_bottom=False) method and it would use a QWebEngineView.loadFinished callback that scrolls to the bottom like this:
class HtmlView
def init(...):
...
self.loadFinished.connect(self._load_finished)
def setHtml(..., scroll_to_bottom = False):
...
self._scroll_to_bottom = scroll_to_bottom
def _load_finished(self, success):
if self._scroll_to_bottom:
self.page().runJavaScript('window.scrollTo(0, document.body.scrollHeight)')
I tried this and it worked.
comment:9 by , 21 months ago
I'm not too excited to implement any of these hacks.
I think we need to address the problem that having a million character log that constantly grows is a recipe for bad performance.
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Alexis provided this screenshot.