Ticket #14542: description.txt

File description.txt, 296.2 KB (added by Tom Goddard, 21 months ago)

This is the full log that had to be truncated because Trac has a 256K limit.

Line 
1The following bug report has been submitted:
2Platform: macOS-13.6.1-arm64-arm-64bit
3ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
4Description
5Log is not auto-scrolling.
6
7When I asked about this in December on the mailing list, Tom requested I open a bug when I saw this.
8
9Unfortunately I do not know exactly when this started happening, or how to reproduce.
10
11I 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.
12
13In 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.
14
15If 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.
16
17Log:
18> set bgColor white
19
20> lighting soft
21
22UCSF ChimeraX version: 1.7.1 (2024-01-23)
23© 2016-2023 Regents of the University of California. All rights reserved.
24How to cite UCSF ChimeraX
25
26> open
27> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729_real_space_refined_000.cif
28
29Summary of feedback from opening
30/Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729_real_space_refined_000.cif
31---
32warnings | Skipping chem_comp category: Missing column 'type' near line 162
33Missing entity information. Treating each chain as a separate entity.
34Invalid residue range for struct_conf "21": invalid chain "H", near line 116
35Invalid residue range for struct_conf "22": invalid chain "H", near line 117
36Invalid residue range for struct_conf "23": invalid chain "I", near line 118
37Invalid residue range for struct_conf "24": invalid chain "I", near line 119
38Invalid residue range for struct_conf "25": invalid chain "L", near line 120
395 messages similar to the above omitted
40Missing or incomplete sequence information. Inferred polymer connectivity.
41
42
43Chain information for STR7729_real_space_refined_000.cif #1
44---
45Chain | Description
46C | No description available
47D | No description available
48H | No description available
49I | No description available
50L | No description available
51M | No description available
52
53
54> open
55> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
56
57Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #2, grid size
58300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
59
60> lighting soft
61
62> volume #2 step 1
63
64> volume #2 level 0.29
65
66> ~show
67
68> ribbon
69
70> dssp
71
72> volume #2 color #b2b2b2ab
73
74> save
75> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729_mod03.pdb
76> models #1
77
78> close
79
80> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
81
82> close
83
84> cd /Users/rohoua/work/Genentech/CD20
85
86Current working directory is: /Users/rohoua/work/Genentech/CD20
87
88> open pdb:6vja name CD20_RTX id 101.1
89
90CD20_RTX title:
91Structure of CD20 in complex with rituximab Fab [more info...]
92
93Chain information for CD20_RTX #1
94---
95Chain | Description | UniProt
96C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
97H I | Rituximab Fab heavy chain |
98L M | Rituximab Fab light chain |
99
100Non-standard residues in CD20_RTX #1
101---
102Y01 — cholesterol hemisuccinate
103
104
105> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
106
107Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb
108---
109warning | Ignored bad PDB record found on line 1
110HEADER STR7668 version_2 2023.12.13
111
112CD20_2H7v16 title:
113Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
114resolution. [more info...]
115
116Chain information for CD20_2H7v16 #1
117---
118Chain | Description
119C D | No description available
120H I | No description available
121L M | No description available
122
123Non-standard residues in CD20_2H7v16 #1
124---
125Y01 — (Y01)
126
127
128> open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
129
130Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
131shown at level 0.0054, step 2, values float32
132
133> volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
134
135> view matrix models
136> #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
137
138> open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
139> 102.10
140
141Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
142Fab.pdb
143---
144warning | Ignored bad PDB record found on line 1
145HEADER STR7487 version_1 2023.05.24
146
1472H7v16_XRay title:
148Structure of 2H7 Fab at 2.45 A resolution. [more info...]
149
150Chain information for 2H7v16_XRay #1
151---
152Chain | Description
153A B X Y | No description available
154
155Non-standard residues in 2H7v16_XRay #1
156---
157CL — (CL)
158
159
160> matchmaker #102.10/A,B to #102.1/H,L
161
162Parameters
163---
164Chain pairing | bb
165Alignment algorithm | Needleman-Wunsch
166Similarity matrix | BLOSUM-62
167SS fraction | 0.3
168Gap open (HH/SS/other) | 18/18/6
169Gap extend | 1
170SS matrix | | | H | S | O
171---|---|---|---
172H | 6 | -9 | -6
173S | | 6 | -6
174O | | | 4
175Iteration cutoff | 2
176
177Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
178sequence alignment score = 1228.2
179RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
1800.804)
181
182
183> open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
184> 103.1
185
186Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb
187---
188warning | Ignored bad PDB record found on line 1
189HEADER STR7717 version_2 2023.12.15
190
191CD20_2H7v166_D56A title:
192Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
193info...]
194
195Chain information for CD20_2H7v166_D56A #1
196---
197Chain | Description
198C D | No description available
199H I | No description available
200L | No description available
201M | No description available
202
203Non-standard residues in CD20_2H7v166_D56A #1
204---
205Y01 — (Y01)
206
207
208> open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
209
210Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
211300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32
212
213> volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
214
215> view matrix models
216> #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
217
218> open CD20_2H7v166_S92A_D56A/STR7729_alito6vja.pdb name
219> CD20_2H7v166_S92A_D56A id 104.1
220
221Summary of feedback from opening CD20_2H7v166_S92A_D56A/STR7729_alito6vja.pdb
222---
223warning | Ignored bad PDB record found on line 1
224HEADER STR7729 version_1 2024.01.12
225
226CD20_2H7v166_S92A_D56A title:
227Structure of ABP1AB10781 and Hs_CD20.M1-P297 at 4.5 A resolution. [more
228info...]
229
230Chain information for CD20_2H7v166_S92A_D56A #1
231---
232Chain | Description
233C | No description available
234D | No description available
235H I | No description available
236L | No description available
237M | No description available
238
239
240> open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
241> id 104.2
242
243Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
244300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
245
246> volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
247
248> view matrix models
249> #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
250
251> rename #101 CD20_RTX
252
253> rename #102 CD20_2H7v16
254
255> rename #103 CD20_2H7v166_D56A
256
257> rename #104 CD20_2H7v166_S92A_D56A
258
259> dssp
260
261> name CD20_RTX #101.1
262
263> name CD20_2H7v16 #102.1
264
265> name CD20_2H7v166_D56A #103.1
266
267> name CD20_2H7v166_S92A_D56A #104.1
268
269> name CD20 /C,D
270
271> name CD20_Monomer /C
272
273> name CD20_H1 /C,D:46-71
274
275> name CD20_ECL1 /C,D:72-79
276
277> name CD20_H2 /C,D:80-105
278
279> name CD20_ICL1 /C,D:106-112
280
281> name CD20_H3 /C,D:113-141
282
283> name CD20_ECL2 /C,D:142-187
284
285> name CD20_ECL2SS /C,D:167,183
286
287> name CD20_H4 /C,D:188-end
288
289> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
290
291> name RTX CD20_RTX & /H,L,I,M
292
293> name RTX_H RTX & /H,I
294
295> name RTX_L RTX & /L,M
296
297> name RTX_Epitope CD20_RTX & /C,D:168-175
298
299> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
300
301> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
302
303> name H7v16 CD20_2H7v16 & /H,L,I,M
304
305> name H7v16_H H7v16 & /H,I
306
307> name H7v16_L H7v16 & /L,M
308
309> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
310
311> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
312
313> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
314
315> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
316
317> name H7v166_D56A_H H7v166_D56A & /H,I
318
319> name H7v166_D56A_L H7v166_D56A & /L,M
320
321> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
322
323> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
324
325> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
326> /H,I:119-end)
327
328> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
329
330> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
331
332> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
333
334> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
335
336> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
337> & /H,I:1-111)
338
339> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
340> (H7v166_S92A_D56A & /H,I:119-end)
341
342> lighting soft
343
344> set bgColor white
345
346> camera ortho
347
348> style stick
349
350Changed 44407 atom styles
351
352> color byhetero
353
354> open CD20_2H7_mutants_color.cxc
355
356> color CD20 burlywood
357
358> color modify CD20_H1 hue - 20
359
360> color modify CD20_H2 hue - 10
361
362> color modify CD20_H3 hue + 0
363
364> color modify CD20_H4 hue + 10
365
366> color modify CD20_ECL1 hue +10
367
368> color modify CD20_ECL2 hue + 40
369
370> color modify CD20 saturation + 80
371
372> color CD20_ECL2 rgb(127,165,90)
373
374> color CD20_H4 rgb(176,215,142)
375
376> color RTX plum
377
378> color modify RTX_H hue - 40
379
380> color H7v16 slate blue
381
382> color modify H7v16_H hue - 40
383
384> color H7v166_D56A dodger blue
385
386> color modify H7v166_D56A_H hue - 40
387
388> color H7v166_S92A_D56A purple
389
390> color modify H7v166_S92A_D56A_H hue - 40
391
392executed CD20_2H7_mutants_color.cxc
393
394> hide
395
396> ribbon
397
398> show CD20_ECL2SS
399
400> style CD20_ECL2SS stick
401
402Changed 96 atom styles
403
404> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
405
406Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
407radius 1, and length 140
408
409> marker #1.1 position 155,155,70
410
411> marker #1.1 position 155,155,210
412
413> select
414> #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
415
416440 atoms, 446 bonds, 54 residues, 1 model selected
417
418> define plane sel name membrane_plane
419
420Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
421normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
422
423> rename ##name=membrane_plane id 10
424
425> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
426
427> combine CD20_RTX name RTX_Va modelId 1001
428
429> select zone (RTX_V & /H,L) 0.1 #1001
430
431Selected 1711 atoms
432
433> delete #1001 & ~sel
434
435> combine #1001 name RTX_Va_copy modelId 1002
436
437> combine CD20_RTX name RTX_Vb modelId 1003
438
439> select zone (RTX_V & /I,M) 0.1 #1003
440
441Selected 1711 atoms
442
443> delete #1003 & ~sel
444
445> combine #1003 name RTX_Vb_copy modelId 1004
446
447> combine CD20_RTX name RTX_Ca modelId 1005
448
449> select zone (RTX_C & /H,L) 0.1 #1005
450
451Selected 1503 atoms
452
453> delete #1005 & ~sel
454
455> combine #1005 name RTX_Ca_copy modelId 1006
456
457> combine CD20_RTX name RTX_Cb modelId 1007
458
459> select zone (RTX_C & /I,M) 0.1 #1007
460
461Selected 1503 atoms
462
463> delete #1007 & ~sel
464
465> combine #1007 name RTX_Ca_copy modelId 1008
466
467> matchmaker #1002/L to #1001/H
468
469Parameters
470---
471Chain pairing | bb
472Alignment algorithm | Needleman-Wunsch
473Similarity matrix | BLOSUM-62
474SS fraction | 0.3
475Gap open (HH/SS/other) | 18/18/6
476Gap extend | 1
477SS matrix | | | H | S | O
478---|---|---|---
479H | 6 | -9 | -6
480S | | 6 | -6
481O | | | 4
482Iteration cutoff | 2
483
484Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
485alignment score = 198.7
486RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
4874.421)
488
489
490> wait 1
491
492> measure rotation #1002 toModel #1001 showSlabs true
493
494Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
495Matrix rotation and translation
4960.65377294 -0.06463426 0.75392530 -36.97668460
4970.02426941 -0.99404163 -0.10626495 318.59247232
4980.75630149 0.08777047 -0.64830888 90.28955685
499Axis 0.90906034 -0.01113250 0.41651574
500Axis point 0.00000000 156.41772375 62.99337678
501Rotation angle (degrees) 173.87355102
502Shift along axis 0.44625393
503
504
505> close #1001 #1002
506
507> define axis #2 name axis_Va
508
509Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
510125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
5110.65062, and length 52.0496
512
513> rename #2 Va_rotation_axis id #101.3.1.1
514
515> rename #3 Va_rotation_slabs id #101.3.2.1
516
517> matchmaker #1004/M to #1003/I
518
519Parameters
520---
521Chain pairing | bb
522Alignment algorithm | Needleman-Wunsch
523Similarity matrix | BLOSUM-62
524SS fraction | 0.3
525Gap open (HH/SS/other) | 18/18/6
526Gap extend | 1
527SS matrix | | | H | S | O
528---|---|---|---
529H | 6 | -9 | -6
530S | | 6 | -6
531O | | | 4
532Iteration cutoff | 2
533
534Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
535alignment score = 214.3
536RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
5374.448)
538
539
540> wait 1
541
542> measure rotation #1004 toModel #1003 showSlabs true
543
544Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
545Matrix rotation and translation
5460.65527690 -0.06129532 -0.75289778 163.48223927
5470.03113398 -0.99366393 0.10799385 290.56686667
548-0.75474688 -0.09420658 -0.64921665 352.74817189
549Axis -0.90945183 0.00831685 0.41572611
550Axis point 0.00000000 156.83903630 204.83255489
551Rotation angle (degrees) 173.61745932
552Shift along axis 0.38400661
553
554
555> close #1004 #1003
556
557> define axis #2 name axis_Vb
558
559Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
560125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
5610.648586, and length 51.8869
562
563> rename #2 Vb_rotation_axis id #101.3.1.2
564
565> rename #3 Vb_rotation_slabs id #101.3.2.2
566
567> matchmaker #1006/L to #1005/H
568
569Parameters
570---
571Chain pairing | bb
572Alignment algorithm | Needleman-Wunsch
573Similarity matrix | BLOSUM-62
574SS fraction | 0.3
575Gap open (HH/SS/other) | 18/18/6
576Gap extend | 1
577SS matrix | | | H | S | O
578---|---|---|---
579H | 6 | -9 | -6
580S | | 6 | -6
581O | | | 4
582Iteration cutoff | 2
583
584Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
585alignment score = 238.2
586RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
5873.308)
588
589
590> wait 1
591
592> measure rotation #1006 toModel #1005 showSlabs true
593
594Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
595Matrix rotation and translation
5960.37780344 0.24165354 0.89379423 -73.66252391
5970.01279825 -0.96661035 0.25593093 273.63534365
5980.92579737 -0.08525258 -0.36828146 68.27322422
599Axis -0.82796624 -0.07766353 -0.55537400
600Axis point 0.00000000 144.62953182 41.62502778
601Rotation angle (degrees) 168.10978391
602Shift along axis 1.82142171
603
604
605> close #1006 #1005
606
607> define axis #2 name axis_Ca
608
609Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
610110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
6110.539289, and length 43.1431
612
613> rename #2 Ca_rotation_axis id #101.3.1.3
614
615> rename #3 Ca_rotation_slabs id #101.3.2.3
616
617> matchmaker #1008/M to #1007/I
618
619Parameters
620---
621Chain pairing | bb
622Alignment algorithm | Needleman-Wunsch
623Similarity matrix | BLOSUM-62
624SS fraction | 0.3
625Gap open (HH/SS/other) | 18/18/6
626Gap extend | 1
627SS matrix | | | H | S | O
628---|---|---|---
629H | 6 | -9 | -6
630S | | 6 | -6
631O | | | 4
632Iteration cutoff | 2
633
634Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
635alignment score = 238.2
636RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
6373.487)
638
639
640> wait 1
641
642> measure rotation #1008 toModel #1007 showSlabs true
643
644Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
645Matrix rotation and translation
6460.37961795 0.24211100 -0.89290116 191.06761259
6470.01296287 -0.96644625 -0.25654164 332.12351027
648-0.92505253 0.08581325 -0.37001879 328.82641259
649Axis 0.82850834 0.07780721 -0.55454483
650Axis point 0.00000000 136.30341759 249.27961172
651Rotation angle (degrees) 168.07628341
652Shift along axis 1.79372450
653
654
655> close #1008 #1007
656
657> define axis #2 name axis_Cb
658
659Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
660110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
6610.53918, and length 43.1344
662
663> rename #2 Cb_rotation_axis id #101.3.1.4
664
665> rename #3 Cb_rotation_slabs id #101.3.2.4
666
667> rename #101.3 geometry
668
669> rename #101.3.1 rotation_axes
670
671> rename #101.3.2 rotation_slabs
672
673executed CD20_RTX_define_pseudo_symmetries.cxc
674
675> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
676
677> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
678
679> select zone (H7v16_V & /H,L) 0.1 #1001
680
681Selected 1754 atoms
682
683> delete #1001 & ~sel
684
685> combine #1001 name 2H7_v16_Va_copy modelId 1002
686
687> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
688
689> select zone (H7v16_V & /I,M) 0.1 #1003
690
691Selected 1710 atoms
692
693> delete #1003 & ~sel
694
695> combine #1003 name 2H7_v16_Vb_copy modelId 1004
696
697> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
698
699> select zone (H7v16_C & /H,L) 0.1 #1005
700
701Selected 1550 atoms
702
703> delete #1005 & ~sel
704
705> combine #1005 name 2H7_v16_Ca_copy modelId 1006
706
707> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
708
709> select zone (H7v16_C & /I,M) 0.1 #1007
710
711Selected 1550 atoms
712
713> delete #1007 & ~sel
714
715> combine #1007 name 2H7_v16_Ca_copy modelId 1008
716
717> matchmaker #1002/L to #1001/H
718
719Parameters
720---
721Chain pairing | bb
722Alignment algorithm | Needleman-Wunsch
723Similarity matrix | BLOSUM-62
724SS fraction | 0.3
725Gap open (HH/SS/other) | 18/18/6
726Gap extend | 1
727SS matrix | | | H | S | O
728---|---|---|---
729H | 6 | -9 | -6
730S | | 6 | -6
731O | | | 4
732Iteration cutoff | 2
733
734Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
735sequence alignment score = 387.9
736RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
7375.340)
738
739
740> wait 1
741
742> measure rotation #1002 toModel #1001 showSlabs true
743
744Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
745Matrix rotation and translation
7460.58985298 0.00233427 0.80750728 -45.05678546
7470.12316682 -0.98855531 -0.08711100 297.16136614
7480.79806228 0.15084078 -0.58338980 65.44859378
749Axis 0.89106916 0.03536916 0.45248731
750Axis point 0.00000000 147.01172040 55.34624717
751Rotation angle (degrees) 172.32693090
752Shift along axis -0.02370559
753
754
755> close #1001 #1002
756
757> define axis #2 name axis_Va
758
759Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
760125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
7610.589874, and length 47.1899
762
763> rename #2 Va_rotation_axis id #102.3.1.1
764
765> rename #3 Va_rotation_slabs id #102.3.2.1
766
767> matchmaker #1004/M to #1003/I
768
769Parameters
770---
771Chain pairing | bb
772Alignment algorithm | Needleman-Wunsch
773Similarity matrix | BLOSUM-62
774SS fraction | 0.3
775Gap open (HH/SS/other) | 18/18/6
776Gap extend | 1
777SS matrix | | | H | S | O
778---|---|---|---
779H | 6 | -9 | -6
780S | | 6 | -6
781O | | | 4
782Iteration cutoff | 2
783
784Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
785sequence alignment score = 378.3
786RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
7874.620)
788
789
790> wait 1
791
792> measure rotation #1004 toModel #1003 showSlabs true
793
794Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
795Matrix rotation and translation
7960.62864598 0.45103819 -0.63353672 71.77949524
7970.53321619 -0.84298968 -0.07105560 212.64664720
798-0.56611370 -0.29314322 -0.77044294 368.84403487
799Axis -0.90200560 -0.27383758 0.33376470
800Axis point -0.00000000 108.05935567 190.41757658
801Rotation angle (degrees) 172.92851049
802Shift along axis 0.13096924
803
804
805> close #1004 #1003
806
807> define axis #2 name axis_Vb
808
809Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
810125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
8110.594923, and length 47.5938
812
813> rename #2 Vb_rotation_axis id #102.3.1.2
814
815> rename #3 Vb_rotation_slabs id #102.3.2.2
816
817> matchmaker #1006/L to #1005/H
818
819Parameters
820---
821Chain pairing | bb
822Alignment algorithm | Needleman-Wunsch
823Similarity matrix | BLOSUM-62
824SS fraction | 0.3
825Gap open (HH/SS/other) | 18/18/6
826Gap extend | 1
827SS matrix | | | H | S | O
828---|---|---|---
829H | 6 | -9 | -6
830S | | 6 | -6
831O | | | 4
832Iteration cutoff | 2
833
834Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
835sequence alignment score = 403.6
836RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
8373.184)
838
839
840> wait 1
841
842> measure rotation #1006 toModel #1005 showSlabs true
843
844Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
845Matrix rotation and translation
846-0.62547004 0.41276667 0.66212605 49.05674876
8470.08546501 -0.80725952 0.58397585 200.07354667
8480.77555333 0.42184801 0.46963954 -95.83522576
849Axis -0.42390521 -0.29657098 -0.85577452
850Axis point 59.57688139 113.83169245 0.00000000
851Rotation angle (degrees) 168.97535276
852Shift along axis 1.88192618
853
854
855> close #1006 #1005
856
857> define axis #2 name axis_Ca
858
859Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
860101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
8610.550437, and length 44.0349
862
863> rename #2 Ca_rotation_axis id #102.3.1.3
864
865> rename #3 Ca_rotation_slabs id #102.3.2.3
866
867> matchmaker #1008/M to #1007/I
868
869Parameters
870---
871Chain pairing | bb
872Alignment algorithm | Needleman-Wunsch
873Similarity matrix | BLOSUM-62
874SS fraction | 0.3
875Gap open (HH/SS/other) | 18/18/6
876Gap extend | 1
877SS matrix | | | H | S | O
878---|---|---|---
879H | 6 | -9 | -6
880S | | 6 | -6
881O | | | 4
882Iteration cutoff | 2
883
884Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
885sequence alignment score = 396
886RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
8873.551)
888
889
890> wait 1
891
892> measure rotation #1008 toModel #1007 showSlabs true
893
894Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
895Matrix rotation and translation
896-0.62894249 0.48033740 -0.61131606 312.62038315
8970.14842286 -0.69766113 -0.70088487 336.12735996
898-0.76315267 -0.53154955 0.36749568 311.24709675
899Axis 0.42085200 0.37736216 -0.82491296
900Axis point 256.37284203 220.04020388 0.00000000
901Rotation angle (degrees) 168.39393838
902Shift along axis 1.65689588
903
904
905> close #1008 #1007
906
907> define axis #2 name axis_Cb
908
909Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
910105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
9110.534846, and length 42.7877
912
913> rename #2 Cb_rotation_axis id #102.3.1.4
914
915> rename #3 Cb_rotation_slabs id #102.3.2.4
916
917> rename #102.3 geometry
918
919> rename #102.3.1 rotation_axes
920
921> rename #102.3.2 rotation_slabs
922
923executed CD20_2H7v16_define_pseudo_symmetries.cxc
924
925> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
926
927> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
928
929> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
930
931Selected 1654 atoms
932
933> delete #1001 & ~sel
934
935> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
936
937> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
938
939> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
940
941Selected 1678 atoms
942
943> delete #1003 & ~sel
944
945> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
946
947> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
948
949> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
950
951Selected 1550 atoms
952
953> delete #1005 & ~sel
954
955> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
956
957> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
958
959> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
960
961Selected 1550 atoms
962
963> delete #1007 & ~sel
964
965> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
966
967> matchmaker #1002/L to #1001/H
968
969Parameters
970---
971Chain pairing | bb
972Alignment algorithm | Needleman-Wunsch
973Similarity matrix | BLOSUM-62
974SS fraction | 0.3
975Gap open (HH/SS/other) | 18/18/6
976Gap extend | 1
977SS matrix | | | H | S | O
978---|---|---|---
979H | 6 | -9 | -6
980S | | 6 | -6
981O | | | 4
982Iteration cutoff | 2
983
984Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
985L (#1002), sequence alignment score = 547.6
986RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
9872.607)
988
989
990> wait 1
991
992> measure rotation #1002 toModel #1001 showSlabs true
993
994Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
995coordinates:
996Matrix rotation and translation
9970.73992366 -0.12116101 0.66168949 -29.70332856
998-0.06116680 -0.99168902 -0.11318795 332.06337928
9990.66990417 0.04327702 -0.74118520 123.44534698
1000Axis 0.93259437 -0.04896279 0.35758970
1001Axis point 0.00000000 162.47254458 74.89799404
1002Rotation angle (degrees) 175.18797763
1003Shift along axis 0.18287681
1004
1005
1006> close #1001 #1002
1007
1008> define axis #2 name axis_Va
1009
1010Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
1011127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
10120.599212, and length 47.937
1013
1014> rename #2 Va_rotation_axis id #103.3.1.1
1015
1016> rename #3 Va_rotation_slabs id #103.3.2.1
1017
1018> matchmaker #1004/M to #1003/I
1019
1020Parameters
1021---
1022Chain pairing | bb
1023Alignment algorithm | Needleman-Wunsch
1024Similarity matrix | BLOSUM-62
1025SS fraction | 0.3
1026Gap open (HH/SS/other) | 18/18/6
1027Gap extend | 1
1028SS matrix | | | H | S | O
1029---|---|---|---
1030H | 6 | -9 | -6
1031S | | 6 | -6
1032O | | | 4
1033Iteration cutoff | 2
1034
1035Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
1036M (#1004), sequence alignment score = 376.5
1037RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
10383.886)
1039
1040
1041> wait 1
1042
1043> measure rotation #1004 toModel #1003 showSlabs true
1044
1045Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
1046coordinates:
1047Matrix rotation and translation
10480.72982969 -0.01372193 -0.68349128 135.94952936
10490.06485007 -0.99390027 0.08920045 287.47713002
1050-0.68054617 -0.10942560 -0.72448806 354.00628960
1051Axis -0.92979963 -0.01378652 0.36780781
1052Axis point 0.00000000 152.92822789 195.61279282
1053Rotation angle (degrees) 173.86847166
1054Shift along axis -0.16285394
1055
1056
1057> close #1004 #1003
1058
1059> define axis #2 name axis_Vb
1060
1061Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
1062126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
10630.597156, and length 47.7725
1064
1065> rename #2 Vb_rotation_axis id #103.3.1.2
1066
1067> rename #3 Vb_rotation_slabs id #103.3.2.2
1068
1069> matchmaker #1006/L to #1005/H
1070
1071Parameters
1072---
1073Chain pairing | bb
1074Alignment algorithm | Needleman-Wunsch
1075Similarity matrix | BLOSUM-62
1076SS fraction | 0.3
1077Gap open (HH/SS/other) | 18/18/6
1078Gap extend | 1
1079SS matrix | | | H | S | O
1080---|---|---|---
1081H | 6 | -9 | -6
1082S | | 6 | -6
1083O | | | 4
1084Iteration cutoff | 2
1085
1086Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
1087L (#1006), sequence alignment score = 554.5
1088RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
10893.119)
1090
1091
1092> wait 1
1093
1094> measure rotation #1006 toModel #1005 showSlabs true
1095
1096Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
1097coordinates:
1098Matrix rotation and translation
1099-0.33391401 0.38072466 0.86229355 -12.40856576
11000.05205532 -0.90595556 0.42016042 245.78035810
11010.94116506 0.18518442 0.28269251 -52.33839393
1102Axis -0.57081123 -0.19159720 -0.79841408
1103Axis point 28.53870248 129.91224226 0.00000000
1104Rotation angle (degrees) 168.12212217
1105Shift along axis 1.77983022
1106
1107
1108> close #1006 #1005
1109
1110> define axis #2 name axis_Ca
1111
1112Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
1113106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
11140.56909, and length 45.5272
1115
1116> rename #2 Ca_rotation_axis id #103.3.1.3
1117
1118> rename #3 Ca_rotation_slabs id #103.3.2.3
1119
1120> matchmaker #1008/M to #1007/I
1121
1122Parameters
1123---
1124Chain pairing | bb
1125Alignment algorithm | Needleman-Wunsch
1126Similarity matrix | BLOSUM-62
1127SS fraction | 0.3
1128Gap open (HH/SS/other) | 18/18/6
1129Gap extend | 1
1130SS matrix | | | H | S | O
1131---|---|---|---
1132H | 6 | -9 | -6
1133S | | 6 | -6
1134O | | | 4
1135Iteration cutoff | 2
1136
1137Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
1138M (#1008), sequence alignment score = 416.6
1139RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
11403.361)
1141
1142
1143> wait 1
1144
1145> measure rotation #1008 toModel #1007 showSlabs true
1146
1147Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
1148coordinates:
1149Matrix rotation and translation
1150-0.50667380 0.40781938 -0.75958213 323.22163731
11510.08178140 -0.85433688 -0.51324487 330.95129120
1152-0.85825023 -0.32216741 0.39951808 287.19953324
1153Axis 0.48922423 0.25262440 -0.83476977
1154Axis point 265.28291179 189.90297685 0.00000000
1155Rotation angle (degrees) 168.73855860
1156Shift along axis 1.98873850
1157
1158
1159> close #1008 #1007
1160
1161> define axis #2 name axis_Cb
1162
1163Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
1164104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
11650.553583, and length 44.2867
1166
1167> rename #2 Cb_rotation_axis id #103.3.1.4
1168
1169> rename #3 Cb_rotation_slabs id #103.3.2.4
1170
1171> rename #103.3 geometry
1172
1173> rename #103.3.1 rotation_axes
1174
1175> rename #103.3.2 rotation_slabs
1176
1177executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
1178
1179> open
1180> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
1181
1182> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
1183
1184> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
1185
1186Selected 1734 atoms
1187
1188> delete #1001 & ~sel
1189
1190> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
1191
1192> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
1193
1194> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
1195
1196Selected 1678 atoms
1197
1198> delete #1003 & ~sel
1199
1200> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
1201
1202> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
1203
1204> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
1205
1206Selected 1550 atoms
1207
1208> delete #1005 & ~sel
1209
1210> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
1211
1212> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
1213
1214> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
1215
1216Selected 1550 atoms
1217
1218> delete #1007 & ~sel
1219
1220> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
1221
1222> matchmaker #1002/L to #1001/H
1223
1224Parameters
1225---
1226Chain pairing | bb
1227Alignment algorithm | Needleman-Wunsch
1228Similarity matrix | BLOSUM-62
1229SS fraction | 0.3
1230Gap open (HH/SS/other) | 18/18/6
1231Gap extend | 1
1232SS matrix | | | H | S | O
1233---|---|---|---
1234H | 6 | -9 | -6
1235S | | 6 | -6
1236O | | | 4
1237Iteration cutoff | 2
1238
1239Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
12402H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 381.4
1241RMSD between 68 pruned atom pairs is 1.006 angstroms; (across all 103 pairs:
12423.728)
1243
1244
1245> wait 1
1246
1247> measure rotation #1002 toModel #1001 showSlabs true
1248
1249Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
1250#1001 coordinates:
1251Matrix rotation and translation
12520.71569156 -0.03206360 0.69768010 -44.96691323
12530.04686485 -0.99448942 -0.09377893 313.22701875
12540.69684236 0.09981346 -0.71024503 107.14739664
1255Axis 0.92598883 0.00400704 0.37752965
1256Axis point 0.00000000 153.67931126 71.60444720
1257Rotation angle (degrees) 173.99975082
1258Shift along axis 0.06757359
1259
1260
1261> close #1001 #1002
1262
1263> define axis #2 name axis_Va
1264
1265Axis 'rotation axis #2/axis_Va' centered at [136.48132211 154.26990862
1266127.24847182] with direction [0.92598883 0.00400704 0.37752965], radius
12670.603729, and length 48.2983
1268
1269> rename #2 Va_rotation_axis id #104.3.1.1
1270
1271> rename #3 Va_rotation_slabs id #104.3.2.1
1272
1273> matchmaker #1004/M to #1003/I
1274
1275Parameters
1276---
1277Chain pairing | bb
1278Alignment algorithm | Needleman-Wunsch
1279Similarity matrix | BLOSUM-62
1280SS fraction | 0.3
1281Gap open (HH/SS/other) | 18/18/6
1282Gap extend | 1
1283SS matrix | | | H | S | O
1284---|---|---|---
1285H | 6 | -9 | -6
1286S | | 6 | -6
1287O | | | 4
1288Iteration cutoff | 2
1289
1290Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
12912H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 348.3
1292RMSD between 69 pruned atom pairs is 1.043 angstroms; (across all 94 pairs:
12934.124)
1294
1295
1296> wait 1
1297
1298> measure rotation #1004 toModel #1003 showSlabs true
1299
1300Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
1301#1003 coordinates:
1302Matrix rotation and translation
13030.73259686 -0.07112185 -0.67693686 143.43240534
13040.01935436 -0.99194728 0.12516391 289.93644026
1305-0.68038757 -0.10479637 -0.72532095 353.04193759
1306Axis -0.93047520 0.01396239 0.36608873
1307Axis point 0.00000000 157.81290376 195.07385462
1308Rotation angle (degrees) 172.90173563
1309Shift along axis -0.16741650
1310
1311
1312> close #1004 #1003
1313
1314> define axis #2 name axis_Vb
1315
1316Axis 'rotation axis #2/axis_Vb' centered at [172.87152644 155.21885305
1317127.05880479] with direction [-0.9304752 0.01396239 0.36608873], radius
13180.606168, and length 48.4934
1319
1320> rename #2 Vb_rotation_axis id #104.3.1.2
1321
1322> rename #3 Vb_rotation_slabs id #104.3.2.2
1323
1324> matchmaker #1006/L to #1005/H
1325
1326Parameters
1327---
1328Chain pairing | bb
1329Alignment algorithm | Needleman-Wunsch
1330Similarity matrix | BLOSUM-62
1331SS fraction | 0.3
1332Gap open (HH/SS/other) | 18/18/6
1333Gap extend | 1
1334SS matrix | | | H | S | O
1335---|---|---|---
1336H | 6 | -9 | -6
1337S | | 6 | -6
1338O | | | 4
1339Iteration cutoff | 2
1340
1341Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
13422H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 396.1
1343RMSD between 52 pruned atom pairs is 0.923 angstroms; (across all 98 pairs:
13443.306)
1345
1346
1347> wait 1
1348
1349> measure rotation #1006 toModel #1005 showSlabs true
1350
1351Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
1352#1005 coordinates:
1353Matrix rotation and translation
1354-0.43925296 0.41144710 0.79860386 4.35549593
13550.03727237 -0.87984204 0.47380244 231.94081966
13560.89758989 0.23788498 0.37113761 -66.19774762
1357Axis -0.52046834 -0.21837763 -0.82548405
1358Axis point 39.20275524 124.36112361 0.00000000
1359Rotation angle (degrees) 166.90068945
1360Shift along axis 1.72760165
1361
1362
1363> close #1006 #1005
1364
1365> define axis #2 name axis_Ca
1366
1367Axis 'rotation axis #2/axis_Ca' centered at [105.62839077 152.23193079
1368105.353773 ] with direction [-0.52046834 -0.21837763 -0.82548405], radius
13690.559049, and length 44.7239
1370
1371> rename #2 Ca_rotation_axis id #104.3.1.3
1372
1373> rename #3 Ca_rotation_slabs id #104.3.2.3
1374
1375> matchmaker #1008/M to #1007/I
1376
1377Parameters
1378---
1379Chain pairing | bb
1380Alignment algorithm | Needleman-Wunsch
1381Similarity matrix | BLOSUM-62
1382SS fraction | 0.3
1383Gap open (HH/SS/other) | 18/18/6
1384Gap extend | 1
1385SS matrix | | | H | S | O
1386---|---|---|---
1387H | 6 | -9 | -6
1388S | | 6 | -6
1389O | | | 4
1390Iteration cutoff | 2
1391
1392Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
13932H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 364.8
1394RMSD between 58 pruned atom pairs is 1.017 angstroms; (across all 98 pairs:
13953.237)
1396
1397
1398> wait 1
1399
1400> measure rotation #1008 toModel #1007 showSlabs true
1401
1402Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
1403#1007 coordinates:
1404Matrix rotation and translation
1405-0.44280624 0.37609436 -0.81392608 322.15113366
14060.04984109 -0.89604575 -0.44115517 333.30838934
1407-0.89523098 -0.23591322 0.37802969 283.50270597
1408Axis 0.52101945 0.20639753 -0.82821422
1409Axis point 270.23926430 182.69476034 0.00000000
1410Rotation angle (degrees) 168.64064548
1411Shift along axis 1.84005980
1412
1413
1414> close #1008 #1007
1415
1416> define axis #2 name axis_Cb
1417
1418Axis 'rotation axis #2/axis_Cb' centered at [203.87494881 156.40508754
1419105.49293398] with direction [ 0.52101945 0.20639753 -0.82821422], radius
14200.566399, and length 45.312
1421
1422> rename #2 Cb_rotation_axis id #104.3.1.4
1423
1424> rename #3 Cb_rotation_slabs id #104.3.2.4
1425
1426> rename #104.3 geometry
1427
1428> rename #104.3.1 rotation_axes
1429
1430> rename #104.3.2 rotation_slabs
1431
1432executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
1433
1434> open CD20_2H7_mutants_define_domain_centroids.cxc
1435
1436> define centroid RTX_C & /L name centroid_RTX_C_L
1437
1438Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
1439
1440> rename ##name=centroid_RTX_C_L id 101.3.3.1
1441
1442> define centroid RTX_C & /M name centroid_RTX_C_M
1443
1444Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
1445
1446> rename ##name=centroid_RTX_C_M id 101.3.3.2
1447
1448> define centroid RTX_C & /H name centroid_RTX_C_H
1449
1450Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
1451
1452> rename ##name=centroid_RTX_C_H id 101.3.3.3
1453
1454> define centroid RTX_C & /I name centroid_RTX_C_I
1455
1456Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
1457
1458> rename ##name=centroid_RTX_C_I id 101.3.3.4
1459
1460> define centroid RTX_V & /L name centroid_RTX_V_L
1461
1462Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
1463
1464> rename ##name=centroid_RTX_V_L id 101.3.3.5
1465
1466> define centroid RTX_V & /M name centroid_RTX_V_M
1467
1468Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
1469
1470> rename ##name=centroid_RTX_V_M id 101.3.3.6
1471
1472> define centroid RTX_V & /H name centroid_RTX_V_H
1473
1474Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
1475
1476> rename ##name=centroid_RTX_V_H id 101.3.3.7
1477
1478> define centroid RTX_V & /I name centroid_RTX_V_I
1479
1480Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
1481
1482> rename ##name=centroid_RTX_V_I id 101.3.3.8
1483
1484> rename #101.3.3 centroids
1485
1486> define centroid H7v16_C & /L name centroid_2H7v16_C_L
1487
1488Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
1489104.71732873]
1490
1491> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
1492
1493> define centroid H7v16_C & /M name centroid_2H7v16_C_M
1494
1495Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
1496109.46892346]
1497
1498> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
1499
1500> define centroid H7v16_C & /H name centroid_2H7v16_C_H
1501
1502Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
1503100.10963479]
1504
1505> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
1506
1507> define centroid H7v16_C & /I name centroid_2H7v16_C_I
1508
1509Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
1510103.22787118]
1511
1512> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
1513
1514> define centroid H7v16_V & /L name centroid_2H7v16_V_L
1515
1516Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
1517124.64938243]
1518
1519> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
1520
1521> define centroid H7v16_V & /M name centroid_2H7v16_V_M
1522
1523Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
1524126.48898691]
1525
1526> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
1527
1528> define centroid H7v16_V & /H name centroid_2H7v16_V_H
1529
1530Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
1531126.96669027]
1532
1533> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
1534
1535> define centroid H7v16_V & /I name centroid_2H7v16_V_I
1536
1537Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
1538126.76187738]
1539
1540> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
1541
1542> rename #102.3.3 centroids
1543
1544> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
1545
1546Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
1547111.74271267]
1548
1549> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
1550
1551> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
1552
1553Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
1554109.3226675 ]
1555
1556> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
1557
1558> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
1559
1560Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
1561105.03944622]
1562
1563> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
1564
1565> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
1566
1567Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
1568103.22947676]
1569
1570> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
1571
1572> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
1573
1574Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
1575127.91858459]
1576
1577> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
1578
1579> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
1580
1581Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
1582127.2169787 ]
1583
1584> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
1585
1586> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
1587
1588Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
1589127.54490507]
1590
1591> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
1592
1593> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
1594
1595Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
1596127.29650809]
1597
1598> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
1599
1600> rename #103.3.3 centroids
1601
1602> define centroid CD20 & /C name centroid_CD20_C
1603
1604Centroid 'centroid_CD20_C' placed at [144.85124361 155.47295008 168.48352542]
1605
1606> rename ##name=centroid_CD20_C id 101.3.3.9
1607
1608> define centroid CD20 & /D name centroid_CD20_D
1609
1610Centroid 'centroid_CD20_D' placed at [165.21151856 155.17682163 168.76082258]
1611
1612> rename ##name=centroid_CD20_D id 101.3.3.10
1613
1614executed CD20_2H7_mutants_define_domain_centroids.cxc
1615
1616> turn x 90
1617
1618> view
1619
1620> hide #101 models
1621
1622> hide #!102.2 models
1623
1624> ~ribbon #102.10/X,Y
1625
1626executed CD20_2H7_mutants_setup.cxc
1627
1628> hide #!104 models
1629
1630> hide #!103 models
1631
1632> show #!102.2 models
1633
1634> show #!101 models
1635
1636> show #101.1 models
1637
1638> show #!101.3 models
1639
1640> show #!101.3.1 models
1641
1642> show #!101.3.2 models
1643
1644> show #!101.3.3 models
1645
1646> hide #!102.2 models
1647
1648> hide #!101.3 models
1649
1650> hide #!102.3 models
1651
1652> hide #!102.10 models
1653
1654> hide #!102 models
1655
1656> show #!101.3 models
1657
1658> hide #!101.3.1 models
1659
1660> show #!101.3.1 models
1661
1662> show #!101.3.1.1 models
1663
1664> show #!101.3.1.2 models
1665
1666> show #!101.3.1.3 models
1667
1668> show #!101.3.1.4 models
1669
1670> show #101.3.3.1 models
1671
1672> show #101.3.3.2 models
1673
1674> show #101.3.3.3 models
1675
1676> show #101.3.3.4 models
1677
1678> show #101.3.3.5 models
1679
1680> show #101.3.3.6 models
1681
1682> show #101.3.3.7 models
1683
1684> show #101.3.3.8 models
1685
1686> show #101.3.3.9 models
1687
1688> show #101.3.3.10 models
1689
1690> show #!102 models
1691
1692> hide #!102 models
1693
1694> hide #101.1 models
1695
1696> show #!102 models
1697
1698> hide #!102.1 models
1699
1700> show #!102.3 models
1701
1702> hide #!102.3.2 models
1703
1704> close
1705
1706> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
1707
1708> close
1709
1710> cd /Users/rohoua/work/Genentech/CD20
1711
1712Current working directory is: /Users/rohoua/work/Genentech/CD20
1713
1714> open pdb:6vja name CD20_RTX id 101.1
1715
1716CD20_RTX title:
1717Structure of CD20 in complex with rituximab Fab [more info...]
1718
1719Chain information for CD20_RTX #1
1720---
1721Chain | Description | UniProt
1722C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
1723H I | Rituximab Fab heavy chain |
1724L M | Rituximab Fab light chain |
1725
1726Non-standard residues in CD20_RTX #1
1727---
1728Y01 — cholesterol hemisuccinate
1729
1730
1731> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
1732
1733Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb
1734---
1735warning | Ignored bad PDB record found on line 1
1736HEADER STR7668 version_2 2023.12.13
1737
1738CD20_2H7v16 title:
1739Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
1740resolution. [more info...]
1741
1742Chain information for CD20_2H7v16 #1
1743---
1744Chain | Description
1745C D | No description available
1746H I | No description available
1747L M | No description available
1748
1749Non-standard residues in CD20_2H7v16 #1
1750---
1751Y01 — (Y01)
1752
1753
1754> open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
1755
1756Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
1757shown at level 0.0054, step 2, values float32
1758
1759> volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
1760
1761> view matrix models
1762> #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
1763
1764> open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
1765> 102.10
1766
1767Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
1768Fab.pdb
1769---
1770warning | Ignored bad PDB record found on line 1
1771HEADER STR7487 version_1 2023.05.24
1772
17732H7v16_XRay title:
1774Structure of 2H7 Fab at 2.45 A resolution. [more info...]
1775
1776Chain information for 2H7v16_XRay #1
1777---
1778Chain | Description
1779A B X Y | No description available
1780
1781Non-standard residues in 2H7v16_XRay #1
1782---
1783CL — (CL)
1784
1785
1786> matchmaker #102.10/A,B to #102.1/H,L
1787
1788Parameters
1789---
1790Chain pairing | bb
1791Alignment algorithm | Needleman-Wunsch
1792Similarity matrix | BLOSUM-62
1793SS fraction | 0.3
1794Gap open (HH/SS/other) | 18/18/6
1795Gap extend | 1
1796SS matrix | | | H | S | O
1797---|---|---|---
1798H | 6 | -9 | -6
1799S | | 6 | -6
1800O | | | 4
1801Iteration cutoff | 2
1802
1803Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
1804sequence alignment score = 1228.2
1805RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
18060.804)
1807
1808
1809> open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
1810> 103.1
1811
1812Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb
1813---
1814warning | Ignored bad PDB record found on line 1
1815HEADER STR7717 version_2 2023.12.15
1816
1817CD20_2H7v166_D56A title:
1818Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
1819info...]
1820
1821Chain information for CD20_2H7v166_D56A #1
1822---
1823Chain | Description
1824C D | No description available
1825H I | No description available
1826L | No description available
1827M | No description available
1828
1829Non-standard residues in CD20_2H7v166_D56A #1
1830---
1831Y01 — (Y01)
1832
1833
1834> open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
1835
1836Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
1837300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32
1838
1839> volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
1840
1841> view matrix models
1842> #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
1843
1844> open CD20_2H7v166_S92A_D56A/STR7729_alito6vja.pdb name
1845> CD20_2H7v166_S92A_D56A id 104.1
1846
1847Summary of feedback from opening CD20_2H7v166_S92A_D56A/STR7729_alito6vja.pdb
1848---
1849warning | Ignored bad PDB record found on line 1
1850HEADER STR7729 version_1 2024.01.12
1851
1852CD20_2H7v166_S92A_D56A title:
1853Structure of ABP1AB10781 and Hs_CD20.M1-P297 at 4.5 A resolution. [more
1854info...]
1855
1856Chain information for CD20_2H7v166_S92A_D56A #1
1857---
1858Chain | Description
1859C | No description available
1860D | No description available
1861H I | No description available
1862L | No description available
1863M | No description available
1864
1865
1866> open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
1867> id 104.2
1868
1869Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
1870300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
1871
1872> volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
1873
1874> view matrix models
1875> #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
1876
1877> rename #101 CD20_RTX
1878
1879> rename #102 CD20_2H7v16
1880
1881> rename #103 CD20_2H7v166_D56A
1882
1883> rename #104 CD20_2H7v166_S92A_D56A
1884
1885> dssp
1886
1887> name CD20_RTX #101.1
1888
1889> name CD20_2H7v16 #102.1
1890
1891> name CD20_2H7v166_D56A #103.1
1892
1893> name CD20_2H7v166_S92A_D56A #104.1
1894
1895> name CD20 /C,D
1896
1897> name CD20_Monomer /C
1898
1899> name CD20_H1 /C,D:46-71
1900
1901> name CD20_ECL1 /C,D:72-79
1902
1903> name CD20_H2 /C,D:80-105
1904
1905> name CD20_ICL1 /C,D:106-112
1906
1907> name CD20_H3 /C,D:113-141
1908
1909> name CD20_ECL2 /C,D:142-187
1910
1911> name CD20_ECL2SS /C,D:167,183
1912
1913> name CD20_H4 /C,D:188-end
1914
1915> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
1916
1917> name RTX CD20_RTX & /H,L,I,M
1918
1919> name RTX_H RTX & /H,I
1920
1921> name RTX_L RTX & /L,M
1922
1923> name RTX_Epitope CD20_RTX & /C,D:168-175
1924
1925> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
1926
1927> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
1928
1929> name H7v16 CD20_2H7v16 & /H,L,I,M
1930
1931> name H7v16_H H7v16 & /H,I
1932
1933> name H7v16_L H7v16 & /L,M
1934
1935> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
1936
1937> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
1938
1939> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
1940
1941> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
1942
1943> name H7v166_D56A_H H7v166_D56A & /H,I
1944
1945> name H7v166_D56A_L H7v166_D56A & /L,M
1946
1947> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
1948
1949> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
1950
1951> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
1952> /H,I:119-end)
1953
1954> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
1955
1956> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
1957
1958> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
1959
1960> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
1961
1962> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
1963> & /H,I:1-111)
1964
1965> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
1966> (H7v166_S92A_D56A & /H,I:119-end)
1967
1968> lighting soft
1969
1970> set bgColor white
1971
1972> camera ortho
1973
1974> style stick
1975
1976Changed 44407 atom styles
1977
1978> color byhetero
1979
1980> open CD20_2H7_mutants_color.cxc
1981
1982> color CD20 burlywood
1983
1984> color modify CD20_H1 hue - 20
1985
1986> color modify CD20_H2 hue - 10
1987
1988> color modify CD20_H3 hue + 0
1989
1990> color modify CD20_H4 hue + 10
1991
1992> color modify CD20_ECL1 hue +10
1993
1994> color modify CD20_ECL2 hue + 40
1995
1996> color modify CD20 saturation + 80
1997
1998> color CD20_ECL2 rgb(127,165,90)
1999
2000> color CD20_H4 rgb(176,215,142)
2001
2002> color RTX plum
2003
2004> color modify RTX_H hue - 40
2005
2006> color H7v16 slate blue
2007
2008> color modify H7v16_H hue - 40
2009
2010> color H7v166_D56A dodger blue
2011
2012> color modify H7v166_D56A_H hue - 40
2013
2014> color H7v166_S92A_D56A purple
2015
2016> color modify H7v166_S92A_D56A_H hue - 40
2017
2018executed CD20_2H7_mutants_color.cxc
2019
2020> hide
2021
2022> ribbon
2023
2024> show CD20_ECL2SS
2025
2026> style CD20_ECL2SS stick
2027
2028Changed 96 atom styles
2029
2030> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
2031
2032Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
2033radius 1, and length 140
2034
2035> marker #1.1 position 155,155,70
2036
2037> marker #1.1 position 155,155,210
2038
2039> select
2040> #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
2041
2042440 atoms, 446 bonds, 54 residues, 1 model selected
2043
2044> define plane sel name membrane_plane
2045
2046Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
2047normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
2048
2049> rename ##name=membrane_plane id 10
2050
2051> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
2052
2053> combine CD20_RTX name RTX_Va modelId 1001
2054
2055> select zone (RTX_V & /H,L) 0.1 #1001
2056
2057Selected 1711 atoms
2058
2059> delete #1001 & ~sel
2060
2061> combine #1001 name RTX_Va_copy modelId 1002
2062
2063> combine CD20_RTX name RTX_Vb modelId 1003
2064
2065> select zone (RTX_V & /I,M) 0.1 #1003
2066
2067Selected 1711 atoms
2068
2069> delete #1003 & ~sel
2070
2071> combine #1003 name RTX_Vb_copy modelId 1004
2072
2073> combine CD20_RTX name RTX_Ca modelId 1005
2074
2075> select zone (RTX_C & /H,L) 0.1 #1005
2076
2077Selected 1503 atoms
2078
2079> delete #1005 & ~sel
2080
2081> combine #1005 name RTX_Ca_copy modelId 1006
2082
2083> combine CD20_RTX name RTX_Cb modelId 1007
2084
2085> select zone (RTX_C & /I,M) 0.1 #1007
2086
2087Selected 1503 atoms
2088
2089> delete #1007 & ~sel
2090
2091> combine #1007 name RTX_Ca_copy modelId 1008
2092
2093> matchmaker #1002/L to #1001/H
2094
2095Parameters
2096---
2097Chain pairing | bb
2098Alignment algorithm | Needleman-Wunsch
2099Similarity matrix | BLOSUM-62
2100SS fraction | 0.3
2101Gap open (HH/SS/other) | 18/18/6
2102Gap extend | 1
2103SS matrix | | | H | S | O
2104---|---|---|---
2105H | 6 | -9 | -6
2106S | | 6 | -6
2107O | | | 4
2108Iteration cutoff | 2
2109
2110Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
2111alignment score = 198.7
2112RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
21134.421)
2114
2115
2116> wait 1
2117
2118> measure rotation #1002 toModel #1001 showSlabs true
2119
2120Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
2121Matrix rotation and translation
21220.65377294 -0.06463426 0.75392530 -36.97668460
21230.02426941 -0.99404163 -0.10626495 318.59247232
21240.75630149 0.08777047 -0.64830888 90.28955685
2125Axis 0.90906034 -0.01113250 0.41651574
2126Axis point 0.00000000 156.41772375 62.99337678
2127Rotation angle (degrees) 173.87355102
2128Shift along axis 0.44625393
2129
2130
2131> close #1001 #1002
2132
2133> define axis #2 name axis_Va
2134
2135Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
2136125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
21370.65062, and length 52.0496
2138
2139> rename #2 Va_rotation_axis id #101.3.1.1
2140
2141> rename #3 Va_rotation_slabs id #101.3.2.1
2142
2143> matchmaker #1004/M to #1003/I
2144
2145Parameters
2146---
2147Chain pairing | bb
2148Alignment algorithm | Needleman-Wunsch
2149Similarity matrix | BLOSUM-62
2150SS fraction | 0.3
2151Gap open (HH/SS/other) | 18/18/6
2152Gap extend | 1
2153SS matrix | | | H | S | O
2154---|---|---|---
2155H | 6 | -9 | -6
2156S | | 6 | -6
2157O | | | 4
2158Iteration cutoff | 2
2159
2160Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
2161alignment score = 214.3
2162RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
21634.448)
2164
2165
2166> wait 1
2167
2168> measure rotation #1004 toModel #1003 showSlabs true
2169
2170Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
2171Matrix rotation and translation
21720.65527690 -0.06129532 -0.75289778 163.48223927
21730.03113398 -0.99366393 0.10799385 290.56686667
2174-0.75474688 -0.09420658 -0.64921665 352.74817189
2175Axis -0.90945183 0.00831685 0.41572611
2176Axis point 0.00000000 156.83903630 204.83255489
2177Rotation angle (degrees) 173.61745932
2178Shift along axis 0.38400661
2179
2180
2181> close #1004 #1003
2182
2183> define axis #2 name axis_Vb
2184
2185Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
2186125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
21870.648586, and length 51.8869
2188
2189> rename #2 Vb_rotation_axis id #101.3.1.2
2190
2191> rename #3 Vb_rotation_slabs id #101.3.2.2
2192
2193> matchmaker #1006/L to #1005/H
2194
2195Parameters
2196---
2197Chain pairing | bb
2198Alignment algorithm | Needleman-Wunsch
2199Similarity matrix | BLOSUM-62
2200SS fraction | 0.3
2201Gap open (HH/SS/other) | 18/18/6
2202Gap extend | 1
2203SS matrix | | | H | S | O
2204---|---|---|---
2205H | 6 | -9 | -6
2206S | | 6 | -6
2207O | | | 4
2208Iteration cutoff | 2
2209
2210Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
2211alignment score = 238.2
2212RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
22133.308)
2214
2215
2216> wait 1
2217
2218> measure rotation #1006 toModel #1005 showSlabs true
2219
2220Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
2221Matrix rotation and translation
22220.37780344 0.24165354 0.89379423 -73.66252391
22230.01279825 -0.96661035 0.25593093 273.63534365
22240.92579737 -0.08525258 -0.36828146 68.27322422
2225Axis -0.82796624 -0.07766353 -0.55537400
2226Axis point 0.00000000 144.62953182 41.62502778
2227Rotation angle (degrees) 168.10978391
2228Shift along axis 1.82142171
2229
2230
2231> close #1006 #1005
2232
2233> define axis #2 name axis_Ca
2234
2235Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
2236110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
22370.539289, and length 43.1431
2238
2239> rename #2 Ca_rotation_axis id #101.3.1.3
2240
2241> rename #3 Ca_rotation_slabs id #101.3.2.3
2242
2243> matchmaker #1008/M to #1007/I
2244
2245Parameters
2246---
2247Chain pairing | bb
2248Alignment algorithm | Needleman-Wunsch
2249Similarity matrix | BLOSUM-62
2250SS fraction | 0.3
2251Gap open (HH/SS/other) | 18/18/6
2252Gap extend | 1
2253SS matrix | | | H | S | O
2254---|---|---|---
2255H | 6 | -9 | -6
2256S | | 6 | -6
2257O | | | 4
2258Iteration cutoff | 2
2259
2260Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
2261alignment score = 238.2
2262RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
22633.487)
2264
2265
2266> wait 1
2267
2268> measure rotation #1008 toModel #1007 showSlabs true
2269
2270Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
2271Matrix rotation and translation
22720.37961795 0.24211100 -0.89290116 191.06761259
22730.01296287 -0.96644625 -0.25654164 332.12351027
2274-0.92505253 0.08581325 -0.37001879 328.82641259
2275Axis 0.82850834 0.07780721 -0.55454483
2276Axis point 0.00000000 136.30341759 249.27961172
2277Rotation angle (degrees) 168.07628341
2278Shift along axis 1.79372450
2279
2280
2281> close #1008 #1007
2282
2283> define axis #2 name axis_Cb
2284
2285Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
2286110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
22870.53918, and length 43.1344
2288
2289> rename #2 Cb_rotation_axis id #101.3.1.4
2290
2291> rename #3 Cb_rotation_slabs id #101.3.2.4
2292
2293> rename #101.3 geometry
2294
2295> rename #101.3.1 rotation_axes
2296
2297> rename #101.3.2 rotation_slabs
2298
2299executed CD20_RTX_define_pseudo_symmetries.cxc
2300
2301> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
2302
2303> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
2304
2305> select zone (H7v16_V & /H,L) 0.1 #1001
2306
2307Selected 1754 atoms
2308
2309> delete #1001 & ~sel
2310
2311> combine #1001 name 2H7_v16_Va_copy modelId 1002
2312
2313> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
2314
2315> select zone (H7v16_V & /I,M) 0.1 #1003
2316
2317Selected 1710 atoms
2318
2319> delete #1003 & ~sel
2320
2321> combine #1003 name 2H7_v16_Vb_copy modelId 1004
2322
2323> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
2324
2325> select zone (H7v16_C & /H,L) 0.1 #1005
2326
2327Selected 1550 atoms
2328
2329> delete #1005 & ~sel
2330
2331> combine #1005 name 2H7_v16_Ca_copy modelId 1006
2332
2333> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
2334
2335> select zone (H7v16_C & /I,M) 0.1 #1007
2336
2337Selected 1550 atoms
2338
2339> delete #1007 & ~sel
2340
2341> combine #1007 name 2H7_v16_Ca_copy modelId 1008
2342
2343> matchmaker #1002/L to #1001/H
2344
2345Parameters
2346---
2347Chain pairing | bb
2348Alignment algorithm | Needleman-Wunsch
2349Similarity matrix | BLOSUM-62
2350SS fraction | 0.3
2351Gap open (HH/SS/other) | 18/18/6
2352Gap extend | 1
2353SS matrix | | | H | S | O
2354---|---|---|---
2355H | 6 | -9 | -6
2356S | | 6 | -6
2357O | | | 4
2358Iteration cutoff | 2
2359
2360Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
2361sequence alignment score = 387.9
2362RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
23635.340)
2364
2365
2366> wait 1
2367
2368> measure rotation #1002 toModel #1001 showSlabs true
2369
2370Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
2371Matrix rotation and translation
23720.58985298 0.00233427 0.80750728 -45.05678546
23730.12316682 -0.98855531 -0.08711100 297.16136614
23740.79806228 0.15084078 -0.58338980 65.44859378
2375Axis 0.89106916 0.03536916 0.45248731
2376Axis point 0.00000000 147.01172040 55.34624717
2377Rotation angle (degrees) 172.32693090
2378Shift along axis -0.02370559
2379
2380
2381> close #1001 #1002
2382
2383> define axis #2 name axis_Va
2384
2385Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
2386125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
23870.589874, and length 47.1899
2388
2389> rename #2 Va_rotation_axis id #102.3.1.1
2390
2391> rename #3 Va_rotation_slabs id #102.3.2.1
2392
2393> matchmaker #1004/M to #1003/I
2394
2395Parameters
2396---
2397Chain pairing | bb
2398Alignment algorithm | Needleman-Wunsch
2399Similarity matrix | BLOSUM-62
2400SS fraction | 0.3
2401Gap open (HH/SS/other) | 18/18/6
2402Gap extend | 1
2403SS matrix | | | H | S | O
2404---|---|---|---
2405H | 6 | -9 | -6
2406S | | 6 | -6
2407O | | | 4
2408Iteration cutoff | 2
2409
2410Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
2411sequence alignment score = 378.3
2412RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
24134.620)
2414
2415
2416> wait 1
2417
2418> measure rotation #1004 toModel #1003 showSlabs true
2419
2420Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
2421Matrix rotation and translation
24220.62864598 0.45103819 -0.63353672 71.77949524
24230.53321619 -0.84298968 -0.07105560 212.64664720
2424-0.56611370 -0.29314322 -0.77044294 368.84403487
2425Axis -0.90200560 -0.27383758 0.33376470
2426Axis point -0.00000000 108.05935567 190.41757658
2427Rotation angle (degrees) 172.92851049
2428Shift along axis 0.13096924
2429
2430
2431> close #1004 #1003
2432
2433> define axis #2 name axis_Vb
2434
2435Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
2436125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
24370.594923, and length 47.5938
2438
2439> rename #2 Vb_rotation_axis id #102.3.1.2
2440
2441> rename #3 Vb_rotation_slabs id #102.3.2.2
2442
2443> matchmaker #1006/L to #1005/H
2444
2445Parameters
2446---
2447Chain pairing | bb
2448Alignment algorithm | Needleman-Wunsch
2449Similarity matrix | BLOSUM-62
2450SS fraction | 0.3
2451Gap open (HH/SS/other) | 18/18/6
2452Gap extend | 1
2453SS matrix | | | H | S | O
2454---|---|---|---
2455H | 6 | -9 | -6
2456S | | 6 | -6
2457O | | | 4
2458Iteration cutoff | 2
2459
2460Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
2461sequence alignment score = 403.6
2462RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
24633.184)
2464
2465
2466> wait 1
2467
2468> measure rotation #1006 toModel #1005 showSlabs true
2469
2470Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
2471Matrix rotation and translation
2472-0.62547004 0.41276667 0.66212605 49.05674876
24730.08546501 -0.80725952 0.58397585 200.07354667
24740.77555333 0.42184801 0.46963954 -95.83522576
2475Axis -0.42390521 -0.29657098 -0.85577452
2476Axis point 59.57688139 113.83169245 0.00000000
2477Rotation angle (degrees) 168.97535276
2478Shift along axis 1.88192618
2479
2480
2481> close #1006 #1005
2482
2483> define axis #2 name axis_Ca
2484
2485Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
2486101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
24870.550437, and length 44.0349
2488
2489> rename #2 Ca_rotation_axis id #102.3.1.3
2490
2491> rename #3 Ca_rotation_slabs id #102.3.2.3
2492
2493> matchmaker #1008/M to #1007/I
2494
2495Parameters
2496---
2497Chain pairing | bb
2498Alignment algorithm | Needleman-Wunsch
2499Similarity matrix | BLOSUM-62
2500SS fraction | 0.3
2501Gap open (HH/SS/other) | 18/18/6
2502Gap extend | 1
2503SS matrix | | | H | S | O
2504---|---|---|---
2505H | 6 | -9 | -6
2506S | | 6 | -6
2507O | | | 4
2508Iteration cutoff | 2
2509
2510Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
2511sequence alignment score = 396
2512RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
25133.551)
2514
2515
2516> wait 1
2517
2518> measure rotation #1008 toModel #1007 showSlabs true
2519
2520Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
2521Matrix rotation and translation
2522-0.62894249 0.48033740 -0.61131606 312.62038315
25230.14842286 -0.69766113 -0.70088487 336.12735996
2524-0.76315267 -0.53154955 0.36749568 311.24709675
2525Axis 0.42085200 0.37736216 -0.82491296
2526Axis point 256.37284203 220.04020388 0.00000000
2527Rotation angle (degrees) 168.39393838
2528Shift along axis 1.65689588
2529
2530
2531> close #1008 #1007
2532
2533> define axis #2 name axis_Cb
2534
2535Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
2536105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
25370.534846, and length 42.7877
2538
2539> rename #2 Cb_rotation_axis id #102.3.1.4
2540
2541> rename #3 Cb_rotation_slabs id #102.3.2.4
2542
2543> rename #102.3 geometry
2544
2545> rename #102.3.1 rotation_axes
2546
2547> rename #102.3.2 rotation_slabs
2548
2549executed CD20_2H7v16_define_pseudo_symmetries.cxc
2550
2551> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
2552
2553> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
2554
2555> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
2556
2557Selected 1654 atoms
2558
2559> delete #1001 & ~sel
2560
2561> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
2562
2563> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
2564
2565> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
2566
2567Selected 1678 atoms
2568
2569> delete #1003 & ~sel
2570
2571> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
2572
2573> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
2574
2575> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
2576
2577Selected 1550 atoms
2578
2579> delete #1005 & ~sel
2580
2581> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
2582
2583> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
2584
2585> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
2586
2587Selected 1550 atoms
2588
2589> delete #1007 & ~sel
2590
2591> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
2592
2593> matchmaker #1002/L to #1001/H
2594
2595Parameters
2596---
2597Chain pairing | bb
2598Alignment algorithm | Needleman-Wunsch
2599Similarity matrix | BLOSUM-62
2600SS fraction | 0.3
2601Gap open (HH/SS/other) | 18/18/6
2602Gap extend | 1
2603SS matrix | | | H | S | O
2604---|---|---|---
2605H | 6 | -9 | -6
2606S | | 6 | -6
2607O | | | 4
2608Iteration cutoff | 2
2609
2610Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
2611L (#1002), sequence alignment score = 547.6
2612RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
26132.607)
2614
2615
2616> wait 1
2617
2618> measure rotation #1002 toModel #1001 showSlabs true
2619
2620Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
2621coordinates:
2622Matrix rotation and translation
26230.73992366 -0.12116101 0.66168949 -29.70332856
2624-0.06116680 -0.99168902 -0.11318795 332.06337928
26250.66990417 0.04327702 -0.74118520 123.44534698
2626Axis 0.93259437 -0.04896279 0.35758970
2627Axis point 0.00000000 162.47254458 74.89799404
2628Rotation angle (degrees) 175.18797763
2629Shift along axis 0.18287681
2630
2631
2632> close #1001 #1002
2633
2634> define axis #2 name axis_Va
2635
2636Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
2637127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
26380.599212, and length 47.937
2639
2640> rename #2 Va_rotation_axis id #103.3.1.1
2641
2642> rename #3 Va_rotation_slabs id #103.3.2.1
2643
2644> matchmaker #1004/M to #1003/I
2645
2646Parameters
2647---
2648Chain pairing | bb
2649Alignment algorithm | Needleman-Wunsch
2650Similarity matrix | BLOSUM-62
2651SS fraction | 0.3
2652Gap open (HH/SS/other) | 18/18/6
2653Gap extend | 1
2654SS matrix | | | H | S | O
2655---|---|---|---
2656H | 6 | -9 | -6
2657S | | 6 | -6
2658O | | | 4
2659Iteration cutoff | 2
2660
2661Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
2662M (#1004), sequence alignment score = 376.5
2663RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
26643.886)
2665
2666
2667> wait 1
2668
2669> measure rotation #1004 toModel #1003 showSlabs true
2670
2671Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
2672coordinates:
2673Matrix rotation and translation
26740.72982969 -0.01372193 -0.68349128 135.94952936
26750.06485007 -0.99390027 0.08920045 287.47713002
2676-0.68054617 -0.10942560 -0.72448806 354.00628960
2677Axis -0.92979963 -0.01378652 0.36780781
2678Axis point 0.00000000 152.92822789 195.61279282
2679Rotation angle (degrees) 173.86847166
2680Shift along axis -0.16285394
2681
2682
2683> close #1004 #1003
2684
2685> define axis #2 name axis_Vb
2686
2687Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
2688126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
26890.597156, and length 47.7725
2690
2691> rename #2 Vb_rotation_axis id #103.3.1.2
2692
2693> rename #3 Vb_rotation_slabs id #103.3.2.2
2694
2695> matchmaker #1006/L to #1005/H
2696
2697Parameters
2698---
2699Chain pairing | bb
2700Alignment algorithm | Needleman-Wunsch
2701Similarity matrix | BLOSUM-62
2702SS fraction | 0.3
2703Gap open (HH/SS/other) | 18/18/6
2704Gap extend | 1
2705SS matrix | | | H | S | O
2706---|---|---|---
2707H | 6 | -9 | -6
2708S | | 6 | -6
2709O | | | 4
2710Iteration cutoff | 2
2711
2712Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
2713L (#1006), sequence alignment score = 554.5
2714RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
27153.119)
2716
2717
2718> wait 1
2719
2720> measure rotation #1006 toModel #1005 showSlabs true
2721
2722Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
2723coordinates:
2724Matrix rotation and translation
2725-0.33391401 0.38072466 0.86229355 -12.40856576
27260.05205532 -0.90595556 0.42016042 245.78035810
27270.94116506 0.18518442 0.28269251 -52.33839393
2728Axis -0.57081123 -0.19159720 -0.79841408
2729Axis point 28.53870248 129.91224226 0.00000000
2730Rotation angle (degrees) 168.12212217
2731Shift along axis 1.77983022
2732
2733
2734> close #1006 #1005
2735
2736> define axis #2 name axis_Ca
2737
2738Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
2739106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
27400.56909, and length 45.5272
2741
2742> rename #2 Ca_rotation_axis id #103.3.1.3
2743
2744> rename #3 Ca_rotation_slabs id #103.3.2.3
2745
2746> matchmaker #1008/M to #1007/I
2747
2748Parameters
2749---
2750Chain pairing | bb
2751Alignment algorithm | Needleman-Wunsch
2752Similarity matrix | BLOSUM-62
2753SS fraction | 0.3
2754Gap open (HH/SS/other) | 18/18/6
2755Gap extend | 1
2756SS matrix | | | H | S | O
2757---|---|---|---
2758H | 6 | -9 | -6
2759S | | 6 | -6
2760O | | | 4
2761Iteration cutoff | 2
2762
2763Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
2764M (#1008), sequence alignment score = 416.6
2765RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
27663.361)
2767
2768
2769> wait 1
2770
2771> measure rotation #1008 toModel #1007 showSlabs true
2772
2773Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
2774coordinates:
2775Matrix rotation and translation
2776-0.50667380 0.40781938 -0.75958213 323.22163731
27770.08178140 -0.85433688 -0.51324487 330.95129120
2778-0.85825023 -0.32216741 0.39951808 287.19953324
2779Axis 0.48922423 0.25262440 -0.83476977
2780Axis point 265.28291179 189.90297685 0.00000000
2781Rotation angle (degrees) 168.73855860
2782Shift along axis 1.98873850
2783
2784
2785> close #1008 #1007
2786
2787> define axis #2 name axis_Cb
2788
2789Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
2790104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
27910.553583, and length 44.2867
2792
2793> rename #2 Cb_rotation_axis id #103.3.1.4
2794
2795> rename #3 Cb_rotation_slabs id #103.3.2.4
2796
2797> rename #103.3 geometry
2798
2799> rename #103.3.1 rotation_axes
2800
2801> rename #103.3.2 rotation_slabs
2802
2803executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
2804
2805> open
2806> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
2807
2808> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
2809
2810> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
2811
2812Selected 1734 atoms
2813
2814> delete #1001 & ~sel
2815
2816> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
2817
2818> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
2819
2820> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
2821
2822Selected 1678 atoms
2823
2824> delete #1003 & ~sel
2825
2826> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
2827
2828> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
2829
2830> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
2831
2832Selected 1550 atoms
2833
2834> delete #1005 & ~sel
2835
2836> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
2837
2838> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
2839
2840> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
2841
2842Selected 1550 atoms
2843
2844> delete #1007 & ~sel
2845
2846> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
2847
2848> matchmaker #1002/L to #1001/H
2849
2850Parameters
2851---
2852Chain pairing | bb
2853Alignment algorithm | Needleman-Wunsch
2854Similarity matrix | BLOSUM-62
2855SS fraction | 0.3
2856Gap open (HH/SS/other) | 18/18/6
2857Gap extend | 1
2858SS matrix | | | H | S | O
2859---|---|---|---
2860H | 6 | -9 | -6
2861S | | 6 | -6
2862O | | | 4
2863Iteration cutoff | 2
2864
2865Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
28662H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 381.4
2867RMSD between 68 pruned atom pairs is 1.006 angstroms; (across all 103 pairs:
28683.728)
2869
2870
2871> wait 1
2872
2873> measure rotation #1002 toModel #1001 showSlabs true
2874
2875Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
2876#1001 coordinates:
2877Matrix rotation and translation
28780.71569156 -0.03206360 0.69768010 -44.96691323
28790.04686485 -0.99448942 -0.09377893 313.22701875
28800.69684236 0.09981346 -0.71024503 107.14739664
2881Axis 0.92598883 0.00400704 0.37752965
2882Axis point 0.00000000 153.67931126 71.60444720
2883Rotation angle (degrees) 173.99975082
2884Shift along axis 0.06757359
2885
2886
2887> close #1001 #1002
2888
2889> define axis #2 name axis_Va
2890
2891Axis 'rotation axis #2/axis_Va' centered at [136.48132211 154.26990862
2892127.24847182] with direction [0.92598883 0.00400704 0.37752965], radius
28930.603729, and length 48.2983
2894
2895> rename #2 Va_rotation_axis id #104.3.1.1
2896
2897> rename #3 Va_rotation_slabs id #104.3.2.1
2898
2899> matchmaker #1004/M to #1003/I
2900
2901Parameters
2902---
2903Chain pairing | bb
2904Alignment algorithm | Needleman-Wunsch
2905Similarity matrix | BLOSUM-62
2906SS fraction | 0.3
2907Gap open (HH/SS/other) | 18/18/6
2908Gap extend | 1
2909SS matrix | | | H | S | O
2910---|---|---|---
2911H | 6 | -9 | -6
2912S | | 6 | -6
2913O | | | 4
2914Iteration cutoff | 2
2915
2916Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
29172H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 348.3
2918RMSD between 69 pruned atom pairs is 1.043 angstroms; (across all 94 pairs:
29194.124)
2920
2921
2922> wait 1
2923
2924> measure rotation #1004 toModel #1003 showSlabs true
2925
2926Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
2927#1003 coordinates:
2928Matrix rotation and translation
29290.73259686 -0.07112185 -0.67693686 143.43240534
29300.01935436 -0.99194728 0.12516391 289.93644026
2931-0.68038757 -0.10479637 -0.72532095 353.04193759
2932Axis -0.93047520 0.01396239 0.36608873
2933Axis point 0.00000000 157.81290376 195.07385462
2934Rotation angle (degrees) 172.90173563
2935Shift along axis -0.16741650
2936
2937
2938> close #1004 #1003
2939
2940> define axis #2 name axis_Vb
2941
2942Axis 'rotation axis #2/axis_Vb' centered at [172.87152644 155.21885305
2943127.05880479] with direction [-0.9304752 0.01396239 0.36608873], radius
29440.606168, and length 48.4934
2945
2946> rename #2 Vb_rotation_axis id #104.3.1.2
2947
2948> rename #3 Vb_rotation_slabs id #104.3.2.2
2949
2950> matchmaker #1006/L to #1005/H
2951
2952Parameters
2953---
2954Chain pairing | bb
2955Alignment algorithm | Needleman-Wunsch
2956Similarity matrix | BLOSUM-62
2957SS fraction | 0.3
2958Gap open (HH/SS/other) | 18/18/6
2959Gap extend | 1
2960SS matrix | | | H | S | O
2961---|---|---|---
2962H | 6 | -9 | -6
2963S | | 6 | -6
2964O | | | 4
2965Iteration cutoff | 2
2966
2967Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
29682H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 396.1
2969RMSD between 52 pruned atom pairs is 0.923 angstroms; (across all 98 pairs:
29703.306)
2971
2972
2973> wait 1
2974
2975> measure rotation #1006 toModel #1005 showSlabs true
2976
2977Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
2978#1005 coordinates:
2979Matrix rotation and translation
2980-0.43925296 0.41144710 0.79860386 4.35549593
29810.03727237 -0.87984204 0.47380244 231.94081966
29820.89758989 0.23788498 0.37113761 -66.19774762
2983Axis -0.52046834 -0.21837763 -0.82548405
2984Axis point 39.20275524 124.36112361 0.00000000
2985Rotation angle (degrees) 166.90068945
2986Shift along axis 1.72760165
2987
2988
2989> close #1006 #1005
2990
2991> define axis #2 name axis_Ca
2992
2993Axis 'rotation axis #2/axis_Ca' centered at [105.62839077 152.23193079
2994105.353773 ] with direction [-0.52046834 -0.21837763 -0.82548405], radius
29950.559049, and length 44.7239
2996
2997> rename #2 Ca_rotation_axis id #104.3.1.3
2998
2999> rename #3 Ca_rotation_slabs id #104.3.2.3
3000
3001> matchmaker #1008/M to #1007/I
3002
3003Parameters
3004---
3005Chain pairing | bb
3006Alignment algorithm | Needleman-Wunsch
3007Similarity matrix | BLOSUM-62
3008SS fraction | 0.3
3009Gap open (HH/SS/other) | 18/18/6
3010Gap extend | 1
3011SS matrix | | | H | S | O
3012---|---|---|---
3013H | 6 | -9 | -6
3014S | | 6 | -6
3015O | | | 4
3016Iteration cutoff | 2
3017
3018Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
30192H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 364.8
3020RMSD between 58 pruned atom pairs is 1.017 angstroms; (across all 98 pairs:
30213.237)
3022
3023
3024> wait 1
3025
3026> measure rotation #1008 toModel #1007 showSlabs true
3027
3028Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
3029#1007 coordinates:
3030Matrix rotation and translation
3031-0.44280624 0.37609436 -0.81392608 322.15113366
30320.04984109 -0.89604575 -0.44115517 333.30838934
3033-0.89523098 -0.23591322 0.37802969 283.50270597
3034Axis 0.52101945 0.20639753 -0.82821422
3035Axis point 270.23926430 182.69476034 0.00000000
3036Rotation angle (degrees) 168.64064548
3037Shift along axis 1.84005980
3038
3039
3040> close #1008 #1007
3041
3042> define axis #2 name axis_Cb
3043
3044Axis 'rotation axis #2/axis_Cb' centered at [203.87494881 156.40508754
3045105.49293398] with direction [ 0.52101945 0.20639753 -0.82821422], radius
30460.566399, and length 45.312
3047
3048> rename #2 Cb_rotation_axis id #104.3.1.4
3049
3050> rename #3 Cb_rotation_slabs id #104.3.2.4
3051
3052> rename #104.3 geometry
3053
3054> rename #104.3.1 rotation_axes
3055
3056> rename #104.3.2 rotation_slabs
3057
3058executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
3059
3060> open CD20_2H7_mutants_define_domain_centroids.cxc
3061
3062> define centroid RTX_C & /L name centroid_RTX_C_L
3063
3064Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
3065
3066> rename ##name=centroid_RTX_C_L id 101.3.3.1
3067
3068> define centroid RTX_C & /M name centroid_RTX_C_M
3069
3070Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
3071
3072> rename ##name=centroid_RTX_C_M id 101.3.3.2
3073
3074> define centroid RTX_C & /H name centroid_RTX_C_H
3075
3076Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
3077
3078> rename ##name=centroid_RTX_C_H id 101.3.3.3
3079
3080> define centroid RTX_C & /I name centroid_RTX_C_I
3081
3082Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
3083
3084> rename ##name=centroid_RTX_C_I id 101.3.3.4
3085
3086> define centroid RTX_V & /L name centroid_RTX_V_L
3087
3088Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
3089
3090> rename ##name=centroid_RTX_V_L id 101.3.3.5
3091
3092> define centroid RTX_V & /M name centroid_RTX_V_M
3093
3094Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
3095
3096> rename ##name=centroid_RTX_V_M id 101.3.3.6
3097
3098> define centroid RTX_V & /H name centroid_RTX_V_H
3099
3100Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
3101
3102> rename ##name=centroid_RTX_V_H id 101.3.3.7
3103
3104> define centroid RTX_V & /I name centroid_RTX_V_I
3105
3106Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
3107
3108> rename ##name=centroid_RTX_V_I id 101.3.3.8
3109
3110> rename #101.3.3 centroids
3111
3112> define centroid H7v16_C & /L name centroid_2H7v16_C_L
3113
3114Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
3115104.71732873]
3116
3117> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
3118
3119> define centroid H7v16_C & /M name centroid_2H7v16_C_M
3120
3121Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
3122109.46892346]
3123
3124> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
3125
3126> define centroid H7v16_C & /H name centroid_2H7v16_C_H
3127
3128Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
3129100.10963479]
3130
3131> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
3132
3133> define centroid H7v16_C & /I name centroid_2H7v16_C_I
3134
3135Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
3136103.22787118]
3137
3138> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
3139
3140> define centroid H7v16_V & /L name centroid_2H7v16_V_L
3141
3142Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
3143124.64938243]
3144
3145> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
3146
3147> define centroid H7v16_V & /M name centroid_2H7v16_V_M
3148
3149Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
3150126.48898691]
3151
3152> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
3153
3154> define centroid H7v16_V & /H name centroid_2H7v16_V_H
3155
3156Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
3157126.96669027]
3158
3159> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
3160
3161> define centroid H7v16_V & /I name centroid_2H7v16_V_I
3162
3163Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
3164126.76187738]
3165
3166> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
3167
3168> rename #102.3.3 centroids
3169
3170> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
3171
3172Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
3173111.74271267]
3174
3175> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
3176
3177> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
3178
3179Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
3180109.3226675 ]
3181
3182> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
3183
3184> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
3185
3186Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
3187105.03944622]
3188
3189> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
3190
3191> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
3192
3193Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
3194103.22947676]
3195
3196> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
3197
3198> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
3199
3200Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
3201127.91858459]
3202
3203> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
3204
3205> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
3206
3207Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
3208127.2169787 ]
3209
3210> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
3211
3212> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
3213
3214Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
3215127.54490507]
3216
3217> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
3218
3219> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
3220
3221Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
3222127.29650809]
3223
3224> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
3225
3226> rename #103.3.3 centroids
3227
3228> define centroid CD20 & /C name centroid_CD20_C
3229
3230Centroid 'centroid_CD20_C' placed at [144.85124361 155.47295008 168.48352542]
3231
3232> rename ##name=centroid_CD20_C id 101.3.3.9
3233
3234> define centroid CD20 & /D name centroid_CD20_D
3235
3236Centroid 'centroid_CD20_D' placed at [165.21151856 155.17682163 168.76082258]
3237
3238> rename ##name=centroid_CD20_D id 101.3.3.10
3239
3240executed CD20_2H7_mutants_define_domain_centroids.cxc
3241
3242> turn x 90
3243
3244> view
3245
3246> hide #101 models
3247
3248> hide #!102.2 models
3249
3250> ~ribbon #102.10/X,Y
3251
3252executed CD20_2H7_mutants_setup.cxc
3253
3254> hide #!102 models
3255
3256> hide #!103 models
3257
3258> hide #!102.1 models
3259
3260> show #!102.1 models
3261
3262> hide #!102 models
3263
3264> hide #!104.2 models
3265
3266> hide #!104.3 models
3267
3268> open /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729v2.pdb
3269
3270Summary of feedback from opening
3271/Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729v2.pdb
3272---
3273warning | Ignored bad PDB record found on line 1
3274HEADER STR7729 version_2 2024.01.29
3275
3276STR7729v2.pdb title:
3277Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
3278resolution. [more info...]
3279
3280Chain information for STR7729v2.pdb #2
3281---
3282Chain | Description
3283C D | No description available
3284H | No description available
3285I | No description available
3286L M | No description available
3287
3288
3289> matchmaker #2 to #104.1
3290
3291Parameters
3292---
3293Chain pairing | bb
3294Alignment algorithm | Needleman-Wunsch
3295Similarity matrix | BLOSUM-62
3296SS fraction | 0.3
3297Gap open (HH/SS/other) | 18/18/6
3298Gap extend | 1
3299SS matrix | | | H | S | O
3300---|---|---|---
3301H | 6 | -9 | -6
3302S | | 6 | -6
3303O | | | 4
3304Iteration cutoff | 2
3305
3306Matchmaker CD20_2H7v166_S92A_D56A, chain I (#104.1) with STR7729v2.pdb, chain
3307I (#2), sequence alignment score = 2027.6
3308RMSD between 229 pruned atom pairs is 0.178 angstroms; (across all 229 pairs:
33090.178)
3310
3311
3312> save
3313> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb
3314> models #2
3315
3316> close
3317
3318> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
3319
3320> close
3321
3322> cd /Users/rohoua/work/Genentech/CD20
3323
3324Current working directory is: /Users/rohoua/work/Genentech/CD20
3325
3326> open pdb:6vja name CD20_RTX id 101.1
3327
3328CD20_RTX title:
3329Structure of CD20 in complex with rituximab Fab [more info...]
3330
3331Chain information for CD20_RTX #1
3332---
3333Chain | Description | UniProt
3334C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
3335H I | Rituximab Fab heavy chain |
3336L M | Rituximab Fab light chain |
3337
3338Non-standard residues in CD20_RTX #1
3339---
3340Y01 — cholesterol hemisuccinate
3341
3342
3343> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
3344
3345Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb
3346---
3347warning | Ignored bad PDB record found on line 1
3348HEADER STR7668 version_2 2023.12.13
3349
3350CD20_2H7v16 title:
3351Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
3352resolution. [more info...]
3353
3354Chain information for CD20_2H7v16 #1
3355---
3356Chain | Description
3357C D | No description available
3358H I | No description available
3359L M | No description available
3360
3361Non-standard residues in CD20_2H7v16 #1
3362---
3363Y01 — (Y01)
3364
3365
3366> open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
3367
3368Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
3369shown at level 0.0054, step 2, values float32
3370
3371> volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
3372
3373> view matrix models
3374> #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
3375
3376> open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
3377> 102.10
3378
3379Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
3380Fab.pdb
3381---
3382warning | Ignored bad PDB record found on line 1
3383HEADER STR7487 version_1 2023.05.24
3384
33852H7v16_XRay title:
3386Structure of 2H7 Fab at 2.45 A resolution. [more info...]
3387
3388Chain information for 2H7v16_XRay #1
3389---
3390Chain | Description
3391A B X Y | No description available
3392
3393Non-standard residues in 2H7v16_XRay #1
3394---
3395CL — (CL)
3396
3397
3398> matchmaker #102.10/A,B to #102.1/H,L
3399
3400Parameters
3401---
3402Chain pairing | bb
3403Alignment algorithm | Needleman-Wunsch
3404Similarity matrix | BLOSUM-62
3405SS fraction | 0.3
3406Gap open (HH/SS/other) | 18/18/6
3407Gap extend | 1
3408SS matrix | | | H | S | O
3409---|---|---|---
3410H | 6 | -9 | -6
3411S | | 6 | -6
3412O | | | 4
3413Iteration cutoff | 2
3414
3415Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
3416sequence alignment score = 1228.2
3417RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
34180.804)
3419
3420
3421> open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
3422> 103.1
3423
3424Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb
3425---
3426warning | Ignored bad PDB record found on line 1
3427HEADER STR7717 version_2 2023.12.15
3428
3429CD20_2H7v166_D56A title:
3430Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
3431info...]
3432
3433Chain information for CD20_2H7v166_D56A #1
3434---
3435Chain | Description
3436C D | No description available
3437H I | No description available
3438L | No description available
3439M | No description available
3440
3441Non-standard residues in CD20_2H7v166_D56A #1
3442---
3443Y01 — (Y01)
3444
3445
3446> open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
3447
3448Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
3449300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32
3450
3451> volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
3452
3453> view matrix models
3454> #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
3455
3456> open CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb name
3457> CD20_2H7v166_S92A_D56A id 104.1
3458
3459Summary of feedback from opening
3460CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb
3461---
3462warning | Ignored bad PDB record found on line 1
3463HEADER STR7729 version_2 2024.01.29
3464
3465CD20_2H7v166_S92A_D56A title:
3466Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
3467resolution. [more info...]
3468
3469Chain information for CD20_2H7v166_S92A_D56A #1
3470---
3471Chain | Description
3472C D | No description available
3473H | No description available
3474I | No description available
3475L M | No description available
3476
3477
3478> open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
3479> id 104.2
3480
3481Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
3482300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
3483
3484> volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
3485
3486> view matrix models
3487> #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
3488
3489> rename #101 CD20_RTX
3490
3491> rename #102 CD20_2H7v16
3492
3493> rename #103 CD20_2H7v166_D56A
3494
3495> rename #104 CD20_2H7v166_S92A_D56A
3496
3497> dssp
3498
3499> name CD20_RTX #101.1
3500
3501> name CD20_2H7v16 #102.1
3502
3503> name CD20_2H7v166_D56A #103.1
3504
3505> name CD20_2H7v166_S92A_D56A #104.1
3506
3507> name CD20 /C,D
3508
3509> name CD20_Monomer /C
3510
3511> name CD20_H1 /C,D:46-71
3512
3513> name CD20_ECL1 /C,D:72-79
3514
3515> name CD20_H2 /C,D:80-105
3516
3517> name CD20_ICL1 /C,D:106-112
3518
3519> name CD20_H3 /C,D:113-141
3520
3521> name CD20_ECL2 /C,D:142-187
3522
3523> name CD20_ECL2SS /C,D:167,183
3524
3525> name CD20_H4 /C,D:188-end
3526
3527> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
3528
3529> name RTX CD20_RTX & /H,L,I,M
3530
3531> name RTX_H RTX & /H,I
3532
3533> name RTX_L RTX & /L,M
3534
3535> name RTX_Epitope CD20_RTX & /C,D:168-175
3536
3537> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
3538
3539> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
3540
3541> name H7v16 CD20_2H7v16 & /H,L,I,M
3542
3543> name H7v16_H H7v16 & /H,I
3544
3545> name H7v16_L H7v16 & /L,M
3546
3547> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
3548
3549> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
3550
3551> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
3552
3553> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
3554
3555> name H7v166_D56A_H H7v166_D56A & /H,I
3556
3557> name H7v166_D56A_L H7v166_D56A & /L,M
3558
3559> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
3560
3561> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
3562
3563> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
3564> /H,I:119-end)
3565
3566> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
3567
3568> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
3569
3570> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
3571
3572> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
3573
3574> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
3575> & /H,I:1-111)
3576
3577> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
3578> (H7v166_S92A_D56A & /H,I:119-end)
3579
3580> lighting soft
3581
3582> set bgColor white
3583
3584> camera ortho
3585
3586> style stick
3587
3588Changed 44237 atom styles
3589
3590> color byhetero
3591
3592> open CD20_2H7_mutants_color.cxc
3593
3594> color CD20 burlywood
3595
3596> color modify CD20_H1 hue - 20
3597
3598> color modify CD20_H2 hue - 10
3599
3600> color modify CD20_H3 hue + 0
3601
3602> color modify CD20_H4 hue + 10
3603
3604> color modify CD20_ECL1 hue +10
3605
3606> color modify CD20_ECL2 hue + 40
3607
3608> color modify CD20 saturation + 80
3609
3610> color CD20_ECL2 rgb(127,165,90)
3611
3612> color CD20_H4 rgb(176,215,142)
3613
3614> color RTX plum
3615
3616> color modify RTX_H hue - 40
3617
3618> color H7v16 slate blue
3619
3620> color modify H7v16_H hue - 40
3621
3622> color H7v166_D56A dodger blue
3623
3624> color modify H7v166_D56A_H hue - 40
3625
3626> color H7v166_S92A_D56A purple
3627
3628> color modify H7v166_S92A_D56A_H hue - 40
3629
3630executed CD20_2H7_mutants_color.cxc
3631
3632> hide
3633
3634> ribbon
3635
3636> show CD20_ECL2SS
3637
3638> style CD20_ECL2SS stick
3639
3640Changed 96 atom styles
3641
3642> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
3643
3644Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
3645radius 1, and length 140
3646
3647> marker #1.1 position 155,155,70
3648
3649> marker #1.1 position 155,155,210
3650
3651> select
3652> #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
3653
3654440 atoms, 446 bonds, 54 residues, 1 model selected
3655
3656> define plane sel name membrane_plane
3657
3658Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
3659normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
3660
3661> rename ##name=membrane_plane id 10
3662
3663> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
3664
3665> combine CD20_RTX name RTX_Va modelId 1001
3666
3667> select zone (RTX_V & /H,L) 0.1 #1001
3668
3669Selected 1711 atoms
3670
3671> delete #1001 & ~sel
3672
3673> combine #1001 name RTX_Va_copy modelId 1002
3674
3675> combine CD20_RTX name RTX_Vb modelId 1003
3676
3677> select zone (RTX_V & /I,M) 0.1 #1003
3678
3679Selected 1711 atoms
3680
3681> delete #1003 & ~sel
3682
3683> combine #1003 name RTX_Vb_copy modelId 1004
3684
3685> combine CD20_RTX name RTX_Ca modelId 1005
3686
3687> select zone (RTX_C & /H,L) 0.1 #1005
3688
3689Selected 1503 atoms
3690
3691> delete #1005 & ~sel
3692
3693> combine #1005 name RTX_Ca_copy modelId 1006
3694
3695> combine CD20_RTX name RTX_Cb modelId 1007
3696
3697> select zone (RTX_C & /I,M) 0.1 #1007
3698
3699Selected 1503 atoms
3700
3701> delete #1007 & ~sel
3702
3703> combine #1007 name RTX_Ca_copy modelId 1008
3704
3705> matchmaker #1002/L to #1001/H
3706
3707Parameters
3708---
3709Chain pairing | bb
3710Alignment algorithm | Needleman-Wunsch
3711Similarity matrix | BLOSUM-62
3712SS fraction | 0.3
3713Gap open (HH/SS/other) | 18/18/6
3714Gap extend | 1
3715SS matrix | | | H | S | O
3716---|---|---|---
3717H | 6 | -9 | -6
3718S | | 6 | -6
3719O | | | 4
3720Iteration cutoff | 2
3721
3722Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
3723alignment score = 198.7
3724RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
37254.421)
3726
3727
3728> wait 1
3729
3730> measure rotation #1002 toModel #1001 showSlabs true
3731
3732Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
3733Matrix rotation and translation
37340.65377294 -0.06463426 0.75392530 -36.97668460
37350.02426941 -0.99404163 -0.10626495 318.59247232
37360.75630149 0.08777047 -0.64830888 90.28955685
3737Axis 0.90906034 -0.01113250 0.41651574
3738Axis point 0.00000000 156.41772375 62.99337678
3739Rotation angle (degrees) 173.87355102
3740Shift along axis 0.44625393
3741
3742
3743> close #1001 #1002
3744
3745> define axis #2 name axis_Va
3746
3747Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
3748125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
37490.65062, and length 52.0496
3750
3751> rename #2 Va_rotation_axis id #101.3.1.1
3752
3753> rename #3 Va_rotation_slabs id #101.3.2.1
3754
3755> matchmaker #1004/M to #1003/I
3756
3757Parameters
3758---
3759Chain pairing | bb
3760Alignment algorithm | Needleman-Wunsch
3761Similarity matrix | BLOSUM-62
3762SS fraction | 0.3
3763Gap open (HH/SS/other) | 18/18/6
3764Gap extend | 1
3765SS matrix | | | H | S | O
3766---|---|---|---
3767H | 6 | -9 | -6
3768S | | 6 | -6
3769O | | | 4
3770Iteration cutoff | 2
3771
3772Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
3773alignment score = 214.3
3774RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
37754.448)
3776
3777
3778> wait 1
3779
3780> measure rotation #1004 toModel #1003 showSlabs true
3781
3782Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
3783Matrix rotation and translation
37840.65527690 -0.06129532 -0.75289778 163.48223927
37850.03113398 -0.99366393 0.10799385 290.56686667
3786-0.75474688 -0.09420658 -0.64921665 352.74817189
3787Axis -0.90945183 0.00831685 0.41572611
3788Axis point 0.00000000 156.83903630 204.83255489
3789Rotation angle (degrees) 173.61745932
3790Shift along axis 0.38400661
3791
3792
3793> close #1004 #1003
3794
3795> define axis #2 name axis_Vb
3796
3797Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
3798125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
37990.648586, and length 51.8869
3800
3801> rename #2 Vb_rotation_axis id #101.3.1.2
3802
3803> rename #3 Vb_rotation_slabs id #101.3.2.2
3804
3805> matchmaker #1006/L to #1005/H
3806
3807Parameters
3808---
3809Chain pairing | bb
3810Alignment algorithm | Needleman-Wunsch
3811Similarity matrix | BLOSUM-62
3812SS fraction | 0.3
3813Gap open (HH/SS/other) | 18/18/6
3814Gap extend | 1
3815SS matrix | | | H | S | O
3816---|---|---|---
3817H | 6 | -9 | -6
3818S | | 6 | -6
3819O | | | 4
3820Iteration cutoff | 2
3821
3822Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
3823alignment score = 238.2
3824RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
38253.308)
3826
3827
3828> wait 1
3829
3830> measure rotation #1006 toModel #1005 showSlabs true
3831
3832Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
3833Matrix rotation and translation
38340.37780344 0.24165354 0.89379423 -73.66252391
38350.01279825 -0.96661035 0.25593093 273.63534365
38360.92579737 -0.08525258 -0.36828146 68.27322422
3837Axis -0.82796624 -0.07766353 -0.55537400
3838Axis point 0.00000000 144.62953182 41.62502778
3839Rotation angle (degrees) 168.10978391
3840Shift along axis 1.82142171
3841
3842
3843> close #1006 #1005
3844
3845> define axis #2 name axis_Ca
3846
3847Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
3848110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
38490.539289, and length 43.1431
3850
3851> rename #2 Ca_rotation_axis id #101.3.1.3
3852
3853> rename #3 Ca_rotation_slabs id #101.3.2.3
3854
3855> matchmaker #1008/M to #1007/I
3856
3857Parameters
3858---
3859Chain pairing | bb
3860Alignment algorithm | Needleman-Wunsch
3861Similarity matrix | BLOSUM-62
3862SS fraction | 0.3
3863Gap open (HH/SS/other) | 18/18/6
3864Gap extend | 1
3865SS matrix | | | H | S | O
3866---|---|---|---
3867H | 6 | -9 | -6
3868S | | 6 | -6
3869O | | | 4
3870Iteration cutoff | 2
3871
3872Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
3873alignment score = 238.2
3874RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
38753.487)
3876
3877
3878> wait 1
3879
3880> measure rotation #1008 toModel #1007 showSlabs true
3881
3882Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
3883Matrix rotation and translation
38840.37961795 0.24211100 -0.89290116 191.06761259
38850.01296287 -0.96644625 -0.25654164 332.12351027
3886-0.92505253 0.08581325 -0.37001879 328.82641259
3887Axis 0.82850834 0.07780721 -0.55454483
3888Axis point 0.00000000 136.30341759 249.27961172
3889Rotation angle (degrees) 168.07628341
3890Shift along axis 1.79372450
3891
3892
3893> close #1008 #1007
3894
3895> define axis #2 name axis_Cb
3896
3897Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
3898110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
38990.53918, and length 43.1344
3900
3901> rename #2 Cb_rotation_axis id #101.3.1.4
3902
3903> rename #3 Cb_rotation_slabs id #101.3.2.4
3904
3905> rename #101.3 geometry
3906
3907> rename #101.3.1 rotation_axes
3908
3909> rename #101.3.2 rotation_slabs
3910
3911executed CD20_RTX_define_pseudo_symmetries.cxc
3912
3913> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
3914
3915> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
3916
3917> select zone (H7v16_V & /H,L) 0.1 #1001
3918
3919Selected 1754 atoms
3920
3921> delete #1001 & ~sel
3922
3923> combine #1001 name 2H7_v16_Va_copy modelId 1002
3924
3925> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
3926
3927> select zone (H7v16_V & /I,M) 0.1 #1003
3928
3929Selected 1710 atoms
3930
3931> delete #1003 & ~sel
3932
3933> combine #1003 name 2H7_v16_Vb_copy modelId 1004
3934
3935> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
3936
3937> select zone (H7v16_C & /H,L) 0.1 #1005
3938
3939Selected 1550 atoms
3940
3941> delete #1005 & ~sel
3942
3943> combine #1005 name 2H7_v16_Ca_copy modelId 1006
3944
3945> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
3946
3947> select zone (H7v16_C & /I,M) 0.1 #1007
3948
3949Selected 1550 atoms
3950
3951> delete #1007 & ~sel
3952
3953> combine #1007 name 2H7_v16_Ca_copy modelId 1008
3954
3955> matchmaker #1002/L to #1001/H
3956
3957Parameters
3958---
3959Chain pairing | bb
3960Alignment algorithm | Needleman-Wunsch
3961Similarity matrix | BLOSUM-62
3962SS fraction | 0.3
3963Gap open (HH/SS/other) | 18/18/6
3964Gap extend | 1
3965SS matrix | | | H | S | O
3966---|---|---|---
3967H | 6 | -9 | -6
3968S | | 6 | -6
3969O | | | 4
3970Iteration cutoff | 2
3971
3972Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
3973sequence alignment score = 387.9
3974RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
39755.340)
3976
3977
3978> wait 1
3979
3980> measure rotation #1002 toModel #1001 showSlabs true
3981
3982Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
3983Matrix rotation and translation
39840.58985298 0.00233427 0.80750728 -45.05678546
39850.12316682 -0.98855531 -0.08711100 297.16136614
39860.79806228 0.15084078 -0.58338980 65.44859378
3987Axis 0.89106916 0.03536916 0.45248731
3988Axis point 0.00000000 147.01172040 55.34624717
3989Rotation angle (degrees) 172.32693090
3990Shift along axis -0.02370559
3991
3992
3993> close #1001 #1002
3994
3995> define axis #2 name axis_Va
3996
3997Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
3998125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
39990.589874, and length 47.1899
4000
4001> rename #2 Va_rotation_axis id #102.3.1.1
4002
4003> rename #3 Va_rotation_slabs id #102.3.2.1
4004
4005> matchmaker #1004/M to #1003/I
4006
4007Parameters
4008---
4009Chain pairing | bb
4010Alignment algorithm | Needleman-Wunsch
4011Similarity matrix | BLOSUM-62
4012SS fraction | 0.3
4013Gap open (HH/SS/other) | 18/18/6
4014Gap extend | 1
4015SS matrix | | | H | S | O
4016---|---|---|---
4017H | 6 | -9 | -6
4018S | | 6 | -6
4019O | | | 4
4020Iteration cutoff | 2
4021
4022Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
4023sequence alignment score = 378.3
4024RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
40254.620)
4026
4027
4028> wait 1
4029
4030> measure rotation #1004 toModel #1003 showSlabs true
4031
4032Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
4033Matrix rotation and translation
40340.62864598 0.45103819 -0.63353672 71.77949524
40350.53321619 -0.84298968 -0.07105560 212.64664720
4036-0.56611370 -0.29314322 -0.77044294 368.84403487
4037Axis -0.90200560 -0.27383758 0.33376470
4038Axis point -0.00000000 108.05935567 190.41757658
4039Rotation angle (degrees) 172.92851049
4040Shift along axis 0.13096924
4041
4042
4043> close #1004 #1003
4044
4045> define axis #2 name axis_Vb
4046
4047Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
4048125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
40490.594923, and length 47.5938
4050
4051> rename #2 Vb_rotation_axis id #102.3.1.2
4052
4053> rename #3 Vb_rotation_slabs id #102.3.2.2
4054
4055> matchmaker #1006/L to #1005/H
4056
4057Parameters
4058---
4059Chain pairing | bb
4060Alignment algorithm | Needleman-Wunsch
4061Similarity matrix | BLOSUM-62
4062SS fraction | 0.3
4063Gap open (HH/SS/other) | 18/18/6
4064Gap extend | 1
4065SS matrix | | | H | S | O
4066---|---|---|---
4067H | 6 | -9 | -6
4068S | | 6 | -6
4069O | | | 4
4070Iteration cutoff | 2
4071
4072Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
4073sequence alignment score = 403.6
4074RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
40753.184)
4076
4077
4078> wait 1
4079
4080> measure rotation #1006 toModel #1005 showSlabs true
4081
4082Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
4083Matrix rotation and translation
4084-0.62547004 0.41276667 0.66212605 49.05674876
40850.08546501 -0.80725952 0.58397585 200.07354667
40860.77555333 0.42184801 0.46963954 -95.83522576
4087Axis -0.42390521 -0.29657098 -0.85577452
4088Axis point 59.57688139 113.83169245 0.00000000
4089Rotation angle (degrees) 168.97535276
4090Shift along axis 1.88192618
4091
4092
4093> close #1006 #1005
4094
4095> define axis #2 name axis_Ca
4096
4097Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
4098101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
40990.550437, and length 44.0349
4100
4101> rename #2 Ca_rotation_axis id #102.3.1.3
4102
4103> rename #3 Ca_rotation_slabs id #102.3.2.3
4104
4105> matchmaker #1008/M to #1007/I
4106
4107Parameters
4108---
4109Chain pairing | bb
4110Alignment algorithm | Needleman-Wunsch
4111Similarity matrix | BLOSUM-62
4112SS fraction | 0.3
4113Gap open (HH/SS/other) | 18/18/6
4114Gap extend | 1
4115SS matrix | | | H | S | O
4116---|---|---|---
4117H | 6 | -9 | -6
4118S | | 6 | -6
4119O | | | 4
4120Iteration cutoff | 2
4121
4122Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
4123sequence alignment score = 396
4124RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
41253.551)
4126
4127
4128> wait 1
4129
4130> measure rotation #1008 toModel #1007 showSlabs true
4131
4132Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
4133Matrix rotation and translation
4134-0.62894249 0.48033740 -0.61131606 312.62038315
41350.14842286 -0.69766113 -0.70088487 336.12735996
4136-0.76315267 -0.53154955 0.36749568 311.24709675
4137Axis 0.42085200 0.37736216 -0.82491296
4138Axis point 256.37284203 220.04020388 0.00000000
4139Rotation angle (degrees) 168.39393838
4140Shift along axis 1.65689588
4141
4142
4143> close #1008 #1007
4144
4145> define axis #2 name axis_Cb
4146
4147Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
4148105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
41490.534846, and length 42.7877
4150
4151> rename #2 Cb_rotation_axis id #102.3.1.4
4152
4153> rename #3 Cb_rotation_slabs id #102.3.2.4
4154
4155> rename #102.3 geometry
4156
4157> rename #102.3.1 rotation_axes
4158
4159> rename #102.3.2 rotation_slabs
4160
4161executed CD20_2H7v16_define_pseudo_symmetries.cxc
4162
4163> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
4164
4165> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
4166
4167> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
4168
4169Selected 1654 atoms
4170
4171> delete #1001 & ~sel
4172
4173> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
4174
4175> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
4176
4177> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
4178
4179Selected 1678 atoms
4180
4181> delete #1003 & ~sel
4182
4183> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
4184
4185> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
4186
4187> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
4188
4189Selected 1550 atoms
4190
4191> delete #1005 & ~sel
4192
4193> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
4194
4195> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
4196
4197> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
4198
4199Selected 1550 atoms
4200
4201> delete #1007 & ~sel
4202
4203> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
4204
4205> matchmaker #1002/L to #1001/H
4206
4207Parameters
4208---
4209Chain pairing | bb
4210Alignment algorithm | Needleman-Wunsch
4211Similarity matrix | BLOSUM-62
4212SS fraction | 0.3
4213Gap open (HH/SS/other) | 18/18/6
4214Gap extend | 1
4215SS matrix | | | H | S | O
4216---|---|---|---
4217H | 6 | -9 | -6
4218S | | 6 | -6
4219O | | | 4
4220Iteration cutoff | 2
4221
4222Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
4223L (#1002), sequence alignment score = 547.6
4224RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
42252.607)
4226
4227
4228> wait 1
4229
4230> measure rotation #1002 toModel #1001 showSlabs true
4231
4232Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
4233coordinates:
4234Matrix rotation and translation
42350.73992366 -0.12116101 0.66168949 -29.70332856
4236-0.06116680 -0.99168902 -0.11318795 332.06337928
42370.66990417 0.04327702 -0.74118520 123.44534698
4238Axis 0.93259437 -0.04896279 0.35758970
4239Axis point 0.00000000 162.47254458 74.89799404
4240Rotation angle (degrees) 175.18797763
4241Shift along axis 0.18287681
4242
4243
4244> close #1001 #1002
4245
4246> define axis #2 name axis_Va
4247
4248Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
4249127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
42500.599212, and length 47.937
4251
4252> rename #2 Va_rotation_axis id #103.3.1.1
4253
4254> rename #3 Va_rotation_slabs id #103.3.2.1
4255
4256> matchmaker #1004/M to #1003/I
4257
4258Parameters
4259---
4260Chain pairing | bb
4261Alignment algorithm | Needleman-Wunsch
4262Similarity matrix | BLOSUM-62
4263SS fraction | 0.3
4264Gap open (HH/SS/other) | 18/18/6
4265Gap extend | 1
4266SS matrix | | | H | S | O
4267---|---|---|---
4268H | 6 | -9 | -6
4269S | | 6 | -6
4270O | | | 4
4271Iteration cutoff | 2
4272
4273Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
4274M (#1004), sequence alignment score = 376.5
4275RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
42763.886)
4277
4278
4279> wait 1
4280
4281> measure rotation #1004 toModel #1003 showSlabs true
4282
4283Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
4284coordinates:
4285Matrix rotation and translation
42860.72982969 -0.01372193 -0.68349128 135.94952936
42870.06485007 -0.99390027 0.08920045 287.47713002
4288-0.68054617 -0.10942560 -0.72448806 354.00628960
4289Axis -0.92979963 -0.01378652 0.36780781
4290Axis point 0.00000000 152.92822789 195.61279282
4291Rotation angle (degrees) 173.86847166
4292Shift along axis -0.16285394
4293
4294
4295> close #1004 #1003
4296
4297> define axis #2 name axis_Vb
4298
4299Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
4300126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
43010.597156, and length 47.7725
4302
4303> rename #2 Vb_rotation_axis id #103.3.1.2
4304
4305> rename #3 Vb_rotation_slabs id #103.3.2.2
4306
4307> matchmaker #1006/L to #1005/H
4308
4309Parameters
4310---
4311Chain pairing | bb
4312Alignment algorithm | Needleman-Wunsch
4313Similarity matrix | BLOSUM-62
4314SS fraction | 0.3
4315Gap open (HH/SS/other) | 18/18/6
4316Gap extend | 1
4317SS matrix | | | H | S | O
4318---|---|---|---
4319H | 6 | -9 | -6
4320S | | 6 | -6
4321O | | | 4
4322Iteration cutoff | 2
4323
4324Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
4325L (#1006), sequence alignment score = 554.5
4326RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
43273.119)
4328
4329
4330> wait 1
4331
4332> measure rotation #1006 toModel #1005 showSlabs true
4333
4334Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
4335coordinates:
4336Matrix rotation and translation
4337-0.33391401 0.38072466 0.86229355 -12.40856576
43380.05205532 -0.90595556 0.42016042 245.78035810
43390.94116506 0.18518442 0.28269251 -52.33839393
4340Axis -0.57081123 -0.19159720 -0.79841408
4341Axis point 28.53870248 129.91224226 0.00000000
4342Rotation angle (degrees) 168.12212217
4343Shift along axis 1.77983022
4344
4345
4346> close #1006 #1005
4347
4348> define axis #2 name axis_Ca
4349
4350Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
4351106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
43520.56909, and length 45.5272
4353
4354> rename #2 Ca_rotation_axis id #103.3.1.3
4355
4356> rename #3 Ca_rotation_slabs id #103.3.2.3
4357
4358> matchmaker #1008/M to #1007/I
4359
4360Parameters
4361---
4362Chain pairing | bb
4363Alignment algorithm | Needleman-Wunsch
4364Similarity matrix | BLOSUM-62
4365SS fraction | 0.3
4366Gap open (HH/SS/other) | 18/18/6
4367Gap extend | 1
4368SS matrix | | | H | S | O
4369---|---|---|---
4370H | 6 | -9 | -6
4371S | | 6 | -6
4372O | | | 4
4373Iteration cutoff | 2
4374
4375Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
4376M (#1008), sequence alignment score = 416.6
4377RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
43783.361)
4379
4380
4381> wait 1
4382
4383> measure rotation #1008 toModel #1007 showSlabs true
4384
4385Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
4386coordinates:
4387Matrix rotation and translation
4388-0.50667380 0.40781938 -0.75958213 323.22163731
43890.08178140 -0.85433688 -0.51324487 330.95129120
4390-0.85825023 -0.32216741 0.39951808 287.19953324
4391Axis 0.48922423 0.25262440 -0.83476977
4392Axis point 265.28291179 189.90297685 0.00000000
4393Rotation angle (degrees) 168.73855860
4394Shift along axis 1.98873850
4395
4396
4397> close #1008 #1007
4398
4399> define axis #2 name axis_Cb
4400
4401Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
4402104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
44030.553583, and length 44.2867
4404
4405> rename #2 Cb_rotation_axis id #103.3.1.4
4406
4407> rename #3 Cb_rotation_slabs id #103.3.2.4
4408
4409> rename #103.3 geometry
4410
4411> rename #103.3.1 rotation_axes
4412
4413> rename #103.3.2 rotation_slabs
4414
4415executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
4416
4417> open
4418> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
4419
4420> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
4421
4422> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
4423
4424Selected 1653 atoms
4425
4426> delete #1001 & ~sel
4427
4428> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
4429
4430> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
4431
4432> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
4433
4434Selected 1678 atoms
4435
4436> delete #1003 & ~sel
4437
4438> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
4439
4440> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
4441
4442> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
4443
4444Selected 1461 atoms
4445
4446> delete #1005 & ~sel
4447
4448> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
4449
4450> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
4451
4452> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
4453
4454Selected 1550 atoms
4455
4456> delete #1007 & ~sel
4457
4458> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
4459
4460> matchmaker #1002/L to #1001/H
4461
4462Parameters
4463---
4464Chain pairing | bb
4465Alignment algorithm | Needleman-Wunsch
4466Similarity matrix | BLOSUM-62
4467SS fraction | 0.3
4468Gap open (HH/SS/other) | 18/18/6
4469Gap extend | 1
4470SS matrix | | | H | S | O
4471---|---|---|---
4472H | 6 | -9 | -6
4473S | | 6 | -6
4474O | | | 4
4475Iteration cutoff | 2
4476
4477Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
44782H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 221.1
4479RMSD between 66 pruned atom pairs is 1.048 angstroms; (across all 87 pairs:
44803.054)
4481
4482
4483> wait 1
4484
4485> measure rotation #1002 toModel #1001 showSlabs true
4486
4487Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
4488#1001 coordinates:
4489Matrix rotation and translation
44900.71841270 -0.03882790 0.69453263 -43.77242719
44910.04474713 -0.99379351 -0.10184377 314.28607160
44920.69417640 0.10424420 -0.71221645 107.06747282
4493Axis 0.92669760 0.00160183 0.37580447
4494Axis point 0.00000000 153.96110044 71.86641580
4495Rotation angle (degrees) 173.61580296
4496Shift along axis 0.17606353
4497
4498
4499> close #1001 #1002
4500
4501> define axis #2 name axis_Va
4502
4503Axis 'rotation axis #2/axis_Va' centered at [136.49236761 154.19703207
4504127.21828189] with direction [0.9266976 0.00160183 0.37580447], radius
45050.603625, and length 48.29
4506
4507> rename #2 Va_rotation_axis id #104.3.1.1
4508
4509> rename #3 Va_rotation_slabs id #104.3.2.1
4510
4511> matchmaker #1004/M to #1003/I
4512
4513Parameters
4514---
4515Chain pairing | bb
4516Alignment algorithm | Needleman-Wunsch
4517Similarity matrix | BLOSUM-62
4518SS fraction | 0.3
4519Gap open (HH/SS/other) | 18/18/6
4520Gap extend | 1
4521SS matrix | | | H | S | O
4522---|---|---|---
4523H | 6 | -9 | -6
4524S | | 6 | -6
4525O | | | 4
4526Iteration cutoff | 2
4527
4528Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
45292H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 228.5
4530RMSD between 66 pruned atom pairs is 1.088 angstroms; (across all 92 pairs:
45313.936)
4532
4533
4534> wait 1
4535
4536> measure rotation #1004 toModel #1003 showSlabs true
4537
4538Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
4539#1003 coordinates:
4540Matrix rotation and translation
45410.73661563 -0.07135580 -0.67253682 142.18618798
45420.02298296 -0.99120309 0.13033888 288.51761976
4543-0.67592100 -0.11146654 -0.72849572 353.55093768
4544Axis -0.93153019 0.01303723 0.36343024
4545Axis point 0.00000000 157.62360929 194.41945478
4546Rotation angle (degrees) 172.54257925
4547Shift along axis -0.19815617
4548
4549
4550> close #1004 #1003
4551
4552> define axis #2 name axis_Vb
4553
4554Axis 'rotation axis #2/axis_Vb' centered at [172.8655548 155.20426996
4555126.97712173] with direction [-0.93153019 0.01303723 0.36343024], radius
45560.60681, and length 48.5448
4557
4558> rename #2 Vb_rotation_axis id #104.3.1.2
4559
4560> rename #3 Vb_rotation_slabs id #104.3.2.2
4561
4562> matchmaker #1006/L to #1005/H
4563
4564Parameters
4565---
4566Chain pairing | bb
4567Alignment algorithm | Needleman-Wunsch
4568Similarity matrix | BLOSUM-62
4569SS fraction | 0.3
4570Gap open (HH/SS/other) | 18/18/6
4571Gap extend | 1
4572SS matrix | | | H | S | O
4573---|---|---|---
4574H | 6 | -9 | -6
4575S | | 6 | -6
4576O | | | 4
4577Iteration cutoff | 2
4578
4579Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
45802H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 229.8
4581RMSD between 50 pruned atom pairs is 0.885 angstroms; (across all 82 pairs:
45823.058)
4583
4584
4585> wait 1
4586
4587> measure rotation #1006 toModel #1005 showSlabs true
4588
4589Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
4590#1005 coordinates:
4591Matrix rotation and translation
4592-0.43223566 0.39105435 0.81255697 5.34243089
45930.04124481 -0.89156204 0.45101662 236.01875124
45940.90081696 0.22845922 0.36923594 -64.79879197
4595Axis -0.52502754 -0.20821113 -0.82522373
4596Axis point 38.63388899 125.78498588 0.00000000
4597Rotation angle (degrees) 167.76344751
4598Shift along axis 1.52684600
4599
4600
4601> close #1006 #1005
4602
4603> define axis #2 name axis_Ca
4604
4605Axis 'rotation axis #2/axis_Ca' centered at [105.63109625 152.35419104
4606105.30435297] with direction [-0.52502754 -0.20821113 -0.82522373], radius
46070.532467, and length 42.5974
4608
4609> rename #2 Ca_rotation_axis id #104.3.1.3
4610
4611> rename #3 Ca_rotation_slabs id #104.3.2.3
4612
4613> matchmaker #1008/M to #1007/I
4614
4615Parameters
4616---
4617Chain pairing | bb
4618Alignment algorithm | Needleman-Wunsch
4619Similarity matrix | BLOSUM-62
4620SS fraction | 0.3
4621Gap open (HH/SS/other) | 18/18/6
4622Gap extend | 1
4623SS matrix | | | H | S | O
4624---|---|---|---
4625H | 6 | -9 | -6
4626S | | 6 | -6
4627O | | | 4
4628Iteration cutoff | 2
4629
4630Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
46312H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 226.4
4632RMSD between 57 pruned atom pairs is 0.983 angstroms; (across all 98 pairs:
46333.247)
4634
4635
4636> wait 1
4637
4638> measure rotation #1008 toModel #1007 showSlabs true
4639
4640Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
4641#1007 coordinates:
4642Matrix rotation and translation
4643-0.44691350 0.37987962 -0.80991345 321.97311814
46440.04334425 -0.89510032 -0.44375297 334.72634524
4645-0.89352650 -0.23342428 0.38356682 282.18198422
4646Axis 0.51860284 0.20616286 -0.82978790
4647Axis point 269.80743377 182.59879005 0.00000000
4648Rotation angle (degrees) 168.30019456
4649Shift along axis 1.83311720
4650
4651
4652> close #1008 #1007
4653
4654> define axis #2 name axis_Cb
4655
4656Axis 'rotation axis #2/axis_Cb' centered at [203.87433587 156.38806637
4657105.49592574] with direction [ 0.51860284 0.20616286 -0.8297879 ], radius
46580.566216, and length 45.2973
4659
4660> rename #2 Cb_rotation_axis id #104.3.1.4
4661
4662> rename #3 Cb_rotation_slabs id #104.3.2.4
4663
4664> rename #104.3 geometry
4665
4666> rename #104.3.1 rotation_axes
4667
4668> rename #104.3.2 rotation_slabs
4669
4670executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
4671
4672> open CD20_2H7_mutants_define_domain_centroids.cxc
4673
4674> define centroid RTX_C & /L name centroid_RTX_C_L
4675
4676Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
4677
4678> rename ##name=centroid_RTX_C_L id 101.3.3.1
4679
4680> define centroid RTX_C & /M name centroid_RTX_C_M
4681
4682Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
4683
4684> rename ##name=centroid_RTX_C_M id 101.3.3.2
4685
4686> define centroid RTX_C & /H name centroid_RTX_C_H
4687
4688Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
4689
4690> rename ##name=centroid_RTX_C_H id 101.3.3.3
4691
4692> define centroid RTX_C & /I name centroid_RTX_C_I
4693
4694Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
4695
4696> rename ##name=centroid_RTX_C_I id 101.3.3.4
4697
4698> define centroid RTX_V & /L name centroid_RTX_V_L
4699
4700Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
4701
4702> rename ##name=centroid_RTX_V_L id 101.3.3.5
4703
4704> define centroid RTX_V & /M name centroid_RTX_V_M
4705
4706Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
4707
4708> rename ##name=centroid_RTX_V_M id 101.3.3.6
4709
4710> define centroid RTX_V & /H name centroid_RTX_V_H
4711
4712Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
4713
4714> rename ##name=centroid_RTX_V_H id 101.3.3.7
4715
4716> define centroid RTX_V & /I name centroid_RTX_V_I
4717
4718Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
4719
4720> rename ##name=centroid_RTX_V_I id 101.3.3.8
4721
4722> rename #101.3.3 centroids
4723
4724> define centroid H7v16_C & /L name centroid_2H7v16_C_L
4725
4726Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
4727104.71732873]
4728
4729> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
4730
4731> define centroid H7v16_C & /M name centroid_2H7v16_C_M
4732
4733Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
4734109.46892346]
4735
4736> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
4737
4738> define centroid H7v16_C & /H name centroid_2H7v16_C_H
4739
4740Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
4741100.10963479]
4742
4743> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
4744
4745> define centroid H7v16_C & /I name centroid_2H7v16_C_I
4746
4747Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
4748103.22787118]
4749
4750> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
4751
4752> define centroid H7v16_V & /L name centroid_2H7v16_V_L
4753
4754Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
4755124.64938243]
4756
4757> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
4758
4759> define centroid H7v16_V & /M name centroid_2H7v16_V_M
4760
4761Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
4762126.48898691]
4763
4764> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
4765
4766> define centroid H7v16_V & /H name centroid_2H7v16_V_H
4767
4768Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
4769126.96669027]
4770
4771> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
4772
4773> define centroid H7v16_V & /I name centroid_2H7v16_V_I
4774
4775Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
4776126.76187738]
4777
4778> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
4779
4780> rename #102.3.3 centroids
4781
4782> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
4783
4784Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
4785111.74271267]
4786
4787> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
4788
4789> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
4790
4791Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
4792109.3226675 ]
4793
4794> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
4795
4796> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
4797
4798Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
4799105.03944622]
4800
4801> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
4802
4803> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
4804
4805Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
4806103.22947676]
4807
4808> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
4809
4810> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
4811
4812Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
4813127.91858459]
4814
4815> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
4816
4817> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
4818
4819Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
4820127.2169787 ]
4821
4822> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
4823
4824> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
4825
4826Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
4827127.54490507]
4828
4829> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
4830
4831> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
4832
4833Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
4834127.29650809]
4835
4836> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
4837
4838> rename #103.3.3 centroids
4839
4840> define centroid CD20 & /C name centroid_CD20_C
4841
4842Centroid 'centroid_CD20_C' placed at [144.8538135 155.45678354 168.48594241]
4843
4844> rename ##name=centroid_CD20_C id 101.3.3.9
4845
4846> define centroid CD20 & /D name centroid_CD20_D
4847
4848Centroid 'centroid_CD20_D' placed at [165.21501485 155.16108662 168.7605414 ]
4849
4850> rename ##name=centroid_CD20_D id 101.3.3.10
4851
4852executed CD20_2H7_mutants_define_domain_centroids.cxc
4853
4854> turn x 90
4855
4856> view
4857
4858> hide #101 models
4859
4860> hide #!102.2 models
4861
4862> ~ribbon #102.10/X,Y
4863
4864executed CD20_2H7_mutants_setup.cxc
4865
4866> help angle
4867
4868> open /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730.pdb
4869
4870Summary of feedback from opening
4871/Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730.pdb
4872---
4873warning | Ignored bad PDB record found on line 1
4874HEADER STR7730 version_1 2024.01.12
4875
4876STR7730.pdb title:
4877Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
4878info...]
4879
4880Chain information for STR7730.pdb #2
4881---
4882Chain | Description
4883C | No description available
4884D | No description available
4885H I | No description available
4886L | No description available
4887M | No description available
4888
4889
4890> matchmaker #2 to #103.1
4891
4892Parameters
4893---
4894Chain pairing | bb
4895Alignment algorithm | Needleman-Wunsch
4896Similarity matrix | BLOSUM-62
4897SS fraction | 0.3
4898Gap open (HH/SS/other) | 18/18/6
4899Gap extend | 1
4900SS matrix | | | H | S | O
4901---|---|---|---
4902H | 6 | -9 | -6
4903S | | 6 | -6
4904O | | | 4
4905Iteration cutoff | 2
4906
4907Matchmaker CD20_2H7v166_D56A, chain I (#103.1) with STR7730.pdb, chain H (#2),
4908sequence alignment score = 1988.6
4909RMSD between 214 pruned atom pairs is 0.839 angstroms; (across all 229 pairs:
49101.558)
4911
4912
4913> save /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730_alito6vja.pdb
4914> models #2
4915
4916> help martrix
4917
4918No help found for 'martrix'
4919
4920> help view matrix
4921
4922> view matrix
4923
4924view matrix camera 1,0,0,148.16,0,1.1102e-16,1,424.33,0,-1,1.1102e-16,137.41
4925view matrix models
4926#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,#104.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.094232,-0.75331,-0.65088,436.99,-0.99412,-0.036109,-0.10213,396.76,0.053436,0.65667,-0.75228,168.36
4927
4928
4929> close
4930
4931> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
4932
4933> close
4934
4935> cd /Users/rohoua/work/Genentech/CD20
4936
4937Current working directory is: /Users/rohoua/work/Genentech/CD20
4938
4939> open pdb:6vja name CD20_RTX id 101.1
4940
4941CD20_RTX title:
4942Structure of CD20 in complex with rituximab Fab [more info...]
4943
4944Chain information for CD20_RTX #1
4945---
4946Chain | Description | UniProt
4947C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
4948H I | Rituximab Fab heavy chain |
4949L M | Rituximab Fab light chain |
4950
4951Non-standard residues in CD20_RTX #1
4952---
4953Y01 — cholesterol hemisuccinate
4954
4955
4956> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
4957
4958Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb
4959---
4960warning | Ignored bad PDB record found on line 1
4961HEADER STR7668 version_2 2023.12.13
4962
4963CD20_2H7v16 title:
4964Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
4965resolution. [more info...]
4966
4967Chain information for CD20_2H7v16 #1
4968---
4969Chain | Description
4970C D | No description available
4971H I | No description available
4972L M | No description available
4973
4974Non-standard residues in CD20_2H7v16 #1
4975---
4976Y01 — (Y01)
4977
4978
4979> open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
4980
4981Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
4982shown at level 0.0054, step 2, values float32
4983
4984> volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
4985
4986> view matrix models
4987> #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
4988
4989> open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
4990> 102.10
4991
4992Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
4993Fab.pdb
4994---
4995warning | Ignored bad PDB record found on line 1
4996HEADER STR7487 version_1 2023.05.24
4997
49982H7v16_XRay title:
4999Structure of 2H7 Fab at 2.45 A resolution. [more info...]
5000
5001Chain information for 2H7v16_XRay #1
5002---
5003Chain | Description
5004A B X Y | No description available
5005
5006Non-standard residues in 2H7v16_XRay #1
5007---
5008CL — (CL)
5009
5010
5011> matchmaker #102.10/A,B to #102.1/H,L
5012
5013Parameters
5014---
5015Chain pairing | bb
5016Alignment algorithm | Needleman-Wunsch
5017Similarity matrix | BLOSUM-62
5018SS fraction | 0.3
5019Gap open (HH/SS/other) | 18/18/6
5020Gap extend | 1
5021SS matrix | | | H | S | O
5022---|---|---|---
5023H | 6 | -9 | -6
5024S | | 6 | -6
5025O | | | 4
5026Iteration cutoff | 2
5027
5028Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
5029sequence alignment score = 1228.2
5030RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
50310.804)
5032
5033
5034> open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
5035> 103.1
5036
5037Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb
5038---
5039warning | Ignored bad PDB record found on line 1
5040HEADER STR7717 version_2 2023.12.15
5041
5042CD20_2H7v166_D56A title:
5043Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
5044info...]
5045
5046Chain information for CD20_2H7v166_D56A #1
5047---
5048Chain | Description
5049C D | No description available
5050H I | No description available
5051L | No description available
5052M | No description available
5053
5054Non-standard residues in CD20_2H7v166_D56A #1
5055---
5056Y01 — (Y01)
5057
5058
5059> open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
5060
5061Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
5062300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32
5063
5064> volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
5065
5066> view matrix models
5067> #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
5068
5069> open CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb name
5070> CD20_2H7v166_S92A_D56A id 104.1
5071
5072Summary of feedback from opening
5073CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb
5074---
5075warning | Ignored bad PDB record found on line 1
5076HEADER STR7729 version_2 2024.01.29
5077
5078CD20_2H7v166_S92A_D56A title:
5079Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
5080resolution. [more info...]
5081
5082Chain information for CD20_2H7v166_S92A_D56A #1
5083---
5084Chain | Description
5085C D | No description available
5086H | No description available
5087I | No description available
5088L M | No description available
5089
5090
5091> open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
5092> id 104.2
5093
5094Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
5095300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
5096
5097> volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
5098
5099> view matrix models
5100> #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
5101
5102> open CD20_2H7v166/STR7730_alito6vja.pdb name CD20_2H7v166 id 105.1
5103
5104Summary of feedback from opening CD20_2H7v166/STR7730_alito6vja.pdb
5105---
5106warning | Ignored bad PDB record found on line 1
5107HEADER STR7730 version_1 2024.01.12
5108
5109CD20_2H7v166 title:
5110Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
5111info...]
5112
5113Chain information for CD20_2H7v166 #1
5114---
5115Chain | Description
5116C | No description available
5117D | No description available
5118H I | No description available
5119L | No description available
5120M | No description available
5121
5122
5123> open CD20_2H7v166/cryosparc_P71_J138_006_volume_map_sharp.mrc id 105.2
5124
5125Opened cryosparc_P71_J138_006_volume_map_sharp.mrc as #1, grid size
5126300,300,300, pixel 1.43, shown at level 0.0428, step 2, values float32
5127
5128> volume #105.2 step 1 level 0.355 color #9999CC transparency 0.5
5129
5130> view matrix models
5131> #105.2,0.094232,-0.75331,-0.65088,436.99,-0.99412,-0.036109,-0.10213,396.76,0.053436,0.65667,-0.75228,168.36
5132
5133> rename #101 CD20_RTX
5134
5135> rename #102 CD20_2H7v16
5136
5137> rename #103 CD20_2H7v166_D56A
5138
5139> rename #104 CD20_2H7v166_S92A_D56A
5140
5141> dssp
5142
5143> name CD20_RTX #101.1
5144
5145> name CD20_2H7v16 #102.1
5146
5147> name CD20_2H7v166_D56A #103.1
5148
5149> name CD20_2H7v166_S92A_D56A #104.1
5150
5151> name CD20 /C,D
5152
5153> name CD20_Monomer /C
5154
5155> name CD20_H1 /C,D:46-71
5156
5157> name CD20_ECL1 /C,D:72-79
5158
5159> name CD20_H2 /C,D:80-105
5160
5161> name CD20_ICL1 /C,D:106-112
5162
5163> name CD20_H3 /C,D:113-141
5164
5165> name CD20_ECL2 /C,D:142-187
5166
5167> name CD20_ECL2SS /C,D:167,183
5168
5169> name CD20_H4 /C,D:188-end
5170
5171> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
5172
5173> name RTX CD20_RTX & /H,L,I,M
5174
5175> name RTX_H RTX & /H,I
5176
5177> name RTX_L RTX & /L,M
5178
5179> name RTX_Epitope CD20_RTX & /C,D:168-175
5180
5181> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
5182
5183> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
5184
5185> name H7v16 CD20_2H7v16 & /H,L,I,M
5186
5187> name H7v16_H H7v16 & /H,I
5188
5189> name H7v16_L H7v16 & /L,M
5190
5191> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
5192
5193> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
5194
5195> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
5196
5197> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
5198
5199> name H7v166_D56A_H H7v166_D56A & /H,I
5200
5201> name H7v166_D56A_L H7v166_D56A & /L,M
5202
5203> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
5204
5205> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
5206
5207> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
5208> /H,I:119-end)
5209
5210> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
5211
5212> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
5213
5214> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
5215
5216> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
5217
5218> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
5219> & /H,I:1-111)
5220
5221> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
5222> (H7v166_S92A_D56A & /H,I:119-end)
5223
5224> lighting soft
5225
5226> set bgColor white
5227
5228> camera ortho
5229
5230> style stick
5231
5232Changed 53488 atom styles
5233
5234> color byhetero
5235
5236> open CD20_2H7_mutants_color.cxc
5237
5238> color CD20 burlywood
5239
5240> color modify CD20_H1 hue - 20
5241
5242> color modify CD20_H2 hue - 10
5243
5244> color modify CD20_H3 hue + 0
5245
5246> color modify CD20_H4 hue + 10
5247
5248> color modify CD20_ECL1 hue +10
5249
5250> color modify CD20_ECL2 hue + 40
5251
5252> color modify CD20 saturation + 80
5253
5254> color CD20_ECL2 rgb(127,165,90)
5255
5256> color CD20_H4 rgb(176,215,142)
5257
5258> color RTX plum
5259
5260> color modify RTX_H hue - 40
5261
5262> color H7v16 slate blue
5263
5264> color modify H7v16_H hue - 40
5265
5266> color H7v166_D56A dodger blue
5267
5268> color modify H7v166_D56A_H hue - 40
5269
5270> color H7v166_S92A_D56A purple
5271
5272> color modify H7v166_S92A_D56A_H hue - 40
5273
5274executed CD20_2H7_mutants_color.cxc
5275
5276> hide
5277
5278> ribbon
5279
5280> show CD20_ECL2SS
5281
5282> style CD20_ECL2SS stick
5283
5284Changed 120 atom styles
5285
5286> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
5287
5288Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
5289radius 1, and length 140
5290
5291> marker #1.1 position 155,155,70
5292
5293> marker #1.1 position 155,155,210
5294
5295> select
5296> #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
5297
5298440 atoms, 446 bonds, 54 residues, 1 model selected
5299
5300> define plane sel name membrane_plane
5301
5302Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
5303normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
5304
5305> rename ##name=membrane_plane id 10
5306
5307> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
5308
5309> combine CD20_RTX name RTX_Va modelId 1001
5310
5311> select zone (RTX_V & /H,L) 0.1 #1001
5312
5313Selected 1711 atoms
5314
5315> delete #1001 & ~sel
5316
5317> combine #1001 name RTX_Va_copy modelId 1002
5318
5319> combine CD20_RTX name RTX_Vb modelId 1003
5320
5321> select zone (RTX_V & /I,M) 0.1 #1003
5322
5323Selected 1711 atoms
5324
5325> delete #1003 & ~sel
5326
5327> combine #1003 name RTX_Vb_copy modelId 1004
5328
5329> combine CD20_RTX name RTX_Ca modelId 1005
5330
5331> select zone (RTX_C & /H,L) 0.1 #1005
5332
5333Selected 1503 atoms
5334
5335> delete #1005 & ~sel
5336
5337> combine #1005 name RTX_Ca_copy modelId 1006
5338
5339> combine CD20_RTX name RTX_Cb modelId 1007
5340
5341> select zone (RTX_C & /I,M) 0.1 #1007
5342
5343Selected 1503 atoms
5344
5345> delete #1007 & ~sel
5346
5347> combine #1007 name RTX_Ca_copy modelId 1008
5348
5349> matchmaker #1002/L to #1001/H
5350
5351Parameters
5352---
5353Chain pairing | bb
5354Alignment algorithm | Needleman-Wunsch
5355Similarity matrix | BLOSUM-62
5356SS fraction | 0.3
5357Gap open (HH/SS/other) | 18/18/6
5358Gap extend | 1
5359SS matrix | | | H | S | O
5360---|---|---|---
5361H | 6 | -9 | -6
5362S | | 6 | -6
5363O | | | 4
5364Iteration cutoff | 2
5365
5366Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
5367alignment score = 198.7
5368RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
53694.421)
5370
5371
5372> wait 1
5373
5374> measure rotation #1002 toModel #1001 showSlabs true
5375
5376Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
5377Matrix rotation and translation
53780.65377294 -0.06463426 0.75392530 -36.97668460
53790.02426941 -0.99404163 -0.10626495 318.59247232
53800.75630149 0.08777047 -0.64830888 90.28955685
5381Axis 0.90906034 -0.01113250 0.41651574
5382Axis point 0.00000000 156.41772375 62.99337678
5383Rotation angle (degrees) 173.87355102
5384Shift along axis 0.44625393
5385
5386
5387> close #1001 #1002
5388
5389> define axis #2 name axis_Va
5390
5391Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
5392125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
53930.65062, and length 52.0496
5394
5395> rename #2 Va_rotation_axis id #101.3.1.1
5396
5397> rename #3 Va_rotation_slabs id #101.3.2.1
5398
5399> matchmaker #1004/M to #1003/I
5400
5401Parameters
5402---
5403Chain pairing | bb
5404Alignment algorithm | Needleman-Wunsch
5405Similarity matrix | BLOSUM-62
5406SS fraction | 0.3
5407Gap open (HH/SS/other) | 18/18/6
5408Gap extend | 1
5409SS matrix | | | H | S | O
5410---|---|---|---
5411H | 6 | -9 | -6
5412S | | 6 | -6
5413O | | | 4
5414Iteration cutoff | 2
5415
5416Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
5417alignment score = 214.3
5418RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
54194.448)
5420
5421
5422> wait 1
5423
5424> measure rotation #1004 toModel #1003 showSlabs true
5425
5426Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
5427Matrix rotation and translation
54280.65527690 -0.06129532 -0.75289778 163.48223927
54290.03113398 -0.99366393 0.10799385 290.56686667
5430-0.75474688 -0.09420658 -0.64921665 352.74817189
5431Axis -0.90945183 0.00831685 0.41572611
5432Axis point 0.00000000 156.83903630 204.83255489
5433Rotation angle (degrees) 173.61745932
5434Shift along axis 0.38400661
5435
5436
5437> close #1004 #1003
5438
5439> define axis #2 name axis_Vb
5440
5441Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
5442125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
54430.648586, and length 51.8869
5444
5445> rename #2 Vb_rotation_axis id #101.3.1.2
5446
5447> rename #3 Vb_rotation_slabs id #101.3.2.2
5448
5449> matchmaker #1006/L to #1005/H
5450
5451Parameters
5452---
5453Chain pairing | bb
5454Alignment algorithm | Needleman-Wunsch
5455Similarity matrix | BLOSUM-62
5456SS fraction | 0.3
5457Gap open (HH/SS/other) | 18/18/6
5458Gap extend | 1
5459SS matrix | | | H | S | O
5460---|---|---|---
5461H | 6 | -9 | -6
5462S | | 6 | -6
5463O | | | 4
5464Iteration cutoff | 2
5465
5466Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
5467alignment score = 238.2
5468RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
54693.308)
5470
5471
5472> wait 1
5473
5474> measure rotation #1006 toModel #1005 showSlabs true
5475
5476Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
5477Matrix rotation and translation
54780.37780344 0.24165354 0.89379423 -73.66252391
54790.01279825 -0.96661035 0.25593093 273.63534365
54800.92579737 -0.08525258 -0.36828146 68.27322422
5481Axis -0.82796624 -0.07766353 -0.55537400
5482Axis point 0.00000000 144.62953182 41.62502778
5483Rotation angle (degrees) 168.10978391
5484Shift along axis 1.82142171
5485
5486
5487> close #1006 #1005
5488
5489> define axis #2 name axis_Ca
5490
5491Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
5492110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
54930.539289, and length 43.1431
5494
5495> rename #2 Ca_rotation_axis id #101.3.1.3
5496
5497> rename #3 Ca_rotation_slabs id #101.3.2.3
5498
5499> matchmaker #1008/M to #1007/I
5500
5501Parameters
5502---
5503Chain pairing | bb
5504Alignment algorithm | Needleman-Wunsch
5505Similarity matrix | BLOSUM-62
5506SS fraction | 0.3
5507Gap open (HH/SS/other) | 18/18/6
5508Gap extend | 1
5509SS matrix | | | H | S | O
5510---|---|---|---
5511H | 6 | -9 | -6
5512S | | 6 | -6
5513O | | | 4
5514Iteration cutoff | 2
5515
5516Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
5517alignment score = 238.2
5518RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
55193.487)
5520
5521
5522> wait 1
5523
5524> measure rotation #1008 toModel #1007 showSlabs true
5525
5526Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
5527Matrix rotation and translation
55280.37961795 0.24211100 -0.89290116 191.06761259
55290.01296287 -0.96644625 -0.25654164 332.12351027
5530-0.92505253 0.08581325 -0.37001879 328.82641259
5531Axis 0.82850834 0.07780721 -0.55454483
5532Axis point 0.00000000 136.30341759 249.27961172
5533Rotation angle (degrees) 168.07628341
5534Shift along axis 1.79372450
5535
5536
5537> close #1008 #1007
5538
5539> define axis #2 name axis_Cb
5540
5541Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
5542110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
55430.53918, and length 43.1344
5544
5545> rename #2 Cb_rotation_axis id #101.3.1.4
5546
5547> rename #3 Cb_rotation_slabs id #101.3.2.4
5548
5549> rename #101.3 geometry
5550
5551> rename #101.3.1 rotation_axes
5552
5553> rename #101.3.2 rotation_slabs
5554
5555executed CD20_RTX_define_pseudo_symmetries.cxc
5556
5557> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
5558
5559> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
5560
5561> select zone (H7v16_V & /H,L) 0.1 #1001
5562
5563Selected 1754 atoms
5564
5565> delete #1001 & ~sel
5566
5567> combine #1001 name 2H7_v16_Va_copy modelId 1002
5568
5569> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
5570
5571> select zone (H7v16_V & /I,M) 0.1 #1003
5572
5573Selected 1710 atoms
5574
5575> delete #1003 & ~sel
5576
5577> combine #1003 name 2H7_v16_Vb_copy modelId 1004
5578
5579> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
5580
5581> select zone (H7v16_C & /H,L) 0.1 #1005
5582
5583Selected 1550 atoms
5584
5585> delete #1005 & ~sel
5586
5587> combine #1005 name 2H7_v16_Ca_copy modelId 1006
5588
5589> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
5590
5591> select zone (H7v16_C & /I,M) 0.1 #1007
5592
5593Selected 1550 atoms
5594
5595> delete #1007 & ~sel
5596
5597> combine #1007 name 2H7_v16_Ca_copy modelId 1008
5598
5599> matchmaker #1002/L to #1001/H
5600
5601Parameters
5602---
5603Chain pairing | bb
5604Alignment algorithm | Needleman-Wunsch
5605Similarity matrix | BLOSUM-62
5606SS fraction | 0.3
5607Gap open (HH/SS/other) | 18/18/6
5608Gap extend | 1
5609SS matrix | | | H | S | O
5610---|---|---|---
5611H | 6 | -9 | -6
5612S | | 6 | -6
5613O | | | 4
5614Iteration cutoff | 2
5615
5616Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
5617sequence alignment score = 387.9
5618RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
56195.340)
5620
5621
5622> wait 1
5623
5624> measure rotation #1002 toModel #1001 showSlabs true
5625
5626Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
5627Matrix rotation and translation
56280.58985298 0.00233427 0.80750728 -45.05678546
56290.12316682 -0.98855531 -0.08711100 297.16136614
56300.79806228 0.15084078 -0.58338980 65.44859378
5631Axis 0.89106916 0.03536916 0.45248731
5632Axis point 0.00000000 147.01172040 55.34624717
5633Rotation angle (degrees) 172.32693090
5634Shift along axis -0.02370559
5635
5636
5637> close #1001 #1002
5638
5639> define axis #2 name axis_Va
5640
5641Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
5642125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
56430.589874, and length 47.1899
5644
5645> rename #2 Va_rotation_axis id #102.3.1.1
5646
5647> rename #3 Va_rotation_slabs id #102.3.2.1
5648
5649> matchmaker #1004/M to #1003/I
5650
5651Parameters
5652---
5653Chain pairing | bb
5654Alignment algorithm | Needleman-Wunsch
5655Similarity matrix | BLOSUM-62
5656SS fraction | 0.3
5657Gap open (HH/SS/other) | 18/18/6
5658Gap extend | 1
5659SS matrix | | | H | S | O
5660---|---|---|---
5661H | 6 | -9 | -6
5662S | | 6 | -6
5663O | | | 4
5664Iteration cutoff | 2
5665
5666Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
5667sequence alignment score = 378.3
5668RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
56694.620)
5670
5671
5672> wait 1
5673
5674> measure rotation #1004 toModel #1003 showSlabs true
5675
5676Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
5677Matrix rotation and translation
56780.62864598 0.45103819 -0.63353672 71.77949524
56790.53321619 -0.84298968 -0.07105560 212.64664720
5680-0.56611370 -0.29314322 -0.77044294 368.84403487
5681Axis -0.90200560 -0.27383758 0.33376470
5682Axis point -0.00000000 108.05935567 190.41757658
5683Rotation angle (degrees) 172.92851049
5684Shift along axis 0.13096924
5685
5686
5687> close #1004 #1003
5688
5689> define axis #2 name axis_Vb
5690
5691Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
5692125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
56930.594923, and length 47.5938
5694
5695> rename #2 Vb_rotation_axis id #102.3.1.2
5696
5697> rename #3 Vb_rotation_slabs id #102.3.2.2
5698
5699> matchmaker #1006/L to #1005/H
5700
5701Parameters
5702---
5703Chain pairing | bb
5704Alignment algorithm | Needleman-Wunsch
5705Similarity matrix | BLOSUM-62
5706SS fraction | 0.3
5707Gap open (HH/SS/other) | 18/18/6
5708Gap extend | 1
5709SS matrix | | | H | S | O
5710---|---|---|---
5711H | 6 | -9 | -6
5712S | | 6 | -6
5713O | | | 4
5714Iteration cutoff | 2
5715
5716Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
5717sequence alignment score = 403.6
5718RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
57193.184)
5720
5721
5722> wait 1
5723
5724> measure rotation #1006 toModel #1005 showSlabs true
5725
5726Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
5727Matrix rotation and translation
5728-0.62547004 0.41276667 0.66212605 49.05674876
57290.08546501 -0.80725952 0.58397585 200.07354667
57300.77555333 0.42184801 0.46963954 -95.83522576
5731Axis -0.42390521 -0.29657098 -0.85577452
5732Axis point 59.57688139 113.83169245 0.00000000
5733Rotation angle (degrees) 168.97535276
5734Shift along axis 1.88192618
5735
5736
5737> close #1006 #1005
5738
5739> define axis #2 name axis_Ca
5740
5741Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
5742101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
57430.550437, and length 44.0349
5744
5745> rename #2 Ca_rotation_axis id #102.3.1.3
5746
5747> rename #3 Ca_rotation_slabs id #102.3.2.3
5748
5749> matchmaker #1008/M to #1007/I
5750
5751Parameters
5752---
5753Chain pairing | bb
5754Alignment algorithm | Needleman-Wunsch
5755Similarity matrix | BLOSUM-62
5756SS fraction | 0.3
5757Gap open (HH/SS/other) | 18/18/6
5758Gap extend | 1
5759SS matrix | | | H | S | O
5760---|---|---|---
5761H | 6 | -9 | -6
5762S | | 6 | -6
5763O | | | 4
5764Iteration cutoff | 2
5765
5766Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
5767sequence alignment score = 396
5768RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
57693.551)
5770
5771
5772> wait 1
5773
5774> measure rotation #1008 toModel #1007 showSlabs true
5775
5776Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
5777Matrix rotation and translation
5778-0.62894249 0.48033740 -0.61131606 312.62038315
57790.14842286 -0.69766113 -0.70088487 336.12735996
5780-0.76315267 -0.53154955 0.36749568 311.24709675
5781Axis 0.42085200 0.37736216 -0.82491296
5782Axis point 256.37284203 220.04020388 0.00000000
5783Rotation angle (degrees) 168.39393838
5784Shift along axis 1.65689588
5785
5786
5787> close #1008 #1007
5788
5789> define axis #2 name axis_Cb
5790
5791Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
5792105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
57930.534846, and length 42.7877
5794
5795> rename #2 Cb_rotation_axis id #102.3.1.4
5796
5797> rename #3 Cb_rotation_slabs id #102.3.2.4
5798
5799> rename #102.3 geometry
5800
5801> rename #102.3.1 rotation_axes
5802
5803> rename #102.3.2 rotation_slabs
5804
5805executed CD20_2H7v16_define_pseudo_symmetries.cxc
5806
5807> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
5808
5809> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
5810
5811> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
5812
5813Selected 1654 atoms
5814
5815> delete #1001 & ~sel
5816
5817> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
5818
5819> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
5820
5821> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
5822
5823Selected 1678 atoms
5824
5825> delete #1003 & ~sel
5826
5827> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
5828
5829> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
5830
5831> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
5832
5833Selected 1550 atoms
5834
5835> delete #1005 & ~sel
5836
5837> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
5838
5839> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
5840
5841> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
5842
5843Selected 1550 atoms
5844
5845> delete #1007 & ~sel
5846
5847> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
5848
5849> matchmaker #1002/L to #1001/H
5850
5851Parameters
5852---
5853Chain pairing | bb
5854Alignment algorithm | Needleman-Wunsch
5855Similarity matrix | BLOSUM-62
5856SS fraction | 0.3
5857Gap open (HH/SS/other) | 18/18/6
5858Gap extend | 1
5859SS matrix | | | H | S | O
5860---|---|---|---
5861H | 6 | -9 | -6
5862S | | 6 | -6
5863O | | | 4
5864Iteration cutoff | 2
5865
5866Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
5867L (#1002), sequence alignment score = 547.6
5868RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
58692.607)
5870
5871
5872> wait 1
5873
5874> measure rotation #1002 toModel #1001 showSlabs true
5875
5876Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
5877coordinates:
5878Matrix rotation and translation
58790.73992366 -0.12116101 0.66168949 -29.70332856
5880-0.06116680 -0.99168902 -0.11318795 332.06337928
58810.66990417 0.04327702 -0.74118520 123.44534698
5882Axis 0.93259437 -0.04896279 0.35758970
5883Axis point 0.00000000 162.47254458 74.89799404
5884Rotation angle (degrees) 175.18797763
5885Shift along axis 0.18287681
5886
5887
5888> close #1001 #1002
5889
5890> define axis #2 name axis_Va
5891
5892Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
5893127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
58940.599212, and length 47.937
5895
5896> rename #2 Va_rotation_axis id #103.3.1.1
5897
5898> rename #3 Va_rotation_slabs id #103.3.2.1
5899
5900> matchmaker #1004/M to #1003/I
5901
5902Parameters
5903---
5904Chain pairing | bb
5905Alignment algorithm | Needleman-Wunsch
5906Similarity matrix | BLOSUM-62
5907SS fraction | 0.3
5908Gap open (HH/SS/other) | 18/18/6
5909Gap extend | 1
5910SS matrix | | | H | S | O
5911---|---|---|---
5912H | 6 | -9 | -6
5913S | | 6 | -6
5914O | | | 4
5915Iteration cutoff | 2
5916
5917Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
5918M (#1004), sequence alignment score = 376.5
5919RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
59203.886)
5921
5922
5923> wait 1
5924
5925> measure rotation #1004 toModel #1003 showSlabs true
5926
5927Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
5928coordinates:
5929Matrix rotation and translation
59300.72982969 -0.01372193 -0.68349128 135.94952936
59310.06485007 -0.99390027 0.08920045 287.47713002
5932-0.68054617 -0.10942560 -0.72448806 354.00628960
5933Axis -0.92979963 -0.01378652 0.36780781
5934Axis point 0.00000000 152.92822789 195.61279282
5935Rotation angle (degrees) 173.86847166
5936Shift along axis -0.16285394
5937
5938
5939> close #1004 #1003
5940
5941> define axis #2 name axis_Vb
5942
5943Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
5944126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
59450.597156, and length 47.7725
5946
5947> rename #2 Vb_rotation_axis id #103.3.1.2
5948
5949> rename #3 Vb_rotation_slabs id #103.3.2.2
5950
5951> matchmaker #1006/L to #1005/H
5952
5953Parameters
5954---
5955Chain pairing | bb
5956Alignment algorithm | Needleman-Wunsch
5957Similarity matrix | BLOSUM-62
5958SS fraction | 0.3
5959Gap open (HH/SS/other) | 18/18/6
5960Gap extend | 1
5961SS matrix | | | H | S | O
5962---|---|---|---
5963H | 6 | -9 | -6
5964S | | 6 | -6
5965O | | | 4
5966Iteration cutoff | 2
5967
5968Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
5969L (#1006), sequence alignment score = 554.5
5970RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
59713.119)
5972
5973
5974> wait 1
5975
5976> measure rotation #1006 toModel #1005 showSlabs true
5977
5978Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
5979coordinates:
5980Matrix rotation and translation
5981-0.33391401 0.38072466 0.86229355 -12.40856576
59820.05205532 -0.90595556 0.42016042 245.78035810
59830.94116506 0.18518442 0.28269251 -52.33839393
5984Axis -0.57081123 -0.19159720 -0.79841408
5985Axis point 28.53870248 129.91224226 0.00000000
5986Rotation angle (degrees) 168.12212217
5987Shift along axis 1.77983022
5988
5989
5990> close #1006 #1005
5991
5992> define axis #2 name axis_Ca
5993
5994Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
5995106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
59960.56909, and length 45.5272
5997
5998> rename #2 Ca_rotation_axis id #103.3.1.3
5999
6000> rename #3 Ca_rotation_slabs id #103.3.2.3
6001
6002> matchmaker #1008/M to #1007/I
6003
6004Parameters
6005---
6006Chain pairing | bb
6007Alignment algorithm | Needleman-Wunsch
6008Similarity matrix | BLOSUM-62
6009SS fraction | 0.3
6010Gap open (HH/SS/other) | 18/18/6
6011Gap extend | 1
6012SS matrix | | | H | S | O
6013---|---|---|---
6014H | 6 | -9 | -6
6015S | | 6 | -6
6016O | | | 4
6017Iteration cutoff | 2
6018
6019Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
6020M (#1008), sequence alignment score = 416.6
6021RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
60223.361)
6023
6024
6025> wait 1
6026
6027> measure rotation #1008 toModel #1007 showSlabs true
6028
6029Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
6030coordinates:
6031Matrix rotation and translation
6032-0.50667380 0.40781938 -0.75958213 323.22163731
60330.08178140 -0.85433688 -0.51324487 330.95129120
6034-0.85825023 -0.32216741 0.39951808 287.19953324
6035Axis 0.48922423 0.25262440 -0.83476977
6036Axis point 265.28291179 189.90297685 0.00000000
6037Rotation angle (degrees) 168.73855860
6038Shift along axis 1.98873850
6039
6040
6041> close #1008 #1007
6042
6043> define axis #2 name axis_Cb
6044
6045Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
6046104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
60470.553583, and length 44.2867
6048
6049> rename #2 Cb_rotation_axis id #103.3.1.4
6050
6051> rename #3 Cb_rotation_slabs id #103.3.2.4
6052
6053> rename #103.3 geometry
6054
6055> rename #103.3.1 rotation_axes
6056
6057> rename #103.3.2 rotation_slabs
6058
6059executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
6060
6061> open
6062> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
6063
6064> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
6065
6066> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
6067
6068Selected 1653 atoms
6069
6070> delete #1001 & ~sel
6071
6072> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
6073
6074> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
6075
6076> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
6077
6078Selected 1678 atoms
6079
6080> delete #1003 & ~sel
6081
6082> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
6083
6084> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
6085
6086> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
6087
6088Selected 1461 atoms
6089
6090> delete #1005 & ~sel
6091
6092> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
6093
6094> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
6095
6096> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
6097
6098Selected 1550 atoms
6099
6100> delete #1007 & ~sel
6101
6102> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
6103
6104> matchmaker #1002/L to #1001/H
6105
6106Parameters
6107---
6108Chain pairing | bb
6109Alignment algorithm | Needleman-Wunsch
6110Similarity matrix | BLOSUM-62
6111SS fraction | 0.3
6112Gap open (HH/SS/other) | 18/18/6
6113Gap extend | 1
6114SS matrix | | | H | S | O
6115---|---|---|---
6116H | 6 | -9 | -6
6117S | | 6 | -6
6118O | | | 4
6119Iteration cutoff | 2
6120
6121Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
61222H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 221.1
6123RMSD between 66 pruned atom pairs is 1.048 angstroms; (across all 87 pairs:
61243.054)
6125
6126
6127> wait 1
6128
6129> measure rotation #1002 toModel #1001 showSlabs true
6130
6131Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
6132#1001 coordinates:
6133Matrix rotation and translation
61340.71841270 -0.03882790 0.69453263 -43.77242719
61350.04474713 -0.99379351 -0.10184377 314.28607160
61360.69417640 0.10424420 -0.71221645 107.06747282
6137Axis 0.92669760 0.00160183 0.37580447
6138Axis point 0.00000000 153.96110044 71.86641580
6139Rotation angle (degrees) 173.61580296
6140Shift along axis 0.17606353
6141
6142
6143> close #1001 #1002
6144
6145> define axis #2 name axis_Va
6146
6147Axis 'rotation axis #2/axis_Va' centered at [136.49236761 154.19703207
6148127.21828189] with direction [0.9266976 0.00160183 0.37580447], radius
61490.603625, and length 48.29
6150
6151> rename #2 Va_rotation_axis id #104.3.1.1
6152
6153> rename #3 Va_rotation_slabs id #104.3.2.1
6154
6155> matchmaker #1004/M to #1003/I
6156
6157Parameters
6158---
6159Chain pairing | bb
6160Alignment algorithm | Needleman-Wunsch
6161Similarity matrix | BLOSUM-62
6162SS fraction | 0.3
6163Gap open (HH/SS/other) | 18/18/6
6164Gap extend | 1
6165SS matrix | | | H | S | O
6166---|---|---|---
6167H | 6 | -9 | -6
6168S | | 6 | -6
6169O | | | 4
6170Iteration cutoff | 2
6171
6172Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
61732H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 228.5
6174RMSD between 66 pruned atom pairs is 1.088 angstroms; (across all 92 pairs:
61753.936)
6176
6177
6178> wait 1
6179
6180> measure rotation #1004 toModel #1003 showSlabs true
6181
6182Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
6183#1003 coordinates:
6184Matrix rotation and translation
61850.73661563 -0.07135580 -0.67253682 142.18618798
61860.02298296 -0.99120309 0.13033888 288.51761976
6187-0.67592100 -0.11146654 -0.72849572 353.55093768
6188Axis -0.93153019 0.01303723 0.36343024
6189Axis point 0.00000000 157.62360929 194.41945478
6190Rotation angle (degrees) 172.54257925
6191Shift along axis -0.19815617
6192
6193
6194> close #1004 #1003
6195
6196> define axis #2 name axis_Vb
6197
6198Axis 'rotation axis #2/axis_Vb' centered at [172.8655548 155.20426996
6199126.97712173] with direction [-0.93153019 0.01303723 0.36343024], radius
62000.60681, and length 48.5448
6201
6202> rename #2 Vb_rotation_axis id #104.3.1.2
6203
6204> rename #3 Vb_rotation_slabs id #104.3.2.2
6205
6206> matchmaker #1006/L to #1005/H
6207
6208Parameters
6209---
6210Chain pairing | bb
6211Alignment algorithm | Needleman-Wunsch
6212Similarity matrix | BLOSUM-62
6213SS fraction | 0.3
6214Gap open (HH/SS/other) | 18/18/6
6215Gap extend | 1
6216SS matrix | | | H | S | O
6217---|---|---|---
6218H | 6 | -9 | -6
6219S | | 6 | -6
6220O | | | 4
6221Iteration cutoff | 2
6222
6223Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
62242H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 229.8
6225RMSD between 50 pruned atom pairs is 0.885 angstroms; (across all 82 pairs:
62263.058)
6227
6228
6229> wait 1
6230
6231> measure rotation #1006 toModel #1005 showSlabs true
6232
6233Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
6234#1005 coordinates:
6235Matrix rotation and translation
6236-0.43223566 0.39105435 0.81255697 5.34243089
62370.04124481 -0.89156204 0.45101662 236.01875124
62380.90081696 0.22845922 0.36923594 -64.79879197
6239Axis -0.52502754 -0.20821113 -0.82522373
6240Axis point 38.63388899 125.78498588 0.00000000
6241Rotation angle (degrees) 167.76344751
6242Shift along axis 1.52684600
6243
6244
6245> close #1006 #1005
6246
6247> define axis #2 name axis_Ca
6248
6249Axis 'rotation axis #2/axis_Ca' centered at [105.63109625 152.35419104
6250105.30435297] with direction [-0.52502754 -0.20821113 -0.82522373], radius
62510.532467, and length 42.5974
6252
6253> rename #2 Ca_rotation_axis id #104.3.1.3
6254
6255> rename #3 Ca_rotation_slabs id #104.3.2.3
6256
6257> matchmaker #1008/M to #1007/I
6258
6259Parameters
6260---
6261Chain pairing | bb
6262Alignment algorithm | Needleman-Wunsch
6263Similarity matrix | BLOSUM-62
6264SS fraction | 0.3
6265Gap open (HH/SS/other) | 18/18/6
6266Gap extend | 1
6267SS matrix | | | H | S | O
6268---|---|---|---
6269H | 6 | -9 | -6
6270S | | 6 | -6
6271O | | | 4
6272Iteration cutoff | 2
6273
6274Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
62752H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 226.4
6276RMSD between 57 pruned atom pairs is 0.983 angstroms; (across all 98 pairs:
62773.247)
6278
6279
6280> wait 1
6281
6282> measure rotation #1008 toModel #1007 showSlabs true
6283
6284Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
6285#1007 coordinates:
6286Matrix rotation and translation
6287-0.44691350 0.37987962 -0.80991345 321.97311814
62880.04334425 -0.89510032 -0.44375297 334.72634524
6289-0.89352650 -0.23342428 0.38356682 282.18198422
6290Axis 0.51860284 0.20616286 -0.82978790
6291Axis point 269.80743377 182.59879005 0.00000000
6292Rotation angle (degrees) 168.30019456
6293Shift along axis 1.83311720
6294
6295
6296> close #1008 #1007
6297
6298> define axis #2 name axis_Cb
6299
6300Axis 'rotation axis #2/axis_Cb' centered at [203.87433587 156.38806637
6301105.49592574] with direction [ 0.51860284 0.20616286 -0.8297879 ], radius
63020.566216, and length 45.2973
6303
6304> rename #2 Cb_rotation_axis id #104.3.1.4
6305
6306> rename #3 Cb_rotation_slabs id #104.3.2.4
6307
6308> rename #104.3 geometry
6309
6310> rename #104.3.1 rotation_axes
6311
6312> rename #104.3.2 rotation_slabs
6313
6314executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
6315
6316> open CD20_2H7_mutants_define_domain_centroids.cxc
6317
6318> define centroid RTX_C & /L name centroid_RTX_C_L
6319
6320Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
6321
6322> rename ##name=centroid_RTX_C_L id 101.3.3.1
6323
6324> define centroid RTX_C & /M name centroid_RTX_C_M
6325
6326Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
6327
6328> rename ##name=centroid_RTX_C_M id 101.3.3.2
6329
6330> define centroid RTX_C & /H name centroid_RTX_C_H
6331
6332Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
6333
6334> rename ##name=centroid_RTX_C_H id 101.3.3.3
6335
6336> define centroid RTX_C & /I name centroid_RTX_C_I
6337
6338Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
6339
6340> rename ##name=centroid_RTX_C_I id 101.3.3.4
6341
6342> define centroid RTX_V & /L name centroid_RTX_V_L
6343
6344Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
6345
6346> rename ##name=centroid_RTX_V_L id 101.3.3.5
6347
6348> define centroid RTX_V & /M name centroid_RTX_V_M
6349
6350Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
6351
6352> rename ##name=centroid_RTX_V_M id 101.3.3.6
6353
6354> define centroid RTX_V & /H name centroid_RTX_V_H
6355
6356Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
6357
6358> rename ##name=centroid_RTX_V_H id 101.3.3.7
6359
6360> define centroid RTX_V & /I name centroid_RTX_V_I
6361
6362Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
6363
6364> rename ##name=centroid_RTX_V_I id 101.3.3.8
6365
6366> rename #101.3.3 centroids
6367
6368> define centroid H7v16_C & /L name centroid_2H7v16_C_L
6369
6370Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
6371104.71732873]
6372
6373> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
6374
6375> define centroid H7v16_C & /M name centroid_2H7v16_C_M
6376
6377Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
6378109.46892346]
6379
6380> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
6381
6382> define centroid H7v16_C & /H name centroid_2H7v16_C_H
6383
6384Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
6385100.10963479]
6386
6387> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
6388
6389> define centroid H7v16_C & /I name centroid_2H7v16_C_I
6390
6391Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
6392103.22787118]
6393
6394> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
6395
6396> define centroid H7v16_V & /L name centroid_2H7v16_V_L
6397
6398Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
6399124.64938243]
6400
6401> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
6402
6403> define centroid H7v16_V & /M name centroid_2H7v16_V_M
6404
6405Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
6406126.48898691]
6407
6408> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
6409
6410> define centroid H7v16_V & /H name centroid_2H7v16_V_H
6411
6412Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
6413126.96669027]
6414
6415> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
6416
6417> define centroid H7v16_V & /I name centroid_2H7v16_V_I
6418
6419Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
6420126.76187738]
6421
6422> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
6423
6424> rename #102.3.3 centroids
6425
6426> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
6427
6428Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
6429111.74271267]
6430
6431> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
6432
6433> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
6434
6435Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
6436109.3226675 ]
6437
6438> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
6439
6440> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
6441
6442Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
6443105.03944622]
6444
6445> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
6446
6447> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
6448
6449Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
6450103.22947676]
6451
6452> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
6453
6454> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
6455
6456Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
6457127.91858459]
6458
6459> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
6460
6461> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
6462
6463Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
6464127.2169787 ]
6465
6466> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
6467
6468> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
6469
6470Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
6471127.54490507]
6472
6473> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
6474
6475> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
6476
6477Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
6478127.29650809]
6479
6480> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
6481
6482> rename #103.3.3 centroids
6483
6484> define centroid CD20 & /C name centroid_CD20_C
6485
6486Centroid 'centroid_CD20_C' placed at [149.05372941 155.2359381 168.42928274]
6487
6488> rename ##name=centroid_CD20_C id 101.3.3.9
6489
6490> define centroid CD20 & /D name centroid_CD20_D
6491
6492Centroid 'centroid_CD20_D' placed at [161.37843923 154.64721755 168.73475111]
6493
6494> rename ##name=centroid_CD20_D id 101.3.3.10
6495
6496executed CD20_2H7_mutants_define_domain_centroids.cxc
6497
6498> turn x 90
6499
6500> view
6501
6502> hide #101 models
6503
6504> hide #!102.2 models
6505
6506> ~ribbon #102.10/X,Y
6507
6508executed CD20_2H7_mutants_setup.cxc
6509
6510> hide #!104 models
6511
6512> hide #!103 models
6513
6514> hide #!102 models
6515
6516> hide #!105 models
6517
6518> show #!105 models
6519
6520> show #!104 models
6521
6522> hide #!104 models
6523
6524> hide #!104.3 models
6525
6526> show #!104 models
6527
6528> hide #!104 models
6529
6530> show #!104 models
6531
6532> hide #!104 models
6533
6534> show #!104 models
6535
6536> hide #!104 models
6537
6538> show #!104 models
6539
6540> hide #!104 models
6541
6542> show #!104 models
6543
6544> hide #!104 models
6545
6546> show #!104 models
6547
6548> hide #!104 models
6549
6550> show #!104 models
6551
6552> hide #!104 models
6553
6554> show #!103 models
6555
6556> hide #!103 models
6557
6558> show #!103 models
6559
6560> hide #!103.3 models
6561
6562> hide #!103 models
6563
6564> show #!103 models
6565
6566> hide #!103 models
6567
6568> show #!103 models
6569
6570> hide #!103 models
6571
6572> show #!103 models
6573
6574> hide #!103 models
6575
6576> show #!103 models
6577
6578> hide #!105.2 models
6579
6580> hide #!103.2 models
6581
6582> hide #!103 models
6583
6584> show #!103 models
6585
6586> hide #!103 models
6587
6588> show #!103 models
6589
6590> hide #!103 models
6591
6592> show #!103 models
6593
6594> hide #!103 models
6595
6596> show #!103 models
6597
6598> hide #!103 models
6599
6600> show #!103 models
6601
6602> hide #!103 models
6603
6604> show #!103 models
6605
6606> hide #!103 models
6607
6608> show #!103 models
6609
6610> hide #!103 models
6611
6612> show #!103 models
6613
6614> hide #!103 models
6615
6616> show #!103 models
6617
6618> hide #!103 models
6619
6620> show #!102 models
6621
6622> hide #!102.10 models
6623
6624> hide #!102.3 models
6625
6626> hide #!102 models
6627
6628> show #!102 models
6629
6630> hide #!102 models
6631
6632> hide #!103.1 models
6633
6634> show #!101 models
6635
6636> hide #!101 models
6637
6638> show #!101 models
6639
6640> show #101.1 models
6641
6642> hide #!101 models
6643
6644> show #!101 models
6645
6646> hide #!101 models
6647
6648> show #!101 models
6649
6650> hide #!101 models
6651
6652> show #!101 models
6653
6654> hide #!101 models
6655
6656> show #!101 models
6657
6658> hide #!101 models
6659
6660> show #!101 models
6661
6662> hide #!101 models
6663
6664> show #!101 models
6665
6666> hide #!101 models
6667
6668> show #!101 models
6669
6670> hide #!101 models
6671
6672> show #!101 models
6673
6674> hide #!101 models
6675
6676> hide #10 models
6677
6678> show #10 models
6679
6680> show #!101 models
6681
6682> hide #!101 models
6683
6684> show #!101 models
6685
6686> hide #!105 models
6687
6688> select add #105
6689
66909251 atoms, 9491 bonds, 1207 residues, 4 models selected
6691
6692> select subtract #105
6693
6694Nothing selected
6695
6696> show #!105 models
6697
6698> hide #!105 models
6699
6700> show #!105 models
6701
6702> hide #!105 models
6703
6704> show #!105 models
6705
6706> hide #!105 models
6707
6708> show #!105 models
6709
6710> hide #!105 models
6711
6712> show #!105 models
6713
6714> hide #!105 models
6715
6716> show #!105 models
6717
6718> hide #!105 models
6719
6720> show #!105 models
6721
6722> hide #!105 models
6723
6724> show #!105 models
6725
6726> hide #!105 models
6727
6728> show #!105 models
6729
6730> hide #!105 models
6731
6732> show #!105 models
6733
6734> hide #!105 models
6735
6736> show #!105 models
6737
6738> hide #!105 models
6739
6740> show #!105 models
6741
6742> hide #!105 models
6743
6744> show #!105 models
6745
6746> hide #!105 models
6747
6748> show #!105 models
6749
6750> hide #!105 models
6751
6752> show #!105 models
6753
6754> hide #!105 models
6755
6756> show #!105 models
6757
6758> hide #!105 models
6759
6760> show #!105 models
6761
6762> hide #!105 models
6763
6764> show #!105 models
6765
6766> hide #!105 models
6767
6768> show #!105 models
6769
6770> hide #!105 models
6771
6772> show #!105 models
6773
6774> hide #!105 models
6775
6776> show #!105 models
6777
6778> hide #!105 models
6779
6780> show #!105 models
6781
6782> hide #!105 models
6783
6784> show #!105 models
6785
6786> hide #!105 models
6787
6788> show #!105 models
6789
6790> hide #!105 models
6791
6792> show #!105 models
6793
6794> hide #!105 models
6795
6796> show #!105 models
6797
6798> hide #!105 models
6799
6800> matchmaker #105.1/C,D to #101.1/C,D
6801
6802Parameters
6803---
6804Chain pairing | bb
6805Alignment algorithm | Needleman-Wunsch
6806Similarity matrix | BLOSUM-62
6807SS fraction | 0.3
6808Gap open (HH/SS/other) | 18/18/6
6809Gap extend | 1
6810SS matrix | | | H | S | O
6811---|---|---|---
6812H | 6 | -9 | -6
6813S | | 6 | -6
6814O | | | 4
6815Iteration cutoff | 2
6816
6817Matchmaker CD20_RTX, chain D (#101.1) with CD20_2H7v166, chain D (#105.1),
6818sequence alignment score = 1150.4
6819RMSD between 148 pruned atom pairs is 0.878 angstroms; (across all 158 pairs:
68201.117)
6821
6822
6823> show #!105 models
6824
6825> hide #!105 models
6826
6827> show #!105 models
6828
6829> hide #!105 models
6830
6831> show #!105 models
6832
6833> hide #!105 models
6834
6835> show #!105 models
6836
6837> hide #!105 models
6838
6839> show #!105 models
6840
6841> hide #!105 models
6842
6843> show #!105 models
6844
6845> hide #!105 models
6846
6847> show #!105 models
6848
6849> hide #!105 models
6850
6851> show #!105 models
6852
6853> hide #!105 models
6854
6855> show #!105 models
6856
6857> hide #!105 models
6858
6859> show #!105 models
6860
6861> hide #!105 models
6862
6863> show #!105 models
6864
6865> hide #!105 models
6866
6867> show #!105 models
6868
6869> hide #!105 models
6870
6871> save /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730_alito6vja.pdb
6872> models #105.1
6873
6874> view matrix
6875
6876view matrix camera
68770.30758,0.083643,0.94784,441.19,-0.95125,0.0031095,0.30841,241.21,0.022849,-0.99649,0.080522,159.68
6878view matrix models
6879#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,#104.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#105,1,0,0,0,0,1,0,0,0,0,1,0,#105.1,-0.9972,-0.068777,0.029474,316.4,0.068287,-0.99752,-0.017317,300.18,0.030591,-0.015255,0.99942,-2.5792,#105.2,0.094232,-0.75331,-0.65088,436.99,-0.99412,-0.036109,-0.10213,396.76,0.053436,0.65667,-0.75228,168.36,#105.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0
6880
6881
6882> ui tool show Log
6883
6884> open /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730.pdb
6885
6886Summary of feedback from opening
6887/Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730.pdb
6888---
6889warning | Ignored bad PDB record found on line 1
6890HEADER STR7730 version_1 2024.01.12
6891
6892STR7730.pdb title:
6893Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
6894info...]
6895
6896Chain information for STR7730.pdb #2
6897---
6898Chain | Description
6899C | No description available
6900D | No description available
6901H I | No description available
6902L | No description available
6903M | No description available
6904
6905
6906> matchmaker #2 to #105.1
6907
6908Parameters
6909---
6910Chain pairing | bb
6911Alignment algorithm | Needleman-Wunsch
6912Similarity matrix | BLOSUM-62
6913SS fraction | 0.3
6914Gap open (HH/SS/other) | 18/18/6
6915Gap extend | 1
6916SS matrix | | | H | S | O
6917---|---|---|---
6918H | 6 | -9 | -6
6919S | | 6 | -6
6920O | | | 4
6921Iteration cutoff | 2
6922
6923Matchmaker CD20_2H7v166, chain C (#105.1) with STR7730.pdb, chain C (#2),
6924sequence alignment score = 2082.4
6925RMSD between 166 pruned atom pairs is 0.001 angstroms; (across all 166 pairs:
69260.001)
6927
6928
6929> view matrix
6930
6931view matrix camera
69320.30758,0.083643,0.94784,441.19,-0.95125,0.0031095,0.30841,241.21,0.022849,-0.99649,0.080522,159.68
6933view matrix models
6934#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,#104.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#105,1,0,0,0,0,1,0,0,0,0,1,0,#105.1,-0.9972,-0.068777,0.029474,316.4,0.068287,-0.99752,-0.017317,300.18,0.030591,-0.015255,0.99942,-2.5792,#105.2,0.094232,-0.75331,-0.65088,436.99,-0.99412,-0.036109,-0.10213,396.76,0.053436,0.65667,-0.75228,168.36,#105.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.024025,0.77304,0.6339,-141.69,0.99715,-0.026789,0.070462,-68.674,0.071451,0.63379,-0.7702,173
6935
6936
6937> close
6938
6939> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
6940
6941> close
6942
6943> cd /Users/rohoua/work/Genentech/CD20
6944
6945Current working directory is: /Users/rohoua/work/Genentech/CD20
6946
6947> open pdb:6vja name CD20_RTX id 101.1
6948
6949CD20_RTX title:
6950Structure of CD20 in complex with rituximab Fab [more info...]
6951
6952Chain information for CD20_RTX #1
6953---
6954Chain | Description | UniProt
6955C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
6956H I | Rituximab Fab heavy chain |
6957L M | Rituximab Fab light chain |
6958
6959Non-standard residues in CD20_RTX #1
6960---
6961Y01 — cholesterol hemisuccinate
6962
6963
6964> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
6965
6966Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb
6967---
6968warning | Ignored bad PDB record found on line 1
6969HEADER STR7668 version_2 2023.12.13
6970
6971CD20_2H7v16 title:
6972Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
6973resolution. [more info...]
6974
6975Chain information for CD20_2H7v16 #1
6976---
6977Chain | Description
6978C D | No description available
6979H I | No description available
6980L M | No description available
6981
6982Non-standard residues in CD20_2H7v16 #1
6983---
6984Y01 — (Y01)
6985
6986
6987> open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
6988
6989Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
6990shown at level 0.0054, step 2, values float32
6991
6992> volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
6993
6994> view matrix models
6995> #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
6996
6997> open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
6998> 102.10
6999
7000Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
7001Fab.pdb
7002---
7003warning | Ignored bad PDB record found on line 1
7004HEADER STR7487 version_1 2023.05.24
7005
70062H7v16_XRay title:
7007Structure of 2H7 Fab at 2.45 A resolution. [more info...]
7008
7009Chain information for 2H7v16_XRay #1
7010---
7011Chain | Description
7012A B X Y | No description available
7013
7014Non-standard residues in 2H7v16_XRay #1
7015---
7016CL — (CL)
7017
7018
7019> matchmaker #102.10/A,B to #102.1/H,L
7020
7021Parameters
7022---
7023Chain pairing | bb
7024Alignment algorithm | Needleman-Wunsch
7025Similarity matrix | BLOSUM-62
7026SS fraction | 0.3
7027Gap open (HH/SS/other) | 18/18/6
7028Gap extend | 1
7029SS matrix | | | H | S | O
7030---|---|---|---
7031H | 6 | -9 | -6
7032S | | 6 | -6
7033O | | | 4
7034Iteration cutoff | 2
7035
7036Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
7037sequence alignment score = 1228.2
7038RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
70390.804)
7040
7041
7042> open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
7043> 103.1
7044
7045Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb
7046---
7047warning | Ignored bad PDB record found on line 1
7048HEADER STR7717 version_2 2023.12.15
7049
7050CD20_2H7v166_D56A title:
7051Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
7052info...]
7053
7054Chain information for CD20_2H7v166_D56A #1
7055---
7056Chain | Description
7057C D | No description available
7058H I | No description available
7059L | No description available
7060M | No description available
7061
7062Non-standard residues in CD20_2H7v166_D56A #1
7063---
7064Y01 — (Y01)
7065
7066
7067> open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
7068
7069Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
7070300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32
7071
7072> volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
7073
7074> view matrix models
7075> #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
7076
7077> open CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb name
7078> CD20_2H7v166_S92A_D56A id 104.1
7079
7080Summary of feedback from opening
7081CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb
7082---
7083warning | Ignored bad PDB record found on line 1
7084HEADER STR7729 version_2 2024.01.29
7085
7086CD20_2H7v166_S92A_D56A title:
7087Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
7088resolution. [more info...]
7089
7090Chain information for CD20_2H7v166_S92A_D56A #1
7091---
7092Chain | Description
7093C D | No description available
7094H | No description available
7095I | No description available
7096L M | No description available
7097
7098
7099> open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
7100> id 104.2
7101
7102Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
7103300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
7104
7105> volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
7106
7107> view matrix models
7108> #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
7109
7110> open CD20_2H7v166/STR7730_alito6vja.pdb name CD20_2H7v166 id 105.1
7111
7112Summary of feedback from opening CD20_2H7v166/STR7730_alito6vja.pdb
7113---
7114warning | Ignored bad PDB record found on line 1
7115HEADER STR7730 version_1 2024.01.12
7116
7117CD20_2H7v166 title:
7118Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
7119info...]
7120
7121Chain information for CD20_2H7v166 #1
7122---
7123Chain | Description
7124C | No description available
7125D | No description available
7126H I | No description available
7127L | No description available
7128M | No description available
7129
7130
7131> open CD20_2H7v166/cryosparc_P71_J138_006_volume_map_sharp.mrc id 105.2
7132
7133Opened cryosparc_P71_J138_006_volume_map_sharp.mrc as #1, grid size
7134300,300,300, pixel 1.43, shown at level 0.0428, step 2, values float32
7135
7136> volume #105.2 step 1 level 0.355 color #9999CC transparency 0.5
7137
7138> view matrix models
7139> #105.2,-0.024025,0.77304,0.6339,-141.69,0.99715,-0.026789,0.070462,-68.674,0.071451,0.63379,-0.7702,173
7140
7141> rename #101 CD20_RTX
7142
7143> rename #102 CD20_2H7v16
7144
7145> rename #103 CD20_2H7v166_D56A
7146
7147> rename #104 CD20_2H7v166_S92A_D56A
7148
7149> dssp
7150
7151> name CD20_RTX #101.1
7152
7153> name CD20_2H7v16 #102.1
7154
7155> name CD20_2H7v166_D56A #103.1
7156
7157> name CD20_2H7v166_S92A_D56A #104.1
7158
7159> name CD20 /C,D
7160
7161> name CD20_Monomer /C
7162
7163> name CD20_H1 /C,D:46-71
7164
7165> name CD20_ECL1 /C,D:72-79
7166
7167> name CD20_H2 /C,D:80-105
7168
7169> name CD20_ICL1 /C,D:106-112
7170
7171> name CD20_H3 /C,D:113-141
7172
7173> name CD20_ECL2 /C,D:142-187
7174
7175> name CD20_ECL2SS /C,D:167,183
7176
7177> name CD20_H4 /C,D:188-end
7178
7179> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
7180
7181> name RTX CD20_RTX & /H,L,I,M
7182
7183> name RTX_H RTX & /H,I
7184
7185> name RTX_L RTX & /L,M
7186
7187> name RTX_Epitope CD20_RTX & /C,D:168-175
7188
7189> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
7190
7191> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
7192
7193> name H7v16 CD20_2H7v16 & /H,L,I,M
7194
7195> name H7v16_H H7v16 & /H,I
7196
7197> name H7v16_L H7v16 & /L,M
7198
7199> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
7200
7201> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
7202
7203> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
7204
7205> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
7206
7207> name H7v166_D56A_H H7v166_D56A & /H,I
7208
7209> name H7v166_D56A_L H7v166_D56A & /L,M
7210
7211> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
7212
7213> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
7214
7215> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
7216> /H,I:119-end)
7217
7218> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
7219
7220> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
7221
7222> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
7223
7224> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
7225
7226> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
7227> & /H,I:1-111)
7228
7229> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
7230> (H7v166_S92A_D56A & /H,I:119-end)
7231
7232> lighting soft
7233
7234> set bgColor white
7235
7236> camera ortho
7237
7238> style stick
7239
7240Changed 53488 atom styles
7241
7242> color byhetero
7243
7244> open CD20_2H7_mutants_color.cxc
7245
7246> color CD20 burlywood
7247
7248> color modify CD20_H1 hue - 20
7249
7250> color modify CD20_H2 hue - 10
7251
7252> color modify CD20_H3 hue + 0
7253
7254> color modify CD20_H4 hue + 10
7255
7256> color modify CD20_ECL1 hue +10
7257
7258> color modify CD20_ECL2 hue + 40
7259
7260> color modify CD20 saturation + 80
7261
7262> color CD20_ECL2 rgb(127,165,90)
7263
7264> color CD20_H4 rgb(176,215,142)
7265
7266> color RTX plum
7267
7268> color modify RTX_H hue - 40
7269
7270> color H7v16 slate blue
7271
7272> color modify H7v16_H hue - 40
7273
7274> color H7v166_D56A dodger blue
7275
7276> color modify H7v166_D56A_H hue - 40
7277
7278> color H7v166_S92A_D56A purple
7279
7280> color modify H7v166_S92A_D56A_H hue - 40
7281
7282executed CD20_2H7_mutants_color.cxc
7283
7284> hide
7285
7286> ribbon
7287
7288> show CD20_ECL2SS
7289
7290> style CD20_ECL2SS stick
7291
7292Changed 120 atom styles
7293
7294> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
7295
7296Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
7297radius 1, and length 140
7298
7299> marker #1.1 position 155,155,70
7300
7301> marker #1.1 position 155,155,210
7302
7303> select
7304> #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
7305
7306440 atoms, 446 bonds, 54 residues, 1 model selected
7307
7308> define plane sel name membrane_plane
7309
7310Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
7311normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
7312
7313> rename ##name=membrane_plane id 10
7314
7315> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
7316
7317> combine CD20_RTX name RTX_Va modelId 1001
7318
7319> select zone (RTX_V & /H,L) 0.1 #1001
7320
7321Selected 1711 atoms
7322
7323> delete #1001 & ~sel
7324
7325> combine #1001 name RTX_Va_copy modelId 1002
7326
7327> combine CD20_RTX name RTX_Vb modelId 1003
7328
7329> select zone (RTX_V & /I,M) 0.1 #1003
7330
7331Selected 1711 atoms
7332
7333> delete #1003 & ~sel
7334
7335> combine #1003 name RTX_Vb_copy modelId 1004
7336
7337> combine CD20_RTX name RTX_Ca modelId 1005
7338
7339> select zone (RTX_C & /H,L) 0.1 #1005
7340
7341Selected 1503 atoms
7342
7343> delete #1005 & ~sel
7344
7345> combine #1005 name RTX_Ca_copy modelId 1006
7346
7347> combine CD20_RTX name RTX_Cb modelId 1007
7348
7349> select zone (RTX_C & /I,M) 0.1 #1007
7350
7351Selected 1503 atoms
7352
7353> delete #1007 & ~sel
7354
7355> combine #1007 name RTX_Ca_copy modelId 1008
7356
7357> matchmaker #1002/L to #1001/H
7358
7359Parameters
7360---
7361Chain pairing | bb
7362Alignment algorithm | Needleman-Wunsch
7363Similarity matrix | BLOSUM-62
7364SS fraction | 0.3
7365Gap open (HH/SS/other) | 18/18/6
7366Gap extend | 1
7367SS matrix | | | H | S | O
7368---|---|---|---
7369H | 6 | -9 | -6
7370S | | 6 | -6
7371O | | | 4
7372Iteration cutoff | 2
7373
7374Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
7375alignment score = 198.7
7376RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
73774.421)
7378
7379
7380> wait 1
7381
7382> measure rotation #1002 toModel #1001 showSlabs true
7383
7384Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
7385Matrix rotation and translation
73860.65377294 -0.06463426 0.75392530 -36.97668460
73870.02426941 -0.99404163 -0.10626495 318.59247232
73880.75630149 0.08777047 -0.64830888 90.28955685
7389Axis 0.90906034 -0.01113250 0.41651574
7390Axis point 0.00000000 156.41772375 62.99337678
7391Rotation angle (degrees) 173.87355102
7392Shift along axis 0.44625393
7393
7394
7395> close #1001 #1002
7396
7397> define axis #2 name axis_Va
7398
7399Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
7400125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
74010.65062, and length 52.0496
7402
7403> rename #2 Va_rotation_axis id #101.3.1.1
7404
7405> rename #3 Va_rotation_slabs id #101.3.2.1
7406
7407> matchmaker #1004/M to #1003/I
7408
7409Parameters
7410---
7411Chain pairing | bb
7412Alignment algorithm | Needleman-Wunsch
7413Similarity matrix | BLOSUM-62
7414SS fraction | 0.3
7415Gap open (HH/SS/other) | 18/18/6
7416Gap extend | 1
7417SS matrix | | | H | S | O
7418---|---|---|---
7419H | 6 | -9 | -6
7420S | | 6 | -6
7421O | | | 4
7422Iteration cutoff | 2
7423
7424Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
7425alignment score = 214.3
7426RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
74274.448)
7428
7429
7430> wait 1
7431
7432> measure rotation #1004 toModel #1003 showSlabs true
7433
7434Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
7435Matrix rotation and translation
74360.65527690 -0.06129532 -0.75289778 163.48223927
74370.03113398 -0.99366393 0.10799385 290.56686667
7438-0.75474688 -0.09420658 -0.64921665 352.74817189
7439Axis -0.90945183 0.00831685 0.41572611
7440Axis point 0.00000000 156.83903630 204.83255489
7441Rotation angle (degrees) 173.61745932
7442Shift along axis 0.38400661
7443
7444
7445> close #1004 #1003
7446
7447> define axis #2 name axis_Vb
7448
7449Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
7450125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
74510.648586, and length 51.8869
7452
7453> rename #2 Vb_rotation_axis id #101.3.1.2
7454
7455> rename #3 Vb_rotation_slabs id #101.3.2.2
7456
7457> matchmaker #1006/L to #1005/H
7458
7459Parameters
7460---
7461Chain pairing | bb
7462Alignment algorithm | Needleman-Wunsch
7463Similarity matrix | BLOSUM-62
7464SS fraction | 0.3
7465Gap open (HH/SS/other) | 18/18/6
7466Gap extend | 1
7467SS matrix | | | H | S | O
7468---|---|---|---
7469H | 6 | -9 | -6
7470S | | 6 | -6
7471O | | | 4
7472Iteration cutoff | 2
7473
7474Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
7475alignment score = 238.2
7476RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
74773.308)
7478
7479
7480> wait 1
7481
7482> measure rotation #1006 toModel #1005 showSlabs true
7483
7484Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
7485Matrix rotation and translation
74860.37780344 0.24165354 0.89379423 -73.66252391
74870.01279825 -0.96661035 0.25593093 273.63534365
74880.92579737 -0.08525258 -0.36828146 68.27322422
7489Axis -0.82796624 -0.07766353 -0.55537400
7490Axis point 0.00000000 144.62953182 41.62502778
7491Rotation angle (degrees) 168.10978391
7492Shift along axis 1.82142171
7493
7494
7495> close #1006 #1005
7496
7497> define axis #2 name axis_Ca
7498
7499Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
7500110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
75010.539289, and length 43.1431
7502
7503> rename #2 Ca_rotation_axis id #101.3.1.3
7504
7505> rename #3 Ca_rotation_slabs id #101.3.2.3
7506
7507> matchmaker #1008/M to #1007/I
7508
7509Parameters
7510---
7511Chain pairing | bb
7512Alignment algorithm | Needleman-Wunsch
7513Similarity matrix | BLOSUM-62
7514SS fraction | 0.3
7515Gap open (HH/SS/other) | 18/18/6
7516Gap extend | 1
7517SS matrix | | | H | S | O
7518---|---|---|---
7519H | 6 | -9 | -6
7520S | | 6 | -6
7521O | | | 4
7522Iteration cutoff | 2
7523
7524Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
7525alignment score = 238.2
7526RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
75273.487)
7528
7529
7530> wait 1
7531
7532> measure rotation #1008 toModel #1007 showSlabs true
7533
7534Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
7535Matrix rotation and translation
75360.37961795 0.24211100 -0.89290116 191.06761259
75370.01296287 -0.96644625 -0.25654164 332.12351027
7538-0.92505253 0.08581325 -0.37001879 328.82641259
7539Axis 0.82850834 0.07780721 -0.55454483
7540Axis point 0.00000000 136.30341759 249.27961172
7541Rotation angle (degrees) 168.07628341
7542Shift along axis 1.79372450
7543
7544
7545> close #1008 #1007
7546
7547> define axis #2 name axis_Cb
7548
7549Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
7550110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
75510.53918, and length 43.1344
7552
7553> rename #2 Cb_rotation_axis id #101.3.1.4
7554
7555> rename #3 Cb_rotation_slabs id #101.3.2.4
7556
7557> rename #101.3 geometry
7558
7559> rename #101.3.1 rotation_axes
7560
7561> rename #101.3.2 rotation_slabs
7562
7563executed CD20_RTX_define_pseudo_symmetries.cxc
7564
7565> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
7566
7567> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
7568
7569> select zone (H7v16_V & /H,L) 0.1 #1001
7570
7571Selected 1754 atoms
7572
7573> delete #1001 & ~sel
7574
7575> combine #1001 name 2H7_v16_Va_copy modelId 1002
7576
7577> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
7578
7579> select zone (H7v16_V & /I,M) 0.1 #1003
7580
7581Selected 1710 atoms
7582
7583> delete #1003 & ~sel
7584
7585> combine #1003 name 2H7_v16_Vb_copy modelId 1004
7586
7587> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
7588
7589> select zone (H7v16_C & /H,L) 0.1 #1005
7590
7591Selected 1550 atoms
7592
7593> delete #1005 & ~sel
7594
7595> combine #1005 name 2H7_v16_Ca_copy modelId 1006
7596
7597> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
7598
7599> select zone (H7v16_C & /I,M) 0.1 #1007
7600
7601Selected 1550 atoms
7602
7603> delete #1007 & ~sel
7604
7605> combine #1007 name 2H7_v16_Ca_copy modelId 1008
7606
7607> matchmaker #1002/L to #1001/H
7608
7609Parameters
7610---
7611Chain pairing | bb
7612Alignment algorithm | Needleman-Wunsch
7613Similarity matrix | BLOSUM-62
7614SS fraction | 0.3
7615Gap open (HH/SS/other) | 18/18/6
7616Gap extend | 1
7617SS matrix | | | H | S | O
7618---|---|---|---
7619H | 6 | -9 | -6
7620S | | 6 | -6
7621O | | | 4
7622Iteration cutoff | 2
7623
7624Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
7625sequence alignment score = 387.9
7626RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
76275.340)
7628
7629
7630> wait 1
7631
7632> measure rotation #1002 toModel #1001 showSlabs true
7633
7634Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
7635Matrix rotation and translation
76360.58985298 0.00233427 0.80750728 -45.05678546
76370.12316682 -0.98855531 -0.08711100 297.16136614
76380.79806228 0.15084078 -0.58338980 65.44859378
7639Axis 0.89106916 0.03536916 0.45248731
7640Axis point 0.00000000 147.01172040 55.34624717
7641Rotation angle (degrees) 172.32693090
7642Shift along axis -0.02370559
7643
7644
7645> close #1001 #1002
7646
7647> define axis #2 name axis_Va
7648
7649Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
7650125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
76510.589874, and length 47.1899
7652
7653> rename #2 Va_rotation_axis id #102.3.1.1
7654
7655> rename #3 Va_rotation_slabs id #102.3.2.1
7656
7657> matchmaker #1004/M to #1003/I
7658
7659Parameters
7660---
7661Chain pairing | bb
7662Alignment algorithm | Needleman-Wunsch
7663Similarity matrix | BLOSUM-62
7664SS fraction | 0.3
7665Gap open (HH/SS/other) | 18/18/6
7666Gap extend | 1
7667SS matrix | | | H | S | O
7668---|---|---|---
7669H | 6 | -9 | -6
7670S | | 6 | -6
7671O | | | 4
7672Iteration cutoff | 2
7673
7674Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
7675sequence alignment score = 378.3
7676RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
76774.620)
7678
7679
7680> wait 1
7681
7682> measure rotation #1004 toModel #1003 showSlabs true
7683
7684Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
7685Matrix rotation and translation
76860.62864598 0.45103819 -0.63353672 71.77949524
76870.53321619 -0.84298968 -0.07105560 212.64664720
7688-0.56611370 -0.29314322 -0.77044294 368.84403487
7689Axis -0.90200560 -0.27383758 0.33376470
7690Axis point -0.00000000 108.05935567 190.41757658
7691Rotation angle (degrees) 172.92851049
7692Shift along axis 0.13096924
7693
7694
7695> close #1004 #1003
7696
7697> define axis #2 name axis_Vb
7698
7699Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
7700125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
77010.594923, and length 47.5938
7702
7703> rename #2 Vb_rotation_axis id #102.3.1.2
7704
7705> rename #3 Vb_rotation_slabs id #102.3.2.2
7706
7707> matchmaker #1006/L to #1005/H
7708
7709Parameters
7710---
7711Chain pairing | bb
7712Alignment algorithm | Needleman-Wunsch
7713Similarity matrix | BLOSUM-62
7714SS fraction | 0.3
7715Gap open (HH/SS/other) | 18/18/6
7716Gap extend | 1
7717SS matrix | | | H | S | O
7718---|---|---|---
7719H | 6 | -9 | -6
7720S | | 6 | -6
7721O | | | 4
7722Iteration cutoff | 2
7723
7724Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
7725sequence alignment score = 403.6
7726RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
77273.184)
7728
7729
7730> wait 1
7731
7732> measure rotation #1006 toModel #1005 showSlabs true
7733
7734Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
7735Matrix rotation and translation
7736-0.62547004 0.41276667 0.66212605 49.05674876
77370.08546501 -0.80725952 0.58397585 200.07354667
77380.77555333 0.42184801 0.46963954 -95.83522576
7739Axis -0.42390521 -0.29657098 -0.85577452
7740Axis point 59.57688139 113.83169245 0.00000000
7741Rotation angle (degrees) 168.97535276
7742Shift along axis 1.88192618
7743
7744
7745> close #1006 #1005
7746
7747> define axis #2 name axis_Ca
7748
7749Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
7750101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
77510.550437, and length 44.0349
7752
7753> rename #2 Ca_rotation_axis id #102.3.1.3
7754
7755> rename #3 Ca_rotation_slabs id #102.3.2.3
7756
7757> matchmaker #1008/M to #1007/I
7758
7759Parameters
7760---
7761Chain pairing | bb
7762Alignment algorithm | Needleman-Wunsch
7763Similarity matrix | BLOSUM-62
7764SS fraction | 0.3
7765Gap open (HH/SS/other) | 18/18/6
7766Gap extend | 1
7767SS matrix | | | H | S | O
7768---|---|---|---
7769H | 6 | -9 | -6
7770S | | 6 | -6
7771O | | | 4
7772Iteration cutoff | 2
7773
7774Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
7775sequence alignment score = 396
7776RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
77773.551)
7778
7779
7780> wait 1
7781
7782> measure rotation #1008 toModel #1007 showSlabs true
7783
7784Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
7785Matrix rotation and translation
7786-0.62894249 0.48033740 -0.61131606 312.62038315
77870.14842286 -0.69766113 -0.70088487 336.12735996
7788-0.76315267 -0.53154955 0.36749568 311.24709675
7789Axis 0.42085200 0.37736216 -0.82491296
7790Axis point 256.37284203 220.04020388 0.00000000
7791Rotation angle (degrees) 168.39393838
7792Shift along axis 1.65689588
7793
7794
7795> close #1008 #1007
7796
7797> define axis #2 name axis_Cb
7798
7799Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
7800105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
78010.534846, and length 42.7877
7802
7803> rename #2 Cb_rotation_axis id #102.3.1.4
7804
7805> rename #3 Cb_rotation_slabs id #102.3.2.4
7806
7807> rename #102.3 geometry
7808
7809> rename #102.3.1 rotation_axes
7810
7811> rename #102.3.2 rotation_slabs
7812
7813executed CD20_2H7v16_define_pseudo_symmetries.cxc
7814
7815> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
7816
7817> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
7818
7819> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
7820
7821Selected 1654 atoms
7822
7823> delete #1001 & ~sel
7824
7825> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
7826
7827> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
7828
7829> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
7830
7831Selected 1678 atoms
7832
7833> delete #1003 & ~sel
7834
7835> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
7836
7837> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
7838
7839> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
7840
7841Selected 1550 atoms
7842
7843> delete #1005 & ~sel
7844
7845> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
7846
7847> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
7848
7849> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
7850
7851Selected 1550 atoms
7852
7853> delete #1007 & ~sel
7854
7855> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
7856
7857> matchmaker #1002/L to #1001/H
7858
7859Parameters
7860---
7861Chain pairing | bb
7862Alignment algorithm | Needleman-Wunsch
7863Similarity matrix | BLOSUM-62
7864SS fraction | 0.3
7865Gap open (HH/SS/other) | 18/18/6
7866Gap extend | 1
7867SS matrix | | | H | S | O
7868---|---|---|---
7869H | 6 | -9 | -6
7870S | | 6 | -6
7871O | | | 4
7872Iteration cutoff | 2
7873
7874Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
7875L (#1002), sequence alignment score = 547.6
7876RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
78772.607)
7878
7879
7880> wait 1
7881
7882> measure rotation #1002 toModel #1001 showSlabs true
7883
7884Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
7885coordinates:
7886Matrix rotation and translation
78870.73992366 -0.12116101 0.66168949 -29.70332856
7888-0.06116680 -0.99168902 -0.11318795 332.06337928
78890.66990417 0.04327702 -0.74118520 123.44534698
7890Axis 0.93259437 -0.04896279 0.35758970
7891Axis point 0.00000000 162.47254458 74.89799404
7892Rotation angle (degrees) 175.18797763
7893Shift along axis 0.18287681
7894
7895
7896> close #1001 #1002
7897
7898> define axis #2 name axis_Va
7899
7900Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
7901127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
79020.599212, and length 47.937
7903
7904> rename #2 Va_rotation_axis id #103.3.1.1
7905
7906> rename #3 Va_rotation_slabs id #103.3.2.1
7907
7908> matchmaker #1004/M to #1003/I
7909
7910Parameters
7911---
7912Chain pairing | bb
7913Alignment algorithm | Needleman-Wunsch
7914Similarity matrix | BLOSUM-62
7915SS fraction | 0.3
7916Gap open (HH/SS/other) | 18/18/6
7917Gap extend | 1
7918SS matrix | | | H | S | O
7919---|---|---|---
7920H | 6 | -9 | -6
7921S | | 6 | -6
7922O | | | 4
7923Iteration cutoff | 2
7924
7925Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
7926M (#1004), sequence alignment score = 376.5
7927RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
79283.886)
7929
7930
7931> wait 1
7932
7933> measure rotation #1004 toModel #1003 showSlabs true
7934
7935Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
7936coordinates:
7937Matrix rotation and translation
79380.72982969 -0.01372193 -0.68349128 135.94952936
79390.06485007 -0.99390027 0.08920045 287.47713002
7940-0.68054617 -0.10942560 -0.72448806 354.00628960
7941Axis -0.92979963 -0.01378652 0.36780781
7942Axis point 0.00000000 152.92822789 195.61279282
7943Rotation angle (degrees) 173.86847166
7944Shift along axis -0.16285394
7945
7946
7947> close #1004 #1003
7948
7949> define axis #2 name axis_Vb
7950
7951Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
7952126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
79530.597156, and length 47.7725
7954
7955> rename #2 Vb_rotation_axis id #103.3.1.2
7956
7957> rename #3 Vb_rotation_slabs id #103.3.2.2
7958
7959> matchmaker #1006/L to #1005/H
7960
7961Parameters
7962---
7963Chain pairing | bb
7964Alignment algorithm | Needleman-Wunsch
7965Similarity matrix | BLOSUM-62
7966SS fraction | 0.3
7967Gap open (HH/SS/other) | 18/18/6
7968Gap extend | 1
7969SS matrix | | | H | S | O
7970---|---|---|---
7971H | 6 | -9 | -6
7972S | | 6 | -6
7973O | | | 4
7974Iteration cutoff | 2
7975
7976Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
7977L (#1006), sequence alignment score = 554.5
7978RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
79793.119)
7980
7981
7982> wait 1
7983
7984> measure rotation #1006 toModel #1005 showSlabs true
7985
7986Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
7987coordinates:
7988Matrix rotation and translation
7989-0.33391401 0.38072466 0.86229355 -12.40856576
79900.05205532 -0.90595556 0.42016042 245.78035810
79910.94116506 0.18518442 0.28269251 -52.33839393
7992Axis -0.57081123 -0.19159720 -0.79841408
7993Axis point 28.53870248 129.91224226 0.00000000
7994Rotation angle (degrees) 168.12212217
7995Shift along axis 1.77983022
7996
7997
7998> close #1006 #1005
7999
8000> define axis #2 name axis_Ca
8001
8002Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
8003106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
80040.56909, and length 45.5272
8005
8006> rename #2 Ca_rotation_axis id #103.3.1.3
8007
8008> rename #3 Ca_rotation_slabs id #103.3.2.3
8009
8010> matchmaker #1008/M to #1007/I
8011
8012Parameters
8013---
8014Chain pairing | bb
8015Alignment algorithm | Needleman-Wunsch
8016Similarity matrix | BLOSUM-62
8017SS fraction | 0.3
8018Gap open (HH/SS/other) | 18/18/6
8019Gap extend | 1
8020SS matrix | | | H | S | O
8021---|---|---|---
8022H | 6 | -9 | -6
8023S | | 6 | -6
8024O | | | 4
8025Iteration cutoff | 2
8026
8027Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
8028M (#1008), sequence alignment score = 416.6
8029RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
80303.361)
8031
8032
8033> wait 1
8034
8035> measure rotation #1008 toModel #1007 showSlabs true
8036
8037Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
8038coordinates:
8039Matrix rotation and translation
8040-0.50667380 0.40781938 -0.75958213 323.22163731
80410.08178140 -0.85433688 -0.51324487 330.95129120
8042-0.85825023 -0.32216741 0.39951808 287.19953324
8043Axis 0.48922423 0.25262440 -0.83476977
8044Axis point 265.28291179 189.90297685 0.00000000
8045Rotation angle (degrees) 168.73855860
8046Shift along axis 1.98873850
8047
8048
8049> close #1008 #1007
8050
8051> define axis #2 name axis_Cb
8052
8053Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
8054104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
80550.553583, and length 44.2867
8056
8057> rename #2 Cb_rotation_axis id #103.3.1.4
8058
8059> rename #3 Cb_rotation_slabs id #103.3.2.4
8060
8061> rename #103.3 geometry
8062
8063> rename #103.3.1 rotation_axes
8064
8065> rename #103.3.2 rotation_slabs
8066
8067executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
8068
8069> open
8070> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
8071
8072> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
8073
8074> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
8075
8076Selected 1653 atoms
8077
8078> delete #1001 & ~sel
8079
8080> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
8081
8082> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
8083
8084> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
8085
8086Selected 1678 atoms
8087
8088> delete #1003 & ~sel
8089
8090> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
8091
8092> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
8093
8094> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
8095
8096Selected 1461 atoms
8097
8098> delete #1005 & ~sel
8099
8100> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
8101
8102> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
8103
8104> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
8105
8106Selected 1550 atoms
8107
8108> delete #1007 & ~sel
8109
8110> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
8111
8112> matchmaker #1002/L to #1001/H
8113
8114Parameters
8115---
8116Chain pairing | bb
8117Alignment algorithm | Needleman-Wunsch
8118Similarity matrix | BLOSUM-62
8119SS fraction | 0.3
8120Gap open (HH/SS/other) | 18/18/6
8121Gap extend | 1
8122SS matrix | | | H | S | O
8123---|---|---|---
8124H | 6 | -9 | -6
8125S | | 6 | -6
8126O | | | 4
8127Iteration cutoff | 2
8128
8129Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
81302H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 221.1
8131RMSD between 66 pruned atom pairs is 1.048 angstroms; (across all 87 pairs:
81323.054)
8133
8134
8135> wait 1
8136
8137> measure rotation #1002 toModel #1001 showSlabs true
8138
8139Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
8140#1001 coordinates:
8141Matrix rotation and translation
81420.71841270 -0.03882790 0.69453263 -43.77242719
81430.04474713 -0.99379351 -0.10184377 314.28607160
81440.69417640 0.10424420 -0.71221645 107.06747282
8145Axis 0.92669760 0.00160183 0.37580447
8146Axis point 0.00000000 153.96110044 71.86641580
8147Rotation angle (degrees) 173.61580296
8148Shift along axis 0.17606353
8149
8150
8151> close #1001 #1002
8152
8153> define axis #2 name axis_Va
8154
8155Axis 'rotation axis #2/axis_Va' centered at [136.49236761 154.19703207
8156127.21828189] with direction [0.9266976 0.00160183 0.37580447], radius
81570.603625, and length 48.29
8158
8159> rename #2 Va_rotation_axis id #104.3.1.1
8160
8161> rename #3 Va_rotation_slabs id #104.3.2.1
8162
8163> matchmaker #1004/M to #1003/I
8164
8165Parameters
8166---
8167Chain pairing | bb
8168Alignment algorithm | Needleman-Wunsch
8169Similarity matrix | BLOSUM-62
8170SS fraction | 0.3
8171Gap open (HH/SS/other) | 18/18/6
8172Gap extend | 1
8173SS matrix | | | H | S | O
8174---|---|---|---
8175H | 6 | -9 | -6
8176S | | 6 | -6
8177O | | | 4
8178Iteration cutoff | 2
8179
8180Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
81812H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 228.5
8182RMSD between 66 pruned atom pairs is 1.088 angstroms; (across all 92 pairs:
81833.936)
8184
8185
8186> wait 1
8187
8188> measure rotation #1004 toModel #1003 showSlabs true
8189
8190Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
8191#1003 coordinates:
8192Matrix rotation and translation
81930.73661563 -0.07135580 -0.67253682 142.18618798
81940.02298296 -0.99120309 0.13033888 288.51761976
8195-0.67592100 -0.11146654 -0.72849572 353.55093768
8196Axis -0.93153019 0.01303723 0.36343024
8197Axis point 0.00000000 157.62360929 194.41945478
8198Rotation angle (degrees) 172.54257925
8199Shift along axis -0.19815617
8200
8201
8202> close #1004 #1003
8203
8204> define axis #2 name axis_Vb
8205
8206Axis 'rotation axis #2/axis_Vb' centered at [172.8655548 155.20426996
8207126.97712173] with direction [-0.93153019 0.01303723 0.36343024], radius
82080.60681, and length 48.5448
8209
8210> rename #2 Vb_rotation_axis id #104.3.1.2
8211
8212> rename #3 Vb_rotation_slabs id #104.3.2.2
8213
8214> matchmaker #1006/L to #1005/H
8215
8216Parameters
8217---
8218Chain pairing | bb
8219Alignment algorithm | Needleman-Wunsch
8220Similarity matrix | BLOSUM-62
8221SS fraction | 0.3
8222Gap open (HH/SS/other) | 18/18/6
8223Gap extend | 1
8224SS matrix | | | H | S | O
8225---|---|---|---
8226H | 6 | -9 | -6
8227S | | 6 | -6
8228O | | | 4
8229Iteration cutoff | 2
8230
8231Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
82322H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 229.8
8233RMSD between 50 pruned atom pairs is 0.885 angstroms; (across all 82 pairs:
82343.058)
8235
8236
8237> wait 1
8238
8239> measure rotation #1006 toModel #1005 showSlabs true
8240
8241Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
8242#1005 coordinates:
8243Matrix rotation and translation
8244-0.43223566 0.39105435 0.81255697 5.34243089
82450.04124481 -0.89156204 0.45101662 236.01875124
82460.90081696 0.22845922 0.36923594 -64.79879197
8247Axis -0.52502754 -0.20821113 -0.82522373
8248Axis point 38.63388899 125.78498588 0.00000000
8249Rotation angle (degrees) 167.76344751
8250Shift along axis 1.52684600
8251
8252
8253> close #1006 #1005
8254
8255> define axis #2 name axis_Ca
8256
8257Axis 'rotation axis #2/axis_Ca' centered at [105.63109625 152.35419104
8258105.30435297] with direction [-0.52502754 -0.20821113 -0.82522373], radius
82590.532467, and length 42.5974
8260
8261> rename #2 Ca_rotation_axis id #104.3.1.3
8262
8263> rename #3 Ca_rotation_slabs id #104.3.2.3
8264
8265> matchmaker #1008/M to #1007/I
8266
8267Parameters
8268---
8269Chain pairing | bb
8270Alignment algorithm | Needleman-Wunsch
8271Similarity matrix | BLOSUM-62
8272SS fraction | 0.3
8273Gap open (HH/SS/other) | 18/18/6
8274Gap extend | 1
8275SS matrix | | | H | S | O
8276---|---|---|---
8277H | 6 | -9 | -6
8278S | | 6 | -6
8279O | | | 4
8280Iteration cutoff | 2
8281
8282Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
82832H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 226.4
8284RMSD between 57 pruned atom pairs is 0.983 angstroms; (across all 98 pairs:
82853.247)
8286
8287
8288> wait 1
8289
8290> measure rotation #1008 toModel #1007 showSlabs true
8291
8292Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
8293#1007 coordinates:
8294Matrix rotation and translation
8295-0.44691350 0.37987962 -0.80991345 321.97311814
82960.04334425 -0.89510032 -0.44375297 334.72634524
8297-0.89352650 -0.23342428 0.38356682 282.18198422
8298Axis 0.51860284 0.20616286 -0.82978790
8299Axis point 269.80743377 182.59879005 0.00000000
8300Rotation angle (degrees) 168.30019456
8301Shift along axis 1.83311720
8302
8303
8304> close #1008 #1007
8305
8306> define axis #2 name axis_Cb
8307
8308Axis 'rotation axis #2/axis_Cb' centered at [203.87433587 156.38806637
8309105.49592574] with direction [ 0.51860284 0.20616286 -0.8297879 ], radius
83100.566216, and length 45.2973
8311
8312> rename #2 Cb_rotation_axis id #104.3.1.4
8313
8314> rename #3 Cb_rotation_slabs id #104.3.2.4
8315
8316> rename #104.3 geometry
8317
8318> rename #104.3.1 rotation_axes
8319
8320> rename #104.3.2 rotation_slabs
8321
8322executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
8323
8324> open CD20_2H7_mutants_define_domain_centroids.cxc
8325
8326> define centroid RTX_C & /L name centroid_RTX_C_L
8327
8328Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
8329
8330> rename ##name=centroid_RTX_C_L id 101.3.3.1
8331
8332> define centroid RTX_C & /M name centroid_RTX_C_M
8333
8334Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
8335
8336> rename ##name=centroid_RTX_C_M id 101.3.3.2
8337
8338> define centroid RTX_C & /H name centroid_RTX_C_H
8339
8340Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
8341
8342> rename ##name=centroid_RTX_C_H id 101.3.3.3
8343
8344> define centroid RTX_C & /I name centroid_RTX_C_I
8345
8346Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
8347
8348> rename ##name=centroid_RTX_C_I id 101.3.3.4
8349
8350> define centroid RTX_V & /L name centroid_RTX_V_L
8351
8352Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
8353
8354> rename ##name=centroid_RTX_V_L id 101.3.3.5
8355
8356> define centroid RTX_V & /M name centroid_RTX_V_M
8357
8358Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
8359
8360> rename ##name=centroid_RTX_V_M id 101.3.3.6
8361
8362> define centroid RTX_V & /H name centroid_RTX_V_H
8363
8364Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
8365
8366> rename ##name=centroid_RTX_V_H id 101.3.3.7
8367
8368> define centroid RTX_V & /I name centroid_RTX_V_I
8369
8370Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
8371
8372> rename ##name=centroid_RTX_V_I id 101.3.3.8
8373
8374> rename #101.3.3 centroids
8375
8376> define centroid H7v16_C & /L name centroid_2H7v16_C_L
8377
8378Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
8379104.71732873]
8380
8381> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
8382
8383> define centroid H7v16_C & /M name centroid_2H7v16_C_M
8384
8385Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
8386109.46892346]
8387
8388> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
8389
8390> define centroid H7v16_C & /H name centroid_2H7v16_C_H
8391
8392Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
8393100.10963479]
8394
8395> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
8396
8397> define centroid H7v16_C & /I name centroid_2H7v16_C_I
8398
8399Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
8400103.22787118]
8401
8402> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
8403
8404> define centroid H7v16_V & /L name centroid_2H7v16_V_L
8405
8406Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
8407124.64938243]
8408
8409> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
8410
8411> define centroid H7v16_V & /M name centroid_2H7v16_V_M
8412
8413Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
8414126.48898691]
8415
8416> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
8417
8418> define centroid H7v16_V & /H name centroid_2H7v16_V_H
8419
8420Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
8421126.96669027]
8422
8423> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
8424
8425> define centroid H7v16_V & /I name centroid_2H7v16_V_I
8426
8427Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
8428126.76187738]
8429
8430> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
8431
8432> rename #102.3.3 centroids
8433
8434> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
8435
8436Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
8437111.74271267]
8438
8439> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
8440
8441> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
8442
8443Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
8444109.3226675 ]
8445
8446> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
8447
8448> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
8449
8450Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
8451105.03944622]
8452
8453> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
8454
8455> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
8456
8457Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
8458103.22947676]
8459
8460> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
8461
8462> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
8463
8464Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
8465127.91858459]
8466
8467> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
8468
8469> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
8470
8471Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
8472127.2169787 ]
8473
8474> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
8475
8476> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
8477
8478Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
8479127.54490507]
8480
8481> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
8482
8483> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
8484
8485Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
8486127.29650809]
8487
8488> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
8489
8490> rename #103.3.3 centroids
8491
8492> define centroid CD20 & /C name centroid_CD20_C
8493
8494Centroid 'centroid_CD20_C' placed at [144.71880576 155.32713058 168.44437979]
8495
8496> rename ##name=centroid_CD20_C id 101.3.3.9
8497
8498> define centroid CD20 & /D name centroid_CD20_D
8499
8500Centroid 'centroid_CD20_D' placed at [165.28259991 155.13681165 168.62706115]
8501
8502> rename ##name=centroid_CD20_D id 101.3.3.10
8503
8504executed CD20_2H7_mutants_define_domain_centroids.cxc
8505
8506> turn x 90
8507
8508> view
8509
8510> hide #101 models
8511
8512> hide #!102.2 models
8513
8514> ~ribbon #102.10/X,Y
8515
8516executed CD20_2H7_mutants_setup.cxc
8517
8518> hide #!105 models
8519
8520> show #!105 models
8521
8522> hide #!104 models
8523
8524> hide #!103 models
8525
8526> hide #!102 models
8527
8528> hide #!105.2 models
8529
8530> show #!101 models
8531
8532> show #101.1 models
8533
8534> hide #!101 models
8535
8536> show #!101 models
8537
8538> hide #!101 models
8539
8540> show #!101 models
8541
8542> hide #!101 models
8543
8544> show #!101 models
8545
8546> hide #!101 models
8547
8548> show #!101 models
8549
8550> hide #!101 models
8551
8552> show #!101 models
8553
8554> hide #!105 models
8555
8556> show #!104 models
8557
8558> hide #!104 models
8559
8560> show #!104 models
8561
8562> hide #!104.2 models
8563
8564> hide #!104.3 models
8565
8566> hide #!104 models
8567
8568> show #!104 models
8569
8570> hide #!104 models
8571
8572> show #!104 models
8573
8574> hide #!104 models
8575
8576> show #!104 models
8577
8578> hide #!104 models
8579
8580> show #!104 models
8581
8582> hide #!104 models
8583
8584> show #!104 models
8585
8586> hide #!104 models
8587
8588> show #!104 models
8589
8590> hide #!104 models
8591
8592> show #!104 models
8593
8594> hide #!104 models
8595
8596> show #!104 models
8597
8598> hide #!104 models
8599
8600> show #!104 models
8601
8602> hide #!104 models
8603
8604> show #!104 models
8605
8606> hide #!104 models
8607
8608> show #!105 models
8609
8610> hide #!105 models
8611
8612> show #!103 models
8613
8614> hide #!103.3 models
8615
8616> hide #!103.2 models
8617
8618> hide #!103.1 models
8619
8620> show #!103.1 models
8621
8622> show #!104 models
8623
8624> hide #!104 models
8625
8626> show #!104 models
8627
8628> hide #!104 models
8629
8630> hide #!103 models
8631
8632> show #!103 models
8633
8634> hide #!103 models
8635
8636> show #!103 models
8637
8638> hide #!103 models
8639
8640> show #!102 models
8641
8642> hide #!102 models
8643
8644> show #!102 models
8645
8646> hide #!102 models
8647
8648> show #!102 models
8649
8650> hide #!102 models
8651
8652> show #!102 models
8653
8654> hide #!102 models
8655
8656> show #!102 models
8657
8658> hide #!102 models
8659
8660> show #!102 models
8661
8662> hide #!102 models
8663
8664> show #!102 models
8665
8666> show #!104 models
8667
8668> hide #!104 models
8669
8670> show #!104 models
8671
8672> hide #!104 models
8673
8674> show #!104 models
8675
8676> hide #!104 models
8677
8678> show #!103 models
8679
8680> hide #!103 models
8681
8682> show #!103 models
8683
8684> hide #!103 models
8685
8686> hide #!102 models
8687
8688> show #!102 models
8689
8690> hide #!102 models
8691
8692> show #!102 models
8693
8694> hide #!102 models
8695
8696> show #!102 models
8697
8698> hide #!102 models
8699
8700> show #!102 models
8701
8702> hide #!102 models
8703
8704> show #!105 models
8705
8706> show #!105.2 models
8707
8708> hide #!101 models
8709
8710> select #105.1/L:48
8711
87128 atoms, 7 bonds, 1 residue, 1 model selected
8713
8714> select #105.1/L:49
8715
871612 atoms, 12 bonds, 1 residue, 1 model selected
8717
8718> select #105.1/L:60
8719
87206 atoms, 5 bonds, 1 residue, 1 model selected
8721
8722> select add #105.1/L:48
8723
872414 atoms, 12 bonds, 2 residues, 1 model selected
8725
8726> select subtract #105.1/L:48
8727
87286 atoms, 5 bonds, 1 residue, 1 model selected
8729
8730> select #105.1/L:49
8731
873212 atoms, 12 bonds, 1 residue, 1 model selected
8733
8734> select #105.1/L:49-60
8735
873681 atoms, 83 bonds, 12 residues, 1 model selected
8737
8738> delete sel
8739
8740> save /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730_alito6vja_v2.pdb
8741> models #105.1
8742
8743> close
8744
8745> open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
8746
8747> close
8748
8749> cd /Users/rohoua/work/Genentech/CD20
8750
8751Current working directory is: /Users/rohoua/work/Genentech/CD20
8752
8753> open pdb:6vja name CD20_RTX id 101.1
8754
8755CD20_RTX title:
8756Structure of CD20 in complex with rituximab Fab [more info...]
8757
8758Chain information for CD20_RTX #1
8759---
8760Chain | Description | UniProt
8761C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
8762H I | Rituximab Fab heavy chain |
8763L M | Rituximab Fab light chain |
8764
8765Non-standard residues in CD20_RTX #1
8766---
8767Y01 — cholesterol hemisuccinate
8768
8769
8770> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
8771
8772Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb
8773---
8774warning | Ignored bad PDB record found on line 1
8775HEADER STR7668 version_2 2023.12.13
8776
8777CD20_2H7v16 title:
8778Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
8779resolution. [more info...]
8780
8781Chain information for CD20_2H7v16 #1
8782---
8783Chain | Description
8784C D | No description available
8785H I | No description available
8786L M | No description available
8787
8788Non-standard residues in CD20_2H7v16 #1
8789---
8790Y01 — (Y01)
8791
8792
8793> open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
8794
8795Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
8796shown at level 0.0054, step 2, values float32
8797
8798> volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
8799
8800> view matrix models
8801> #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
8802
8803> open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
8804> 102.10
8805
8806Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
8807Fab.pdb
8808---
8809warning | Ignored bad PDB record found on line 1
8810HEADER STR7487 version_1 2023.05.24
8811
88122H7v16_XRay title:
8813Structure of 2H7 Fab at 2.45 A resolution. [more info...]
8814
8815Chain information for 2H7v16_XRay #1
8816---
8817Chain | Description
8818A B X Y | No description available
8819
8820Non-standard residues in 2H7v16_XRay #1
8821---
8822CL — (CL)
8823
8824
8825> matchmaker #102.10/A,B to #102.1/H,L
8826
8827Parameters
8828---
8829Chain pairing | bb
8830Alignment algorithm | Needleman-Wunsch
8831Similarity matrix | BLOSUM-62
8832SS fraction | 0.3
8833Gap open (HH/SS/other) | 18/18/6
8834Gap extend | 1
8835SS matrix | | | H | S | O
8836---|---|---|---
8837H | 6 | -9 | -6
8838S | | 6 | -6
8839O | | | 4
8840Iteration cutoff | 2
8841
8842Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
8843sequence alignment score = 1228.2
8844RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
88450.804)
8846
8847
8848> open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
8849> 103.1
8850
8851Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb
8852---
8853warning | Ignored bad PDB record found on line 1
8854HEADER STR7717 version_2 2023.12.15
8855
8856CD20_2H7v166_D56A title:
8857Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
8858info...]
8859
8860Chain information for CD20_2H7v166_D56A #1
8861---
8862Chain | Description
8863C D | No description available
8864H I | No description available
8865L | No description available
8866M | No description available
8867
8868Non-standard residues in CD20_2H7v166_D56A #1
8869---
8870Y01 — (Y01)
8871
8872
8873> open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
8874
8875Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
8876300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32
8877
8878> volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
8879
8880> view matrix models
8881> #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
8882
8883> open CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb name
8884> CD20_2H7v166_S92A_D56A id 104.1
8885
8886Summary of feedback from opening
8887CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb
8888---
8889warning | Ignored bad PDB record found on line 1
8890HEADER STR7729 version_2 2024.01.29
8891
8892CD20_2H7v166_S92A_D56A title:
8893Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
8894resolution. [more info...]
8895
8896Chain information for CD20_2H7v166_S92A_D56A #1
8897---
8898Chain | Description
8899C D | No description available
8900H | No description available
8901I | No description available
8902L M | No description available
8903
8904
8905> open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
8906> id 104.2
8907
8908Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
8909300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32
8910
8911> volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
8912
8913> view matrix models
8914> #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
8915
8916> open CD20_2H7v166/STR7730_alito6vja_v2.pdb name CD20_2H7v166 id 105.1
8917
8918Summary of feedback from opening CD20_2H7v166/STR7730_alito6vja_v2.pdb
8919---
8920warning | Ignored bad PDB record found on line 1
8921HEADER STR7730 version_1 2024.01.12
8922
8923CD20_2H7v166 title:
8924Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
8925info...]
8926
8927Chain information for CD20_2H7v166 #1
8928---
8929Chain | Description
8930C | No description available
8931D | No description available
8932H I | No description available
8933L | No description available
8934M | No description available
8935
8936
8937> open CD20_2H7v166/cryosparc_P71_J138_006_volume_map_sharp.mrc id 105.2
8938
8939Opened cryosparc_P71_J138_006_volume_map_sharp.mrc as #1, grid size
8940300,300,300, pixel 1.43, shown at level 0.0428, step 2, values float32
8941
8942> volume #105.2 step 1 level 0.355 color #9999CC transparency 0.5
8943
8944> view matrix models
8945> #105.2,-0.024025,0.77304,0.6339,-141.69,0.99715,-0.026789,0.070462,-68.674,0.071451,0.63379,-0.7702,173
8946
8947> rename #101 CD20_RTX
8948
8949> rename #102 CD20_2H7v16
8950
8951> rename #103 CD20_2H7v166_D56A
8952
8953> rename #104 CD20_2H7v166_S92A_D56A
8954
8955> rename #105 CD20_2H7v166
8956
8957> dssp
8958
8959> name CD20_RTX #101.1
8960
8961> name CD20_2H7v16 #102.1
8962
8963> name CD20_2H7v166_D56A #103.1
8964
8965> name CD20_2H7v166_S92A_D56A #104.1
8966
8967> name CD20_2H7v166 #105.1
8968
8969> name CD20 /C,D
8970
8971> name CD20_Monomer /C
8972
8973> name CD20_H1 /C,D:46-71
8974
8975> name CD20_ECL1 /C,D:72-79
8976
8977> name CD20_H2 /C,D:80-105
8978
8979> name CD20_ICL1 /C,D:106-112
8980
8981> name CD20_H3 /C,D:113-141
8982
8983> name CD20_ECL2 /C,D:142-187
8984
8985> name CD20_ECL2SS /C,D:167,183
8986
8987> name CD20_H4 /C,D:188-end
8988
8989> name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
8990
8991> name RTX CD20_RTX & /H,L,I,M
8992
8993> name RTX_H RTX & /H,I
8994
8995> name RTX_L RTX & /L,M
8996
8997> name RTX_Epitope CD20_RTX & /C,D:168-175
8998
8999> name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
9000
9001> name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
9002
9003> name H7v16 CD20_2H7v16 & /H,L,I,M
9004
9005> name H7v16_H H7v16 & /H,I
9006
9007> name H7v16_L H7v16 & /L,M
9008
9009> name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
9010
9011> name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
9012
9013> name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
9014
9015> name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
9016
9017> name H7v166_D56A_H H7v166_D56A & /H,I
9018
9019> name H7v166_D56A_L H7v166_D56A & /L,M
9020
9021> name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
9022
9023> name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
9024
9025> name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
9026> /H,I:119-end)
9027
9028> name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
9029
9030> name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
9031
9032> name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
9033
9034> name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
9035
9036> name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
9037> & /H,I:1-111)
9038
9039> name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
9040> (H7v166_S92A_D56A & /H,I:119-end)
9041
9042> name H7v166 CD20_2H7v166 & /H,L,I,M
9043
9044> name H7v166_H H7v166 & /H,I
9045
9046> name H7v166_L H7v166 & /L,M
9047
9048> name H7v166_Epitope CD20_2H7v166 & /C,D:168-175
9049
9050> name H7v166_V (H7v166 & /L,M:1-107) | (H7v166 & /H,I:1-111)
9051
9052> name H7v166_C (H7v166 & /L,M:112-end) | (H7v166 & /H,I:119-end)
9053
9054> lighting soft
9055
9056> set bgColor white
9057
9058> camera ortho
9059
9060> style stick
9061
9062Changed 53407 atom styles
9063
9064> color byhetero
9065
9066> open CD20_2H7_mutants_color.cxc
9067
9068> color CD20 burlywood
9069
9070> color modify CD20_H1 hue - 20
9071
9072> color modify CD20_H2 hue - 10
9073
9074> color modify CD20_H3 hue + 0
9075
9076> color modify CD20_H4 hue + 10
9077
9078> color modify CD20_ECL1 hue +10
9079
9080> color modify CD20_ECL2 hue + 40
9081
9082> color modify CD20 saturation + 80
9083
9084> color CD20_ECL2 rgb(127,165,90)
9085
9086> color CD20_H4 rgb(176,215,142)
9087
9088> color RTX plum
9089
9090> color modify RTX_H hue - 40
9091
9092> color H7v16 slate blue
9093
9094> color modify H7v16_H hue - 40
9095
9096> color H7v166_D56A dodger blue
9097
9098> color modify H7v166_D56A_H hue - 40
9099
9100> color H7v166_S92A_D56A purple
9101
9102> color modify H7v166_S92A_D56A_H hue - 40
9103
9104executed CD20_2H7_mutants_color.cxc
9105
9106> hide
9107
9108> ribbon
9109
9110> show CD20_ECL2SS
9111
9112> style CD20_ECL2SS stick
9113
9114Changed 120 atom styles
9115
9116> define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
9117
9118Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
9119radius 1, and length 140
9120
9121> marker #1.1 position 155,155,70
9122
9123> marker #1.1 position 155,155,210
9124
9125> select
9126> #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
9127
9128440 atoms, 446 bonds, 54 residues, 1 model selected
9129
9130> define plane sel name membrane_plane
9131
9132Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
9133normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3
9134
9135> rename ##name=membrane_plane id 10
9136
9137> open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
9138
9139> combine CD20_RTX name RTX_Va modelId 1001
9140
9141> select zone (RTX_V & /H,L) 0.1 #1001
9142
9143Selected 1711 atoms
9144
9145> delete #1001 & ~sel
9146
9147> combine #1001 name RTX_Va_copy modelId 1002
9148
9149> combine CD20_RTX name RTX_Vb modelId 1003
9150
9151> select zone (RTX_V & /I,M) 0.1 #1003
9152
9153Selected 1711 atoms
9154
9155> delete #1003 & ~sel
9156
9157> combine #1003 name RTX_Vb_copy modelId 1004
9158
9159> combine CD20_RTX name RTX_Ca modelId 1005
9160
9161> select zone (RTX_C & /H,L) 0.1 #1005
9162
9163Selected 1503 atoms
9164
9165> delete #1005 & ~sel
9166
9167> combine #1005 name RTX_Ca_copy modelId 1006
9168
9169> combine CD20_RTX name RTX_Cb modelId 1007
9170
9171> select zone (RTX_C & /I,M) 0.1 #1007
9172
9173Selected 1503 atoms
9174
9175> delete #1007 & ~sel
9176
9177> combine #1007 name RTX_Ca_copy modelId 1008
9178
9179> matchmaker #1002/L to #1001/H
9180
9181Parameters
9182---
9183Chain pairing | bb
9184Alignment algorithm | Needleman-Wunsch
9185Similarity matrix | BLOSUM-62
9186SS fraction | 0.3
9187Gap open (HH/SS/other) | 18/18/6
9188Gap extend | 1
9189SS matrix | | | H | S | O
9190---|---|---|---
9191H | 6 | -9 | -6
9192S | | 6 | -6
9193O | | | 4
9194Iteration cutoff | 2
9195
9196Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
9197alignment score = 198.7
9198RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
91994.421)
9200
9201
9202> wait 1
9203
9204> measure rotation #1002 toModel #1001 showSlabs true
9205
9206Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates:
9207Matrix rotation and translation
92080.65377294 -0.06463426 0.75392530 -36.97668460
92090.02426941 -0.99404163 -0.10626495 318.59247232
92100.75630149 0.08777047 -0.64830888 90.28955685
9211Axis 0.90906034 -0.01113250 0.41651574
9212Axis point 0.00000000 156.41772375 62.99337678
9213Rotation angle (degrees) 173.87355102
9214Shift along axis 0.44625393
9215
9216
9217> close #1001 #1002
9218
9219> define axis #2 name axis_Va
9220
9221Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
9222125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
92230.65062, and length 52.0496
9224
9225> rename #2 Va_rotation_axis id #101.3.1.1
9226
9227> rename #3 Va_rotation_slabs id #101.3.2.1
9228
9229> matchmaker #1004/M to #1003/I
9230
9231Parameters
9232---
9233Chain pairing | bb
9234Alignment algorithm | Needleman-Wunsch
9235Similarity matrix | BLOSUM-62
9236SS fraction | 0.3
9237Gap open (HH/SS/other) | 18/18/6
9238Gap extend | 1
9239SS matrix | | | H | S | O
9240---|---|---|---
9241H | 6 | -9 | -6
9242S | | 6 | -6
9243O | | | 4
9244Iteration cutoff | 2
9245
9246Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
9247alignment score = 214.3
9248RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
92494.448)
9250
9251
9252> wait 1
9253
9254> measure rotation #1004 toModel #1003 showSlabs true
9255
9256Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates:
9257Matrix rotation and translation
92580.65527690 -0.06129532 -0.75289778 163.48223927
92590.03113398 -0.99366393 0.10799385 290.56686667
9260-0.75474688 -0.09420658 -0.64921665 352.74817189
9261Axis -0.90945183 0.00831685 0.41572611
9262Axis point 0.00000000 156.83903630 204.83255489
9263Rotation angle (degrees) 173.61745932
9264Shift along axis 0.38400661
9265
9266
9267> close #1004 #1003
9268
9269> define axis #2 name axis_Vb
9270
9271Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
9272125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
92730.648586, and length 51.8869
9274
9275> rename #2 Vb_rotation_axis id #101.3.1.2
9276
9277> rename #3 Vb_rotation_slabs id #101.3.2.2
9278
9279> matchmaker #1006/L to #1005/H
9280
9281Parameters
9282---
9283Chain pairing | bb
9284Alignment algorithm | Needleman-Wunsch
9285Similarity matrix | BLOSUM-62
9286SS fraction | 0.3
9287Gap open (HH/SS/other) | 18/18/6
9288Gap extend | 1
9289SS matrix | | | H | S | O
9290---|---|---|---
9291H | 6 | -9 | -6
9292S | | 6 | -6
9293O | | | 4
9294Iteration cutoff | 2
9295
9296Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
9297alignment score = 238.2
9298RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
92993.308)
9300
9301
9302> wait 1
9303
9304> measure rotation #1006 toModel #1005 showSlabs true
9305
9306Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates:
9307Matrix rotation and translation
93080.37780344 0.24165354 0.89379423 -73.66252391
93090.01279825 -0.96661035 0.25593093 273.63534365
93100.92579737 -0.08525258 -0.36828146 68.27322422
9311Axis -0.82796624 -0.07766353 -0.55537400
9312Axis point 0.00000000 144.62953182 41.62502778
9313Rotation angle (degrees) 168.10978391
9314Shift along axis 1.82142171
9315
9316
9317> close #1006 #1005
9318
9319> define axis #2 name axis_Ca
9320
9321Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
9322110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
93230.539289, and length 43.1431
9324
9325> rename #2 Ca_rotation_axis id #101.3.1.3
9326
9327> rename #3 Ca_rotation_slabs id #101.3.2.3
9328
9329> matchmaker #1008/M to #1007/I
9330
9331Parameters
9332---
9333Chain pairing | bb
9334Alignment algorithm | Needleman-Wunsch
9335Similarity matrix | BLOSUM-62
9336SS fraction | 0.3
9337Gap open (HH/SS/other) | 18/18/6
9338Gap extend | 1
9339SS matrix | | | H | S | O
9340---|---|---|---
9341H | 6 | -9 | -6
9342S | | 6 | -6
9343O | | | 4
9344Iteration cutoff | 2
9345
9346Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
9347alignment score = 238.2
9348RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
93493.487)
9350
9351
9352> wait 1
9353
9354> measure rotation #1008 toModel #1007 showSlabs true
9355
9356Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates:
9357Matrix rotation and translation
93580.37961795 0.24211100 -0.89290116 191.06761259
93590.01296287 -0.96644625 -0.25654164 332.12351027
9360-0.92505253 0.08581325 -0.37001879 328.82641259
9361Axis 0.82850834 0.07780721 -0.55454483
9362Axis point 0.00000000 136.30341759 249.27961172
9363Rotation angle (degrees) 168.07628341
9364Shift along axis 1.79372450
9365
9366
9367> close #1008 #1007
9368
9369> define axis #2 name axis_Cb
9370
9371Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
9372110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
93730.53918, and length 43.1344
9374
9375> rename #2 Cb_rotation_axis id #101.3.1.4
9376
9377> rename #3 Cb_rotation_slabs id #101.3.2.4
9378
9379> rename #101.3 geometry
9380
9381> rename #101.3.1 rotation_axes
9382
9383> rename #101.3.2 rotation_slabs
9384
9385executed CD20_RTX_define_pseudo_symmetries.cxc
9386
9387> open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
9388
9389> combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
9390
9391> select zone (H7v16_V & /H,L) 0.1 #1001
9392
9393Selected 1754 atoms
9394
9395> delete #1001 & ~sel
9396
9397> combine #1001 name 2H7_v16_Va_copy modelId 1002
9398
9399> combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
9400
9401> select zone (H7v16_V & /I,M) 0.1 #1003
9402
9403Selected 1710 atoms
9404
9405> delete #1003 & ~sel
9406
9407> combine #1003 name 2H7_v16_Vb_copy modelId 1004
9408
9409> combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
9410
9411> select zone (H7v16_C & /H,L) 0.1 #1005
9412
9413Selected 1550 atoms
9414
9415> delete #1005 & ~sel
9416
9417> combine #1005 name 2H7_v16_Ca_copy modelId 1006
9418
9419> combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
9420
9421> select zone (H7v16_C & /I,M) 0.1 #1007
9422
9423Selected 1550 atoms
9424
9425> delete #1007 & ~sel
9426
9427> combine #1007 name 2H7_v16_Ca_copy modelId 1008
9428
9429> matchmaker #1002/L to #1001/H
9430
9431Parameters
9432---
9433Chain pairing | bb
9434Alignment algorithm | Needleman-Wunsch
9435Similarity matrix | BLOSUM-62
9436SS fraction | 0.3
9437Gap open (HH/SS/other) | 18/18/6
9438Gap extend | 1
9439SS matrix | | | H | S | O
9440---|---|---|---
9441H | 6 | -9 | -6
9442S | | 6 | -6
9443O | | | 4
9444Iteration cutoff | 2
9445
9446Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
9447sequence alignment score = 387.9
9448RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
94495.340)
9450
9451
9452> wait 1
9453
9454> measure rotation #1002 toModel #1001 showSlabs true
9455
9456Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates:
9457Matrix rotation and translation
94580.58985298 0.00233427 0.80750728 -45.05678546
94590.12316682 -0.98855531 -0.08711100 297.16136614
94600.79806228 0.15084078 -0.58338980 65.44859378
9461Axis 0.89106916 0.03536916 0.45248731
9462Axis point 0.00000000 147.01172040 55.34624717
9463Rotation angle (degrees) 172.32693090
9464Shift along axis -0.02370559
9465
9466
9467> close #1001 #1002
9468
9469> define axis #2 name axis_Va
9470
9471Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
9472125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
94730.589874, and length 47.1899
9474
9475> rename #2 Va_rotation_axis id #102.3.1.1
9476
9477> rename #3 Va_rotation_slabs id #102.3.2.1
9478
9479> matchmaker #1004/M to #1003/I
9480
9481Parameters
9482---
9483Chain pairing | bb
9484Alignment algorithm | Needleman-Wunsch
9485Similarity matrix | BLOSUM-62
9486SS fraction | 0.3
9487Gap open (HH/SS/other) | 18/18/6
9488Gap extend | 1
9489SS matrix | | | H | S | O
9490---|---|---|---
9491H | 6 | -9 | -6
9492S | | 6 | -6
9493O | | | 4
9494Iteration cutoff | 2
9495
9496Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
9497sequence alignment score = 378.3
9498RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
94994.620)
9500
9501
9502> wait 1
9503
9504> measure rotation #1004 toModel #1003 showSlabs true
9505
9506Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates:
9507Matrix rotation and translation
95080.62864598 0.45103819 -0.63353672 71.77949524
95090.53321619 -0.84298968 -0.07105560 212.64664720
9510-0.56611370 -0.29314322 -0.77044294 368.84403487
9511Axis -0.90200560 -0.27383758 0.33376470
9512Axis point -0.00000000 108.05935567 190.41757658
9513Rotation angle (degrees) 172.92851049
9514Shift along axis 0.13096924
9515
9516
9517> close #1004 #1003
9518
9519> define axis #2 name axis_Vb
9520
9521Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
9522125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
95230.594923, and length 47.5938
9524
9525> rename #2 Vb_rotation_axis id #102.3.1.2
9526
9527> rename #3 Vb_rotation_slabs id #102.3.2.2
9528
9529> matchmaker #1006/L to #1005/H
9530
9531Parameters
9532---
9533Chain pairing | bb
9534Alignment algorithm | Needleman-Wunsch
9535Similarity matrix | BLOSUM-62
9536SS fraction | 0.3
9537Gap open (HH/SS/other) | 18/18/6
9538Gap extend | 1
9539SS matrix | | | H | S | O
9540---|---|---|---
9541H | 6 | -9 | -6
9542S | | 6 | -6
9543O | | | 4
9544Iteration cutoff | 2
9545
9546Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
9547sequence alignment score = 403.6
9548RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
95493.184)
9550
9551
9552> wait 1
9553
9554> measure rotation #1006 toModel #1005 showSlabs true
9555
9556Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates:
9557Matrix rotation and translation
9558-0.62547004 0.41276667 0.66212605 49.05674876
95590.08546501 -0.80725952 0.58397585 200.07354667
95600.77555333 0.42184801 0.46963954 -95.83522576
9561Axis -0.42390521 -0.29657098 -0.85577452
9562Axis point 59.57688139 113.83169245 0.00000000
9563Rotation angle (degrees) 168.97535276
9564Shift along axis 1.88192618
9565
9566
9567> close #1006 #1005
9568
9569> define axis #2 name axis_Ca
9570
9571Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
9572101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
95730.550437, and length 44.0349
9574
9575> rename #2 Ca_rotation_axis id #102.3.1.3
9576
9577> rename #3 Ca_rotation_slabs id #102.3.2.3
9578
9579> matchmaker #1008/M to #1007/I
9580
9581Parameters
9582---
9583Chain pairing | bb
9584Alignment algorithm | Needleman-Wunsch
9585Similarity matrix | BLOSUM-62
9586SS fraction | 0.3
9587Gap open (HH/SS/other) | 18/18/6
9588Gap extend | 1
9589SS matrix | | | H | S | O
9590---|---|---|---
9591H | 6 | -9 | -6
9592S | | 6 | -6
9593O | | | 4
9594Iteration cutoff | 2
9595
9596Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
9597sequence alignment score = 396
9598RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
95993.551)
9600
9601
9602> wait 1
9603
9604> measure rotation #1008 toModel #1007 showSlabs true
9605
9606Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates:
9607Matrix rotation and translation
9608-0.62894249 0.48033740 -0.61131606 312.62038315
96090.14842286 -0.69766113 -0.70088487 336.12735996
9610-0.76315267 -0.53154955 0.36749568 311.24709675
9611Axis 0.42085200 0.37736216 -0.82491296
9612Axis point 256.37284203 220.04020388 0.00000000
9613Rotation angle (degrees) 168.39393838
9614Shift along axis 1.65689588
9615
9616
9617> close #1008 #1007
9618
9619> define axis #2 name axis_Cb
9620
9621Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
9622105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
96230.534846, and length 42.7877
9624
9625> rename #2 Cb_rotation_axis id #102.3.1.4
9626
9627> rename #3 Cb_rotation_slabs id #102.3.2.4
9628
9629> rename #102.3 geometry
9630
9631> rename #102.3.1 rotation_axes
9632
9633> rename #102.3.2 rotation_slabs
9634
9635executed CD20_2H7v16_define_pseudo_symmetries.cxc
9636
9637> open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
9638
9639> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
9640
9641> select zone (H7v166_D56A_V & /H,L) 0.1 #1001
9642
9643Selected 1654 atoms
9644
9645> delete #1001 & ~sel
9646
9647> combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
9648
9649> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
9650
9651> select zone (H7v166_D56A_V & /I,M) 0.1 #1003
9652
9653Selected 1678 atoms
9654
9655> delete #1003 & ~sel
9656
9657> combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
9658
9659> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
9660
9661> select zone (H7v166_D56A_C & /H,L) 0.1 #1005
9662
9663Selected 1550 atoms
9664
9665> delete #1005 & ~sel
9666
9667> combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
9668
9669> combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
9670
9671> select zone (H7v166_D56A_C & /I,M) 0.1 #1007
9672
9673Selected 1550 atoms
9674
9675> delete #1007 & ~sel
9676
9677> combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
9678
9679> matchmaker #1002/L to #1001/H
9680
9681Parameters
9682---
9683Chain pairing | bb
9684Alignment algorithm | Needleman-Wunsch
9685Similarity matrix | BLOSUM-62
9686SS fraction | 0.3
9687Gap open (HH/SS/other) | 18/18/6
9688Gap extend | 1
9689SS matrix | | | H | S | O
9690---|---|---|---
9691H | 6 | -9 | -6
9692S | | 6 | -6
9693O | | | 4
9694Iteration cutoff | 2
9695
9696Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
9697L (#1002), sequence alignment score = 547.6
9698RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
96992.607)
9700
9701
9702> wait 1
9703
9704> measure rotation #1002 toModel #1001 showSlabs true
9705
9706Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
9707coordinates:
9708Matrix rotation and translation
97090.73992366 -0.12116101 0.66168949 -29.70332856
9710-0.06116680 -0.99168902 -0.11318795 332.06337928
97110.66990417 0.04327702 -0.74118520 123.44534698
9712Axis 0.93259437 -0.04896279 0.35758970
9713Axis point 0.00000000 162.47254458 74.89799404
9714Rotation angle (degrees) 175.18797763
9715Shift along axis 0.18287681
9716
9717
9718> close #1001 #1002
9719
9720> define axis #2 name axis_Va
9721
9722Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
9723127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
97240.599212, and length 47.937
9725
9726> rename #2 Va_rotation_axis id #103.3.1.1
9727
9728> rename #3 Va_rotation_slabs id #103.3.2.1
9729
9730> matchmaker #1004/M to #1003/I
9731
9732Parameters
9733---
9734Chain pairing | bb
9735Alignment algorithm | Needleman-Wunsch
9736Similarity matrix | BLOSUM-62
9737SS fraction | 0.3
9738Gap open (HH/SS/other) | 18/18/6
9739Gap extend | 1
9740SS matrix | | | H | S | O
9741---|---|---|---
9742H | 6 | -9 | -6
9743S | | 6 | -6
9744O | | | 4
9745Iteration cutoff | 2
9746
9747Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
9748M (#1004), sequence alignment score = 376.5
9749RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
97503.886)
9751
9752
9753> wait 1
9754
9755> measure rotation #1004 toModel #1003 showSlabs true
9756
9757Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
9758coordinates:
9759Matrix rotation and translation
97600.72982969 -0.01372193 -0.68349128 135.94952936
97610.06485007 -0.99390027 0.08920045 287.47713002
9762-0.68054617 -0.10942560 -0.72448806 354.00628960
9763Axis -0.92979963 -0.01378652 0.36780781
9764Axis point 0.00000000 152.92822789 195.61279282
9765Rotation angle (degrees) 173.86847166
9766Shift along axis -0.16285394
9767
9768
9769> close #1004 #1003
9770
9771> define axis #2 name axis_Vb
9772
9773Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
9774126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
97750.597156, and length 47.7725
9776
9777> rename #2 Vb_rotation_axis id #103.3.1.2
9778
9779> rename #3 Vb_rotation_slabs id #103.3.2.2
9780
9781> matchmaker #1006/L to #1005/H
9782
9783Parameters
9784---
9785Chain pairing | bb
9786Alignment algorithm | Needleman-Wunsch
9787Similarity matrix | BLOSUM-62
9788SS fraction | 0.3
9789Gap open (HH/SS/other) | 18/18/6
9790Gap extend | 1
9791SS matrix | | | H | S | O
9792---|---|---|---
9793H | 6 | -9 | -6
9794S | | 6 | -6
9795O | | | 4
9796Iteration cutoff | 2
9797
9798Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
9799L (#1006), sequence alignment score = 554.5
9800RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
98013.119)
9802
9803
9804> wait 1
9805
9806> measure rotation #1006 toModel #1005 showSlabs true
9807
9808Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
9809coordinates:
9810Matrix rotation and translation
9811-0.33391401 0.38072466 0.86229355 -12.40856576
98120.05205532 -0.90595556 0.42016042 245.78035810
98130.94116506 0.18518442 0.28269251 -52.33839393
9814Axis -0.57081123 -0.19159720 -0.79841408
9815Axis point 28.53870248 129.91224226 0.00000000
9816Rotation angle (degrees) 168.12212217
9817Shift along axis 1.77983022
9818
9819
9820> close #1006 #1005
9821
9822> define axis #2 name axis_Ca
9823
9824Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
9825106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
98260.56909, and length 45.5272
9827
9828> rename #2 Ca_rotation_axis id #103.3.1.3
9829
9830> rename #3 Ca_rotation_slabs id #103.3.2.3
9831
9832> matchmaker #1008/M to #1007/I
9833
9834Parameters
9835---
9836Chain pairing | bb
9837Alignment algorithm | Needleman-Wunsch
9838Similarity matrix | BLOSUM-62
9839SS fraction | 0.3
9840Gap open (HH/SS/other) | 18/18/6
9841Gap extend | 1
9842SS matrix | | | H | S | O
9843---|---|---|---
9844H | 6 | -9 | -6
9845S | | 6 | -6
9846O | | | 4
9847Iteration cutoff | 2
9848
9849Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
9850M (#1008), sequence alignment score = 416.6
9851RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
98523.361)
9853
9854
9855> wait 1
9856
9857> measure rotation #1008 toModel #1007 showSlabs true
9858
9859Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
9860coordinates:
9861Matrix rotation and translation
9862-0.50667380 0.40781938 -0.75958213 323.22163731
98630.08178140 -0.85433688 -0.51324487 330.95129120
9864-0.85825023 -0.32216741 0.39951808 287.19953324
9865Axis 0.48922423 0.25262440 -0.83476977
9866Axis point 265.28291179 189.90297685 0.00000000
9867Rotation angle (degrees) 168.73855860
9868Shift along axis 1.98873850
9869
9870
9871> close #1008 #1007
9872
9873> define axis #2 name axis_Cb
9874
9875Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
9876104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
98770.553583, and length 44.2867
9878
9879> rename #2 Cb_rotation_axis id #103.3.1.4
9880
9881> rename #3 Cb_rotation_slabs id #103.3.2.4
9882
9883> rename #103.3 geometry
9884
9885> rename #103.3.1 rotation_axes
9886
9887> rename #103.3.2 rotation_slabs
9888
9889executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
9890
9891> open
9892> CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
9893
9894> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
9895
9896> select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
9897
9898Selected 1653 atoms
9899
9900> delete #1001 & ~sel
9901
9902> combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
9903
9904> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
9905
9906> select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
9907
9908Selected 1678 atoms
9909
9910> delete #1003 & ~sel
9911
9912> combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
9913
9914> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
9915
9916> select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
9917
9918Selected 1461 atoms
9919
9920> delete #1005 & ~sel
9921
9922> combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
9923
9924> combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
9925
9926> select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
9927
9928Selected 1550 atoms
9929
9930> delete #1007 & ~sel
9931
9932> combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
9933
9934> matchmaker #1002/L to #1001/H
9935
9936Parameters
9937---
9938Chain pairing | bb
9939Alignment algorithm | Needleman-Wunsch
9940Similarity matrix | BLOSUM-62
9941SS fraction | 0.3
9942Gap open (HH/SS/other) | 18/18/6
9943Gap extend | 1
9944SS matrix | | | H | S | O
9945---|---|---|---
9946H | 6 | -9 | -6
9947S | | 6 | -6
9948O | | | 4
9949Iteration cutoff | 2
9950
9951Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
99522H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 221.1
9953RMSD between 66 pruned atom pairs is 1.048 angstroms; (across all 87 pairs:
99543.054)
9955
9956
9957> wait 1
9958
9959> measure rotation #1002 toModel #1001 showSlabs true
9960
9961Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
9962#1001 coordinates:
9963Matrix rotation and translation
99640.71841270 -0.03882790 0.69453263 -43.77242719
99650.04474713 -0.99379351 -0.10184377 314.28607160
99660.69417640 0.10424420 -0.71221645 107.06747282
9967Axis 0.92669760 0.00160183 0.37580447
9968Axis point 0.00000000 153.96110044 71.86641580
9969Rotation angle (degrees) 173.61580296
9970Shift along axis 0.17606353
9971
9972
9973> close #1001 #1002
9974
9975> define axis #2 name axis_Va
9976
9977Axis 'rotation axis #2/axis_Va' centered at [136.49236761 154.19703207
9978127.21828189] with direction [0.9266976 0.00160183 0.37580447], radius
99790.603625, and length 48.29
9980
9981> rename #2 Va_rotation_axis id #104.3.1.1
9982
9983> rename #3 Va_rotation_slabs id #104.3.2.1
9984
9985> matchmaker #1004/M to #1003/I
9986
9987Parameters
9988---
9989Chain pairing | bb
9990Alignment algorithm | Needleman-Wunsch
9991Similarity matrix | BLOSUM-62
9992SS fraction | 0.3
9993Gap open (HH/SS/other) | 18/18/6
9994Gap extend | 1
9995SS matrix | | | H | S | O
9996---|---|---|---
9997H | 6 | -9 | -6
9998S | | 6 | -6
9999O | | | 4
10000Iteration cutoff | 2
10001
10002Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
100032H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 228.5
10004RMSD between 66 pruned atom pairs is 1.088 angstroms; (across all 92 pairs:
100053.936)
10006
10007
10008> wait 1
10009
10010> measure rotation #1004 toModel #1003 showSlabs true
10011
10012Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
10013#1003 coordinates:
10014Matrix rotation and translation
100150.73661563 -0.07135580 -0.67253682 142.18618798
100160.02298296 -0.99120309 0.13033888 288.51761976
10017-0.67592100 -0.11146654 -0.72849572 353.55093768
10018Axis -0.93153019 0.01303723 0.36343024
10019Axis point 0.00000000 157.62360929 194.41945478
10020Rotation angle (degrees) 172.54257925
10021Shift along axis -0.19815617
10022
10023
10024> close #1004 #1003
10025
10026> define axis #2 name axis_Vb
10027
10028Axis 'rotation axis #2/axis_Vb' centered at [172.8655548 155.20426996
10029126.97712173] with direction [-0.93153019 0.01303723 0.36343024], radius
100300.60681, and length 48.5448
10031
10032> rename #2 Vb_rotation_axis id #104.3.1.2
10033
10034> rename #3 Vb_rotation_slabs id #104.3.2.2
10035
10036> matchmaker #1006/L to #1005/H
10037
10038Parameters
10039---
10040Chain pairing | bb
10041Alignment algorithm | Needleman-Wunsch
10042Similarity matrix | BLOSUM-62
10043SS fraction | 0.3
10044Gap open (HH/SS/other) | 18/18/6
10045Gap extend | 1
10046SS matrix | | | H | S | O
10047---|---|---|---
10048H | 6 | -9 | -6
10049S | | 6 | -6
10050O | | | 4
10051Iteration cutoff | 2
10052
10053Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
100542H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 229.8
10055RMSD between 50 pruned atom pairs is 0.885 angstroms; (across all 82 pairs:
100563.058)
10057
10058
10059> wait 1
10060
10061> measure rotation #1006 toModel #1005 showSlabs true
10062
10063Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
10064#1005 coordinates:
10065Matrix rotation and translation
10066-0.43223566 0.39105435 0.81255697 5.34243089
100670.04124481 -0.89156204 0.45101662 236.01875124
100680.90081696 0.22845922 0.36923594 -64.79879197
10069Axis -0.52502754 -0.20821113 -0.82522373
10070Axis point 38.63388899 125.78498588 0.00000000
10071Rotation angle (degrees) 167.76344751
10072Shift along axis 1.52684600
10073
10074
10075> close #1006 #1005
10076
10077> define axis #2 name axis_Ca
10078
10079Axis 'rotation axis #2/axis_Ca' centered at [105.63109625 152.35419104
10080105.30435297] with direction [-0.52502754 -0.20821113 -0.82522373], radius
100810.532467, and length 42.5974
10082
10083> rename #2 Ca_rotation_axis id #104.3.1.3
10084
10085> rename #3 Ca_rotation_slabs id #104.3.2.3
10086
10087> matchmaker #1008/M to #1007/I
10088
10089Parameters
10090---
10091Chain pairing | bb
10092Alignment algorithm | Needleman-Wunsch
10093Similarity matrix | BLOSUM-62
10094SS fraction | 0.3
10095Gap open (HH/SS/other) | 18/18/6
10096Gap extend | 1
10097SS matrix | | | H | S | O
10098---|---|---|---
10099H | 6 | -9 | -6
10100S | | 6 | -6
10101O | | | 4
10102Iteration cutoff | 2
10103
10104Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
101052H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 226.4
10106RMSD between 57 pruned atom pairs is 0.983 angstroms; (across all 98 pairs:
101073.247)
10108
10109
10110> wait 1
10111
10112> measure rotation #1008 toModel #1007 showSlabs true
10113
10114Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
10115#1007 coordinates:
10116Matrix rotation and translation
10117-0.44691350 0.37987962 -0.80991345 321.97311814
101180.04334425 -0.89510032 -0.44375297 334.72634524
10119-0.89352650 -0.23342428 0.38356682 282.18198422
10120Axis 0.51860284 0.20616286 -0.82978790
10121Axis point 269.80743377 182.59879005 0.00000000
10122Rotation angle (degrees) 168.30019456
10123Shift along axis 1.83311720
10124
10125
10126> close #1008 #1007
10127
10128> define axis #2 name axis_Cb
10129
10130Axis 'rotation axis #2/axis_Cb' centered at [203.87433587 156.38806637
10131105.49592574] with direction [ 0.51860284 0.20616286 -0.8297879 ], radius
101320.566216, and length 45.2973
10133
10134> rename #2 Cb_rotation_axis id #104.3.1.4
10135
10136> rename #3 Cb_rotation_slabs id #104.3.2.4
10137
10138> rename #104.3 geometry
10139
10140> rename #104.3.1 rotation_axes
10141
10142> rename #104.3.2 rotation_slabs
10143
10144executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
10145
10146> open CD20_2H7v166/CD20_2H7v166_define_pseudo_symmetries.cxc
10147
10148> combine CD20_2H7v166 name 2H7_v166_Va modelId 1001
10149
10150> select zone (H7v166_V & /H,L) 0.1 #1001
10151
10152Selected 1657 atoms
10153
10154> delete #1001 & ~sel
10155
10156> combine #1001 name 2H7_v166_Va_copy modelId 1002
10157
10158> combine CD20_2H7v166 name 2H7_v166_Vb modelId 1003
10159
10160> select zone (H7v166_V & /I,M) 0.1 #1003
10161
10162Selected 1682 atoms
10163
10164> delete #1003 & ~sel
10165
10166> combine #1003 name 2H7_v166_Vb_copy modelId 1004
10167
10168> combine CD20_2H7v166 name 2H7_v166_Ca modelId 1005
10169
10170> select zone (H7v166_C & /H,L) 0.1 #1005
10171
10172Selected 1550 atoms
10173
10174> delete #1005 & ~sel
10175
10176> combine #1005 name 2H7_v166_Ca_copy modelId 1006
10177
10178> combine CD20_2H7v166 name 2H7_v166_Cb modelId 1007
10179
10180> select zone (H7v166_C & /I,M) 0.1 #1007
10181
10182Selected 1550 atoms
10183
10184> delete #1007 & ~sel
10185
10186> combine #1007 name 2H7_v166_Ca_copy modelId 1008
10187
10188> matchmaker #1002/L to #1001/H
10189
10190Parameters
10191---
10192Chain pairing | bb
10193Alignment algorithm | Needleman-Wunsch
10194Similarity matrix | BLOSUM-62
10195SS fraction | 0.3
10196Gap open (HH/SS/other) | 18/18/6
10197Gap extend | 1
10198SS matrix | | | H | S | O
10199---|---|---|---
10200H | 6 | -9 | -6
10201S | | 6 | -6
10202O | | | 4
10203Iteration cutoff | 2
10204
10205Matchmaker 2H7_v166_Va, chain H (#1001) with 2H7_v166_Va_copy, chain L
10206(#1002), sequence alignment score = 377
10207RMSD between 66 pruned atom pairs is 1.022 angstroms; (across all 90 pairs:
102082.960)
10209
10210
10211> wait 1
10212
10213> measure rotation #1002 toModel #1001 showSlabs true
10214
10215Position of 2H7_v166_Va_copy #1002 relative to 2H7_v166_Va #1001 coordinates:
10216Matrix rotation and translation
102170.74036052 -0.11371993 0.66252101 -31.23158610
10218-0.02845388 -0.99000464 -0.13813468 329.18077129
102190.67160754 0.08341817 -0.73619612 115.46673824
10220Axis 0.93258730 -0.03824813 0.35891226
10221Axis point 0.00000000 160.25696876 74.26207800
10222Rotation angle (degrees) 173.17807255
10223Shift along axis -0.27430151
10224
10225
10226> close #1001 #1002
10227
10228> define axis #2 name axis_Va
10229
10230Axis 'rotation axis #2/axis_Va' centered at [135.68943718 154.69194858
10231126.48303609] with direction [ 0.9325873 -0.03824813 0.35891226], radius
102320.590651, and length 47.2521
10233
10234> rename #2 Va_rotation_axis id #105.3.1.1
10235
10236> rename #3 Va_rotation_slabs id #105.3.2.1
10237
10238> matchmaker #1004/M to #1003/I
10239
10240Parameters
10241---
10242Chain pairing | bb
10243Alignment algorithm | Needleman-Wunsch
10244Similarity matrix | BLOSUM-62
10245SS fraction | 0.3
10246Gap open (HH/SS/other) | 18/18/6
10247Gap extend | 1
10248SS matrix | | | H | S | O
10249---|---|---|---
10250H | 6 | -9 | -6
10251S | | 6 | -6
10252O | | | 4
10253Iteration cutoff | 2
10254
10255Matchmaker 2H7_v166_Vb, chain I (#1003) with 2H7_v166_Vb_copy, chain M
10256(#1004), sequence alignment score = 358.4
10257RMSD between 69 pruned atom pairs is 0.979 angstroms; (across all 95 pairs:
102584.646)
10259
10260
10261> wait 1
10262
10263> measure rotation #1004 toModel #1003 showSlabs true
10264
10265Position of 2H7_v166_Vb_copy #1004 relative to 2H7_v166_Vb #1003 coordinates:
10266Matrix rotation and translation
102670.75743859 0.04690774 -0.65121920 117.86722740
102680.12590076 -0.98918973 0.07518427 279.29903150
10269-0.64065262 -0.13893646 -0.75515620 355.61680478
10270Axis -0.93718783 -0.04624900 0.34574559
10271Axis point 0.00000000 147.61804807 191.01165258
10272Rotation angle (degrees) 173.44045283
10273Shift along axis -0.42808976
10274
10275
10276> close #1004 #1003
10277
10278> define axis #2 name axis_Vb
10279
10280Axis 'rotation axis #2/axis_Vb' centered at [173.55590691 156.18280566
10281126.98373076] with direction [-0.93718783 -0.046249 0.34574559], radius
102820.594071, and length 47.5257
10283
10284> rename #2 Vb_rotation_axis id #105.3.1.2
10285
10286> rename #3 Vb_rotation_slabs id #105.3.2.2
10287
10288> matchmaker #1006/L to #1005/H
10289
10290Parameters
10291---
10292Chain pairing | bb
10293Alignment algorithm | Needleman-Wunsch
10294Similarity matrix | BLOSUM-62
10295SS fraction | 0.3
10296Gap open (HH/SS/other) | 18/18/6
10297Gap extend | 1
10298SS matrix | | | H | S | O
10299---|---|---|---
10300H | 6 | -9 | -6
10301S | | 6 | -6
10302O | | | 4
10303Iteration cutoff | 2
10304
10305Matchmaker 2H7_v166_Ca, chain H (#1005) with 2H7_v166_Ca_copy, chain L
10306(#1006), sequence alignment score = 399.2
10307RMSD between 58 pruned atom pairs is 1.052 angstroms; (across all 98 pairs:
103083.123)
10309
10310
10311> wait 1
10312
10313> measure rotation #1006 toModel #1005 showSlabs true
10314
10315Position of 2H7_v166_Ca_copy #1006 relative to 2H7_v166_Ca #1005 coordinates:
10316Matrix rotation and translation
10317-0.36716667 0.38456866 0.84693305 -6.67078745
103180.04496994 -0.90212482 0.42912530 243.63516386
103190.92906746 0.19564703 0.31393613 -56.48454371
10320Axis -0.55560865 -0.19545541 -0.80814369
10321Axis point 32.11829117 129.02332751 0.00000000
10322Rotation angle (degrees) 167.87118034
10323Shift along axis 1.73416361
10324
10325
10326> close #1006 #1005
10327
10328> define axis #2 name axis_Ca
10329
10330Axis 'rotation axis #2/axis_Ca' centered at [104.82226786 154.59957746
10331105.74936185] with direction [-0.55560865 -0.19545541 -0.80814369], radius
103320.570192, and length 45.6153
10333
10334> rename #2 Ca_rotation_axis id #105.3.1.3
10335
10336> rename #3 Ca_rotation_slabs id #105.3.2.3
10337
10338> matchmaker #1008/M to #1007/I
10339
10340Parameters
10341---
10342Chain pairing | bb
10343Alignment algorithm | Needleman-Wunsch
10344Similarity matrix | BLOSUM-62
10345SS fraction | 0.3
10346Gap open (HH/SS/other) | 18/18/6
10347Gap extend | 1
10348SS matrix | | | H | S | O
10349---|---|---|---
10350H | 6 | -9 | -6
10351S | | 6 | -6
10352O | | | 4
10353Iteration cutoff | 2
10354
10355Matchmaker 2H7_v166_Cb, chain I (#1007) with 2H7_v166_Ca_copy, chain M
10356(#1008), sequence alignment score = 402
10357RMSD between 56 pruned atom pairs is 0.960 angstroms; (across all 98 pairs:
103583.231)
10359
10360
10361> wait 1
10362
10363> measure rotation #1008 toModel #1007 showSlabs true
10364
10365Position of 2H7_v166_Ca_copy #1008 relative to 2H7_v166_Cb #1007 coordinates:
10366Matrix rotation and translation
10367-0.45572784 0.44991832 -0.76804013 308.16221430
103680.12623181 -0.82146310 -0.55611502 324.81402868
10369-0.88112296 -0.35038819 0.31756960 307.00257135
10370Axis 0.51450327 0.28280942 -0.80950925
10371Axis point 271.86890530 196.87368907 0.00000000
10372Rotation angle (degrees) 168.46727340
10373Shift along axis 1.88951223
10374
10375
10376> close #1008 #1007
10377
10378> define axis #2 name axis_Cb
10379
10380Axis 'rotation axis #2/axis_Cb' centered at [204.54770711 159.86893059
10381105.92183993] with direction [ 0.51450327 0.28280942 -0.80950925], radius
103820.553089, and length 44.2472
10383
10384> rename #2 Cb_rotation_axis id #105.3.1.4
10385
10386> rename #3 Cb_rotation_slabs id #105.3.2.4
10387
10388> rename #105.3 geometry
10389
10390> rename #105.3.1 rotation_axes
10391
10392> rename #105.3.2 rotation_slabs
10393
10394executed CD20_2H7v166_define_pseudo_symmetries.cxc
10395
10396> open CD20_2H7_mutants_define_domain_centroids.cxc
10397
10398> define centroid RTX_C & /L name centroid_RTX_C_L
10399
10400Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556]
10401
10402> rename ##name=centroid_RTX_C_L id 101.3.3.1
10403
10404> define centroid RTX_C & /M name centroid_RTX_C_M
10405
10406Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025]
10407
10408> rename ##name=centroid_RTX_C_M id 101.3.3.2
10409
10410> define centroid RTX_C & /H name centroid_RTX_C_H
10411
10412Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761]
10413
10414> rename ##name=centroid_RTX_C_H id 101.3.3.3
10415
10416> define centroid RTX_C & /I name centroid_RTX_C_I
10417
10418Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456]
10419
10420> rename ##name=centroid_RTX_C_I id 101.3.3.4
10421
10422> define centroid RTX_V & /L name centroid_RTX_V_L
10423
10424Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216]
10425
10426> rename ##name=centroid_RTX_V_L id 101.3.3.5
10427
10428> define centroid RTX_V & /M name centroid_RTX_V_M
10429
10430Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698]
10431
10432> rename ##name=centroid_RTX_V_M id 101.3.3.6
10433
10434> define centroid RTX_V & /H name centroid_RTX_V_H
10435
10436Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601]
10437
10438> rename ##name=centroid_RTX_V_H id 101.3.3.7
10439
10440> define centroid RTX_V & /I name centroid_RTX_V_I
10441
10442Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082]
10443
10444> rename ##name=centroid_RTX_V_I id 101.3.3.8
10445
10446> rename #101.3.3 centroids
10447
10448> define centroid H7v16_C & /L name centroid_2H7v16_C_L
10449
10450Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
10451104.71732873]
10452
10453> rename ##name=centroid_2H7v16_C_L id 102.3.3.1
10454
10455> define centroid H7v16_C & /M name centroid_2H7v16_C_M
10456
10457Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
10458109.46892346]
10459
10460> rename ##name=centroid_2H7v16_C_M id 102.3.3.2
10461
10462> define centroid H7v16_C & /H name centroid_2H7v16_C_H
10463
10464Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
10465100.10963479]
10466
10467> rename ##name=centroid_2H7v16_C_H id 102.3.3.3
10468
10469> define centroid H7v16_C & /I name centroid_2H7v16_C_I
10470
10471Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
10472103.22787118]
10473
10474> rename ##name=centroid_2H7v16_C_I id 102.3.3.4
10475
10476> define centroid H7v16_V & /L name centroid_2H7v16_V_L
10477
10478Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
10479124.64938243]
10480
10481> rename ##name=centroid_2H7v16_V_L id 102.3.3.5
10482
10483> define centroid H7v16_V & /M name centroid_2H7v16_V_M
10484
10485Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
10486126.48898691]
10487
10488> rename ##name=centroid_2H7v16_V_M id 102.3.3.6
10489
10490> define centroid H7v16_V & /H name centroid_2H7v16_V_H
10491
10492Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
10493126.96669027]
10494
10495> rename ##name=centroid_2H7v16_V_H id 102.3.3.7
10496
10497> define centroid H7v16_V & /I name centroid_2H7v16_V_I
10498
10499Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
10500126.76187738]
10501
10502> rename ##name=centroid_2H7v16_V_I id 102.3.3.8
10503
10504> rename #102.3.3 centroids
10505
10506> define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
10507
10508Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
10509111.74271267]
10510
10511> rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
10512
10513> define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
10514
10515Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
10516109.3226675 ]
10517
10518> rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
10519
10520> define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
10521
10522Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
10523105.03944622]
10524
10525> rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
10526
10527> define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
10528
10529Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
10530103.22947676]
10531
10532> rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
10533
10534> define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
10535
10536Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
10537127.91858459]
10538
10539> rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
10540
10541> define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
10542
10543Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
10544127.2169787 ]
10545
10546> rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
10547
10548> define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
10549
10550Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
10551127.54490507]
10552
10553> rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
10554
10555> define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
10556
10557Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
10558127.29650809]
10559
10560> rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
10561
10562> rename #103.3.3 centroids
10563
10564> define centroid CD20 & /C name centroid_CD20_C
10565
10566Centroid 'centroid_CD20_C' placed at [144.71880576 155.32713058 168.44437979]
10567
10568> rename ##name=centroid_CD20_C id 101.3.3.9
10569
10570> define centroid CD20 & /D name centroid_CD20_D
10571
10572Centroid 'centroid_CD20_D' placed at [165.28259991 155.13681165 168.62706115]
10573
10574> rename ##name=centroid_CD20_D id 101.3.3.10
10575
10576executed CD20_2H7_mutants_define_domain_centroids.cxc
10577
10578> turn x 90
10579
10580> view
10581
10582> hide #101 models
10583
10584> hide #!102.2 models
10585
10586> ~ribbon #102.10/X,Y
10587
10588executed CD20_2H7_mutants_setup.cxc
10589
10590> show #!102.2 models
10591
10592> show #!101 models
10593
10594> show #101.1 models
10595
10596> show #!101.3 models
10597
10598> hide #!101 models
10599
10600> hide #!102 models
10601
10602> hide #!103 models
10603
10604> hide #!104 models
10605
10606> hide #!105 models
10607
10608> show #!101 models
10609
10610> show #!102 models
10611
10612> hide #!102 models
10613
10614> show #!102 models
10615
10616> hide #!102.10 models
10617
10618> hide #!102.2 models
10619
10620> hide #!102 models
10621
10622> show #!102 models
10623
10624> hide #!102.3 models
10625
10626> hide #!102 models
10627
10628> show #!102 models
10629
10630> hide #!102 models
10631
10632> show #!102 models
10633
10634> hide #!102 models
10635
10636> show #!102 models
10637
10638> hide #!102 models
10639
10640> show #!102 models
10641
10642> hide #!102 models
10643
10644> show #!102 models
10645
10646> hide #!102 models
10647
10648> show #!102 models
10649
10650> hide #!102 models
10651
10652> show #!102 models
10653
10654> hide #!102 models
10655
10656> open /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A/STR7731.pdb
10657
10658Summary of feedback from opening
10659/Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A/STR7731.pdb
10660---
10661warning | Ignored bad PDB record found on line 1
10662HEADER STR7731 version_1 2024.01.12
10663
10664STR7731.pdb title:
10665Structure of 2H7v166 LC.S92A Fab and Hs_CD20.M1-P297 at 4.5 A resolut ion.
10666[more info...]
10667
10668Chain information for STR7731.pdb #2
10669---
10670Chain | Description
10671C | No description available
10672D | No description available
10673H I | No description available
10674L | No description available
10675M | No description available
10676
10677
10678> select ~sel & ##selected
10679
10680Nothing selected
10681
10682> matchmaker #2/C,D to #101/C,D
10683
10684Parameters
10685---
10686Chain pairing | bb
10687Alignment algorithm | Needleman-Wunsch
10688Similarity matrix | BLOSUM-62
10689SS fraction | 0.3
10690Gap open (HH/SS/other) | 18/18/6
10691Gap extend | 1
10692SS matrix | | | H | S | O
10693---|---|---|---
10694H | 6 | -9 | -6
10695S | | 6 | -6
10696O | | | 4
10697Iteration cutoff | 2
10698
10699Matchmaker CD20_RTX, chain D (#101.1) with STR7731.pdb, chain D (#2), sequence
10700alignment score = 1147.4
10701RMSD between 149 pruned atom pairs is 0.818 angstroms; (across all 158 pairs:
107021.025)
10703
10704
10705> view matrix
10706
10707view matrix camera
107080.97626,0.15017,0.1561,198.03,-0.2019,0.36983,0.9069,440.11,0.078453,-0.91688,0.39137,230.3
10709view matrix models
10710#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,#104.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#105,1,0,0,0,0,1,0,0,0,0,1,0,#105.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.2,-0.024025,0.77304,0.6339,-141.69,0.99715,-0.026789,0.070462,-68.674,0.071451,0.63379,-0.7702,173,#105.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#2,-1,-0.0003813,0.0027977,355.86,0.0003427,-0.9999,-0.013785,358.24,0.0028027,-0.013784,0.9999,-35.444
10711
10712
10713> save
10714> /Users/rohoua/work/Genentech/CD20/CD20_2H7v166_S92A/STR7731_alito6vja.pdb
10715> models #2
10716
10717> view matrix
10718
10719view matrix camera
107200.97626,0.15017,0.1561,198.03,-0.2019,0.36983,0.9069,440.11,0.078453,-0.91688,0.39137,230.3
10721view matrix models
10722#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,#104.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#105,1,0,0,0,0,1,0,0,0,0,1,0,#105.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.2,-0.024025,0.77304,0.6339,-141.69,0.99715,-0.026789,0.070462,-68.674,0.071451,0.63379,-0.7702,173,#105.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#105.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#2,-1,-0.0003813,0.0027977,355.86,0.0003427,-0.9999,-0.013785,358.24,0.0028027,-0.013784,0.9999,-35.444
10723
10724
10725
10726
10727
10728OpenGL version: 4.1 Metal - 83.1
10729OpenGL renderer: Apple M2
10730OpenGL vendor: Apple
10731
10732Python: 3.11.2
10733Locale: UTF-8
10734Qt version: PyQt6 6.3.1, Qt 6.3.1
10735Qt runtime version: 6.3.2
10736Qt platform: cocoa
10737Hardware:
10738
10739 Hardware Overview:
10740
10741 Model Name: MacBook Pro
10742 Model Identifier: Mac14,7
10743 Model Number: Z16T0006PLL/A
10744 Chip: Apple M2
10745 Total Number of Cores: 8 (4 performance and 4 efficiency)
10746 Memory: 16 GB
10747 System Firmware Version: 10151.61.4
10748 OS Loader Version: 8422.141.2.700.1
10749
10750Software:
10751
10752 System Software Overview:
10753
10754 System Version: macOS 13.6.1 (22G313)
10755 Kernel Version: Darwin 22.6.0
10756 Time since boot: 26 days, 21 hours, 57 minutes
10757
10758Graphics/Displays:
10759
10760 Apple M2:
10761
10762 Chipset Model: Apple M2
10763 Type: GPU
10764 Bus: Built-In
10765 Total Number of Cores: 10
10766 Vendor: Apple (0x106b)
10767 Metal Support: Metal 3
10768 Displays:
10769 Color LCD:
10770 Display Type: Built-In Retina LCD
10771 Resolution: 2560 x 1600 Retina
10772 Main Display: Yes
10773 Mirror: Off
10774 Online: Yes
10775 Automatically Adjust Brightness: Yes
10776 Connection Type: Internal
10777
10778
10779Installed Packages:
10780 alabaster: 0.7.16
10781 appdirs: 1.4.4
10782 appnope: 0.1.3
10783 asttokens: 2.4.1
10784 Babel: 2.14.0
10785 backcall: 0.2.0
10786 beautifulsoup4: 4.11.2
10787 blockdiag: 3.0.0
10788 blosc2: 2.0.0
10789 build: 0.10.0
10790 certifi: 2022.12.7
10791 cftime: 1.6.3
10792 charset-normalizer: 3.3.2
10793 ChimeraX-AddCharge: 1.5.13
10794 ChimeraX-AddH: 2.2.5
10795 ChimeraX-AlignmentAlgorithms: 2.0.1
10796 ChimeraX-AlignmentHdrs: 3.4.1
10797 ChimeraX-AlignmentMatrices: 2.1
10798 ChimeraX-Alignments: 2.12.2
10799 ChimeraX-AlphaFold: 1.0
10800 ChimeraX-AltlocExplorer: 1.1.1
10801 ChimeraX-AmberInfo: 1.0
10802 ChimeraX-Arrays: 1.1
10803 ChimeraX-Atomic: 1.49.1
10804 ChimeraX-AtomicLibrary: 12.1.5
10805 ChimeraX-AtomSearch: 2.0.1
10806 ChimeraX-AxesPlanes: 2.3.2
10807 ChimeraX-BasicActions: 1.1.2
10808 ChimeraX-BILD: 1.0
10809 ChimeraX-BlastProtein: 2.1.2
10810 ChimeraX-BondRot: 2.0.4
10811 ChimeraX-BugReporter: 1.0.1
10812 ChimeraX-BuildStructure: 2.10.5
10813 ChimeraX-Bumps: 1.0
10814 ChimeraX-BundleBuilder: 1.2.2
10815 ChimeraX-ButtonPanel: 1.0.1
10816 ChimeraX-CageBuilder: 1.0.1
10817 ChimeraX-CellPack: 1.0
10818 ChimeraX-Centroids: 1.3.2
10819 ChimeraX-ChangeChains: 1.1
10820 ChimeraX-CheckWaters: 1.3.2
10821 ChimeraX-ChemGroup: 2.0.1
10822 ChimeraX-Clashes: 2.2.4
10823 ChimeraX-Clipper: 0.22.2
10824 ChimeraX-ColorActions: 1.0.3
10825 ChimeraX-ColorGlobe: 1.0
10826 ChimeraX-ColorKey: 1.5.5
10827 ChimeraX-CommandLine: 1.2.5
10828 ChimeraX-ConnectStructure: 2.0.1
10829 ChimeraX-Contacts: 1.0.1
10830 ChimeraX-Core: 1.7.1
10831 ChimeraX-CoreFormats: 1.2
10832 ChimeraX-coulombic: 1.4.2
10833 ChimeraX-Crosslinks: 1.0
10834 ChimeraX-Crystal: 1.0
10835 ChimeraX-CrystalContacts: 1.0.1
10836 ChimeraX-DataFormats: 1.2.3
10837 ChimeraX-Dicom: 1.2
10838 ChimeraX-DistMonitor: 1.4
10839 ChimeraX-DockPrep: 1.1.3
10840 ChimeraX-Dssp: 2.0
10841 ChimeraX-EMDB-SFF: 1.0
10842 ChimeraX-ESMFold: 1.0
10843 ChimeraX-FileHistory: 1.0.1
10844 ChimeraX-FunctionKey: 1.0.1
10845 ChimeraX-Geometry: 1.3
10846 ChimeraX-gltf: 1.0
10847 ChimeraX-Graphics: 1.1.1
10848 ChimeraX-Hbonds: 2.4
10849 ChimeraX-Help: 1.2.2
10850 ChimeraX-HKCage: 1.3
10851 ChimeraX-IHM: 1.1
10852 ChimeraX-ImageFormats: 1.2
10853 ChimeraX-IMOD: 1.0
10854 ChimeraX-IO: 1.0.1
10855 ChimeraX-ISOLDE: 1.7rc1
10856 ChimeraX-ItemsInspection: 1.0.1
10857 ChimeraX-IUPAC: 1.0
10858 ChimeraX-Label: 1.1.8
10859 ChimeraX-ListInfo: 1.2.2
10860 ChimeraX-Log: 1.1.6
10861 ChimeraX-LookingGlass: 1.1
10862 ChimeraX-Maestro: 1.9.1
10863 ChimeraX-Map: 1.1.4
10864 ChimeraX-MapData: 2.0
10865 ChimeraX-MapEraser: 1.0.1
10866 ChimeraX-MapFilter: 2.0.1
10867 ChimeraX-MapFit: 2.0
10868 ChimeraX-MapSeries: 2.1.1
10869 ChimeraX-Markers: 1.0.1
10870 ChimeraX-Mask: 1.0.2
10871 ChimeraX-MatchMaker: 2.1.2
10872 ChimeraX-MCopy: 1.0
10873 ChimeraX-MDcrds: 2.6.1
10874 ChimeraX-MedicalToolbar: 1.0.2
10875 ChimeraX-Meeting: 1.0.1
10876 ChimeraX-MLP: 1.1.1
10877 ChimeraX-mmCIF: 2.12.1
10878 ChimeraX-MMTF: 2.2
10879 ChimeraX-Modeller: 1.5.14
10880 ChimeraX-ModelPanel: 1.4
10881 ChimeraX-ModelSeries: 1.0.1
10882 ChimeraX-Mol2: 2.0.3
10883 ChimeraX-Mole: 1.0
10884 ChimeraX-Morph: 1.0.2
10885 ChimeraX-MouseModes: 1.2
10886 ChimeraX-Movie: 1.0
10887 ChimeraX-Neuron: 1.0
10888 ChimeraX-Nifti: 1.1
10889 ChimeraX-NRRD: 1.1
10890 ChimeraX-Nucleotides: 2.0.3
10891 ChimeraX-OpenCommand: 1.13.1
10892 ChimeraX-PDB: 2.7.3
10893 ChimeraX-PDBBio: 1.0.1
10894 ChimeraX-PDBLibrary: 1.0.4
10895 ChimeraX-PDBMatrices: 1.0
10896 ChimeraX-PickBlobs: 1.0.1
10897 ChimeraX-Positions: 1.0
10898 ChimeraX-PresetMgr: 1.1
10899 ChimeraX-PubChem: 2.1
10900 ChimeraX-ReadPbonds: 1.0.1
10901 ChimeraX-Registration: 1.1.2
10902 ChimeraX-RemoteControl: 1.0
10903 ChimeraX-RenderByAttr: 1.1
10904 ChimeraX-RenumberResidues: 1.1
10905 ChimeraX-ResidueFit: 1.0.1
10906 ChimeraX-RestServer: 1.2
10907 ChimeraX-RNALayout: 1.0
10908 ChimeraX-RotamerLibMgr: 4.0
10909 ChimeraX-RotamerLibsDunbrack: 2.0
10910 ChimeraX-RotamerLibsDynameomics: 2.0
10911 ChimeraX-RotamerLibsRichardson: 2.0
10912 ChimeraX-SaveCommand: 1.5.1
10913 ChimeraX-SchemeMgr: 1.0
10914 ChimeraX-SDF: 2.0.2
10915 ChimeraX-Segger: 1.0
10916 ChimeraX-Segment: 1.0.1
10917 ChimeraX-SelInspector: 1.0
10918 ChimeraX-SeqView: 2.11
10919 ChimeraX-Shape: 1.0.1
10920 ChimeraX-Shell: 1.0.1
10921 ChimeraX-Shortcuts: 1.1.1
10922 ChimeraX-ShowSequences: 1.0.2
10923 ChimeraX-SideView: 1.0.1
10924 ChimeraX-Smiles: 2.1.2
10925 ChimeraX-SmoothLines: 1.0
10926 ChimeraX-SpaceNavigator: 1.0
10927 ChimeraX-StdCommands: 1.12.4
10928 ChimeraX-STL: 1.0.1
10929 ChimeraX-Storm: 1.0
10930 ChimeraX-StructMeasure: 1.1.2
10931 ChimeraX-Struts: 1.0.1
10932 ChimeraX-Surface: 1.0.1
10933 ChimeraX-SwapAA: 2.0.1
10934 ChimeraX-SwapRes: 2.2.2
10935 ChimeraX-TapeMeasure: 1.0
10936 ChimeraX-TaskManager: 1.0
10937 ChimeraX-Test: 1.0
10938 ChimeraX-Toolbar: 1.1.2
10939 ChimeraX-ToolshedUtils: 1.2.4
10940 ChimeraX-Topography: 1.0
10941 ChimeraX-ToQuest: 1.0
10942 ChimeraX-Tug: 1.0.1
10943 ChimeraX-UI: 1.33.3
10944 ChimeraX-uniprot: 2.3
10945 ChimeraX-UnitCell: 1.0.1
10946 ChimeraX-ViewDockX: 1.3.2
10947 ChimeraX-VIPERdb: 1.0
10948 ChimeraX-Vive: 1.1
10949 ChimeraX-VolumeMenu: 1.0.1
10950 ChimeraX-vrml: 1.0
10951 ChimeraX-VTK: 1.0
10952 ChimeraX-WavefrontOBJ: 1.0
10953 ChimeraX-WebCam: 1.0.2
10954 ChimeraX-WebServices: 1.1.3
10955 ChimeraX-Zone: 1.0.1
10956 colorama: 0.4.6
10957 comm: 0.2.1
10958 contourpy: 1.2.0
10959 cxservices: 1.2.2
10960 cycler: 0.12.1
10961 Cython: 0.29.33
10962 debugpy: 1.8.0
10963 decorator: 5.1.1
10964 docutils: 0.19
10965 executing: 2.0.1
10966 filelock: 3.9.0
10967 fonttools: 4.47.2
10968 funcparserlib: 2.0.0a0
10969 glfw: 2.6.4
10970 grako: 3.16.5
10971 h5py: 3.10.0
10972 html2text: 2020.1.16
10973 idna: 3.6
10974 ihm: 0.38
10975 imagecodecs: 2023.9.18
10976 imagesize: 1.4.1
10977 ipykernel: 6.23.2
10978 ipython: 8.14.0
10979 ipython-genutils: 0.2.0
10980 ipywidgets: 8.1.1
10981 jedi: 0.18.2
10982 Jinja2: 3.1.2
10983 jupyter-client: 8.2.0
10984 jupyter-core: 5.7.1
10985 jupyterlab-widgets: 3.0.9
10986 kiwisolver: 1.4.5
10987 line-profiler: 4.0.2
10988 lxml: 4.9.2
10989 lz4: 4.3.2
10990 MarkupSafe: 2.1.4
10991 matplotlib: 3.7.2
10992 matplotlib-inline: 0.1.6
10993 msgpack: 1.0.4
10994 nest-asyncio: 1.6.0
10995 netCDF4: 1.6.2
10996 networkx: 3.1
10997 nibabel: 5.0.1
10998 nptyping: 2.5.0
10999 numexpr: 2.8.8
11000 numpy: 1.25.1
11001 openvr: 1.23.701
11002 packaging: 21.3
11003 ParmEd: 3.4.3
11004 parso: 0.8.3
11005 pep517: 0.13.0
11006 pexpect: 4.9.0
11007 pickleshare: 0.7.5
11008 pillow: 10.2.0
11009 pip: 23.0
11010 pkginfo: 1.9.6
11011 platformdirs: 4.1.0
11012 prompt-toolkit: 3.0.43
11013 psutil: 5.9.5
11014 ptyprocess: 0.7.0
11015 pure-eval: 0.2.2
11016 py-cpuinfo: 9.0.0
11017 pycollada: 0.7.2
11018 pydicom: 2.3.0
11019 Pygments: 2.16.1
11020 pynrrd: 1.0.0
11021 PyOpenGL: 3.1.7
11022 PyOpenGL-accelerate: 3.1.7
11023 pyopenxr: 1.0.2801
11024 pyparsing: 3.0.9
11025 pyproject-hooks: 1.0.0
11026 PyQt6-commercial: 6.3.1
11027 PyQt6-Qt6: 6.3.2
11028 PyQt6-sip: 13.4.0
11029 PyQt6-WebEngine-commercial: 6.3.1
11030 PyQt6-WebEngine-Qt6: 6.3.2
11031 python-dateutil: 2.8.2
11032 pytz: 2023.3.post1
11033 pyzmq: 25.1.2
11034 qtconsole: 5.4.3
11035 QtPy: 2.4.1
11036 RandomWords: 0.4.0
11037 requests: 2.31.0
11038 scipy: 1.11.1
11039 setuptools: 67.4.0
11040 setuptools-scm: 7.0.5
11041 sfftk-rw: 0.7.3
11042 six: 1.16.0
11043 snowballstemmer: 2.2.0
11044 sortedcontainers: 2.4.0
11045 soupsieve: 2.5
11046 sphinx: 6.1.3
11047 sphinx-autodoc-typehints: 1.22
11048 sphinxcontrib-applehelp: 1.0.8
11049 sphinxcontrib-blockdiag: 3.0.0
11050 sphinxcontrib-devhelp: 1.0.6
11051 sphinxcontrib-htmlhelp: 2.0.5
11052 sphinxcontrib-jsmath: 1.0.1
11053 sphinxcontrib-qthelp: 1.0.7
11054 sphinxcontrib-serializinghtml: 1.1.10
11055 stack-data: 0.6.3
11056 superqt: 0.5.0
11057 tables: 3.8.0
11058 tcia-utils: 1.5.1
11059 tifffile: 2023.7.18
11060 tinyarray: 1.2.4
11061 tomli: 2.0.1
11062 tornado: 6.4
11063 traitlets: 5.9.0
11064 typing-extensions: 4.9.0
11065 tzdata: 2023.4
11066 urllib3: 2.1.0
11067 wcwidth: 0.2.13
11068 webcolors: 1.12
11069 wheel: 0.38.4
11070 wheel-filename: 1.4.1
11071 widgetsnbextension: 4.0.9