Changes between Initial Version and Version 1 of Ticket #15615


Ignore:
Timestamp:
Jul 16, 2024, 1:59:20 PM (15 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #15615

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash changing display configuration on Mac

  • Ticket #15615 – Description

    initial v1  
    5353  "threads" : 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     55[deleted to fit within ticket limits]
    155056],
    155157  "sharedCache" : {
    … …  
    40742580 
    40752581
    4076 > hide sel cartoons
    4077 
    4078 > color #52 dodgerblue
    4079 
    4080 > color #53 dodgerblue
    4081 
    4082 > color #54 #00b305ff
    4083 
    4084 > color #55 #00b305ff
    4085 
    4086 > color #56 #f15839ff
    4087 
    4088 > select #1.12/A
    4089 
    4090 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4091 
    4092 > show sel cartoons
    4093 
    4094 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4095 
    4096 Chain information for AF3 E1 1-421.pdb #57 
    4097 --- 
    4098 Chain | Description 
    4099 A | No description available 
    4100  
    4101 
    4102 > matchmaker #57 to #1.12 & sel
    4103 
    4104 Parameters 
    4105 --- 
    4106 Chain pairing | bb 
    4107 Alignment algorithm | Needleman-Wunsch 
    4108 Similarity matrix | BLOSUM-62 
    4109 SS fraction | 0.3 
    4110 Gap open (HH/SS/other) | 18/18/6 
    4111 Gap extend | 1 
    4112 SS matrix |  |  | H | S | O 
    4113 ---|---|---|--- 
    4114 H | 6 | -9 | -6 
    4115 S |  | 6 | -6 
    4116 O |  |  | 4 
    4117 Iteration cutoff | 2 
    4118  
    4119 Matchmaker 3j0c.pdb1, chain A (#1.12) with AF3 E1 1-421.pdb, chain A (#57),
    4120 sequence alignment score = 1060.7 
    4121 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4122 3.020) 
    4123  
    4124 
    4125 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4126 
    4127 Chain information for AF3 E1 422-461.pdb #58 
    4128 --- 
    4129 Chain | Description 
    4130 A | No description available 
    4131  
    4132 
    4133 > matchmaker #58 to #1.12 & sel
    4134 
    4135 Parameters 
    4136 --- 
    4137 Chain pairing | bb 
    4138 Alignment algorithm | Needleman-Wunsch 
    4139 Similarity matrix | BLOSUM-62 
    4140 SS fraction | 0.3 
    4141 Gap open (HH/SS/other) | 18/18/6 
    4142 Gap extend | 1 
    4143 SS matrix |  |  | H | S | O 
    4144 ---|---|---|--- 
    4145 H | 6 | -9 | -6 
    4146 S |  | 6 | -6 
    4147 O |  |  | 4 
    4148 Iteration cutoff | 2 
    4149  
    4150 Matchmaker 3j0c.pdb1, chain A (#1.12) with AF3 E1 422-461.pdb, chain A (#58),
    4151 sequence alignment score = 626.9 
    4152 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    4153 2.776) 
    4154  
    4155 
    4156 > hide sel cartoons
    4157 
    4158 > select #1.12/B
    4159 
    4160 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4161 
    4162 > show sel cartoons
    4163 
    4164 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4165 
    4166 Chain information for AF3 E2 1-352.pdb #59 
    4167 --- 
    4168 Chain | Description 
    4169 B | No description available 
    4170  
    4171 
    4172 > matchmaker #59 to #1.12 & sel
    4173 
    4174 Parameters 
    4175 --- 
    4176 Chain pairing | bb 
    4177 Alignment algorithm | Needleman-Wunsch 
    4178 Similarity matrix | BLOSUM-62 
    4179 SS fraction | 0.3 
    4180 Gap open (HH/SS/other) | 18/18/6 
    4181 Gap extend | 1 
    4182 SS matrix |  |  | H | S | O 
    4183 ---|---|---|--- 
    4184 H | 6 | -9 | -6 
    4185 S |  | 6 | -6 
    4186 O |  |  | 4 
    4187 Iteration cutoff | 2 
    4188  
    4189 Matchmaker 3j0c.pdb1, chain B (#1.12) with AF3 E2 1-352.pdb, chain B (#59),
    4190 sequence alignment score = 583.7 
    4191 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4192 5.933) 
    4193  
    4194 
    4195 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4196 
    4197 Chain information for AF3 E2 353-438.pdb #60 
    4198 --- 
    4199 Chain | Description 
    4200 B | No description available 
    4201  
    4202 
    4203 > matchmaker #60 to #1.12 & sel
    4204 
    4205 Parameters 
    4206 --- 
    4207 Chain pairing | bb 
    4208 Alignment algorithm | Needleman-Wunsch 
    4209 Similarity matrix | BLOSUM-62 
    4210 SS fraction | 0.3 
    4211 Gap open (HH/SS/other) | 18/18/6 
    4212 Gap extend | 1 
    4213 SS matrix |  |  | H | S | O 
    4214 ---|---|---|--- 
    4215 H | 6 | -9 | -6 
    4216 S |  | 6 | -6 
    4217 O |  |  | 4 
    4218 Iteration cutoff | 2 
    4219  
    4220 Matchmaker 3j0c.pdb1, chain B (#1.12) with AF3 E2 353-438.pdb, chain B (#60),
    4221 sequence alignment score = 333.4 
    4222 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4223 8.411) 
    4224  
    4225 
    4226 > hide sel cartoons
    4227 
    4228 > select #1.12/C
    4229 
    4230 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4231 
    4232 > show sel cartoons
    4233 
    4234 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4235 
    4236 Chain information for AF3 CA.pdb #61 
    4237 --- 
    4238 Chain | Description 
    4239 A | No description available 
    4240  
    4241 
    4242 > matchmaker #61 to #1.12 & sel
    4243 
    4244 Parameters 
    4245 --- 
    4246 Chain pairing | bb 
    4247 Alignment algorithm | Needleman-Wunsch 
    4248 Similarity matrix | BLOSUM-62 
    4249 SS fraction | 0.3 
    4250 Gap open (HH/SS/other) | 18/18/6 
    4251 Gap extend | 1 
    4252 SS matrix |  |  | H | S | O 
    4253 ---|---|---|--- 
    4254 H | 6 | -9 | -6 
    4255 S |  | 6 | -6 
    4256 O |  |  | 4 
    4257 Iteration cutoff | 2 
    4258  
    4259 Matchmaker 3j0c.pdb1, chain C (#1.12) with AF3 CA.pdb, chain A (#61), sequence
    4260 alignment score = 328.1 
    4261 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4262 2.714) 
    4263  
    4264 
    4265 > hide sel cartoons
    4266 
    4267 > hide #57 models
    4268 
    4269 > show #57 models
    4270 
    4271 > color #57 dodgerblue
    4272 
    4273 > color #58 dodgerblue
    4274 
    4275 > color #59 #00b305ff
    4276 
    4277 > color #60 #00b305ff
    4278 
    4279 > color #61 #f15839ff
    4280 
    4281 > select #1.13/A
    4282 
    4283 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4284 
    4285 > show sel cartoons
    4286 
    4287 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4288 
    4289 Chain information for AF3 E1 1-421.pdb #62 
    4290 --- 
    4291 Chain | Description 
    4292 A | No description available 
    4293  
    4294 
    4295 > matchmaker #62 to #1.12 & sel
    4296 
    4297 No 'to' model specified 
    4298 
    4299 > matchmaker #62 to #1.13 & sel
    4300 
    4301 Parameters 
    4302 --- 
    4303 Chain pairing | bb 
    4304 Alignment algorithm | Needleman-Wunsch 
    4305 Similarity matrix | BLOSUM-62 
    4306 SS fraction | 0.3 
    4307 Gap open (HH/SS/other) | 18/18/6 
    4308 Gap extend | 1 
    4309 SS matrix |  |  | H | S | O 
    4310 ---|---|---|--- 
    4311 H | 6 | -9 | -6 
    4312 S |  | 6 | -6 
    4313 O |  |  | 4 
    4314 Iteration cutoff | 2 
    4315  
    4316 Matchmaker 3j0c.pdb1, chain A (#1.13) with AF3 E1 1-421.pdb, chain A (#62),
    4317 sequence alignment score = 1060.7 
    4318 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4319 3.020) 
    4320  
    4321 
    4322 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4323 
    4324 Chain information for AF3 E1 422-461.pdb #63 
    4325 --- 
    4326 Chain | Description 
    4327 A | No description available 
    4328  
    4329 
    4330 > matchmaker #63 to #1.13 & sel
    4331 
    4332 Parameters 
    4333 --- 
    4334 Chain pairing | bb 
    4335 Alignment algorithm | Needleman-Wunsch 
    4336 Similarity matrix | BLOSUM-62 
    4337 SS fraction | 0.3 
    4338 Gap open (HH/SS/other) | 18/18/6 
    4339 Gap extend | 1 
    4340 SS matrix |  |  | H | S | O 
    4341 ---|---|---|--- 
    4342 H | 6 | -9 | -6 
    4343 S |  | 6 | -6 
    4344 O |  |  | 4 
    4345 Iteration cutoff | 2 
    4346  
    4347 Matchmaker 3j0c.pdb1, chain A (#1.13) with AF3 E1 422-461.pdb, chain A (#63),
    4348 sequence alignment score = 626.9 
    4349 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    4350 2.775) 
    4351  
    4352 
    4353 > hide sel cartoons
    4354 
    4355 > select #1.13/B
    4356 
    4357 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4358 
    4359 > show sel cartoons
    4360 
    4361 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4362 
    4363 Chain information for AF3 E2 1-352.pdb #64 
    4364 --- 
    4365 Chain | Description 
    4366 B | No description available 
    4367  
    4368 
    4369 > matchmaker #64 to #1.13 & sel
    4370 
    4371 Parameters 
    4372 --- 
    4373 Chain pairing | bb 
    4374 Alignment algorithm | Needleman-Wunsch 
    4375 Similarity matrix | BLOSUM-62 
    4376 SS fraction | 0.3 
    4377 Gap open (HH/SS/other) | 18/18/6 
    4378 Gap extend | 1 
    4379 SS matrix |  |  | H | S | O 
    4380 ---|---|---|--- 
    4381 H | 6 | -9 | -6 
    4382 S |  | 6 | -6 
    4383 O |  |  | 4 
    4384 Iteration cutoff | 2 
    4385  
    4386 Matchmaker 3j0c.pdb1, chain B (#1.13) with AF3 E2 1-352.pdb, chain B (#64),
    4387 sequence alignment score = 583.7 
    4388 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4389 5.933) 
    4390  
    4391 
    4392 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4393 
    4394 Chain information for AF3 E2 353-438.pdb #65 
    4395 --- 
    4396 Chain | Description 
    4397 B | No description available 
    4398  
    4399 
    4400 > matchmaker #65 to #1.13 & sel
    4401 
    4402 Parameters 
    4403 --- 
    4404 Chain pairing | bb 
    4405 Alignment algorithm | Needleman-Wunsch 
    4406 Similarity matrix | BLOSUM-62 
    4407 SS fraction | 0.3 
    4408 Gap open (HH/SS/other) | 18/18/6 
    4409 Gap extend | 1 
    4410 SS matrix |  |  | H | S | O 
    4411 ---|---|---|--- 
    4412 H | 6 | -9 | -6 
    4413 S |  | 6 | -6 
    4414 O |  |  | 4 
    4415 Iteration cutoff | 2 
    4416  
    4417 Matchmaker 3j0c.pdb1, chain B (#1.13) with AF3 E2 353-438.pdb, chain B (#65),
    4418 sequence alignment score = 322.6 
    4419 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4420 8.411) 
    4421  
    4422 
    4423 > select #1.13/C
    4424 
    4425 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4426 
    4427 > show sel cartoons
    4428 
    4429 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4430 
    4431 Chain information for AF3 CA.pdb #66 
    4432 --- 
    4433 Chain | Description 
    4434 A | No description available 
    4435  
    4436 
    4437 > matchmaker #66 to #1.13 & sel
    4438 
    4439 Parameters 
    4440 --- 
    4441 Chain pairing | bb 
    4442 Alignment algorithm | Needleman-Wunsch 
    4443 Similarity matrix | BLOSUM-62 
    4444 SS fraction | 0.3 
    4445 Gap open (HH/SS/other) | 18/18/6 
    4446 Gap extend | 1 
    4447 SS matrix |  |  | H | S | O 
    4448 ---|---|---|--- 
    4449 H | 6 | -9 | -6 
    4450 S |  | 6 | -6 
    4451 O |  |  | 4 
    4452 Iteration cutoff | 2 
    4453  
    4454 Matchmaker 3j0c.pdb1, chain C (#1.13) with AF3 CA.pdb, chain A (#66), sequence
    4455 alignment score = 328.1 
    4456 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4457 2.714) 
    4458  
    4459 
    4460 > hide sel cartoons
    4461 
    4462 > select #1.13/B
    4463 
    4464 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4465 
    4466 > hide sel cartoons
    4467 
    4468 > color #62 dodgerblue
    4469 
    4470 > color #63 dodgerblue
    4471 
    4472 > color #64 #00b305ff
    4473 
    4474 > color #65 #00b305ff
    4475 
    4476 > color #66 #f15839ff
    4477 
    4478 > select #1.14/A
    4479 
    4480 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4481 
    4482 > show sel cartoons
    4483 
    4484 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4485 
    4486 Chain information for AF3 E1 1-421.pdb #67 
    4487 --- 
    4488 Chain | Description 
    4489 A | No description available 
    4490  
    4491 
    4492 > matchmaker #67 to #1.13 & sel
    4493 
    4494 No 'to' model specified 
    4495 
    4496 > matchmaker #67 to #1.14 & sel
    4497 
    4498 Parameters 
    4499 --- 
    4500 Chain pairing | bb 
    4501 Alignment algorithm | Needleman-Wunsch 
    4502 Similarity matrix | BLOSUM-62 
    4503 SS fraction | 0.3 
    4504 Gap open (HH/SS/other) | 18/18/6 
    4505 Gap extend | 1 
    4506 SS matrix |  |  | H | S | O 
    4507 ---|---|---|--- 
    4508 H | 6 | -9 | -6 
    4509 S |  | 6 | -6 
    4510 O |  |  | 4 
    4511 Iteration cutoff | 2 
    4512  
    4513 Matchmaker 3j0c.pdb1, chain A (#1.14) with AF3 E1 1-421.pdb, chain A (#67),
    4514 sequence alignment score = 1060.7 
    4515 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4516 3.020) 
    4517  
    4518 
    4519 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4520 
    4521 Chain information for AF3 E1 422-461.pdb #68 
    4522 --- 
    4523 Chain | Description 
    4524 A | No description available 
    4525  
    4526 
    4527 > matchmaker #68 to #1.14 & sel
    4528 
    4529 Parameters 
    4530 --- 
    4531 Chain pairing | bb 
    4532 Alignment algorithm | Needleman-Wunsch 
    4533 Similarity matrix | BLOSUM-62 
    4534 SS fraction | 0.3 
    4535 Gap open (HH/SS/other) | 18/18/6 
    4536 Gap extend | 1 
    4537 SS matrix |  |  | H | S | O 
    4538 ---|---|---|--- 
    4539 H | 6 | -9 | -6 
    4540 S |  | 6 | -6 
    4541 O |  |  | 4 
    4542 Iteration cutoff | 2 
    4543  
    4544 Matchmaker 3j0c.pdb1, chain A (#1.14) with AF3 E1 422-461.pdb, chain A (#68),
    4545 sequence alignment score = 626.9 
    4546 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    4547 2.775) 
    4548  
    4549 
    4550 > hide sel cartoons
    4551 
    4552 > select #1.14/B
    4553 
    4554 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4555 
    4556 > show sel cartoons
    4557 
    4558 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4559 
    4560 Chain information for AF3 E2 1-352.pdb #69 
    4561 --- 
    4562 Chain | Description 
    4563 B | No description available 
    4564  
    4565 
    4566 > matchmaker #69 to #1.14 & sel
    4567 
    4568 Parameters 
    4569 --- 
    4570 Chain pairing | bb 
    4571 Alignment algorithm | Needleman-Wunsch 
    4572 Similarity matrix | BLOSUM-62 
    4573 SS fraction | 0.3 
    4574 Gap open (HH/SS/other) | 18/18/6 
    4575 Gap extend | 1 
    4576 SS matrix |  |  | H | S | O 
    4577 ---|---|---|--- 
    4578 H | 6 | -9 | -6 
    4579 S |  | 6 | -6 
    4580 O |  |  | 4 
    4581 Iteration cutoff | 2 
    4582  
    4583 Matchmaker 3j0c.pdb1, chain B (#1.14) with AF3 E2 1-352.pdb, chain B (#69),
    4584 sequence alignment score = 583.7 
    4585 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4586 5.933) 
    4587  
    4588 
    4589 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4590 
    4591 Chain information for AF3 E2 353-438.pdb #70 
    4592 --- 
    4593 Chain | Description 
    4594 B | No description available 
    4595  
    4596 
    4597 > matchmaker #70 to #1.14 & sel
    4598 
    4599 Parameters 
    4600 --- 
    4601 Chain pairing | bb 
    4602 Alignment algorithm | Needleman-Wunsch 
    4603 Similarity matrix | BLOSUM-62 
    4604 SS fraction | 0.3 
    4605 Gap open (HH/SS/other) | 18/18/6 
    4606 Gap extend | 1 
    4607 SS matrix |  |  | H | S | O 
    4608 ---|---|---|--- 
    4609 H | 6 | -9 | -6 
    4610 S |  | 6 | -6 
    4611 O |  |  | 4 
    4612 Iteration cutoff | 2 
    4613  
    4614 Matchmaker 3j0c.pdb1, chain B (#1.14) with AF3 E2 353-438.pdb, chain B (#70),
    4615 sequence alignment score = 322.6 
    4616 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4617 8.411) 
    4618  
    4619 
    4620 > hide sel cartoons
    4621 
    4622 > select #1.14/C
    4623 
    4624 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4625 
    4626 > show sel cartoons
    4627 
    4628 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4629 
    4630 Chain information for AF3 CA.pdb #71 
    4631 --- 
    4632 Chain | Description 
    4633 A | No description available 
    4634  
    4635 
    4636 > matchmaker #71 to #1.14 & sel
    4637 
    4638 Parameters 
    4639 --- 
    4640 Chain pairing | bb 
    4641 Alignment algorithm | Needleman-Wunsch 
    4642 Similarity matrix | BLOSUM-62 
    4643 SS fraction | 0.3 
    4644 Gap open (HH/SS/other) | 18/18/6 
    4645 Gap extend | 1 
    4646 SS matrix |  |  | H | S | O 
    4647 ---|---|---|--- 
    4648 H | 6 | -9 | -6 
    4649 S |  | 6 | -6 
    4650 O |  |  | 4 
    4651 Iteration cutoff | 2 
    4652  
    4653 Matchmaker 3j0c.pdb1, chain C (#1.14) with AF3 CA.pdb, chain A (#71), sequence
    4654 alignment score = 328.1 
    4655 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4656 2.714) 
    4657  
    4658 
    4659 > hide sel cartoons
    4660 
    4661 > color #67 dodgerblue
    4662 
    4663 > color #68 dodgerblue
    4664 
    4665 > color #69 #00b305ff
    4666 
    4667 > color #70 #00b305ff
    4668 
    4669 > color #71 #f15839ff
    4670 
    4671 > select #1.15/A
    4672 
    4673 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4674 
    4675 > show sel cartoons
    4676 
    4677 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4678 
    4679 Chain information for AF3 E1 1-421.pdb #72 
    4680 --- 
    4681 Chain | Description 
    4682 A | No description available 
    4683  
    4684 
    4685 > matchmaker #72 to #1.15 & sel
    4686 
    4687 Parameters 
    4688 --- 
    4689 Chain pairing | bb 
    4690 Alignment algorithm | Needleman-Wunsch 
    4691 Similarity matrix | BLOSUM-62 
    4692 SS fraction | 0.3 
    4693 Gap open (HH/SS/other) | 18/18/6 
    4694 Gap extend | 1 
    4695 SS matrix |  |  | H | S | O 
    4696 ---|---|---|--- 
    4697 H | 6 | -9 | -6 
    4698 S |  | 6 | -6 
    4699 O |  |  | 4 
    4700 Iteration cutoff | 2 
    4701  
    4702 Matchmaker 3j0c.pdb1, chain A (#1.15) with AF3 E1 1-421.pdb, chain A (#72),
    4703 sequence alignment score = 1060.7 
    4704 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4705 3.020) 
    4706  
    4707 
    4708 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4709 
    4710 Chain information for AF3 E1 422-461.pdb #73 
    4711 --- 
    4712 Chain | Description 
    4713 A | No description available 
    4714  
    4715 
    4716 > matchmaker #73 to #1.15 & sel
    4717 
    4718 Parameters 
    4719 --- 
    4720 Chain pairing | bb 
    4721 Alignment algorithm | Needleman-Wunsch 
    4722 Similarity matrix | BLOSUM-62 
    4723 SS fraction | 0.3 
    4724 Gap open (HH/SS/other) | 18/18/6 
    4725 Gap extend | 1 
    4726 SS matrix |  |  | H | S | O 
    4727 ---|---|---|--- 
    4728 H | 6 | -9 | -6 
    4729 S |  | 6 | -6 
    4730 O |  |  | 4 
    4731 Iteration cutoff | 2 
    4732  
    4733 Matchmaker 3j0c.pdb1, chain A (#1.15) with AF3 E1 422-461.pdb, chain A (#73),
    4734 sequence alignment score = 626.9 
    4735 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    4736 2.776) 
    4737  
    4738 
    4739 > hide sel cartoons
    4740 
    4741 > select #1.15/B
    4742 
    4743 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4744 
    4745 > show sel cartoons
    4746 
    4747 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4748 
    4749 Chain information for AF3 E2 1-352.pdb #74 
    4750 --- 
    4751 Chain | Description 
    4752 B | No description available 
    4753  
    4754 
    4755 > matchmaker #74 to #1.15 & sel
    4756 
    4757 Parameters 
    4758 --- 
    4759 Chain pairing | bb 
    4760 Alignment algorithm | Needleman-Wunsch 
    4761 Similarity matrix | BLOSUM-62 
    4762 SS fraction | 0.3 
    4763 Gap open (HH/SS/other) | 18/18/6 
    4764 Gap extend | 1 
    4765 SS matrix |  |  | H | S | O 
    4766 ---|---|---|--- 
    4767 H | 6 | -9 | -6 
    4768 S |  | 6 | -6 
    4769 O |  |  | 4 
    4770 Iteration cutoff | 2 
    4771  
    4772 Matchmaker 3j0c.pdb1, chain B (#1.15) with AF3 E2 1-352.pdb, chain B (#74),
    4773 sequence alignment score = 583.7 
    4774 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4775 5.933) 
    4776  
    4777 
    4778 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4779 
    4780 Chain information for AF3 E2 353-438.pdb #75 
    4781 --- 
    4782 Chain | Description 
    4783 B | No description available 
    4784  
    4785 
    4786 > matchmaker #75 to #1.15 & sel
    4787 
    4788 Parameters 
    4789 --- 
    4790 Chain pairing | bb 
    4791 Alignment algorithm | Needleman-Wunsch 
    4792 Similarity matrix | BLOSUM-62 
    4793 SS fraction | 0.3 
    4794 Gap open (HH/SS/other) | 18/18/6 
    4795 Gap extend | 1 
    4796 SS matrix |  |  | H | S | O 
    4797 ---|---|---|--- 
    4798 H | 6 | -9 | -6 
    4799 S |  | 6 | -6 
    4800 O |  |  | 4 
    4801 Iteration cutoff | 2 
    4802  
    4803 Matchmaker 3j0c.pdb1, chain B (#1.15) with AF3 E2 353-438.pdb, chain B (#75),
    4804 sequence alignment score = 333.4 
    4805 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4806 8.411) 
    4807  
    4808 
    4809 > hide sel cartoons
    4810 
    4811 > select #1.15/C
    4812 
    4813 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4814 
    4815 > show sel cartoons
    4816 
    4817 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4818 
    4819 Chain information for AF3 CA.pdb #76 
    4820 --- 
    4821 Chain | Description 
    4822 A | No description available 
    4823  
    4824 
    4825 > matchmaker #76 to #1.15 & sel
    4826 
    4827 Parameters 
    4828 --- 
    4829 Chain pairing | bb 
    4830 Alignment algorithm | Needleman-Wunsch 
    4831 Similarity matrix | BLOSUM-62 
    4832 SS fraction | 0.3 
    4833 Gap open (HH/SS/other) | 18/18/6 
    4834 Gap extend | 1 
    4835 SS matrix |  |  | H | S | O 
    4836 ---|---|---|--- 
    4837 H | 6 | -9 | -6 
    4838 S |  | 6 | -6 
    4839 O |  |  | 4 
    4840 Iteration cutoff | 2 
    4841  
    4842 Matchmaker 3j0c.pdb1, chain C (#1.15) with AF3 CA.pdb, chain A (#76), sequence
    4843 alignment score = 328.1 
    4844 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4845 2.714) 
    4846  
    4847 
    4848 > hide sel cartoons
    4849 
    4850 > color #72 dodgerblue
    4851 
    4852 > color #73 dodgerblue
    4853 
    4854 > color #74 #00b305ff
    4855 
    4856 > color #75 #00b305ff
    4857 
    4858 > color #76 #f15839ff
    4859 
    4860 > select #1.16/A
    4861 
    4862 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4863 
    4864 > show sel cartoons
    4865 
    4866 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4867 
    4868 Chain information for AF3 E1 1-421.pdb #77 
    4869 --- 
    4870 Chain | Description 
    4871 A | No description available 
    4872  
    4873 
    4874 > matchmaker #77 to #1.16 & sel
    4875 
    4876 Parameters 
    4877 --- 
    4878 Chain pairing | bb 
    4879 Alignment algorithm | Needleman-Wunsch 
    4880 Similarity matrix | BLOSUM-62 
    4881 SS fraction | 0.3 
    4882 Gap open (HH/SS/other) | 18/18/6 
    4883 Gap extend | 1 
    4884 SS matrix |  |  | H | S | O 
    4885 ---|---|---|--- 
    4886 H | 6 | -9 | -6 
    4887 S |  | 6 | -6 
    4888 O |  |  | 4 
    4889 Iteration cutoff | 2 
    4890  
    4891 Matchmaker 3j0c.pdb1, chain A (#1.16) with AF3 E1 1-421.pdb, chain A (#77),
    4892 sequence alignment score = 1060.7 
    4893 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4894 3.020) 
    4895  
    4896 
    4897 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4898 
    4899 Chain information for AF3 E1 422-461.pdb #78 
    4900 --- 
    4901 Chain | Description 
    4902 A | No description available 
    4903  
    4904 
    4905 > matchmaker #78 to #1.16 & sel
    4906 
    4907 Parameters 
    4908 --- 
    4909 Chain pairing | bb 
    4910 Alignment algorithm | Needleman-Wunsch 
    4911 Similarity matrix | BLOSUM-62 
    4912 SS fraction | 0.3 
    4913 Gap open (HH/SS/other) | 18/18/6 
    4914 Gap extend | 1 
    4915 SS matrix |  |  | H | S | O 
    4916 ---|---|---|--- 
    4917 H | 6 | -9 | -6 
    4918 S |  | 6 | -6 
    4919 O |  |  | 4 
    4920 Iteration cutoff | 2 
    4921  
    4922 Matchmaker 3j0c.pdb1, chain A (#1.16) with AF3 E1 422-461.pdb, chain A (#78),
    4923 sequence alignment score = 626.9 
    4924 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    4925 2.775) 
    4926  
    4927 
    4928 > hide sel cartoons
    4929 
    4930 > select #1.16/B
    4931 
    4932 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4933 
    4934 > show sel cartoons
    4935 
    4936 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4937 
    4938 Chain information for AF3 E2 1-352.pdb #79 
    4939 --- 
    4940 Chain | Description 
    4941 B | No description available 
    4942  
    4943 
    4944 > matchmaker #79 to #1.16 & sel
    4945 
    4946 Parameters 
    4947 --- 
    4948 Chain pairing | bb 
    4949 Alignment algorithm | Needleman-Wunsch 
    4950 Similarity matrix | BLOSUM-62 
    4951 SS fraction | 0.3 
    4952 Gap open (HH/SS/other) | 18/18/6 
    4953 Gap extend | 1 
    4954 SS matrix |  |  | H | S | O 
    4955 ---|---|---|--- 
    4956 H | 6 | -9 | -6 
    4957 S |  | 6 | -6 
    4958 O |  |  | 4 
    4959 Iteration cutoff | 2 
    4960  
    4961 Matchmaker 3j0c.pdb1, chain B (#1.16) with AF3 E2 1-352.pdb, chain B (#79),
    4962 sequence alignment score = 583.7 
    4963 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4964 5.933) 
    4965  
    4966 
    4967 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4968 
    4969 Chain information for AF3 E2 353-438.pdb #80 
    4970 --- 
    4971 Chain | Description 
    4972 B | No description available 
    4973  
    4974 
    4975 > matchmaker #80 to #1.16 & sel
    4976 
    4977 Parameters 
    4978 --- 
    4979 Chain pairing | bb 
    4980 Alignment algorithm | Needleman-Wunsch 
    4981 Similarity matrix | BLOSUM-62 
    4982 SS fraction | 0.3 
    4983 Gap open (HH/SS/other) | 18/18/6 
    4984 Gap extend | 1 
    4985 SS matrix |  |  | H | S | O 
    4986 ---|---|---|--- 
    4987 H | 6 | -9 | -6 
    4988 S |  | 6 | -6 
    4989 O |  |  | 4 
    4990 Iteration cutoff | 2 
    4991  
    4992 Matchmaker 3j0c.pdb1, chain B (#1.16) with AF3 E2 353-438.pdb, chain B (#80),
    4993 sequence alignment score = 322.6 
    4994 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4995 8.411) 
    4996  
    4997 
    4998 > hide sel cartoons
    4999 
    5000 > select #1.16/C
    5001 
    5002 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5003 
    5004 > show sel cartoons
    5005 
    5006 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5007 
    5008 Chain information for AF3 CA.pdb #81 
    5009 --- 
    5010 Chain | Description 
    5011 A | No description available 
    5012  
    5013 
    5014 > matchmaker #81 to #1.16 & sel
    5015 
    5016 Parameters 
    5017 --- 
    5018 Chain pairing | bb 
    5019 Alignment algorithm | Needleman-Wunsch 
    5020 Similarity matrix | BLOSUM-62 
    5021 SS fraction | 0.3 
    5022 Gap open (HH/SS/other) | 18/18/6 
    5023 Gap extend | 1 
    5024 SS matrix |  |  | H | S | O 
    5025 ---|---|---|--- 
    5026 H | 6 | -9 | -6 
    5027 S |  | 6 | -6 
    5028 O |  |  | 4 
    5029 Iteration cutoff | 2 
    5030  
    5031 Matchmaker 3j0c.pdb1, chain C (#1.16) with AF3 CA.pdb, chain A (#81), sequence
    5032 alignment score = 328.1 
    5033 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5034 2.714) 
    5035  
    5036 
    5037 > hide sel cartoons
    5038 
    5039 > color #77 dodgerblue
    5040 
    5041 > color #78 dodgerblue
    5042 
    5043 > color #79 #00b305ff
    5044 
    5045 > color #80 #00b305ff
    5046 
    5047 > color #81 #f15839ff
    5048 
    5049 > select #1.17/A
    5050 
    5051 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5052 
    5053 > show sel cartoons
    5054 
    5055 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5056 
    5057 Chain information for AF3 E1 1-421.pdb #82 
    5058 --- 
    5059 Chain | Description 
    5060 A | No description available 
    5061  
    5062 
    5063 > matchmaker #82 to #1.17 & sel
    5064 
    5065 Parameters 
    5066 --- 
    5067 Chain pairing | bb 
    5068 Alignment algorithm | Needleman-Wunsch 
    5069 Similarity matrix | BLOSUM-62 
    5070 SS fraction | 0.3 
    5071 Gap open (HH/SS/other) | 18/18/6 
    5072 Gap extend | 1 
    5073 SS matrix |  |  | H | S | O 
    5074 ---|---|---|--- 
    5075 H | 6 | -9 | -6 
    5076 S |  | 6 | -6 
    5077 O |  |  | 4 
    5078 Iteration cutoff | 2 
    5079  
    5080 Matchmaker 3j0c.pdb1, chain A (#1.17) with AF3 E1 1-421.pdb, chain A (#82),
    5081 sequence alignment score = 1060.7 
    5082 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5083 3.020) 
    5084  
    5085 
    5086 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5087 
    5088 Chain information for AF3 E1 422-461.pdb #83 
    5089 --- 
    5090 Chain | Description 
    5091 A | No description available 
    5092  
    5093 
    5094 > matchmaker #83 to #1.17 & sel
    5095 
    5096 Parameters 
    5097 --- 
    5098 Chain pairing | bb 
    5099 Alignment algorithm | Needleman-Wunsch 
    5100 Similarity matrix | BLOSUM-62 
    5101 SS fraction | 0.3 
    5102 Gap open (HH/SS/other) | 18/18/6 
    5103 Gap extend | 1 
    5104 SS matrix |  |  | H | S | O 
    5105 ---|---|---|--- 
    5106 H | 6 | -9 | -6 
    5107 S |  | 6 | -6 
    5108 O |  |  | 4 
    5109 Iteration cutoff | 2 
    5110  
    5111 Matchmaker 3j0c.pdb1, chain A (#1.17) with AF3 E1 422-461.pdb, chain A (#83),
    5112 sequence alignment score = 626.9 
    5113 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    5114 2.776) 
    5115  
    5116 
    5117 > hide sel cartoons
    5118 
    5119 > select #1.17/B
    5120 
    5121 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5122 
    5123 > show sel cartoons
    5124 
    5125 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5126 
    5127 Chain information for AF3 E2 1-352.pdb #84 
    5128 --- 
    5129 Chain | Description 
    5130 B | No description available 
    5131  
    5132 
    5133 > matchmaker #84 to #1.17 & sel
    5134 
    5135 Parameters 
    5136 --- 
    5137 Chain pairing | bb 
    5138 Alignment algorithm | Needleman-Wunsch 
    5139 Similarity matrix | BLOSUM-62 
    5140 SS fraction | 0.3 
    5141 Gap open (HH/SS/other) | 18/18/6 
    5142 Gap extend | 1 
    5143 SS matrix |  |  | H | S | O 
    5144 ---|---|---|--- 
    5145 H | 6 | -9 | -6 
    5146 S |  | 6 | -6 
    5147 O |  |  | 4 
    5148 Iteration cutoff | 2 
    5149  
    5150 Matchmaker 3j0c.pdb1, chain B (#1.17) with AF3 E2 1-352.pdb, chain B (#84),
    5151 sequence alignment score = 583.7 
    5152 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5153 5.933) 
    5154  
    5155 
    5156 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5157 
    5158 Chain information for AF3 E2 353-438.pdb #85 
    5159 --- 
    5160 Chain | Description 
    5161 B | No description available 
    5162  
    5163 
    5164 > matchmaker #85 to #1.17 & sel
    5165 
    5166 Parameters 
    5167 --- 
    5168 Chain pairing | bb 
    5169 Alignment algorithm | Needleman-Wunsch 
    5170 Similarity matrix | BLOSUM-62 
    5171 SS fraction | 0.3 
    5172 Gap open (HH/SS/other) | 18/18/6 
    5173 Gap extend | 1 
    5174 SS matrix |  |  | H | S | O 
    5175 ---|---|---|--- 
    5176 H | 6 | -9 | -6 
    5177 S |  | 6 | -6 
    5178 O |  |  | 4 
    5179 Iteration cutoff | 2 
    5180  
    5181 Matchmaker 3j0c.pdb1, chain B (#1.17) with AF3 E2 353-438.pdb, chain B (#85),
    5182 sequence alignment score = 322.6 
    5183 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5184 8.411) 
    5185  
    5186 
    5187 > hide sel cartoons
    5188 
    5189 > select #1.17/C
    5190 
    5191 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5192 
    5193 > show sel cartoons
    5194 
    5195 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5196 
    5197 Chain information for AF3 CA.pdb #86 
    5198 --- 
    5199 Chain | Description 
    5200 A | No description available 
    5201  
    5202 
    5203 > matchmaker #86 to #1.17 & sel
    5204 
    5205 Parameters 
    5206 --- 
    5207 Chain pairing | bb 
    5208 Alignment algorithm | Needleman-Wunsch 
    5209 Similarity matrix | BLOSUM-62 
    5210 SS fraction | 0.3 
    5211 Gap open (HH/SS/other) | 18/18/6 
    5212 Gap extend | 1 
    5213 SS matrix |  |  | H | S | O 
    5214 ---|---|---|--- 
    5215 H | 6 | -9 | -6 
    5216 S |  | 6 | -6 
    5217 O |  |  | 4 
    5218 Iteration cutoff | 2 
    5219  
    5220 Matchmaker 3j0c.pdb1, chain C (#1.17) with AF3 CA.pdb, chain A (#86), sequence
    5221 alignment score = 328.1 
    5222 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5223 2.714) 
    5224  
    5225 
    5226 > hide sel cartoons
    5227 
    5228 > color #82 dodgerblue
    5229 
    5230 > color #83 dodgerblue
    5231 
    5232 > color #84 #00b305ff
    5233 
    5234 > color #85 #00b305ff
    5235 
    5236 > color #86 #f15839ff
    5237 
    5238 > select #1.18/A
    5239 
    5240 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5241 
    5242 > show sel cartoons
    5243 
    5244 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5245 
    5246 Chain information for AF3 E1 1-421.pdb #87 
    5247 --- 
    5248 Chain | Description 
    5249 A | No description available 
    5250  
    5251 
    5252 > matchmaker #87 to #1.18 & sel
    5253 
    5254 Parameters 
    5255 --- 
    5256 Chain pairing | bb 
    5257 Alignment algorithm | Needleman-Wunsch 
    5258 Similarity matrix | BLOSUM-62 
    5259 SS fraction | 0.3 
    5260 Gap open (HH/SS/other) | 18/18/6 
    5261 Gap extend | 1 
    5262 SS matrix |  |  | H | S | O 
    5263 ---|---|---|--- 
    5264 H | 6 | -9 | -6 
    5265 S |  | 6 | -6 
    5266 O |  |  | 4 
    5267 Iteration cutoff | 2 
    5268  
    5269 Matchmaker 3j0c.pdb1, chain A (#1.18) with AF3 E1 1-421.pdb, chain A (#87),
    5270 sequence alignment score = 1060.7 
    5271 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5272 3.020) 
    5273  
    5274 
    5275 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5276 
    5277 Chain information for AF3 E1 422-461.pdb #88 
    5278 --- 
    5279 Chain | Description 
    5280 A | No description available 
    5281  
    5282 
    5283 > matchmaker #88 to #1.18 & sel
    5284 
    5285 Parameters 
    5286 --- 
    5287 Chain pairing | bb 
    5288 Alignment algorithm | Needleman-Wunsch 
    5289 Similarity matrix | BLOSUM-62 
    5290 SS fraction | 0.3 
    5291 Gap open (HH/SS/other) | 18/18/6 
    5292 Gap extend | 1 
    5293 SS matrix |  |  | H | S | O 
    5294 ---|---|---|--- 
    5295 H | 6 | -9 | -6 
    5296 S |  | 6 | -6 
    5297 O |  |  | 4 
    5298 Iteration cutoff | 2 
    5299  
    5300 Matchmaker 3j0c.pdb1, chain A (#1.18) with AF3 E1 422-461.pdb, chain A (#88),
    5301 sequence alignment score = 626.9 
    5302 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    5303 2.776) 
    5304  
    5305 
    5306 > hide sel cartoons
    5307 
    5308 > select #1.18/B
    5309 
    5310 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5311 
    5312 > show sel cartoons
    5313 
    5314 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5315 
    5316 Chain information for AF3 E2 1-352.pdb #89 
    5317 --- 
    5318 Chain | Description 
    5319 B | No description available 
    5320  
    5321 
    5322 > matchmaker #89 to #1.18 & sel
    5323 
    5324 Parameters 
    5325 --- 
    5326 Chain pairing | bb 
    5327 Alignment algorithm | Needleman-Wunsch 
    5328 Similarity matrix | BLOSUM-62 
    5329 SS fraction | 0.3 
    5330 Gap open (HH/SS/other) | 18/18/6 
    5331 Gap extend | 1 
    5332 SS matrix |  |  | H | S | O 
    5333 ---|---|---|--- 
    5334 H | 6 | -9 | -6 
    5335 S |  | 6 | -6 
    5336 O |  |  | 4 
    5337 Iteration cutoff | 2 
    5338  
    5339 Matchmaker 3j0c.pdb1, chain B (#1.18) with AF3 E2 1-352.pdb, chain B (#89),
    5340 sequence alignment score = 583.7 
    5341 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5342 5.933) 
    5343  
    5344 
    5345 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5346 
    5347 Chain information for AF3 E2 353-438.pdb #90 
    5348 --- 
    5349 Chain | Description 
    5350 B | No description available 
    5351  
    5352 
    5353 > matchmaker #90 to #1.18 & sel
    5354 
    5355 Parameters 
    5356 --- 
    5357 Chain pairing | bb 
    5358 Alignment algorithm | Needleman-Wunsch 
    5359 Similarity matrix | BLOSUM-62 
    5360 SS fraction | 0.3 
    5361 Gap open (HH/SS/other) | 18/18/6 
    5362 Gap extend | 1 
    5363 SS matrix |  |  | H | S | O 
    5364 ---|---|---|--- 
    5365 H | 6 | -9 | -6 
    5366 S |  | 6 | -6 
    5367 O |  |  | 4 
    5368 Iteration cutoff | 2 
    5369  
    5370 Matchmaker 3j0c.pdb1, chain B (#1.18) with AF3 E2 353-438.pdb, chain B (#90),
    5371 sequence alignment score = 333.4 
    5372 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5373 8.411) 
    5374  
    5375 
    5376 > hide sel cartoons
    5377 
    5378 > select #1.18/C
    5379 
    5380 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5381 
    5382 > show sel cartoons
    5383 
    5384 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5385 
    5386 Chain information for AF3 CA.pdb #91 
    5387 --- 
    5388 Chain | Description 
    5389 A | No description available 
    5390  
    5391 
    5392 > matchmaker #91 to #1.18 & sel
    5393 
    5394 Parameters 
    5395 --- 
    5396 Chain pairing | bb 
    5397 Alignment algorithm | Needleman-Wunsch 
    5398 Similarity matrix | BLOSUM-62 
    5399 SS fraction | 0.3 
    5400 Gap open (HH/SS/other) | 18/18/6 
    5401 Gap extend | 1 
    5402 SS matrix |  |  | H | S | O 
    5403 ---|---|---|--- 
    5404 H | 6 | -9 | -6 
    5405 S |  | 6 | -6 
    5406 O |  |  | 4 
    5407 Iteration cutoff | 2 
    5408  
    5409 Matchmaker 3j0c.pdb1, chain C (#1.18) with AF3 CA.pdb, chain A (#91), sequence
    5410 alignment score = 328.1 
    5411 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5412 2.714) 
    5413  
    5414 
    5415 > hide sel cartoons
    5416 
    5417 > color #87 dodgerblue
    5418 
    5419 > color #88 dodgerblue
    5420 
    5421 > color #89 #00b305ff
    5422 
    5423 > color #90 #00b305ff
    5424 
    5425 > color #91 #f15839ff
    5426 
    5427 > select #1.19/A
    5428 
    5429 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5430 
    5431 > show sel cartoons
    5432 
    5433 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5434 
    5435 Chain information for AF3 E1 1-421.pdb #92 
    5436 --- 
    5437 Chain | Description 
    5438 A | No description available 
    5439  
    5440 
    5441 > matchmaker #92 to #1.19 & sel
    5442 
    5443 Parameters 
    5444 --- 
    5445 Chain pairing | bb 
    5446 Alignment algorithm | Needleman-Wunsch 
    5447 Similarity matrix | BLOSUM-62 
    5448 SS fraction | 0.3 
    5449 Gap open (HH/SS/other) | 18/18/6 
    5450 Gap extend | 1 
    5451 SS matrix |  |  | H | S | O 
    5452 ---|---|---|--- 
    5453 H | 6 | -9 | -6 
    5454 S |  | 6 | -6 
    5455 O |  |  | 4 
    5456 Iteration cutoff | 2 
    5457  
    5458 Matchmaker 3j0c.pdb1, chain A (#1.19) with AF3 E1 1-421.pdb, chain A (#92),
    5459 sequence alignment score = 1060.7 
    5460 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5461 3.020) 
    5462  
    5463 
    5464 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5465 
    5466 Chain information for AF3 E1 422-461.pdb #93 
    5467 --- 
    5468 Chain | Description 
    5469 A | No description available 
    5470  
    5471 
    5472 > matchmaker #93 to #1.19 & sel
    5473 
    5474 Parameters 
    5475 --- 
    5476 Chain pairing | bb 
    5477 Alignment algorithm | Needleman-Wunsch 
    5478 Similarity matrix | BLOSUM-62 
    5479 SS fraction | 0.3 
    5480 Gap open (HH/SS/other) | 18/18/6 
    5481 Gap extend | 1 
    5482 SS matrix |  |  | H | S | O 
    5483 ---|---|---|--- 
    5484 H | 6 | -9 | -6 
    5485 S |  | 6 | -6 
    5486 O |  |  | 4 
    5487 Iteration cutoff | 2 
    5488  
    5489 Matchmaker 3j0c.pdb1, chain A (#1.19) with AF3 E1 422-461.pdb, chain A (#93),
    5490 sequence alignment score = 626.9 
    5491 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    5492 2.775) 
    5493  
    5494 
    5495 > hide sel cartoons
    5496 
    5497 > select #1.19/B
    5498 
    5499 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5500 
    5501 > show sel cartoons
    5502 
    5503 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5504 
    5505 Chain information for AF3 E2 1-352.pdb #94 
    5506 --- 
    5507 Chain | Description 
    5508 B | No description available 
    5509  
    5510 
    5511 > matchmaker #94 to #1.19 & sel
    5512 
    5513 Parameters 
    5514 --- 
    5515 Chain pairing | bb 
    5516 Alignment algorithm | Needleman-Wunsch 
    5517 Similarity matrix | BLOSUM-62 
    5518 SS fraction | 0.3 
    5519 Gap open (HH/SS/other) | 18/18/6 
    5520 Gap extend | 1 
    5521 SS matrix |  |  | H | S | O 
    5522 ---|---|---|--- 
    5523 H | 6 | -9 | -6 
    5524 S |  | 6 | -6 
    5525 O |  |  | 4 
    5526 Iteration cutoff | 2 
    5527  
    5528 Matchmaker 3j0c.pdb1, chain B (#1.19) with AF3 E2 1-352.pdb, chain B (#94),
    5529 sequence alignment score = 583.7 
    5530 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5531 5.933) 
    5532  
    5533 
    5534 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5535 
    5536 Chain information for AF3 E2 353-438.pdb #95 
    5537 --- 
    5538 Chain | Description 
    5539 B | No description available 
    5540  
    5541 
    5542 > matchmaker #95 to #1.19 & sel
    5543 
    5544 Parameters 
    5545 --- 
    5546 Chain pairing | bb 
    5547 Alignment algorithm | Needleman-Wunsch 
    5548 Similarity matrix | BLOSUM-62 
    5549 SS fraction | 0.3 
    5550 Gap open (HH/SS/other) | 18/18/6 
    5551 Gap extend | 1 
    5552 SS matrix |  |  | H | S | O 
    5553 ---|---|---|--- 
    5554 H | 6 | -9 | -6 
    5555 S |  | 6 | -6 
    5556 O |  |  | 4 
    5557 Iteration cutoff | 2 
    5558  
    5559 Matchmaker 3j0c.pdb1, chain B (#1.19) with AF3 E2 353-438.pdb, chain B (#95),
    5560 sequence alignment score = 322.6 
    5561 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5562 8.411) 
    5563  
    5564 
    5565 > hide sel cartoons
    5566 
    5567 > select #1.19/C
    5568 
    5569 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5570 
    5571 > show sel cartoons
    5572 
    5573 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5574 
    5575 Chain information for AF3 CA.pdb #96 
    5576 --- 
    5577 Chain | Description 
    5578 A | No description available 
    5579  
    5580 
    5581 > matchmaker #96 to #1.19 & sel
    5582 
    5583 Parameters 
    5584 --- 
    5585 Chain pairing | bb 
    5586 Alignment algorithm | Needleman-Wunsch 
    5587 Similarity matrix | BLOSUM-62 
    5588 SS fraction | 0.3 
    5589 Gap open (HH/SS/other) | 18/18/6 
    5590 Gap extend | 1 
    5591 SS matrix |  |  | H | S | O 
    5592 ---|---|---|--- 
    5593 H | 6 | -9 | -6 
    5594 S |  | 6 | -6 
    5595 O |  |  | 4 
    5596 Iteration cutoff | 2 
    5597  
    5598 Matchmaker 3j0c.pdb1, chain C (#1.19) with AF3 CA.pdb, chain A (#96), sequence
    5599 alignment score = 328.1 
    5600 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5601 2.714) 
    5602  
    5603 
    5604 > hide sel cartoons
    5605 
    5606 > color #92 dodgerblue
    5607 
    5608 > color #93 dodgerblue
    5609 
    5610 > color #94 dodgerblue
    5611 
    5612 > color #94 #00b305ff
    5613 
    5614 > color #95 #00b305ff
    5615 
    5616 > color #96 #f15839ff
    5617 
    5618 > select #1.20/A
    5619 
    5620 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5621 
    5622 > show sel cartoons
    5623 
    5624 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5625 
    5626 Chain information for AF3 E1 1-421.pdb #97 
    5627 --- 
    5628 Chain | Description 
    5629 A | No description available 
    5630  
    5631 
    5632 > matchmaker #97 to #1.20 & sel
    5633 
    5634 Parameters 
    5635 --- 
    5636 Chain pairing | bb 
    5637 Alignment algorithm | Needleman-Wunsch 
    5638 Similarity matrix | BLOSUM-62 
    5639 SS fraction | 0.3 
    5640 Gap open (HH/SS/other) | 18/18/6 
    5641 Gap extend | 1 
    5642 SS matrix |  |  | H | S | O 
    5643 ---|---|---|--- 
    5644 H | 6 | -9 | -6 
    5645 S |  | 6 | -6 
    5646 O |  |  | 4 
    5647 Iteration cutoff | 2 
    5648  
    5649 Matchmaker 3j0c.pdb1, chain A (#1.20) with AF3 E1 1-421.pdb, chain A (#97),
    5650 sequence alignment score = 1060.7 
    5651 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5652 3.020) 
    5653  
    5654 
    5655 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5656 
    5657 Chain information for AF3 E1 422-461.pdb #98 
    5658 --- 
    5659 Chain | Description 
    5660 A | No description available 
    5661  
    5662 
    5663 > matchmaker #98 to #1.20 & sel
    5664 
    5665 Parameters 
    5666 --- 
    5667 Chain pairing | bb 
    5668 Alignment algorithm | Needleman-Wunsch 
    5669 Similarity matrix | BLOSUM-62 
    5670 SS fraction | 0.3 
    5671 Gap open (HH/SS/other) | 18/18/6 
    5672 Gap extend | 1 
    5673 SS matrix |  |  | H | S | O 
    5674 ---|---|---|--- 
    5675 H | 6 | -9 | -6 
    5676 S |  | 6 | -6 
    5677 O |  |  | 4 
    5678 Iteration cutoff | 2 
    5679  
    5680 Matchmaker 3j0c.pdb1, chain A (#1.20) with AF3 E1 422-461.pdb, chain A (#98),
    5681 sequence alignment score = 626.9 
    5682 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    5683 2.775) 
    5684  
    5685 
    5686 > hide sel cartoons
    5687 
    5688 > select #1.20/B
    5689 
    5690 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5691 
    5692 > show sel cartoons
    5693 
    5694 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5695 
    5696 Chain information for AF3 E2 1-352.pdb #99 
    5697 --- 
    5698 Chain | Description 
    5699 B | No description available 
    5700  
    5701 
    5702 > matchmaker #99 to #1.20 & sel
    5703 
    5704 Parameters 
    5705 --- 
    5706 Chain pairing | bb 
    5707 Alignment algorithm | Needleman-Wunsch 
    5708 Similarity matrix | BLOSUM-62 
    5709 SS fraction | 0.3 
    5710 Gap open (HH/SS/other) | 18/18/6 
    5711 Gap extend | 1 
    5712 SS matrix |  |  | H | S | O 
    5713 ---|---|---|--- 
    5714 H | 6 | -9 | -6 
    5715 S |  | 6 | -6 
    5716 O |  |  | 4 
    5717 Iteration cutoff | 2 
    5718  
    5719 Matchmaker 3j0c.pdb1, chain B (#1.20) with AF3 E2 1-352.pdb, chain B (#99),
    5720 sequence alignment score = 583.7 
    5721 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5722 5.933) 
    5723  
    5724 
    5725 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5726 
    5727 Chain information for AF3 E2 353-438.pdb #100 
    5728 --- 
    5729 Chain | Description 
    5730 B | No description available 
    5731  
    5732 
    5733 > matchmaker #100 to #1.20 & sel
    5734 
    5735 Parameters 
    5736 --- 
    5737 Chain pairing | bb 
    5738 Alignment algorithm | Needleman-Wunsch 
    5739 Similarity matrix | BLOSUM-62 
    5740 SS fraction | 0.3 
    5741 Gap open (HH/SS/other) | 18/18/6 
    5742 Gap extend | 1 
    5743 SS matrix |  |  | H | S | O 
    5744 ---|---|---|--- 
    5745 H | 6 | -9 | -6 
    5746 S |  | 6 | -6 
    5747 O |  |  | 4 
    5748 Iteration cutoff | 2 
    5749  
    5750 Matchmaker 3j0c.pdb1, chain B (#1.20) with AF3 E2 353-438.pdb, chain B (#100),
    5751 sequence alignment score = 322.6 
    5752 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5753 8.411) 
    5754  
    5755 
    5756 > hide sel cartoons
    5757 
    5758 > select #1.20/C
    5759 
    5760 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5761 
    5762 > show sel cartoons
    5763 
    5764 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5765 
    5766 Chain information for AF3 CA.pdb #101 
    5767 --- 
    5768 Chain | Description 
    5769 A | No description available 
    5770  
    5771 
    5772 > matchmaker #101 to #1.20 & sel
    5773 
    5774 Parameters 
    5775 --- 
    5776 Chain pairing | bb 
    5777 Alignment algorithm | Needleman-Wunsch 
    5778 Similarity matrix | BLOSUM-62 
    5779 SS fraction | 0.3 
    5780 Gap open (HH/SS/other) | 18/18/6 
    5781 Gap extend | 1 
    5782 SS matrix |  |  | H | S | O 
    5783 ---|---|---|--- 
    5784 H | 6 | -9 | -6 
    5785 S |  | 6 | -6 
    5786 O |  |  | 4 
    5787 Iteration cutoff | 2 
    5788  
    5789 Matchmaker 3j0c.pdb1, chain C (#1.20) with AF3 CA.pdb, chain A (#101),
    5790 sequence alignment score = 328.1 
    5791 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5792 2.714) 
    5793  
    5794 
    5795 > hide sel cartoons
    5796 
    5797 > color #97 dodgerblue
    5798 
    5799 > color #98 dodgerblue
    5800 
    5801 > color #99 #00b305ff
    5802 
    5803 > color #100 #00b305ff
    5804 
    5805 > color #101 #f15839ff
    5806 
    5807 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    5808 
    5809 > select #1.21/A
    5810 
    5811 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5812 
    5813 > show sel cartoons
    5814 
    5815 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5816 
    5817 Chain information for AF3 E1 1-421.pdb #102 
    5818 --- 
    5819 Chain | Description 
    5820 A | No description available 
    5821  
    5822 
    5823 > matchmaker #102 to #1.21 & sel
    5824 
    5825 Parameters 
    5826 --- 
    5827 Chain pairing | bb 
    5828 Alignment algorithm | Needleman-Wunsch 
    5829 Similarity matrix | BLOSUM-62 
    5830 SS fraction | 0.3 
    5831 Gap open (HH/SS/other) | 18/18/6 
    5832 Gap extend | 1 
    5833 SS matrix |  |  | H | S | O 
    5834 ---|---|---|--- 
    5835 H | 6 | -9 | -6 
    5836 S |  | 6 | -6 
    5837 O |  |  | 4 
    5838 Iteration cutoff | 2 
    5839  
    5840 Matchmaker 3j0c.pdb1, chain A (#1.21) with AF3 E1 1-421.pdb, chain A (#102),
    5841 sequence alignment score = 1060.7 
    5842 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5843 3.020) 
    5844  
    5845 
    5846 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5847 
    5848 Chain information for AF3 E1 422-461.pdb #103 
    5849 --- 
    5850 Chain | Description 
    5851 A | No description available 
    5852  
    5853 
    5854 > matchmaker #103 to #1.21 & sel
    5855 
    5856 Parameters 
    5857 --- 
    5858 Chain pairing | bb 
    5859 Alignment algorithm | Needleman-Wunsch 
    5860 Similarity matrix | BLOSUM-62 
    5861 SS fraction | 0.3 
    5862 Gap open (HH/SS/other) | 18/18/6 
    5863 Gap extend | 1 
    5864 SS matrix |  |  | H | S | O 
    5865 ---|---|---|--- 
    5866 H | 6 | -9 | -6 
    5867 S |  | 6 | -6 
    5868 O |  |  | 4 
    5869 Iteration cutoff | 2 
    5870  
    5871 Matchmaker 3j0c.pdb1, chain A (#1.21) with AF3 E1 422-461.pdb, chain A (#103),
    5872 sequence alignment score = 626.9 
    5873 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    5874 2.775) 
    5875  
    5876 
    5877 > hide sel cartoons
    5878 
    5879 > select #1.21/B
    5880 
    5881 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5882 
    5883 > show sel cartoons
    5884 
    5885 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5886 
    5887 Chain information for AF3 E2 1-352.pdb #104 
    5888 --- 
    5889 Chain | Description 
    5890 B | No description available 
    5891  
    5892 
    5893 > matchmaker #104 to #1.21 & sel
    5894 
    5895 Parameters 
    5896 --- 
    5897 Chain pairing | bb 
    5898 Alignment algorithm | Needleman-Wunsch 
    5899 Similarity matrix | BLOSUM-62 
    5900 SS fraction | 0.3 
    5901 Gap open (HH/SS/other) | 18/18/6 
    5902 Gap extend | 1 
    5903 SS matrix |  |  | H | S | O 
    5904 ---|---|---|--- 
    5905 H | 6 | -9 | -6 
    5906 S |  | 6 | -6 
    5907 O |  |  | 4 
    5908 Iteration cutoff | 2 
    5909  
    5910 Matchmaker 3j0c.pdb1, chain B (#1.21) with AF3 E2 1-352.pdb, chain B (#104),
    5911 sequence alignment score = 583.7 
    5912 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5913 5.933) 
    5914  
    5915 
    5916 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5917 
    5918 Chain information for AF3 E2 353-438.pdb #105 
    5919 --- 
    5920 Chain | Description 
    5921 B | No description available 
    5922  
    5923 
    5924 > matchmaker #105 to #1.21 & sel
    5925 
    5926 Parameters 
    5927 --- 
    5928 Chain pairing | bb 
    5929 Alignment algorithm | Needleman-Wunsch 
    5930 Similarity matrix | BLOSUM-62 
    5931 SS fraction | 0.3 
    5932 Gap open (HH/SS/other) | 18/18/6 
    5933 Gap extend | 1 
    5934 SS matrix |  |  | H | S | O 
    5935 ---|---|---|--- 
    5936 H | 6 | -9 | -6 
    5937 S |  | 6 | -6 
    5938 O |  |  | 4 
    5939 Iteration cutoff | 2 
    5940  
    5941 Matchmaker 3j0c.pdb1, chain B (#1.21) with AF3 E2 353-438.pdb, chain B (#105),
    5942 sequence alignment score = 322.6 
    5943 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5944 8.411) 
    5945  
    5946 
    5947 > hide sel cartoons
    5948 
    5949 > select #1.21/C
    5950 
    5951 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5952 
    5953 > show sel cartoons
    5954 
    5955 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5956 
    5957 Chain information for AF3 CA.pdb #106 
    5958 --- 
    5959 Chain | Description 
    5960 A | No description available 
    5961  
    5962 
    5963 > matchmaker #106 to #1.21 & sel
    5964 
    5965 Parameters 
    5966 --- 
    5967 Chain pairing | bb 
    5968 Alignment algorithm | Needleman-Wunsch 
    5969 Similarity matrix | BLOSUM-62 
    5970 SS fraction | 0.3 
    5971 Gap open (HH/SS/other) | 18/18/6 
    5972 Gap extend | 1 
    5973 SS matrix |  |  | H | S | O 
    5974 ---|---|---|--- 
    5975 H | 6 | -9 | -6 
    5976 S |  | 6 | -6 
    5977 O |  |  | 4 
    5978 Iteration cutoff | 2 
    5979  
    5980 Matchmaker 3j0c.pdb1, chain C (#1.21) with AF3 CA.pdb, chain A (#106),
    5981 sequence alignment score = 328.1 
    5982 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5983 2.714) 
    5984  
    5985 
    5986 > hide sel cartoons
    5987 
    5988 > color #102 dodgerblue
    5989 
    5990 > color #103 dodgerblue
    5991 
    5992 > color #104 #00b305ff
    5993 
    5994 > color #105 #00b305ff
    5995 
    5996 > color #106 #f15839ff
    5997 
    5998 > select #1.22/A
    5999 
    6000 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6001 
    6002 > show sel cartoons
    6003 
    6004 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6005 
    6006 Chain information for AF3 E1 1-421.pdb #107 
    6007 --- 
    6008 Chain | Description 
    6009 A | No description available 
    6010  
    6011 
    6012 > matchmaker #107 to #1.22 & sel
    6013 
    6014 Parameters 
    6015 --- 
    6016 Chain pairing | bb 
    6017 Alignment algorithm | Needleman-Wunsch 
    6018 Similarity matrix | BLOSUM-62 
    6019 SS fraction | 0.3 
    6020 Gap open (HH/SS/other) | 18/18/6 
    6021 Gap extend | 1 
    6022 SS matrix |  |  | H | S | O 
    6023 ---|---|---|--- 
    6024 H | 6 | -9 | -6 
    6025 S |  | 6 | -6 
    6026 O |  |  | 4 
    6027 Iteration cutoff | 2 
    6028  
    6029 Matchmaker 3j0c.pdb1, chain A (#1.22) with AF3 E1 1-421.pdb, chain A (#107),
    6030 sequence alignment score = 1060.7 
    6031 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6032 3.020) 
    6033  
    6034 
    6035 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6036 
    6037 Chain information for AF3 E1 422-461.pdb #108 
    6038 --- 
    6039 Chain | Description 
    6040 A | No description available 
    6041  
    6042 
    6043 > matchmaker #108 to #1.22 & sel
    6044 
    6045 Parameters 
    6046 --- 
    6047 Chain pairing | bb 
    6048 Alignment algorithm | Needleman-Wunsch 
    6049 Similarity matrix | BLOSUM-62 
    6050 SS fraction | 0.3 
    6051 Gap open (HH/SS/other) | 18/18/6 
    6052 Gap extend | 1 
    6053 SS matrix |  |  | H | S | O 
    6054 ---|---|---|--- 
    6055 H | 6 | -9 | -6 
    6056 S |  | 6 | -6 
    6057 O |  |  | 4 
    6058 Iteration cutoff | 2 
    6059  
    6060 Matchmaker 3j0c.pdb1, chain A (#1.22) with AF3 E1 422-461.pdb, chain A (#108),
    6061 sequence alignment score = 626.9 
    6062 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    6063 2.776) 
    6064  
    6065 
    6066 > hide sel cartoons
    6067 
    6068 > select #1.22/B
    6069 
    6070 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6071 
    6072 > show sel cartoons
    6073 
    6074 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6075 
    6076 Chain information for AF3 E2 1-352.pdb #109 
    6077 --- 
    6078 Chain | Description 
    6079 B | No description available 
    6080  
    6081 
    6082 > matchmaker #109 to #1.22 & sel
    6083 
    6084 Parameters 
    6085 --- 
    6086 Chain pairing | bb 
    6087 Alignment algorithm | Needleman-Wunsch 
    6088 Similarity matrix | BLOSUM-62 
    6089 SS fraction | 0.3 
    6090 Gap open (HH/SS/other) | 18/18/6 
    6091 Gap extend | 1 
    6092 SS matrix |  |  | H | S | O 
    6093 ---|---|---|--- 
    6094 H | 6 | -9 | -6 
    6095 S |  | 6 | -6 
    6096 O |  |  | 4 
    6097 Iteration cutoff | 2 
    6098  
    6099 Matchmaker 3j0c.pdb1, chain B (#1.22) with AF3 E2 1-352.pdb, chain B (#109),
    6100 sequence alignment score = 583.7 
    6101 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6102 5.933) 
    6103  
    6104 
    6105 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6106 
    6107 Chain information for AF3 E2 353-438.pdb #110 
    6108 --- 
    6109 Chain | Description 
    6110 B | No description available 
    6111  
    6112 
    6113 > matchmaker #110 to #1.22 & sel
    6114 
    6115 Parameters 
    6116 --- 
    6117 Chain pairing | bb 
    6118 Alignment algorithm | Needleman-Wunsch 
    6119 Similarity matrix | BLOSUM-62 
    6120 SS fraction | 0.3 
    6121 Gap open (HH/SS/other) | 18/18/6 
    6122 Gap extend | 1 
    6123 SS matrix |  |  | H | S | O 
    6124 ---|---|---|--- 
    6125 H | 6 | -9 | -6 
    6126 S |  | 6 | -6 
    6127 O |  |  | 4 
    6128 Iteration cutoff | 2 
    6129  
    6130 Matchmaker 3j0c.pdb1, chain B (#1.22) with AF3 E2 353-438.pdb, chain B (#110),
    6131 sequence alignment score = 322.6 
    6132 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6133 8.411) 
    6134  
    6135 
    6136 > hide sel cartoons
    6137 
    6138 > select #1.22/C
    6139 
    6140 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6141 
    6142 > show sel cartoons
    6143 
    6144 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6145 
    6146 Chain information for AF3 CA.pdb #111 
    6147 --- 
    6148 Chain | Description 
    6149 A | No description available 
    6150  
    6151 
    6152 > matchmaker #111 to #1.22 & sel
    6153 
    6154 Parameters 
    6155 --- 
    6156 Chain pairing | bb 
    6157 Alignment algorithm | Needleman-Wunsch 
    6158 Similarity matrix | BLOSUM-62 
    6159 SS fraction | 0.3 
    6160 Gap open (HH/SS/other) | 18/18/6 
    6161 Gap extend | 1 
    6162 SS matrix |  |  | H | S | O 
    6163 ---|---|---|--- 
    6164 H | 6 | -9 | -6 
    6165 S |  | 6 | -6 
    6166 O |  |  | 4 
    6167 Iteration cutoff | 2 
    6168  
    6169 Matchmaker 3j0c.pdb1, chain C (#1.22) with AF3 CA.pdb, chain A (#111),
    6170 sequence alignment score = 328.1 
    6171 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6172 2.714) 
    6173  
    6174 
    6175 > hide sel cartoons
    6176 
    6177 > color #107 dodgerblue
    6178 
    6179 > color #108 dodgerblue
    6180 
    6181 > color #109 #00b305ff
    6182 
    6183 > color #110 #00b305ff
    6184 
    6185 > color #111 #f15839ff
    6186 
    6187 > select #1.23/A
    6188 
    6189 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6190 
    6191 > show sel cartoons
    6192 
    6193 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6194 
    6195 Chain information for AF3 E1 1-421.pdb #112 
    6196 --- 
    6197 Chain | Description 
    6198 A | No description available 
    6199  
    6200 
    6201 > matchmaker #112 to #1.23 & sel
    6202 
    6203 Parameters 
    6204 --- 
    6205 Chain pairing | bb 
    6206 Alignment algorithm | Needleman-Wunsch 
    6207 Similarity matrix | BLOSUM-62 
    6208 SS fraction | 0.3 
    6209 Gap open (HH/SS/other) | 18/18/6 
    6210 Gap extend | 1 
    6211 SS matrix |  |  | H | S | O 
    6212 ---|---|---|--- 
    6213 H | 6 | -9 | -6 
    6214 S |  | 6 | -6 
    6215 O |  |  | 4 
    6216 Iteration cutoff | 2 
    6217  
    6218 Matchmaker 3j0c.pdb1, chain A (#1.23) with AF3 E1 1-421.pdb, chain A (#112),
    6219 sequence alignment score = 1060.7 
    6220 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6221 3.020) 
    6222  
    6223 
    6224 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6225 
    6226 Chain information for AF3 E1 422-461.pdb #113 
    6227 --- 
    6228 Chain | Description 
    6229 A | No description available 
    6230  
    6231 
    6232 > matchmaker #113 to #1.23 & sel
    6233 
    6234 Parameters 
    6235 --- 
    6236 Chain pairing | bb 
    6237 Alignment algorithm | Needleman-Wunsch 
    6238 Similarity matrix | BLOSUM-62 
    6239 SS fraction | 0.3 
    6240 Gap open (HH/SS/other) | 18/18/6 
    6241 Gap extend | 1 
    6242 SS matrix |  |  | H | S | O 
    6243 ---|---|---|--- 
    6244 H | 6 | -9 | -6 
    6245 S |  | 6 | -6 
    6246 O |  |  | 4 
    6247 Iteration cutoff | 2 
    6248  
    6249 Matchmaker 3j0c.pdb1, chain A (#1.23) with AF3 E1 422-461.pdb, chain A (#113),
    6250 sequence alignment score = 626.9 
    6251 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    6252 2.776) 
    6253  
    6254 
    6255 > hide sel cartoons
    6256 
    6257 [Repeated 1 time(s)]
    6258 
    6259 > select #1.23/B
    6260 
    6261 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6262 
    6263 > show sel cartoons
    6264 
    6265 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6266 
    6267 Chain information for AF3 E2 1-352.pdb #114 
    6268 --- 
    6269 Chain | Description 
    6270 B | No description available 
    6271  
    6272 
    6273 > matchmaker #114 to #1.23 & sel
    6274 
    6275 Parameters 
    6276 --- 
    6277 Chain pairing | bb 
    6278 Alignment algorithm | Needleman-Wunsch 
    6279 Similarity matrix | BLOSUM-62 
    6280 SS fraction | 0.3 
    6281 Gap open (HH/SS/other) | 18/18/6 
    6282 Gap extend | 1 
    6283 SS matrix |  |  | H | S | O 
    6284 ---|---|---|--- 
    6285 H | 6 | -9 | -6 
    6286 S |  | 6 | -6 
    6287 O |  |  | 4 
    6288 Iteration cutoff | 2 
    6289  
    6290 Matchmaker 3j0c.pdb1, chain B (#1.23) with AF3 E2 1-352.pdb, chain B (#114),
    6291 sequence alignment score = 583.7 
    6292 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6293 5.933) 
    6294  
    6295 
    6296 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6297 
    6298 Chain information for AF3 E2 353-438.pdb #115 
    6299 --- 
    6300 Chain | Description 
    6301 B | No description available 
    6302  
    6303 
    6304 > matchmaker #115 to #1.23 & sel
    6305 
    6306 Parameters 
    6307 --- 
    6308 Chain pairing | bb 
    6309 Alignment algorithm | Needleman-Wunsch 
    6310 Similarity matrix | BLOSUM-62 
    6311 SS fraction | 0.3 
    6312 Gap open (HH/SS/other) | 18/18/6 
    6313 Gap extend | 1 
    6314 SS matrix |  |  | H | S | O 
    6315 ---|---|---|--- 
    6316 H | 6 | -9 | -6 
    6317 S |  | 6 | -6 
    6318 O |  |  | 4 
    6319 Iteration cutoff | 2 
    6320  
    6321 Matchmaker 3j0c.pdb1, chain B (#1.23) with AF3 E2 353-438.pdb, chain B (#115),
    6322 sequence alignment score = 333.4 
    6323 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6324 8.411) 
    6325  
    6326 
    6327 > hide sel cartoons
    6328 
    6329 > select #1.23/C
    6330 
    6331 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6332 
    6333 > show sel cartoons
    6334 
    6335 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6336 
    6337 Chain information for AF3 CA.pdb #116 
    6338 --- 
    6339 Chain | Description 
    6340 A | No description available 
    6341  
    6342 
    6343 > matchmaker #116 to #1.23 & sel
    6344 
    6345 Parameters 
    6346 --- 
    6347 Chain pairing | bb 
    6348 Alignment algorithm | Needleman-Wunsch 
    6349 Similarity matrix | BLOSUM-62 
    6350 SS fraction | 0.3 
    6351 Gap open (HH/SS/other) | 18/18/6 
    6352 Gap extend | 1 
    6353 SS matrix |  |  | H | S | O 
    6354 ---|---|---|--- 
    6355 H | 6 | -9 | -6 
    6356 S |  | 6 | -6 
    6357 O |  |  | 4 
    6358 Iteration cutoff | 2 
    6359  
    6360 Matchmaker 3j0c.pdb1, chain C (#1.23) with AF3 CA.pdb, chain A (#116),
    6361 sequence alignment score = 328.1 
    6362 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6363 2.714) 
    6364  
    6365 
    6366 > hide sel cartoons
    6367 
    6368 > color #112 dodgerblue
    6369 
    6370 > color #113 dodgerblue
    6371 
    6372 > color #114 #00b305ff
    6373 
    6374 > color #115 #00b305ff
    6375 
    6376 > color #116 #f15839ff
    6377 
    6378 > select #1.24/A
    6379 
    6380 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6381 
    6382 > show sel cartoons
    6383 
    6384 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6385 
    6386 Chain information for AF3 E1 1-421.pdb #117 
    6387 --- 
    6388 Chain | Description 
    6389 A | No description available 
    6390  
    6391 
    6392 > matchmaker #117 to #1.24 & sel
    6393 
    6394 Parameters 
    6395 --- 
    6396 Chain pairing | bb 
    6397 Alignment algorithm | Needleman-Wunsch 
    6398 Similarity matrix | BLOSUM-62 
    6399 SS fraction | 0.3 
    6400 Gap open (HH/SS/other) | 18/18/6 
    6401 Gap extend | 1 
    6402 SS matrix |  |  | H | S | O 
    6403 ---|---|---|--- 
    6404 H | 6 | -9 | -6 
    6405 S |  | 6 | -6 
    6406 O |  |  | 4 
    6407 Iteration cutoff | 2 
    6408  
    6409 Matchmaker 3j0c.pdb1, chain A (#1.24) with AF3 E1 1-421.pdb, chain A (#117),
    6410 sequence alignment score = 1060.7 
    6411 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6412 3.020) 
    6413  
    6414 
    6415 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6416 
    6417 Chain information for AF3 E1 422-461.pdb #118 
    6418 --- 
    6419 Chain | Description 
    6420 A | No description available 
    6421  
    6422 
    6423 > matchmaker #118 to #1.24 & sel
    6424 
    6425 Parameters 
    6426 --- 
    6427 Chain pairing | bb 
    6428 Alignment algorithm | Needleman-Wunsch 
    6429 Similarity matrix | BLOSUM-62 
    6430 SS fraction | 0.3 
    6431 Gap open (HH/SS/other) | 18/18/6 
    6432 Gap extend | 1 
    6433 SS matrix |  |  | H | S | O 
    6434 ---|---|---|--- 
    6435 H | 6 | -9 | -6 
    6436 S |  | 6 | -6 
    6437 O |  |  | 4 
    6438 Iteration cutoff | 2 
    6439  
    6440 Matchmaker 3j0c.pdb1, chain A (#1.24) with AF3 E1 422-461.pdb, chain A (#118),
    6441 sequence alignment score = 626.9 
    6442 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    6443 2.775) 
    6444  
    6445 
    6446 > hide sel cartoons
    6447 
    6448 > select #1.24/B
    6449 
    6450 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6451 
    6452 > show sel cartoons
    6453 
    6454 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6455 
    6456 Chain information for AF3 E2 1-352.pdb #119 
    6457 --- 
    6458 Chain | Description 
    6459 B | No description available 
    6460  
    6461 
    6462 > matchmaker #119 to #1.24 & sel
    6463 
    6464 Parameters 
    6465 --- 
    6466 Chain pairing | bb 
    6467 Alignment algorithm | Needleman-Wunsch 
    6468 Similarity matrix | BLOSUM-62 
    6469 SS fraction | 0.3 
    6470 Gap open (HH/SS/other) | 18/18/6 
    6471 Gap extend | 1 
    6472 SS matrix |  |  | H | S | O 
    6473 ---|---|---|--- 
    6474 H | 6 | -9 | -6 
    6475 S |  | 6 | -6 
    6476 O |  |  | 4 
    6477 Iteration cutoff | 2 
    6478  
    6479 Matchmaker 3j0c.pdb1, chain B (#1.24) with AF3 E2 1-352.pdb, chain B (#119),
    6480 sequence alignment score = 583.7 
    6481 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6482 5.933) 
    6483  
    6484 
    6485 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6486 
    6487 Chain information for AF3 E2 353-438.pdb #120 
    6488 --- 
    6489 Chain | Description 
    6490 B | No description available 
    6491  
    6492 
    6493 > matchmaker #120 to #1.24 & sel
    6494 
    6495 Parameters 
    6496 --- 
    6497 Chain pairing | bb 
    6498 Alignment algorithm | Needleman-Wunsch 
    6499 Similarity matrix | BLOSUM-62 
    6500 SS fraction | 0.3 
    6501 Gap open (HH/SS/other) | 18/18/6 
    6502 Gap extend | 1 
    6503 SS matrix |  |  | H | S | O 
    6504 ---|---|---|--- 
    6505 H | 6 | -9 | -6 
    6506 S |  | 6 | -6 
    6507 O |  |  | 4 
    6508 Iteration cutoff | 2 
    6509  
    6510 Matchmaker 3j0c.pdb1, chain B (#1.24) with AF3 E2 353-438.pdb, chain B (#120),
    6511 sequence alignment score = 333.4 
    6512 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6513 8.411) 
    6514  
    6515 
    6516 > hide sel cartoons
    6517 
    6518 > select #1.24/C
    6519 
    6520 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6521 
    6522 > show sel cartoons
    6523 
    6524 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6525 
    6526 Chain information for AF3 CA.pdb #121 
    6527 --- 
    6528 Chain | Description 
    6529 A | No description available 
    6530  
    6531 
    6532 > matchmaker #121 to #1.24 & sel
    6533 
    6534 Parameters 
    6535 --- 
    6536 Chain pairing | bb 
    6537 Alignment algorithm | Needleman-Wunsch 
    6538 Similarity matrix | BLOSUM-62 
    6539 SS fraction | 0.3 
    6540 Gap open (HH/SS/other) | 18/18/6 
    6541 Gap extend | 1 
    6542 SS matrix |  |  | H | S | O 
    6543 ---|---|---|--- 
    6544 H | 6 | -9 | -6 
    6545 S |  | 6 | -6 
    6546 O |  |  | 4 
    6547 Iteration cutoff | 2 
    6548  
    6549 Matchmaker 3j0c.pdb1, chain C (#1.24) with AF3 CA.pdb, chain A (#121),
    6550 sequence alignment score = 328.1 
    6551 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6552 2.714) 
    6553  
    6554 
    6555 > hide sel cartoons
    6556 
    6557 > color #117 dodgerblue
    6558 
    6559 > color #118 dodgerblue
    6560 
    6561 > color #119 #00b305ff
    6562 
    6563 > color #120 #00b305ff
    6564 
    6565 > color #121 #f15839ff
    6566 
    6567 > select #1.25/A
    6568 
    6569 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6570 
    6571 > show sel cartoons
    6572 
    6573 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6574 
    6575 Chain information for AF3 E1 1-421.pdb #122 
    6576 --- 
    6577 Chain | Description 
    6578 A | No description available 
    6579  
    6580 
    6581 > matchmaker #122 to #1.25 & sel
    6582 
    6583 Parameters 
    6584 --- 
    6585 Chain pairing | bb 
    6586 Alignment algorithm | Needleman-Wunsch 
    6587 Similarity matrix | BLOSUM-62 
    6588 SS fraction | 0.3 
    6589 Gap open (HH/SS/other) | 18/18/6 
    6590 Gap extend | 1 
    6591 SS matrix |  |  | H | S | O 
    6592 ---|---|---|--- 
    6593 H | 6 | -9 | -6 
    6594 S |  | 6 | -6 
    6595 O |  |  | 4 
    6596 Iteration cutoff | 2 
    6597  
    6598 Matchmaker 3j0c.pdb1, chain A (#1.25) with AF3 E1 1-421.pdb, chain A (#122),
    6599 sequence alignment score = 1060.7 
    6600 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6601 3.020) 
    6602  
    6603 
    6604 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6605 
    6606 Chain information for AF3 E1 422-461.pdb #123 
    6607 --- 
    6608 Chain | Description 
    6609 A | No description available 
    6610  
    6611 
    6612 > matchmaker #123 to #1.25 & sel
    6613 
    6614 Parameters 
    6615 --- 
    6616 Chain pairing | bb 
    6617 Alignment algorithm | Needleman-Wunsch 
    6618 Similarity matrix | BLOSUM-62 
    6619 SS fraction | 0.3 
    6620 Gap open (HH/SS/other) | 18/18/6 
    6621 Gap extend | 1 
    6622 SS matrix |  |  | H | S | O 
    6623 ---|---|---|--- 
    6624 H | 6 | -9 | -6 
    6625 S |  | 6 | -6 
    6626 O |  |  | 4 
    6627 Iteration cutoff | 2 
    6628  
    6629 Matchmaker 3j0c.pdb1, chain A (#1.25) with AF3 E1 422-461.pdb, chain A (#123),
    6630 sequence alignment score = 626.9 
    6631 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    6632 2.776) 
    6633  
    6634 
    6635 > hide sel cartoons
    6636 
    6637 > select #1.25/B
    6638 
    6639 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6640 
    6641 > show sel cartoons
    6642 
    6643 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6644 
    6645 Chain information for AF3 E2 1-352.pdb #124 
    6646 --- 
    6647 Chain | Description 
    6648 B | No description available 
    6649  
    6650 
    6651 > matchmaker #124 to #1.25 & sel
    6652 
    6653 Parameters 
    6654 --- 
    6655 Chain pairing | bb 
    6656 Alignment algorithm | Needleman-Wunsch 
    6657 Similarity matrix | BLOSUM-62 
    6658 SS fraction | 0.3 
    6659 Gap open (HH/SS/other) | 18/18/6 
    6660 Gap extend | 1 
    6661 SS matrix |  |  | H | S | O 
    6662 ---|---|---|--- 
    6663 H | 6 | -9 | -6 
    6664 S |  | 6 | -6 
    6665 O |  |  | 4 
    6666 Iteration cutoff | 2 
    6667  
    6668 Matchmaker 3j0c.pdb1, chain B (#1.25) with AF3 E2 1-352.pdb, chain B (#124),
    6669 sequence alignment score = 583.7 
    6670 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6671 5.933) 
    6672  
    6673 
    6674 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6675 
    6676 Chain information for AF3 E2 353-438.pdb #125 
    6677 --- 
    6678 Chain | Description 
    6679 B | No description available 
    6680  
    6681 
    6682 > matchmaker #125 to #1.25 & sel
    6683 
    6684 Parameters 
    6685 --- 
    6686 Chain pairing | bb 
    6687 Alignment algorithm | Needleman-Wunsch 
    6688 Similarity matrix | BLOSUM-62 
    6689 SS fraction | 0.3 
    6690 Gap open (HH/SS/other) | 18/18/6 
    6691 Gap extend | 1 
    6692 SS matrix |  |  | H | S | O 
    6693 ---|---|---|--- 
    6694 H | 6 | -9 | -6 
    6695 S |  | 6 | -6 
    6696 O |  |  | 4 
    6697 Iteration cutoff | 2 
    6698  
    6699 Matchmaker 3j0c.pdb1, chain B (#1.25) with AF3 E2 353-438.pdb, chain B (#125),
    6700 sequence alignment score = 333.4 
    6701 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6702 8.411) 
    6703  
    6704 
    6705 > hide sel cartoons
    6706 
    6707 > select #1.25/C
    6708 
    6709 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6710 
    6711 > show sel cartoons
    6712 
    6713 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6714 
    6715 Chain information for AF3 CA.pdb #126 
    6716 --- 
    6717 Chain | Description 
    6718 A | No description available 
    6719  
    6720 
    6721 > matchmaker #126 to #1.25 & sel
    6722 
    6723 Parameters 
    6724 --- 
    6725 Chain pairing | bb 
    6726 Alignment algorithm | Needleman-Wunsch 
    6727 Similarity matrix | BLOSUM-62 
    6728 SS fraction | 0.3 
    6729 Gap open (HH/SS/other) | 18/18/6 
    6730 Gap extend | 1 
    6731 SS matrix |  |  | H | S | O 
    6732 ---|---|---|--- 
    6733 H | 6 | -9 | -6 
    6734 S |  | 6 | -6 
    6735 O |  |  | 4 
    6736 Iteration cutoff | 2 
    6737  
    6738 Matchmaker 3j0c.pdb1, chain C (#1.25) with AF3 CA.pdb, chain A (#126),
    6739 sequence alignment score = 328.1 
    6740 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6741 2.714) 
    6742  
    6743 
    6744 > hide sel cartoons
    6745 
    6746 > color #122 dodgerblue
    6747 
    6748 > color #123 dodgerblue
    6749 
    6750 > color #124 #00b305ff
    6751 
    6752 > color #125 #00b305ff
    6753 
    6754 > color #126 #f15839ff
    6755 
    6756 > select #1.26/A
    6757 
    6758 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6759 
    6760 > show sel cartoons
    6761 
    6762 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6763 
    6764 Chain information for AF3 E1 1-421.pdb #127 
    6765 --- 
    6766 Chain | Description 
    6767 A | No description available 
    6768  
    6769 
    6770 > matchmaker #127 to #1.26 & sel
    6771 
    6772 Parameters 
    6773 --- 
    6774 Chain pairing | bb 
    6775 Alignment algorithm | Needleman-Wunsch 
    6776 Similarity matrix | BLOSUM-62 
    6777 SS fraction | 0.3 
    6778 Gap open (HH/SS/other) | 18/18/6 
    6779 Gap extend | 1 
    6780 SS matrix |  |  | H | S | O 
    6781 ---|---|---|--- 
    6782 H | 6 | -9 | -6 
    6783 S |  | 6 | -6 
    6784 O |  |  | 4 
    6785 Iteration cutoff | 2 
    6786  
    6787 Matchmaker 3j0c.pdb1, chain A (#1.26) with AF3 E1 1-421.pdb, chain A (#127),
    6788 sequence alignment score = 1060.7 
    6789 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6790 3.020) 
    6791  
    6792 
    6793 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6794 
    6795 Chain information for AF3 E1 422-461.pdb #128 
    6796 --- 
    6797 Chain | Description 
    6798 A | No description available 
    6799  
    6800 
    6801 > matchmaker #128 to #1.26 & sel
    6802 
    6803 Parameters 
    6804 --- 
    6805 Chain pairing | bb 
    6806 Alignment algorithm | Needleman-Wunsch 
    6807 Similarity matrix | BLOSUM-62 
    6808 SS fraction | 0.3 
    6809 Gap open (HH/SS/other) | 18/18/6 
    6810 Gap extend | 1 
    6811 SS matrix |  |  | H | S | O 
    6812 ---|---|---|--- 
    6813 H | 6 | -9 | -6 
    6814 S |  | 6 | -6 
    6815 O |  |  | 4 
    6816 Iteration cutoff | 2 
    6817  
    6818 Matchmaker 3j0c.pdb1, chain A (#1.26) with AF3 E1 422-461.pdb, chain A (#128),
    6819 sequence alignment score = 626.9 
    6820 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    6821 2.775) 
    6822  
    6823 
    6824 > hide sel cartoons
    6825 
    6826 > select #1.26/B
    6827 
    6828 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6829 
    6830 > show sel cartoons
    6831 
    6832 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6833 
    6834 Chain information for AF3 E2 1-352.pdb #129 
    6835 --- 
    6836 Chain | Description 
    6837 B | No description available 
    6838  
    6839 
    6840 > matchmaker #129 to #1.26 & sel
    6841 
    6842 Parameters 
    6843 --- 
    6844 Chain pairing | bb 
    6845 Alignment algorithm | Needleman-Wunsch 
    6846 Similarity matrix | BLOSUM-62 
    6847 SS fraction | 0.3 
    6848 Gap open (HH/SS/other) | 18/18/6 
    6849 Gap extend | 1 
    6850 SS matrix |  |  | H | S | O 
    6851 ---|---|---|--- 
    6852 H | 6 | -9 | -6 
    6853 S |  | 6 | -6 
    6854 O |  |  | 4 
    6855 Iteration cutoff | 2 
    6856  
    6857 Matchmaker 3j0c.pdb1, chain B (#1.26) with AF3 E2 1-352.pdb, chain B (#129),
    6858 sequence alignment score = 583.7 
    6859 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6860 5.933) 
    6861  
    6862 
    6863 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6864 
    6865 Chain information for AF3 E2 353-438.pdb #130 
    6866 --- 
    6867 Chain | Description 
    6868 B | No description available 
    6869  
    6870 
    6871 > matchmaker #130 to #1.26 & sel
    6872 
    6873 Parameters 
    6874 --- 
    6875 Chain pairing | bb 
    6876 Alignment algorithm | Needleman-Wunsch 
    6877 Similarity matrix | BLOSUM-62 
    6878 SS fraction | 0.3 
    6879 Gap open (HH/SS/other) | 18/18/6 
    6880 Gap extend | 1 
    6881 SS matrix |  |  | H | S | O 
    6882 ---|---|---|--- 
    6883 H | 6 | -9 | -6 
    6884 S |  | 6 | -6 
    6885 O |  |  | 4 
    6886 Iteration cutoff | 2 
    6887  
    6888 Matchmaker 3j0c.pdb1, chain B (#1.26) with AF3 E2 353-438.pdb, chain B (#130),
    6889 sequence alignment score = 322.6 
    6890 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6891 8.411) 
    6892  
    6893 
    6894 > hide sel cartoons
    6895 
    6896 > select #1.26/C
    6897 
    6898 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6899 
    6900 > show sel cartoons
    6901 
    6902 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6903 
    6904 Chain information for AF3 CA.pdb #131 
    6905 --- 
    6906 Chain | Description 
    6907 A | No description available 
    6908  
    6909 
    6910 > matchmaker #131 to #1.26 & sel
    6911 
    6912 Parameters 
    6913 --- 
    6914 Chain pairing | bb 
    6915 Alignment algorithm | Needleman-Wunsch 
    6916 Similarity matrix | BLOSUM-62 
    6917 SS fraction | 0.3 
    6918 Gap open (HH/SS/other) | 18/18/6 
    6919 Gap extend | 1 
    6920 SS matrix |  |  | H | S | O 
    6921 ---|---|---|--- 
    6922 H | 6 | -9 | -6 
    6923 S |  | 6 | -6 
    6924 O |  |  | 4 
    6925 Iteration cutoff | 2 
    6926  
    6927 Matchmaker 3j0c.pdb1, chain C (#1.26) with AF3 CA.pdb, chain A (#131),
    6928 sequence alignment score = 328.1 
    6929 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6930 2.714) 
    6931  
    6932 
    6933 > hide sel cartoons
    6934 
    6935 > color #127 dodgerblue
    6936 
    6937 > color #128 dodgerblue
    6938 
    6939 > color #129 #00b305ff
    6940 
    6941 > color #130 #00b305ff
    6942 
    6943 > color #131 #f15839ff
    6944 
    6945 > select #1.27/A
    6946 
    6947 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6948 
    6949 > show sel cartoons
    6950 
    6951 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6952 
    6953 Chain information for AF3 E1 1-421.pdb #132 
    6954 --- 
    6955 Chain | Description 
    6956 A | No description available 
    6957  
    6958 
    6959 > matchmaker #132 to #1.27 & sel
    6960 
    6961 Parameters 
    6962 --- 
    6963 Chain pairing | bb 
    6964 Alignment algorithm | Needleman-Wunsch 
    6965 Similarity matrix | BLOSUM-62 
    6966 SS fraction | 0.3 
    6967 Gap open (HH/SS/other) | 18/18/6 
    6968 Gap extend | 1 
    6969 SS matrix |  |  | H | S | O 
    6970 ---|---|---|--- 
    6971 H | 6 | -9 | -6 
    6972 S |  | 6 | -6 
    6973 O |  |  | 4 
    6974 Iteration cutoff | 2 
    6975  
    6976 Matchmaker 3j0c.pdb1, chain A (#1.27) with AF3 E1 1-421.pdb, chain A (#132),
    6977 sequence alignment score = 1060.7 
    6978 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6979 3.020) 
    6980  
    6981 
    6982 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6983 
    6984 Chain information for AF3 E1 422-461.pdb #133 
    6985 --- 
    6986 Chain | Description 
    6987 A | No description available 
    6988  
    6989 
    6990 > matchmaker #133 to #1.27 & sel
    6991 
    6992 Parameters 
    6993 --- 
    6994 Chain pairing | bb 
    6995 Alignment algorithm | Needleman-Wunsch 
    6996 Similarity matrix | BLOSUM-62 
    6997 SS fraction | 0.3 
    6998 Gap open (HH/SS/other) | 18/18/6 
    6999 Gap extend | 1 
    7000 SS matrix |  |  | H | S | O 
    7001 ---|---|---|--- 
    7002 H | 6 | -9 | -6 
    7003 S |  | 6 | -6 
    7004 O |  |  | 4 
    7005 Iteration cutoff | 2 
    7006  
    7007 Matchmaker 3j0c.pdb1, chain A (#1.27) with AF3 E1 422-461.pdb, chain A (#133),
    7008 sequence alignment score = 626.9 
    7009 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    7010 2.775) 
    7011  
    7012 
    7013 > hide sel cartoons
    7014 
    7015 > select #1.27/B
    7016 
    7017 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7018 
    7019 > show sel cartoons
    7020 
    7021 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7022 
    7023 Chain information for AF3 E2 1-352.pdb #134 
    7024 --- 
    7025 Chain | Description 
    7026 B | No description available 
    7027  
    7028 
    7029 > matchmaker #134 to #1.27 & sel
    7030 
    7031 Parameters 
    7032 --- 
    7033 Chain pairing | bb 
    7034 Alignment algorithm | Needleman-Wunsch 
    7035 Similarity matrix | BLOSUM-62 
    7036 SS fraction | 0.3 
    7037 Gap open (HH/SS/other) | 18/18/6 
    7038 Gap extend | 1 
    7039 SS matrix |  |  | H | S | O 
    7040 ---|---|---|--- 
    7041 H | 6 | -9 | -6 
    7042 S |  | 6 | -6 
    7043 O |  |  | 4 
    7044 Iteration cutoff | 2 
    7045  
    7046 Matchmaker 3j0c.pdb1, chain B (#1.27) with AF3 E2 1-352.pdb, chain B (#134),
    7047 sequence alignment score = 583.7 
    7048 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7049 5.933) 
    7050  
    7051 
    7052 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7053 
    7054 Chain information for AF3 E2 353-438.pdb #135 
    7055 --- 
    7056 Chain | Description 
    7057 B | No description available 
    7058  
    7059 
    7060 > matchmaker #135 to #1.27 & sel
    7061 
    7062 Parameters 
    7063 --- 
    7064 Chain pairing | bb 
    7065 Alignment algorithm | Needleman-Wunsch 
    7066 Similarity matrix | BLOSUM-62 
    7067 SS fraction | 0.3 
    7068 Gap open (HH/SS/other) | 18/18/6 
    7069 Gap extend | 1 
    7070 SS matrix |  |  | H | S | O 
    7071 ---|---|---|--- 
    7072 H | 6 | -9 | -6 
    7073 S |  | 6 | -6 
    7074 O |  |  | 4 
    7075 Iteration cutoff | 2 
    7076  
    7077 Matchmaker 3j0c.pdb1, chain B (#1.27) with AF3 E2 353-438.pdb, chain B (#135),
    7078 sequence alignment score = 333.4 
    7079 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7080 8.411) 
    7081  
    7082 
    7083 > hide sel cartoons
    7084 
    7085 > select #1.27/C
    7086 
    7087 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7088 
    7089 > show sel cartoons
    7090 
    7091 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7092 
    7093 Chain information for AF3 CA.pdb #136 
    7094 --- 
    7095 Chain | Description 
    7096 A | No description available 
    7097  
    7098 
    7099 > matchmaker #136 to #1.27 & sel
    7100 
    7101 Parameters 
    7102 --- 
    7103 Chain pairing | bb 
    7104 Alignment algorithm | Needleman-Wunsch 
    7105 Similarity matrix | BLOSUM-62 
    7106 SS fraction | 0.3 
    7107 Gap open (HH/SS/other) | 18/18/6 
    7108 Gap extend | 1 
    7109 SS matrix |  |  | H | S | O 
    7110 ---|---|---|--- 
    7111 H | 6 | -9 | -6 
    7112 S |  | 6 | -6 
    7113 O |  |  | 4 
    7114 Iteration cutoff | 2 
    7115  
    7116 Matchmaker 3j0c.pdb1, chain C (#1.27) with AF3 CA.pdb, chain A (#136),
    7117 sequence alignment score = 328.1 
    7118 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7119 2.714) 
    7120  
    7121 
    7122 > hide sel cartoons
    7123 
    7124 > color #132 dodgerblue
    7125 
    7126 > color #133 dodgerblue
    7127 
    7128 > color #134 #00b305ff
    7129 
    7130 > color #135 #00b305ff
    7131 
    7132 > color #136 #f15839ff
    7133 
    7134 > select #1.28/A
    7135 
    7136 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7137 
    7138 > show sel cartoons
    7139 
    7140 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7141 
    7142 Chain information for AF3 E1 1-421.pdb #137 
    7143 --- 
    7144 Chain | Description 
    7145 A | No description available 
    7146  
    7147 
    7148 > matchmaker #137 to #1.28 & sel
    7149 
    7150 Parameters 
    7151 --- 
    7152 Chain pairing | bb 
    7153 Alignment algorithm | Needleman-Wunsch 
    7154 Similarity matrix | BLOSUM-62 
    7155 SS fraction | 0.3 
    7156 Gap open (HH/SS/other) | 18/18/6 
    7157 Gap extend | 1 
    7158 SS matrix |  |  | H | S | O 
    7159 ---|---|---|--- 
    7160 H | 6 | -9 | -6 
    7161 S |  | 6 | -6 
    7162 O |  |  | 4 
    7163 Iteration cutoff | 2 
    7164  
    7165 Matchmaker 3j0c.pdb1, chain A (#1.28) with AF3 E1 1-421.pdb, chain A (#137),
    7166 sequence alignment score = 1060.7 
    7167 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7168 3.020) 
    7169  
    7170 
    7171 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7172 
    7173 Chain information for AF3 E1 422-461.pdb #138 
    7174 --- 
    7175 Chain | Description 
    7176 A | No description available 
    7177  
    7178 
    7179 > matchmaker #138 to #1.28 & sel
    7180 
    7181 Parameters 
    7182 --- 
    7183 Chain pairing | bb 
    7184 Alignment algorithm | Needleman-Wunsch 
    7185 Similarity matrix | BLOSUM-62 
    7186 SS fraction | 0.3 
    7187 Gap open (HH/SS/other) | 18/18/6 
    7188 Gap extend | 1 
    7189 SS matrix |  |  | H | S | O 
    7190 ---|---|---|--- 
    7191 H | 6 | -9 | -6 
    7192 S |  | 6 | -6 
    7193 O |  |  | 4 
    7194 Iteration cutoff | 2 
    7195  
    7196 Matchmaker 3j0c.pdb1, chain A (#1.28) with AF3 E1 422-461.pdb, chain A (#138),
    7197 sequence alignment score = 626.9 
    7198 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    7199 2.776) 
    7200  
    7201 
    7202 > hide sel cartoons
    7203 
    7204 > select #1.28/B
    7205 
    7206 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7207 
    7208 > show sel cartoons
    7209 
    7210 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7211 
    7212 Chain information for AF3 E2 1-352.pdb #139 
    7213 --- 
    7214 Chain | Description 
    7215 B | No description available 
    7216  
    7217 
    7218 > matchmaker #139 to #1.28 & sel
    7219 
    7220 Parameters 
    7221 --- 
    7222 Chain pairing | bb 
    7223 Alignment algorithm | Needleman-Wunsch 
    7224 Similarity matrix | BLOSUM-62 
    7225 SS fraction | 0.3 
    7226 Gap open (HH/SS/other) | 18/18/6 
    7227 Gap extend | 1 
    7228 SS matrix |  |  | H | S | O 
    7229 ---|---|---|--- 
    7230 H | 6 | -9 | -6 
    7231 S |  | 6 | -6 
    7232 O |  |  | 4 
    7233 Iteration cutoff | 2 
    7234  
    7235 Matchmaker 3j0c.pdb1, chain B (#1.28) with AF3 E2 1-352.pdb, chain B (#139),
    7236 sequence alignment score = 583.7 
    7237 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7238 5.933) 
    7239  
    7240 
    7241 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7242 
    7243 Chain information for AF3 E2 353-438.pdb #140 
    7244 --- 
    7245 Chain | Description 
    7246 B | No description available 
    7247  
    7248 
    7249 > matchmaker #140 to #1.28 & sel
    7250 
    7251 Parameters 
    7252 --- 
    7253 Chain pairing | bb 
    7254 Alignment algorithm | Needleman-Wunsch 
    7255 Similarity matrix | BLOSUM-62 
    7256 SS fraction | 0.3 
    7257 Gap open (HH/SS/other) | 18/18/6 
    7258 Gap extend | 1 
    7259 SS matrix |  |  | H | S | O 
    7260 ---|---|---|--- 
    7261 H | 6 | -9 | -6 
    7262 S |  | 6 | -6 
    7263 O |  |  | 4 
    7264 Iteration cutoff | 2 
    7265  
    7266 Matchmaker 3j0c.pdb1, chain B (#1.28) with AF3 E2 353-438.pdb, chain B (#140),
    7267 sequence alignment score = 333.4 
    7268 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7269 8.411) 
    7270  
    7271 
    7272 > hide sel cartoons
    7273 
    7274 > select #1.28/C
    7275 
    7276 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7277 
    7278 > show sel cartoons
    7279 
    7280 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7281 
    7282 Chain information for AF3 CA.pdb #141 
    7283 --- 
    7284 Chain | Description 
    7285 A | No description available 
    7286  
    7287 
    7288 > matchmaker #141 to #1.28 & sel
    7289 
    7290 Parameters 
    7291 --- 
    7292 Chain pairing | bb 
    7293 Alignment algorithm | Needleman-Wunsch 
    7294 Similarity matrix | BLOSUM-62 
    7295 SS fraction | 0.3 
    7296 Gap open (HH/SS/other) | 18/18/6 
    7297 Gap extend | 1 
    7298 SS matrix |  |  | H | S | O 
    7299 ---|---|---|--- 
    7300 H | 6 | -9 | -6 
    7301 S |  | 6 | -6 
    7302 O |  |  | 4 
    7303 Iteration cutoff | 2 
    7304  
    7305 Matchmaker 3j0c.pdb1, chain C (#1.28) with AF3 CA.pdb, chain A (#141),
    7306 sequence alignment score = 328.1 
    7307 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7308 2.714) 
    7309  
    7310 
    7311 > hide sel cartoons
    7312 
    7313 > color #137 dodgerblue
    7314 
    7315 > color #138 dodgerblue
    7316 
    7317 > color #139 #00b305ff
    7318 
    7319 > color #140 #00b305ff
    7320 
    7321 > color #141 #f15839ff
    7322 
    7323 > select #1.29/A
    7324 
    7325 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7326 
    7327 > show sel cartoons
    7328 
    7329 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7330 
    7331 Chain information for AF3 E1 1-421.pdb #142 
    7332 --- 
    7333 Chain | Description 
    7334 A | No description available 
    7335  
    7336 
    7337 > matchmaker #142 to #1.29 & sel
    7338 
    7339 Parameters 
    7340 --- 
    7341 Chain pairing | bb 
    7342 Alignment algorithm | Needleman-Wunsch 
    7343 Similarity matrix | BLOSUM-62 
    7344 SS fraction | 0.3 
    7345 Gap open (HH/SS/other) | 18/18/6 
    7346 Gap extend | 1 
    7347 SS matrix |  |  | H | S | O 
    7348 ---|---|---|--- 
    7349 H | 6 | -9 | -6 
    7350 S |  | 6 | -6 
    7351 O |  |  | 4 
    7352 Iteration cutoff | 2 
    7353  
    7354 Matchmaker 3j0c.pdb1, chain A (#1.29) with AF3 E1 1-421.pdb, chain A (#142),
    7355 sequence alignment score = 1060.7 
    7356 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7357 3.020) 
    7358  
    7359 
    7360 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7361 
    7362 Chain information for AF3 E1 422-461.pdb #143 
    7363 --- 
    7364 Chain | Description 
    7365 A | No description available 
    7366  
    7367 
    7368 > matchmaker #143 to #1.29 & sel
    7369 
    7370 Parameters 
    7371 --- 
    7372 Chain pairing | bb 
    7373 Alignment algorithm | Needleman-Wunsch 
    7374 Similarity matrix | BLOSUM-62 
    7375 SS fraction | 0.3 
    7376 Gap open (HH/SS/other) | 18/18/6 
    7377 Gap extend | 1 
    7378 SS matrix |  |  | H | S | O 
    7379 ---|---|---|--- 
    7380 H | 6 | -9 | -6 
    7381 S |  | 6 | -6 
    7382 O |  |  | 4 
    7383 Iteration cutoff | 2 
    7384  
    7385 Matchmaker 3j0c.pdb1, chain A (#1.29) with AF3 E1 422-461.pdb, chain A (#143),
    7386 sequence alignment score = 626.9 
    7387 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    7388 2.775) 
    7389  
    7390 
    7391 > hide sel cartoons
    7392 
    7393 > select #1.29/B
    7394 
    7395 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7396 
    7397 > show sel cartoons
    7398 
    7399 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7400 
    7401 Chain information for AF3 E2 1-352.pdb #144 
    7402 --- 
    7403 Chain | Description 
    7404 B | No description available 
    7405  
    7406 
    7407 > matchmaker #144 to #1.29 & sel
    7408 
    7409 Parameters 
    7410 --- 
    7411 Chain pairing | bb 
    7412 Alignment algorithm | Needleman-Wunsch 
    7413 Similarity matrix | BLOSUM-62 
    7414 SS fraction | 0.3 
    7415 Gap open (HH/SS/other) | 18/18/6 
    7416 Gap extend | 1 
    7417 SS matrix |  |  | H | S | O 
    7418 ---|---|---|--- 
    7419 H | 6 | -9 | -6 
    7420 S |  | 6 | -6 
    7421 O |  |  | 4 
    7422 Iteration cutoff | 2 
    7423  
    7424 Matchmaker 3j0c.pdb1, chain B (#1.29) with AF3 E2 1-352.pdb, chain B (#144),
    7425 sequence alignment score = 583.7 
    7426 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7427 5.933) 
    7428  
    7429 
    7430 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7431 
    7432 Chain information for AF3 E2 353-438.pdb #145 
    7433 --- 
    7434 Chain | Description 
    7435 B | No description available 
    7436  
    7437 
    7438 > matchmaker #145 to #1.29 & sel
    7439 
    7440 Parameters 
    7441 --- 
    7442 Chain pairing | bb 
    7443 Alignment algorithm | Needleman-Wunsch 
    7444 Similarity matrix | BLOSUM-62 
    7445 SS fraction | 0.3 
    7446 Gap open (HH/SS/other) | 18/18/6 
    7447 Gap extend | 1 
    7448 SS matrix |  |  | H | S | O 
    7449 ---|---|---|--- 
    7450 H | 6 | -9 | -6 
    7451 S |  | 6 | -6 
    7452 O |  |  | 4 
    7453 Iteration cutoff | 2 
    7454  
    7455 Matchmaker 3j0c.pdb1, chain B (#1.29) with AF3 E2 353-438.pdb, chain B (#145),
    7456 sequence alignment score = 333.4 
    7457 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7458 8.411) 
    7459  
    7460 
    7461 > hide sel cartoons
    7462 
    7463 > select #1.29/C
    7464 
    7465 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7466 
    7467 > show sel cartoons
    7468 
    7469 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7470 
    7471 Chain information for AF3 CA.pdb #146 
    7472 --- 
    7473 Chain | Description 
    7474 A | No description available 
    7475  
    7476 
    7477 > matchmaker #146 to #1.29 & sel
    7478 
    7479 Parameters 
    7480 --- 
    7481 Chain pairing | bb 
    7482 Alignment algorithm | Needleman-Wunsch 
    7483 Similarity matrix | BLOSUM-62 
    7484 SS fraction | 0.3 
    7485 Gap open (HH/SS/other) | 18/18/6 
    7486 Gap extend | 1 
    7487 SS matrix |  |  | H | S | O 
    7488 ---|---|---|--- 
    7489 H | 6 | -9 | -6 
    7490 S |  | 6 | -6 
    7491 O |  |  | 4 
    7492 Iteration cutoff | 2 
    7493  
    7494 Matchmaker 3j0c.pdb1, chain C (#1.29) with AF3 CA.pdb, chain A (#146),
    7495 sequence alignment score = 328.1 
    7496 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7497 2.714) 
    7498  
    7499 
    7500 > hide sel cartoons
    7501 
    7502 > color #142 dodgerblue
    7503 
    7504 > color #143 dodgerblue
    7505 
    7506 > color #144 #00b305ff
    7507 
    7508 > color #145 #00b305ff
    7509 
    7510 > color #146 #f15839ff
    7511 
    7512 > select #1.30/A
    7513 
    7514 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7515 
    7516 > show sel cartoons
    7517 
    7518 > select #1.30/B
    7519 
    7520 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7521 
    7522 > select #1.30/A
    7523 
    7524 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7525 
    7526 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7527 
    7528 Chain information for AF3 E1 1-421.pdb #147 
    7529 --- 
    7530 Chain | Description 
    7531 A | No description available 
    7532  
    7533 
    7534 > matchmaker #147 to #1.30 & sel
    7535 
    7536 Parameters 
    7537 --- 
    7538 Chain pairing | bb 
    7539 Alignment algorithm | Needleman-Wunsch 
    7540 Similarity matrix | BLOSUM-62 
    7541 SS fraction | 0.3 
    7542 Gap open (HH/SS/other) | 18/18/6 
    7543 Gap extend | 1 
    7544 SS matrix |  |  | H | S | O 
    7545 ---|---|---|--- 
    7546 H | 6 | -9 | -6 
    7547 S |  | 6 | -6 
    7548 O |  |  | 4 
    7549 Iteration cutoff | 2 
    7550  
    7551 Matchmaker 3j0c.pdb1, chain A (#1.30) with AF3 E1 1-421.pdb, chain A (#147),
    7552 sequence alignment score = 1060.7 
    7553 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7554 3.020) 
    7555  
    7556 
    7557 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7558 
    7559 Chain information for AF3 E1 422-461.pdb #148 
    7560 --- 
    7561 Chain | Description 
    7562 A | No description available 
    7563  
    7564 
    7565 > matchmaker #148 to #1.30 & sel
    7566 
    7567 Parameters 
    7568 --- 
    7569 Chain pairing | bb 
    7570 Alignment algorithm | Needleman-Wunsch 
    7571 Similarity matrix | BLOSUM-62 
    7572 SS fraction | 0.3 
    7573 Gap open (HH/SS/other) | 18/18/6 
    7574 Gap extend | 1 
    7575 SS matrix |  |  | H | S | O 
    7576 ---|---|---|--- 
    7577 H | 6 | -9 | -6 
    7578 S |  | 6 | -6 
    7579 O |  |  | 4 
    7580 Iteration cutoff | 2 
    7581  
    7582 Matchmaker 3j0c.pdb1, chain A (#1.30) with AF3 E1 422-461.pdb, chain A (#148),
    7583 sequence alignment score = 626.9 
    7584 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    7585 2.775) 
    7586  
    7587 
    7588 > hide sel cartoons
    7589 
    7590 > select #1.30/B
    7591 
    7592 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7593 
    7594 > show sel cartoons
    7595 
    7596 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7597 
    7598 Chain information for AF3 E2 1-352.pdb #149 
    7599 --- 
    7600 Chain | Description 
    7601 B | No description available 
    7602  
    7603 
    7604 > matchmaker #149 to #1.30 & sel
    7605 
    7606 Parameters 
    7607 --- 
    7608 Chain pairing | bb 
    7609 Alignment algorithm | Needleman-Wunsch 
    7610 Similarity matrix | BLOSUM-62 
    7611 SS fraction | 0.3 
    7612 Gap open (HH/SS/other) | 18/18/6 
    7613 Gap extend | 1 
    7614 SS matrix |  |  | H | S | O 
    7615 ---|---|---|--- 
    7616 H | 6 | -9 | -6 
    7617 S |  | 6 | -6 
    7618 O |  |  | 4 
    7619 Iteration cutoff | 2 
    7620  
    7621 Matchmaker 3j0c.pdb1, chain B (#1.30) with AF3 E2 1-352.pdb, chain B (#149),
    7622 sequence alignment score = 583.7 
    7623 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7624 5.933) 
    7625  
    7626 
    7627 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7628 
    7629 Chain information for AF3 E2 353-438.pdb #150 
    7630 --- 
    7631 Chain | Description 
    7632 B | No description available 
    7633  
    7634 
    7635 > matchmaker #150 to #1.30 & sel
    7636 
    7637 Parameters 
    7638 --- 
    7639 Chain pairing | bb 
    7640 Alignment algorithm | Needleman-Wunsch 
    7641 Similarity matrix | BLOSUM-62 
    7642 SS fraction | 0.3 
    7643 Gap open (HH/SS/other) | 18/18/6 
    7644 Gap extend | 1 
    7645 SS matrix |  |  | H | S | O 
    7646 ---|---|---|--- 
    7647 H | 6 | -9 | -6 
    7648 S |  | 6 | -6 
    7649 O |  |  | 4 
    7650 Iteration cutoff | 2 
    7651  
    7652 Matchmaker 3j0c.pdb1, chain B (#1.30) with AF3 E2 353-438.pdb, chain B (#150),
    7653 sequence alignment score = 333.4 
    7654 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7655 8.411) 
    7656  
    7657 
    7658 > hide sel cartoons
    7659 
    7660 > select #1.30/C
    7661 
    7662 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7663 
    7664 > show sel cartoons
    7665 
    7666 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7667 
    7668 Chain information for AF3 CA.pdb #151 
    7669 --- 
    7670 Chain | Description 
    7671 A | No description available 
    7672  
    7673 
    7674 > matchmaker #151 to #1.30 & sel
    7675 
    7676 Parameters 
    7677 --- 
    7678 Chain pairing | bb 
    7679 Alignment algorithm | Needleman-Wunsch 
    7680 Similarity matrix | BLOSUM-62 
    7681 SS fraction | 0.3 
    7682 Gap open (HH/SS/other) | 18/18/6 
    7683 Gap extend | 1 
    7684 SS matrix |  |  | H | S | O 
    7685 ---|---|---|--- 
    7686 H | 6 | -9 | -6 
    7687 S |  | 6 | -6 
    7688 O |  |  | 4 
    7689 Iteration cutoff | 2 
    7690  
    7691 Matchmaker 3j0c.pdb1, chain C (#1.30) with AF3 CA.pdb, chain A (#151),
    7692 sequence alignment score = 328.1 
    7693 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7694 2.714) 
    7695  
    7696 
    7697 > hide sel cartoons
    7698 
    7699 > color #147 dodgerblue
    7700 
    7701 > color #148 dodgerblue
    7702 
    7703 > color #149 #00b305ff
    7704 
    7705 > color #150 #00b305ff
    7706 
    7707 > color #151 #f15839ff
    7708 
    7709 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    7710 
    7711 > select #1.31/A
    7712 
    7713 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7714 
    7715 > show sel cartoons
    7716 
    7717 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7718 
    7719 Chain information for AF3 E1 1-421.pdb #152 
    7720 --- 
    7721 Chain | Description 
    7722 A | No description available 
    7723  
    7724 
    7725 > matchmaker #152 to #1.31 & sel
    7726 
    7727 Parameters 
    7728 --- 
    7729 Chain pairing | bb 
    7730 Alignment algorithm | Needleman-Wunsch 
    7731 Similarity matrix | BLOSUM-62 
    7732 SS fraction | 0.3 
    7733 Gap open (HH/SS/other) | 18/18/6 
    7734 Gap extend | 1 
    7735 SS matrix |  |  | H | S | O 
    7736 ---|---|---|--- 
    7737 H | 6 | -9 | -6 
    7738 S |  | 6 | -6 
    7739 O |  |  | 4 
    7740 Iteration cutoff | 2 
    7741  
    7742 Matchmaker 3j0c.pdb1, chain A (#1.31) with AF3 E1 1-421.pdb, chain A (#152),
    7743 sequence alignment score = 1060.7 
    7744 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7745 3.020) 
    7746  
    7747 
    7748 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7749 
    7750 Chain information for AF3 E1 422-461.pdb #153 
    7751 --- 
    7752 Chain | Description 
    7753 A | No description available 
    7754  
    7755 
    7756 > matchmaker #153 to #1.31 & sel
    7757 
    7758 Parameters 
    7759 --- 
    7760 Chain pairing | bb 
    7761 Alignment algorithm | Needleman-Wunsch 
    7762 Similarity matrix | BLOSUM-62 
    7763 SS fraction | 0.3 
    7764 Gap open (HH/SS/other) | 18/18/6 
    7765 Gap extend | 1 
    7766 SS matrix |  |  | H | S | O 
    7767 ---|---|---|--- 
    7768 H | 6 | -9 | -6 
    7769 S |  | 6 | -6 
    7770 O |  |  | 4 
    7771 Iteration cutoff | 2 
    7772  
    7773 Matchmaker 3j0c.pdb1, chain A (#1.31) with AF3 E1 422-461.pdb, chain A (#153),
    7774 sequence alignment score = 626.9 
    7775 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    7776 2.775) 
    7777  
    7778 
    7779 > hide sel cartoons
    7780 
    7781 > select #1.31/B
    7782 
    7783 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7784 
    7785 > show sel cartoons
    7786 
    7787 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7788 
    7789 Chain information for AF3 E2 1-352.pdb #154 
    7790 --- 
    7791 Chain | Description 
    7792 B | No description available 
    7793  
    7794 
    7795 > matchmaker #154 to #1.31 & sel
    7796 
    7797 Parameters 
    7798 --- 
    7799 Chain pairing | bb 
    7800 Alignment algorithm | Needleman-Wunsch 
    7801 Similarity matrix | BLOSUM-62 
    7802 SS fraction | 0.3 
    7803 Gap open (HH/SS/other) | 18/18/6 
    7804 Gap extend | 1 
    7805 SS matrix |  |  | H | S | O 
    7806 ---|---|---|--- 
    7807 H | 6 | -9 | -6 
    7808 S |  | 6 | -6 
    7809 O |  |  | 4 
    7810 Iteration cutoff | 2 
    7811  
    7812 Matchmaker 3j0c.pdb1, chain B (#1.31) with AF3 E2 1-352.pdb, chain B (#154),
    7813 sequence alignment score = 583.7 
    7814 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7815 5.933) 
    7816  
    7817 
    7818 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7819 
    7820 Chain information for AF3 E2 353-438.pdb #155 
    7821 --- 
    7822 Chain | Description 
    7823 B | No description available 
    7824  
    7825 
    7826 > matchmaker #155 to #1.31 & sel
    7827 
    7828 Parameters 
    7829 --- 
    7830 Chain pairing | bb 
    7831 Alignment algorithm | Needleman-Wunsch 
    7832 Similarity matrix | BLOSUM-62 
    7833 SS fraction | 0.3 
    7834 Gap open (HH/SS/other) | 18/18/6 
    7835 Gap extend | 1 
    7836 SS matrix |  |  | H | S | O 
    7837 ---|---|---|--- 
    7838 H | 6 | -9 | -6 
    7839 S |  | 6 | -6 
    7840 O |  |  | 4 
    7841 Iteration cutoff | 2 
    7842  
    7843 Matchmaker 3j0c.pdb1, chain B (#1.31) with AF3 E2 353-438.pdb, chain B (#155),
    7844 sequence alignment score = 333.4 
    7845 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7846 8.411) 
    7847  
    7848 
    7849 > select #1.31/C
    7850 
    7851 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7852 
    7853 > show sel cartoons
    7854 
    7855 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7856 
    7857 Chain information for AF3 CA.pdb #156 
    7858 --- 
    7859 Chain | Description 
    7860 A | No description available 
    7861  
    7862 
    7863 > matchmaker #156 to #1.31 & sel
    7864 
    7865 Parameters 
    7866 --- 
    7867 Chain pairing | bb 
    7868 Alignment algorithm | Needleman-Wunsch 
    7869 Similarity matrix | BLOSUM-62 
    7870 SS fraction | 0.3 
    7871 Gap open (HH/SS/other) | 18/18/6 
    7872 Gap extend | 1 
    7873 SS matrix |  |  | H | S | O 
    7874 ---|---|---|--- 
    7875 H | 6 | -9 | -6 
    7876 S |  | 6 | -6 
    7877 O |  |  | 4 
    7878 Iteration cutoff | 2 
    7879  
    7880 Matchmaker 3j0c.pdb1, chain C (#1.31) with AF3 CA.pdb, chain A (#156),
    7881 sequence alignment score = 328.1 
    7882 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7883 2.714) 
    7884  
    7885 
    7886 > hide sel cartoons
    7887 
    7888 > select #1.31/B
    7889 
    7890 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7891 
    7892 > hide sel cartoons
    7893 
    7894 > color #152 dodgerblue
    7895 
    7896 > color #153 dodgerblue
    7897 
    7898 > color #154 #00b305ff
    7899 
    7900 > color #155 #00b305ff
    7901 
    7902 > color #156 #f15839ff
    7903 
    7904 > select #1.32/A
    7905 
    7906 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7907 
    7908 > show sel cartoons
    7909 
    7910 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7911 
    7912 Chain information for AF3 E1 1-421.pdb #157 
    7913 --- 
    7914 Chain | Description 
    7915 A | No description available 
    7916  
    7917 
    7918 > matchmaker #157 to #1.32 & sel
    7919 
    7920 Parameters 
    7921 --- 
    7922 Chain pairing | bb 
    7923 Alignment algorithm | Needleman-Wunsch 
    7924 Similarity matrix | BLOSUM-62 
    7925 SS fraction | 0.3 
    7926 Gap open (HH/SS/other) | 18/18/6 
    7927 Gap extend | 1 
    7928 SS matrix |  |  | H | S | O 
    7929 ---|---|---|--- 
    7930 H | 6 | -9 | -6 
    7931 S |  | 6 | -6 
    7932 O |  |  | 4 
    7933 Iteration cutoff | 2 
    7934  
    7935 Matchmaker 3j0c.pdb1, chain A (#1.32) with AF3 E1 1-421.pdb, chain A (#157),
    7936 sequence alignment score = 1060.7 
    7937 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7938 3.020) 
    7939  
    7940 
    7941 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7942 
    7943 Chain information for AF3 E1 422-461.pdb #158 
    7944 --- 
    7945 Chain | Description 
    7946 A | No description available 
    7947  
    7948 
    7949 > matchmaker #158 to #1.32 & sel
    7950 
    7951 Parameters 
    7952 --- 
    7953 Chain pairing | bb 
    7954 Alignment algorithm | Needleman-Wunsch 
    7955 Similarity matrix | BLOSUM-62 
    7956 SS fraction | 0.3 
    7957 Gap open (HH/SS/other) | 18/18/6 
    7958 Gap extend | 1 
    7959 SS matrix |  |  | H | S | O 
    7960 ---|---|---|--- 
    7961 H | 6 | -9 | -6 
    7962 S |  | 6 | -6 
    7963 O |  |  | 4 
    7964 Iteration cutoff | 2 
    7965  
    7966 Matchmaker 3j0c.pdb1, chain A (#1.32) with AF3 E1 422-461.pdb, chain A (#158),
    7967 sequence alignment score = 626.9 
    7968 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    7969 2.775) 
    7970  
    7971 
    7972 > hide sel cartoons
    7973 
    7974 > select #1.32/B
    7975 
    7976 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7977 
    7978 > show sel cartoons
    7979 
    7980 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7981 
    7982 Chain information for AF3 E2 1-352.pdb #159 
    7983 --- 
    7984 Chain | Description 
    7985 B | No description available 
    7986  
    7987 
    7988 > matchmaker #159 to #1.32 & sel
    7989 
    7990 Parameters 
    7991 --- 
    7992 Chain pairing | bb 
    7993 Alignment algorithm | Needleman-Wunsch 
    7994 Similarity matrix | BLOSUM-62 
    7995 SS fraction | 0.3 
    7996 Gap open (HH/SS/other) | 18/18/6 
    7997 Gap extend | 1 
    7998 SS matrix |  |  | H | S | O 
    7999 ---|---|---|--- 
    8000 H | 6 | -9 | -6 
    8001 S |  | 6 | -6 
    8002 O |  |  | 4 
    8003 Iteration cutoff | 2 
    8004  
    8005 Matchmaker 3j0c.pdb1, chain B (#1.32) with AF3 E2 1-352.pdb, chain B (#159),
    8006 sequence alignment score = 583.7 
    8007 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8008 5.933) 
    8009  
    8010 
    8011 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8012 
    8013 Chain information for AF3 E2 353-438.pdb #160 
    8014 --- 
    8015 Chain | Description 
    8016 B | No description available 
    8017  
    8018 
    8019 > matchmaker #160 to #1.32 & sel
    8020 
    8021 Parameters 
    8022 --- 
    8023 Chain pairing | bb 
    8024 Alignment algorithm | Needleman-Wunsch 
    8025 Similarity matrix | BLOSUM-62 
    8026 SS fraction | 0.3 
    8027 Gap open (HH/SS/other) | 18/18/6 
    8028 Gap extend | 1 
    8029 SS matrix |  |  | H | S | O 
    8030 ---|---|---|--- 
    8031 H | 6 | -9 | -6 
    8032 S |  | 6 | -6 
    8033 O |  |  | 4 
    8034 Iteration cutoff | 2 
    8035  
    8036 Matchmaker 3j0c.pdb1, chain B (#1.32) with AF3 E2 353-438.pdb, chain B (#160),
    8037 sequence alignment score = 322.6 
    8038 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8039 8.411) 
    8040  
    8041 
    8042 > hide sel cartoons
    8043 
    8044 > select #1.32/C
    8045 
    8046 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8047 
    8048 > show sel cartoons
    8049 
    8050 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8051 
    8052 Chain information for AF3 CA.pdb #161 
    8053 --- 
    8054 Chain | Description 
    8055 A | No description available 
    8056  
    8057 
    8058 > matchmaker #161 to #1.32 & sel
    8059 
    8060 Parameters 
    8061 --- 
    8062 Chain pairing | bb 
    8063 Alignment algorithm | Needleman-Wunsch 
    8064 Similarity matrix | BLOSUM-62 
    8065 SS fraction | 0.3 
    8066 Gap open (HH/SS/other) | 18/18/6 
    8067 Gap extend | 1 
    8068 SS matrix |  |  | H | S | O 
    8069 ---|---|---|--- 
    8070 H | 6 | -9 | -6 
    8071 S |  | 6 | -6 
    8072 O |  |  | 4 
    8073 Iteration cutoff | 2 
    8074  
    8075 Matchmaker 3j0c.pdb1, chain C (#1.32) with AF3 CA.pdb, chain A (#161),
    8076 sequence alignment score = 328.1 
    8077 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8078 2.714) 
    8079  
    8080 
    8081 > hide sel cartoons
    8082 
    8083 > color #157 dodgerblue
    8084 
    8085 > color #158 dodgerblue
    8086 
    8087 > color #159 #00b305ff
    8088 
    8089 > color #160 #00b305ff
    8090 
    8091 > color #161 #f15839ff
    8092 
    8093 > select #1.33/A
    8094 
    8095 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8096 
    8097 > show sel cartoons
    8098 
    8099 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8100 
    8101 Chain information for AF3 E1 1-421.pdb #162 
    8102 --- 
    8103 Chain | Description 
    8104 A | No description available 
    8105  
    8106 
    8107 > matchmaker #162 to #1.33 & sel
    8108 
    8109 Parameters 
    8110 --- 
    8111 Chain pairing | bb 
    8112 Alignment algorithm | Needleman-Wunsch 
    8113 Similarity matrix | BLOSUM-62 
    8114 SS fraction | 0.3 
    8115 Gap open (HH/SS/other) | 18/18/6 
    8116 Gap extend | 1 
    8117 SS matrix |  |  | H | S | O 
    8118 ---|---|---|--- 
    8119 H | 6 | -9 | -6 
    8120 S |  | 6 | -6 
    8121 O |  |  | 4 
    8122 Iteration cutoff | 2 
    8123  
    8124 Matchmaker 3j0c.pdb1, chain A (#1.33) with AF3 E1 1-421.pdb, chain A (#162),
    8125 sequence alignment score = 1060.7 
    8126 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8127 3.020) 
    8128  
    8129 
    8130 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8131 
    8132 Chain information for AF3 E1 422-461.pdb #163 
    8133 --- 
    8134 Chain | Description 
    8135 A | No description available 
    8136  
    8137 
    8138 > matchmaker #163 to #1.33 & sel
    8139 
    8140 Parameters 
    8141 --- 
    8142 Chain pairing | bb 
    8143 Alignment algorithm | Needleman-Wunsch 
    8144 Similarity matrix | BLOSUM-62 
    8145 SS fraction | 0.3 
    8146 Gap open (HH/SS/other) | 18/18/6 
    8147 Gap extend | 1 
    8148 SS matrix |  |  | H | S | O 
    8149 ---|---|---|--- 
    8150 H | 6 | -9 | -6 
    8151 S |  | 6 | -6 
    8152 O |  |  | 4 
    8153 Iteration cutoff | 2 
    8154  
    8155 Matchmaker 3j0c.pdb1, chain A (#1.33) with AF3 E1 422-461.pdb, chain A (#163),
    8156 sequence alignment score = 626.9 
    8157 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    8158 2.775) 
    8159  
    8160 
    8161 > hide sel cartoons
    8162 
    8163 > select #1.33/B
    8164 
    8165 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8166 
    8167 > show sel cartoons
    8168 
    8169 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8170 
    8171 Chain information for AF3 E2 1-352.pdb #164 
    8172 --- 
    8173 Chain | Description 
    8174 B | No description available 
    8175  
    8176 
    8177 > matchmaker #164 to #1.33 & sel
    8178 
    8179 Parameters 
    8180 --- 
    8181 Chain pairing | bb 
    8182 Alignment algorithm | Needleman-Wunsch 
    8183 Similarity matrix | BLOSUM-62 
    8184 SS fraction | 0.3 
    8185 Gap open (HH/SS/other) | 18/18/6 
    8186 Gap extend | 1 
    8187 SS matrix |  |  | H | S | O 
    8188 ---|---|---|--- 
    8189 H | 6 | -9 | -6 
    8190 S |  | 6 | -6 
    8191 O |  |  | 4 
    8192 Iteration cutoff | 2 
    8193  
    8194 Matchmaker 3j0c.pdb1, chain B (#1.33) with AF3 E2 1-352.pdb, chain B (#164),
    8195 sequence alignment score = 583.7 
    8196 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8197 5.933) 
    8198  
    8199 
    8200 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8201 
    8202 Chain information for AF3 E2 353-438.pdb #165 
    8203 --- 
    8204 Chain | Description 
    8205 B | No description available 
    8206  
    8207 
    8208 > matchmaker #165 to #1.33 & sel
    8209 
    8210 Parameters 
    8211 --- 
    8212 Chain pairing | bb 
    8213 Alignment algorithm | Needleman-Wunsch 
    8214 Similarity matrix | BLOSUM-62 
    8215 SS fraction | 0.3 
    8216 Gap open (HH/SS/other) | 18/18/6 
    8217 Gap extend | 1 
    8218 SS matrix |  |  | H | S | O 
    8219 ---|---|---|--- 
    8220 H | 6 | -9 | -6 
    8221 S |  | 6 | -6 
    8222 O |  |  | 4 
    8223 Iteration cutoff | 2 
    8224  
    8225 Matchmaker 3j0c.pdb1, chain B (#1.33) with AF3 E2 353-438.pdb, chain B (#165),
    8226 sequence alignment score = 322.6 
    8227 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8228 8.411) 
    8229  
    8230 
    8231 > hide sel cartoons
    8232 
    8233 > select #1.33/C
    8234 
    8235 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8236 
    8237 > show sel cartoons
    8238 
    8239 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8240 
    8241 Chain information for AF3 CA.pdb #166 
    8242 --- 
    8243 Chain | Description 
    8244 A | No description available 
    8245  
    8246 
    8247 > matchmaker #166 to #1.33 & sel
    8248 
    8249 Parameters 
    8250 --- 
    8251 Chain pairing | bb 
    8252 Alignment algorithm | Needleman-Wunsch 
    8253 Similarity matrix | BLOSUM-62 
    8254 SS fraction | 0.3 
    8255 Gap open (HH/SS/other) | 18/18/6 
    8256 Gap extend | 1 
    8257 SS matrix |  |  | H | S | O 
    8258 ---|---|---|--- 
    8259 H | 6 | -9 | -6 
    8260 S |  | 6 | -6 
    8261 O |  |  | 4 
    8262 Iteration cutoff | 2 
    8263  
    8264 Matchmaker 3j0c.pdb1, chain C (#1.33) with AF3 CA.pdb, chain A (#166),
    8265 sequence alignment score = 328.1 
    8266 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8267 2.714) 
    8268  
    8269 
    8270 > hide sel cartoons
    8271 
    8272 > color #162 dodgerblue
    8273 
    8274 > color #163 dodgerblue
    8275 
    8276 > color #164 #00b305ff
    8277 
    8278 > color #165 #00b305ff
    8279 
    8280 > color #166 #f15839ff
    8281 
    8282 > select #1.34/A
    8283 
    8284 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8285 
    8286 > show sel cartoons
    8287 
    8288 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8289 
    8290 Chain information for AF3 E1 1-421.pdb #167 
    8291 --- 
    8292 Chain | Description 
    8293 A | No description available 
    8294  
    8295 
    8296 > matchmaker #167 to #1.34 & sel
    8297 
    8298 Parameters 
    8299 --- 
    8300 Chain pairing | bb 
    8301 Alignment algorithm | Needleman-Wunsch 
    8302 Similarity matrix | BLOSUM-62 
    8303 SS fraction | 0.3 
    8304 Gap open (HH/SS/other) | 18/18/6 
    8305 Gap extend | 1 
    8306 SS matrix |  |  | H | S | O 
    8307 ---|---|---|--- 
    8308 H | 6 | -9 | -6 
    8309 S |  | 6 | -6 
    8310 O |  |  | 4 
    8311 Iteration cutoff | 2 
    8312  
    8313 Matchmaker 3j0c.pdb1, chain A (#1.34) with AF3 E1 1-421.pdb, chain A (#167),
    8314 sequence alignment score = 1060.7 
    8315 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8316 3.020) 
    8317  
    8318 
    8319 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8320 
    8321 Chain information for AF3 E1 422-461.pdb #168 
    8322 --- 
    8323 Chain | Description 
    8324 A | No description available 
    8325  
    8326 
    8327 > matchmaker #168 to #1.34 & sel
    8328 
    8329 Parameters 
    8330 --- 
    8331 Chain pairing | bb 
    8332 Alignment algorithm | Needleman-Wunsch 
    8333 Similarity matrix | BLOSUM-62 
    8334 SS fraction | 0.3 
    8335 Gap open (HH/SS/other) | 18/18/6 
    8336 Gap extend | 1 
    8337 SS matrix |  |  | H | S | O 
    8338 ---|---|---|--- 
    8339 H | 6 | -9 | -6 
    8340 S |  | 6 | -6 
    8341 O |  |  | 4 
    8342 Iteration cutoff | 2 
    8343  
    8344 Matchmaker 3j0c.pdb1, chain A (#1.34) with AF3 E1 422-461.pdb, chain A (#168),
    8345 sequence alignment score = 626.9 
    8346 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    8347 2.776) 
    8348  
    8349 
    8350 > hide sel cartoons
    8351 
    8352 > select #1.34/B
    8353 
    8354 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8355 
    8356 > show sel cartoons
    8357 
    8358 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8359 
    8360 Chain information for AF3 E2 1-352.pdb #169 
    8361 --- 
    8362 Chain | Description 
    8363 B | No description available 
    8364  
    8365 
    8366 > matchmaker #169 to #1.34 & sel
    8367 
    8368 Parameters 
    8369 --- 
    8370 Chain pairing | bb 
    8371 Alignment algorithm | Needleman-Wunsch 
    8372 Similarity matrix | BLOSUM-62 
    8373 SS fraction | 0.3 
    8374 Gap open (HH/SS/other) | 18/18/6 
    8375 Gap extend | 1 
    8376 SS matrix |  |  | H | S | O 
    8377 ---|---|---|--- 
    8378 H | 6 | -9 | -6 
    8379 S |  | 6 | -6 
    8380 O |  |  | 4 
    8381 Iteration cutoff | 2 
    8382  
    8383 Matchmaker 3j0c.pdb1, chain B (#1.34) with AF3 E2 1-352.pdb, chain B (#169),
    8384 sequence alignment score = 583.7 
    8385 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8386 5.933) 
    8387  
    8388 
    8389 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8390 
    8391 Chain information for AF3 E2 353-438.pdb #170 
    8392 --- 
    8393 Chain | Description 
    8394 B | No description available 
    8395  
    8396 
    8397 > matchmaker #170 to #1.34 & sel
    8398 
    8399 Parameters 
    8400 --- 
    8401 Chain pairing | bb 
    8402 Alignment algorithm | Needleman-Wunsch 
    8403 Similarity matrix | BLOSUM-62 
    8404 SS fraction | 0.3 
    8405 Gap open (HH/SS/other) | 18/18/6 
    8406 Gap extend | 1 
    8407 SS matrix |  |  | H | S | O 
    8408 ---|---|---|--- 
    8409 H | 6 | -9 | -6 
    8410 S |  | 6 | -6 
    8411 O |  |  | 4 
    8412 Iteration cutoff | 2 
    8413  
    8414 Matchmaker 3j0c.pdb1, chain B (#1.34) with AF3 E2 353-438.pdb, chain B (#170),
    8415 sequence alignment score = 333.4 
    8416 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8417 8.411) 
    8418  
    8419 
    8420 > hide sel cartoons
    8421 
    8422 > select #1.34/C
    8423 
    8424 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8425 
    8426 > show sel cartoons
    8427 
    8428 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8429 
    8430 Chain information for AF3 CA.pdb #171 
    8431 --- 
    8432 Chain | Description 
    8433 A | No description available 
    8434  
    8435 
    8436 > matchmaker #171 to #1.34 & sel
    8437 
    8438 Parameters 
    8439 --- 
    8440 Chain pairing | bb 
    8441 Alignment algorithm | Needleman-Wunsch 
    8442 Similarity matrix | BLOSUM-62 
    8443 SS fraction | 0.3 
    8444 Gap open (HH/SS/other) | 18/18/6 
    8445 Gap extend | 1 
    8446 SS matrix |  |  | H | S | O 
    8447 ---|---|---|--- 
    8448 H | 6 | -9 | -6 
    8449 S |  | 6 | -6 
    8450 O |  |  | 4 
    8451 Iteration cutoff | 2 
    8452  
    8453 Matchmaker 3j0c.pdb1, chain C (#1.34) with AF3 CA.pdb, chain A (#171),
    8454 sequence alignment score = 328.1 
    8455 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8456 2.714) 
    8457  
    8458 
    8459 > hide sel cartoons
    8460 
    8461 > color #167 dodgerblue
    8462 
    8463 > color #168 dodgerblue
    8464 
    8465 > color #169 #00b305ff
    8466 
    8467 > color #170 #00b305ff
    8468 
    8469 > color #171 #f15839ff
    8470 
    8471 > select #1.35/A
    8472 
    8473 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8474 
    8475 > show sel cartoons
    8476 
    8477 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8478 
    8479 Chain information for AF3 E1 1-421.pdb #172 
    8480 --- 
    8481 Chain | Description 
    8482 A | No description available 
    8483  
    8484 
    8485 > matchmaker #172 to #1.35 & sel
    8486 
    8487 Parameters 
    8488 --- 
    8489 Chain pairing | bb 
    8490 Alignment algorithm | Needleman-Wunsch 
    8491 Similarity matrix | BLOSUM-62 
    8492 SS fraction | 0.3 
    8493 Gap open (HH/SS/other) | 18/18/6 
    8494 Gap extend | 1 
    8495 SS matrix |  |  | H | S | O 
    8496 ---|---|---|--- 
    8497 H | 6 | -9 | -6 
    8498 S |  | 6 | -6 
    8499 O |  |  | 4 
    8500 Iteration cutoff | 2 
    8501  
    8502 Matchmaker 3j0c.pdb1, chain A (#1.35) with AF3 E1 1-421.pdb, chain A (#172),
    8503 sequence alignment score = 1060.7 
    8504 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8505 3.020) 
    8506  
    8507 
    8508 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8509 
    8510 Chain information for AF3 E1 422-461.pdb #173 
    8511 --- 
    8512 Chain | Description 
    8513 A | No description available 
    8514  
    8515 
    8516 > matchmaker #173 to #1.35 & sel
    8517 
    8518 Parameters 
    8519 --- 
    8520 Chain pairing | bb 
    8521 Alignment algorithm | Needleman-Wunsch 
    8522 Similarity matrix | BLOSUM-62 
    8523 SS fraction | 0.3 
    8524 Gap open (HH/SS/other) | 18/18/6 
    8525 Gap extend | 1 
    8526 SS matrix |  |  | H | S | O 
    8527 ---|---|---|--- 
    8528 H | 6 | -9 | -6 
    8529 S |  | 6 | -6 
    8530 O |  |  | 4 
    8531 Iteration cutoff | 2 
    8532  
    8533 Matchmaker 3j0c.pdb1, chain A (#1.35) with AF3 E1 422-461.pdb, chain A (#173),
    8534 sequence alignment score = 626.9 
    8535 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    8536 2.775) 
    8537  
    8538 
    8539 > hide sel cartoons
    8540 
    8541 > select #1.35/B
    8542 
    8543 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8544 
    8545 > show sel cartoons
    8546 
    8547 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8548 
    8549 Chain information for AF3 E2 1-352.pdb #174 
    8550 --- 
    8551 Chain | Description 
    8552 B | No description available 
    8553  
    8554 
    8555 > matchmaker #174 to #1.35 & sel
    8556 
    8557 Parameters 
    8558 --- 
    8559 Chain pairing | bb 
    8560 Alignment algorithm | Needleman-Wunsch 
    8561 Similarity matrix | BLOSUM-62 
    8562 SS fraction | 0.3 
    8563 Gap open (HH/SS/other) | 18/18/6 
    8564 Gap extend | 1 
    8565 SS matrix |  |  | H | S | O 
    8566 ---|---|---|--- 
    8567 H | 6 | -9 | -6 
    8568 S |  | 6 | -6 
    8569 O |  |  | 4 
    8570 Iteration cutoff | 2 
    8571  
    8572 Matchmaker 3j0c.pdb1, chain B (#1.35) with AF3 E2 1-352.pdb, chain B (#174),
    8573 sequence alignment score = 583.7 
    8574 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8575 5.933) 
    8576  
    8577 
    8578 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8579 
    8580 Chain information for AF3 E2 353-438.pdb #175 
    8581 --- 
    8582 Chain | Description 
    8583 B | No description available 
    8584  
    8585 
    8586 > matchmaker #175 to #1.35 & sel
    8587 
    8588 Parameters 
    8589 --- 
    8590 Chain pairing | bb 
    8591 Alignment algorithm | Needleman-Wunsch 
    8592 Similarity matrix | BLOSUM-62 
    8593 SS fraction | 0.3 
    8594 Gap open (HH/SS/other) | 18/18/6 
    8595 Gap extend | 1 
    8596 SS matrix |  |  | H | S | O 
    8597 ---|---|---|--- 
    8598 H | 6 | -9 | -6 
    8599 S |  | 6 | -6 
    8600 O |  |  | 4 
    8601 Iteration cutoff | 2 
    8602  
    8603 Matchmaker 3j0c.pdb1, chain B (#1.35) with AF3 E2 353-438.pdb, chain B (#175),
    8604 sequence alignment score = 333.4 
    8605 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8606 8.411) 
    8607  
    8608 
    8609 > hide sel cartoons
    8610 
    8611 > select #1.35/C
    8612 
    8613 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8614 
    8615 > show sel cartoons
    8616 
    8617 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8618 
    8619 Chain information for AF3 CA.pdb #176 
    8620 --- 
    8621 Chain | Description 
    8622 A | No description available 
    8623  
    8624 
    8625 > matchmaker #176 to #1.35 & sel
    8626 
    8627 Parameters 
    8628 --- 
    8629 Chain pairing | bb 
    8630 Alignment algorithm | Needleman-Wunsch 
    8631 Similarity matrix | BLOSUM-62 
    8632 SS fraction | 0.3 
    8633 Gap open (HH/SS/other) | 18/18/6 
    8634 Gap extend | 1 
    8635 SS matrix |  |  | H | S | O 
    8636 ---|---|---|--- 
    8637 H | 6 | -9 | -6 
    8638 S |  | 6 | -6 
    8639 O |  |  | 4 
    8640 Iteration cutoff | 2 
    8641  
    8642 Matchmaker 3j0c.pdb1, chain C (#1.35) with AF3 CA.pdb, chain A (#176),
    8643 sequence alignment score = 328.1 
    8644 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8645 2.714) 
    8646  
    8647 
    8648 > hide sel cartoons
    8649 
    8650 > color #172 dodgerblue
    8651 
    8652 > color #173 dodgerblue
    8653 
    8654 > color #174 #00b305ff
    8655 
    8656 > color #175 #00b305ff
    8657 
    8658 > color #176 #f15839ff
    8659 
    8660 > select #1.36/A
    8661 
    8662 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8663 
    8664 > show sel cartoons
    8665 
    8666 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8667 
    8668 Chain information for AF3 E1 1-421.pdb #177 
    8669 --- 
    8670 Chain | Description 
    8671 A | No description available 
    8672  
    8673 
    8674 > matchmaker #177 to #1.36 & sel
    8675 
    8676 Parameters 
    8677 --- 
    8678 Chain pairing | bb 
    8679 Alignment algorithm | Needleman-Wunsch 
    8680 Similarity matrix | BLOSUM-62 
    8681 SS fraction | 0.3 
    8682 Gap open (HH/SS/other) | 18/18/6 
    8683 Gap extend | 1 
    8684 SS matrix |  |  | H | S | O 
    8685 ---|---|---|--- 
    8686 H | 6 | -9 | -6 
    8687 S |  | 6 | -6 
    8688 O |  |  | 4 
    8689 Iteration cutoff | 2 
    8690  
    8691 Matchmaker 3j0c.pdb1, chain A (#1.36) with AF3 E1 1-421.pdb, chain A (#177),
    8692 sequence alignment score = 1060.7 
    8693 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8694 3.020) 
    8695  
    8696 
    8697 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8698 
    8699 Chain information for AF3 E1 422-461.pdb #178 
    8700 --- 
    8701 Chain | Description 
    8702 A | No description available 
    8703  
    8704 
    8705 > matchmaker #178 to #1.36 & sel
    8706 
    8707 Parameters 
    8708 --- 
    8709 Chain pairing | bb 
    8710 Alignment algorithm | Needleman-Wunsch 
    8711 Similarity matrix | BLOSUM-62 
    8712 SS fraction | 0.3 
    8713 Gap open (HH/SS/other) | 18/18/6 
    8714 Gap extend | 1 
    8715 SS matrix |  |  | H | S | O 
    8716 ---|---|---|--- 
    8717 H | 6 | -9 | -6 
    8718 S |  | 6 | -6 
    8719 O |  |  | 4 
    8720 Iteration cutoff | 2 
    8721  
    8722 Matchmaker 3j0c.pdb1, chain A (#1.36) with AF3 E1 422-461.pdb, chain A (#178),
    8723 sequence alignment score = 626.9 
    8724 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    8725 2.776) 
    8726  
    8727 
    8728 > hide sel cartoons
    8729 
    8730 > select #1.36/B
    8731 
    8732 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8733 
    8734 > show sel cartoons
    8735 
    8736 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8737 
    8738 Chain information for AF3 E2 1-352.pdb #179 
    8739 --- 
    8740 Chain | Description 
    8741 B | No description available 
    8742  
    8743 
    8744 > matchmaker #179 to #1.36 & sel
    8745 
    8746 Parameters 
    8747 --- 
    8748 Chain pairing | bb 
    8749 Alignment algorithm | Needleman-Wunsch 
    8750 Similarity matrix | BLOSUM-62 
    8751 SS fraction | 0.3 
    8752 Gap open (HH/SS/other) | 18/18/6 
    8753 Gap extend | 1 
    8754 SS matrix |  |  | H | S | O 
    8755 ---|---|---|--- 
    8756 H | 6 | -9 | -6 
    8757 S |  | 6 | -6 
    8758 O |  |  | 4 
    8759 Iteration cutoff | 2 
    8760  
    8761 Matchmaker 3j0c.pdb1, chain B (#1.36) with AF3 E2 1-352.pdb, chain B (#179),
    8762 sequence alignment score = 583.7 
    8763 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8764 5.933) 
    8765  
    8766 
    8767 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8768 
    8769 Chain information for AF3 E2 353-438.pdb #180 
    8770 --- 
    8771 Chain | Description 
    8772 B | No description available 
    8773  
    8774 
    8775 > matchmaker #180 to #1.36 & sel
    8776 
    8777 Parameters 
    8778 --- 
    8779 Chain pairing | bb 
    8780 Alignment algorithm | Needleman-Wunsch 
    8781 Similarity matrix | BLOSUM-62 
    8782 SS fraction | 0.3 
    8783 Gap open (HH/SS/other) | 18/18/6 
    8784 Gap extend | 1 
    8785 SS matrix |  |  | H | S | O 
    8786 ---|---|---|--- 
    8787 H | 6 | -9 | -6 
    8788 S |  | 6 | -6 
    8789 O |  |  | 4 
    8790 Iteration cutoff | 2 
    8791  
    8792 Matchmaker 3j0c.pdb1, chain B (#1.36) with AF3 E2 353-438.pdb, chain B (#180),
    8793 sequence alignment score = 333.4 
    8794 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8795 8.411) 
    8796  
    8797 
    8798 > hide sel cartoons
    8799 
    8800 > select #1.36/C
    8801 
    8802 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8803 
    8804 > show sel cartoons
    8805 
    8806 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8807 
    8808 Chain information for AF3 CA.pdb #181 
    8809 --- 
    8810 Chain | Description 
    8811 A | No description available 
    8812  
    8813 
    8814 > matchmaker #181 to #1.36 & sel
    8815 
    8816 Parameters 
    8817 --- 
    8818 Chain pairing | bb 
    8819 Alignment algorithm | Needleman-Wunsch 
    8820 Similarity matrix | BLOSUM-62 
    8821 SS fraction | 0.3 
    8822 Gap open (HH/SS/other) | 18/18/6 
    8823 Gap extend | 1 
    8824 SS matrix |  |  | H | S | O 
    8825 ---|---|---|--- 
    8826 H | 6 | -9 | -6 
    8827 S |  | 6 | -6 
    8828 O |  |  | 4 
    8829 Iteration cutoff | 2 
    8830  
    8831 Matchmaker 3j0c.pdb1, chain C (#1.36) with AF3 CA.pdb, chain A (#181),
    8832 sequence alignment score = 328.1 
    8833 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8834 2.714) 
    8835  
    8836 
    8837 > hide sel cartoons
    8838 
    8839 > color #177 dodgerblue
    8840 
    8841 > color #178 dodgerblue
    8842 
    8843 > color #179 #00b305ff
    8844 
    8845 > color #180 #00b305ff
    8846 
    8847 > color #181 #f15839ff
    8848 
    8849 > select #1.37/A
    8850 
    8851 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8852 
    8853 > show sel cartoons
    8854 
    8855 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8856 
    8857 Chain information for AF3 E1 1-421.pdb #182 
    8858 --- 
    8859 Chain | Description 
    8860 A | No description available 
    8861  
    8862 
    8863 > matchmaker #182 to #1.37 & sel
    8864 
    8865 Parameters 
    8866 --- 
    8867 Chain pairing | bb 
    8868 Alignment algorithm | Needleman-Wunsch 
    8869 Similarity matrix | BLOSUM-62 
    8870 SS fraction | 0.3 
    8871 Gap open (HH/SS/other) | 18/18/6 
    8872 Gap extend | 1 
    8873 SS matrix |  |  | H | S | O 
    8874 ---|---|---|--- 
    8875 H | 6 | -9 | -6 
    8876 S |  | 6 | -6 
    8877 O |  |  | 4 
    8878 Iteration cutoff | 2 
    8879  
    8880 Matchmaker 3j0c.pdb1, chain A (#1.37) with AF3 E1 1-421.pdb, chain A (#182),
    8881 sequence alignment score = 1060.7 
    8882 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8883 3.020) 
    8884  
    8885 
    8886 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8887 
    8888 Chain information for AF3 E1 422-461.pdb #183 
    8889 --- 
    8890 Chain | Description 
    8891 A | No description available 
    8892  
    8893 
    8894 > matchmaker #183 to #1.37 & sel
    8895 
    8896 Parameters 
    8897 --- 
    8898 Chain pairing | bb 
    8899 Alignment algorithm | Needleman-Wunsch 
    8900 Similarity matrix | BLOSUM-62 
    8901 SS fraction | 0.3 
    8902 Gap open (HH/SS/other) | 18/18/6 
    8903 Gap extend | 1 
    8904 SS matrix |  |  | H | S | O 
    8905 ---|---|---|--- 
    8906 H | 6 | -9 | -6 
    8907 S |  | 6 | -6 
    8908 O |  |  | 4 
    8909 Iteration cutoff | 2 
    8910  
    8911 Matchmaker 3j0c.pdb1, chain A (#1.37) with AF3 E1 422-461.pdb, chain A (#183),
    8912 sequence alignment score = 626.9 
    8913 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    8914 2.775) 
    8915  
    8916 
    8917 > hide sel cartoons
    8918 
    8919 > select #1.37/B
    8920 
    8921 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8922 
    8923 > show sel cartoons
    8924 
    8925 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8926 
    8927 Chain information for AF3 E2 1-352.pdb #184 
    8928 --- 
    8929 Chain | Description 
    8930 B | No description available 
    8931  
    8932 
    8933 > matchmaker #184 to #1.37 & sel
    8934 
    8935 Parameters 
    8936 --- 
    8937 Chain pairing | bb 
    8938 Alignment algorithm | Needleman-Wunsch 
    8939 Similarity matrix | BLOSUM-62 
    8940 SS fraction | 0.3 
    8941 Gap open (HH/SS/other) | 18/18/6 
    8942 Gap extend | 1 
    8943 SS matrix |  |  | H | S | O 
    8944 ---|---|---|--- 
    8945 H | 6 | -9 | -6 
    8946 S |  | 6 | -6 
    8947 O |  |  | 4 
    8948 Iteration cutoff | 2 
    8949  
    8950 Matchmaker 3j0c.pdb1, chain B (#1.37) with AF3 E2 1-352.pdb, chain B (#184),
    8951 sequence alignment score = 583.7 
    8952 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8953 5.933) 
    8954  
    8955 
    8956 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8957 
    8958 Chain information for AF3 E2 353-438.pdb #185 
    8959 --- 
    8960 Chain | Description 
    8961 B | No description available 
    8962  
    8963 
    8964 > matchmaker #185 to #1.37 & sel
    8965 
    8966 Parameters 
    8967 --- 
    8968 Chain pairing | bb 
    8969 Alignment algorithm | Needleman-Wunsch 
    8970 Similarity matrix | BLOSUM-62 
    8971 SS fraction | 0.3 
    8972 Gap open (HH/SS/other) | 18/18/6 
    8973 Gap extend | 1 
    8974 SS matrix |  |  | H | S | O 
    8975 ---|---|---|--- 
    8976 H | 6 | -9 | -6 
    8977 S |  | 6 | -6 
    8978 O |  |  | 4 
    8979 Iteration cutoff | 2 
    8980  
    8981 Matchmaker 3j0c.pdb1, chain B (#1.37) with AF3 E2 353-438.pdb, chain B (#185),
    8982 sequence alignment score = 333.4 
    8983 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8984 8.411) 
    8985  
    8986 
    8987 > hide sel cartoons
    8988 
    8989 > select #1.37/C
    8990 
    8991 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8992 
    8993 > show sel cartoons
    8994 
    8995 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8996 
    8997 Chain information for AF3 CA.pdb #186 
    8998 --- 
    8999 Chain | Description 
    9000 A | No description available 
    9001  
    9002 
    9003 > matchmaker #186 to #1.37 & sel
    9004 
    9005 Parameters 
    9006 --- 
    9007 Chain pairing | bb 
    9008 Alignment algorithm | Needleman-Wunsch 
    9009 Similarity matrix | BLOSUM-62 
    9010 SS fraction | 0.3 
    9011 Gap open (HH/SS/other) | 18/18/6 
    9012 Gap extend | 1 
    9013 SS matrix |  |  | H | S | O 
    9014 ---|---|---|--- 
    9015 H | 6 | -9 | -6 
    9016 S |  | 6 | -6 
    9017 O |  |  | 4 
    9018 Iteration cutoff | 2 
    9019  
    9020 Matchmaker 3j0c.pdb1, chain C (#1.37) with AF3 CA.pdb, chain A (#186),
    9021 sequence alignment score = 328.1 
    9022 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9023 2.714) 
    9024  
    9025 
    9026 > hide sel cartoons
    9027 
    9028 > color #182 dodgerblue
    9029 
    9030 > color #183 dodgerblue
    9031 
    9032 > color #184 #00b305ff
    9033 
    9034 > color #185 #00b305ff
    9035 
    9036 > color #186 #f15839ff
    9037 
    9038 > select #1.38/A
    9039 
    9040 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9041 
    9042 > show sel cartoons
    9043 
    9044 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9045 
    9046 Chain information for AF3 E1 1-421.pdb #187 
    9047 --- 
    9048 Chain | Description 
    9049 A | No description available 
    9050  
    9051 
    9052 > matchmaker #187 to #1.38 & sel
    9053 
    9054 Parameters 
    9055 --- 
    9056 Chain pairing | bb 
    9057 Alignment algorithm | Needleman-Wunsch 
    9058 Similarity matrix | BLOSUM-62 
    9059 SS fraction | 0.3 
    9060 Gap open (HH/SS/other) | 18/18/6 
    9061 Gap extend | 1 
    9062 SS matrix |  |  | H | S | O 
    9063 ---|---|---|--- 
    9064 H | 6 | -9 | -6 
    9065 S |  | 6 | -6 
    9066 O |  |  | 4 
    9067 Iteration cutoff | 2 
    9068  
    9069 Matchmaker 3j0c.pdb1, chain A (#1.38) with AF3 E1 1-421.pdb, chain A (#187),
    9070 sequence alignment score = 1060.7 
    9071 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9072 3.020) 
    9073  
    9074 
    9075 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9076 
    9077 Chain information for AF3 E1 422-461.pdb #188 
    9078 --- 
    9079 Chain | Description 
    9080 A | No description available 
    9081  
    9082 
    9083 > matchmaker #188 to #1.38 & sel
    9084 
    9085 Parameters 
    9086 --- 
    9087 Chain pairing | bb 
    9088 Alignment algorithm | Needleman-Wunsch 
    9089 Similarity matrix | BLOSUM-62 
    9090 SS fraction | 0.3 
    9091 Gap open (HH/SS/other) | 18/18/6 
    9092 Gap extend | 1 
    9093 SS matrix |  |  | H | S | O 
    9094 ---|---|---|--- 
    9095 H | 6 | -9 | -6 
    9096 S |  | 6 | -6 
    9097 O |  |  | 4 
    9098 Iteration cutoff | 2 
    9099  
    9100 Matchmaker 3j0c.pdb1, chain A (#1.38) with AF3 E1 422-461.pdb, chain A (#188),
    9101 sequence alignment score = 626.9 
    9102 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9103 2.776) 
    9104  
    9105 
    9106 > hide sel cartoons
    9107 
    9108 > select #1.38/B
    9109 
    9110 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9111 
    9112 > show sel cartoons
    9113 
    9114 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9115 
    9116 Chain information for AF3 E2 1-352.pdb #189 
    9117 --- 
    9118 Chain | Description 
    9119 B | No description available 
    9120  
    9121 
    9122 > matchmaker #189 to #1.38 & sel
    9123 
    9124 Parameters 
    9125 --- 
    9126 Chain pairing | bb 
    9127 Alignment algorithm | Needleman-Wunsch 
    9128 Similarity matrix | BLOSUM-62 
    9129 SS fraction | 0.3 
    9130 Gap open (HH/SS/other) | 18/18/6 
    9131 Gap extend | 1 
    9132 SS matrix |  |  | H | S | O 
    9133 ---|---|---|--- 
    9134 H | 6 | -9 | -6 
    9135 S |  | 6 | -6 
    9136 O |  |  | 4 
    9137 Iteration cutoff | 2 
    9138  
    9139 Matchmaker 3j0c.pdb1, chain B (#1.38) with AF3 E2 1-352.pdb, chain B (#189),
    9140 sequence alignment score = 583.7 
    9141 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9142 5.933) 
    9143  
    9144 
    9145 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9146 
    9147 Chain information for AF3 E2 353-438.pdb #190 
    9148 --- 
    9149 Chain | Description 
    9150 B | No description available 
    9151  
    9152 
    9153 > matchmaker #190 to #1.38 & sel
    9154 
    9155 Parameters 
    9156 --- 
    9157 Chain pairing | bb 
    9158 Alignment algorithm | Needleman-Wunsch 
    9159 Similarity matrix | BLOSUM-62 
    9160 SS fraction | 0.3 
    9161 Gap open (HH/SS/other) | 18/18/6 
    9162 Gap extend | 1 
    9163 SS matrix |  |  | H | S | O 
    9164 ---|---|---|--- 
    9165 H | 6 | -9 | -6 
    9166 S |  | 6 | -6 
    9167 O |  |  | 4 
    9168 Iteration cutoff | 2 
    9169  
    9170 Matchmaker 3j0c.pdb1, chain B (#1.38) with AF3 E2 353-438.pdb, chain B (#190),
    9171 sequence alignment score = 322.6 
    9172 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9173 8.411) 
    9174  
    9175 
    9176 > hide sel cartoons
    9177 
    9178 > select #1.38/C
    9179 
    9180 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9181 
    9182 > show sel cartoons
    9183 
    9184 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9185 
    9186 Chain information for AF3 CA.pdb #191 
    9187 --- 
    9188 Chain | Description 
    9189 A | No description available 
    9190  
    9191 
    9192 > matchmaker #191 to #1.38 & sel
    9193 
    9194 Parameters 
    9195 --- 
    9196 Chain pairing | bb 
    9197 Alignment algorithm | Needleman-Wunsch 
    9198 Similarity matrix | BLOSUM-62 
    9199 SS fraction | 0.3 
    9200 Gap open (HH/SS/other) | 18/18/6 
    9201 Gap extend | 1 
    9202 SS matrix |  |  | H | S | O 
    9203 ---|---|---|--- 
    9204 H | 6 | -9 | -6 
    9205 S |  | 6 | -6 
    9206 O |  |  | 4 
    9207 Iteration cutoff | 2 
    9208  
    9209 Matchmaker 3j0c.pdb1, chain C (#1.38) with AF3 CA.pdb, chain A (#191),
    9210 sequence alignment score = 328.1 
    9211 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9212 2.714) 
    9213  
    9214 
    9215 > hide sel cartoons
    9216 
    9217 > color #187 dodgerblue
    9218 
    9219 > color #188 dodgerblue
    9220 
    9221 > color #189 #00b305ff
    9222 
    9223 > color #190 #00b305ff
    9224 
    9225 > color #191 #f15839ff
    9226 
    9227 > select #1.39/A
    9228 
    9229 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9230 
    9231 > show sel cartoons
    9232 
    9233 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9234 
    9235 Chain information for AF3 E1 1-421.pdb #192 
    9236 --- 
    9237 Chain | Description 
    9238 A | No description available 
    9239  
    9240 
    9241 > matchmaker #192 to #1.39 & sel
    9242 
    9243 Parameters 
    9244 --- 
    9245 Chain pairing | bb 
    9246 Alignment algorithm | Needleman-Wunsch 
    9247 Similarity matrix | BLOSUM-62 
    9248 SS fraction | 0.3 
    9249 Gap open (HH/SS/other) | 18/18/6 
    9250 Gap extend | 1 
    9251 SS matrix |  |  | H | S | O 
    9252 ---|---|---|--- 
    9253 H | 6 | -9 | -6 
    9254 S |  | 6 | -6 
    9255 O |  |  | 4 
    9256 Iteration cutoff | 2 
    9257  
    9258 Matchmaker 3j0c.pdb1, chain A (#1.39) with AF3 E1 1-421.pdb, chain A (#192),
    9259 sequence alignment score = 1060.7 
    9260 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9261 3.020) 
    9262  
    9263 
    9264 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9265 
    9266 Chain information for AF3 E1 422-461.pdb #193 
    9267 --- 
    9268 Chain | Description 
    9269 A | No description available 
    9270  
    9271 
    9272 > matchmaker #193 to #1.39 & sel
    9273 
    9274 Parameters 
    9275 --- 
    9276 Chain pairing | bb 
    9277 Alignment algorithm | Needleman-Wunsch 
    9278 Similarity matrix | BLOSUM-62 
    9279 SS fraction | 0.3 
    9280 Gap open (HH/SS/other) | 18/18/6 
    9281 Gap extend | 1 
    9282 SS matrix |  |  | H | S | O 
    9283 ---|---|---|--- 
    9284 H | 6 | -9 | -6 
    9285 S |  | 6 | -6 
    9286 O |  |  | 4 
    9287 Iteration cutoff | 2 
    9288  
    9289 Matchmaker 3j0c.pdb1, chain A (#1.39) with AF3 E1 422-461.pdb, chain A (#193),
    9290 sequence alignment score = 626.9 
    9291 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9292 2.776) 
    9293  
    9294 
    9295 > hide sel cartoons
    9296 
    9297 > select #1.39/B
    9298 
    9299 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9300 
    9301 > show sel cartoons
    9302 
    9303 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9304 
    9305 Chain information for AF3 E2 1-352.pdb #194 
    9306 --- 
    9307 Chain | Description 
    9308 B | No description available 
    9309  
    9310 
    9311 > matchmaker #194 to #1.39 & sel
    9312 
    9313 Parameters 
    9314 --- 
    9315 Chain pairing | bb 
    9316 Alignment algorithm | Needleman-Wunsch 
    9317 Similarity matrix | BLOSUM-62 
    9318 SS fraction | 0.3 
    9319 Gap open (HH/SS/other) | 18/18/6 
    9320 Gap extend | 1 
    9321 SS matrix |  |  | H | S | O 
    9322 ---|---|---|--- 
    9323 H | 6 | -9 | -6 
    9324 S |  | 6 | -6 
    9325 O |  |  | 4 
    9326 Iteration cutoff | 2 
    9327  
    9328 Matchmaker 3j0c.pdb1, chain B (#1.39) with AF3 E2 1-352.pdb, chain B (#194),
    9329 sequence alignment score = 583.7 
    9330 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9331 5.933) 
    9332  
    9333 
    9334 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9335 
    9336 Chain information for AF3 E2 353-438.pdb #195 
    9337 --- 
    9338 Chain | Description 
    9339 B | No description available 
    9340  
    9341 
    9342 > matchmaker #195 to #1.39 & sel
    9343 
    9344 Parameters 
    9345 --- 
    9346 Chain pairing | bb 
    9347 Alignment algorithm | Needleman-Wunsch 
    9348 Similarity matrix | BLOSUM-62 
    9349 SS fraction | 0.3 
    9350 Gap open (HH/SS/other) | 18/18/6 
    9351 Gap extend | 1 
    9352 SS matrix |  |  | H | S | O 
    9353 ---|---|---|--- 
    9354 H | 6 | -9 | -6 
    9355 S |  | 6 | -6 
    9356 O |  |  | 4 
    9357 Iteration cutoff | 2 
    9358  
    9359 Matchmaker 3j0c.pdb1, chain B (#1.39) with AF3 E2 353-438.pdb, chain B (#195),
    9360 sequence alignment score = 322.6 
    9361 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9362 8.411) 
    9363  
    9364 
    9365 > hide sel cartoons
    9366 
    9367 > select #1.39/C
    9368 
    9369 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9370 
    9371 > show sel atoms
    9372 
    9373 > hide sel atoms
    9374 
    9375 > show sel cartoons
    9376 
    9377 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9378 
    9379 Chain information for AF3 CA.pdb #196 
    9380 --- 
    9381 Chain | Description 
    9382 A | No description available 
    9383  
    9384 
    9385 > matchmaker #196 to #1.39 & sel
    9386 
    9387 Parameters 
    9388 --- 
    9389 Chain pairing | bb 
    9390 Alignment algorithm | Needleman-Wunsch 
    9391 Similarity matrix | BLOSUM-62 
    9392 SS fraction | 0.3 
    9393 Gap open (HH/SS/other) | 18/18/6 
    9394 Gap extend | 1 
    9395 SS matrix |  |  | H | S | O 
    9396 ---|---|---|--- 
    9397 H | 6 | -9 | -6 
    9398 S |  | 6 | -6 
    9399 O |  |  | 4 
    9400 Iteration cutoff | 2 
    9401  
    9402 Matchmaker 3j0c.pdb1, chain C (#1.39) with AF3 CA.pdb, chain A (#196),
    9403 sequence alignment score = 328.1 
    9404 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9405 2.714) 
    9406  
    9407 
    9408 > hide sel cartoons
    9409 
    9410 > color #192 dodgerblue
    9411 
    9412 > color #193 dodgerblue
    9413 
    9414 > color #194 #00b305ff
    9415 
    9416 > color #195 #00b305ff
    9417 
    9418 > color #196 #f15839ff
    9419 
    9420 > select #1.40/A
    9421 
    9422 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9423 
    9424 > show sel cartoons
    9425 
    9426 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9427 
    9428 Chain information for AF3 E1 1-421.pdb #197 
    9429 --- 
    9430 Chain | Description 
    9431 A | No description available 
    9432  
    9433 
    9434 > matchmaker #197 to #1.40 & sel
    9435 
    9436 Parameters 
    9437 --- 
    9438 Chain pairing | bb 
    9439 Alignment algorithm | Needleman-Wunsch 
    9440 Similarity matrix | BLOSUM-62 
    9441 SS fraction | 0.3 
    9442 Gap open (HH/SS/other) | 18/18/6 
    9443 Gap extend | 1 
    9444 SS matrix |  |  | H | S | O 
    9445 ---|---|---|--- 
    9446 H | 6 | -9 | -6 
    9447 S |  | 6 | -6 
    9448 O |  |  | 4 
    9449 Iteration cutoff | 2 
    9450  
    9451 Matchmaker 3j0c.pdb1, chain A (#1.40) with AF3 E1 1-421.pdb, chain A (#197),
    9452 sequence alignment score = 1060.7 
    9453 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9454 3.020) 
    9455  
    9456 
    9457 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9458 
    9459 Chain information for AF3 E1 422-461.pdb #198 
    9460 --- 
    9461 Chain | Description 
    9462 A | No description available 
    9463  
    9464 
    9465 > matchmaker #198 to #1.40 & sel
    9466 
    9467 Parameters 
    9468 --- 
    9469 Chain pairing | bb 
    9470 Alignment algorithm | Needleman-Wunsch 
    9471 Similarity matrix | BLOSUM-62 
    9472 SS fraction | 0.3 
    9473 Gap open (HH/SS/other) | 18/18/6 
    9474 Gap extend | 1 
    9475 SS matrix |  |  | H | S | O 
    9476 ---|---|---|--- 
    9477 H | 6 | -9 | -6 
    9478 S |  | 6 | -6 
    9479 O |  |  | 4 
    9480 Iteration cutoff | 2 
    9481  
    9482 Matchmaker 3j0c.pdb1, chain A (#1.40) with AF3 E1 422-461.pdb, chain A (#198),
    9483 sequence alignment score = 626.9 
    9484 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9485 2.775) 
    9486  
    9487 
    9488 > hide sel cartoons
    9489 
    9490 [Repeated 1 time(s)]
    9491 
    9492 > select #1.40/B
    9493 
    9494 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9495 
    9496 > show sel cartoons
    9497 
    9498 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9499 
    9500 Chain information for AF3 E2 1-352.pdb #199 
    9501 --- 
    9502 Chain | Description 
    9503 B | No description available 
    9504  
    9505 
    9506 > matchmaker #199 to #1.40 & sel
    9507 
    9508 Parameters 
    9509 --- 
    9510 Chain pairing | bb 
    9511 Alignment algorithm | Needleman-Wunsch 
    9512 Similarity matrix | BLOSUM-62 
    9513 SS fraction | 0.3 
    9514 Gap open (HH/SS/other) | 18/18/6 
    9515 Gap extend | 1 
    9516 SS matrix |  |  | H | S | O 
    9517 ---|---|---|--- 
    9518 H | 6 | -9 | -6 
    9519 S |  | 6 | -6 
    9520 O |  |  | 4 
    9521 Iteration cutoff | 2 
    9522  
    9523 Matchmaker 3j0c.pdb1, chain B (#1.40) with AF3 E2 1-352.pdb, chain B (#199),
    9524 sequence alignment score = 583.7 
    9525 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9526 5.933) 
    9527  
    9528 
    9529 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9530 
    9531 Chain information for AF3 E2 353-438.pdb #200 
    9532 --- 
    9533 Chain | Description 
    9534 B | No description available 
    9535  
    9536 
    9537 > matchmaker #200 to #1.40 & sel
    9538 
    9539 Parameters 
    9540 --- 
    9541 Chain pairing | bb 
    9542 Alignment algorithm | Needleman-Wunsch 
    9543 Similarity matrix | BLOSUM-62 
    9544 SS fraction | 0.3 
    9545 Gap open (HH/SS/other) | 18/18/6 
    9546 Gap extend | 1 
    9547 SS matrix |  |  | H | S | O 
    9548 ---|---|---|--- 
    9549 H | 6 | -9 | -6 
    9550 S |  | 6 | -6 
    9551 O |  |  | 4 
    9552 Iteration cutoff | 2 
    9553  
    9554 Matchmaker 3j0c.pdb1, chain B (#1.40) with AF3 E2 353-438.pdb, chain B (#200),
    9555 sequence alignment score = 333.4 
    9556 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9557 8.411) 
    9558  
    9559 
    9560 > hide sel cartoons
    9561 
    9562 > select #1.40/C
    9563 
    9564 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9565 
    9566 > show sel cartoons
    9567 
    9568 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9569 
    9570 Chain information for AF3 CA.pdb #201 
    9571 --- 
    9572 Chain | Description 
    9573 A | No description available 
    9574  
    9575 
    9576 > matchmaker #201 to #1.40 & sel
    9577 
    9578 Parameters 
    9579 --- 
    9580 Chain pairing | bb 
    9581 Alignment algorithm | Needleman-Wunsch 
    9582 Similarity matrix | BLOSUM-62 
    9583 SS fraction | 0.3 
    9584 Gap open (HH/SS/other) | 18/18/6 
    9585 Gap extend | 1 
    9586 SS matrix |  |  | H | S | O 
    9587 ---|---|---|--- 
    9588 H | 6 | -9 | -6 
    9589 S |  | 6 | -6 
    9590 O |  |  | 4 
    9591 Iteration cutoff | 2 
    9592  
    9593 Matchmaker 3j0c.pdb1, chain C (#1.40) with AF3 CA.pdb, chain A (#201),
    9594 sequence alignment score = 328.1 
    9595 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9596 2.714) 
    9597  
    9598 
    9599 > hide sel cartoons
    9600 
    9601 > color #197 dodgerblue
    9602 
    9603 > color #198 dodgerblue
    9604 
    9605 > color #199 #00b305ff
    9606 
    9607 > color #200 #00b305ff
    9608 
    9609 > color #201 #f15839ff
    9610 
    9611 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    9612 
    9613 > select #1.41/A
    9614 
    9615 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9616 
    9617 > show sel cartoons
    9618 
    9619 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9620 
    9621 Chain information for AF3 E1 1-421.pdb #202 
    9622 --- 
    9623 Chain | Description 
    9624 A | No description available 
    9625  
    9626 
    9627 > matchmaker #202 to #1.41 & sel
    9628 
    9629 Parameters 
    9630 --- 
    9631 Chain pairing | bb 
    9632 Alignment algorithm | Needleman-Wunsch 
    9633 Similarity matrix | BLOSUM-62 
    9634 SS fraction | 0.3 
    9635 Gap open (HH/SS/other) | 18/18/6 
    9636 Gap extend | 1 
    9637 SS matrix |  |  | H | S | O 
    9638 ---|---|---|--- 
    9639 H | 6 | -9 | -6 
    9640 S |  | 6 | -6 
    9641 O |  |  | 4 
    9642 Iteration cutoff | 2 
    9643  
    9644 Matchmaker 3j0c.pdb1, chain A (#1.41) with AF3 E1 1-421.pdb, chain A (#202),
    9645 sequence alignment score = 1060.7 
    9646 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9647 3.020) 
    9648  
    9649 
    9650 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9651 
    9652 Chain information for AF3 E1 422-461.pdb #203 
    9653 --- 
    9654 Chain | Description 
    9655 A | No description available 
    9656  
    9657 
    9658 > matchmaker #203 to #1.41 & sel
    9659 
    9660 Parameters 
    9661 --- 
    9662 Chain pairing | bb 
    9663 Alignment algorithm | Needleman-Wunsch 
    9664 Similarity matrix | BLOSUM-62 
    9665 SS fraction | 0.3 
    9666 Gap open (HH/SS/other) | 18/18/6 
    9667 Gap extend | 1 
    9668 SS matrix |  |  | H | S | O 
    9669 ---|---|---|--- 
    9670 H | 6 | -9 | -6 
    9671 S |  | 6 | -6 
    9672 O |  |  | 4 
    9673 Iteration cutoff | 2 
    9674  
    9675 Matchmaker 3j0c.pdb1, chain A (#1.41) with AF3 E1 422-461.pdb, chain A (#203),
    9676 sequence alignment score = 626.9 
    9677 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9678 2.776) 
    9679  
    9680 
    9681 > hide sel cartoons
    9682 
    9683 [Repeated 1 time(s)]
    9684 
    9685 > select #1.41/B
    9686 
    9687 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9688 
    9689 > show sel cartoons
    9690 
    9691 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9692 
    9693 Chain information for AF3 E2 1-352.pdb #204 
    9694 --- 
    9695 Chain | Description 
    9696 B | No description available 
    9697  
    9698 
    9699 > matchmaker #204 to #1.41 & sel
    9700 
    9701 Parameters 
    9702 --- 
    9703 Chain pairing | bb 
    9704 Alignment algorithm | Needleman-Wunsch 
    9705 Similarity matrix | BLOSUM-62 
    9706 SS fraction | 0.3 
    9707 Gap open (HH/SS/other) | 18/18/6 
    9708 Gap extend | 1 
    9709 SS matrix |  |  | H | S | O 
    9710 ---|---|---|--- 
    9711 H | 6 | -9 | -6 
    9712 S |  | 6 | -6 
    9713 O |  |  | 4 
    9714 Iteration cutoff | 2 
    9715  
    9716 Matchmaker 3j0c.pdb1, chain B (#1.41) with AF3 E2 1-352.pdb, chain B (#204),
    9717 sequence alignment score = 583.7 
    9718 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9719 5.933) 
    9720  
    9721 
    9722 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9723 
    9724 Chain information for AF3 E2 353-438.pdb #205 
    9725 --- 
    9726 Chain | Description 
    9727 B | No description available 
    9728  
    9729 
    9730 > matchmaker #205 to #1.41 & sel
    9731 
    9732 Parameters 
    9733 --- 
    9734 Chain pairing | bb 
    9735 Alignment algorithm | Needleman-Wunsch 
    9736 Similarity matrix | BLOSUM-62 
    9737 SS fraction | 0.3 
    9738 Gap open (HH/SS/other) | 18/18/6 
    9739 Gap extend | 1 
    9740 SS matrix |  |  | H | S | O 
    9741 ---|---|---|--- 
    9742 H | 6 | -9 | -6 
    9743 S |  | 6 | -6 
    9744 O |  |  | 4 
    9745 Iteration cutoff | 2 
    9746  
    9747 Matchmaker 3j0c.pdb1, chain B (#1.41) with AF3 E2 353-438.pdb, chain B (#205),
    9748 sequence alignment score = 322.6 
    9749 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9750 8.411) 
    9751  
    9752 
    9753 > hide sel cartoons
    9754 
    9755 > select #1.41/C
    9756 
    9757 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9758 
    9759 > show sel cartoons
    9760 
    9761 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9762 
    9763 Chain information for AF3 CA.pdb #206 
    9764 --- 
    9765 Chain | Description 
    9766 A | No description available 
    9767  
    9768 
    9769 > matchmaker #206 to #1.41 & sel
    9770 
    9771 Parameters 
    9772 --- 
    9773 Chain pairing | bb 
    9774 Alignment algorithm | Needleman-Wunsch 
    9775 Similarity matrix | BLOSUM-62 
    9776 SS fraction | 0.3 
    9777 Gap open (HH/SS/other) | 18/18/6 
    9778 Gap extend | 1 
    9779 SS matrix |  |  | H | S | O 
    9780 ---|---|---|--- 
    9781 H | 6 | -9 | -6 
    9782 S |  | 6 | -6 
    9783 O |  |  | 4 
    9784 Iteration cutoff | 2 
    9785  
    9786 Matchmaker 3j0c.pdb1, chain C (#1.41) with AF3 CA.pdb, chain A (#206),
    9787 sequence alignment score = 328.1 
    9788 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9789 2.714) 
    9790  
    9791 
    9792 > hide sel cartoons
    9793 
    9794 > color #202 dodgerblue
    9795 
    9796 > color #203 dodgerblue
    9797 
    9798 > color #204 #00b305ff
    9799 
    9800 > color #205 #00b305ff
    9801 
    9802 > color #206 #f15839ff
    9803 
    9804 > select #1.42/A
    9805 
    9806 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9807 
    9808 > show sel cartoons
    9809 
    9810 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9811 
    9812 Chain information for AF3 E1 1-421.pdb #207 
    9813 --- 
    9814 Chain | Description 
    9815 A | No description available 
    9816  
    9817 
    9818 > matchmaker #207 to #1.42 & sel
    9819 
    9820 Parameters 
    9821 --- 
    9822 Chain pairing | bb 
    9823 Alignment algorithm | Needleman-Wunsch 
    9824 Similarity matrix | BLOSUM-62 
    9825 SS fraction | 0.3 
    9826 Gap open (HH/SS/other) | 18/18/6 
    9827 Gap extend | 1 
    9828 SS matrix |  |  | H | S | O 
    9829 ---|---|---|--- 
    9830 H | 6 | -9 | -6 
    9831 S |  | 6 | -6 
    9832 O |  |  | 4 
    9833 Iteration cutoff | 2 
    9834  
    9835 Matchmaker 3j0c.pdb1, chain A (#1.42) with AF3 E1 1-421.pdb, chain A (#207),
    9836 sequence alignment score = 1060.7 
    9837 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9838 3.020) 
    9839  
    9840 
    9841 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9842 
    9843 Chain information for AF3 E1 422-461.pdb #208 
    9844 --- 
    9845 Chain | Description 
    9846 A | No description available 
    9847  
    9848 
    9849 > matchmaker #208 to #1.42 & sel
    9850 
    9851 Parameters 
    9852 --- 
    9853 Chain pairing | bb 
    9854 Alignment algorithm | Needleman-Wunsch 
    9855 Similarity matrix | BLOSUM-62 
    9856 SS fraction | 0.3 
    9857 Gap open (HH/SS/other) | 18/18/6 
    9858 Gap extend | 1 
    9859 SS matrix |  |  | H | S | O 
    9860 ---|---|---|--- 
    9861 H | 6 | -9 | -6 
    9862 S |  | 6 | -6 
    9863 O |  |  | 4 
    9864 Iteration cutoff | 2 
    9865  
    9866 Matchmaker 3j0c.pdb1, chain A (#1.42) with AF3 E1 422-461.pdb, chain A (#208),
    9867 sequence alignment score = 626.9 
    9868 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9869 2.776) 
    9870  
    9871 
    9872 > hide sel cartoons
    9873 
    9874 > select #1.42/B
    9875 
    9876 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9877 
    9878 > show sel cartoons
    9879 
    9880 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9881 
    9882 Chain information for AF3 E2 1-352.pdb #209 
    9883 --- 
    9884 Chain | Description 
    9885 B | No description available 
    9886  
    9887 
    9888 > matchmaker #209 to #1.42 & sel
    9889 
    9890 Parameters 
    9891 --- 
    9892 Chain pairing | bb 
    9893 Alignment algorithm | Needleman-Wunsch 
    9894 Similarity matrix | BLOSUM-62 
    9895 SS fraction | 0.3 
    9896 Gap open (HH/SS/other) | 18/18/6 
    9897 Gap extend | 1 
    9898 SS matrix |  |  | H | S | O 
    9899 ---|---|---|--- 
    9900 H | 6 | -9 | -6 
    9901 S |  | 6 | -6 
    9902 O |  |  | 4 
    9903 Iteration cutoff | 2 
    9904  
    9905 Matchmaker 3j0c.pdb1, chain B (#1.42) with AF3 E2 1-352.pdb, chain B (#209),
    9906 sequence alignment score = 583.7 
    9907 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9908 5.933) 
    9909  
    9910 
    9911 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9912 
    9913 Chain information for AF3 E2 353-438.pdb #210 
    9914 --- 
    9915 Chain | Description 
    9916 B | No description available 
    9917  
    9918 
    9919 > matchmaker #210 to #1.42 & sel
    9920 
    9921 Parameters 
    9922 --- 
    9923 Chain pairing | bb 
    9924 Alignment algorithm | Needleman-Wunsch 
    9925 Similarity matrix | BLOSUM-62 
    9926 SS fraction | 0.3 
    9927 Gap open (HH/SS/other) | 18/18/6 
    9928 Gap extend | 1 
    9929 SS matrix |  |  | H | S | O 
    9930 ---|---|---|--- 
    9931 H | 6 | -9 | -6 
    9932 S |  | 6 | -6 
    9933 O |  |  | 4 
    9934 Iteration cutoff | 2 
    9935  
    9936 Matchmaker 3j0c.pdb1, chain B (#1.42) with AF3 E2 353-438.pdb, chain B (#210),
    9937 sequence alignment score = 322.6 
    9938 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9939 8.411) 
    9940  
    9941 
    9942 > hide sel cartoons
    9943 
    9944 > select #1.42/C
    9945 
    9946 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9947 
    9948 > show sel cartoons
    9949 
    9950 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9951 
    9952 Chain information for AF3 CA.pdb #211 
    9953 --- 
    9954 Chain | Description 
    9955 A | No description available 
    9956  
    9957 
    9958 > matchmaker #211 to #1.42 & sel
    9959 
    9960 Parameters 
    9961 --- 
    9962 Chain pairing | bb 
    9963 Alignment algorithm | Needleman-Wunsch 
    9964 Similarity matrix | BLOSUM-62 
    9965 SS fraction | 0.3 
    9966 Gap open (HH/SS/other) | 18/18/6 
    9967 Gap extend | 1 
    9968 SS matrix |  |  | H | S | O 
    9969 ---|---|---|--- 
    9970 H | 6 | -9 | -6 
    9971 S |  | 6 | -6 
    9972 O |  |  | 4 
    9973 Iteration cutoff | 2 
    9974  
    9975 Matchmaker 3j0c.pdb1, chain C (#1.42) with AF3 CA.pdb, chain A (#211),
    9976 sequence alignment score = 328.1 
    9977 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9978 2.714) 
    9979  
    9980 
    9981 > hide sel cartoons
    9982 
    9983 > color #207 dodgerblue
    9984 
    9985 > color #208 dodgerblue
    9986 
    9987 > color #209 #00b305ff
    9988 
    9989 > color #210 #00b305ff
    9990 
    9991 > color #211 #f15839ff
    9992 
    9993 > select #1.43/A
    9994 
    9995 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9996 
    9997 > show sel cartoons
    9998 
    9999 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10000 
    10001 Chain information for AF3 E1 1-421.pdb #212 
    10002 --- 
    10003 Chain | Description 
    10004 A | No description available 
    10005  
    10006 
    10007 > matchmaker #212 to #1.43 & sel
    10008 
    10009 Parameters 
    10010 --- 
    10011 Chain pairing | bb 
    10012 Alignment algorithm | Needleman-Wunsch 
    10013 Similarity matrix | BLOSUM-62 
    10014 SS fraction | 0.3 
    10015 Gap open (HH/SS/other) | 18/18/6 
    10016 Gap extend | 1 
    10017 SS matrix |  |  | H | S | O 
    10018 ---|---|---|--- 
    10019 H | 6 | -9 | -6 
    10020 S |  | 6 | -6 
    10021 O |  |  | 4 
    10022 Iteration cutoff | 2 
    10023  
    10024 Matchmaker 3j0c.pdb1, chain A (#1.43) with AF3 E1 1-421.pdb, chain A (#212),
    10025 sequence alignment score = 1060.7 
    10026 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10027 3.020) 
    10028  
    10029 
    10030 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10031 
    10032 Chain information for AF3 E1 422-461.pdb #213 
    10033 --- 
    10034 Chain | Description 
    10035 A | No description available 
    10036  
    10037 
    10038 > matchmaker #213 to #1.43 & sel
    10039 
    10040 Parameters 
    10041 --- 
    10042 Chain pairing | bb 
    10043 Alignment algorithm | Needleman-Wunsch 
    10044 Similarity matrix | BLOSUM-62 
    10045 SS fraction | 0.3 
    10046 Gap open (HH/SS/other) | 18/18/6 
    10047 Gap extend | 1 
    10048 SS matrix |  |  | H | S | O 
    10049 ---|---|---|--- 
    10050 H | 6 | -9 | -6 
    10051 S |  | 6 | -6 
    10052 O |  |  | 4 
    10053 Iteration cutoff | 2 
    10054  
    10055 Matchmaker 3j0c.pdb1, chain A (#1.43) with AF3 E1 422-461.pdb, chain A (#213),
    10056 sequence alignment score = 626.9 
    10057 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    10058 2.775) 
    10059  
    10060 
    10061 > hide sel cartoons
    10062 
    10063 > select #1.43/B
    10064 
    10065 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10066 
    10067 > show sel cartoons
    10068 
    10069 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10070 
    10071 Chain information for AF3 E2 1-352.pdb #214 
    10072 --- 
    10073 Chain | Description 
    10074 B | No description available 
    10075  
    10076 
    10077 > matchmaker #214 to #1.43 & sel
    10078 
    10079 Parameters 
    10080 --- 
    10081 Chain pairing | bb 
    10082 Alignment algorithm | Needleman-Wunsch 
    10083 Similarity matrix | BLOSUM-62 
    10084 SS fraction | 0.3 
    10085 Gap open (HH/SS/other) | 18/18/6 
    10086 Gap extend | 1 
    10087 SS matrix |  |  | H | S | O 
    10088 ---|---|---|--- 
    10089 H | 6 | -9 | -6 
    10090 S |  | 6 | -6 
    10091 O |  |  | 4 
    10092 Iteration cutoff | 2 
    10093  
    10094 Matchmaker 3j0c.pdb1, chain B (#1.43) with AF3 E2 1-352.pdb, chain B (#214),
    10095 sequence alignment score = 583.7 
    10096 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10097 5.933) 
    10098  
    10099 
    10100 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10101 
    10102 Chain information for AF3 E2 353-438.pdb #215 
    10103 --- 
    10104 Chain | Description 
    10105 B | No description available 
    10106  
    10107 
    10108 > matchmaker #215 to #1.43 & sel
    10109 
    10110 Parameters 
    10111 --- 
    10112 Chain pairing | bb 
    10113 Alignment algorithm | Needleman-Wunsch 
    10114 Similarity matrix | BLOSUM-62 
    10115 SS fraction | 0.3 
    10116 Gap open (HH/SS/other) | 18/18/6 
    10117 Gap extend | 1 
    10118 SS matrix |  |  | H | S | O 
    10119 ---|---|---|--- 
    10120 H | 6 | -9 | -6 
    10121 S |  | 6 | -6 
    10122 O |  |  | 4 
    10123 Iteration cutoff | 2 
    10124  
    10125 Matchmaker 3j0c.pdb1, chain B (#1.43) with AF3 E2 353-438.pdb, chain B (#215),
    10126 sequence alignment score = 333.4 
    10127 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10128 8.411) 
    10129  
    10130 
    10131 > hide sel cartoons
    10132 
    10133 > select #1.43/C
    10134 
    10135 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10136 
    10137 > show sel cartoons
    10138 
    10139 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10140 
    10141 Chain information for AF3 CA.pdb #216 
    10142 --- 
    10143 Chain | Description 
    10144 A | No description available 
    10145  
    10146 
    10147 > matchmaker #216 to #1.43 & sel
    10148 
    10149 Parameters 
    10150 --- 
    10151 Chain pairing | bb 
    10152 Alignment algorithm | Needleman-Wunsch 
    10153 Similarity matrix | BLOSUM-62 
    10154 SS fraction | 0.3 
    10155 Gap open (HH/SS/other) | 18/18/6 
    10156 Gap extend | 1 
    10157 SS matrix |  |  | H | S | O 
    10158 ---|---|---|--- 
    10159 H | 6 | -9 | -6 
    10160 S |  | 6 | -6 
    10161 O |  |  | 4 
    10162 Iteration cutoff | 2 
    10163  
    10164 Matchmaker 3j0c.pdb1, chain C (#1.43) with AF3 CA.pdb, chain A (#216),
    10165 sequence alignment score = 328.1 
    10166 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10167 2.714) 
    10168  
    10169 
    10170 > hide sel cartoons
    10171 
    10172 > color #212 dodgerblue
    10173 
    10174 > color #213 dodgerblue
    10175 
    10176 > color #214 #00b305ff
    10177 
    10178 > color #215 #00b305ff
    10179 
    10180 > color #216 #f15839ff
    10181 
    10182 > select #1.44/A
    10183 
    10184 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10185 
    10186 > show sel cartoons
    10187 
    10188 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10189 
    10190 Chain information for AF3 E1 1-421.pdb #217 
    10191 --- 
    10192 Chain | Description 
    10193 A | No description available 
    10194  
    10195 
    10196 > matchmaker #217 to #1.43 & sel
    10197 
    10198 No 'to' model specified 
    10199 
    10200 > matchmaker #217 to #1.44 & sel
    10201 
    10202 Parameters 
    10203 --- 
    10204 Chain pairing | bb 
    10205 Alignment algorithm | Needleman-Wunsch 
    10206 Similarity matrix | BLOSUM-62 
    10207 SS fraction | 0.3 
    10208 Gap open (HH/SS/other) | 18/18/6 
    10209 Gap extend | 1 
    10210 SS matrix |  |  | H | S | O 
    10211 ---|---|---|--- 
    10212 H | 6 | -9 | -6 
    10213 S |  | 6 | -6 
    10214 O |  |  | 4 
    10215 Iteration cutoff | 2 
    10216  
    10217 Matchmaker 3j0c.pdb1, chain A (#1.44) with AF3 E1 1-421.pdb, chain A (#217),
    10218 sequence alignment score = 1060.7 
    10219 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10220 3.020) 
    10221  
    10222 
    10223 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10224 
    10225 Chain information for AF3 E1 422-461.pdb #218 
    10226 --- 
    10227 Chain | Description 
    10228 A | No description available 
    10229  
    10230 
    10231 > matchmaker #218 to #1.44 & sel
    10232 
    10233 Parameters 
    10234 --- 
    10235 Chain pairing | bb 
    10236 Alignment algorithm | Needleman-Wunsch 
    10237 Similarity matrix | BLOSUM-62 
    10238 SS fraction | 0.3 
    10239 Gap open (HH/SS/other) | 18/18/6 
    10240 Gap extend | 1 
    10241 SS matrix |  |  | H | S | O 
    10242 ---|---|---|--- 
    10243 H | 6 | -9 | -6 
    10244 S |  | 6 | -6 
    10245 O |  |  | 4 
    10246 Iteration cutoff | 2 
    10247  
    10248 Matchmaker 3j0c.pdb1, chain A (#1.44) with AF3 E1 422-461.pdb, chain A (#218),
    10249 sequence alignment score = 626.9 
    10250 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    10251 2.775) 
    10252  
    10253 
    10254 > hide sel cartoons
    10255 
    10256 > select #1.44/B
    10257 
    10258 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10259 
    10260 > show sel cartoons
    10261 
    10262 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10263 
    10264 Chain information for AF3 E2 1-352.pdb #219 
    10265 --- 
    10266 Chain | Description 
    10267 B | No description available 
    10268  
    10269 
    10270 > matchmaker #219 to #1.44 & sel
    10271 
    10272 Parameters 
    10273 --- 
    10274 Chain pairing | bb 
    10275 Alignment algorithm | Needleman-Wunsch 
    10276 Similarity matrix | BLOSUM-62 
    10277 SS fraction | 0.3 
    10278 Gap open (HH/SS/other) | 18/18/6 
    10279 Gap extend | 1 
    10280 SS matrix |  |  | H | S | O 
    10281 ---|---|---|--- 
    10282 H | 6 | -9 | -6 
    10283 S |  | 6 | -6 
    10284 O |  |  | 4 
    10285 Iteration cutoff | 2 
    10286  
    10287 Matchmaker 3j0c.pdb1, chain B (#1.44) with AF3 E2 1-352.pdb, chain B (#219),
    10288 sequence alignment score = 583.7 
    10289 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10290 5.933) 
    10291  
    10292 
    10293 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10294 
    10295 Chain information for AF3 E2 353-438.pdb #220 
    10296 --- 
    10297 Chain | Description 
    10298 B | No description available 
    10299  
    10300 
    10301 > matchmaker #220 to #1.44 & sel
    10302 
    10303 Parameters 
    10304 --- 
    10305 Chain pairing | bb 
    10306 Alignment algorithm | Needleman-Wunsch 
    10307 Similarity matrix | BLOSUM-62 
    10308 SS fraction | 0.3 
    10309 Gap open (HH/SS/other) | 18/18/6 
    10310 Gap extend | 1 
    10311 SS matrix |  |  | H | S | O 
    10312 ---|---|---|--- 
    10313 H | 6 | -9 | -6 
    10314 S |  | 6 | -6 
    10315 O |  |  | 4 
    10316 Iteration cutoff | 2 
    10317  
    10318 Matchmaker 3j0c.pdb1, chain B (#1.44) with AF3 E2 353-438.pdb, chain B (#220),
    10319 sequence alignment score = 333.4 
    10320 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10321 8.411) 
    10322  
    10323 
    10324 > hide sel cartoons
    10325 
    10326 > select #1.44/C
    10327 
    10328 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10329 
    10330 > show sel cartoons
    10331 
    10332 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10333 
    10334 Chain information for AF3 CA.pdb #221 
    10335 --- 
    10336 Chain | Description 
    10337 A | No description available 
    10338  
    10339 
    10340 > matchmaker #221 to #1.44 & sel
    10341 
    10342 Parameters 
    10343 --- 
    10344 Chain pairing | bb 
    10345 Alignment algorithm | Needleman-Wunsch 
    10346 Similarity matrix | BLOSUM-62 
    10347 SS fraction | 0.3 
    10348 Gap open (HH/SS/other) | 18/18/6 
    10349 Gap extend | 1 
    10350 SS matrix |  |  | H | S | O 
    10351 ---|---|---|--- 
    10352 H | 6 | -9 | -6 
    10353 S |  | 6 | -6 
    10354 O |  |  | 4 
    10355 Iteration cutoff | 2 
    10356  
    10357 Matchmaker 3j0c.pdb1, chain C (#1.44) with AF3 CA.pdb, chain A (#221),
    10358 sequence alignment score = 328.1 
    10359 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10360 2.714) 
    10361  
    10362 
    10363 > hide sel cartoons
    10364 
    10365 > color #217 dodgerblue
    10366 
    10367 > color #218 dodgerblue
    10368 
    10369 > color #219 #00b305ff
    10370 
    10371 > color #220 #00b305ff
    10372 
    10373 > color #221 #f15839ff
    10374 
    10375 > select #1.45/A
    10376 
    10377 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10378 
    10379 > show sel cartoons
    10380 
    10381 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10382 
    10383 Chain information for AF3 E1 1-421.pdb #222 
    10384 --- 
    10385 Chain | Description 
    10386 A | No description available 
    10387  
    10388 
    10389 > matchmaker #222 to #1.45 & sel
    10390 
    10391 Parameters 
    10392 --- 
    10393 Chain pairing | bb 
    10394 Alignment algorithm | Needleman-Wunsch 
    10395 Similarity matrix | BLOSUM-62 
    10396 SS fraction | 0.3 
    10397 Gap open (HH/SS/other) | 18/18/6 
    10398 Gap extend | 1 
    10399 SS matrix |  |  | H | S | O 
    10400 ---|---|---|--- 
    10401 H | 6 | -9 | -6 
    10402 S |  | 6 | -6 
    10403 O |  |  | 4 
    10404 Iteration cutoff | 2 
    10405  
    10406 Matchmaker 3j0c.pdb1, chain A (#1.45) with AF3 E1 1-421.pdb, chain A (#222),
    10407 sequence alignment score = 1060.7 
    10408 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10409 3.020) 
    10410  
    10411 
    10412 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10413 
    10414 Chain information for AF3 E1 422-461.pdb #223 
    10415 --- 
    10416 Chain | Description 
    10417 A | No description available 
    10418  
    10419 
    10420 > matchmaker #223 to #1.45 & sel
    10421 
    10422 Parameters 
    10423 --- 
    10424 Chain pairing | bb 
    10425 Alignment algorithm | Needleman-Wunsch 
    10426 Similarity matrix | BLOSUM-62 
    10427 SS fraction | 0.3 
    10428 Gap open (HH/SS/other) | 18/18/6 
    10429 Gap extend | 1 
    10430 SS matrix |  |  | H | S | O 
    10431 ---|---|---|--- 
    10432 H | 6 | -9 | -6 
    10433 S |  | 6 | -6 
    10434 O |  |  | 4 
    10435 Iteration cutoff | 2 
    10436  
    10437 Matchmaker 3j0c.pdb1, chain A (#1.45) with AF3 E1 422-461.pdb, chain A (#223),
    10438 sequence alignment score = 626.9 
    10439 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    10440 2.775) 
    10441  
    10442 
    10443 > hide sel cartoons
    10444 
    10445 [Repeated 1 time(s)]
    10446 
    10447 > select #1.45/B
    10448 
    10449 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10450 
    10451 > show sel cartoons
    10452 
    10453 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10454 
    10455 Chain information for AF3 E2 1-352.pdb #224 
    10456 --- 
    10457 Chain | Description 
    10458 B | No description available 
    10459  
    10460 
    10461 > matchmaker #224 to #1.45 & sel
    10462 
    10463 Parameters 
    10464 --- 
    10465 Chain pairing | bb 
    10466 Alignment algorithm | Needleman-Wunsch 
    10467 Similarity matrix | BLOSUM-62 
    10468 SS fraction | 0.3 
    10469 Gap open (HH/SS/other) | 18/18/6 
    10470 Gap extend | 1 
    10471 SS matrix |  |  | H | S | O 
    10472 ---|---|---|--- 
    10473 H | 6 | -9 | -6 
    10474 S |  | 6 | -6 
    10475 O |  |  | 4 
    10476 Iteration cutoff | 2 
    10477  
    10478 Matchmaker 3j0c.pdb1, chain B (#1.45) with AF3 E2 1-352.pdb, chain B (#224),
    10479 sequence alignment score = 583.7 
    10480 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10481 5.933) 
    10482  
    10483 
    10484 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10485 
    10486 Chain information for AF3 E2 353-438.pdb #225 
    10487 --- 
    10488 Chain | Description 
    10489 B | No description available 
    10490  
    10491 
    10492 > matchmaker #225 to #1.45 & sel
    10493 
    10494 Parameters 
    10495 --- 
    10496 Chain pairing | bb 
    10497 Alignment algorithm | Needleman-Wunsch 
    10498 Similarity matrix | BLOSUM-62 
    10499 SS fraction | 0.3 
    10500 Gap open (HH/SS/other) | 18/18/6 
    10501 Gap extend | 1 
    10502 SS matrix |  |  | H | S | O 
    10503 ---|---|---|--- 
    10504 H | 6 | -9 | -6 
    10505 S |  | 6 | -6 
    10506 O |  |  | 4 
    10507 Iteration cutoff | 2 
    10508  
    10509 Matchmaker 3j0c.pdb1, chain B (#1.45) with AF3 E2 353-438.pdb, chain B (#225),
    10510 sequence alignment score = 333.4 
    10511 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10512 8.411) 
    10513  
    10514 
    10515 > hide sel cartoons
    10516 
    10517 > select #1.45/C
    10518 
    10519 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10520 
    10521 > show sel cartoons
    10522 
    10523 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10524 
    10525 Chain information for AF3 CA.pdb #226 
    10526 --- 
    10527 Chain | Description 
    10528 A | No description available 
    10529  
    10530 
    10531 > matchmaker #226 to #1.45 & sel
    10532 
    10533 Parameters 
    10534 --- 
    10535 Chain pairing | bb 
    10536 Alignment algorithm | Needleman-Wunsch 
    10537 Similarity matrix | BLOSUM-62 
    10538 SS fraction | 0.3 
    10539 Gap open (HH/SS/other) | 18/18/6 
    10540 Gap extend | 1 
    10541 SS matrix |  |  | H | S | O 
    10542 ---|---|---|--- 
    10543 H | 6 | -9 | -6 
    10544 S |  | 6 | -6 
    10545 O |  |  | 4 
    10546 Iteration cutoff | 2 
    10547  
    10548 Matchmaker 3j0c.pdb1, chain C (#1.45) with AF3 CA.pdb, chain A (#226),
    10549 sequence alignment score = 328.1 
    10550 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10551 2.714) 
    10552  
    10553 
    10554 > hide sel cartoons
    10555 
    10556 > color #222 dodgerblue
    10557 
    10558 > color #223 dodgerblue
    10559 
    10560 > color #224 #00b305ff
    10561 
    10562 > color #225 #00b305ff
    10563 
    10564 > color #226 #f15839ff
    10565 
    10566 > select #1.46/A
    10567 
    10568 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10569 
    10570 > show sel cartoons
    10571 
    10572 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10573 
    10574 Chain information for AF3 E1 1-421.pdb #227 
    10575 --- 
    10576 Chain | Description 
    10577 A | No description available 
    10578  
    10579 
    10580 > matchmaker #227 to #1.46 & sel
    10581 
    10582 Parameters 
    10583 --- 
    10584 Chain pairing | bb 
    10585 Alignment algorithm | Needleman-Wunsch 
    10586 Similarity matrix | BLOSUM-62 
    10587 SS fraction | 0.3 
    10588 Gap open (HH/SS/other) | 18/18/6 
    10589 Gap extend | 1 
    10590 SS matrix |  |  | H | S | O 
    10591 ---|---|---|--- 
    10592 H | 6 | -9 | -6 
    10593 S |  | 6 | -6 
    10594 O |  |  | 4 
    10595 Iteration cutoff | 2 
    10596  
    10597 Matchmaker 3j0c.pdb1, chain A (#1.46) with AF3 E1 1-421.pdb, chain A (#227),
    10598 sequence alignment score = 1060.7 
    10599 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10600 3.020) 
    10601  
    10602 
    10603 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10604 
    10605 Chain information for AF3 E1 422-461.pdb #228 
    10606 --- 
    10607 Chain | Description 
    10608 A | No description available 
    10609  
    10610 
    10611 > matchmaker #228 to #1.46 & sel
    10612 
    10613 Parameters 
    10614 --- 
    10615 Chain pairing | bb 
    10616 Alignment algorithm | Needleman-Wunsch 
    10617 Similarity matrix | BLOSUM-62 
    10618 SS fraction | 0.3 
    10619 Gap open (HH/SS/other) | 18/18/6 
    10620 Gap extend | 1 
    10621 SS matrix |  |  | H | S | O 
    10622 ---|---|---|--- 
    10623 H | 6 | -9 | -6 
    10624 S |  | 6 | -6 
    10625 O |  |  | 4 
    10626 Iteration cutoff | 2 
    10627  
    10628 Matchmaker 3j0c.pdb1, chain A (#1.46) with AF3 E1 422-461.pdb, chain A (#228),
    10629 sequence alignment score = 626.9 
    10630 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    10631 2.776) 
    10632  
    10633 
    10634 > hide sel cartoons
    10635 
    10636 > select #1.46/B
    10637 
    10638 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10639 
    10640 > show sel cartoons
    10641 
    10642 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10643 
    10644 Chain information for AF3 E2 1-352.pdb #229 
    10645 --- 
    10646 Chain | Description 
    10647 B | No description available 
    10648  
    10649 
    10650 > matchmaker #229 to #1.46 & sel
    10651 
    10652 Parameters 
    10653 --- 
    10654 Chain pairing | bb 
    10655 Alignment algorithm | Needleman-Wunsch 
    10656 Similarity matrix | BLOSUM-62 
    10657 SS fraction | 0.3 
    10658 Gap open (HH/SS/other) | 18/18/6 
    10659 Gap extend | 1 
    10660 SS matrix |  |  | H | S | O 
    10661 ---|---|---|--- 
    10662 H | 6 | -9 | -6 
    10663 S |  | 6 | -6 
    10664 O |  |  | 4 
    10665 Iteration cutoff | 2 
    10666  
    10667 Matchmaker 3j0c.pdb1, chain B (#1.46) with AF3 E2 1-352.pdb, chain B (#229),
    10668 sequence alignment score = 583.7 
    10669 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10670 5.933) 
    10671  
    10672 
    10673 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10674 
    10675 Chain information for AF3 E2 353-438.pdb #230 
    10676 --- 
    10677 Chain | Description 
    10678 B | No description available 
    10679  
    10680 
    10681 > matchmaker #230 to #1.46 & sel
    10682 
    10683 Parameters 
    10684 --- 
    10685 Chain pairing | bb 
    10686 Alignment algorithm | Needleman-Wunsch 
    10687 Similarity matrix | BLOSUM-62 
    10688 SS fraction | 0.3 
    10689 Gap open (HH/SS/other) | 18/18/6 
    10690 Gap extend | 1 
    10691 SS matrix |  |  | H | S | O 
    10692 ---|---|---|--- 
    10693 H | 6 | -9 | -6 
    10694 S |  | 6 | -6 
    10695 O |  |  | 4 
    10696 Iteration cutoff | 2 
    10697  
    10698 Matchmaker 3j0c.pdb1, chain B (#1.46) with AF3 E2 353-438.pdb, chain B (#230),
    10699 sequence alignment score = 333.4 
    10700 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10701 8.411) 
    10702  
    10703 
    10704 > hide sel cartoons
    10705 
    10706 > select #1.46/C
    10707 
    10708 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10709 
    10710 > show sel cartoons
    10711 
    10712 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10713 
    10714 Chain information for AF3 CA.pdb #231 
    10715 --- 
    10716 Chain | Description 
    10717 A | No description available 
    10718  
    10719 
    10720 > matchmaker #231 to #1.46 & sel
    10721 
    10722 Parameters 
    10723 --- 
    10724 Chain pairing | bb 
    10725 Alignment algorithm | Needleman-Wunsch 
    10726 Similarity matrix | BLOSUM-62 
    10727 SS fraction | 0.3 
    10728 Gap open (HH/SS/other) | 18/18/6 
    10729 Gap extend | 1 
    10730 SS matrix |  |  | H | S | O 
    10731 ---|---|---|--- 
    10732 H | 6 | -9 | -6 
    10733 S |  | 6 | -6 
    10734 O |  |  | 4 
    10735 Iteration cutoff | 2 
    10736  
    10737 Matchmaker 3j0c.pdb1, chain C (#1.46) with AF3 CA.pdb, chain A (#231),
    10738 sequence alignment score = 328.1 
    10739 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10740 2.714) 
    10741  
    10742 
    10743 > hide sel cartoons
    10744 
    10745 > color #227 #408ca2ff
    10746 
    10747 > color #227 dodgerblue
    10748 
    10749 > color #228 dodgerblue
    10750 
    10751 > color #229 #00b305ff
    10752 
    10753 > color #230 #00b305ff
    10754 
    10755 > color #231 #f15839ff
    10756 
    10757 > view sel
    10758 
    10759 No displayed objects specified. 
    10760 
    10761 > select
    10762 > #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#2/A#3/A#6/A#7/A#8/A#11/A#12/A#13/A#16/A#17/A#18/A#21/A#22/A#23/A#26/A#27/A#28/A#31/A#32/A#33/A#36/A#37/A#38/A#41/A#42/A#43/A#46/A#47/A#48/A#51/A#52/A#53/A#56/A#57/A#58/A#61/A#62/A#63/A#66/A#67/A#68/A#71/A#72/A#73/A#76/A#77/A#78/A#81/A#82/A#83/A#86/A#87/A#88/A#91/A#92/A#93/A#96/A#97/A#98/A#101/A#102/A#103/A#106/A#107/A#108/A#111/A#112/A#113/A#116/A#117/A#118/A#121/A#122/A#123/A#126/A#127/A#128/A#131/A#132/A#133/A#136/A#137/A#138/A#141/A#142/A#143/A#146/A#147/A#148/A#151/A#152/A#153/A#156/A#157/A#158/A#161/A#162/A#163/A#166/A#167/A#168/A#171/A#172/A#173/A#176/A#177/A#178/A#181/A#182/A#183/A#186/A#187/A#188/A#191/A#192/A#193/A#196/A#197/A#198/A#201/A#202/A#203/A#206/A#207/A#208/A#211/A#212/A#213/A#216/A#217/A#218/A#221/A#222/A#223/A#226/A#227/A#228/A#231/A
    10763 
    10764 418952 atoms, 429570 bonds, 55178 residues, 198 models selected 
    10765 
    10766 > view sel
    10767 
    10768 > select clear
    10769 
    10770 > select #1.47/A
    10771 
    10772 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10773 
    10774 > show sel cartoons
    10775 
    10776 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10777 
    10778 Chain information for AF3 E1 1-421.pdb #232 
    10779 --- 
    10780 Chain | Description 
    10781 A | No description available 
    10782  
    10783 
    10784 > matchmaker #232 to #1.47 & sel
    10785 
    10786 Parameters 
    10787 --- 
    10788 Chain pairing | bb 
    10789 Alignment algorithm | Needleman-Wunsch 
    10790 Similarity matrix | BLOSUM-62 
    10791 SS fraction | 0.3 
    10792 Gap open (HH/SS/other) | 18/18/6 
    10793 Gap extend | 1 
    10794 SS matrix |  |  | H | S | O 
    10795 ---|---|---|--- 
    10796 H | 6 | -9 | -6 
    10797 S |  | 6 | -6 
    10798 O |  |  | 4 
    10799 Iteration cutoff | 2 
    10800  
    10801 Matchmaker 3j0c.pdb1, chain A (#1.47) with AF3 E1 1-421.pdb, chain A (#232),
    10802 sequence alignment score = 1060.7 
    10803 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10804 3.020) 
    10805  
    10806 
    10807 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10808 
    10809 Chain information for AF3 E1 422-461.pdb #233 
    10810 --- 
    10811 Chain | Description 
    10812 A | No description available 
    10813  
    10814 
    10815 > matchmaker #233 to #1.47 & sel
    10816 
    10817 Parameters 
    10818 --- 
    10819 Chain pairing | bb 
    10820 Alignment algorithm | Needleman-Wunsch 
    10821 Similarity matrix | BLOSUM-62 
    10822 SS fraction | 0.3 
    10823 Gap open (HH/SS/other) | 18/18/6 
    10824 Gap extend | 1 
    10825 SS matrix |  |  | H | S | O 
    10826 ---|---|---|--- 
    10827 H | 6 | -9 | -6 
    10828 S |  | 6 | -6 
    10829 O |  |  | 4 
    10830 Iteration cutoff | 2 
    10831  
    10832 Matchmaker 3j0c.pdb1, chain A (#1.47) with AF3 E1 422-461.pdb, chain A (#233),
    10833 sequence alignment score = 626.9 
    10834 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    10835 2.775) 
    10836  
    10837 
    10838 > hide sel cartoons
    10839 
    10840 > select #1.47/B
    10841 
    10842 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10843 
    10844 > show sel cartoons
    10845 
    10846 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10847 
    10848 Chain information for AF3 E2 1-352.pdb #234 
    10849 --- 
    10850 Chain | Description 
    10851 B | No description available 
    10852  
    10853 
    10854 > matchmaker #234 to #1.47 & sel
    10855 
    10856 Parameters 
    10857 --- 
    10858 Chain pairing | bb 
    10859 Alignment algorithm | Needleman-Wunsch 
    10860 Similarity matrix | BLOSUM-62 
    10861 SS fraction | 0.3 
    10862 Gap open (HH/SS/other) | 18/18/6 
    10863 Gap extend | 1 
    10864 SS matrix |  |  | H | S | O 
    10865 ---|---|---|--- 
    10866 H | 6 | -9 | -6 
    10867 S |  | 6 | -6 
    10868 O |  |  | 4 
    10869 Iteration cutoff | 2 
    10870  
    10871 Matchmaker 3j0c.pdb1, chain B (#1.47) with AF3 E2 1-352.pdb, chain B (#234),
    10872 sequence alignment score = 583.7 
    10873 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10874 5.933) 
    10875  
    10876 
    10877 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10878 
    10879 Chain information for AF3 E2 353-438.pdb #235 
    10880 --- 
    10881 Chain | Description 
    10882 B | No description available 
    10883  
    10884 
    10885 > matchmaker #235 to #1.47 & sel
    10886 
    10887 Parameters 
    10888 --- 
    10889 Chain pairing | bb 
    10890 Alignment algorithm | Needleman-Wunsch 
    10891 Similarity matrix | BLOSUM-62 
    10892 SS fraction | 0.3 
    10893 Gap open (HH/SS/other) | 18/18/6 
    10894 Gap extend | 1 
    10895 SS matrix |  |  | H | S | O 
    10896 ---|---|---|--- 
    10897 H | 6 | -9 | -6 
    10898 S |  | 6 | -6 
    10899 O |  |  | 4 
    10900 Iteration cutoff | 2 
    10901  
    10902 Matchmaker 3j0c.pdb1, chain B (#1.47) with AF3 E2 353-438.pdb, chain B (#235),
    10903 sequence alignment score = 322.6 
    10904 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10905 8.411) 
    10906  
    10907 
    10908 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10909 
    10910 Chain information for AF3 CA.pdb #236 
    10911 --- 
    10912 Chain | Description 
    10913 A | No description available 
    10914  
    10915 
    10916 > hide sel cartoons
    10917 
    10918 > select #1.47/C
    10919 
    10920 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10921 
    10922 > show sel cartoons
    10923 
    10924 > matchmaker #236 to #1.47 & sel
    10925 
    10926 Parameters 
    10927 --- 
    10928 Chain pairing | bb 
    10929 Alignment algorithm | Needleman-Wunsch 
    10930 Similarity matrix | BLOSUM-62 
    10931 SS fraction | 0.3 
    10932 Gap open (HH/SS/other) | 18/18/6 
    10933 Gap extend | 1 
    10934 SS matrix |  |  | H | S | O 
    10935 ---|---|---|--- 
    10936 H | 6 | -9 | -6 
    10937 S |  | 6 | -6 
    10938 O |  |  | 4 
    10939 Iteration cutoff | 2 
    10940  
    10941 Matchmaker 3j0c.pdb1, chain C (#1.47) with AF3 CA.pdb, chain A (#236),
    10942 sequence alignment score = 328.1 
    10943 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10944 2.714) 
    10945  
    10946 
    10947 > hide sel cartoons
    10948 
    10949 > color #232 dodgerblue
    10950 
    10951 > color #233 dodgerblue
    10952 
    10953 > color #234 #00b305ff
    10954 
    10955 > color #235 #00b305ff
    10956 
    10957 > color #236 #f15839ff
    10958 
    10959 > select #1.48/A
    10960 
    10961 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10962 
    10963 > show sel cartoons
    10964 
    10965 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10966 
    10967 Chain information for AF3 E1 1-421.pdb #237 
    10968 --- 
    10969 Chain | Description 
    10970 A | No description available 
    10971  
    10972 
    10973 > matchmaker #237 to #1.48 & sel
    10974 
    10975 Parameters 
    10976 --- 
    10977 Chain pairing | bb 
    10978 Alignment algorithm | Needleman-Wunsch 
    10979 Similarity matrix | BLOSUM-62 
    10980 SS fraction | 0.3 
    10981 Gap open (HH/SS/other) | 18/18/6 
    10982 Gap extend | 1 
    10983 SS matrix |  |  | H | S | O 
    10984 ---|---|---|--- 
    10985 H | 6 | -9 | -6 
    10986 S |  | 6 | -6 
    10987 O |  |  | 4 
    10988 Iteration cutoff | 2 
    10989  
    10990 Matchmaker 3j0c.pdb1, chain A (#1.48) with AF3 E1 1-421.pdb, chain A (#237),
    10991 sequence alignment score = 1060.7 
    10992 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10993 3.020) 
    10994  
    10995 
    10996 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10997 
    10998 Chain information for AF3 E1 422-461.pdb #238 
    10999 --- 
    11000 Chain | Description 
    11001 A | No description available 
    11002  
    11003 
    11004 > matchmaker #238 to #1.48 & sel
    11005 
    11006 Parameters 
    11007 --- 
    11008 Chain pairing | bb 
    11009 Alignment algorithm | Needleman-Wunsch 
    11010 Similarity matrix | BLOSUM-62 
    11011 SS fraction | 0.3 
    11012 Gap open (HH/SS/other) | 18/18/6 
    11013 Gap extend | 1 
    11014 SS matrix |  |  | H | S | O 
    11015 ---|---|---|--- 
    11016 H | 6 | -9 | -6 
    11017 S |  | 6 | -6 
    11018 O |  |  | 4 
    11019 Iteration cutoff | 2 
    11020  
    11021 Matchmaker 3j0c.pdb1, chain A (#1.48) with AF3 E1 422-461.pdb, chain A (#238),
    11022 sequence alignment score = 626.9 
    11023 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    11024 2.775) 
    11025  
    11026 
    11027 > hide sel cartoons
    11028 
    11029 > select #1.48/B
    11030 
    11031 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11032 
    11033 > show sel cartoons
    11034 
    11035 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11036 
    11037 Chain information for AF3 E2 1-352.pdb #239 
    11038 --- 
    11039 Chain | Description 
    11040 B | No description available 
    11041  
    11042 
    11043 > matchmaker #239 to #1.48 & sel
    11044 
    11045 Parameters 
    11046 --- 
    11047 Chain pairing | bb 
    11048 Alignment algorithm | Needleman-Wunsch 
    11049 Similarity matrix | BLOSUM-62 
    11050 SS fraction | 0.3 
    11051 Gap open (HH/SS/other) | 18/18/6 
    11052 Gap extend | 1 
    11053 SS matrix |  |  | H | S | O 
    11054 ---|---|---|--- 
    11055 H | 6 | -9 | -6 
    11056 S |  | 6 | -6 
    11057 O |  |  | 4 
    11058 Iteration cutoff | 2 
    11059  
    11060 Matchmaker 3j0c.pdb1, chain B (#1.48) with AF3 E2 1-352.pdb, chain B (#239),
    11061 sequence alignment score = 583.7 
    11062 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11063 5.933) 
    11064  
    11065 
    11066 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11067 
    11068 Chain information for AF3 E2 353-438.pdb #240 
    11069 --- 
    11070 Chain | Description 
    11071 B | No description available 
    11072  
    11073 
    11074 > matchmaker #240 to #1.48 & sel
    11075 
    11076 Parameters 
    11077 --- 
    11078 Chain pairing | bb 
    11079 Alignment algorithm | Needleman-Wunsch 
    11080 Similarity matrix | BLOSUM-62 
    11081 SS fraction | 0.3 
    11082 Gap open (HH/SS/other) | 18/18/6 
    11083 Gap extend | 1 
    11084 SS matrix |  |  | H | S | O 
    11085 ---|---|---|--- 
    11086 H | 6 | -9 | -6 
    11087 S |  | 6 | -6 
    11088 O |  |  | 4 
    11089 Iteration cutoff | 2 
    11090  
    11091 Matchmaker 3j0c.pdb1, chain B (#1.48) with AF3 E2 353-438.pdb, chain B (#240),
    11092 sequence alignment score = 322.6 
    11093 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11094 8.411) 
    11095  
    11096 
    11097 > hide sel cartoons
    11098 
    11099 > select #1.48/B
    11100 
    11101 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11102 
    11103 > show sel cartoons
    11104 
    11105 > hide sel cartoons
    11106 
    11107 > select #1.48/C
    11108 
    11109 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11110 
    11111 > show sel cartoons
    11112 
    11113 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11114 
    11115 Chain information for AF3 CA.pdb #241 
    11116 --- 
    11117 Chain | Description 
    11118 A | No description available 
    11119  
    11120 
    11121 > matchmaker #241 to #1.48 & sel
    11122 
    11123 Parameters 
    11124 --- 
    11125 Chain pairing | bb 
    11126 Alignment algorithm | Needleman-Wunsch 
    11127 Similarity matrix | BLOSUM-62 
    11128 SS fraction | 0.3 
    11129 Gap open (HH/SS/other) | 18/18/6 
    11130 Gap extend | 1 
    11131 SS matrix |  |  | H | S | O 
    11132 ---|---|---|--- 
    11133 H | 6 | -9 | -6 
    11134 S |  | 6 | -6 
    11135 O |  |  | 4 
    11136 Iteration cutoff | 2 
    11137  
    11138 Matchmaker 3j0c.pdb1, chain C (#1.48) with AF3 CA.pdb, chain A (#241),
    11139 sequence alignment score = 328.1 
    11140 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11141 2.714) 
    11142  
    11143 
    11144 > hide sel cartoons
    11145 
    11146 > color #237 dodgerblue
    11147 
    11148 > color #238 dodgerblue
    11149 
    11150 > color #239 #00b305ff
    11151 
    11152 > color #241 #f15839ff
    11153 
    11154 > color #240 #00b305ff
    11155 
    11156 > select #1.49/A
    11157 
    11158 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11159 
    11160 > show sel cartoons
    11161 
    11162 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11163 
    11164 Chain information for AF3 E1 1-421.pdb #242 
    11165 --- 
    11166 Chain | Description 
    11167 A | No description available 
    11168  
    11169 
    11170 > matchmaker #242 to #1.49 & sel
    11171 
    11172 Parameters 
    11173 --- 
    11174 Chain pairing | bb 
    11175 Alignment algorithm | Needleman-Wunsch 
    11176 Similarity matrix | BLOSUM-62 
    11177 SS fraction | 0.3 
    11178 Gap open (HH/SS/other) | 18/18/6 
    11179 Gap extend | 1 
    11180 SS matrix |  |  | H | S | O 
    11181 ---|---|---|--- 
    11182 H | 6 | -9 | -6 
    11183 S |  | 6 | -6 
    11184 O |  |  | 4 
    11185 Iteration cutoff | 2 
    11186  
    11187 Matchmaker 3j0c.pdb1, chain A (#1.49) with AF3 E1 1-421.pdb, chain A (#242),
    11188 sequence alignment score = 1060.7 
    11189 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11190 3.020) 
    11191  
    11192 
    11193 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11194 
    11195 Chain information for AF3 E1 422-461.pdb #243 
    11196 --- 
    11197 Chain | Description 
    11198 A | No description available 
    11199  
    11200 
    11201 > matchmaker #243 to #1.49 & sel
    11202 
    11203 Parameters 
    11204 --- 
    11205 Chain pairing | bb 
    11206 Alignment algorithm | Needleman-Wunsch 
    11207 Similarity matrix | BLOSUM-62 
    11208 SS fraction | 0.3 
    11209 Gap open (HH/SS/other) | 18/18/6 
    11210 Gap extend | 1 
    11211 SS matrix |  |  | H | S | O 
    11212 ---|---|---|--- 
    11213 H | 6 | -9 | -6 
    11214 S |  | 6 | -6 
    11215 O |  |  | 4 
    11216 Iteration cutoff | 2 
    11217  
    11218 Matchmaker 3j0c.pdb1, chain A (#1.49) with AF3 E1 422-461.pdb, chain A (#243),
    11219 sequence alignment score = 626.9 
    11220 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    11221 2.776) 
    11222  
    11223 
    11224 > hide sel cartoons
    11225 
    11226 > select #1.49/B
    11227 
    11228 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11229 
    11230 > show sel cartoons
    11231 
    11232 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11233 
    11234 Chain information for AF3 E2 1-352.pdb #244 
    11235 --- 
    11236 Chain | Description 
    11237 B | No description available 
    11238  
    11239 
    11240 > matchmaker #244 to #1.49 & sel
    11241 
    11242 Parameters 
    11243 --- 
    11244 Chain pairing | bb 
    11245 Alignment algorithm | Needleman-Wunsch 
    11246 Similarity matrix | BLOSUM-62 
    11247 SS fraction | 0.3 
    11248 Gap open (HH/SS/other) | 18/18/6 
    11249 Gap extend | 1 
    11250 SS matrix |  |  | H | S | O 
    11251 ---|---|---|--- 
    11252 H | 6 | -9 | -6 
    11253 S |  | 6 | -6 
    11254 O |  |  | 4 
    11255 Iteration cutoff | 2 
    11256  
    11257 Matchmaker 3j0c.pdb1, chain B (#1.49) with AF3 E2 1-352.pdb, chain B (#244),
    11258 sequence alignment score = 583.7 
    11259 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11260 5.933) 
    11261  
    11262 
    11263 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11264 
    11265 Chain information for AF3 E2 353-438.pdb #245 
    11266 --- 
    11267 Chain | Description 
    11268 B | No description available 
    11269  
    11270 
    11271 > matchmaker #245 to #1.49 & sel
    11272 
    11273 Parameters 
    11274 --- 
    11275 Chain pairing | bb 
    11276 Alignment algorithm | Needleman-Wunsch 
    11277 Similarity matrix | BLOSUM-62 
    11278 SS fraction | 0.3 
    11279 Gap open (HH/SS/other) | 18/18/6 
    11280 Gap extend | 1 
    11281 SS matrix |  |  | H | S | O 
    11282 ---|---|---|--- 
    11283 H | 6 | -9 | -6 
    11284 S |  | 6 | -6 
    11285 O |  |  | 4 
    11286 Iteration cutoff | 2 
    11287  
    11288 Matchmaker 3j0c.pdb1, chain B (#1.49) with AF3 E2 353-438.pdb, chain B (#245),
    11289 sequence alignment score = 333.4 
    11290 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11291 8.411) 
    11292  
    11293 
    11294 > hide sel cartoons
    11295 
    11296 > select #1.49/C
    11297 
    11298 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11299 
    11300 > show sel cartoons
    11301 
    11302 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11303 
    11304 Chain information for AF3 CA.pdb #246 
    11305 --- 
    11306 Chain | Description 
    11307 A | No description available 
    11308  
    11309 
    11310 > matchmaker #246 to #1.49 & sel
    11311 
    11312 Parameters 
    11313 --- 
    11314 Chain pairing | bb 
    11315 Alignment algorithm | Needleman-Wunsch 
    11316 Similarity matrix | BLOSUM-62 
    11317 SS fraction | 0.3 
    11318 Gap open (HH/SS/other) | 18/18/6 
    11319 Gap extend | 1 
    11320 SS matrix |  |  | H | S | O 
    11321 ---|---|---|--- 
    11322 H | 6 | -9 | -6 
    11323 S |  | 6 | -6 
    11324 O |  |  | 4 
    11325 Iteration cutoff | 2 
    11326  
    11327 Matchmaker 3j0c.pdb1, chain C (#1.49) with AF3 CA.pdb, chain A (#246),
    11328 sequence alignment score = 328.1 
    11329 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11330 2.714) 
    11331  
    11332 
    11333 > hide sel cartoons
    11334 
    11335 > color #242 dodgerblue
    11336 
    11337 > color #243 dodgerblue
    11338 
    11339 > color #244 #00b305ff
    11340 
    11341 > color #245 #00b305ff
    11342 
    11343 > color #245 #f15839ff
    11344 
    11345 > color #245 #00b305ff
    11346 
    11347 > color #246 #f15839ff
    11348 
    11349 > select #1.50/A
    11350 
    11351 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11352 
    11353 > show sel cartoons
    11354 
    11355 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11356 
    11357 Chain information for AF3 E1 1-421.pdb #247 
    11358 --- 
    11359 Chain | Description 
    11360 A | No description available 
    11361  
    11362 
    11363 > matchmaker #247 to #1.49 & sel
    11364 
    11365 No 'to' model specified 
    11366 
    11367 > matchmaker #247 to #1.50 & sel
    11368 
    11369 Parameters 
    11370 --- 
    11371 Chain pairing | bb 
    11372 Alignment algorithm | Needleman-Wunsch 
    11373 Similarity matrix | BLOSUM-62 
    11374 SS fraction | 0.3 
    11375 Gap open (HH/SS/other) | 18/18/6 
    11376 Gap extend | 1 
    11377 SS matrix |  |  | H | S | O 
    11378 ---|---|---|--- 
    11379 H | 6 | -9 | -6 
    11380 S |  | 6 | -6 
    11381 O |  |  | 4 
    11382 Iteration cutoff | 2 
    11383  
    11384 Matchmaker 3j0c.pdb1, chain A (#1.50) with AF3 E1 1-421.pdb, chain A (#247),
    11385 sequence alignment score = 1060.7 
    11386 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11387 3.020) 
    11388  
    11389 
    11390 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11391 
    11392 Chain information for AF3 E1 422-461.pdb #248 
    11393 --- 
    11394 Chain | Description 
    11395 A | No description available 
    11396  
    11397 
    11398 > matchmaker #248 to #1.50 & sel
    11399 
    11400 Parameters 
    11401 --- 
    11402 Chain pairing | bb 
    11403 Alignment algorithm | Needleman-Wunsch 
    11404 Similarity matrix | BLOSUM-62 
    11405 SS fraction | 0.3 
    11406 Gap open (HH/SS/other) | 18/18/6 
    11407 Gap extend | 1 
    11408 SS matrix |  |  | H | S | O 
    11409 ---|---|---|--- 
    11410 H | 6 | -9 | -6 
    11411 S |  | 6 | -6 
    11412 O |  |  | 4 
    11413 Iteration cutoff | 2 
    11414  
    11415 Matchmaker 3j0c.pdb1, chain A (#1.50) with AF3 E1 422-461.pdb, chain A (#248),
    11416 sequence alignment score = 626.9 
    11417 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    11418 2.776) 
    11419  
    11420 
    11421 > hide sel cartoons
    11422 
    11423 > select #1.50/B
    11424 
    11425 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11426 
    11427 > show sel cartoons
    11428 
    11429 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11430 
    11431 Chain information for AF3 E2 1-352.pdb #249 
    11432 --- 
    11433 Chain | Description 
    11434 B | No description available 
    11435  
    11436 
    11437 > matchmaker #249 to #1.50 & sel
    11438 
    11439 Parameters 
    11440 --- 
    11441 Chain pairing | bb 
    11442 Alignment algorithm | Needleman-Wunsch 
    11443 Similarity matrix | BLOSUM-62 
    11444 SS fraction | 0.3 
    11445 Gap open (HH/SS/other) | 18/18/6 
    11446 Gap extend | 1 
    11447 SS matrix |  |  | H | S | O 
    11448 ---|---|---|--- 
    11449 H | 6 | -9 | -6 
    11450 S |  | 6 | -6 
    11451 O |  |  | 4 
    11452 Iteration cutoff | 2 
    11453  
    11454 Matchmaker 3j0c.pdb1, chain B (#1.50) with AF3 E2 1-352.pdb, chain B (#249),
    11455 sequence alignment score = 583.7 
    11456 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11457 5.933) 
    11458  
    11459 
    11460 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11461 
    11462 Chain information for AF3 E2 353-438.pdb #250 
    11463 --- 
    11464 Chain | Description 
    11465 B | No description available 
    11466  
    11467 
    11468 > matchmaker #250 to #1.50 & sel
    11469 
    11470 Parameters 
    11471 --- 
    11472 Chain pairing | bb 
    11473 Alignment algorithm | Needleman-Wunsch 
    11474 Similarity matrix | BLOSUM-62 
    11475 SS fraction | 0.3 
    11476 Gap open (HH/SS/other) | 18/18/6 
    11477 Gap extend | 1 
    11478 SS matrix |  |  | H | S | O 
    11479 ---|---|---|--- 
    11480 H | 6 | -9 | -6 
    11481 S |  | 6 | -6 
    11482 O |  |  | 4 
    11483 Iteration cutoff | 2 
    11484  
    11485 Matchmaker 3j0c.pdb1, chain B (#1.50) with AF3 E2 353-438.pdb, chain B (#250),
    11486 sequence alignment score = 333.4 
    11487 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11488 8.411) 
    11489  
    11490 
    11491 > hide sel cartoons
    11492 
    11493 > select #1.50/C
    11494 
    11495 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11496 
    11497 > show sel cartoons
    11498 
    11499 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11500 
    11501 Chain information for AF3 CA.pdb #251 
    11502 --- 
    11503 Chain | Description 
    11504 A | No description available 
    11505  
    11506 
    11507 > matchmaker #251 to #1.50 & sel
    11508 
    11509 Parameters 
    11510 --- 
    11511 Chain pairing | bb 
    11512 Alignment algorithm | Needleman-Wunsch 
    11513 Similarity matrix | BLOSUM-62 
    11514 SS fraction | 0.3 
    11515 Gap open (HH/SS/other) | 18/18/6 
    11516 Gap extend | 1 
    11517 SS matrix |  |  | H | S | O 
    11518 ---|---|---|--- 
    11519 H | 6 | -9 | -6 
    11520 S |  | 6 | -6 
    11521 O |  |  | 4 
    11522 Iteration cutoff | 2 
    11523  
    11524 Matchmaker 3j0c.pdb1, chain C (#1.50) with AF3 CA.pdb, chain A (#251),
    11525 sequence alignment score = 328.1 
    11526 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11527 2.714) 
    11528  
    11529 
    11530 > hide sel cartoons
    11531 
    11532 > color #247 dodgerblue
    11533 
    11534 > color #248 dodgerblue
    11535 
    11536 > color #249 #00b305ff
    11537 
    11538 > color #250 #00b305ff
    11539 
    11540 > color #251 #f15839ff
    11541 
    11542 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    11543 
    11544 > select #1.51/A
    11545 
    11546 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11547 
    11548 > show sel cartoons
    11549 
    11550 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11551 
    11552 Chain information for AF3 E1 1-421.pdb #252 
    11553 --- 
    11554 Chain | Description 
    11555 A | No description available 
    11556  
    11557 
    11558 > matchmaker #252 to #1.51 & sel
    11559 
    11560 Parameters 
    11561 --- 
    11562 Chain pairing | bb 
    11563 Alignment algorithm | Needleman-Wunsch 
    11564 Similarity matrix | BLOSUM-62 
    11565 SS fraction | 0.3 
    11566 Gap open (HH/SS/other) | 18/18/6 
    11567 Gap extend | 1 
    11568 SS matrix |  |  | H | S | O 
    11569 ---|---|---|--- 
    11570 H | 6 | -9 | -6 
    11571 S |  | 6 | -6 
    11572 O |  |  | 4 
    11573 Iteration cutoff | 2 
    11574  
    11575 Matchmaker 3j0c.pdb1, chain A (#1.51) with AF3 E1 1-421.pdb, chain A (#252),
    11576 sequence alignment score = 1060.7 
    11577 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11578 3.020) 
    11579  
    11580 
    11581 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11582 
    11583 Chain information for AF3 E1 422-461.pdb #253 
    11584 --- 
    11585 Chain | Description 
    11586 A | No description available 
    11587  
    11588 
    11589 > matchmaker #253 to #1.51 & sel
    11590 
    11591 Parameters 
    11592 --- 
    11593 Chain pairing | bb 
    11594 Alignment algorithm | Needleman-Wunsch 
    11595 Similarity matrix | BLOSUM-62 
    11596 SS fraction | 0.3 
    11597 Gap open (HH/SS/other) | 18/18/6 
    11598 Gap extend | 1 
    11599 SS matrix |  |  | H | S | O 
    11600 ---|---|---|--- 
    11601 H | 6 | -9 | -6 
    11602 S |  | 6 | -6 
    11603 O |  |  | 4 
    11604 Iteration cutoff | 2 
    11605  
    11606 Matchmaker 3j0c.pdb1, chain A (#1.51) with AF3 E1 422-461.pdb, chain A (#253),
    11607 sequence alignment score = 626.9 
    11608 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    11609 2.776) 
    11610  
    11611 
    11612 > hide sel cartoons
    11613 
    11614 > select #1.51/B
    11615 
    11616 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11617 
    11618 > show sel cartoons
    11619 
    11620 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11621 
    11622 Chain information for AF3 E2 1-352.pdb #254 
    11623 --- 
    11624 Chain | Description 
    11625 B | No description available 
    11626  
    11627 
    11628 > matchmaker #254 to #1.51 & sel
    11629 
    11630 Parameters 
    11631 --- 
    11632 Chain pairing | bb 
    11633 Alignment algorithm | Needleman-Wunsch 
    11634 Similarity matrix | BLOSUM-62 
    11635 SS fraction | 0.3 
    11636 Gap open (HH/SS/other) | 18/18/6 
    11637 Gap extend | 1 
    11638 SS matrix |  |  | H | S | O 
    11639 ---|---|---|--- 
    11640 H | 6 | -9 | -6 
    11641 S |  | 6 | -6 
    11642 O |  |  | 4 
    11643 Iteration cutoff | 2 
    11644  
    11645 Matchmaker 3j0c.pdb1, chain B (#1.51) with AF3 E2 1-352.pdb, chain B (#254),
    11646 sequence alignment score = 583.7 
    11647 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11648 5.933) 
    11649  
    11650 
    11651 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11652 
    11653 Chain information for AF3 E2 353-438.pdb #255 
    11654 --- 
    11655 Chain | Description 
    11656 B | No description available 
    11657  
    11658 
    11659 > matchmaker #255 to #1.51 & sel
    11660 
    11661 Parameters 
    11662 --- 
    11663 Chain pairing | bb 
    11664 Alignment algorithm | Needleman-Wunsch 
    11665 Similarity matrix | BLOSUM-62 
    11666 SS fraction | 0.3 
    11667 Gap open (HH/SS/other) | 18/18/6 
    11668 Gap extend | 1 
    11669 SS matrix |  |  | H | S | O 
    11670 ---|---|---|--- 
    11671 H | 6 | -9 | -6 
    11672 S |  | 6 | -6 
    11673 O |  |  | 4 
    11674 Iteration cutoff | 2 
    11675  
    11676 Matchmaker 3j0c.pdb1, chain B (#1.51) with AF3 E2 353-438.pdb, chain B (#255),
    11677 sequence alignment score = 322.6 
    11678 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11679 8.411) 
    11680  
    11681 
    11682 > hide sel cartoons
    11683 
    11684 > select #1.51/C
    11685 
    11686 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11687 
    11688 > show sel cartoons
    11689 
    11690 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11691 
    11692 Chain information for AF3 CA.pdb #256 
    11693 --- 
    11694 Chain | Description 
    11695 A | No description available 
    11696  
    11697 
    11698 > matchmaker #256 to #1.51 & sel
    11699 
    11700 Parameters 
    11701 --- 
    11702 Chain pairing | bb 
    11703 Alignment algorithm | Needleman-Wunsch 
    11704 Similarity matrix | BLOSUM-62 
    11705 SS fraction | 0.3 
    11706 Gap open (HH/SS/other) | 18/18/6 
    11707 Gap extend | 1 
    11708 SS matrix |  |  | H | S | O 
    11709 ---|---|---|--- 
    11710 H | 6 | -9 | -6 
    11711 S |  | 6 | -6 
    11712 O |  |  | 4 
    11713 Iteration cutoff | 2 
    11714  
    11715 Matchmaker 3j0c.pdb1, chain C (#1.51) with AF3 CA.pdb, chain A (#256),
    11716 sequence alignment score = 328.1 
    11717 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11718 2.714) 
    11719  
    11720 
    11721 > matchmaker #256 to #1.51 & sel
    11722 
    11723 Parameters 
    11724 --- 
    11725 Chain pairing | bb 
    11726 Alignment algorithm | Needleman-Wunsch 
    11727 Similarity matrix | BLOSUM-62 
    11728 SS fraction | 0.3 
    11729 Gap open (HH/SS/other) | 18/18/6 
    11730 Gap extend | 1 
    11731 SS matrix |  |  | H | S | O 
    11732 ---|---|---|--- 
    11733 H | 6 | -9 | -6 
    11734 S |  | 6 | -6 
    11735 O |  |  | 4 
    11736 Iteration cutoff | 2 
    11737  
    11738 Matchmaker 3j0c.pdb1, chain C (#1.51) with AF3 CA.pdb, chain A (#256),
    11739 sequence alignment score = 328.1 
    11740 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11741 2.714) 
    11742  
    11743 
    11744 > hide sel cartoons
    11745 
    11746 > color #252 dodgerblue
    11747 
    11748 > color #253 dodgerblue
    11749 
    11750 > color #254 #00b305ff
    11751 
    11752 > color #255 #00b305ff
    11753 
    11754 > color #256 #f15839ff
    11755 
    11756 > select #1.52/A
    11757 
    11758 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11759 
    11760 > show sel cartoons
    11761 
    11762 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11763 
    11764 Chain information for AF3 E1 1-421.pdb #257 
    11765 --- 
    11766 Chain | Description 
    11767 A | No description available 
    11768  
    11769 
    11770 > matchmaker #257 to #1.52 & sel
    11771 
    11772 Parameters 
    11773 --- 
    11774 Chain pairing | bb 
    11775 Alignment algorithm | Needleman-Wunsch 
    11776 Similarity matrix | BLOSUM-62 
    11777 SS fraction | 0.3 
    11778 Gap open (HH/SS/other) | 18/18/6 
    11779 Gap extend | 1 
    11780 SS matrix |  |  | H | S | O 
    11781 ---|---|---|--- 
    11782 H | 6 | -9 | -6 
    11783 S |  | 6 | -6 
    11784 O |  |  | 4 
    11785 Iteration cutoff | 2 
    11786  
    11787 Matchmaker 3j0c.pdb1, chain A (#1.52) with AF3 E1 1-421.pdb, chain A (#257),
    11788 sequence alignment score = 1060.7 
    11789 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11790 3.020) 
    11791  
    11792 
    11793 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11794 
    11795 Chain information for AF3 E1 422-461.pdb #258 
    11796 --- 
    11797 Chain | Description 
    11798 A | No description available 
    11799  
    11800 
    11801 > matchmaker #258 to #1.52 & sel
    11802 
    11803 Parameters 
    11804 --- 
    11805 Chain pairing | bb 
    11806 Alignment algorithm | Needleman-Wunsch 
    11807 Similarity matrix | BLOSUM-62 
    11808 SS fraction | 0.3 
    11809 Gap open (HH/SS/other) | 18/18/6 
    11810 Gap extend | 1 
    11811 SS matrix |  |  | H | S | O 
    11812 ---|---|---|--- 
    11813 H | 6 | -9 | -6 
    11814 S |  | 6 | -6 
    11815 O |  |  | 4 
    11816 Iteration cutoff | 2 
    11817  
    11818 Matchmaker 3j0c.pdb1, chain A (#1.52) with AF3 E1 422-461.pdb, chain A (#258),
    11819 sequence alignment score = 626.9 
    11820 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    11821 2.775) 
    11822  
    11823 
    11824 > hide sel cartoons
    11825 
    11826 > select #1.52/B
    11827 
    11828 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11829 
    11830 > show sel cartoons
    11831 
    11832 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11833 
    11834 Chain information for AF3 E2 1-352.pdb #259 
    11835 --- 
    11836 Chain | Description 
    11837 B | No description available 
    11838  
    11839 
    11840 > matchmaker #259 to #1.52 & sel
    11841 
    11842 Parameters 
    11843 --- 
    11844 Chain pairing | bb 
    11845 Alignment algorithm | Needleman-Wunsch 
    11846 Similarity matrix | BLOSUM-62 
    11847 SS fraction | 0.3 
    11848 Gap open (HH/SS/other) | 18/18/6 
    11849 Gap extend | 1 
    11850 SS matrix |  |  | H | S | O 
    11851 ---|---|---|--- 
    11852 H | 6 | -9 | -6 
    11853 S |  | 6 | -6 
    11854 O |  |  | 4 
    11855 Iteration cutoff | 2 
    11856  
    11857 Matchmaker 3j0c.pdb1, chain B (#1.52) with AF3 E2 1-352.pdb, chain B (#259),
    11858 sequence alignment score = 583.7 
    11859 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11860 5.933) 
    11861  
    11862 
    11863 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11864 
    11865 Chain information for AF3 E2 353-438.pdb #260 
    11866 --- 
    11867 Chain | Description 
    11868 B | No description available 
    11869  
    11870 
    11871 > matchmaker #260 to #1.52 & sel
    11872 
    11873 Parameters 
    11874 --- 
    11875 Chain pairing | bb 
    11876 Alignment algorithm | Needleman-Wunsch 
    11877 Similarity matrix | BLOSUM-62 
    11878 SS fraction | 0.3 
    11879 Gap open (HH/SS/other) | 18/18/6 
    11880 Gap extend | 1 
    11881 SS matrix |  |  | H | S | O 
    11882 ---|---|---|--- 
    11883 H | 6 | -9 | -6 
    11884 S |  | 6 | -6 
    11885 O |  |  | 4 
    11886 Iteration cutoff | 2 
    11887  
    11888 Matchmaker 3j0c.pdb1, chain B (#1.52) with AF3 E2 353-438.pdb, chain B (#260),
    11889 sequence alignment score = 333.4 
    11890 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11891 8.411) 
    11892  
     2582[deleted to fit within ticket limits]
    118932583
    118942584> hide sel cartoons