Changes between Initial Version and Version 1 of Ticket #19302


Ignore:
Timestamp:
Nov 6, 2025, 2:38:03 PM (4 weeks ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19302

    • Property Component Unassigned → Sequence
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → sequence align: 'StructureSeq' object has no attribute 'atomspec'

  • Ticket #19302 – Description

    initial v1  
    41714171RMSD between 324 atom pairs is 0.000 angstroms 
    41724172
    4173 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4174 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4175 > for interface design.cxs"
    4176 
    4177 > show #9.9 models
    4178 
    4179 > hide #9.9 models
    4180 
    4181 > show #9.9 models
    4182 
    4183 > select #2.2/A:1485@C#9.9:365@N
    4184 
    4185 2 atoms, 2 residues, 2 models selected 
    4186 
    4187 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4188 
    4189 > align #2.2.1/A:365-368 toAtoms #8:365-368 matchAtomNames true move residues
    4190 
    4191 RMSD between 16 atom pairs is 0.000 angstroms 
    4192 
    4193 > select #2.2/A:368@C#2.2/B:392@N
    4194 
    4195 2 atoms, 2 residues, 2 models selected 
    4196 
    4197 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4198 
    4199 > align #2.2.1/A:1877-1905 toAtoms #4/B:392-420 matchAtomNames true move
    4200 > residues
    4201 
    4202 RMSD between 242 atom pairs is 0.000 angstroms 
    4203 
    4204 > show #9.10 models
    4205 
    4206 > select #2.2/A:1905@C#9.10:398@N
    4207 
    4208 2 atoms, 2 residues, 2 models selected 
    4209 
    4210 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4211 
    4212 > align #2.2.1/A:398-401 toAtoms #8:398-401 matchAtomNames true move residues
    4213 
    4214 RMSD between 16 atom pairs is 0.000 angstroms 
    4215 
    4216 > select #2.2/A:401@C#2.2/B:535@N
    4217 
    4218 2 atoms, 2 residues, 2 models selected 
    4219 
    4220 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4221 
    4222 > align #2.2.1/A:2440-2480 toAtoms #4/B:535-575 matchAtomNames true move
    4223 > residues
    4224 
    4225 RMSD between 299 atom pairs is 0.000 angstroms 
    4226 
    4227 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4228 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4229 > for interface design.cxs"
    4230 
    4231 > show #9.11 models
    4232 
    4233 > select #2.2/A:2480@C#9.11:443@N
    4234 
    4235 2 atoms, 2 residues, 2 models selected 
    4236 
    4237 > select #2.2/A:2480@C#9.11:443@N
    4238 
    4239 2 atoms, 2 residues, 2 models selected 
    4240 
    4241 > show #8 models
    4242 
    4243 > select #2.2/A
    4244 
    4245 3282 atoms, 3377 bonds, 443 residues, 1 model selected 
    4246 
    4247 > show sel cartoons
    4248 
    4249 > hide #2.2.1.14 models
    4250 
    4251 > show #2.2.1.14 models
    4252 
    4253 > hide #2.2.1.14 models
    4254 
    4255 > show #2.2.1.14 models
    4256 
    4257 > hide #2.2.1.10 models
    4258 
    4259 > show #2.2.1.10 models
    4260 
    4261 > hide #2.2.1.14 models
    4262 
    4263 > show #2.2.1.14 models
    4264 
    4265 > select #2.2/A:2480@C#9.11:443@N
    4266 
    4267 2 atoms, 2 residues, 2 models selected 
    4268 
    4269 > hide #8 models
    4270 
    4271 > show #8 models
    4272 
    4273 > hide #8 models
    4274 
    4275 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4276 
    4277 > align #2.2.1/A:443-470 toAtoms #8:443-470 matchAtomNames true move residues
    4278 
    4279 RMSD between 112 atom pairs is 0.000 angstroms 
    4280 
    4281 > show #9.12 models
    4282 
    4283 > hide #9.12 models
    4284 
    4285 > show #8 models
    4286 
    4287 > hide #8 models
    4288 
    4289 > select #2.2/A:470@C#2.2/C:2@N
    4290 
    4291 2 atoms, 2 residues, 2 models selected 
    4292 
    4293 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4294 
    4295 > align #2.2.1/A:2482-2561 toAtoms #4/C:2-81 matchAtomNames true move residues
    4296 
    4297 RMSD between 612 atom pairs is 0.000 angstroms 
    4298 
    4299 > show #!4 models
    4300 
    4301 > hide #!4 models
    4302 
    4303 > show #!4 models
    4304 
    4305 > hide #!4 models
    4306 
    4307 > show #!4 models
    4308 
    4309 > hide #!4 models
    4310 
    4311 > show #!4 models
    4312 
    4313 > align #2.2.1/A:3002-3003 toAtoms #4/C:3002-3003 matchAtomNames true move
    4314 > residues
    4315 
    4316 RMSD between 16 atom pairs is 0.000 angstroms 
    4317 
    4318 > hide #!4 models
    4319 
    4320 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4321 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4322 > for interface design.cxs"
    4323 
    4324 > show #9.12 models
    4325 
    4326 > select #2.2/A:2561@C#9.11:551@N
    4327 
    4328 1 atom, 1 residue, 1 model selected 
    4329 
    4330 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4331 
    4332 No nitrogens in specified atoms 
    4333 
    4334 > select #2.2/A:2561@C#9.12:551@N
    4335 
    4336 2 atoms, 2 residues, 2 models selected 
    4337 
    4338 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4339 
    4340 > show #8 models
    4341 
    4342 > hide #8 models
    4343 
    4344 > show #8 models
    4345 
    4346 > align #2.2.1/A:3112-3147 toAtoms #8:551-586 matchAtomNames true move
    4347 > residues
    4348 
    4349 RMSD between 144 atom pairs is 0.000 angstroms 
    4350 
    4351 > hide #8 models
    4352 
    4353 > show #!4 models
    4354 
    4355 > hide #2.2.1.10 models
    4356 
    4357 > hide #2.2.1.12 models
    4358 
    4359 > show #2.2.1.12 models
    4360 
    4361 > hide #2.2.1.12 models
    4362 
    4363 > show #2.2.1.12 models
    4364 
    4365 > hide #2.2.1.12 models
    4366 
    4367 > show #2.2.1.12 models
    4368 
    4369 > hide #2.2.1.12 models
    4370 
    4371 > hide #2.2.1.13 models
    4372 
    4373 > hide #!2.2.1.14 models
    4374 
    4375 > show #!2.2.1.14 models
    4376 
    4377 > show #9.13 models
    4378 
    4379 > hide #9.13 models
    4380 
    4381 > show #9.13 models
    4382 
    4383 > hide #9.13 models
    4384 
    4385 > show #9.13 models
    4386 
    4387 > hide #9.13 models
    4388 
    4389 > hide #!4 models
    4390 
    4391 > show #2.2.1.13 models
    4392 
    4393 > hide #2.2.1.13 models
    4394 
    4395 > show #2.2.1.12 models
    4396 
    4397 > select #2/D:69
    4398 
    4399 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4400 
    4401 > hide sel cartoons
    4402 
    4403 > show sel atoms
    4404 
    4405 > color sel byhetero
    4406 
    4407 > select #2.2/A:3147@C#2.2/D:69@N
    4408 
    4409 2 atoms, 2 residues, 2 models selected 
    4410 
    4411 > build join peptide sel length 1.33 omega 180 phi -120 move N
    4412 
    4413 > align #2.2.1/A:3216-3358 toAtoms #4/D:69-211 matchAtomNames true move
    4414 > residues
    4415 
    4416 RMSD between 1132 atom pairs is 0.000 angstroms 
    4417 
    4418 > show #!4 models
    4419 
    4420 > hide #!4 models
    4421 
    4422 > show #2.2.1.10 models
    4423 
    4424 > hide #2.2.1.10 models
    4425 
    4426 > show #2.2.1.10 models
    4427 
    4428 > show #9.13 models
    4429 
    4430 > show #!4 models
    4431 
    4432 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4433 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4434 > for interface design.cxs"
    4435 
    4436 ——— End of log from Sat May 18 17:13:54 2024 ———
    4437 
    4438 opened ChimeraX session 
    4439 
    4440 > close #2.2
    4441 
    4442 > hide #!4 models
    4443 
    4444 > show #!4 models
    4445 
    4446 > hide #!4 models
    4447 
    4448 > show #!4 models
    4449 
    4450 > hide #!4 models
    4451 
    4452 > show #!4 models
    4453 
    4454 > hide #!4 models
    4455 
    4456 > show #!4 models
    4457 
    4458 > close #6
    4459 
    4460 > close #8#9
    4461 
    4462 > close #7
    4463 
    4464 > close #3
    4465 
    4466 > close #5
    4467 
    4468 > hide #!2.1 models
    4469 
    4470 > show #!2.1 models
    4471 
    4472 > close #2
    4473 
    4474 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4475 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4476 > v2.cxs"
    4477 
    4478 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4479 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single
    4480 > chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb" format pdb
    4481 
    4482 Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-
    4483 Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single
    4484 chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb 
    4485 --- 
    4486 warnings | Ignored bad PDB record found on line 34701 
    4487 SEQRES *** A 830 
    4488  
    4489 Ignored bad PDB record found on line 34702 
    4490 SEQRES *** A 830 
    4491  
    4492 Ignored bad PDB record found on line 34703 
    4493 SEQRES *** A 830 
    4494  
    4495 Ignored bad PDB record found on line 34704 
    4496 SEQRES *** A 830 
    4497  
    4498 Ignored bad PDB record found on line 34705 
    4499 SEQRES *** A 830 
    4500  
    4501 92885266 messages similar to the above omitted 
    4502  
    4503 Chain information for SingleChainStromalRidge_PetF_Fdn.pdb #2 
    4504 --- 
    4505 Chain | Description 
    4506 A | No description available 
    4507 M | No description available 
    4508 N | No description available 
    4509  
    4510 
    4511 > help help:user/tools/modelpanel.html
    4512 
    4513 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4514 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single
    4515 > chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb" models #2
    4516 
    4517 > hide #!4 models
    4518 
    4519 > select #2/N
    4520 
    4521 728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected 
    4522 
    4523 > hide sel cartoons
    4524 
    4525 > show sel cartoons
    4526 
    4527 > select #2
    4528 
    4529 7455 atoms, 7544 bonds, 23 pseudobonds, 1082 residues, 3 models selected 
    4530 
    4531 > ui tool show "Color Actions"
    4532 
    4533 > color sel bychain
    4534 
    4535 > select #2:FES,SF4
    4536 
    4537 44 atoms, 64 bonds, 6 residues, 1 model selected 
    4538 
    4539 > color sel byhetero
    4540 
    4541 > select #2
    4542 
    4543 7455 atoms, 7544 bonds, 23 pseudobonds, 1082 residues, 3 models selected 
    4544 
    4545 > color sel byhetero
    4546 
    4547 > show sel atoms
    4548 
    4549 [Repeated 1 time(s)]
    4550 
    4551 > hide sel atoms
    4552 
    4553 > select #2:FES,SF4,CYS
    4554 
    4555 238 atoms, 231 bonds, 19 pseudobonds, 33 residues, 2 models selected 
    4556 
    4557 > show sel atoms
    4558 
    4559 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4560 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4561 > v2.cxs"
    4562 
    4563 ——— End of log from Sat May 18 22:45:24 2024 ———
    4564 
    4565 opened ChimeraX session 
    4566 
    4567 > hide #!2 models
    4568 
    4569 > show #!4 models
    4570 
    4571 > close #2
    4572 
    4573 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4574 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4575 > v3.cxs"
    4576 
    4577 > ui tool show "Show Sequence Viewer"
    4578 
    4579 > sequence chain #4/A
    4580 
    4581 Alignment identifier is 4/A 
    4582 
    4583 > select #4/A:729
    4584 
    4585 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4586 
    4587 > select #4/A:729
    4588 
    4589 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4590 
    4591 > rename #4 id 2
    4592 
    4593 > select #2/A:16-73,191-200,315-354,417-442,562-595,695-729
    4594 
    4595 1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected 
    4596 
    4597 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4598 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4599 > v3.cxs"
    4600 
    4601 > select #2/A:16-73
    4602 
    4603 474 atoms, 490 bonds, 58 residues, 1 model selected 
    4604 
    4605 > ui tool show "Renumber Residues"
    4606 
    4607 > renumber #2/A:16-73 start 1
    4608 
    4609 58 residues renumbered 
    4610 
    4611 > select #2/A:191
    4612 
    4613 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4614 
    4615 > select #2/A:191
    4616 
    4617 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4618 
    4619 > select #2/A:191-200
    4620 
    4621 89 atoms, 92 bonds, 10 residues, 1 model selected 
    4622 
    4623 > renumber #2/A:191-200 start 63
    4624 
    4625 10 residues renumbered 
    4626 
    4627 > select #2/A:315-354
    4628 
    4629 322 atoms, 333 bonds, 40 residues, 1 model selected 
    4630 
    4631 > renumber #2/A:315-354 start 77
    4632 
    4633 40 residues renumbered 
    4634 
    4635 > select #2/A:417-442
    4636 
    4637 228 atoms, 232 bonds, 26 residues, 1 model selected 
    4638 
    4639 > renumber #2/A:417-442 start 121
    4640 
    4641 26 residues renumbered 
    4642 
    4643 > select #2/A:562-595
    4644 
    4645 257 atoms, 264 bonds, 34 residues, 1 model selected 
    4646 
    4647 > renumber #2/A:562-595 start 151
    4648 
    4649 34 residues renumbered 
    4650 
    4651 > select #2/A:695-729
    4652 
    4653 279 atoms, 286 bonds, 35 residues, 1 model selected 
    4654 
    4655 > renumber #2/A:695-729 start 193
    4656 
    4657 35 residues renumbered 
    4658 
    4659 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4660 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
    4661 > v3.cxs"
    4662 
    4663 > ui tool show "Show Sequence Viewer"
    4664 
    4665 > sequence chain #2/B
    4666 
    4667 Alignment identifier is 2/B 
    4668 
    4669 > select #2/B:2-44,162-176,291-331,392-420,535-575,665-696/A:227
    4670 
    4671 1639 atoms, 1681 bonds, 5 pseudobonds, 202 residues, 2 models selected 
    4672 
    4673 > select #2/B:2-44/A:227
    4674 
    4675 365 atoms, 374 bonds, 44 residues, 1 model selected 
    4676 
    4677 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4678 > 2024/Nanda Noy 2023/Models/PSI stromal ridge single
    4679 > chain/PSI_stromal_ridge_0.pdb"
    4680 
    4681 Chain information for PSI_stromal_ridge_0.pdb #3 
    4682 --- 
    4683 Chain | Description 
    4684 A | No description available 
    4685  
    4686 
    4687 > ui tool show Matchmaker
    4688 
    4689 > matchmaker #3 to #2
    4690 
    4691 Parameters 
    4692 --- 
    4693 Chain pairing | bb 
    4694 Alignment algorithm | Needleman-Wunsch 
    4695 Similarity matrix | BLOSUM-62 
    4696 SS fraction | 0.3 
    4697 Gap open (HH/SS/other) | 18/18/6 
    4698 Gap extend | 1 
    4699 SS matrix |  |  | H | S | O 
    4700 ---|---|---|--- 
    4701 H | 6 | -9 | -6 
    4702 S |  | 6 | -6 
    4703 O |  |  | 4 
    4704 Iteration cutoff | 2 
    4705  
    4706 Matchmaker combination, chain A (#2) with PSI_stromal_ridge_0.pdb, chain A
    4707 (#3), sequence alignment score = 924.3 
    4708 RMSD between 203 pruned atom pairs is 0.259 angstroms; (across all 203 pairs:
    4709 0.259) 
    4710  
    4711 
    4712 > select #2/B:2-44/A:227
    4713 
    4714 365 atoms, 374 bonds, 44 residues, 1 model selected 
    4715 
    4716 > hide #3 models
    4717 
    4718 > show #3 models
    4719 
    4720 > select #2/B:2-44
    4721 
    4722 356 atoms, 366 bonds, 43 residues, 1 model selected 
    4723 
    4724 > renumber #2/B:2-44 start 258
    4725 
    4726 Proposed renumbering conflicts with existing residue combination #2/B TYR 291 
    4727 
    4728 > select #2/B:2-44,162-176,291-331,392-420,535-575,665-696
    4729 
    4730 1630 atoms, 1673 bonds, 5 pseudobonds, 201 residues, 2 models selected 
    4731 
    4732 > select #2/B:2-44,162-176,291-331,392-420,535-575,665-696
    4733 
    4734 1630 atoms, 1673 bonds, 5 pseudobonds, 201 residues, 2 models selected 
    4735 
    4736 > renumber #2/B:2-696 start 1002
    4737 
    4738 201 residues renumbered 
    4739 
    4740 > select #2/B:697
    4741 
    4742 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4743 
    4744 > select #2/B:697-707
    4745 
    4746 81 atoms, 81 bonds, 11 residues, 1 model selected 
    4747 
    4748 > renumber #2/B:697-707 start 1697
    4749 
    4750 11 residues renumbered 
    4751 
    4752 > select #3 sequence GGGG
    4753 
    4754 676 atoms, 663 bonds, 169 residues, 1 model selected 
    4755 
    4756 > color sel cyan
    4757 
    4758 > hide #3 models
    4759 
    4760 > show #3 models
    4761 
    4762 > hide #3 models
    4763 
    4764 > select #2/B:1002-1044
    4765 
    4766 356 atoms, 366 bonds, 43 residues, 1 model selected 
    4767 
    4768 > show #3 models
    4769 
    4770 > renumber #2/B:1002-1044 start 258
    4771 
    4772 43 residues renumbered 
    4773 
    4774 > select #2/B:1162-1176
    4775 
    4776 124 atoms, 127 bonds, 15 residues, 1 model selected 
    4777 
    4778 > select #2/B:300
    4779 
    4780 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4781 
    4782 > select #2/B:300-1162
    4783 
    4784 18 atoms, 16 bonds, 1 pseudobond, 2 residues, 2 models selected 
    4785 
    4786 > select #2/B:1162-1176
    4787 
    4788 124 atoms, 127 bonds, 15 residues, 1 model selected 
    4789 
    4790 > renumber #2/B:1162-1176 start 305
    4791 
    4792 15 residues renumbered 
    4793 
    4794 > select #2/B:319
    4795 
    4796 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4797 
    4798 > select #2/B:319-1291
    4799 
    4800 20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected 
    4801 
    4802 > select #2/B:1291-1331
    4803 
    4804 324 atoms, 333 bonds, 41 residues, 1 model selected 
    4805 
    4806 > hide #3 models
    4807 
    4808 > hide #!2 models
    4809 
    4810 > show #!2 models
    4811 
    4812 > select #2/N
    4813 
    4814 728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected 
    4815 
    4816 > hide sel atoms
    4817 
    4818 > hide sel cartoons
    4819 
    4820 > show #!1 models
    4821 
    4822 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4823 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion
    4824 > round1/PSI_fdn_0.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-
    4825 > Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    4826 > interface/RFdiffusion round1/PSI_fdn_1.pdb"
    4827 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    4828 > Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_2.pdb"
    4829 
    4830 Chain information for PSI_fdn_0.pdb #4 
    4831 --- 
    4832 Chain | Description 
    4833 A | No description available 
    4834  
    4835 Chain information for PSI_fdn_1.pdb #5 
    4836 --- 
    4837 Chain | Description 
    4838 A | No description available 
    4839  
    4840 Chain information for PSI_fdn_2.pdb #6 
    4841 --- 
    4842 Chain | Description 
    4843 A | No description available 
    4844  
    4845 
    4846 > ui tool show Matchmaker
    4847 
    4848 > matchmaker #4-6 to #1
    4849 
    4850 Parameters 
    4851 --- 
    4852 Chain pairing | bb 
    4853 Alignment algorithm | Needleman-Wunsch 
    4854 Similarity matrix | BLOSUM-62 
    4855 SS fraction | 0.3 
    4856 Gap open (HH/SS/other) | 18/18/6 
    4857 Gap extend | 1 
    4858 SS matrix |  |  | H | S | O 
    4859 ---|---|---|--- 
    4860 H | 6 | -9 | -6 
    4861 S |  | 6 | -6 
    4862 O |  |  | 4 
    4863 Iteration cutoff | 2 
    4864  
    4865 Matchmaker 2fdn, chain M (#1) with PSI_fdn_0.pdb, chain A (#4), sequence
    4866 alignment score = 139.6 
    4867 RMSD between 46 pruned atom pairs is 0.501 angstroms; (across all 53 pairs:
    4868 2.902) 
    4869  
    4870 Matchmaker 2fdn, chain M (#1) with PSI_fdn_1.pdb, chain A (#5), sequence
    4871 alignment score = 147.1 
    4872 RMSD between 47 pruned atom pairs is 0.590 angstroms; (across all 53 pairs:
    4873 2.756) 
    4874  
    4875 Matchmaker 2fdn, chain M (#1) with PSI_fdn_2.pdb, chain A (#6), sequence
    4876 alignment score = 135.4 
    4877 RMSD between 44 pruned atom pairs is 0.540 angstroms; (across all 48 pairs:
    4878 2.878) 
    4879  
    4880 
    4881 > select #4-6/A
    4882 
    4883 10668 atoms, 10665 bonds, 2667 residues, 3 models selected 
    4884 
    4885 > select #4-6:1-831
    4886 
    4887 9972 atoms, 9969 bonds, 2493 residues, 3 models selected 
    4888 
    4889 > hide sel atoms
    4890 
    4891 > hide sel cartoons
    4892 
    4893 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    4894 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
    4895 > fdn large target.cxs"
    4896 
    4897 > show #3 models
    4898 
    4899 > hide #3 models
    4900 
    4901 > close #4-6
    4902 
    4903 > select #2/B:1291-1331
    4904 
    4905 324 atoms, 333 bonds, 41 residues, 1 model selected 
    4906 
    4907 > show #3 models
    4908 
    4909 > select #2/B:319
    4910 
    4911 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4912 
    4913 > select #2/B:319-1291
    4914 
    4915 20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected 
    4916 
    4917 > select #2/B:1291-1331
    4918 
    4919 324 atoms, 333 bonds, 41 residues, 1 model selected 
    4920 
    4921 > renumber #2/B:1291-1331 start 305
    4922 
    4923 Proposed renumbering conflicts with existing residue combination #2/B LYS 305 
    4924 
    4925 > select #2/B:305
    4926 
    4927 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4928 
    4929 > select #2/B:2-44,162-176,291-331,392-420,535-575,665-696
    4930 
    4931 208 atoms, 211 bonds, 1 pseudobond, 25 residues, 2 models selected 
    4932 
    4933 > hide #3 models
    4934 
    4935 > select #2/B:1291-1331
    4936 
    4937 324 atoms, 333 bonds, 41 residues, 1 model selected 
    4938 
    4939 > show #3 models
    4940 
    4941 > renumber #2/B:1291-1331 start 324
    4942 
    4943 41 residues renumbered 
    4944 
    4945 > select #2/B:1392-1420
    4946 
    4947 242 atoms, 246 bonds, 29 residues, 1 model selected 
    4948 
    4949 > select #2/B:364
    4950 
    4951 10 atoms, 10 bonds, 1 residue, 1 model selected 
    4952 
    4953 > select #2/B:364-1392
    4954 
    4955 18 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected 
    4956 
    4957 > select #2/B:1392-1420
    4958 
    4959 242 atoms, 246 bonds, 29 residues, 1 model selected 
    4960 
    4961 > select #2/B:364
    4962 
    4963 10 atoms, 10 bonds, 1 residue, 1 model selected 
    4964 
    4965 > select #2/B:364-1392
    4966 
    4967 18 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected 
    4968 
    4969 > select #2/B:1392-1420
    4970 
    4971 242 atoms, 246 bonds, 29 residues, 1 model selected 
    4972 
    4973 > renumber #2/B:1392-1420 start 369
    4974 
    4975 29 residues renumbered 
    4976 
    4977 > select #2/B:397
    4978 
    4979 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4980 
    4981 > select #2/B:397-1535
    4982 
    4983 13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected 
    4984 
    4985 > select #2/B:1535-1575
    4986 
    4987 299 atoms, 306 bonds, 41 residues, 1 model selected 
    4988 
    4989 > renumber #2/B:1535-1575 start 402
    4990 
    4991 41 residues renumbered 
    4992 
    4993 > select #2/B:1665-1696
    4994 
    4995 285 atoms, 295 bonds, 32 residues, 1 model selected 
    4996 
    4997 > select #2/B:442
    4998 
    4999 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5000 
    5001 > select #2/B:442-1665
    5002 
    5003 13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected 
    5004 
    5005 > select #2/B:1665-1696
    5006 
    5007 285 atoms, 295 bonds, 32 residues, 1 model selected 
    5008 
    5009 > select #2/B:1665-170
    5010 
    5011 Nothing selected 
    5012 
    5013 > show cartoons
    5014 
    5015 > select #2/B:1665-1707
    5016 
    5017 366 atoms, 377 bonds, 43 residues, 1 model selected 
    5018 
    5019 > show sel cartoons
    5020 
    5021 > renumber #2/B:1665-1707 start 451
    5022 
    5023 43 residues renumbered 
    5024 
    5025 > hide #3 models
    5026 
    5027 > select #2/B
    5028 
    5029 1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected 
    5030 
    5031 > select #2/B
    5032 
    5033 1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected 
    5034 
    5035 > select #2/C
    5036 
    5037 628 atoms, 649 bonds, 8 pseudobonds, 82 residues, 3 models selected 
    5038 
    5039 > select #2/C
    5040 
    5041 628 atoms, 649 bonds, 8 pseudobonds, 82 residues, 3 models selected 
    5042 
    5043 > select #2/C:2-81
    5044 
    5045 612 atoms, 625 bonds, 80 residues, 1 model selected 
    5046 
    5047 > show sel cartoons
    5048 
    5049 > select #2/C:2
    5050 
    5051 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5052 
    5053 > show #3 models
    5054 
    5055 > renumber #2/C:2 start 471
    5056 
    5057 1 residues renumbered 
    5058 
    5059 > ui tool show "Show Sequence Viewer"
    5060 
    5061 > sequence chain #2/C
    5062 
    5063 Alignment identifier is 2/C 
    5064 
    5065 > select #2/C:2-81
    5066 
    5067 606 atoms, 619 bonds, 79 residues, 1 model selected 
    5068 
    5069 > renumber #2/C:3-81 start 472
    5070 
    5071 79 residues renumbered 
    5072 
    5073 > select #2/D
    5074 
    5075 1132 atoms, 1163 bonds, 143 residues, 1 model selected 
    5076 
    5077 > select #2/D
    5078 
    5079 1132 atoms, 1163 bonds, 143 residues, 1 model selected 
    5080 
    5081 > renumber #2/D start 587
    5082 
    5083 143 residues renumbered 
    5084 
    5085 > select #2/E
    5086 
    5087 528 atoms, 540 bonds, 66 residues, 1 model selected 
    5088 
    5089 > renumber #2/E start 764
    5090 
    5091 66 residues renumbered 
    5092 
    5093 > hide #3 models
    5094 
    5095 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5096 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
    5097 > fdn large target reunumbered.cxs"
    5098 
    5099 > ui tool show "Show Sequence Viewer"
    5100 
    5101 > sequence chain #2/D
    5102 
    5103 Alignment identifier is 2/D 
    5104 
    5105 > ui tool show "Show Sequence Viewer"
    5106 
    5107 > sequence chain #2/E
    5108 
    5109 Alignment identifier is 2/E 
    5110 
    5111 > select #2/D
    5112 
    5113 1132 atoms, 1163 bonds, 143 residues, 1 model selected 
    5114 
    5115 > select #2/D:701-729
    5116 
    5117 224 atoms, 228 bonds, 29 residues, 1 model selected 
    5118 
    5119 > hide sel cartoons
    5120 
    5121 > select #2/B
    5122 
    5123 1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected 
    5124 
    5125 > hide sel cartoons
    5126 
    5127 > show sel cartoons
    5128 
    5129 [Repeated 1 time(s)]
    5130 
    5131 > hide sel cartoons
    5132 
    5133 > select #2/A:1-15
    5134 
    5135 119 atoms, 120 bonds, 15 residues, 1 model selected 
    5136 
    5137 > hide sel cartoons
    5138 
    5139 > select #2/A:1-15,63-115
    5140 
    5141 516 atoms, 529 bonds, 1 pseudobond, 64 residues, 2 models selected 
    5142 
    5143 > select #2/A:1-15,63-146
    5144 
    5145 758 atoms, 777 bonds, 2 pseudobonds, 91 residues, 2 models selected 
    5146 
    5147 > hide sel cartoons
    5148 
    5149 > select #2/A:1-15,63-146/C/D:587-700/E
    5150 
    5151 2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected 
    5152 
    5153 > ui tool show "Change Chain IDs"
    5154 
    5155 > changechains sel A
    5156 
    5157 Cannot reassign chain ID to only part of polymeric chain (combination #2/A) 
    5158 
    5159 > combine #2
    5160 
    5161 > rename #4 "Stromal ridge small"
    5162 
    5163 > select #2/A:1-15,63-146/C/D:587-700/E
    5164 
    5165 2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected 
    5166 
    5167 > hide sel cartoons
    5168 
    5169 [Repeated 1 time(s)]
    5170 
    5171 > show sel cartoons
    5172 
    5173 > hide #!2 models
    5174 
    5175 > select #4/A:1-15,63-146/C/D:587-700/E
    5176 
    5177 2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected 
    5178 
    5179 > hide sel cartoons
    5180 
    5181 [Repeated 1 time(s)]
    5182 
    5183 > show sel cartoons
    5184 
    5185 [Repeated 1 time(s)]
    5186 
    5187 > hide sel cartoons
    5188 
    5189 [Repeated 1 time(s)]
    5190 
    5191 > show sel cartoons
    5192 
    5193 > hide sel cartoons
    5194 
    5195 > show sel cartoons
    5196 
    5197 > show #!2 models
    5198 
    5199 > hide #!4 models
    5200 
    5201 > select #2/A:1-15,63-146/C/D:587-700/E
    5202 
    5203 2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected 
    5204 
    5205 > select #2/A:16-62,147/C/D:587-700/E
    5206 
    5207 2419 atoms, 2492 bonds, 17 pseudobonds, 305 residues, 3 models selected 
    5208 
    5209 > select #2/A:16-62,147-227/C/D:587-700/E
    5210 
    5211 2955 atoms, 3042 bonds, 18 pseudobonds, 374 residues, 4 models selected 
    5212 
    5213 > select #2/A:16-62,147-227,3001/C/D:587-700/E
    5214 
    5215 2963 atoms, 3054 bonds, 20 pseudobonds, 375 residues, 4 models selected 
    5216 
    5217 > select #4/A:1-15,63-146/B/D:701-729
    5218 
    5219 2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected 
    5220 
    5221 > select #4/A:1-15,63-146/B/D:701-729
    5222 
    5223 2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected 
    5224 
    5225 > select #4/A:1-15,63-146/B/D:701-729
    5226 
    5227 2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected 
    5228 
    5229 > show #!4 models
    5230 
    5231 > hide #!2 models
    5232 
    5233 > select #4/A:1-15,63-146/D:701-729
    5234 
    5235 982 atoms, 1005 bonds, 2 pseudobonds, 120 residues, 2 models selected 
    5236 
    5237 > hide sel cartoons
    5238 
    5239 > select #4/A:1-12,46-146/D:701-729
    5240 
    5241 1065 atoms, 1090 bonds, 3 pseudobonds, 130 residues, 2 models selected 
    5242 
    5243 > select #4/A:1-12,55-146/D:701-729
    5244 
    5245 994 atoms, 1016 bonds, 3 pseudobonds, 121 residues, 2 models selected 
    5246 
    5247 > hide sel cartoons
    5248 
    5249 > select #4/B
    5250 
    5251 1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected 
    5252 
    5253 > show sel cartoons
    5254 
    5255 > select #4/B &~:425-436
    5256 
    5257 1635 atoms, 1676 bonds, 5 pseudobonds, 200 residues, 2 models selected 
    5258 
    5259 > hide sel cartoons
    5260 
    5261 > select #4/A:16-54,151-227,3001/C/D:587-700/E
    5262 
    5263 2929 atoms, 3020 bonds, 20 pseudobonds, 371 residues, 4 models selected 
    5264 
    5265 > hide sel cartoons
    5266 
    5267 > show sel cartoons
    5268 
    5269 > select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
    5270 
    5271 3005 atoms, 3097 bonds, 22 pseudobonds, 383 residues, 4 models selected 
    5272 
    5273 > hide sel cartoons
    5274 
    5275 > show sel cartoons
    5276 
    5277 > surface #4 enclose #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
    5278 
    5279 > coulombic sel
    5280 
    5281 Using Amber 20 recommended default charges and atom types for standard
    5282 residues 
    5283 Coulombic values for Stromal ridge small_A SES surface #4.5: minimum, -23.39,
    5284 mean -1.01, maximum 11.65 
    5285 Coulombic values for Stromal ridge small_B SES surface #4.6: minimum, -18.54,
    5286 mean 0.17, maximum 12.46 
    5287 Coulombic values for Stromal ridge small_C SES surface #4.7: minimum, -12.54,
    5288 mean -0.30, maximum 9.66 
    5289 Coulombic values for Stromal ridge small_D SES surface #4.8: minimum, -11.89,
    5290 mean 1.48, maximum 14.01 
    5291 Coulombic values for Stromal ridge small_E SES surface #4.9: minimum, -13.21,
    5292 mean 1.18, maximum 10.80 
    5293 To also show corresponding color key, enter the above coulombic command and
    5294 add key true 
    5295 
    5296 > close #4.5-9
    5297 
    5298 > select add #4.4
    5299 
    5300 3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected 
    5301 
    5302 > select subtract #4.4
    5303 
    5304 3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected 
    5305 
    5306 > select add #4.4
    5307 
    5308 3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected 
    5309 
    5310 > select subtract #4.4
    5311 
    5312 3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected 
    5313 
    5314 > select add #4.4
    5315 
    5316 3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected 
    5317 
    5318 > close #4.4
    5319 
    5320 > select #4/M
    5321 
    5322 Nothing selected 
    5323 
    5324 > select #4/N
    5325 
    5326 728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected 
    5327 
    5328 > hide #!1 models
    5329 
    5330 > hide sel cartoons
    5331 
    5332 > hide sel atoms
    5333 
    5334 > select #4 &@@display
    5335 
    5336 184 atoms, 176 bonds, 15 pseudobonds, 24 residues, 3 models selected 
    5337 
    5338 > select #4 &@@~display
    5339 
    5340 184 atoms, 176 bonds, 15 pseudobonds, 24 residues, 3 models selected 
    5341 
    5342 > show sel atoms
    5343 
    5344 > select #4 &~@@display
    5345 
    5346 6200 atoms, 6338 bonds, 4 pseudobonds, 784 residues, 2 models selected 
    5347 
    5348 > show sel atoms
    5349 
    5350 > hide sel atoms
    5351 
    5352 > select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
    5353 
    5354 3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected 
    5355 
    5356 > hide sel cartoons
    5357 
    5358 > hide sel atoms
    5359 
    5360 > show sel cartoons
    5361 
    5362 > show sel atoms
    5363 
    5364 > select #4
    5365 
    5366 6384 atoms, 6556 bonds, 46 pseudobonds, 805 residues, 4 models selected 
    5367 
    5368 > ui tool show "Change Chain IDs"
    5369 
    5370 > changechains sel A
    5371 
    5372 Proposed chain ID change would produce multiple residues with the samechain-
    5373 ID/number/insertion-code combo (A/477/) 
    5374 
    5375 > select #4/B
    5376 
    5377 1711 atoms, 1755 bonds, 212 residues, 1 model selected 
    5378 
    5379 > show sel cartoons
    5380 
    5381 > show #3 models
    5382 
    5383 > hide sel cartoons
    5384 
    5385 > select #4/B:402-442
    5386 
    5387 299 atoms, 306 bonds, 41 residues, 1 model selected 
    5388 
    5389 > show sel cartoons
    5390 
    5391 > hide #3 models
    5392 
    5393 > select #4/A:402-442
    5394 
    5395 Nothing selected 
    5396 
    5397 > select #4/C:402-442
    5398 
    5399 Nothing selected 
    5400 
    5401 > select #4/D:402-442
    5402 
    5403 Nothing selected 
    5404 
    5405 > select #4/E:402-442
    5406 
    5407 Nothing selected 
    5408 
    5409 > select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
    5410 
    5411 3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected 
    5412 
    5413 > select #4&~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
    5414 
    5415 3379 atoms, 3454 bonds, 4 pseudobonds, 422 residues, 2 models selected 
    5416 
    5417 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5418 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
    5419 > fdn small target.cxs"
    5420 
    5421 > select #4&~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
    5422 
    5423 3379 atoms, 3454 bonds, 4 pseudobonds, 422 residues, 2 models selected 
    5424 
    5425 > delete atoms (#!4 & sel)
    5426 
    5427 > delete bonds (#!4 & sel)
    5428 
    5429 > select #4
    5430 
    5431 3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected 
    5432 
    5433 > ui tool show "Change Chain IDs"
    5434 
    5435 > changechains sel A
    5436 
    5437 Chain IDs of 274 residues changed 
    5438 
    5439 > changechains sel A
    5440 
    5441 Chain IDs of 0 residues changed 
    5442 
    5443 > select #4/A
    5444 
    5445 3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected 
    5446 
    5447 > show #!1 models
    5448 
    5449 > hide #!1 models
    5450 
    5451 > show #!1 models
    5452 
    5453 > hide #!1 models
    5454 
    5455 > show #!1 models
    5456 
    5457 > hide #!1 models
    5458 
    5459 > combine #4#5
    5460 
    5461 > rename #5 "Stromal ridge and 2fdn"
    5462 
    5463 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5464 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
    5465 > fdn small target.cxs"
    5466 
    5467 > select #5/A &protein
    5468 
    5469 2981 atoms, 3061 bonds, 9 pseudobonds, 380 residues, 2 models selected 
    5470 
    5471 > hide sel atoms
    5472 
    5473 > hide #!4 models
    5474 
    5475 > select #5/A:27, 31, 504, 807,818, 481, 485, 528
    5476 
    5477 72 atoms, 66 bonds, 8 residues, 1 model selected 
    5478 
    5479 > show sel atoms
    5480 
    5481 > show #!2 models
    5482 
    5483 > hide sel atoms
    5484 
    5485 > select #2/A:27, 31, 504, 807,818, 481, 485, 528
    5486 
    5487 20 atoms, 18 bonds, 2 residues, 1 model selected 
    5488 
    5489 > hide #!2 models
    5490 
    5491 > show #!1 models
    5492 
    5493 > hide #!1 models
    5494 
    5495 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5496 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
    5497 > fdn small target.cxs"
    5498 
    5499 ——— End of log from Sun May 19 17:29:55 2024 ———
    5500 
    5501 opened ChimeraX session 
    5502 
    5503 > show #!4 models
    5504 
    5505 > hide #!4 models
    5506 
    5507 > hide #!5 models
    5508 
    5509 > show #!5 models
    5510 
    5511 > show #3 models
    5512 
    5513 > hide #3 models
    5514 
    5515 > close #3
    5516 
    5517 > show #!2 models
    5518 
    5519 > hide #!2 models
    5520 
    5521 > show #!2 models
    5522 
    5523 > hide #!2 models
    5524 
    5525 > show #!2 models
    5526 
    5527 > rename #2 "PSI chains"
    5528 
    5529 > select #5/M
    5530 
    5531 Nothing selected 
    5532 
    5533 > split #2
    5534 
    5535 Split PSI chains (#2) into 6 models 
    5536 Chain information for PSI chains A #2.1 
    5537 --- 
    5538 Chain | Description 
    5539 A | No description available 
    5540  
    5541 Chain information for PSI chains B #2.2 
    5542 --- 
    5543 Chain | Description 
    5544 B | No description available 
    5545  
    5546 Chain information for PSI chains C #2.3 
    5547 --- 
    5548 Chain | Description 
    5549 C | No description available 
    5550  
    5551 Chain information for PSI chains D #2.4 
    5552 --- 
    5553 Chain | Description 
    5554 D | No description available 
    5555  
    5556 Chain information for PSI chains E #2.5 
    5557 --- 
    5558 Chain | Description 
    5559 E | No description available 
    5560  
    5561 Chain information for PSI chains N #2.6 
    5562 --- 
    5563 Chain | Description 
    5564 N | No description available 
    5565  
    5566 
    5567 > hide #!2.1 models
    5568 
    5569 > hide #!2.2 models
    5570 
    5571 > hide #!2.3 models
    5572 
    5573 > hide #2.4 models
    5574 
    5575 > hide #2.5 models
    5576 
    5577 > rename #2 "PSI 6yez chains"
    5578 
    5579 > show #!2.1 models
    5580 
    5581 > hide #!2.1 models
    5582 
    5583 > show #!2.1 models
    5584 
    5585 > hide #!2.1 models
    5586 
    5587 > show #!4 models
    5588 
    5589 > hide #!5 models
    5590 
    5591 > hide #!4 models
    5592 
    5593 > show #!5 models
    5594 
    5595 > hide #!2 models
    5596 
    5597 > split #5/B
    5598 
    5599 > select #5/B
    5600 
    5601 Nothing selected 
    5602 
    5603 > show #!2 models
    5604 
    5605 > show #!1 models
    5606 
    5607 > show #!4 models
    5608 
    5609 > hide #!4 models
    5610 
    5611 > close #4
    5612 
    5613 > rename #5 id 3
    5614 
    5615 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5616 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    5617 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best.pdb"
    5618 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5619 > Noy 2023/Models/BacetrioFdx PSI
    5620 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design7.pdb"
    5621 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5622 > Noy 2023/Models/BacetrioFdx PSI
    5623 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design6.pdb"
    5624 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5625 > Noy 2023/Models/BacetrioFdx PSI
    5626 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design5.pdb"
    5627 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5628 > Noy 2023/Models/BacetrioFdx PSI
    5629 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design4.pdb"
    5630 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5631 > Noy 2023/Models/BacetrioFdx PSI
    5632 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design3.pdb"
    5633 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5634 > Noy 2023/Models/BacetrioFdx PSI
    5635 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design2.pdb"
    5636 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5637 > Noy 2023/Models/BacetrioFdx PSI
    5638 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design1.pdb"
    5639 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5640 > Noy 2023/Models/BacetrioFdx PSI
    5641 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design0.pdb"
    5642 
    5643 Chain information for best.pdb #4 
    5644 --- 
    5645 Chain | Description 
    5646 A | No description available 
    5647 B | No description available 
    5648  
    5649 Chain information for best_design7.pdb #5 
    5650 --- 
    5651 Chain | Description 
    5652 A | No description available 
    5653 B | No description available 
    5654  
    5655 Chain information for best_design6.pdb #6 
    5656 --- 
    5657 Chain | Description 
    5658 A | No description available 
    5659 B | No description available 
    5660  
    5661 Chain information for best_design5.pdb #7 
    5662 --- 
    5663 Chain | Description 
    5664 A | No description available 
    5665 B | No description available 
    5666  
    5667 Chain information for best_design4.pdb #8 
    5668 --- 
    5669 Chain | Description 
    5670 A | No description available 
    5671 B | No description available 
    5672  
    5673 Chain information for best_design3.pdb #9 
    5674 --- 
    5675 Chain | Description 
    5676 A | No description available 
    5677 B | No description available 
    5678  
    5679 Chain information for best_design2.pdb #10 
    5680 --- 
    5681 Chain | Description 
    5682 A | No description available 
    5683 B | No description available 
    5684  
    5685 Chain information for best_design1.pdb #11 
    5686 --- 
    5687 Chain | Description 
    5688 A | No description available 
    5689 B | No description available 
    5690  
    5691 Chain information for best_design0.pdb #12 
    5692 --- 
    5693 Chain | Description 
    5694 A | No description available 
    5695 B | No description available 
    5696  
    5697 
    5698 > ui tool show Matchmaker
    5699 
    5700 > rename #3 "Stromal ridge target"
    5701 
    5702 > hide #!3 models
    5703 
    5704 > show #!3 models
    5705 
    5706 > ui tool show Matchmaker
    5707 
    5708 > matchmaker #!4-12 to #3
    5709 
    5710 Parameters 
    5711 --- 
    5712 Chain pairing | bb 
    5713 Alignment algorithm | Needleman-Wunsch 
    5714 Similarity matrix | BLOSUM-62 
    5715 SS fraction | 0.3 
    5716 Gap open (HH/SS/other) | 18/18/6 
    5717 Gap extend | 1 
    5718 SS matrix |  |  | H | S | O 
    5719 ---|---|---|--- 
    5720 H | 6 | -9 | -6 
    5721 S |  | 6 | -6 
    5722 O |  |  | 4 
    5723 Iteration cutoff | 2 
    5724  
    5725 Matchmaker Stromal ridge target, chain A (#3) with best.pdb, chain A (#4),
    5726 sequence alignment score = 561.8 
    5727 RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs:
    5728 0.365) 
    5729  
    5730 Matchmaker Stromal ridge target, chain A (#3) with best_design7.pdb, chain A
    5731 (#5), sequence alignment score = 561.8 
    5732 RMSD between 114 pruned atom pairs is 0.362 angstroms; (across all 114 pairs:
    5733 0.362) 
    5734  
    5735 Matchmaker Stromal ridge target, chain A (#3) with best_design6.pdb, chain A
    5736 (#6), sequence alignment score = 561.8 
    5737 RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs:
    5738 0.365) 
    5739  
    5740 Matchmaker Stromal ridge target, chain A (#3) with best_design5.pdb, chain A
    5741 (#7), sequence alignment score = 561.8 
    5742 RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs:
    5743 0.366) 
    5744  
    5745 Matchmaker Stromal ridge target, chain A (#3) with best_design4.pdb, chain A
    5746 (#8), sequence alignment score = 561.8 
    5747 RMSD between 114 pruned atom pairs is 0.367 angstroms; (across all 114 pairs:
    5748 0.367) 
    5749  
    5750 Matchmaker Stromal ridge target, chain A (#3) with best_design3.pdb, chain A
    5751 (#9), sequence alignment score = 561.8 
    5752 RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs:
    5753 0.366) 
    5754  
    5755 Matchmaker Stromal ridge target, chain A (#3) with best_design2.pdb, chain A
    5756 (#10), sequence alignment score = 561.8 
    5757 RMSD between 114 pruned atom pairs is 0.364 angstroms; (across all 114 pairs:
    5758 0.364) 
    5759  
    5760 Matchmaker Stromal ridge target, chain A (#3) with best_design1.pdb, chain A
    5761 (#11), sequence alignment score = 561.8 
    5762 RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs:
    5763 0.365) 
    5764  
    5765 Matchmaker Stromal ridge target, chain A (#3) with best_design0.pdb, chain A
    5766 (#12), sequence alignment score = 561.8 
    5767 RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs:
    5768 0.366) 
    5769  
    5770 
    5771 > hide #!2 models
    5772 
    5773 > hide #!5 models
    5774 
    5775 > hide #!6 models
    5776 
    5777 > hide #!7 models
    5778 
    5779 > hide #!8 models
    5780 
    5781 > hide #!9 models
    5782 
    5783 > hide #!10 models
    5784 
    5785 > hide #!11 models
    5786 
    5787 > hide #!12 models
    5788 
    5789 > select #4/B:8-11,14-18,38-41,44-48
    5790 
    5791 112 atoms, 108 bonds, 18 residues, 1 model selected 
    5792 
    5793 > show sel atoms
    5794 
    5795 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5796 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    5797 > interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"
    5798 
    5799 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5800 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    5801 > interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb"
    5802 
    5803 Chain information for
    5804 Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #13 
    5805 --- 
    5806 Chain | Description 
    5807 A | No description available 
    5808  
    5809 
    5810 > ui tool show Matchmaker
    5811 
    5812 > matchmaker #13 to #4 showAlignment true
    5813 
    5814 Parameters 
    5815 --- 
    5816 Chain pairing | bb 
    5817 Alignment algorithm | Needleman-Wunsch 
    5818 Similarity matrix | BLOSUM-62 
    5819 SS fraction | 0.3 
    5820 Gap open (HH/SS/other) | 18/18/6 
    5821 Gap extend | 1 
    5822 SS matrix |  |  | H | S | O 
    5823 ---|---|---|--- 
    5824 H | 6 | -9 | -6 
    5825 S |  | 6 | -6 
    5826 O |  |  | 4 
    5827 Iteration cutoff | 2 
    5828  
    5829 Matchmaker best.pdb, chain B (#4) with
    5830 Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
    5831 chain A (#13), sequence alignment score = 242.6 
    5832 Alignment identifier is 1 
    5833 Showing conservation header ("seq_conservation" residue attribute) for
    5834 alignment 1 
    5835 Hiding conservation header for alignment 1 
    5836 Chains used in RMSD evaluation for alignment 1: best.pdb #4/B,
    5837 Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb
    5838 #13/A 
    5839 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    5840 RMSD between 36 pruned atom pairs is 0.894 angstroms; (across all 54 pairs:
    5841 2.833) 
    5842  
    5843 
    5844 > sequence header consensus show
    5845 
    5846 Showing consensus header ("seq_consensus" residue attribute) for alignment 1 
    5847 
    5848 > rename #13 Best_alphafold2_rank5.pdb
    5849 
    5850 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5851 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    5852 > interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb"
    5853 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5854 > Noy 2023/Models/BacetrioFdx PSI
    5855 > interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
    5856 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5857 > Noy 2023/Models/BacetrioFdx PSI
    5858 > interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb"
    5859 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
    5860 > Noy 2023/Models/BacetrioFdx PSI
    5861 > interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb"
    5862 
    5863 Chain information for
    5864 Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb #14 
    5865 --- 
    5866 Chain | Description 
    5867 A | No description available 
    5868  
    5869 Chain information for
    5870 Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #15 
    5871 --- 
    5872 Chain | Description 
    5873 A | No description available 
    5874  
    5875 Chain information for
    5876 Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #16 
    5877 --- 
    5878 Chain | Description 
    5879 A | No description available 
    5880  
    5881 Chain information for
    5882 Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb #17 
    5883 --- 
    5884 Chain | Description 
    5885 A | No description available 
    5886  
    5887 
    5888 > rename #14 Best_alphafold2_rank3.pdb
    5889 
    5890 > rename #15 Best_alphafold2_rank1.pdb
    5891 
    5892 > rename #16 Best_alphafold2_rank2.pdb
    5893 
    5894 > rename #17 Best_alphafold2_rank4.pdb
    5895 
    5896 > rename #13 id 18
    5897 
    5898 > rename #15 id 13
    5899 
    5900 > rename #14 id 15
    5901 
    5902 > rename #16 id 14
    5903 
    5904 > rename #18 id 17
    5905 
    5906 > rename #17.1 id 18
    5907 
    5908 > rename #17 id 16
    5909 
    5910 > rename #18 id 17
    5911 
    5912 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    5913 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    5914 > interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"
    5915 
    5916 > ui tool show Matchmaker
    5917 
    5918 > matchmaker #13-17 to #4
    5919 
    5920 Parameters 
    5921 --- 
    5922 Chain pairing | bb 
    5923 Alignment algorithm | Needleman-Wunsch 
    5924 Similarity matrix | BLOSUM-62 
    5925 SS fraction | 0.3 
    5926 Gap open (HH/SS/other) | 18/18/6 
    5927 Gap extend | 1 
    5928 SS matrix |  |  | H | S | O 
    5929 ---|---|---|--- 
    5930 H | 6 | -9 | -6 
    5931 S |  | 6 | -6 
    5932 O |  |  | 4 
    5933 Iteration cutoff | 2 
    5934  
    5935 Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank1.pdb, chain A
    5936 (#13), sequence alignment score = 235.1 
    5937 RMSD between 34 pruned atom pairs is 0.831 angstroms; (across all 54 pairs:
    5938 3.025) 
    5939  
    5940 Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank2.pdb, chain A
    5941 (#14), sequence alignment score = 228.2 
    5942 RMSD between 32 pruned atom pairs is 0.678 angstroms; (across all 54 pairs:
    5943 3.041) 
    5944  
    5945 Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank3.pdb, chain A
    5946 (#15), sequence alignment score = 235.1 
    5947 RMSD between 32 pruned atom pairs is 0.771 angstroms; (across all 54 pairs:
    5948 3.139) 
    5949  
    5950 Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank4.pdb, chain A
    5951 (#16), sequence alignment score = 235.1 
    5952 RMSD between 34 pruned atom pairs is 0.832 angstroms; (across all 54 pairs:
    5953 3.177) 
    5954  
    5955 Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank5.pdb, chain A
    5956 (#17), sequence alignment score = 242.6 
    5957 RMSD between 36 pruned atom pairs is 0.894 angstroms; (across all 54 pairs:
    5958 2.833) 
    5959  
    5960 
    5961 > hide #14 models
    5962 
    5963 > hide #15 models
    5964 
    5965 > hide #16 models
    5966 
    5967 > hide #17 models
    5968 
    5969 > hide #!3 models
    5970 
    5971 > hide #!4 models
    5972 
    5973 > select #13/B:8-11,14-18,38-41,44-48
    5974 
    5975 Nothing selected 
    5976 
    5977 > select #13/A:8-11,14-18,38-41,44-48
    5978 
    5979 112 atoms, 108 bonds, 18 residues, 1 model selected 
    5980 
    5981 > show #14 models
    5982 
    5983 > show #15 models
    5984 
    5985 > show #16 models
    5986 
    5987 > show #17 models
    5988 
    5989 > show sel atoms
    5990 
    5991 > hide #17 models
    5992 
    5993 > hide #16 models
    5994 
    5995 > hide #15 models
    5996 
    5997 > hide #14 models
    5998 
    5999 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    6000 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    6001 > interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"
    6002 
    6003 ——— End of log from Sat Jun 1 14:26:44 2024 ———
    6004 
    6005 opened ChimeraX session 
    6006 
    6007 > hide #!1 models
    6008 
    6009 > show #!4 models
    6010 
    6011 > hide #13 models
    6012 
    6013 > show #!3 models
    6014 
    6015 > hide #!4 models
    6016 
    6017 > help help:user
    6018 
    6019 > hide #!3 models
    6020 
    6021 > show #!4 models
    6022 
    6023 > hide #!4 models
    6024 
    6025 > show #!3 models
    6026 
    6027 > info #3/A:16 rescolor
    6028 
    6029 Expected a keyword 
    6030 
    6031 > help help:user
    6032 
    6033 > info rescolor #3/A:16
    6034 
    6035 #3/A:16 color #b89a8c 
    6036 
    6037 > show #!2 models
    6038 
    6039 > hide #!3 models
    6040 
    6041 > show #!3 models
    6042 
    6043 > hide #!3 models
    6044 
    6045 > hide #!2.6 models
    6046 
    6047 > show #!2.2 models
    6048 
    6049 > show #!3 models
    6050 
    6051 > hide #!2.2 models
    6052 
    6053 > select #3/A &@@color=#b89a8c
    6054 
    6055 Expected a keyword 
    6056 bad color: b89a8c: Invalid color name or specifier 
    6057 
    6058 > select #3/A &@@color#b89a8c
    6059 
    6060 Expected a keyword 
    6061 
    6062 > select #3/A &@@color='#b89a8c'
    6063 
    6064 518 atoms, 413 bonds, 104 residues, 1 model selected 
    6065 
    6066 > select #3/A &@@color='plum'
    6067 
    6068 Nothing selected 
    6069 
    6070 > info rescolor #3/A:430
    6071 
    6072 #3/A:430 color #d9b3f5 
    6073 
    6074 > info rescolor #3/A:804
    6075 
    6076 #3/A:804 color #ebe6fb 
    6077 
    6078 > info rescolor #3/A:498
    6079 
    6080 #3/A:498 color #b88eb1 
    6081 
    6082 > info rescolor #3/A:685
    6083 
    6084 #3/A:685 color #c8e69e 
    6085 
    6086 > select #3/A &@@color='#b89a8c'
    6087 
    6088 518 atoms, 413 bonds, 104 residues, 1 model selected 
    6089 
    6090 > info residues sel attribute num
    6091 
    6092  
    6093 
    6094 > info residues #3/A &@@color='#b89a8c' attribute num
    6095 
    6096  
    6097 
    6098 > info residues #3/A &@@color='#b89a8c' attribute number
    6099 
    6100 residue id #3/A:16 number 16 index 15 
    6101 residue id #3/A:17 number 17 index 16 
    6102 residue id #3/A:18 number 18 index 17 
    6103 residue id #3/A:152 number 152 index 135 
    6104 residue id #3/A:153 number 153 index 136 
    6105 residue id #3/A:154 number 154 index 137 
    6106 residue id #3/A:155 number 155 index 138 
    6107 residue id #3/A:156 number 156 index 139 
    6108 residue id #3/A:157 number 157 index 140 
    6109 residue id #3/A:158 number 158 index 141 
    6110 residue id #3/A:159 number 159 index 142 
    6111 residue id #3/A:160 number 160 index 143 
    6112 residue id #3/A:161 number 161 index 144 
    6113 residue id #3/A:162 number 162 index 145 
    6114 residue id #3/A:163 number 163 index 146 
    6115 residue id #3/A:164 number 164 index 147 
    6116 residue id #3/A:165 number 165 index 148 
    6117 residue id #3/A:166 number 166 index 149 
    6118 residue id #3/A:52 number 52 index 51 
    6119 residue id #3/A:53 number 53 index 52 
    6120 residue id #3/A:54 number 54 index 53 
    6121 residue id #3/A:19 number 19 index 18 
    6122 residue id #3/A:20 number 20 index 19 
    6123 residue id #3/A:21 number 21 index 20 
    6124 residue id #3/A:22 number 22 index 21 
    6125 residue id #3/A:23 number 23 index 22 
    6126 residue id #3/A:24 number 24 index 23 
    6127 residue id #3/A:25 number 25 index 24 
    6128 residue id #3/A:26 number 26 index 25 
    6129 residue id #3/A:27 number 27 index 26 
    6130 residue id #3/A:28 number 28 index 27 
    6131 residue id #3/A:29 number 29 index 28 
    6132 residue id #3/A:30 number 30 index 29 
    6133 residue id #3/A:31 number 31 index 30 
    6134 residue id #3/A:32 number 32 index 31 
    6135 residue id #3/A:33 number 33 index 32 
    6136 residue id #3/A:34 number 34 index 33 
    6137 residue id #3/A:35 number 35 index 34 
    6138 residue id #3/A:36 number 36 index 35 
    6139 residue id #3/A:37 number 37 index 36 
    6140 residue id #3/A:38 number 38 index 37 
    6141 residue id #3/A:39 number 39 index 38 
    6142 residue id #3/A:40 number 40 index 39 
    6143 residue id #3/A:41 number 41 index 40 
    6144 residue id #3/A:42 number 42 index 41 
    6145 residue id #3/A:43 number 43 index 42 
    6146 residue id #3/A:44 number 44 index 43 
    6147 residue id #3/A:45 number 45 index 44 
    6148 residue id #3/A:46 number 46 index 45 
    6149 residue id #3/A:47 number 47 index 46 
    6150 residue id #3/A:48 number 48 index 47 
    6151 residue id #3/A:49 number 49 index 48 
    6152 residue id #3/A:50 number 50 index 49 
    6153 residue id #3/A:51 number 51 index 50 
    6154 residue id #3/A:209 number 209 index 184 
    6155 residue id #3/A:210 number 210 index 185 
    6156 residue id #3/A:211 number 211 index 186 
    6157 residue id #3/A:212 number 212 index 187 
    6158 residue id #3/A:213 number 213 index 188 
    6159 residue id #3/A:214 number 214 index 189 
    6160 residue id #3/A:215 number 215 index 190 
    6161 residue id #3/A:216 number 216 index 191 
    6162 residue id #3/A:217 number 217 index 192 
    6163 residue id #3/A:218 number 218 index 193 
    6164 residue id #3/A:219 number 219 index 194 
    6165 residue id #3/A:220 number 220 index 195 
    6166 residue id #3/A:221 number 221 index 196 
    6167 residue id #3/A:222 number 222 index 197 
    6168 residue id #3/A:223 number 223 index 198 
    6169 residue id #3/A:224 number 224 index 199 
    6170 residue id #3/A:225 number 225 index 200 
    6171 residue id #3/A:226 number 226 index 201 
    6172 residue id #3/A:167 number 167 index 150 
    6173 residue id #3/A:168 number 168 index 151 
    6174 residue id #3/A:169 number 169 index 152 
    6175 residue id #3/A:170 number 170 index 153 
    6176 residue id #3/A:171 number 171 index 154 
    6177 residue id #3/A:172 number 172 index 155 
    6178 residue id #3/A:173 number 173 index 156 
    6179 residue id #3/A:174 number 174 index 157 
    6180 residue id #3/A:175 number 175 index 158 
    6181 residue id #3/A:176 number 176 index 159 
    6182 residue id #3/A:177 number 177 index 160 
    6183 residue id #3/A:178 number 178 index 161 
    6184 residue id #3/A:179 number 179 index 162 
    6185 residue id #3/A:180 number 180 index 163 
    6186 residue id #3/A:181 number 181 index 164 
    6187 residue id #3/A:182 number 182 index 165 
    6188 residue id #3/A:183 number 183 index 166 
    6189 residue id #3/A:194 number 194 index 169 
    6190 residue id #3/A:195 number 195 index 170 
    6191 residue id #3/A:196 number 196 index 171 
    6192 residue id #3/A:197 number 197 index 172 
    6193 residue id #3/A:198 number 198 index 173 
    6194 residue id #3/A:199 number 199 index 174 
    6195 residue id #3/A:200 number 200 index 175 
    6196 residue id #3/A:201 number 201 index 176 
    6197 residue id #3/A:202 number 202 index 177 
    6198 residue id #3/A:203 number 203 index 178 
    6199 residue id #3/A:204 number 204 index 179 
    6200 residue id #3/A:205 number 205 index 180 
    6201 residue id #3/A:206 number 206 index 181 
    6202 residue id #3/A:207 number 207 index 182 
    6203 residue id #3/A:208 number 208 index 183 
    6204 
    6205 > info residues sel attribute number
    6206 
    6207 residue id #3/A:16 number 16 index 15 
    6208 residue id #3/A:17 number 17 index 16 
    6209 residue id #3/A:18 number 18 index 17 
    6210 residue id #3/A:152 number 152 index 135 
    6211 residue id #3/A:153 number 153 index 136 
    6212 residue id #3/A:154 number 154 index 137 
    6213 residue id #3/A:155 number 155 index 138 
    6214 residue id #3/A:156 number 156 index 139 
    6215 residue id #3/A:157 number 157 index 140 
    6216 residue id #3/A:158 number 158 index 141 
    6217 residue id #3/A:159 number 159 index 142 
    6218 residue id #3/A:160 number 160 index 143 
    6219 residue id #3/A:161 number 161 index 144 
    6220 residue id #3/A:162 number 162 index 145 
    6221 residue id #3/A:163 number 163 index 146 
    6222 residue id #3/A:164 number 164 index 147 
    6223 residue id #3/A:165 number 165 index 148 
    6224 residue id #3/A:166 number 166 index 149 
    6225 residue id #3/A:52 number 52 index 51 
    6226 residue id #3/A:53 number 53 index 52 
    6227 residue id #3/A:54 number 54 index 53 
    6228 residue id #3/A:19 number 19 index 18 
    6229 residue id #3/A:20 number 20 index 19 
    6230 residue id #3/A:21 number 21 index 20 
    6231 residue id #3/A:22 number 22 index 21 
    6232 residue id #3/A:23 number 23 index 22 
    6233 residue id #3/A:24 number 24 index 23 
    6234 residue id #3/A:25 number 25 index 24 
    6235 residue id #3/A:26 number 26 index 25 
    6236 residue id #3/A:27 number 27 index 26 
    6237 residue id #3/A:28 number 28 index 27 
    6238 residue id #3/A:29 number 29 index 28 
    6239 residue id #3/A:30 number 30 index 29 
    6240 residue id #3/A:31 number 31 index 30 
    6241 residue id #3/A:32 number 32 index 31 
    6242 residue id #3/A:33 number 33 index 32 
    6243 residue id #3/A:34 number 34 index 33 
    6244 residue id #3/A:35 number 35 index 34 
    6245 residue id #3/A:36 number 36 index 35 
    6246 residue id #3/A:37 number 37 index 36 
    6247 residue id #3/A:38 number 38 index 37 
    6248 residue id #3/A:39 number 39 index 38 
    6249 residue id #3/A:40 number 40 index 39 
    6250 residue id #3/A:41 number 41 index 40 
    6251 residue id #3/A:42 number 42 index 41 
    6252 residue id #3/A:43 number 43 index 42 
    6253 residue id #3/A:44 number 44 index 43 
    6254 residue id #3/A:45 number 45 index 44 
    6255 residue id #3/A:46 number 46 index 45 
    6256 residue id #3/A:47 number 47 index 46 
    6257 residue id #3/A:48 number 48 index 47 
    6258 residue id #3/A:49 number 49 index 48 
    6259 residue id #3/A:50 number 50 index 49 
    6260 residue id #3/A:51 number 51 index 50 
    6261 residue id #3/A:209 number 209 index 184 
    6262 residue id #3/A:210 number 210 index 185 
    6263 residue id #3/A:211 number 211 index 186 
    6264 residue id #3/A:212 number 212 index 187 
    6265 residue id #3/A:213 number 213 index 188 
    6266 residue id #3/A:214 number 214 index 189 
    6267 residue id #3/A:215 number 215 index 190 
    6268 residue id #3/A:216 number 216 index 191 
    6269 residue id #3/A:217 number 217 index 192 
    6270 residue id #3/A:218 number 218 index 193 
    6271 residue id #3/A:219 number 219 index 194 
    6272 residue id #3/A:220 number 220 index 195 
    6273 residue id #3/A:221 number 221 index 196 
    6274 residue id #3/A:222 number 222 index 197 
    6275 residue id #3/A:223 number 223 index 198 
    6276 residue id #3/A:224 number 224 index 199 
    6277 residue id #3/A:225 number 225 index 200 
    6278 residue id #3/A:226 number 226 index 201 
    6279 residue id #3/A:167 number 167 index 150 
    6280 residue id #3/A:168 number 168 index 151 
    6281 residue id #3/A:169 number 169 index 152 
    6282 residue id #3/A:170 number 170 index 153 
    6283 residue id #3/A:171 number 171 index 154 
    6284 residue id #3/A:172 number 172 index 155 
    6285 residue id #3/A:173 number 173 index 156 
    6286 residue id #3/A:174 number 174 index 157 
    6287 residue id #3/A:175 number 175 index 158 
    6288 residue id #3/A:176 number 176 index 159 
    6289 residue id #3/A:177 number 177 index 160 
    6290 residue id #3/A:178 number 178 index 161 
    6291 residue id #3/A:179 number 179 index 162 
    6292 residue id #3/A:180 number 180 index 163 
    6293 residue id #3/A:181 number 181 index 164 
    6294 residue id #3/A:182 number 182 index 165 
    6295 residue id #3/A:183 number 183 index 166 
    6296 residue id #3/A:194 number 194 index 169 
    6297 residue id #3/A:195 number 195 index 170 
    6298 residue id #3/A:196 number 196 index 171 
    6299 residue id #3/A:197 number 197 index 172 
    6300 residue id #3/A:198 number 198 index 173 
    6301 residue id #3/A:199 number 199 index 174 
    6302 residue id #3/A:200 number 200 index 175 
    6303 residue id #3/A:201 number 201 index 176 
    6304 residue id #3/A:202 number 202 index 177 
    6305 residue id #3/A:203 number 203 index 178 
    6306 residue id #3/A:204 number 204 index 179 
    6307 residue id #3/A:205 number 205 index 180 
    6308 residue id #3/A:206 number 206 index 181 
    6309 residue id #3/A:207 number 207 index 182 
    6310 residue id #3/A:208 number 208 index 183 
    6311 
    6312 > info residues #3/A &@@color='#b89a8c' attribute number
    6313 
    6314 residue id #3/A:16 number 16 index 15 
    6315 residue id #3/A:17 number 17 index 16 
    6316 residue id #3/A:18 number 18 index 17 
    6317 residue id #3/A:152 number 152 index 135 
    6318 residue id #3/A:153 number 153 index 136 
    6319 residue id #3/A:154 number 154 index 137 
    6320 residue id #3/A:155 number 155 index 138 
    6321 residue id #3/A:156 number 156 index 139 
    6322 residue id #3/A:157 number 157 index 140 
    6323 residue id #3/A:158 number 158 index 141 
    6324 residue id #3/A:159 number 159 index 142 
    6325 residue id #3/A:160 number 160 index 143 
    6326 residue id #3/A:161 number 161 index 144 
    6327 residue id #3/A:162 number 162 index 145 
    6328 residue id #3/A:163 number 163 index 146 
    6329 residue id #3/A:164 number 164 index 147 
    6330 residue id #3/A:165 number 165 index 148 
    6331 residue id #3/A:166 number 166 index 149 
    6332 residue id #3/A:52 number 52 index 51 
    6333 residue id #3/A:53 number 53 index 52 
    6334 residue id #3/A:54 number 54 index 53 
    6335 residue id #3/A:19 number 19 index 18 
    6336 residue id #3/A:20 number 20 index 19 
    6337 residue id #3/A:21 number 21 index 20 
    6338 residue id #3/A:22 number 22 index 21 
    6339 residue id #3/A:23 number 23 index 22 
    6340 residue id #3/A:24 number 24 index 23 
    6341 residue id #3/A:25 number 25 index 24 
    6342 residue id #3/A:26 number 26 index 25 
    6343 residue id #3/A:27 number 27 index 26 
    6344 residue id #3/A:28 number 28 index 27 
    6345 residue id #3/A:29 number 29 index 28 
    6346 residue id #3/A:30 number 30 index 29 
    6347 residue id #3/A:31 number 31 index 30 
    6348 residue id #3/A:32 number 32 index 31 
    6349 residue id #3/A:33 number 33 index 32 
    6350 residue id #3/A:34 number 34 index 33 
    6351 residue id #3/A:35 number 35 index 34 
    6352 residue id #3/A:36 number 36 index 35 
    6353 residue id #3/A:37 number 37 index 36 
    6354 residue id #3/A:38 number 38 index 37 
    6355 residue id #3/A:39 number 39 index 38 
    6356 residue id #3/A:40 number 40 index 39 
    6357 residue id #3/A:41 number 41 index 40 
    6358 residue id #3/A:42 number 42 index 41 
    6359 residue id #3/A:43 number 43 index 42 
    6360 residue id #3/A:44 number 44 index 43 
    6361 residue id #3/A:45 number 45 index 44 
    6362 residue id #3/A:46 number 46 index 45 
    6363 residue id #3/A:47 number 47 index 46 
    6364 residue id #3/A:48 number 48 index 47 
    6365 residue id #3/A:49 number 49 index 48 
    6366 residue id #3/A:50 number 50 index 49 
    6367 residue id #3/A:51 number 51 index 50 
    6368 residue id #3/A:209 number 209 index 184 
    6369 residue id #3/A:210 number 210 index 185 
    6370 residue id #3/A:211 number 211 index 186 
    6371 residue id #3/A:212 number 212 index 187 
    6372 residue id #3/A:213 number 213 index 188 
    6373 residue id #3/A:214 number 214 index 189 
    6374 residue id #3/A:215 number 215 index 190 
    6375 residue id #3/A:216 number 216 index 191 
    6376 residue id #3/A:217 number 217 index 192 
    6377 residue id #3/A:218 number 218 index 193 
    6378 residue id #3/A:219 number 219 index 194 
    6379 residue id #3/A:220 number 220 index 195 
    6380 residue id #3/A:221 number 221 index 196 
    6381 residue id #3/A:222 number 222 index 197 
    6382 residue id #3/A:223 number 223 index 198 
    6383 residue id #3/A:224 number 224 index 199 
    6384 residue id #3/A:225 number 225 index 200 
    6385 residue id #3/A:226 number 226 index 201 
    6386 residue id #3/A:167 number 167 index 150 
    6387 residue id #3/A:168 number 168 index 151 
    6388 residue id #3/A:169 number 169 index 152 
    6389 residue id #3/A:170 number 170 index 153 
    6390 residue id #3/A:171 number 171 index 154 
    6391 residue id #3/A:172 number 172 index 155 
    6392 residue id #3/A:173 number 173 index 156 
    6393 residue id #3/A:174 number 174 index 157 
    6394 residue id #3/A:175 number 175 index 158 
    6395 residue id #3/A:176 number 176 index 159 
    6396 residue id #3/A:177 number 177 index 160 
    6397 residue id #3/A:178 number 178 index 161 
    6398 residue id #3/A:179 number 179 index 162 
    6399 residue id #3/A:180 number 180 index 163 
    6400 residue id #3/A:181 number 181 index 164 
    6401 residue id #3/A:182 number 182 index 165 
    6402 residue id #3/A:183 number 183 index 166 
    6403 residue id #3/A:194 number 194 index 169 
    6404 residue id #3/A:195 number 195 index 170 
    6405 residue id #3/A:196 number 196 index 171 
    6406 residue id #3/A:197 number 197 index 172 
    6407 residue id #3/A:198 number 198 index 173 
    6408 residue id #3/A:199 number 199 index 174 
    6409 residue id #3/A:200 number 200 index 175 
    6410 residue id #3/A:201 number 201 index 176 
    6411 residue id #3/A:202 number 202 index 177 
    6412 residue id #3/A:203 number 203 index 178 
    6413 residue id #3/A:204 number 204 index 179 
    6414 residue id #3/A:205 number 205 index 180 
    6415 residue id #3/A:206 number 206 index 181 
    6416 residue id #3/A:207 number 207 index 182 
    6417 residue id #3/A:208 number 208 index 183 
    6418 
    6419 > show #!4 models
    6420 
    6421 > hide #!3 models
    6422 
    6423 > show #!3 models
    6424 
    6425 > select #4/A:1-227
    6426 
    6427 857 atoms, 885 bonds, 2 pseudobonds, 108 residues, 2 models selected 
    6428 
    6429 > ui tool show "Color Actions"
    6430 
    6431 > color sel tan
    6432 
    6433 > hide #!3 models
    6434 
    6435 > show #!3 models
    6436 
    6437 > select #4/A:425-436
    6438 
    6439 Nothing selected 
    6440 
    6441 > hide #!3 models
    6442 
    6443 > select #4/A:410-421
    6444 
    6445 76 atoms, 77 bonds, 12 residues, 1 model selected 
    6446 
    6447 > color sel peru
    6448 
    6449 > select #4/A:456-535
    6450 
    6451 611 atoms, 624 bonds, 80 residues, 1 model selected 
    6452 
    6453 > show #!3 models
    6454 
    6455 > hide #!3 models
    6456 
    6457 > color sel violet
    6458 
    6459 > select #4/A:572-685
    6460 
    6461 908 atoms, 934 bonds, 114 residues, 1 model selected 
    6462 
    6463 > color sel light steel blue
    6464 
    6465 > color sel powder blue
    6466 
    6467 > color sel sky blue
    6468 
    6469 > color sel medium orchid
    6470 
    6471 > color sel light pink
    6472 
    6473 > color sel light coral
    6474 
    6475 > color sel light pink
    6476 
    6477 > select #4/A:749-814
    6478 
    6479 528 atoms, 540 bonds, 66 residues, 1 model selected 
    6480 
    6481 > color sel light coral
    6482 
    6483 > show #!1 models
    6484 
    6485 > show #!2.3 models
    6486 
    6487 > show #!2.1 models
    6488 
    6489 > hide #!2.1 models
    6490 
    6491 > hide #!2.3 models
    6492 
    6493 > show #!3 models
    6494 
    6495 > hide #!3 models
    6496 
    6497 > show #!2.1 models
    6498 
    6499 > show #!2.3 models
    6500 
    6501 > show #2.4 models
    6502 
    6503 > show #2.5 models
    6504 
    6505 > select #2/A:1-16
    6506 
    6507 130 atoms, 132 bonds, 16 residues, 1 model selected 
    6508 
    6509 > hide sel cartoons
    6510 
    6511 > select #2/A:1-16,54-58
    6512 
    6513 170 atoms, 171 bonds, 21 residues, 1 model selected 
    6514 
    6515 > select #2/A:1-16,54-146
    6516 
    6517 809 atoms, 828 bonds, 3 pseudobonds, 97 residues, 2 models selected 
    6518 
    6519 > hide sel cartoons
    6520 
    6521 > select #2:SF4 :<3 &#2/A-E
    6522 
    6523 109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected 
    6524 
    6525 > hide #!1 models
    6526 
    6527 > hide #!4 models
    6528 
    6529 > show #!2.2 models
    6530 
    6531 > show #!3 models
    6532 
    6533 > select add #2.2
    6534 
    6535 1804 atoms, 1850 bonds, 14 pseudobonds, 226 residues, 6 models selected 
    6536 
    6537 > show sel cartoons
    6538 
    6539 > hide sel cartoons
    6540 
    6541 > select subtract #2.2
    6542 
    6543 93 atoms, 95 bonds, 9 pseudobonds, 14 residues, 4 models selected 
    6544 
    6545 > select #2/B:425-436
    6546 
    6547 76 atoms, 77 bonds, 12 residues, 1 model selected 
    6548 
    6549 > show sel cartoons
    6550 
    6551 > hide #!3 models
    6552 
    6553 > show #!3 models
    6554 
    6555 > hide #!3 models
    6556 
    6557 > show #!3 models
    6558 
    6559 > hide #!2 models
    6560 
    6561 > show #!2 models
    6562 
    6563 > hide #!2 models
    6564 
    6565 > show #!2 models
    6566 
    6567 > hide #!2 models
    6568 
    6569 > show #!2 models
    6570 
    6571 > hide #!2 models
    6572 
    6573 > show #!2 models
    6574 
    6575 > hide #!3 models
    6576 
    6577 > select #2:SF4 :<3 &#2/A-E
    6578 
    6579 109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected 
    6580 
    6581 > select #2:SF4 :<3 &#2/A-E
    6582 
    6583 109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected 
    6584 
    6585 > show sel atoms
    6586 
    6587 > color sel byhetero
    6588 
    6589 > show sel cartoons
    6590 
    6591 > show #!4 models
    6592 
    6593 > select #4/A:456-535
    6594 
    6595 611 atoms, 624 bonds, 80 residues, 1 model selected 
    6596 
    6597 > hide #!2.2 models
    6598 
    6599 > hide #!2.1 models
    6600 
    6601 > hide #2.4 models
    6602 
    6603 > hide #2.5 models
    6604 
    6605 > ui tool show Matchmaker
    6606 
    6607 > matchmaker #!4 & sel to #2.3/C pairing bs showAlignment true
    6608 
    6609 Parameters 
    6610 --- 
    6611 Chain pairing | bs 
    6612 Alignment algorithm | Needleman-Wunsch 
    6613 Similarity matrix | BLOSUM-62 
    6614 SS fraction | 0.3 
    6615 Gap open (HH/SS/other) | 18/18/6 
    6616 Gap extend | 1 
    6617 SS matrix |  |  | H | S | O 
    6618 ---|---|---|--- 
    6619 H | 6 | -9 | -6 
    6620 S |  | 6 | -6 
    6621 O |  |  | 4 
    6622 Iteration cutoff | 2 
    6623  
    6624 Matchmaker PSI chains C, chain C (#2.3) with best.pdb, chain A (#4), sequence
    6625 alignment score = 401 
    6626 Alignment identifier is 1 
    6627 Showing conservation header ("seq_conservation" residue attribute) for
    6628 alignment 1 
    6629 Hiding conservation header for alignment 1 
    6630 Chains used in RMSD evaluation for alignment 1: PSI chains C #2.3/C, best.pdb
    6631 #4/A 
    6632 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    6633 RMSD between 80 pruned atom pairs is 0.395 angstroms; (across all 80 pairs:
    6634 0.395) 
    6635  
    6636 
    6637 > show #!2.1 models
    6638 
    6639 > hide #!2.1 models
    6640 
    6641 > show #!2.1 models
    6642 
    6643 > show #!2.2 models
    6644 
    6645 > select #4/A:CYS
    6646 
    6647 84 atoms, 70 bonds, 14 residues, 1 model selected 
    6648 
    6649 > show sel atoms
    6650 
    6651 > color sel byhetero
    6652 
    6653 > hide #!2 models
    6654 
    6655 > show #!2 models
    6656 
    6657 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    6658 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    6659 > interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"
    6660 
    6661 > split #2.1 atoms :SF4
    6662 
    6663 Split PSI chains A (#2.1) into 2 models 
    6664 Chain information for PSI chains A 2 #2.1.2 
    6665 --- 
    6666 Chain | Description 
    6667 A | No description available 
    6668  
    6669 
    6670 > hide #!2.1.2 models
    6671 
    6672 > split #2.3 atoms :SF4
    6673 
    6674 Split PSI chains C (#2.3) into 2 models 
    6675 Chain information for PSI chains C 2 #2.3.2 
    6676 --- 
    6677 Chain | Description 
    6678 C | No description available 
    6679  
    6680 Associated PSI chains C 2 (2.3.2) chain C to best.pdb, chain A with 0
    6681 mismatches 
    6682 Chains used in RMSD evaluation for alignment 1: PSI chains C 2 #2.3.2/C,
    6683 best.pdb #4/A 
    6684 
    6685 > hide #2.3.2 models
    6686 
    6687 > hide #2.3.1 models
    6688 
    6689 > show #2.3.1 models
    6690 
    6691 > hide #2.3.1 models
    6692 
    6693 > show #2.3.1 models
    6694 
    6695 > rename #3 id 20
    6696 
    6697 > combine #2.1.1#2.3.1
    6698 
    6699 > hide #!2 models
    6700 
    6701 > rename #3 "Fe4S4 clusters"
    6702 
    6703 > show #!1 models
    6704 
    6705 > select #1 &!@@color='lime'
    6706 
    6707 Expected a keyword 
    6708 
    6709 > select #1 &~@@color='lime'
    6710 
    6711 669 atoms, 451 bonds, 8 pseudobonds, 151 residues, 2 models selected 
    6712 
    6713 > color sel orange
    6714 
    6715 > color sel dark orange
    6716 
    6717 > color sel byhetero
    6718 
    6719 > select #1 &H
    6720 
    6721 272 atoms, 48 residues, 1 model selected 
    6722 
    6723 > hide sel atoms
    6724 
    6725 > select #1
    6726 
    6727 762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected 
    6728 
    6729 > color sel byhetero
    6730 
    6731 > select clear
    6732 
    6733 > combine #1
    6734 
    6735 > hide #!1 models
    6736 
    6737 > ui tool show Matchmaker
    6738 
    6739 > matchmaker #!18 to #4/B pairing bs showAlignment true
    6740 
    6741 Parameters 
    6742 --- 
    6743 Chain pairing | bs 
    6744 Alignment algorithm | Needleman-Wunsch 
    6745 Similarity matrix | BLOSUM-62 
    6746 SS fraction | 0.3 
    6747 Gap open (HH/SS/other) | 18/18/6 
    6748 Gap extend | 1 
    6749 SS matrix |  |  | H | S | O 
    6750 ---|---|---|--- 
    6751 H | 6 | -9 | -6 
    6752 S |  | 6 | -6 
    6753 O |  |  | 4 
    6754 Iteration cutoff | 2 
    6755  
    6756 Matchmaker best.pdb, chain B (#4) with copy of 2fdn, chain M (#18), sequence
    6757 alignment score = 157.4 
    6758 Alignment identifier is 1 
    6759 Showing conservation header ("seq_conservation" residue attribute) for
    6760 alignment 1 
    6761 Hiding conservation header for alignment 1 
    6762 Chains used in RMSD evaluation for alignment 1: best.pdb #4/B, copy of 2fdn
    6763 #18/M 
    6764 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    6765 RMSD between 38 pruned atom pairs is 0.829 angstroms; (across all 51 pairs:
    6766 2.274) 
    6767  
    6768 
    6769 > select #4:CYS
    6770 
    6771 132 atoms, 110 bonds, 22 residues, 1 model selected 
    6772 
    6773 > select #4/B:CYS
    6774 
    6775 48 atoms, 40 bonds, 8 residues, 1 model selected 
    6776 
    6777 > show #!5 models
    6778 
    6779 > hide #!4 models
    6780 
    6781 > hide #!5 models
    6782 
    6783 > show #!4 models
    6784 
    6785 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    6786 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    6787 > interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"
    6788 
    6789 > show #!5 models
    6790 
    6791 > hide #!5 models
    6792 
    6793 > help help:user
    6794 
    6795 > color #5-18/A:1-227 tan
    6796 
    6797 > color #5-18/A:410-421 peru
    6798 
    6799 > color #5-18/A:456-535 violet
    6800 
    6801 > color #5-18/A:572-685 light pink
    6802 
    6803 > color #5-18/A:749-814 light coral
    6804 
    6805 > show #!5 models
    6806 
    6807 > hide #!4 models
    6808 
    6809 > hide #!5 models
    6810 
    6811 > show #!6 models
    6812 
    6813 > hide #!6 models
    6814 
    6815 > show #!7 models
    6816 
    6817 > hide #!7 models
    6818 
    6819 > show #!8 models
    6820 
    6821 > hide #!8 models
    6822 
    6823 > show #!9 models
    6824 
    6825 > hide #!9 models
    6826 
    6827 > show #!10 models
    6828 
    6829 > show #!9 models
    6830 
    6831 > show #!7 models
    6832 
    6833 > show #!8 models
    6834 
    6835 > show #!6 models
    6836 
    6837 > show #!5 models
    6838 
    6839 > hide #3 models
    6840 
    6841 > show #!4 models
    6842 
    6843 > show #3 models
    6844 
    6845 > show #!11 models
    6846 
    6847 > show #!12 models
    6848 
    6849 > show #13 models
    6850 
    6851 > show #14 models
    6852 
    6853 > show #15 models
    6854 
    6855 > hide #15 models
    6856 
    6857 > hide #14 models
    6858 
    6859 > show #14 models
    6860 
    6861 > hide #14 models
    6862 
    6863 > hide #13 models
    6864 
    6865 > close #13-17
    6866 
    6867 > hide #!5 models
    6868 
    6869 > hide #!6 models
    6870 
    6871 > hide #!7 models
    6872 
    6873 > hide #!8 models
    6874 
    6875 > hide #!9 models
    6876 
    6877 > hide #!10 models
    6878 
    6879 > hide #!11 models
    6880 
    6881 > hide #!12 models
    6882 
    6883 > hide #!18 models
    6884 
    6885 > show #!5 models
    6886 
    6887 > show #!6 models
    6888 
    6889 > show #!7 models
    6890 
    6891 > show #!8 models
    6892 
    6893 > show #!9 models
    6894 
    6895 > show #!10 models
    6896 
    6897 > show #!11 models
    6898 
    6899 > show #!12 models
    6900 
    6901 > select add #4
    6902 
    6903 3337 atoms, 3419 bonds, 6 pseudobonds, 434 residues, 2 models selected 
    6904 
    6905 > select subtract #4
    6906 
    6907 Nothing selected 
    6908 
    6909 > ui tool show Matchmaker
    6910 
    6911 > help help:user
    6912 
    6913 > show #!1 models
    6914 
    6915 > hide #!1 models
    6916 
    6917 > show #!1 models
    6918 
    6919 > hide #!1 models
    6920 
    6921 > select #1:CYS
    6922 
    6923 80 atoms, 72 bonds, 8 residues, 1 model selected 
    6924 
    6925 > align #18:CYS toAtoms #4:CYS matchAtomNames true move nothing
    6926 
    6927 Pairing dropped 32 atoms and 84 reference atoms 
    6928 RMSD between 48 atom pairs is 8.311 angstroms 
    6929 
    6930 > align #18:CYS toAtoms #1:CYS matchAtomNames true move nothing
    6931 
    6932 RMSD between 80 atom pairs is 0.000 angstroms 
    6933 
    6934 > align #18:CYS toAtoms #5:CYS matchAtomNames true move nothing
    6935 
    6936 Pairing dropped 32 atoms and 84 reference atoms 
    6937 RMSD between 48 atom pairs is 8.316 angstroms 
    6938 
    6939 > align #18:CYS toAtoms #6:CYS matchAtomNames true move nothing
    6940 
    6941 Pairing dropped 32 atoms and 84 reference atoms 
    6942 RMSD between 48 atom pairs is 8.305 angstroms 
    6943 
    6944 > align #18:CYS toAtoms #7:CYS matchAtomNames true move nothing
    6945 
    6946 Pairing dropped 32 atoms and 84 reference atoms 
    6947 RMSD between 48 atom pairs is 8.308 angstroms 
    6948 
    6949 > align #18:CYS toAtoms #8:CYS matchAtomNames true move nothing
    6950 
    6951 Pairing dropped 32 atoms and 84 reference atoms 
    6952 RMSD between 48 atom pairs is 8.316 angstroms 
    6953 
    6954 > align #18:CYS toAtoms #9:CYS matchAtomNames true move nothing
    6955 
    6956 Pairing dropped 32 atoms and 84 reference atoms 
    6957 RMSD between 48 atom pairs is 8.306 angstroms 
    6958 
    6959 > align #18:CYS toAtoms #10:CYS matchAtomNames true move nothing
    6960 
    6961 Pairing dropped 32 atoms and 84 reference atoms 
    6962 RMSD between 48 atom pairs is 8.309 angstroms 
    6963 
    6964 > align #18:CYS toAtoms #11:CYS matchAtomNames true move nothing
    6965 
    6966 Pairing dropped 32 atoms and 84 reference atoms 
    6967 RMSD between 48 atom pairs is 8.311 angstroms 
    6968 
    6969 > align #18:CYS toAtoms #12:CYS matchAtomNames true move nothing
    6970 
    6971 Pairing dropped 32 atoms and 84 reference atoms 
    6972 RMSD between 48 atom pairs is 8.309 angstroms 
    6973 
    6974 > select #5-12
    6975 
    6976 26753 atoms, 27419 bonds, 48 pseudobonds, 3472 residues, 16 models selected 
    6977 
    6978 > select #5-12/B:CYS
    6979 
    6980 384 atoms, 320 bonds, 64 residues, 8 models selected 
    6981 
    6982 > show sel atoms
    6983 
    6984 > color sel byhetero
    6985 
    6986 > align #18:CYS toAtoms #4/B:CYS matchAtomNames true move nothing
    6987 
    6988 Pairing dropped 32 atoms and 0 reference atoms 
    6989 RMSD between 48 atom pairs is 1.745 angstroms 
    6990 
    6991 > align #18:CYS toAtoms #5/B:CYS matchAtomNames true move nothing
    6992 
    6993 Pairing dropped 32 atoms and 0 reference atoms 
    6994 RMSD between 48 atom pairs is 1.738 angstroms 
    6995 
    6996 > align #18:CYS toAtoms #6/B:CYS matchAtomNames true move nothing
    6997 
    6998 Pairing dropped 32 atoms and 0 reference atoms 
    6999 RMSD between 48 atom pairs is 1.898 angstroms 
    7000 
    7001 > align #18:CYS toAtoms #7/B:CYS matchAtomNames true move nothing
    7002 
    7003 Pairing dropped 32 atoms and 0 reference atoms 
    7004 RMSD between 48 atom pairs is 1.823 angstroms 
    7005 
    7006 > align #18:CYS toAtoms #8/B:CYS matchAtomNames true move nothing
    7007 
    7008 Pairing dropped 32 atoms and 0 reference atoms 
    7009 RMSD between 48 atom pairs is 1.953 angstroms 
    7010 
    7011 > align #18:CYS toAtoms #9/B:CYS matchAtomNames true move nothing
    7012 
    7013 Pairing dropped 32 atoms and 0 reference atoms 
    7014 RMSD between 48 atom pairs is 1.867 angstroms 
    7015 
    7016 > align #18:CYS toAtoms #10/B:CYS matchAtomNames true move nothing
    7017 
    7018 Pairing dropped 32 atoms and 0 reference atoms 
    7019 RMSD between 48 atom pairs is 1.898 angstroms 
    7020 
    7021 > align #18:CYS toAtoms #11/B:CYS matchAtomNames true move nothing
    7022 
    7023 Pairing dropped 32 atoms and 0 reference atoms 
    7024 RMSD between 48 atom pairs is 1.745 angstroms 
    7025 
    7026 > align #18:CYS toAtoms #12/B:CYS matchAtomNames true move nothing
    7027 
    7028 Pairing dropped 32 atoms and 0 reference atoms 
    7029 RMSD between 48 atom pairs is 1.874 angstroms 
    7030 
    7031 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    7032 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    7033 > interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"
    7034 
    7035 ——— End of log from Tue Jun 4 18:24:08 2024 ———
    7036 
    7037 opened ChimeraX session 
    7038 
    7039 > hide #!12 models
    7040 
    7041 > hide #!10 models
    7042 
    7043 > hide #!9 models
    7044 
    7045 > hide #!8 models
    7046 
    7047 > hide #!7 models
    7048 
    7049 > hide #!6 models
    7050 
    7051 > show #!18 models
    7052 
    7053 > hide #!5 models
    7054 
    7055 > hide #!4 models
    7056 
    7057 > hide #!11 models
    7058 
    7059 > select #18/A:CYS
    7060 
    7061 Nothing selected 
    7062 
    7063 > select #18/A:CYS
    7064 
    7065 Nothing selected 
    7066 
    7067 > select #18:CYS
    7068 
    7069 80 atoms, 72 bonds, 8 residues, 1 model selected 
    7070 
    7071 > ui tool show "Color Actions"
    7072 
    7073 > color sel cyan
    7074 
    7075 > color sel byhetero
    7076 
    7077 > select #4/B:CYS
    7078 
    7079 48 atoms, 40 bonds, 8 residues, 1 model selected 
    7080 
    7081 > show #3#!18 atoms
    7082 
    7083 > hide #3#!18 atoms
    7084 
    7085 > select #3
    7086 
    7087 24 atoms, 36 bonds, 3 residues, 1 model selected 
    7088 
    7089 > show sel atoms
    7090 
    7091 > select #18:CYS
    7092 
    7093 80 atoms, 72 bonds, 8 residues, 1 model selected 
    7094 
    7095 > show sel atoms
    7096 
    7097 > select H
    7098 
    7099 544 atoms, 96 residues, 2 models selected 
    7100 
    7101 > hide sel & #!18 atoms
    7102 
    7103 > select #18:FS4
    7104 
    7105 Nothing selected 
    7106 
    7107 > select #18:SF4
    7108 
    7109 16 atoms, 24 bonds, 2 residues, 1 model selected 
    7110 
    7111 > show sel atoms
    7112 
    7113 > select add #18
    7114 
    7115 762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected 
    7116 
    7117 > select subtract #18
    7118 
    7119 Nothing selected 
    7120 
    7121 > show #!4 models
    7122 
    7123 > select #4/B:CYS
    7124 
    7125 48 atoms, 40 bonds, 8 residues, 1 model selected 
    7126 
    7127 > hide #!4 models
    7128 
    7129 > show #!5 models
    7130 
    7131 > show #!11 models
    7132 
    7133 > hide #!5 models
    7134 
    7135 > show #!5 models
    7136 
    7137 > show #!4 models
    7138 
    7139 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    7140 > 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
    7141 > interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"
    7142 
    7143 ——— End of log from Tue Jun 4 19:01:21 2024 ———
    7144 
    7145 opened ChimeraX session 
    7146 
    7147 > hide #3 models
    7148 
    7149 > hide #!5 models
    7150 
    7151 > hide #!18 models
    7152 
    7153 > hide #!11 models
    7154 
    7155 > show #!11 models
    7156 
    7157 > hide #!11 models
    7158 
    7159 > show #!12 models
    7160 
    7161 > hide #!12 models
    7162 
    7163 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    7164 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI
    7165 > interface/PSI_fdn_8designs_result/PSI_fdn_8designs/design.fasta"
    7166 
    7167 Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-
    7168 Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI
    7169 interface/PSI_fdn_8designs_result/PSI_fdn_8designs/design.fasta 
    7170 --- 
    7171 notes | Alignment identifier is design.fasta 
    7172 Associated PSI chains E (2.5) chain E to design:7
    7173 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches 
    7174 Associated PSI chains C 2 (2.3.2) chain C to design:7
    7175 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches 
    7176 Associated best.pdb chain A to design:7
    7177 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches 
    7178 Associated best.pdb chain B to design:1
    7179 n:5|mpnn:1.001|plddt:0.854|ptm:0.806|pae:6.003|rmsd:0.817 with 0 mismatches 
    7180 Associated best_design7.pdb chain A to design:7
    7181 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches 
    7182 Associated best_design7.pdb chain B to design:7
    7183 n:0|mpnn:1.127|plddt:0.849|ptm:0.800|pae:6.051|rmsd:0.819 with 0 mismatches 
    7184 Associated best_design6.pdb chain A to design:7
    7185 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches 
    7186 Associated best_design6.pdb chain B to design:6
    7187 n:0|mpnn:1.068|plddt:0.846|ptm:0.805|pae:6.080|rmsd:0.975 with 0 mismatches 
    7188 Associated best_design5.pdb chain A to design:7
    7189 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches 
    7190 11 messages similar to the above omitted 
    7191 Associated Stromal ridge target chain A to design:7
    7192 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches 
    7193 Associated Stromal ridge target chain A to design:7
    7194 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches 
    7195 Showing conservation header ("seq_conservation" residue attribute) for
    7196 alignment design.fasta 
    7197  
    7198 Opened 64 sequences from design.fasta 
    7199 
    7200 > show #!11 models
    7201 
    7202 > ui tool show Matchmaker
    7203 
    7204 > matchmaker #11/B to #4/B pairing ss showAlignment true
    7205 
    7206 Parameters 
    7207 --- 
    7208 Chain pairing | ss 
    7209 Alignment algorithm | Needleman-Wunsch 
    7210 Similarity matrix | BLOSUM-62 
    7211 SS fraction | 0.3 
    7212 Gap open (HH/SS/other) | 18/18/6 
    7213 Gap extend | 1 
    7214 SS matrix |  |  | H | S | O 
    7215 ---|---|---|--- 
    7216 H | 6 | -9 | -6 
    7217 S |  | 6 | -6 
    7218 O |  |  | 4 
    7219 Iteration cutoff | 2 
    7220  
    7221 Matchmaker best.pdb, chain B (#4) with best_design1.pdb, chain B (#11),
    7222 sequence alignment score = 287.3 
    7223 Alignment identifier is 2 
    7224 Showing conservation header ("seq_conservation" residue attribute) for
    7225 alignment 2 
    7226 Hiding conservation header for alignment 2 
    7227 Chains used in RMSD evaluation for alignment 2: best.pdb #4/B,
    7228 best_design1.pdb #11/B 
    7229 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    7230 RMSD between 54 pruned atom pairs is 0.000 angstroms; (across all 54 pairs:
    7231 0.000) 
    7232  
    7233 
    7234 > sequence header 2 consensus show
    7235 
    7236 Showing consensus header ("seq_consensus" residue attribute) for alignment 2 
    7237 
    7238 > rename #4 "best (best design1).pdb"
    7239 
    7240 > hide #!4 models
    7241 
    7242 > show #!4 models
    7243 
    7244 > hide #!4 models
    7245 
    7246 > show #!4 models
    7247 
    7248 > hide #!4 models
    7249 
    7250 > show #!4 models
    7251 
    7252 > hide #!4 models
    7253 
    7254 > show #!4 models
    7255 
    7256 > hide #!4 models
    7257 
    7258 > show #!2 models
    7259 
    7260 > hide #!2.1 models
    7261 
    7262 > show #!2.1 models
    7263 
    7264 > show #2.5 models
    7265 
    7266 > show #!2.6 models
    7267 
    7268 > hide #!2.6 models
    7269 
    7270 > show #2.4 models
    7271 
    7272 > hide #2.5 models
    7273 
    7274 > hide #2.4 models
    7275 
    7276 > show #3 models
    7277 
    7278 > hide #!2 models
    7279 
    7280 > select #4/B:53-54 #11/B:53-54
    7281 
    7282 28 atoms, 26 bonds, 4 residues, 2 models selected 
    7283 
    7284 > select #4/B:24-54 #11/B:24-54
    7285 
    7286 418 atoms, 418 bonds, 62 residues, 2 models selected 
    7287 
    7288 > select clear
    7289 
    7290 [Repeated 1 time(s)]
    7291 
    7292 > select add #11/B:1
    7293 
    7294 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7295 
    7296 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    7297 > 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs"
    7298 
    7299 ——— End of log from Thu Sep 19 17:01:48 2024 ———
    7300 
    7301 opened ChimeraX session 
    7302 
    7303 > hide #3 models
    7304 
    7305 > show #3 models
    7306 
    7307 > hide #3 models
    7308 
    7309 > show #3 models
    7310 
    7311 > show #!2 models
    7312 
    7313 > hide #!2 models
    7314 
    7315 > show #!4 models
    7316 
    7317 > hide #!4 models
    7318 
    7319 > show #!4 models
    7320 
    7321 > hide #!4 models
    7322 
    7323 > show #!4 models
    7324 
    7325 > hide #!4 models
    7326 
    7327 > show #!4 models
    7328 
    7329 > hide #!11 models
    7330 
    7331 > show #!1 models
    7332 
    7333 > hide #!1 models
    7334 
    7335 > show #!18 models
    7336 
    7337 > show #!2 models
    7338 
    7339 > hide #!2 models
    7340 
    7341 > show #!2 models
    7342 
    7343 > hide #!2 models
    7344 
    7345 > hide #3 models
    7346 
    7347 > show #3 models
    7348 
    7349 > close #2
    7350 
    7351 Cell requested for row 10 is out of bounds for table with 14 rows! Resizing
    7352 table model. 
    7353 
    7354 > show #!11 models
    7355 
    7356 > hide #!11 models
    7357 
    7358 Cell requested for row 2 is out of bounds for table with 14 rows! Resizing
    7359 table model. 
    7360 
    7361 > hide #!4 models
    7362 
    7363 > show #!4 models
    7364 
    7365 > hide #!4 models
    7366 
    7367 > show #!4 models
    7368 
    7369 > hide #!4 models
    7370 
    7371 > show #!4 models
    7372 
    7373 > show #!5 models
    7374 
    7375 > hide #!5 models
    7376 
    7377 > show #!11 models
    7378 
    7379 > hide #!4 models
    7380 
    7381 > show #!4 models
    7382 
    7383 > show #!20 models
    7384 
    7385 > hide #!20 models
    7386 
    7387 > hide #!11 models
    7388 
    7389 > close #5-12
    7390 
    7391 > show #!1 models
    7392 
    7393 > ui tool show Matchmaker
    7394 
    7395 > matchmaker #1/M to #4/B pairing ss showAlignment true
    7396 
    7397 Parameters 
    7398 --- 
    7399 Chain pairing | ss 
    7400 Alignment algorithm | Needleman-Wunsch 
    7401 Similarity matrix | BLOSUM-62 
    7402 SS fraction | 0.3 
    7403 Gap open (HH/SS/other) | 18/18/6 
    7404 Gap extend | 1 
    7405 SS matrix |  |  | H | S | O 
    7406 ---|---|---|--- 
    7407 H | 6 | -9 | -6 
    7408 S |  | 6 | -6 
    7409 O |  |  | 4 
    7410 Iteration cutoff | 2 
    7411  
    7412 Matchmaker best (best design1).pdb, chain B (#4) with 2fdn, chain M (#1),
    7413 sequence alignment score = 157.4 
    7414 Alignment identifier is 1 
    7415 Showing conservation header ("seq_conservation" residue attribute) for
    7416 alignment 1 
    7417 Hiding conservation header for alignment 1 
    7418 Chains used in RMSD evaluation for alignment 1: 2fdn #1/M, best (best
    7419 design1).pdb #4/B 
    7420 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    7421 RMSD between 40 pruned atom pairs is 0.905 angstroms; (across all 51 pairs:
    7422 2.218) 
    7423  
    7424 
    7425 > sequence header 1 consensus show
    7426 
    7427 Showing consensus header ("seq_consensus" residue attribute) for alignment 1 
    7428 
    7429 > select #4/B:9
    7430 
    7431 4 atoms, 3 bonds, 1 residue, 1 model selected 
    7432 
    7433 > select #4/B:9
    7434 
    7435 4 atoms, 3 bonds, 1 residue, 1 model selected 
    7436 
    7437 > select #4/B:9
    7438 
    7439 4 atoms, 3 bonds, 1 residue, 1 model selected 
    7440 
    7441 > select #4/B:9
    7442 
    7443 4 atoms, 3 bonds, 1 residue, 1 model selected 
    7444 
    7445 > show sel atoms
    7446 
    7447 > select #4/B:9,23-30
    7448 
    7449 64 atoms, 62 bonds, 9 residues, 1 model selected 
    7450 
    7451 > select #4/B:9,23-32
    7452 
    7453 77 atoms, 75 bonds, 11 residues, 1 model selected 
    7454 
    7455 > hide #!18 models
    7456 
    7457 > hide #3 models
    7458 
    7459 > hide #!1 models
    7460 
    7461 > ui tool show Contacts
    7462 
    7463 > select #4/B
    7464 
    7465 357 atoms, 359 bonds, 54 residues, 1 model selected 
    7466 
    7467 > contacts sel restrict #4/A resSeparation 5 interModel false intraMol false
    7468 > color #76d6ff radius 0.2 reveal true log true
    7469    
    7470    
    7471     Allowed overlap: -0.4
    7472     H-bond overlap reduction: 0.4
    7473     Ignore contacts between atoms separated by 4 bonds or less
    7474     Ignore contacts between atoms in residues less than 5 apart in sequence
    7475     Detect intra-residue contacts: False
    7476     Detect intra-molecule contacts: False
    7477    
    7478     22 contacts
    7479                      atom1                                    atom2                    overlap  distance
    7480     best (best design1).pdb #4/B ALA 7 CB    best (best design1).pdb #4/A ARG 473 NH2   0.873    2.647
    7481     best (best design1).pdb #4/B GLU 16 OE1  best (best design1).pdb #4/A THR 802 CB    0.734    2.566
    7482     best (best design1).pdb #4/B GLU 16 OE1  best (best design1).pdb #4/A THR 802 OG1   0.578    1.902
    7483     best (best design1).pdb #4/B GLY 10 O    best (best design1).pdb #4/A ILE 466 CD1   0.308    2.992
    7484     best (best design1).pdb #4/B GLU 16 CD   best (best design1).pdb #4/A THR 802 OG1   0.249    3.091
    7485     best (best design1).pdb #4/B GLU 30 CG   best (best design1).pdb #4/A LYS 489 CE    0.245    3.515
    7486     best (best design1).pdb #4/B ALA 7 CB    best (best design1).pdb #4/A ARG 473 CZ    0.119    3.371
    7487     best (best design1).pdb #4/B CYS 11 CA   best (best design1).pdb #4/A ILE 466 CD1   0.070    3.690
    7488     best (best design1).pdb #4/B GLU 16 CD   best (best design1).pdb #4/A THR 802 CB    -0.041    3.801
    7489     best (best design1).pdb #4/B ALA 7 CB    best (best design1).pdb #4/A ARG 473 NH1   -0.058    3.578
    7490     best (best design1).pdb #4/B VAL 25 CG2  best (best design1).pdb #4/A VAL 776 CG1   -0.063    3.823
    7491     best (best design1).pdb #4/B GLU 30 CG   best (best design1).pdb #4/A LYS 489 NZ    -0.072    3.592
    7492     best (best design1).pdb #4/B GLU 30 OE1  best (best design1).pdb #4/A LYS 489 CE    -0.103    3.403
    7493     best (best design1).pdb #4/B GLY 10 O    best (best design1).pdb #4/A ILE 466 CG1   -0.116    3.416
    7494     best (best design1).pdb #4/B CYS 11 CB   best (best design1).pdb #4/A CYS 468 SG    -0.142    3.792
    7495     best (best design1).pdb #4/B GLU 30 CD   best (best design1).pdb #4/A LYS 489 CE    -0.168    3.928
    7496     best (best design1).pdb #4/B GLU 30 CD   best (best design1).pdb #4/A LYS 489 NZ    -0.185    3.705
    7497     best (best design1).pdb #4/B GLU 46 OE1  best (best design1).pdb #4/A ARG 12 NH1    -0.272    2.932
    7498     best (best design1).pdb #4/B GLU 26 CG   best (best design1).pdb #4/A ALA 777 CB    -0.283    4.043
    7499     best (best design1).pdb #4/B GLU 16 OE1  best (best design1).pdb #4/A THR 802 CA    -0.299    3.599
    7500     best (best design1).pdb #4/B ALA 7 CA    best (best design1).pdb #4/A ARG 473 NH2   -0.367    3.887
    7501     best (best design1).pdb #4/B VAL 25 CG1  best (best design1).pdb #4/A VAL 789 CG1   -0.391    4.151
    7502    
    7503 
    7504  
    7505 22 contacts 
    7506 
    7507 > hide #4.2 models
    7508 
    7509 > show #4.2 models
    7510 
    7511 > select add #4.2
    7512 
    7513 357 atoms, 359 bonds, 22 pseudobonds, 54 residues, 2 models selected 
    7514 
    7515 > select subtract #4.2
    7516 
    7517 357 atoms, 359 bonds, 54 residues, 1 model selected 
    7518 
    7519 > hide #4.2 models
    7520 
    7521 > show #4.2 models
    7522 
    7523 > select #4/B:7,10-11,16,25-26,30/A:473,802,466,489,776-777,468,12,789
    7524 
    7525 120 atoms, 107 bonds, 21 pseudobonds, 16 residues, 2 models selected 
    7526 
    7527 > style sel ball
    7528 
    7529 Changed 120 atom styles 
    7530 
    7531 > color sel byhetero
    7532 
    7533 > ui tool show "Selection Inspector"
    7534 
    7535 > setattr sel r ribbon_hide_backbone false
    7536 
    7537 Assigning ribbon_hide_backbone attribute to 16 items 
    7538 
    7539 > name frozen contacts sel
    7540 
    7541 > select #4/B
    7542 
    7543 357 atoms, 359 bonds, 54 residues, 1 model selected 
    7544 
    7545 > ui tool show Clashes
    7546 
    7547 > clashes sel restrict #4/A resSeparation 5 interModel false intraMol false
    7548 > color #fffb00 reveal true log true
    7549    
    7550    
    7551     Allowed overlap: 0.6
    7552     H-bond overlap reduction: 0.4
    7553     Ignore clashes between atoms separated by 4 bonds or less
    7554     Ignore clashes between atoms in residues less than 5 apart in sequence
    7555     Detect intra-residue clashes: False
    7556     Detect intra-molecule clashes: False
    7557    
    7558     2 clashes
    7559                      atom1                                    atom2                    overlap  distance
    7560     best (best design1).pdb #4/B ALA 7 CB    best (best design1).pdb #4/A ARG 473 NH2   0.873    2.647
    7561     best (best design1).pdb #4/B GLU 16 OE1  best (best design1).pdb #4/A THR 802 CB    0.734    2.566
    7562    
    7563 
    7564  
    7565 2 clashes 
    7566 
    7567 > select #4/B:7,16
    7568 
    7569 14 atoms, 12 bonds, 2 residues, 1 model selected 
    7570 
    7571 > select #4/B
    7572 
    7573 357 atoms, 359 bonds, 54 residues, 1 model selected 
    7574 
    7575 > ui tool show H-Bonds
    7576 
    7577 > hbonds sel color #0096ff restrict #4/A interModel false intraMol false
    7578 > intraRes false reveal true log true
    7579    
    7580    
    7581     Finding intramodel H-bonds
    7582     Constraints relaxed by 0.4 angstroms and 20 degrees
    7583     Models used:
    7584         4 best (best design1).pdb
    7585    
    7586     4 H-bonds
    7587     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7588     best (best design1).pdb #4/A ARG 12 NH1   best (best design1).pdb #4/B GLU 46 OE1  no hydrogen  2.932  N/A
    7589     best (best design1).pdb #4/A LYS 489 NZ   best (best design1).pdb #4/B GLU 26 O    no hydrogen  3.483  N/A
    7590     best (best design1).pdb #4/A LYS 489 NZ   best (best design1).pdb #4/B GLU 30 OE1  no hydrogen  3.116  N/A
    7591     best (best design1).pdb #4/A THR 802 OG1  best (best design1).pdb #4/B GLU 16 OE1  no hydrogen  1.902  N/A
    7592    
    7593 
    7594  
    7595 4 hydrogen bonds found 
    7596 
    7597 > select #4/B:46,26,30,16/A:12,489,802
    7598 
    7599 63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected 
    7600 
    7601 > style sel ball
    7602 
    7603 Changed 63 atom styles 
    7604 
    7605 > hide #4.2 models
    7606 
    7607 > hide #4.3 models
    7608 
    7609 > select #4/B:46,26,30,16/A:12,489,802
    7610 
    7611 63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected 
    7612 
    7613 > select clear
    7614 
    7615 > select #4/B:1-6,10-23,33-48,51-54 #1/M:1-6,10-23,32-47,52-55
    7616 
    7617 755 atoms, 754 bonds, 80 residues, 2 models selected 
    7618 
    7619 > select clear
    7620 
    7621 > select #4/B:46,26,30,16/A:12,489,802
    7622 
    7623 63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected 
    7624 
    7625 > select contacts &~#4/B:46,26,30,16/A:12,489,802
    7626 
    7627 66 atoms, 58 bonds, 11 pseudobonds, 10 residues, 3 models selected 
    7628 
    7629 > style sel sphere
    7630 
    7631 Changed 66 atom styles 
    7632 
    7633 > color sel byhetero
    7634 
    7635 [Repeated 1 time(s)]
    7636 
    7637 > select #4/B:26 &~backbone
    7638 
    7639 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7640 
    7641 > style sel sphere
    7642 
    7643 Changed 5 atom styles 
    7644 
    7645 > show #4.2 models
    7646 
    7647 > style sel ball
    7648 
    7649 Changed 5 atom styles 
    7650 
    7651 > hide #4.4 models
    7652 
    7653 > show #4.4 models
    7654 
    7655 > hide #4.2 models
    7656 
    7657 > show #4.2 models
    7658 
    7659 > hide #4.2 models
    7660 
    7661 > select #4/B:26 &~backbone
    7662 
    7663 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7664 
    7665 > style sel sphere
    7666 
    7667 Changed 5 atom styles 
    7668 
    7669 > surface #4/A
    7670 
    7671 > surface #4/B
    7672 
    7673 > coulombic #4/B surfaces #4.6
    7674 
    7675 Using Amber 20 recommended default charges and atom types for standard
    7676 residues 
    7677 Coulombic values for best (best design1).pdb_B SES surface #4.6: minimum,
    7678 -17.76, mean -5.37, maximum 4.03 
    7679 
    7680 > coulombic #4/A surfaces #4.5
    7681 
    7682 Using Amber 20 recommended default charges and atom types for standard
    7683 residues 
    7684 Coulombic values for best (best design1).pdb_A SES surface #4.5: minimum,
    7685 -15.01, mean 1.13, maximum 14.51 
    7686 
    7687 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    7688 > Models/PSI Fdx best MPNN .cxs"
    7689 
    7690 > select clear
    7691 
    7692 > open 6yez
    7693 
    7694 6yez title: 
    7695 Plant PSI-ferredoxin-plastocyanin supercomplex [more info...] 
    7696  
    7697 Chain information for 6yez #2 
    7698 --- 
    7699 Chain | Description | UniProt 
    7700 1 | Lhca1 |   
    7701 2 | Chlorophyll a-b binding protein, chloroplastic | Q41038_PEA 58-265 
    7702 3 | Chlorophyll a-b binding protein 3, chloroplastic | CB23_PEA 55-275 
    7703 4 | Chlorophyll a-b binding protein P4, chloroplastic | CB24_PEA 52-249 
    7704 A | Photosystem I P700 chlorophyll a apoprotein A1 | A0A0F6NFW5_PEA 16-758 
    7705 B | Photosystem I P700 chlorophyll a apoprotein A2 | A0A0F6NGI2_PEA 2-734 
    7706 C | Photosystem I iron-sulfur center | PSAC_PEA 2-81 
    7707 D | PsaD |   
    7708 E | PsaE |   
    7709 F | PsaF |   
    7710 G | PsaG |   
    7711 H | PsaH |   
    7712 I | Photosystem I reaction center subunit VIII | PSAI_PEA 2-32 
    7713 J | PsaJ |   
    7714 K | Photosystem I reaction center subunit X psaK | E1C9L3_PEA 46-126 
    7715 L | PsaL |   
    7716 N | Ferredoxin-1, chloroplastic | FER1_PEA 1-97 
    7717 P | Plastocyanin, chloroplastic | PLAS_PEA 1-99 
    7718  
    7719 Non-standard residues in 6yez #2 
    7720 --- 
    7721 3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid) 
    7722 BCR — β-carotene 
    7723 C7Z —
    7724 (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-
    7725 cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol 
    7726 CA — calcium ion 
    7727 CHL — chlorophyll B 
    7728 CL0 — chlorophyll A isomer 
    7729 CLA — chlorophyll A 
    7730 CU — copper (II) ion 
    7731 DGD — digalactosyl diacyl glycerol (DGDG) 
    7732 FES — FE2/S2 (inorganic) cluster 
    7733 LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole 
    7734 LMG — 1,2-distearoyl-monogalactosyl-diglyceride 
    7735 LMT — dodecyl-β-D-maltoside 
    7736 LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
    7737 ((3R,3'R)-β,β-carotene-3,3'-diol; lutein) 
    7738 PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone) 
    7739 SF4 — iron/sulfur cluster 
    7740 XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
    7741 tetrahydro-β,β-carotene-3,3'-diol (violaxanthin) 
    7742  
    7743 Associated 6yez chain C to design:0
    7744 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches 
    7745 Associated 6yez chain E to design:0
    7746 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches 
    7747 
    7748 > select #2 &protein
    7749 
    7750 26851 atoms, 27685 bonds, 3438 residues, 1 model selected 
    7751 
    7752 > hide sel cartoons
    7753 
    7754 > hide sel atoms
    7755 
    7756 > show sel cartoons
    7757 
    7758 > hide #4.6 models
    7759 
    7760 > hide #4.5 models
    7761 
    7762 > ui tool show Matchmaker
    7763 
    7764 > matchmaker #2/C to #4/A pairing ss
    7765 
    7766 Parameters 
    7767 --- 
    7768 Chain pairing | ss 
    7769 Alignment algorithm | Needleman-Wunsch 
    7770 Similarity matrix | BLOSUM-62 
    7771 SS fraction | 0.3 
    7772 Gap open (HH/SS/other) | 18/18/6 
    7773 Gap extend | 1 
    7774 SS matrix |  |  | H | S | O 
    7775 ---|---|---|--- 
    7776 H | 6 | -9 | -6 
    7777 S |  | 6 | -6 
    7778 O |  |  | 4 
    7779 Iteration cutoff | 2 
    7780  
    7781 Matchmaker best (best design1).pdb, chain A (#4) with 6yez, chain C (#2),
    7782 sequence alignment score = 401 
    7783 RMSD between 80 pruned atom pairs is 0.395 angstroms; (across all 80 pairs:
    7784 0.395) 
    7785  
    7786 
    7787 > show #4.6 models
    7788 
    7789 > hide #4.6 models
    7790 
    7791 > show #4.6 models
    7792 
    7793 > hide #4.6 models
    7794 
    7795 > show #4.6 models
    7796 
    7797 > hide #4.6 models
    7798 
    7799 > show #4.5 models
    7800 
    7801 > hide #4.5 models
    7802 
    7803 > coulombic #2/E
    7804 
    7805 The following heavy (non-hydrogen) atoms are missing, which may result in
    7806 inaccurate electrostatics: 
    7807 6yez #2/E LYS 129 OXT 
    7808 
    7809 Using Amber 20 recommended default charges and atom types for standard
    7810 residues 
    7811 Coulombic values for 6yez_E SES surface #2.2: minimum, -13.31, mean 0.69,
    7812 maximum 9.65 
    7813 
    7814 > hide #!4 models
    7815 
    7816 > coulombic #2/C:2-81
    7817 
    7818 Using Amber 20 recommended default charges and atom types for standard
    7819 residues 
    7820 Coulombic values for 6yez_C SES surface #2.3: minimum, -12.54, mean -0.30,
    7821 maximum 9.66 
    7822 
    7823 > coulombic #2/D
    7824 
    7825 The following heavy (non-hydrogen) atoms are missing, which may result in
    7826 inaccurate electrostatics: 
    7827 6yez #2/D LEU 211 OXT 
    7828 
    7829 Using Amber 20 recommended default charges and atom types for standard
    7830 residues 
    7831 Coulombic values for 6yez_D SES surface #2.4: minimum, -11.93, mean 1.16,
    7832 maximum 13.86 
    7833 
    7834 > toolshed show
    7835 
    7836 > volume showOutlineBox true
    7837 
    7838 No volumes specified 
    7839 
    7840 > show #3 models
    7841 
    7842 > show #!4 models
    7843 
    7844 > select #2/N/P
    7845 
    7846 1457 atoms, 1483 bonds, 7 pseudobonds, 198 residues, 2 models selected 
    7847 
    7848 > hide sel cartoons
    7849 
    7850 > hide sel atoms
    7851 
    7852 > select #2:3001
    7853 
    7854 8 atoms, 12 bonds, 1 residue, 1 model selected 
    7855 
    7856 > cofr sel
    7857 
    7858 > select #4/A
    7859 
    7860 2980 atoms, 3060 bonds, 6 pseudobonds, 380 residues, 2 models selected 
    7861 
    7862 > hide sel cartoons
    7863 
    7864 > select contacts :<1 &#2
    7865 
    7866 128 atoms, 118 bonds, 17 residues, 1 model selected 
    7867 
    7868 > show sel atoms
    7869 
    7870 > hide sel atoms
    7871 
    7872 > hide #2.4 models
    7873 
    7874 > hide #2.3 models
    7875 
    7876 > hide #2.2 models
    7877 
    7878 > select #4/A
    7879 
    7880 2980 atoms, 3060 bonds, 7 pseudobonds, 380 residues, 3 models selected 
    7881 
    7882 > show sel cartoons
    7883 
    7884 > show #4.5 models
    7885 
    7886 > show #4.6 models
    7887 
    7888 > select #2:CA,CU,DGD,3PH,C7Z,LHG
    7889 
    7890 739 atoms, 735 bonds, 20 residues, 1 model selected 
    7891 
    7892 > select #2/1
    7893 
    7894 2580 atoms, 2690 bonds, 61 pseudobonds, 214 residues, 2 models selected 
    7895 
    7896 > select #2/1-4
    7897 
    7898 10673 atoms, 11130 bonds, 241 pseudobonds, 907 residues, 2 models selected 
    7899 
    7900 > hide sel cartoons
    7901 
    7902 > hide sel atoms
    7903 
    7904 > select #2/C-E
    7905 
    7906 2288 atoms, 2352 bonds, 7 pseudobonds, 291 residues, 2 models selected 
    7907 
    7908 > hide sel cartoons
    7909 
    7910 > set bgColor white
    7911 
    7912 > select clear
    7913 
    7914 > graphics silhouettes true
    7915 
    7916 > hide #!4 models
    7917 
    7918 > show #!4 models
    7919 
    7920 > hide #4.4 models
    7921 
    7922 > hide #4.5 models
    7923 
    7924 > show #4.4 models
    7925 
    7926 > hide #4.6 models
    7927 
    7928 > show #4.5 models
    7929 
    7930 > hide #4.5 models
    7931 
    7932 > surface #2 enclose #2/A-B/F-L
    7933 
    7934 > close #2.5
    7935 
    7936 > select contacts :<1 &#2
    7937 
    7938 128 atoms, 118 bonds, 17 residues, 1 model selected 
    7939 
    7940 > select #4/A :<1 &#2
    7941 
    7942 3059 atoms, 3141 bonds, 4 pseudobonds, 382 residues, 2 models selected 
    7943 
    7944 > select #4/A :<1 &#2 &protein
    7945 
    7946 2994 atoms, 3072 bonds, 381 residues, 1 model selected 
    7947 
    7948 > name frozen minAB sel
    7949 
    7950 > select #2/A-B/F-L &~minAB
    7951 
    7952 23858 atoms, 24789 bonds, 418 pseudobonds, 2167 residues, 2 models selected 
    7953 
    7954 > surface #2 enclose #2/A-B/F-L &~minAB
    7955 
    7956 > show #4.5 models
    7957 
    7958 > show #4.6 models
    7959 
    7960 > hide #4.6 models
    7961 
    7962 > select clear
    7963 
    7964 > select #1:SF4
    7965 
    7966 16 atoms, 24 bonds, 2 residues, 1 model selected 
    7967 
    7968 > show #!1 models
    7969 
    7970 > select #1:1-55
    7971 
    7972 652 atoms, 657 bonds, 55 residues, 1 model selected 
    7973 
    7974 > hide sel cartoons
    7975 
    7976 > hide sel atoms
    7977 
    7978 > select #4/A &contacts
    7979 
    7980 71 atoms, 63 bonds, 9 residues, 1 model selected 
    7981 
    7982 > style sel stick
    7983 
    7984 Changed 71 atom styles 
    7985 
    7986 > select :CL0,CLA
    7987 
    7988 8422 atoms, 8990 bonds, 568 pseudobonds, 142 residues, 2 models selected 
    7989 
    7990 > color (#!2 & sel) lime
    7991 
    7992 > color sel byhetero
    7993 
    7994 > select clear
    7995 
    7996 Cell requested for row 8 is out of bounds for table with 17 rows! Resizing
    7997 table model. 
    7998 
    7999 > select add #4.5
    8000 
    8001 2980 atoms, 380 residues, 1 model selected 
    8002 
    8003 > transparency (#!4 & sel) 30
    8004 
    8005 > transparency (#!4 & sel) 20
    8006 
    8007 > select clear
    8008 
    8009 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    8010 > Models/PSI Fdx best MPNN .cxs"
    8011 
    8012 > view name front
    8013 
    8014 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    8015 > MPNN/PSI-Fdx front .png" width 845 height 690 supersample 3
    8016 > transparentBackground true
    8017 
    8018 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    8019 > MPNN/PSI-Fdx front .png" width 1470 height 1200 supersample 3
    8020 > transparentBackground true
    8021 
    8022 > select contacts
    8023 
    8024 120 atoms, 107 bonds, 26 pseudobonds, 16 residues, 4 models selected 
    8025 
    8026 > style sel stick
    8027 
    8028 Changed 120 atom styles 
    8029 
    8030 > show #4.6 models
    8031 
    8032 > select clear
    8033 
    8034 > select add #4.6
    8035 
    8036 357 atoms, 54 residues, 1 model selected 
    8037 
    8038 > transparency (#!4 & sel) 20
    8039 
    8040 > select clear
    8041 
    8042 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    8043 > MPNN/PSI-Fdx 2 surfaces front .png" width 1470 height 1200 supersample 3
    8044 > transparentBackground true
    8045 
    8046 > hide #4.5 models
    8047 
    8048 > hide #4.6 models
    8049 
    8050 > select contacts
    8051 
    8052 120 atoms, 107 bonds, 26 pseudobonds, 16 residues, 4 models selected 
    8053 
    8054 > style sel sphere
    8055 
    8056 Changed 120 atom styles 
    8057 
    8058 > show #4.5 models
    8059 
    8060 > hide #4.5 models
    8061 
    8062 > show #4.5 models
    8063 
    8064 > hide #4.5 models
    8065 
    8066 > show #4.6 models
    8067 
    8068 > select #4/B &contacts
    8069 
    8070 49 atoms, 44 bonds, 7 residues, 1 model selected 
    8071 
    8072 > style sel stick
    8073 
    8074 Changed 49 atom styles 
    8075 
    8076 > select clear
    8077 
    8078 > view name back
    8079 
    8080 > show #4.5 models
    8081 
    8082 > hide #4.5 models
    8083 
    8084 > hide #4.6 models
    8085 
    8086 > show #4.6 models
    8087 
    8088 > hide #4.6 models
    8089 
    8090 > select #4/A:489
    8091 
    8092 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8093 
    8094 > style sel stick
    8095 
    8096 Changed 9 atom styles 
    8097 
    8098 > show #4.6 models
    8099 
    8100 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    8101 > MPNN/PSI-Fdx back .png" width 1470 height 1200 supersample 3
    8102 > transparentBackground true
    8103 
    8104 > select clear
    8105 
    8106 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    8107 > MPNN/PSI-Fdx back .png" width 1470 height 1200 supersample 3
    8108 > transparentBackground true
    8109 
    8110 > view front
    8111 
    8112 > select #4/A:12
    8113 
    8114 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8115 
    8116 > style sel stick
    8117 
    8118 Changed 11 atom styles 
    8119 
    8120 > show #4.5 models
    8121 
    8122 > select clear
    8123 
    8124 > hide #4.6 models
    8125 
    8126 > select #4/B:16,30,46
    8127 
    8128 27 atoms, 24 bonds, 3 residues, 1 model selected 
    8129 
    8130 > style sel ball
    8131 
    8132 Changed 27 atom styles 
    8133 
    8134 > select #4/B:26 &backbone
    8135 
    8136 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8137 
    8138 > style sel ball
    8139 
    8140 Changed 4 atom styles 
    8141 
    8142 > view front
    8143 
    8144 > select clear
    8145 
    8146 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    8147 > Models/PSI Fdx best MPNN .cxs"
    8148 
    8149 > hide #4.5 models
    8150 
    8151 > select #4/A &contacts &~489,802
    8152 
    8153 Expected a keyword 
    8154 
    8155 > select #4/A &contacts &~:489,802
    8156 
    8157 55 atoms, 49 bonds, 7 residues, 1 model selected 
    8158 
    8159 > style sel stick
    8160 
    8161 Changed 55 atom styles 
    8162 
    8163 > select #4/A:12,489,802
    8164 
    8165 27 atoms, 24 bonds, 3 residues, 1 model selected 
    8166 
    8167 > style sel ball
    8168 
    8169 Changed 27 atom styles 
    8170 
    8171 > show #4.5 models
    8172 
    8173 > select clear
    8174 
    8175 > hide #4.5 models
    8176 
    8177 > show #4.5 models
    8178 
    8179 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    8180 > Models/PSI Fdx best MPNN .cxs"
    8181 
    8182 > hide #4.5 models
    8183 
    8184 > show #4.5 models
    8185 
    8186 > select #4/B:16,26,30,46/A:12,489,802
    8187 
    8188 63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected 
    8189 
    8190 > name frozen hBonds sel
    8191 
    8192 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    8193 > Models/PSI Fdx best MPNN .cxs"
    8194 
    8195 > select clear
    8196 
    8197 > select #4/B &contacts &~hBonds
    8198 
    8199 22 atoms, 19 bonds, 4 residues, 1 model selected 
    8200 
    8201 > style sel sphere
    8202 
    8203 Changed 22 atom styles 
    8204 
    8205 > select #4/B:26 &~backbone
    8206 
    8207 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8208 
    8209 > style sel sphere
    8210 
    8211 Changed 5 atom styles 
    8212 
    8213 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    8214 > Models/PSI Fdx best MPNN .cxs"
    8215 
    8216 > select clear
    8217 
    8218 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    8219 > MPNN/PSI-Fdx front .png" width 1568 height 1280 supersample 3
    8220 > transparentBackground true
    8221 
    8222 > select #4/B &contacts &~hBonds
    8223 
    8224 22 atoms, 19 bonds, 4 residues, 1 model selected 
    8225 
    8226 > style sel stick
    8227 
    8228 Changed 22 atom styles 
    8229 
    8230 > select #4/B:26 &~backbone
    8231 
    8232 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8233 
    8234 > style sel stick
    8235 
    8236 Changed 5 atom styles 
    8237 
    8238 > show #4.6 models
    8239 
    8240 > select clear
    8241 
    8242 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    8243 > MPNN/PSI-Fdx 2 surfaces front .png" width 1568 height 1280 supersample 3
    8244 > transparentBackground true
    8245 
    8246 > hide #4.6 models
    8247 
    8248 > hide #4.5 models
    8249 
    8250 > show #4.6 models
    8251 
    8252 > view back
    8253 
    8254 > select #4/A &contacts &~hBonds
    8255 
    8256 44 atoms, 39 bonds, 6 residues, 1 model selected 
    8257 
    8258 > style sel sphere
    8259 
    8260 Changed 44 atom styles 
    8261 
    8262 > select clear
    8263 
    8264 > select minAB
    8265 
    8266 3213 atoms, 3072 bonds, 410 residues, 1 model selected 
    8267 
    8268 > hide sel cartoons
    8269 
    8270 > hide sel atoms
    8271 
    8272 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    8273 > MPNN/PSI-Fdx 2 surfaces front .png" width 1568 height 1280 supersample 3
    8274 > transparentBackground true
    8275 
    8276 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    8277 > Models/PSI Fdx best MPNN .cxs"
    8278 
    8279 ——— End of log from Mon Sep 30 14:03:27 2024 ———
    8280 
    8281 opened ChimeraX session 
    8282 
    8283 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    8284 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    8285 > RoesttaDock H2ase BFdx dock/fdn_Alt/neurosnap-66fc65140db6770388b10541
    8286 > 2/relaxed_structure.pdb"
    8287 
    8288 Chain information for relaxed_structure.pdb #5 
    8289 --- 
    8290 Chain | Description 
    8291 A | No description available 
    8292 B | No description available 
    8293  
    8294 Associated relaxed_structure.pdb chain A to design:0
    8295 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches 
    8296 
    8297 > ui tool show Matchmaker
    8298 
    8299 > hide #5 models
    8300 
    8301 > show #5 models
    8302 
    8303 > ui tool show Matchmaker
    8304 
    8305 > matchmaker #5/A to #2/C pairing ss
    8306 
    8307 Parameters 
    8308 --- 
    8309 Chain pairing | ss 
    8310 Alignment algorithm | Needleman-Wunsch 
    8311 Similarity matrix | BLOSUM-62 
    8312 SS fraction | 0.3 
    8313 Gap open (HH/SS/other) | 18/18/6 
    8314 Gap extend | 1 
    8315 SS matrix |  |  | H | S | O 
    8316 ---|---|---|--- 
    8317 H | 6 | -9 | -6 
    8318 S |  | 6 | -6 
    8319 O |  |  | 4 
    8320 Iteration cutoff | 2 
    8321  
    8322 Matchmaker 6yez, chain C (#2) with relaxed_structure.pdb, chain A (#5),
    8323 sequence alignment score = 364.4 
    8324 RMSD between 73 pruned atom pairs is 0.691 angstroms; (across all 80 pairs:
    8325 2.602) 
    8326  
    8327 
    8328 > hide #!4 models
    8329 
    8330 > hide #!2 models
    8331 
    8332 > close #5
    8333 
    8334 > show #!4 models
    8335 
    8336 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    8337 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    8338 > RoesttaDock H2ase BFdx
    8339 > dock/fdn_Alt/neurosnap-66fc7cd10db6770388b1055a/relaxed_structure.pdb"
    8340 
    8341 Chain information for relaxed_structure.pdb #5 
    8342 --- 
    8343 Chain | Description 
    8344 A | No description available 
    8345 B | No description available 
    8346 C | No description available 
    8347 D | No description available 
    8348 E | No description available 
    8349 F | No description available 
    8350  
    8351 Associated relaxed_structure.pdb chain C to design:0
    8352 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches 
    8353 Associated relaxed_structure.pdb chain E to design:0
    8354 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches 
    8355 
    8356 > select #5 &protein
    8357 
    8358 28495 atoms, 28969 bonds, 1826 residues, 1 model selected 
    8359 
    8360 > hide sel atoms
    8361 
    8362 > show sel cartoons
    8363 
    8364 > hide #!4 models
    8365 
    8366 > hide #!1 models
    8367 
    8368 > show #!2 models
    8369 
    8370 > view front
    8371 
    8372 > select clear
    8373 
    8374 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    8375 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on
    8376 > PSI.cxs"
    8377 
    8378 > hide #2.5 models
    8379 
    8380 > hide #!2 models
    8381 
    8382 > surface #5
    8383 
    8384 > show #!2 models
    8385 
    8386 > coulombic #5/A surfaces #5.1
    8387 
    8388 Using Amber 20 recommended default charges and atom types for standard
    8389 residues 
    8390 Coulombic values for relaxed_structure.pdb_A SES surface #5.1: minimum,
    8391 -11.84, mean -0.24, maximum 17.92 
    8392 
    8393 > coulombic #5/B surfaces #5.2
    8394 
    8395 Using Amber 20 recommended default charges and atom types for standard
    8396 residues 
    8397 Coulombic values for relaxed_structure.pdb_B SES surface #5.2: minimum,
    8398 -13.17, mean 0.31, maximum 13.60 
    8399 
    8400 > coulombic #5/C surfaces #5.3
    8401 
    8402 Using Amber 20 recommended default charges and atom types for standard
    8403 residues 
    8404 Coulombic values for relaxed_structure.pdb_C SES surface #5.3: minimum,
    8405 -14.28, mean 0.87, maximum 12.27 
    8406 
    8407 > coulombic #5/D surfaces #5.4
    8408 
    8409 Using Amber 20 recommended default charges and atom types for standard
    8410 residues 
    8411 Coulombic values for relaxed_structure.pdb_D SES surface #5.4: minimum, -9.85,
    8412 mean 2.10, maximum 15.14 
    8413 
    8414 > coulombic #5/E surfaces #5.5
    8415 
    8416 Using Amber 20 recommended default charges and atom types for standard
    8417 residues 
    8418 Coulombic values for relaxed_structure.pdb_E SES surface #5.5: minimum,
    8419 -10.97, mean 1.53, maximum 12.30 
    8420 
    8421 > coulombic #5/F surfaces #5.6
    8422 
    8423 Using Amber 20 recommended default charges and atom types for standard
    8424 residues 
    8425 Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum,
    8426 -13.89, mean -3.67, maximum 7.01 
    8427 
    8428 > select add #5.1
    8429 
    8430 11581 atoms, 743 residues, 1 model selected 
    8431 
    8432 > select add #5.2
    8433 
    8434 23096 atoms, 1476 residues, 2 models selected 
    8435 
    8436 > select add #5.3
    8437 
    8438 24310 atoms, 1556 residues, 3 models selected 
    8439 
    8440 > select add #5.4
    8441 
    8442 26587 atoms, 1699 residues, 4 models selected 
    8443 
    8444 > select add #5.5
    8445 
    8446 27646 atoms, 1765 residues, 5 models selected 
    8447 
    8448 > select subtract #5.4
    8449 
    8450 25369 atoms, 1622 residues, 6 models selected 
    8451 
    8452 > select subtract #5.5
    8453 
    8454 24310 atoms, 1556 residues, 5 models selected 
    8455 
    8456 > select add #5.6
    8457 
    8458 25159 atoms, 1617 residues, 4 models selected 
    8459 
    8460 > select add #5.4
    8461 
    8462 27436 atoms, 1760 residues, 5 models selected 
    8463 
    8464 > select add #5.5
    8465 
    8466 28495 atoms, 1826 residues, 6 models selected 
    8467 
    8468 > transparency (#!5 & sel) 20
    8469 
    8470 > show #!1 models
    8471 
    8472 > hide #5.6 models
    8473 
    8474 > select #5/C/F &:Cys &~H
    8475 
    8476 102 atoms, 85 bonds, 17 residues, 1 model selected 
    8477 
    8478 > show sel atoms
    8479 
    8480 > color sel byhetero
    8481 
    8482 > style sel stick
    8483 
    8484 Changed 102 atom styles 
    8485 
    8486 > select #5/F#1/M &:CYS
    8487 
    8488 168 atoms, 152 bonds, 16 residues, 2 models selected 
    8489 
    8490 > ui tool show Matchmaker
    8491 
    8492 > matchmaker #1/M & sel to #5/F & sel pairing ss
    8493 
    8494 Parameters 
    8495 --- 
    8496 Chain pairing | ss 
    8497 Alignment algorithm | Needleman-Wunsch 
    8498 Similarity matrix | BLOSUM-62 
    8499 SS fraction | 0.3 
    8500 Gap open (HH/SS/other) | 18/18/6 
    8501 Gap extend | 1 
    8502 SS matrix |  |  | H | S | O 
    8503 ---|---|---|--- 
    8504 H | 6 | -9 | -6 
    8505 S |  | 6 | -6 
    8506 O |  |  | 4 
    8507 Iteration cutoff | 2 
    8508  
    8509 Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#1),
    8510 sequence alignment score = 48 
    8511 RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
    8512 1.008) 
    8513  
    8514 
    8515 > select #5/A-E
    8516 
    8517 27646 atoms, 28113 bonds, 1765 residues, 1 model selected 
    8518 
    8519 > ui tool show Clashes
    8520 
    8521 > clashes sel restrict #5/F resSeparation 5 interModel false intraMol false
    8522 > color #fffb00 reveal true log true
    8523    
    8524    
    8525     Allowed overlap: 0.6
    8526     H-bond overlap reduction: 0.4
    8527     Ignore clashes between atoms separated by 4 bonds or less
    8528     Ignore clashes between atoms in residues less than 5 apart in sequence
    8529     Detect intra-residue clashes: False
    8530     Detect intra-molecule clashes: False
    8531    
    8532     0 clashes
    8533     atom1  atom2  overlap  distance
    8534    
    8535 
    8536  
    8537 No clashes 
    8538 
    8539 > ui tool show Contacts
    8540 
    8541 > contacts sel restrict #15/B resSeparation 5 interModel false intraMol false
    8542 > color #76d6ff radius 0.2 reveal true log true
    8543    
    8544    
    8545     Allowed overlap: -0.4
    8546     H-bond overlap reduction: 0.4
    8547     Ignore contacts between atoms separated by 4 bonds or less
    8548     Ignore contacts between atoms in residues less than 5 apart in sequence
    8549     Detect intra-residue contacts: False
    8550     Detect intra-molecule contacts: False
    8551    
    8552     0 contacts
    8553     atom1  atom2  overlap  distance
    8554    
    8555 
    8556  
    8557 No contacts 
    8558 
    8559 > contacts sel restrict #5/F resSeparation 5 interModel false intraMol false
    8560 > color #76d6ff radius 0.2 reveal true log true
    8561    
    8562    
    8563     Allowed overlap: -0.4
    8564     H-bond overlap reduction: 0.4
    8565     Ignore contacts between atoms separated by 4 bonds or less
    8566     Ignore contacts between atoms in residues less than 5 apart in sequence
    8567     Detect intra-residue contacts: False
    8568     Detect intra-molecule contacts: False
    8569    
    8570     160 contacts
    8571                     atom1                                   atom2                   overlap  distance
    8572     relaxed_structure.pdb #5/C ARG 18 HH11  relaxed_structure.pdb #5/F GLU 17 CD     0.421    2.279
    8573     relaxed_structure.pdb #5/D LYS 109 HZ2  relaxed_structure.pdb #5/F GLU 19 CD     0.387    2.313
    8574     relaxed_structure.pdb #5/E THR 54 HG1   relaxed_structure.pdb #5/F GLU 9 OE2     0.371    1.709
    8575     relaxed_structure.pdb #5/D LYS 109 HZ2  relaxed_structure.pdb #5/F GLU 19 OE1    0.357    1.723
    8576     relaxed_structure.pdb #5/A LYS 31 HZ2   relaxed_structure.pdb #5/F ASP 30 OD2    0.353    1.727
    8577     relaxed_structure.pdb #5/A ARG 27 HH21  relaxed_structure.pdb #5/F ASP 30 OD1    0.348    1.732
    8578     relaxed_structure.pdb #5/D LYS 109 NZ   relaxed_structure.pdb #5/F GLU 19 CD     0.340    2.985
    8579     relaxed_structure.pdb #5/E ARG 43 HH21  relaxed_structure.pdb #5/F GLU 9 OE1     0.335    1.745
    8580     relaxed_structure.pdb #5/E THR 54 HG1   relaxed_structure.pdb #5/F GLU 9 CD      0.326    2.374
    8581     relaxed_structure.pdb #5/C ARG 18 HH22  relaxed_structure.pdb #5/F GLU 17 OE2    0.323    1.757
    8582     relaxed_structure.pdb #5/A ARG 27 HH11  relaxed_structure.pdb #5/F ASP 30 OD1    0.313    1.767
    8583     relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 HH22   0.308    1.772
    8584     relaxed_structure.pdb #5/E ARG 43 HH22  relaxed_structure.pdb #5/F ALA 7 O       0.213    1.867
    8585     relaxed_structure.pdb #5/C PRO 58 CB    relaxed_structure.pdb #5/F ILE 11 CD1    0.169    3.231
    8586     relaxed_structure.pdb #5/A ARG 27 HH21  relaxed_structure.pdb #5/F ASP 30 CG     0.166    2.534
    8587     relaxed_structure.pdb #5/E ARG 43 NH2   relaxed_structure.pdb #5/F THR 8 HA      0.161    2.464
    8588     relaxed_structure.pdb #5/A THR 28 OG1   relaxed_structure.pdb #5/F ARG 32 HE     0.158    1.942
    8589     relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F GLY 14 N      0.152    3.098
    8590     relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 HH12   0.146    1.934
    8591     relaxed_structure.pdb #5/D LYS 109 HZ1  relaxed_structure.pdb #5/F PRO 18 O      0.146    1.934
    8592     relaxed_structure.pdb #5/C ARG 18 HH11  relaxed_structure.pdb #5/F GLU 17 OE1    0.136    1.944
    8593     relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F PRO 18 HG2    0.085    2.540
    8594     relaxed_structure.pdb #5/C ARG 18 NH1   relaxed_structure.pdb #5/F GLU 17 CD     0.062    3.263
    8595     relaxed_structure.pdb #5/A ARG 27 CZ    relaxed_structure.pdb #5/F ASP 30 OD1    0.055    3.125
    8596     relaxed_structure.pdb #5/C ARG 18 HH11  relaxed_structure.pdb #5/F GLU 17 OE2    0.055    2.025
    8597     relaxed_structure.pdb #5/D LYS 109 HZ3  relaxed_structure.pdb #5/F GLU 19 OE2    0.047    2.033
    8598     relaxed_structure.pdb #5/A ARG 27 NH2   relaxed_structure.pdb #5/F ASP 30 OD1    0.038    2.667
    8599     relaxed_structure.pdb #5/C GLN 15 CD    relaxed_structure.pdb #5/F SER 12 O      0.034    3.146
    8600     relaxed_structure.pdb #5/D LYS 109 NZ   relaxed_structure.pdb #5/F GLU 19 OE1    0.032    2.673
    8601     relaxed_structure.pdb #5/C ALA 35 CB    relaxed_structure.pdb #5/F VAL 51 HA     0.028    2.672
    8602     relaxed_structure.pdb #5/A LYS 31 NZ    relaxed_structure.pdb #5/F ASP 30 OD2    0.025    2.680
    8603     relaxed_structure.pdb #5/A ARG 27 NH1   relaxed_structure.pdb #5/F ASP 30 OD1    0.020    2.685
    8604     relaxed_structure.pdb #5/C LYS 34 C     relaxed_structure.pdb #5/F GLY 50 O      0.019    3.161
    8605     relaxed_structure.pdb #5/C PRO 58 CG    relaxed_structure.pdb #5/F ILE 11 CD1    0.015    3.385
    8606     relaxed_structure.pdb #5/C ILE 11 CD1   relaxed_structure.pdb #5/F PRO 53 HB3    0.012    2.688
    8607     relaxed_structure.pdb #5/D LYS 109 NZ   relaxed_structure.pdb #5/F GLU 19 OE2    0.011    2.694
    8608     relaxed_structure.pdb #5/E THR 54 OG1   relaxed_structure.pdb #5/F GLU 9 CD      -0.001    3.201
    8609     relaxed_structure.pdb #5/A ARG 27 HH11  relaxed_structure.pdb #5/F ASP 30 CG     -0.002    2.702
    8610     relaxed_structure.pdb #5/C THR 14 HG1   relaxed_structure.pdb #5/F ALA 15 HB3    -0.006    2.006
    8611     relaxed_structure.pdb #5/C CYS 13 O     relaxed_structure.pdb #5/F ALA 15 HB3    -0.012    2.492
    8612     relaxed_structure.pdb #5/D LYS 109 HZ3  relaxed_structure.pdb #5/F GLU 19 CD     -0.015    2.715
    8613     relaxed_structure.pdb #5/C PRO 58 HG3   relaxed_structure.pdb #5/F ILE 11 CD1    -0.017    2.717
    8614     relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 NH2    -0.023    2.728
    8615     relaxed_structure.pdb #5/C PRO 58 CB    relaxed_structure.pdb #5/F ILE 11 HD11   -0.027    2.727
    8616     relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F GLU 17 OE2    -0.028    2.733
    8617     relaxed_structure.pdb #5/E ARG 43 NH2   relaxed_structure.pdb #5/F GLU 9 OE1     -0.044    2.749
    8618     relaxed_structure.pdb #5/C ARG 18 CZ    relaxed_structure.pdb #5/F GLY 14 O      -0.062    3.242
    8619     relaxed_structure.pdb #5/C ARG 18 HH22  relaxed_structure.pdb #5/F GLU 17 CD     -0.064    2.764
    8620     relaxed_structure.pdb #5/A ARG 27 NH2   relaxed_structure.pdb #5/F ASP 30 CG     -0.076    3.401
    8621     relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 CZ     -0.080    3.260
    8622     relaxed_structure.pdb #5/E THR 54 OG1   relaxed_structure.pdb #5/F GLU 9 OE2     -0.082    2.662
    8623     relaxed_structure.pdb #5/A ASP 34 CG    relaxed_structure.pdb #5/F ARG 32 HH12   -0.083    2.783
    8624     relaxed_structure.pdb #5/A LYS 31 HZ2   relaxed_structure.pdb #5/F ASP 30 CG     -0.084    2.784
    8625     relaxed_structure.pdb #5/E SER 53 C     relaxed_structure.pdb #5/F GLU 9 OE2     -0.087    3.267
    8626     relaxed_structure.pdb #5/C CYS 13 CB    relaxed_structure.pdb #5/F PRO 53 HG3    -0.088    2.788
    8627     relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F ALA 15 N      -0.094    3.344
    8628     relaxed_structure.pdb #5/C ARG 18 HH21  relaxed_structure.pdb #5/F PRO 18 HG2    -0.099    2.099
    8629     relaxed_structure.pdb #5/C ARG 18 CZ    relaxed_structure.pdb #5/F GLU 17 OE2    -0.103    3.283
    8630     relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F PRO 53 O      -0.106    2.586
    8631     relaxed_structure.pdb #5/C ILE 11 O     relaxed_structure.pdb #5/F PRO 53 HB2    -0.106    2.586
    8632     relaxed_structure.pdb #5/A ARG 27 HH21  relaxed_structure.pdb #5/F ASP 30 HA     -0.109    2.109
    8633     relaxed_structure.pdb #5/E SER 53 H     relaxed_structure.pdb #5/F GLU 9 OE2     -0.109    2.189
    8634     relaxed_structure.pdb #5/C ILE 11 O     relaxed_structure.pdb #5/F PRO 53 HA     -0.113    2.593
    8635     relaxed_structure.pdb #5/C THR 14 HG1   relaxed_structure.pdb #5/F ALA 15 CB     -0.115    2.815
    8636     relaxed_structure.pdb #5/C PRO 58 CB    relaxed_structure.pdb #5/F ILE 11 HD13   -0.120    2.820
    8637     relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F GLY 14 C      -0.122    3.447
    8638     relaxed_structure.pdb #5/C ILE 11 HG13  relaxed_structure.pdb #5/F PRO 53 CB     -0.123    2.823
    8639     relaxed_structure.pdb #5/D LYS 109 NZ   relaxed_structure.pdb #5/F PRO 18 O      -0.123    2.828
    8640     relaxed_structure.pdb #5/C CYS 13 C     relaxed_structure.pdb #5/F ALA 15 HB3    -0.125    2.825
    8641     relaxed_structure.pdb #5/C ARG 18 NH1   relaxed_structure.pdb #5/F GLU 17 OE1    -0.132    2.837
    8642     relaxed_structure.pdb #5/C ILE 11 CG1   relaxed_structure.pdb #5/F PRO 53 CB     -0.134    3.534
    8643     relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F PRO 18 CG     -0.138    3.463
    8644     relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 NH1    -0.139    2.844
    8645     relaxed_structure.pdb #5/C GLN 15 HG2   relaxed_structure.pdb #5/F SER 12 O      -0.148    2.628
    8646     relaxed_structure.pdb #5/E THR 54 OG1   relaxed_structure.pdb #5/F MET 54 CE     -0.150    3.350
    8647     relaxed_structure.pdb #5/C GLN 15 CG    relaxed_structure.pdb #5/F SER 12 O      -0.153    3.333
    8648     relaxed_structure.pdb #5/E ARG 43 NH2   relaxed_structure.pdb #5/F ALA 7 O       -0.157    2.862
    8649     relaxed_structure.pdb #5/A ARG 27 NH2   relaxed_structure.pdb #5/F ASP 30 HA     -0.159    2.784
    8650     relaxed_structure.pdb #5/C ILE 11 CD1   relaxed_structure.pdb #5/F PRO 53 CB     -0.177    3.577
    8651     relaxed_structure.pdb #5/C GLN 15 CG    relaxed_structure.pdb #5/F CYS 13 HA     -0.183    2.883
    8652     relaxed_structure.pdb #5/E ARG 43 NH2   relaxed_structure.pdb #5/F THR 8 CA      -0.185    3.510
    8653     relaxed_structure.pdb #5/C ALA 35 CA    relaxed_structure.pdb #5/F VAL 51 HA     -0.194    2.894
    8654     relaxed_structure.pdb #5/C GLN 15 HE21  relaxed_structure.pdb #5/F GLY 14 C      -0.195    2.895
    8655     relaxed_structure.pdb #5/D LYS 109 HG2  relaxed_structure.pdb #5/F GLU 19 OE1    -0.202    2.682
    8656     relaxed_structure.pdb #5/C ARG 18 NH1   relaxed_structure.pdb #5/F GLU 17 OE2    -0.203    2.908
    8657     relaxed_structure.pdb #5/E THR 54 O     relaxed_structure.pdb #5/F MET 54 CE     -0.206    3.386
    8658     relaxed_structure.pdb #5/C GLN 15 OE1   relaxed_structure.pdb #5/F SER 12 O      -0.206    3.166
    8659     relaxed_structure.pdb #5/C GLN 15 CD    relaxed_structure.pdb #5/F GLY 14 N      -0.207    3.532
    8660     relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F GLY 14 CA     -0.208    3.533
    8661     relaxed_structure.pdb #5/C PRO 58 HB2   relaxed_structure.pdb #5/F ILE 11 CD1    -0.211    2.911
    8662     relaxed_structure.pdb #5/E ARG 43 HH22  relaxed_structure.pdb #5/F ALA 7 C       -0.212    2.912
    8663     relaxed_structure.pdb #5/A THR 28 OG1   relaxed_structure.pdb #5/F ARG 32 NE     -0.215    2.940
    8664     relaxed_structure.pdb #5/C ILE 11 CD1   relaxed_structure.pdb #5/F MET 54 SD     -0.218    3.700
    8665     relaxed_structure.pdb #5/E THR 54 O     relaxed_structure.pdb #5/F MET 54 HE2    -0.218    2.698
    8666     relaxed_structure.pdb #5/C LYS 34 CB    relaxed_structure.pdb #5/F GLY 50 O      -0.221    3.401
    8667     relaxed_structure.pdb #5/A THR 28 HG1   relaxed_structure.pdb #5/F ARG 32 HH21   -0.224    2.224
    8668     relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F PRO 53 HB3    -0.227    2.227
    8669     relaxed_structure.pdb #5/E ARG 43 HH22  relaxed_structure.pdb #5/F THR 8 HA      -0.229    2.229
    8670     relaxed_structure.pdb #5/C ILE 11 O     relaxed_structure.pdb #5/F PRO 53 CB     -0.230    3.410
    8671     relaxed_structure.pdb #5/E THR 54 CG2   relaxed_structure.pdb #5/F GLU 9 OE1     -0.230    3.410
    8672     relaxed_structure.pdb #5/E SER 53 CA    relaxed_structure.pdb #5/F GLU 9 OE2     -0.230    3.410
    8673     relaxed_structure.pdb #5/C CYS 13 CB    relaxed_structure.pdb #5/F PRO 53 CG     -0.231    3.631
    8674     relaxed_structure.pdb #5/C PRO 58 CG    relaxed_structure.pdb #5/F ILE 11 HD13   -0.233    2.933
    8675     relaxed_structure.pdb #5/C THR 14 HG1   relaxed_structure.pdb #5/F ALA 15 CA     -0.234    2.934
    8676     relaxed_structure.pdb #5/A ARG 27 NH1   relaxed_structure.pdb #5/F ASP 30 CG     -0.235    3.560
    8677     relaxed_structure.pdb #5/C PRO 58 HB3   relaxed_structure.pdb #5/F ILE 11 HD11   -0.242    2.242
    8678     relaxed_structure.pdb #5/C ALA 35 CA    relaxed_structure.pdb #5/F GLY 50 O      -0.243    3.423
    8679     relaxed_structure.pdb #5/C ALA 35 HB3   relaxed_structure.pdb #5/F VAL 51 HA     -0.244    2.244
    8680     relaxed_structure.pdb #5/A LYS 31 HZ1   relaxed_structure.pdb #5/F ASP 30 O      -0.246    2.326
    8681     relaxed_structure.pdb #5/C ILE 11 O     relaxed_structure.pdb #5/F PRO 53 CA     -0.247    3.427
    8682     relaxed_structure.pdb #5/C CYS 13 HB2   relaxed_structure.pdb #5/F PRO 53 HG3    -0.250    2.250
    8683     relaxed_structure.pdb #5/A THR 28 HB    relaxed_structure.pdb #5/F GLY 31 HA2    -0.251    2.251
    8684     relaxed_structure.pdb #5/C CYS 13 HB3   relaxed_structure.pdb #5/F PRO 53 CB     -0.254    2.954
    8685     relaxed_structure.pdb #5/A ARG 27 HH21  relaxed_structure.pdb #5/F ASP 30 CA     -0.255    2.955
    8686     relaxed_structure.pdb #5/C CYS 13 HB3   relaxed_structure.pdb #5/F PRO 53 HB2    -0.260    2.260
    8687     relaxed_structure.pdb #5/C PRO 58 HG3   relaxed_structure.pdb #5/F ILE 11 HD13   -0.265    2.265
    8688     relaxed_structure.pdb #5/A LYS 31 NZ    relaxed_structure.pdb #5/F ASP 30 O      -0.269    2.974
    8689     relaxed_structure.pdb #5/C PRO 58 HB2   relaxed_structure.pdb #5/F ILE 11 HD13   -0.269    2.269
    8690     relaxed_structure.pdb #5/C ALA 35 HA    relaxed_structure.pdb #5/F VAL 51 HA     -0.270    2.270
    8691     relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F PRO 53 C      -0.274    2.974
    8692     relaxed_structure.pdb #5/E ARG 43 HH21  relaxed_structure.pdb #5/F GLU 9 CD      -0.276    2.976
    8693     relaxed_structure.pdb #5/C GLN 15 CD    relaxed_structure.pdb #5/F GLY 14 H      -0.276    2.976
    8694     relaxed_structure.pdb #5/A ASP 34 CG    relaxed_structure.pdb #5/F ARG 32 HH22   -0.283    2.983
    8695     relaxed_structure.pdb #5/E THR 54 N     relaxed_structure.pdb #5/F GLU 9 OE2     -0.285    2.990
    8696     relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F GLY 14 H      -0.288    2.913
    8697     relaxed_structure.pdb #5/D LYS 109 HZ1  relaxed_structure.pdb #5/F PRO 18 C      -0.290    2.990
    8698     relaxed_structure.pdb #5/E ARG 43 CZ    relaxed_structure.pdb #5/F GLU 9 OE1     -0.291    3.471
    8699     relaxed_structure.pdb #5/C THR 14 HG22  relaxed_structure.pdb #5/F ALA 15 CB     -0.292    2.992
    8700     relaxed_structure.pdb #5/E THR 54 OG1   relaxed_structure.pdb #5/F MET 54 HE1    -0.299    2.799
    8701     relaxed_structure.pdb #5/E THR 54 CB    relaxed_structure.pdb #5/F GLU 9 OE2     -0.302    3.482
    8702     relaxed_structure.pdb #5/C CYS 13 HA    relaxed_structure.pdb #5/F PRO 53 HD3    -0.306    2.306
    8703     relaxed_structure.pdb #5/C ILE 11 CG1   relaxed_structure.pdb #5/F PRO 53 HB3    -0.311    3.011
    8704     relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F GLY 14 O      -0.312    3.017
    8705     relaxed_structure.pdb #5/A THR 28 HB    relaxed_structure.pdb #5/F GLY 31 C      -0.313    3.013
    8706     relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F GLU 17 CD     -0.314    3.639
    8707     relaxed_structure.pdb #5/A ARG 27 NH2   relaxed_structure.pdb #5/F ASP 30 CA     -0.317    3.642
    8708     relaxed_structure.pdb #5/C CYS 13 CB    relaxed_structure.pdb #5/F PRO 53 CB     -0.318    3.718
    8709     relaxed_structure.pdb #5/C ILE 11 HG13  relaxed_structure.pdb #5/F PRO 53 HB2    -0.319    2.319
    8710     relaxed_structure.pdb #5/C CYS 13 CB    relaxed_structure.pdb #5/F PRO 53 HB2    -0.326    3.026
    8711     relaxed_structure.pdb #5/E VAL 52 HG21  relaxed_structure.pdb #5/F ILE 11 CG2    -0.326    3.026
    8712     relaxed_structure.pdb #5/C CYS 13 O     relaxed_structure.pdb #5/F ALA 15 CB     -0.332    3.512
    8713     relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F CYS 13 C      -0.336    3.661
    8714     relaxed_structure.pdb #5/D LYS 109 HZ2  relaxed_structure.pdb #5/F GLU 19 OE2    -0.338    2.418
    8715     relaxed_structure.pdb #5/C ALA 35 CB    relaxed_structure.pdb #5/F VAL 51 CA     -0.340    3.740
    8716     relaxed_structure.pdb #5/E SER 53 N     relaxed_structure.pdb #5/F GLU 9 OE2     -0.349    3.054
    8717     relaxed_structure.pdb #5/A THR 28 HB    relaxed_structure.pdb #5/F GLY 31 CA     -0.353    3.053
    8718     relaxed_structure.pdb #5/C ARG 18 HH22  relaxed_structure.pdb #5/F PRO 18 HG2    -0.353    2.353
    8719     relaxed_structure.pdb #5/C ILE 11 HB    relaxed_structure.pdb #5/F PRO 53 O      -0.354    2.834
    8720     relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F MET 54 SD     -0.357    3.139
    8721     relaxed_structure.pdb #5/C PRO 58 HB3   relaxed_structure.pdb #5/F ILE 11 CD1    -0.364    3.064
    8722     relaxed_structure.pdb #5/C GLN 15 CD    relaxed_structure.pdb #5/F CYS 13 HA     -0.364    3.064
    8723     relaxed_structure.pdb #5/A LYS 31 NZ    relaxed_structure.pdb #5/F ASP 30 CG     -0.369    3.694
    8724     relaxed_structure.pdb #5/C THR 14 HG22  relaxed_structure.pdb #5/F ALA 15 HB3    -0.370    2.370
    8725     relaxed_structure.pdb #5/A THR 28 OG1   relaxed_structure.pdb #5/F ARG 32 CZ     -0.377    3.577
    8726     relaxed_structure.pdb #5/C ALA 35 N     relaxed_structure.pdb #5/F GLY 50 O      -0.377    3.082
    8727     relaxed_structure.pdb #5/C GLN 15 HE21  relaxed_structure.pdb #5/F GLY 14 CA     -0.381    3.081
    8728     relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F PRO 18 CD     -0.381    3.706
    8729     relaxed_structure.pdb #5/C ARG 18 HH22  relaxed_structure.pdb #5/F PRO 18 CG     -0.386    3.086
    8730     relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F PRO 53 CB     -0.388    3.088
    8731     relaxed_structure.pdb #5/E THR 54 HG22  relaxed_structure.pdb #5/F GLU 9 OE1     -0.396    2.876
    8732    
    8733 
    8734  
    8735 160 contacts 
    8736 
    8737 > color sel byhetero
    8738 
    8739 > select #5/A-F
    8740 
    8741 28495 atoms, 28969 bonds, 160 pseudobonds, 1826 residues, 2 models selected 
    8742 
    8743 > color sel byhetero
    8744 
    8745 > coulombic #5/A surfaces #5.1
    8746 
    8747 Coulombic values for relaxed_structure.pdb_A SES surface #5.1: minimum,
    8748 -11.84, mean -0.24, maximum 17.92 
    8749 
    8750 > coulombic #5/B surfaces #5.2
    8751 
    8752 Coulombic values for relaxed_structure.pdb_B SES surface #5.2: minimum,
    8753 -13.17, mean 0.31, maximum 13.60 
    8754 
    8755 > coulombic #5/C surfaces #5.3
    8756 
    8757 Coulombic values for relaxed_structure.pdb_C SES surface #5.3: minimum,
    8758 -14.28, mean 0.87, maximum 12.27 
    8759 
    8760 > coulombic #5/D surfaces #5.4
    8761 
    8762 Coulombic values for relaxed_structure.pdb_D SES surface #5.4: minimum, -9.85,
    8763 mean 2.10, maximum 15.14 
    8764 
    8765 > coulombic #5/E surfaces #5.5
    8766 
    8767 Coulombic values for relaxed_structure.pdb_E SES surface #5.5: minimum,
    8768 -10.97, mean 1.53, maximum 12.30 
    8769 
    8770 > select H
    8771 
    8772 14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected 
    8773 
    8774 > hide sel & #!1,5 atoms
    8775 
    8776 > select #5/A-E
    8777 
    8778 27646 atoms, 28113 bonds, 1765 residues, 1 model selected 
    8779 
    8780 > hide #5.1 models
    8781 
    8782 > hide #5.2 models
    8783 
    8784 > hide #5.3 models
    8785 
    8786 > hide #5.4 models
    8787 
    8788 > hide #5.5 models
    8789 
    8790 > hide #!2 models
    8791 
    8792 > ui tool show H-Bonds
    8793 
    8794 > hbonds sel color #0096ff restrict #5/F interModel false intraMol false
    8795 > intraRes false reveal true log true
    8796    
    8797    
    8798     Finding intramodel H-bonds
    8799     Constraints relaxed by 0.4 angstroms and 20 degrees
    8800     Models used:
    8801         5 relaxed_structure.pdb
    8802    
    8803     18 H-bonds
    8804     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8805     relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH11  2.685  1.767
    8806     relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH21  2.667  1.732
    8807     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 O    relaxed_structure.pdb #5/A LYS 31 HZ1   2.974  2.326
    8808     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 OD2  relaxed_structure.pdb #5/A LYS 31 HZ2   2.680  1.727
    8809     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE1  relaxed_structure.pdb #5/C ARG 18 HH11  2.837  1.944
    8810     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH11  2.908  2.025
    8811     relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH22  2.733  1.757
    8812     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F PRO 18 O    relaxed_structure.pdb #5/D LYS 109 HZ1  2.828  1.934
    8813     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE1  relaxed_structure.pdb #5/D LYS 109 HZ2  2.673  1.723
    8814     relaxed_structure.pdb #5/E ARG 43 NE   relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HE    3.322  2.487
    8815     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F ALA 7 O     relaxed_structure.pdb #5/E ARG 43 HH22  2.862  1.867
    8816     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HH21  2.749  1.745
    8817     relaxed_structure.pdb #5/E SER 53 N    relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E SER 53 H     3.054  2.189
    8818     relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E THR 54 HG1   2.662  1.709
    8819     relaxed_structure.pdb #5/F ARG 32 NE   relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HE    2.940  1.942
    8820     relaxed_structure.pdb #5/F ARG 32 NH1  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH12  2.844  1.934
    8821     relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HH21  3.342  2.567
    8822     relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH22  2.728  1.772
    8823    
    8824 
    8825  
    8826 18 hydrogen bonds found 
    8827 
    8828 > select #5/F:7,9,17-19,30,28,30,34
    8829 
    8830 111 atoms, 106 bonds, 8 residues, 1 model selected 
    8831 
    8832 > style sel stick
    8833 
    8834 Changed 111 atom styles 
    8835 
    8836 > select #5/F:28,34
    8837 
    8838 30 atoms, 28 bonds, 2 residues, 1 model selected 
    8839 
    8840 > style sel sphere
    8841 
    8842 Changed 30 atom styles 
    8843 
    8844 > select #5/F:32
    8845 
    8846 24 atoms, 23 bonds, 1 residue, 1 model selected 
    8847 
    8848 > style sel stick
    8849 
    8850 Changed 24 atom styles 
    8851 
    8852 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54
    8853 
    8854 167 atoms, 160 bonds, 9 residues, 1 model selected 
    8855 
    8856 > style sel stick
    8857 
    8858 Changed 167 atom styles 
    8859 
    8860 > show sel atoms
    8861 
    8862 > hide #5.8 models
    8863 
    8864 > ui tool show "Selection Inspector"
    8865 
    8866 > setattr sel r ribbon_hide_backbone false
    8867 
    8868 Assigning ribbon_hide_backbone attribute to 9 items 
    8869 
    8870 > select #5/F:7,9,17-19,30,32
    8871 
    8872 105 atoms, 101 bonds, 7 residues, 1 model selected 
    8873 
    8874 > setattr sel r ribbon_hide_backbone false
    8875 
    8876 Assigning ribbon_hide_backbone attribute to 7 items 
    8877 
    8878 > select clear
    8879 
    8880 > select :SF4
    8881 
    8882 104 atoms, 156 bonds, 13 residues, 5 models selected 
    8883 
    8884 > style sel & #3#!1 ball
    8885 
    8886 Changed 40 atom styles 
    8887 
    8888 > style sel & #3#!1 ball
    8889 
    8890 Changed 40 atom styles 
    8891 
    8892 > select clear
    8893 
    8894 > view front
    8895 
    8896 [Repeated 1 time(s)]
    8897 
    8898 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    8899 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on
    8900 > PSI.cxs"
    8901 
    8902 > view name hbond1
    8903 
    8904 > view front
    8905 
    8906 > view hbond1
    8907 
    8908 > view name hbond2
    8909 
    8910 > view name hbond3
    8911 
    8912 > view front
    8913 
    8914 > view back
    8915 
    8916 > view front
    8917 
    8918 [Repeated 1 time(s)]
    8919 
    8920 > select #1/M:61@FE1
    8921 
    8922 1 atom, 1 residue, 1 model selected 
    8923 
    8924 > select #1/M:61@FE2
    8925 
    8926 1 atom, 1 residue, 1 model selected 
    8927 
    8928 > select #1/M:61@FE2#3/C:3003@FE2
    8929 
    8930 2 atoms, 2 residues, 2 models selected 
    8931 
    8932 > ui tool show Distances
    8933 
    8934 > distance style color #797979
    8935 
    8936 [Repeated 2 time(s)]
    8937 
    8938 > distance style decimalPlaces 2
    8939 
    8940 [Repeated 2 time(s)]
    8941 
    8942 > distance style radius 0.2
    8943 
    8944 [Repeated 2 time(s)]
    8945 
    8946 > distance #1/M:61@FE2 #3/C:3003@FE2
    8947 
    8948 Distance between 2fdn #1/M SF4 61 FE2 and Fe4S4 clusters #3/C SF4 3003 FE2:
    8949 11.23Å 
    8950 
    8951 > ~distance #1/M:61@FE2 #3/C:3003@FE2
    8952 
    8953 > select #1/M:61@FE2#3/C:3003@FE1
    8954 
    8955 2 atoms, 2 residues, 2 models selected 
    8956 
    8957 > distance #1/M:61@FE2 #3/C:3003@FE1
    8958 
    8959 Distance between 2fdn #1/M SF4 61 FE2 and Fe4S4 clusters #3/C SF4 3003 FE1:
    8960 8.79Å 
    8961 
    8962 > select clear
    8963 
    8964 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    8965 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on
    8966 > PSI.cxs"
    8967 
    8968 [Repeated 1 time(s)]
    8969 
    8970 ——— End of log from Thu Oct 3 09:47:21 2024 ———
    8971 
    8972 opened ChimeraX session 
    8973 
    8974 > view front
    8975 
    8976 > view back
    8977 
    8978 > view hBond1
    8979 
    8980 Expected an objects specifier or a view name or a keyword 
    8981 
    8982 > view hbond1
    8983 
    8984 > hide #6.1 models
    8985 
    8986 > view hbond2
    8987 
    8988 > view hbond3
    8989 
    8990 > view front
    8991 
    8992 > show #5.1 models
    8993 
    8994 > show #5.2 models
    8995 
    8996 > show #5.3 models
    8997 
    8998 > show #5.4 models
    8999 
    9000 > show #5.5 models
    9001 
    9002 > select add #5.5
    9003 
    9004 1059 atoms, 66 residues, 1 model selected 
    9005 
    9006 > select add #5.4
    9007 
    9008 3336 atoms, 209 residues, 2 models selected 
    9009 
    9010 > select add #5.3
    9011 
    9012 4550 atoms, 289 residues, 3 models selected 
    9013 
    9014 > select add #5.2
    9015 
    9016 16065 atoms, 1022 residues, 4 models selected 
    9017 
    9018 > select add #5.1
    9019 
    9020 27646 atoms, 1765 residues, 5 models selected 
    9021 
    9022 > transparency (#!5 & sel) 20
    9023 
    9024 > transparency (#!5 & sel) 30
    9025 
    9026 > select clear
    9027 
    9028 > graphics silhouettes false
    9029 
    9030 > graphics silhouettes true
    9031 
    9032 > show #!2 models
    9033 
    9034 > hide #!2 models
    9035 
    9036 > show #!2 models
    9037 
    9038 > select #2/F
    9039 
    9040 1633 atoms, 1673 bonds, 9 pseudobonds, 164 residues, 2 models selected 
    9041 
    9042 > hide sel atoms
    9043 
    9044 > hide sel cartoons
    9045 
    9046 > select #2/J
    9047 
    9048 528 atoms, 546 bonds, 5 pseudobonds, 46 residues, 2 models selected 
    9049 
    9050 > hide sel cartoons
    9051 
    9052 > hide sel atoms
    9053 
    9054 > select #2:BCR
    9055 
    9056 1080 atoms, 1107 bonds, 27 residues, 1 model selected 
    9057 
    9058 > select #2:BCR,LUT
    9059 
    9060 1374 atoms, 1408 bonds, 34 residues, 1 model selected 
    9061 
    9062 > color sel orange
    9063 
    9064 > color sel byhetero
    9065 
    9066 > select clear
    9067 
    9068 > show #5.6 models
    9069 
    9070 > coulombic #5/F surfaces #5.6
    9071 
    9072 Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum,
    9073 -13.89, mean -3.67, maximum 7.01 
    9074 
    9075 > select subtract #5.7
    9076 
    9077 Nothing selected 
    9078 
    9079 > select add #5.6
    9080 
    9081 849 atoms, 61 residues, 1 model selected 
    9082 
    9083 > transparency (#!5 & sel) 30
    9084 
    9085 > select clear
    9086 
    9087 > view front
    9088 
    9089 > hide #5.6 models
    9090 
    9091 > hide #5.5 models
    9092 
    9093 > hide #5.4 models
    9094 
    9095 > hide #5.3 models
    9096 
    9097 > hide #5.2 models
    9098 
    9099 > hide #5.1 models
    9100 
    9101 > show #5.1 models
    9102 
    9103 > show #5.2 models
    9104 
    9105 > show #5.3 models
    9106 
    9107 > show #5.4 models
    9108 
    9109 > show #5.5 models
    9110 
    9111 > hide #5.5 models
    9112 
    9113 > show #5.5 models
    9114 
    9115 > hide #5.5 models
    9116 
    9117 > show #5.5 models
    9118 
    9119 > show #5.6 models
    9120 
    9121 > help help:user
    9122 
    9123 > view name front
    9124 
    9125 > turn x 180
    9126 
    9127 > view front
    9128 
    9129 > turn y 180
    9130 
    9131 > hide #5.3 models
    9132 
    9133 > hide #5.4 models
    9134 
    9135 > hide #5.5 models
    9136 
    9137 > hide #5.6 models
    9138 
    9139 > show #5.3 models
    9140 
    9141 > show #5.4 models
    9142 
    9143 > show #5.5 models
    9144 
    9145 > show #5.6 models
    9146 
    9147 > hide #5.5 models
    9148 
    9149 > hide #5.4 models
    9150 
    9151 > hide #5.3 models
    9152 
    9153 > show #5.4 models
    9154 
    9155 > show #5.5 models
    9156 
    9157 > hide #5.4 models
    9158 
    9159 > hide #5.5 models
    9160 
    9161 > show #5.4 models
    9162 
    9163 > hide #5.4 models
    9164 
    9165 > turn y 180
    9166 
    9167 [Repeated 1 time(s)]
    9168 
    9169 > view name back
    9170 
    9171 > view front
    9172 
    9173 > view back
    9174 
    9175 > select #2/I/H/L
    9176 
    9177 2569 atoms, 2652 bonds, 18 pseudobonds, 292 residues, 2 models selected 
    9178 
    9179 > hide sel cartoons
    9180 
    9181 > hide sel atoms
    9182 
    9183 > hide #5.6 models
    9184 
    9185 > view name back
    9186 
    9187 > show #5.6 models
    9188 
    9189 > show #5.4 models
    9190 
    9191 > hide #5.4 models
    9192 
    9193 > hide #5.6 models
    9194 
    9195 > view name back
    9196 
    9197 > view front
    9198 
    9199 > view back
    9200 
    9201 > view front
    9202 
    9203 > show #5.3 models
    9204 
    9205 > show #5.4 models
    9206 
    9207 > show #5.5 models
    9208 
    9209 > hide #5.5 models
    9210 
    9211 > hide #5.4 models
    9212 
    9213 > hide #5.3 models
    9214 
    9215 > show #5.3 models
    9216 
    9217 > show #5.4 models
    9218 
    9219 > show #5.5 models
    9220 
    9221 > show #5.6 models
    9222 
    9223 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    9224 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    9225 
    9226 ——— End of log from Thu Oct 3 21:28:49 2024 ———
    9227 
    9228 opened ChimeraX session 
    9229 
    9230 > view front
    9231 
    9232 > view backZoom
    9233 
    9234 Expected an objects specifier or a view name or a keyword 
    9235 
    9236 > view hbond2
    9237 
    9238 > view back
    9239 
    9240 > hide #5.6 models
    9241 
    9242 > show #5.6 models
    9243 
    9244 > show #!4 models
    9245 
    9246 > hide #!5 models
    9247 
    9248 > show #!5 models
    9249 
    9250 > hide #!4 models
    9251 
    9252 > hide #5.6 models
    9253 
    9254 > show #5.6 models
    9255 
    9256 > hide #5.6 models
    9257 
    9258 > show #5.6 models
    9259 
    9260 > view front
    9261 
    9262 > hide #5.6 models
    9263 
    9264 > hide #!1 models
    9265 
    9266 > show #!18 models
    9267 
    9268 > rename #6 id #8
    9269 
    9270 > select add #8
    9271 
    9272 2569 atoms, 2652 bonds, 19 pseudobonds, 292 residues, 4 models selected 
    9273 
    9274 > hide #5.5 models
    9275 
    9276 > hide #5.4 models
    9277 
    9278 > hide #5.3 models
    9279 
    9280 > show #!1 models
    9281 
    9282 > show #8.1 models
    9283 
    9284 > rename #1 id #6
    9285 
    9286 > rename #2 id #1
    9287 
    9288 > rename #3 id #2
    9289 
    9290 > rename #4 id #3
    9291 
    9292 > rename #18 id #4
    9293 
    9294 > hide #!4 models
    9295 
    9296 > ui tool show Matchmaker
    9297 
    9298 > matchmaker #!6 to #5/B pairing bs
    9299 
    9300 Parameters 
    9301 --- 
    9302 Chain pairing | bs 
    9303 Alignment algorithm | Needleman-Wunsch 
    9304 Similarity matrix | BLOSUM-62 
    9305 SS fraction | 0.3 
    9306 Gap open (HH/SS/other) | 18/18/6 
    9307 Gap extend | 1 
    9308 SS matrix |  |  | H | S | O 
    9309 ---|---|---|--- 
    9310 H | 6 | -9 | -6 
    9311 S |  | 6 | -6 
    9312 O |  |  | 4 
    9313 Iteration cutoff | 2 
    9314  
    9315 Matchmaker relaxed_structure.pdb, chain B (#5) with 2fdn, chain M (#6),
    9316 sequence alignment score = 4 
    9317 Fewer than 3 residues aligned; cannot match relaxed_structure.pdb, chain B
    9318 with 2fdn, chain M 
    9319 
    9320 > ui tool show Matchmaker
    9321 
    9322 > matchmaker #!6 to #5/F pairing bs
    9323 
    9324 Parameters 
    9325 --- 
    9326 Chain pairing | bs 
    9327 Alignment algorithm | Needleman-Wunsch 
    9328 Similarity matrix | BLOSUM-62 
    9329 SS fraction | 0.3 
    9330 Gap open (HH/SS/other) | 18/18/6 
    9331 Gap extend | 1 
    9332 SS matrix |  |  | H | S | O 
    9333 ---|---|---|--- 
    9334 H | 6 | -9 | -6 
    9335 S |  | 6 | -6 
    9336 O |  |  | 4 
    9337 Iteration cutoff | 2 
    9338  
    9339 Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
    9340 sequence alignment score = 170.3 
    9341 RMSD between 41 pruned atom pairs is 0.850 angstroms; (across all 54 pairs:
    9342 2.909) 
    9343  
    9344 
    9345 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    9346 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    9347 
    9348 > select #5@@draw_mode=0
    9349 
    9350 28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected 
    9351 
    9352 > hide #5.1 models
    9353 
    9354 > hide #5.7 models
    9355 
    9356 > select subtract #5.7
    9357 
    9358 28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 8 models selected 
    9359 
    9360 > select subtract #5.6
    9361 
    9362 27425 atoms, 27831 bonds, 1756 residues, 7 models selected 
    9363 
    9364 > select subtract #5.5
    9365 
    9366 26415 atoms, 26811 bonds, 1693 residues, 6 models selected 
    9367 
    9368 > select subtract #5.4
    9369 
    9370 24160 atoms, 24526 bonds, 1551 residues, 5 models selected 
    9371 
    9372 > select subtract #5.3
    9373 
    9374 23024 atoms, 23432 bonds, 1472 residues, 4 models selected 
    9375 
    9376 > select subtract #5.2
    9377 
    9378 11509 atoms, 11705 bonds, 739 residues, 3 models selected 
    9379 
    9380 > select subtract #5.1
    9381 
    9382 1 model selected 
    9383 
    9384 > hide #5.2 models
    9385 
    9386 > select #5/A-F@@draw_mode=0
    9387 
    9388 28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected 
    9389 
    9390 > select clear
    9391 
    9392 > select subtract #5.7
    9393 
    9394 Nothing selected 
    9395 
    9396 > hide #!5 models
    9397 
    9398 > show #!5 models
    9399 
    9400 > select #5/F:1-55@@draw_mode=0
    9401 
    9402 600 atoms, 555 bonds, 48 residues, 1 model selected 
    9403 
    9404 > select #5 &protein &@@draw_mode=0
    9405 
    9406 28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected 
    9407 
    9408 > select #5/C:1-100 &@@draw_mode=0
    9409 
    9410 1136 atoms, 1094 bonds, 79 residues, 1 model selected 
    9411 
    9412 > select #5/C:1-100@@draw_mode=0
    9413 
    9414 1136 atoms, 1094 bonds, 79 residues, 1 model selected 
    9415 
    9416 > select subtract #5.3
    9417 
    9418 1 model selected 
    9419 
    9420 > select #5/C:1-100@@draw_mode=0
    9421 
    9422 1136 atoms, 1094 bonds, 79 residues, 1 model selected 
    9423 
    9424 > select #5/C:11,14-15,34-35/E:52/F:8,52-54
    9425 
    9426 154 atoms, 149 bonds, 17 pseudobonds, 10 residues, 2 models selected 
    9427 
    9428 > select #5/C:11,14-15,34-35/E:52/F:8,51-54
    9429 
    9430 170 atoms, 165 bonds, 22 pseudobonds, 11 residues, 2 models selected 
    9431 
    9432 > select #5/C:11,14-15,34-35/E:52/F:8,51,53,54
    9433 
    9434 159 atoms, 153 bonds, 22 pseudobonds, 10 residues, 2 models selected 
    9435 
    9436 > select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54
    9437 
    9438 169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 2 models selected 
    9439 
    9440 > select subtract #5.7
    9441 
    9442 169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 5 models selected 
    9443 
    9444 > select subtract #5.6
    9445 
    9446 98 atoms, 94 bonds, 6 residues, 4 models selected 
    9447 
    9448 > select subtract #5.5
    9449 
    9450 82 atoms, 79 bonds, 5 residues, 3 models selected 
    9451 
    9452 > select subtract #5.3
    9453 
    9454 1 model selected 
    9455 
    9456 > select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54
    9457 
    9458 169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 2 models selected 
    9459 
    9460 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    9461 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    9462 
    9463 > hide sel atoms
    9464 
    9465 > select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54
    9466 
    9467 202 atoms, 194 bonds, 40 pseudobonds, 13 residues, 2 models selected 
    9468 
    9469 > hide sel atoms
    9470 
    9471 > show sel atoms
    9472 
    9473 > select H
    9474 
    9475 14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected 
    9476 
    9477 > hide sel & #!5-6 atoms
    9478 
    9479 > style sel & #!5-6 stick
    9480 
    9481 Changed 14343 atom styles 
    9482 
    9483 > select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54
    9484 
    9485 202 atoms, 194 bonds, 40 pseudobonds, 13 residues, 2 models selected 
    9486 
    9487 > style sel stick
    9488 
    9489 Changed 202 atom styles 
    9490 
    9491 > select #5/F:Cys
    9492 
    9493 88 atoms, 80 bonds, 8 residues, 1 model selected 
    9494 
    9495 > select #5/F:Cys|#6:Cys
    9496 
    9497 168 atoms, 152 bonds, 16 residues, 2 models selected 
    9498 
    9499 > ui tool show Matchmaker
    9500 
    9501 > matchmaker #!6 & sel to #5/B & sel pairing bs
    9502 
    9503 No 'to' chains specified 
    9504 
    9505 > ui tool show Matchmaker
    9506 
    9507 > matchmaker #!6 & sel to #5/F & sel pairing bs
    9508 
    9509 Parameters 
    9510 --- 
    9511 Chain pairing | bs 
    9512 Alignment algorithm | Needleman-Wunsch 
    9513 Similarity matrix | BLOSUM-62 
    9514 SS fraction | 0.3 
    9515 Gap open (HH/SS/other) | 18/18/6 
    9516 Gap extend | 1 
    9517 SS matrix |  |  | H | S | O 
    9518 ---|---|---|--- 
    9519 H | 6 | -9 | -6 
    9520 S |  | 6 | -6 
    9521 O |  |  | 4 
    9522 Iteration cutoff | 2 
    9523  
    9524 Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
    9525 sequence alignment score = 48 
    9526 RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
    9527 1.008) 
    9528  
    9529 
    9530 > select #6:Cys
    9531 
    9532 80 atoms, 72 bonds, 8 residues, 1 model selected 
    9533 
    9534 > show sel atoms
    9535 
    9536 > select #5:11-14
    9537 
    9538 355 atoms, 352 bonds, 24 residues, 1 model selected 
    9539 
    9540 > show sel atoms
    9541 
    9542 > style sel stick
    9543 
    9544 Changed 355 atom styles 
    9545 
    9546 > hide #!6 models
    9547 
    9548 > select H
    9549 
    9550 14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected 
    9551 
    9552 > hide (#!5 & sel) target a
    9553 
    9554 > show #!6 models
    9555 
    9556 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    9557 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    9558 
    9559 ——— End of log from Fri Oct 4 09:37:44 2024 ———
    9560 
    9561 opened ChimeraX session 
    9562 
    9563 > select #5/F:13
    9564 
    9565 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9566 
    9567 > ui tool show Rotamers
    9568 
    9569 > swapaa interactive sel CYH rotLib Dunbrack
    9570 
    9571 relaxed_structure.pdb #5/F CYS 13: phi -84.1, psi 65.7 trans 
    9572 Changed 9 bond radii 
    9573 
    9574 > swapaa #!5/F:13 CYH criteria 2 rotLib Dunbrack
    9575 
    9576 Using Dunbrack library 
    9577 relaxed_structure.pdb #!5/F CYS 13: phi -84.1, psi 65.7 trans 
    9578 Applying CYS rotamer (chi angles: -178.7) to relaxed_structure.pdb #!5/F CYS
    9579 13 
    9580 
    9581 > select #6:Cys
    9582 
    9583 80 atoms, 72 bonds, 8 residues, 1 model selected 
    9584 
    9585 > hide sel atoms
    9586 
    9587 > view front
    9588 
    9589 > hide #!6 models
    9590 
    9591 > show #!6 models
    9592 
    9593 > select #5/F:Cys|#6:Cys
    9594 
    9595 165 atoms, 149 bonds, 16 residues, 2 models selected 
    9596 
    9597 > ui tool show Matchmaker
    9598 
    9599 > matchmaker #!6 & sel to #5/F & sel pairing bs
    9600 
    9601 Parameters 
    9602 --- 
    9603 Chain pairing | bs 
    9604 Alignment algorithm | Needleman-Wunsch 
    9605 Similarity matrix | BLOSUM-62 
    9606 SS fraction | 0.3 
    9607 Gap open (HH/SS/other) | 18/18/6 
    9608 Gap extend | 1 
    9609 SS matrix |  |  | H | S | O 
    9610 ---|---|---|--- 
    9611 H | 6 | -9 | -6 
    9612 S |  | 6 | -6 
    9613 O |  |  | 4 
    9614 Iteration cutoff | 2 
    9615  
    9616 Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
    9617 sequence alignment score = 48 
    9618 RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
    9619 1.008) 
    9620  
    9621 
    9622 > view front
    9623 
    9624 > matchmaker #!6 & sel to #5/F & sel pairing bs
    9625 
    9626 Parameters 
    9627 --- 
    9628 Chain pairing | bs 
    9629 Alignment algorithm | Needleman-Wunsch 
    9630 Similarity matrix | BLOSUM-62 
    9631 SS fraction | 0.3 
    9632 Gap open (HH/SS/other) | 18/18/6 
    9633 Gap extend | 1 
    9634 SS matrix |  |  | H | S | O 
    9635 ---|---|---|--- 
    9636 H | 6 | -9 | -6 
    9637 S |  | 6 | -6 
    9638 O |  |  | 4 
    9639 Iteration cutoff | 2 
    9640  
    9641 Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
    9642 sequence alignment score = 48 
    9643 RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
    9644 1.008) 
    9645  
    9646 
    9647 > view front
    9648 
    9649 > matchmaker #!6 & sel to #5/F & sel pairing bs
    9650 
    9651 Parameters 
    9652 --- 
    9653 Chain pairing | bs 
    9654 Alignment algorithm | Needleman-Wunsch 
    9655 Similarity matrix | BLOSUM-62 
    9656 SS fraction | 0.3 
    9657 Gap open (HH/SS/other) | 18/18/6 
    9658 Gap extend | 1 
    9659 SS matrix |  |  | H | S | O 
    9660 ---|---|---|--- 
    9661 H | 6 | -9 | -6 
    9662 S |  | 6 | -6 
    9663 O |  |  | 4 
    9664 Iteration cutoff | 2 
    9665  
    9666 Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
    9667 sequence alignment score = 48 
    9668 RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
    9669 1.008) 
    9670  
    9671 
    9672 > view name front
    9673 
    9674 > turn y 180
    9675 
    9676 > view front
    9677 
    9678 > turn y 180
    9679 
    9680 > turn x 30
    9681 
    9682 > show #5.1 models
    9683 
    9684 > show #5.2 models
    9685 
    9686 > show #5.3 models
    9687 
    9688 > show #5.4 models
    9689 
    9690 > show #5.5 models
    9691 
    9692 > hide #5.5 models
    9693 
    9694 > show #5.5 models
    9695 
    9696 > show #5.6 models
    9697 
    9698 > hide #5.3 models
    9699 
    9700 > hide #5.4 models
    9701 
    9702 > coulombic #5/F surfaces #5.6
    9703 
    9704 Using Amber 20 recommended default charges and atom types for standard
    9705 residues 
    9706 Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum,
    9707 -13.91, mean -3.63, maximum 7.03 
    9708 
    9709 > show #5.3 models
    9710 
    9711 > show #5.4 models
    9712 
    9713 > hide #5.4 models
    9714 
    9715 > hide #5.3 models
    9716 
    9717 > transparency (#!5-6 & sel) 30
    9718 
    9719 > select clear
    9720 
    9721 > select add #5.6
    9722 
    9723 844 atoms, 61 residues, 1 model selected 
    9724 
    9725 > transparency (#!5 & sel) 30
    9726 
    9727 > select clear
    9728 
    9729 > view name back
    9730 
    9731 > help help:user
    9732 
    9733 > view list
    9734 
    9735 Named views: back, front, hbond1, hbond2, hbond3 
    9736 
    9737 > view delete hbond1 hbond2 hbond3
    9738 
    9739 Expected fewer arguments 
    9740 
    9741 > view list
    9742 
    9743 Named views: back, front, hbond1, hbond2, hbond3 
    9744 
    9745 > help help:user
    9746 
    9747 > view delete hbond1
    9748 
    9749 > view delete hbond2
    9750 
    9751 > view delete hbond3
    9752 
    9753 > view list
    9754 
    9755 Named views: back, front 
    9756 
    9757 > view front
    9758 
    9759 > hide #5.5 models
    9760 
    9761 > hide #5.6 models
    9762 
    9763 > view back
    9764 
    9765 > show #5.8 models
    9766 
    9767 > select add #5.8
    9768 
    9769 160 pseudobonds, 1 model selected 
    9770 
    9771 > select subtract #5.7
    9772 
    9773 160 pseudobonds, 1 model selected 
    9774 
    9775 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    9776 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    9777 
    9778 ——— End of log from Fri Oct 4 10:09:32 2024 ———
    9779 
    9780 opened ChimeraX session 
    9781 
    9782 > select #5/A-E
    9783 
    9784 27646 atoms, 28113 bonds, 1765 residues, 1 model selected 
    9785 
    9786 > select #5/A-E &~H
    9787 
    9788 13989 atoms, 14456 bonds, 1765 residues, 1 model selected 
    9789 
    9790 > ui tool show Contacts
    9791 
    9792 > contacts sel setAttrs true restrict "#5/F &~H" resSeparation 5 interModel
    9793 > false intraMol false select true color #76d6ff radius 0.2 reveal true log
    9794 > true
    9795    
    9796    
    9797     Allowed overlap: -0.4
    9798     H-bond overlap reduction: 0.4
    9799     Ignore contacts between atoms separated by 4 bonds or less
    9800     Ignore contacts between atoms in residues less than 5 apart in sequence
    9801     Detect intra-residue contacts: False
    9802     Detect intra-molecule contacts: False
    9803    
    9804     66 contacts
    9805                     atom1                                  atom2                  overlap  distance
    9806     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 CD    0.340    2.985
    9807     relaxed_structure.pdb #5/C PRO 58 CB   relaxed_structure.pdb #5/F ILE 11 CD1   0.169    3.231
    9808     relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F GLY 14 N     0.152    3.098
    9809     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 CD    0.062    3.263
    9810     relaxed_structure.pdb #5/A ARG 27 CZ   relaxed_structure.pdb #5/F ASP 30 OD1   0.055    3.125
    9811     relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 OD1   0.038    2.667
    9812     relaxed_structure.pdb #5/C GLN 15 CD   relaxed_structure.pdb #5/F SER 12 O     0.034    3.146
    9813     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE1   0.032    2.673
    9814     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 OD2   0.025    2.680
    9815     relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 OD1   0.020    2.685
    9816     relaxed_structure.pdb #5/C LYS 34 C    relaxed_structure.pdb #5/F GLY 50 O     0.019    3.161
    9817     relaxed_structure.pdb #5/C PRO 58 CG   relaxed_structure.pdb #5/F ILE 11 CD1   0.015    3.385
    9818     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE2   0.011    2.694
    9819     relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 CD     -0.001    3.201
    9820     relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 NH2   -0.023    2.728
    9821     relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 OE2   -0.028    2.733
    9822     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F GLU 9 OE1    -0.044    2.749
    9823     relaxed_structure.pdb #5/C ARG 18 CZ   relaxed_structure.pdb #5/F GLY 14 O     -0.062    3.242
    9824     relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 CG    -0.076    3.401
    9825     relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 CZ    -0.080    3.260
    9826     relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 OE2    -0.082    2.662
    9827     relaxed_structure.pdb #5/E SER 53 C    relaxed_structure.pdb #5/F GLU 9 OE2    -0.087    3.267
    9828     relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F ALA 15 N     -0.094    3.344
    9829     relaxed_structure.pdb #5/C ARG 18 CZ   relaxed_structure.pdb #5/F GLU 17 OE2   -0.103    3.283
    9830     relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F GLY 14 C     -0.122    3.447
    9831     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F PRO 18 O     -0.123    2.828
    9832     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE1   -0.132    2.837
    9833     relaxed_structure.pdb #5/C ILE 11 CG1  relaxed_structure.pdb #5/F PRO 53 CB    -0.134    3.534
    9834     relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F PRO 18 CG    -0.138    3.463
    9835     relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 NH1   -0.139    2.844
    9836     relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F MET 54 CE    -0.150    3.350
    9837     relaxed_structure.pdb #5/C GLN 15 CG   relaxed_structure.pdb #5/F SER 12 O     -0.153    3.333
    9838     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F ALA 7 O      -0.157    2.862
    9839     relaxed_structure.pdb #5/C ILE 11 CD1  relaxed_structure.pdb #5/F PRO 53 CB    -0.177    3.577
    9840     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F THR 8 CA     -0.185    3.510
    9841     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE2   -0.203    2.908
    9842     relaxed_structure.pdb #5/E THR 54 O    relaxed_structure.pdb #5/F MET 54 CE    -0.206    3.386
    9843     relaxed_structure.pdb #5/C GLN 15 OE1  relaxed_structure.pdb #5/F SER 12 O     -0.206    3.166
    9844     relaxed_structure.pdb #5/C GLN 15 CD   relaxed_structure.pdb #5/F GLY 14 N     -0.207    3.532
    9845     relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F GLY 14 CA    -0.208    3.533
    9846     relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 NE    -0.215    2.940
    9847     relaxed_structure.pdb #5/C ILE 11 CD1  relaxed_structure.pdb #5/F MET 54 SD    -0.218    3.700
    9848     relaxed_structure.pdb #5/C LYS 34 CB   relaxed_structure.pdb #5/F GLY 50 O     -0.221    3.401
    9849     relaxed_structure.pdb #5/C ILE 11 O    relaxed_structure.pdb #5/F PRO 53 CB    -0.230    3.410
    9850     relaxed_structure.pdb #5/E THR 54 CG2  relaxed_structure.pdb #5/F GLU 9 OE1    -0.230    3.410
    9851     relaxed_structure.pdb #5/E SER 53 CA   relaxed_structure.pdb #5/F GLU 9 OE2    -0.230    3.410
    9852     relaxed_structure.pdb #5/C CYS 13 CB   relaxed_structure.pdb #5/F PRO 53 CG    -0.231    3.631
    9853     relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 CG    -0.235    3.560
    9854     relaxed_structure.pdb #5/C ALA 35 CA   relaxed_structure.pdb #5/F GLY 50 O     -0.243    3.423
    9855     relaxed_structure.pdb #5/C ILE 11 O    relaxed_structure.pdb #5/F PRO 53 CA    -0.247    3.427
    9856     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 O     -0.269    2.974
    9857     relaxed_structure.pdb #5/E THR 54 N    relaxed_structure.pdb #5/F GLU 9 OE2    -0.285    2.990
    9858     relaxed_structure.pdb #5/E ARG 43 CZ   relaxed_structure.pdb #5/F GLU 9 OE1    -0.291    3.471
    9859     relaxed_structure.pdb #5/E THR 54 CB   relaxed_structure.pdb #5/F GLU 9 OE2    -0.302    3.482
    9860     relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLY 14 O     -0.312    3.017
    9861     relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 CD    -0.314    3.639
    9862     relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 CA    -0.317    3.642
    9863     relaxed_structure.pdb #5/C CYS 13 CB   relaxed_structure.pdb #5/F PRO 53 CB    -0.318    3.718
    9864     relaxed_structure.pdb #5/C CYS 13 O    relaxed_structure.pdb #5/F ALA 15 CB    -0.332    3.512
    9865     relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F CYS 13 C     -0.336    3.661
    9866     relaxed_structure.pdb #5/C ALA 35 CB   relaxed_structure.pdb #5/F VAL 51 CA    -0.340    3.740
    9867     relaxed_structure.pdb #5/E SER 53 N    relaxed_structure.pdb #5/F GLU 9 OE2    -0.349    3.054
    9868     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 CG    -0.369    3.694
    9869     relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 CZ    -0.377    3.577
    9870     relaxed_structure.pdb #5/C ALA 35 N    relaxed_structure.pdb #5/F GLY 50 O     -0.377    3.082
    9871     relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F PRO 18 CD    -0.381    3.706
    9872    
    9873 
    9874  
    9875 66 contacts 
    9876 
    9877 > style sel sphere
    9878 
    9879 Changed 75 atom styles 
    9880 
    9881 > name frozen contacts sel
    9882 
    9883 > select clear
    9884 
    9885 > select contacts
    9886 
    9887 16975 atoms, 38 bonds, 66 pseudobonds, 1093 residues, 2 models selected 
    9888 
    9889 > help help:user
    9890 
    9891 > help help:user/selectcontacts.html
    9892 
    9893 [Repeated 1 time(s)]
    9894 
    9895 > interfaces select #5/A & ::polymer_type>0 contacting #5/F & ::polymer_type>0
    9896 > areaCutoff 0
    9897 
    9898 4 contacting residues 
    9899 
    9900 > select contacts
    9901 
    9902 16975 atoms, 38 bonds, 66 pseudobonds, 1093 residues, 2 models selected 
    9903 
    9904 > style sel stick
    9905 
    9906 Changed 16975 atom styles 
    9907 
    9908 > hide #5.8 models
    9909 
    9910 > select subtract #5.8
    9911 
    9912 16975 atoms, 38 bonds, 1093 residues, 6 models selected 
    9913 
    9914 > close #5.8
    9915 
    9916 > hide #5.9 models
    9917 
    9918 > show #5.9 models
    9919 
    9920 > close #5.9
    9921 
    9922 > close #5.7
    9923 
    9924 > ui tool show H-Bonds
    9925 
    9926 > select #5/A-E
    9927 
    9928 27646 atoms, 28113 bonds, 1765 residues, 1 model selected 
    9929 
    9930 > hbonds sel color #0096ff restrict #5/F interModel false intraMol false
    9931 > intraRes false reveal true log true
    9932    
    9933    
    9934     Finding intramodel H-bonds
    9935     Constraints relaxed by 0.4 angstroms and 20 degrees
    9936     Models used:
    9937         5 relaxed_structure.pdb
    9938    
    9939     19 H-bonds
    9940     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9941     relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH11  2.685  1.767
    9942     relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH21  2.667  1.732
    9943     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 O    relaxed_structure.pdb #5/A LYS 31 HZ1   2.974  2.326
    9944     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 OD2  relaxed_structure.pdb #5/A LYS 31 HZ2   2.680  1.727
    9945     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE1  relaxed_structure.pdb #5/C ARG 18 HH11  2.837  1.944
    9946     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH11  2.908  2.025
    9947     relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH22  2.733  1.757
    9948     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F PRO 18 O    relaxed_structure.pdb #5/D LYS 109 HZ1  2.828  1.934
    9949     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE1  relaxed_structure.pdb #5/D LYS 109 HZ2  2.673  1.723
    9950     relaxed_structure.pdb #5/E ARG 43 NE   relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HE    3.322  2.487
    9951     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F ALA 7 O     relaxed_structure.pdb #5/E ARG 43 HH22  2.862  1.867
    9952     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HH21  2.749  1.745
    9953     relaxed_structure.pdb #5/E SER 53 N    relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E SER 53 H     3.054  2.189
    9954     relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E THR 54 HG1   2.662  1.709
    9955     relaxed_structure.pdb #5/F CYS 13 SG   relaxed_structure.pdb #5/C CYS 13 O    no hydrogen                             3.816  N/A
    9956     relaxed_structure.pdb #5/F ARG 32 NE   relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HE    2.940  1.942
    9957     relaxed_structure.pdb #5/F ARG 32 NH1  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH12  2.844  1.934
    9958     relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HH21  3.342  2.567
    9959     relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH22  2.728  1.772
    9960    
    9961 
    9962  
    9963 19 hydrogen bonds found 
    9964 
    9965 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
    9966 
    9967 272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected 
    9968 
    9969 > select H
    9970 
    9971 14612 atoms, 1922 residues, 3 models selected 
    9972 
    9973 > hide sel & #!5-6 atoms
    9974 
    9975 > select #5/A-E
    9976 
    9977 27646 atoms, 28113 bonds, 1765 residues, 1 model selected 
    9978 
    9979 > hbonds sel color #0096ff restrict #5/F interModel false intraMol false
    9980 > intraRes false reveal true log true
    9981    
    9982    
    9983     Finding intramodel H-bonds
    9984     Constraints relaxed by 0.4 angstroms and 20 degrees
    9985     Models used:
    9986         5 relaxed_structure.pdb
    9987    
    9988     19 H-bonds
    9989     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9990     relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH11  2.685  1.767
    9991     relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH21  2.667  1.732
    9992     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 O    relaxed_structure.pdb #5/A LYS 31 HZ1   2.974  2.326
    9993     relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 OD2  relaxed_structure.pdb #5/A LYS 31 HZ2   2.680  1.727
    9994     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE1  relaxed_structure.pdb #5/C ARG 18 HH11  2.837  1.944
    9995     relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH11  2.908  2.025
    9996     relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH22  2.733  1.757
    9997     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F PRO 18 O    relaxed_structure.pdb #5/D LYS 109 HZ1  2.828  1.934
    9998     relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE1  relaxed_structure.pdb #5/D LYS 109 HZ2  2.673  1.723
    9999     relaxed_structure.pdb #5/E ARG 43 NE   relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HE    3.322  2.487
    10000     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F ALA 7 O     relaxed_structure.pdb #5/E ARG 43 HH22  2.862  1.867
    10001     relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HH21  2.749  1.745
    10002     relaxed_structure.pdb #5/E SER 53 N    relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E SER 53 H     3.054  2.189
    10003     relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E THR 54 HG1   2.662  1.709
    10004     relaxed_structure.pdb #5/F CYS 13 SG   relaxed_structure.pdb #5/C CYS 13 O    no hydrogen                             3.816  N/A
    10005     relaxed_structure.pdb #5/F ARG 32 NE   relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HE    2.940  1.942
    10006     relaxed_structure.pdb #5/F ARG 32 NH1  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH12  2.844  1.934
    10007     relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HH21  3.342  2.567
    10008     relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH22  2.728  1.772
    10009    
    10010 
    10011  
    10012 19 hydrogen bonds found 
    10013 
    10014 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
    10015 
    10016 272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected 
    10017 
    10018 > style sel ball
    10019 
    10020 Changed 272 atom styles 
    10021 
    10022 > style sel stick
    10023 
    10024 Changed 272 atom styles 
    10025 
    10026 > name frozen hBonds sel
    10027 
    10028 [Repeated 1 time(s)]
    10029 
    10030 > help help:user
    10031 
    10032 > name delete all
    10033 
    10034 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
    10035 
    10036 272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected 
    10037 
    10038 > name frozen Hbonds sel
    10039 
    10040 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    10041 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    10042 
    10043 > view front
    10044 
    10045 > interfaces select #5/A & ::polymer_type>0 contacting #5/F & ::polymer_type>0
    10046 > areaCutoff 0
    10047 
    10048 4 contacting residues 
    10049 
    10050 > hide #5.1 models
    10051 
    10052 > hide #5.2 models
    10053 
    10054 > interfaces select #5/B & ::polymer_type>0 contacting #5/F & ::polymer_type>0
    10055 > areaCutoff 0
    10056 
    10057 0 contacting residues 
    10058 
    10059 > interfaces select #5/C & ::polymer_type>0 contacting #5/F & ::polymer_type>0
    10060 > areaCutoff 0
    10061 
    10062 9 contacting residues 
    10063 
    10064 > help help:user
    10065 
    10066 > info residues sel
    10067 
    10068 residue id #5/C:11 name ILE index 10 
    10069 residue id #5/C:13 name CYS index 12 
    10070 residue id #5/C:14 name THR index 13 
    10071 residue id #5/C:15 name GLN index 14 
    10072 residue id #5/C:18 name ARG index 17 
    10073 residue id #5/C:34 name LYS index 33 
    10074 residue id #5/C:35 name ALA index 34 
    10075 residue id #5/C:37 name GLN index 36 
    10076 residue id #5/C:58 name PRO index 57 
    10077 
    10078 > interfaces select #5/C#5/F & ::polymer_type>0 contacting #1/1 &
    10079 > ::polymer_type>0 areaCutoff 0
    10080 
    10081 0 contacting residues 
    10082 
    10083 > interfaces select #5/F & ::polymer_type>0 contacting #5/C & ::polymer_type>0
    10084 > areaCutoff 0
    10085 
    10086 10 contacting residues 
    10087 
    10088 > interfaces select #5/F & ::polymer_type>0 contacting #5/A#5/B#5/C#5/D &
    10089 > ::polymer_type>0 areaCutoff 0
    10090 
    10091 15 contacting residues 
    10092 
    10093 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    10094 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    10095 
    10096 > info residues sel
    10097 
    10098 residue id #5/F:11 name ILE index 10 
    10099 residue id #5/F:12 name SER index 11 
    10100 residue id #5/F:13 name CYS index 12 
    10101 residue id #5/F:14 name GLY index 13 
    10102 residue id #5/F:15 name ALA index 14 
    10103 residue id #5/F:17 name GLU index 16 
    10104 residue id #5/F:18 name PRO index 17 
    10105 residue id #5/F:19 name GLU index 18 
    10106 residue id #5/F:30 name ASP index 29 
    10107 residue id #5/F:31 name GLY index 30 
    10108 residue id #5/F:32 name ARG index 31 
    10109 residue id #5/F:50 name GLY index 49 
    10110 residue id #5/F:51 name VAL index 50 
    10111 residue id #5/F:53 name PRO index 52 
    10112 residue id #5/F:54 name MET index 53 
    10113 
    10114 > select #5/F:11-15,19,29,31,49,50,52,53
    10115 
    10116 131 atoms, 126 bonds, 12 residues, 1 model selected 
    10117 
    10118 > select #5/F:11-15,29,31,49,50,52,53
    10119 
    10120 116 atoms, 112 bonds, 11 residues, 1 model selected 
    10121 
    10122 > select #5/F:11-15,29,31,49,50,52,53
    10123 
    10124 116 atoms, 112 bonds, 11 residues, 1 model selected 
    10125 
    10126 > ui tool show "Selection Inspector"
    10127 
    10128 > setattr sel r ribbon_hide_backbone false
    10129 
    10130 Assigning ribbon_hide_backbone attribute to 11 items 
    10131 
    10132 > select #5/F:11-15,29,31,49,50,52,53
    10133 
    10134 116 atoms, 112 bonds, 11 residues, 1 model selected 
    10135 
    10136 > name frozen buriedFchain sel
    10137 
    10138 > style sel sphere
    10139 
    10140 Changed 116 atom styles 
    10141 
    10142 > interfaces select #5/A#5/B#5/C#5/D#5/E & ::polymer_type>0 contacting #5/F &
    10143 > ::polymer_type>0 areaCutoff 0
    10144 
    10145 20 contacting residues 
    10146 
    10147 > info residues sel
    10148 
    10149 residue id #5/A:27 name ARG index 26 
    10150 residue id #5/A:28 name THR index 27 
    10151 residue id #5/A:31 name LYS index 30 
    10152 residue id #5/A:34 name ASP index 33 
    10153 residue id #5/C:11 name ILE index 10 
    10154 residue id #5/C:13 name CYS index 12 
    10155 residue id #5/C:14 name THR index 13 
    10156 residue id #5/C:15 name GLN index 14 
    10157 residue id #5/C:18 name ARG index 17 
    10158 residue id #5/C:34 name LYS index 33 
    10159 residue id #5/C:35 name ALA index 34 
    10160 residue id #5/C:37 name GLN index 36 
    10161 residue id #5/C:58 name PRO index 57 
    10162 residue id #5/D:109 name LYS index 108 
    10163 residue id #5/E:41 name VAL index 40 
    10164 residue id #5/E:43 name ARG index 42 
    10165 residue id #5/E:51 name ASN index 50 
    10166 residue id #5/E:52 name VAL index 51 
    10167 residue id #5/E:54 name THR index 53 
    10168 residue id #5/E:56 name ASN index 55 
    10169 
    10170 > select #5/C:11,13-15,34-37,58/E:41,51-52,56
    10171 
    10172 206 atoms, 200 bonds, 13 residues, 1 model selected 
    10173 
    10174 > show sel atoms
    10175 
    10176 > style sel sphere
    10177 
    10178 Changed 206 atom styles 
    10179 
    10180 > select H
    10181 
    10182 14612 atoms, 1922 residues, 3 models selected 
    10183 
    10184 > hide sel & #!5-6 atoms
    10185 
    10186 > select clear
    10187 
    10188 > select #5/C:11,13-15,34-37,58/E:41,51-52,56
    10189 
    10190 206 atoms, 200 bonds, 13 residues, 1 model selected 
    10191 
    10192 > name frozen buriedA_Echain sel
    10193 
    10194 > select clear
    10195 
    10196 > select buriedA_Echain|buriedFChain
    10197 
    10198 Expected an objects specifier or a keyword 
    10199 
    10200 > select buriedA_Echain | buriedFChain
    10201 
    10202 Expected a keyword 
    10203 
    10204 > select buriedA_Echain
    10205 
    10206 2273 atoms, 200 bonds, 146 residues, 1 model selected 
    10207 
    10208 > select buriedA_Echain | buriedFchain
    10209 
    10210 3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected 
    10211 
    10212 > select buriedA_Echain
    10213 
    10214 2273 atoms, 200 bonds, 146 residues, 1 model selected 
    10215 
    10216 > select buriedA_Echain | buriedFchain
    10217 
    10218 3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected 
    10219 
    10220 > select Hbonds
    10221 
    10222 16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected 
    10223 
    10224 > show sel atoms
    10225 
    10226 > hide sel atoms
    10227 
    10228 > select buriedA_Echain | buriedFchain
    10229 
    10230 3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected 
    10231 
    10232 > name frozen A_EinterfaceF sel
    10233 
    10234 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
    10235 
    10236 272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected 
    10237 
    10238 > show sel atoms
    10239 
    10240 > select #5/C:Cys/F:Cys &~H &~/C:33
    10241 
    10242 96 atoms, 157 bonds, 1 pseudobond, 16 residues, 2 models selected 
    10243 
    10244 > show sel atoms
    10245 
    10246 > select buriedA_Echain | buriedFchain
    10247 
    10248 3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected 
    10249 
    10250 > select buriedA_Echain
    10251 
    10252 2273 atoms, 200 bonds, 146 residues, 1 model selected 
    10253 
    10254 > select #5/C:11,13-15,34-37,58/E:41,51-52,56
    10255 
    10256 206 atoms, 200 bonds, 13 residues, 1 model selected 
    10257 
    10258 > select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53
    10259 
    10260 322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected 
    10261 
    10262 > select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H
    10263 
    10264 162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected 
    10265 
    10266 > show sel atoms
    10267 
    10268 > view front
    10269 
    10270 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    10271 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    10272 
    10273 > name delete all
    10274 
    10275 > select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H
    10276 
    10277 162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected 
    10278 
    10279 > name frozen interfaceNoHB sel
    10280 
    10281 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
    10282 
    10283 272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected 
    10284 
    10285 > name frozen interfaceHB sel
    10286 
    10287 > select interfaceHB
    10288 
    10289 16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected 
    10290 
    10291 > style sel ball
    10292 
    10293 Changed 16975 atom styles 
    10294 
    10295 > style sel sphere
    10296 
    10297 Changed 16975 atom styles 
    10298 
    10299 > select interfaceHB
    10300 
    10301 16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected 
    10302 
    10303 > style sel stick
    10304 
    10305 Changed 16975 atom styles 
    10306 
    10307 > select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H
    10308 
    10309 162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected 
    10310 
    10311 > style sel sphere
    10312 
    10313 Changed 162 atom styles 
    10314 
    10315 > select clear
    10316 
    10317 > view front
    10318 
    10319 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    10320 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    10321 
    10322 > show #5.1 models
    10323 
    10324 > show #5.2 models
    10325 
    10326 > show #5.3 models
    10327 
    10328 > show #5.4 models
    10329 
    10330 > show #5.5 models
    10331 
    10332 > show #5.6 models
    10333 
    10334 > view front
    10335 
    10336 > hide #8.1 models
    10337 
    10338 > ui tool show "Color Key"
    10339 
    10340 > ui mousemode right "color key"
    10341 
    10342 > key blue-white-red :min : :+
    10343 
    10344 > key blue-white-red :min :0 :+
    10345 
    10346 > key blue-white-red :+ :0 :+
    10347 
    10348 > key blue-white-red :+ :0 :-
    10349 
    10350 > key bold true
    10351 
    10352 > key fontSize 23
    10353 
    10354 > key fontSize 22
    10355 
    10356 > key fontSize 21
    10357 
    10358 > key fontSize 20
    10359 
    10360 > key fontSize 19
    10361 
    10362 > key fontSize 18
    10363 
    10364 > key fontSize 17
    10365 
    10366 > key fontSize 16
    10367 
    10368 > key fontSize 15
    10369 
    10370 > key fontSize 14
    10371 
    10372 > key fontSize 13
    10373 
    10374 > key fontSize 14
    10375 
    10376 > key fontSize 15
    10377 
    10378 > key fontSize 16
    10379 
    10380 > key ticks true
    10381 
    10382 > key tickLength 8.0
    10383 
    10384 > key tickThickness 3.0
    10385 
    10386 > key tickLength 6.0
    10387 
    10388 > key tickLength 4.0
    10389 
    10390 > key tickLength 2.0
    10391 
    10392 > key tickLength 0.0
    10393 
    10394 > key tickLength 2.0
    10395 
    10396 > key tickLength 4.0
    10397 
    10398 > key size 0.25000,0.04000
    10399 
    10400 > key size 0.25000,0.03000
    10401 
    10402 > key size 0.25000,0.02000
    10403 
    10404 > key size 0.25000,0.01000
    10405 
    10406 > key pos 0.71000,0.08000
    10407 
    10408 > key pos 0.70000,0.08000
    10409 
    10410 > key pos 0.69000,0.08000
    10411 
    10412 > key pos 0.68000,0.08000
    10413 
    10414 > key pos 0.67000,0.08000
    10415 
    10416 > key pos 0.66000,0.08000
    10417 
    10418 > key pos 0.65000,0.08000
    10419 
    10420 > key pos 0.64000,0.08000
    10421 
    10422 > key pos 0.63000,0.08000
    10423 
    10424 > key pos 0.62000,0.08000
    10425 
    10426 > key pos 0.61000,0.08000
    10427 
    10428 > key pos 0.60000,0.08000
    10429 
    10430 > key pos 0.59000,0.08000
    10431 
    10432 > key pos 0.58000,0.08000
    10433 
    10434 > key pos 0.57000,0.08000
    10435 
    10436 > key pos 0.56000,0.08000
    10437 
    10438 > key pos 0.55000,0.08000
    10439 
    10440 > key pos 0.54000,0.08000
    10441 
    10442 > key pos 0.53000,0.08000
    10443 
    10444 > key pos 0.52000,0.08000
    10445 
    10446 > key pos 0.51000,0.08000
    10447 
    10448 > key pos 0.50000,0.08000
    10449 
    10450 > key pos 0.49000,0.08000
    10451 
    10452 > key pos 0.48000,0.08000
    10453 
    10454 > key pos 0.47000,0.08000
    10455 
    10456 > key pos 0.46000,0.08000
    10457 
    10458 > key pos 0.45000,0.08000
    10459 
    10460 > key pos 0.44000,0.08000
    10461 
    10462 > key pos 0.43000,0.08000
    10463 
    10464 > key pos 0.42000,0.08000
    10465 
    10466 > key pos 0.41000,0.08000
    10467 
    10468 > key pos 0.40000,0.08000
    10469 
    10470 > key pos 0.39000,0.08000
    10471 
    10472 > key pos 0.38000,0.08000
    10473 
    10474 > key pos 0.37000,0.08000
    10475 
    10476 > key pos 0.36000,0.08000
    10477 
    10478 > key pos 0.35000,0.08000
    10479 
    10480 > key pos 0.34000,0.08000
    10481 
    10482 > key pos 0.33000,0.08000
    10483 
    10484 > key pos 0.32000,0.08000
    10485 
    10486 > key pos 0.31000,0.08000
    10487 
    10488 > key pos 0.30000,0.08000
    10489 
    10490 > key pos 0.29000,0.08000
    10491 
    10492 > key pos 0.28000,0.08000
    10493 
    10494 > key pos 0.27000,0.08000
    10495 
    10496 > key pos 0.26000,0.08000
    10497 
    10498 > key pos 0.25000,0.08000
    10499 
    10500 > key pos 0.24000,0.08000
    10501 
    10502 > key pos 0.23000,0.08000
    10503 
    10504 > key pos 0.22000,0.08000
    10505 
    10506 > key pos 0.21000,0.08000
    10507 
    10508 > key pos 0.20000,0.08000
    10509 
    10510 > key pos 0.19000,0.08000
    10511 
    10512 > key pos 0.18000,0.08000
    10513 
    10514 > key pos 0.17000,0.08000
    10515 
    10516 > key pos 0.16000,0.08000
    10517 
    10518 > key pos 0.15000,0.08000
    10519 
    10520 > key pos 0.14000,0.08000
    10521 
    10522 > key pos 0.13000,0.08000
    10523 
    10524 > key pos 0.12000,0.08000
    10525 
    10526 > key pos 0.11000,0.08000
    10527 
    10528 > key pos 0.10000,0.08000
    10529 
    10530 > key pos 0.09000,0.08000
    10531 
    10532 > key pos 0.08000,0.08000
    10533 
    10534 > key pos 0.07000,0.08000
    10535 
    10536 > key pos 0.06000,0.08000
    10537 
    10538 > key pos 0.05000,0.08000
    10539 
    10540 > key pos 0.04000,0.08000
    10541 
    10542 > key pos 0.03000,0.08000
    10543 
    10544 > key pos 0.02000,0.08000
    10545 
    10546 > key pos 0.02000,0.09000
    10547 
    10548 > key pos 0.02000,0.10000
    10549 
    10550 > key pos 0.02000,0.11000
    10551 
    10552 > key pos 0.02000,0.12000
    10553 
    10554 > key pos 0.02000,0.13000
    10555 
    10556 > key pos 0.02000,0.14000
    10557 
    10558 > key pos 0.02000,0.15000
    10559 
    10560 > key pos 0.02000,0.16000
    10561 
    10562 > key pos 0.02000,0.17000
    10563 
    10564 > key pos 0.02000,0.18000
    10565 
    10566 > key pos 0.02000,0.19000
    10567 
    10568 > key pos 0.02000,0.20000
    10569 
    10570 > key pos 0.02000,0.21000
    10571 
    10572 > key pos 0.02000,0.22000
    10573 
    10574 > key pos 0.02000,0.23000
    10575 
    10576 > key pos 0.02000,0.24000
    10577 
    10578 > key pos 0.02000,0.25000
    10579 
    10580 > key pos 0.02000,0.26000
    10581 
    10582 > key pos 0.02000,0.27000
    10583 
    10584 > key pos 0.02000,0.28000
    10585 
    10586 > key pos 0.02000,0.29000
    10587 
    10588 > key pos 0.02000,0.30000
    10589 
    10590 > key pos 0.02000,0.31000
    10591 
    10592 > key pos 0.02000,0.32000
    10593 
    10594 > key pos 0.02000,0.33000
    10595 
    10596 > key pos 0.02000,0.34000
    10597 
    10598 > key pos 0.02000,0.35000
    10599 
    10600 > key pos 0.02000,0.36000
    10601 
    10602 > key pos 0.02000,0.37000
    10603 
    10604 > key pos 0.02000,0.38000
    10605 
    10606 > key pos 0.02000,0.39000
    10607 
    10608 > key pos 0.02000,0.40000
    10609 
    10610 > key pos 0.02000,0.41000
    10611 
    10612 > key pos 0.02000,0.42000
    10613 
    10614 > key pos 0.02000,0.43000
    10615 
    10616 > key pos 0.02000,0.44000
    10617 
    10618 > key pos 0.02000,0.45000
    10619 
    10620 > key pos 0.02000,0.46000
    10621 
    10622 > key pos 0.02000,0.47000
    10623 
    10624 > key pos 0.02000,0.48000
    10625 
    10626 > key pos 0.02000,0.49000
    10627 
    10628 > key pos 0.02000,0.50000
    10629 
    10630 > key pos 0.02000,0.51000
    10631 
    10632 > key pos 0.02000,0.52000
    10633 
    10634 > key pos 0.02000,0.53000
    10635 
    10636 > key pos 0.02000,0.54000
    10637 
    10638 > key pos 0.02000,0.55000
    10639 
    10640 > key pos 0.02000,0.56000
    10641 
    10642 > key pos 0.02000,0.57000
    10643 
    10644 > key pos 0.02000,0.58000
    10645 
    10646 > key pos 0.02000,0.59000
    10647 
    10648 > key pos 0.02000,0.60000
    10649 
    10650 > key pos 0.02000,0.61000
    10651 
    10652 > key pos 0.02000,0.62000
    10653 
    10654 > key pos 0.02000,0.63000
    10655 
    10656 > key pos 0.02000,0.64000
    10657 
    10658 > key pos 0.02000,0.65000
    10659 
    10660 > key pos 0.02000,0.66000
    10661 
    10662 > key pos 0.02000,0.67000
    10663 
    10664 > key pos 0.02000,0.68000
    10665 
    10666 > key pos 0.02000,0.69000
    10667 
    10668 > key pos 0.02000,0.70000
    10669 
    10670 > key pos 0.02000,0.71000
    10671 
    10672 > key pos 0.02000,0.72000
    10673 
    10674 > key pos 0.02000,0.73000
    10675 
    10676 > key pos 0.02000,0.74000
    10677 
    10678 > key pos 0.02000,0.75000
    10679 
    10680 > key pos 0.02000,0.76000
    10681 
    10682 > key pos 0.02000,0.77000
    10683 
    10684 > key pos 0.02000,0.78000
    10685 
    10686 > key pos 0.02000,0.79000
    10687 
    10688 > key pos 0.02000,0.80000
    10689 
    10690 > key pos 0.02000,0.81000
    10691 
    10692 > key pos 0.02000,0.82000
    10693 
    10694 > key pos 0.02000,0.83000
    10695 
    10696 > key pos 0.02000,0.84000
    10697 
    10698 > key pos 0.02000,0.85000
    10699 
    10700 > key pos 0.02000,0.86000
    10701 
    10702 > key pos 0.02000,0.87000
    10703 
    10704 > key pos 0.02000,0.88000
    10705 
    10706 > key pos 0.02000,0.89000
    10707 
    10708 > key pos 0.02000,0.90000
    10709 
    10710 > key pos 0.02000,0.91000
    10711 
    10712 > key pos 0.02000,0.92000
    10713 
    10714 > key pos 0.02000,0.93000
    10715 
    10716 > key pos 0.02000,0.94000
    10717 
    10718 > key pos 0.02000,0.95000
    10719 
    10720 > key pos 0.02000,0.96000
    10721 
    10722 > key pos 0.02000,0.97000
    10723 
    10724 > key pos 0.02000,0.98000
    10725 
    10726 > key pos 0.03000,0.98000
    10727 
    10728 > key pos 0.04000,0.98000
    10729 
    10730 > key pos 0.05000,0.98000
    10731 
    10732 > key pos 0.06000,0.98000
    10733 
    10734 > key pos 0.07000,0.98000
    10735 
    10736 > key pos 0.08000,0.98000
    10737 
    10738 > key pos 0.09000,0.98000
    10739 
    10740 > key pos 0.10000,0.98000
    10741 
    10742 > key pos 0.11000,0.98000
    10743 
    10744 > key pos 0.12000,0.98000
    10745 
    10746 > key pos 0.13000,0.98000
    10747 
    10748 > key pos 0.14000,0.98000
    10749 
    10750 > key pos 0.15000,0.98000
    10751 
    10752 > key pos 0.16000,0.98000
    10753 
    10754 > key pos 0.17000,0.98000
    10755 
    10756 > key pos 0.18000,0.98000
    10757 
    10758 > key pos 0.19000,0.98000
    10759 
    10760 > key pos 0.20000,0.98000
    10761 
    10762 > key pos 0.21000,0.98000
    10763 
    10764 > key pos 0.22000,0.98000
    10765 
    10766 > key pos 0.23000,0.98000
    10767 
    10768 > key pos 0.24000,0.98000
    10769 
    10770 > key pos 0.25000,0.98000
    10771 
    10772 > key pos 0.26000,0.98000
    10773 
    10774 > key pos 0.27000,0.98000
    10775 
    10776 > key pos 0.28000,0.98000
    10777 
    10778 > key pos 0.29000,0.98000
    10779 
    10780 > key pos 0.30000,0.98000
    10781 
    10782 > key pos 0.31000,0.98000
    10783 
    10784 > key pos 0.32000,0.98000
    10785 
    10786 > key pos 0.33000,0.98000
    10787 
    10788 > key pos 0.34000,0.98000
    10789 
    10790 > key pos 0.35000,0.98000
    10791 
    10792 > key pos 0.36000,0.98000
    10793 
    10794 > key pos 0.37000,0.98000
    10795 
    10796 > key pos 0.38000,0.98000
    10797 
    10798 > key pos 0.39000,0.98000
    10799 
    10800 > key pos 0.40000,0.98000
    10801 
    10802 > key pos 0.41000,0.98000
    10803 
    10804 > key pos 0.42000,0.98000
    10805 
    10806 > key pos 0.43000,0.98000
    10807 
    10808 > key pos 0.44000,0.98000
    10809 
    10810 > key pos 0.45000,0.98000
    10811 
    10812 > key pos 0.46000,0.98000
    10813 
    10814 > key pos 0.47000,0.98000
    10815 
    10816 > key pos 0.48000,0.98000
    10817 
    10818 > key pos 0.49000,0.98000
    10819 
    10820 > key pos 0.50000,0.98000
    10821 
    10822 > key pos 0.51000,0.98000
    10823 
    10824 > key pos 0.52000,0.98000
    10825 
    10826 > key pos 0.53000,0.98000
    10827 
    10828 > key pos 0.54000,0.98000
    10829 
    10830 > key pos 0.55000,0.98000
    10831 
    10832 > key pos 0.56000,0.98000
    10833 
    10834 > key pos 0.57000,0.98000
    10835 
    10836 > key pos 0.58000,0.98000
    10837 
    10838 > key pos 0.59000,0.98000
    10839 
    10840 > key pos 0.60000,0.98000
    10841 
    10842 > key pos 0.61000,0.98000
    10843 
    10844 > key pos 0.62000,0.98000
    10845 
    10846 > key pos 0.63000,0.98000
    10847 
    10848 > key pos 0.64000,0.98000
    10849 
    10850 > key pos 0.65000,0.98000
    10851 
    10852 > key pos 0.66000,0.98000
    10853 
    10854 > key pos 0.67000,0.98000
    10855 
    10856 > key pos 0.68000,0.98000
    10857 
    10858 > key pos 0.69000,0.98000
    10859 
    10860 > key pos 0.70000,0.98000
    10861 
    10862 > key pos 0.71000,0.98000
    10863 
    10864 > key pos 0.72000,0.98000
    10865 
    10866 > key pos 0.73000,0.98000
    10867 
    10868 > key pos 0.74000,0.98000
    10869 
    10870 > key pos 0.73000,0.98000
    10871 
    10872 > ui mousemode right translate
    10873 
    10874 > hide #7 models
    10875 
    10876 > show #7 models
    10877 
    10878 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    10879 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    10880 
    10881 > hide #5.6 models
    10882 
    10883 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
    10884 
    10885 272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected 
    10886 
    10887 > select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H
    10888 
    10889 162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected 
    10890 
    10891 > transparency (#!5 & sel) 80
    10892 
    10893 > transparency (#!5 & sel) 100
    10894 
    10895 > select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53
    10896 
    10897 322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected 
    10898 
    10899 > transparency (#!5 & sel) 100
    10900 
    10901 > select clear
    10902 
    10903 > select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53
    10904 
    10905 322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected 
    10906 
    10907 > transparency (#!5 & sel) 90
    10908 
    10909 > transparency (#!5 & sel) 70
    10910 
    10911 > transparency (#!5 & sel) 100
    10912 
    10913 > hide #5.5 models
    10914 
    10915 > show #5.5 models
    10916 
    10917 > hide #5.5 models
    10918 
    10919 > show #5.5 models
    10920 
    10921 > hide #5.5 models
    10922 
    10923 > show #5.5 models
    10924 
    10925 > hide #5.5 models
    10926 
    10927 > select clear
    10928 
    10929 > show #5.6 models
    10930 
    10931 > hide #5.6 models
    10932 
    10933 > show #5.5 models
    10934 
    10935 > select add #5.6
    10936 
    10937 844 atoms, 61 residues, 1 model selected 
    10938 
    10939 > select add #5.5
    10940 
    10941 1903 atoms, 127 residues, 2 models selected 
    10942 
    10943 > select add #5.4
    10944 
    10945 4180 atoms, 270 residues, 3 models selected 
    10946 
    10947 > select add #5.3
    10948 
    10949 5394 atoms, 350 residues, 4 models selected 
    10950 
    10951 > select add #5.2
    10952 
    10953 16909 atoms, 1083 residues, 5 models selected 
    10954 
    10955 > select add #5.1
    10956 
    10957 28490 atoms, 1826 residues, 6 models selected 
    10958 
    10959 > show #5.6 models
    10960 
    10961 > transparency (#!5 & sel) 30
    10962 
    10963 > select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53
    10964 
    10965 322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected 
    10966 
    10967 > style sel stick
    10968 
    10969 Changed 322 atom styles 
    10970 
    10971 > view front
    10972 
    10973 > select clear
    10974 
    10975 > hide #5.6 models
    10976 
    10977 > show #5.6 models
    10978 
    10979 > hide #5.6 models
    10980 
    10981 > show #5.6 models
    10982 
    10983 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    10984 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    10985 
    10986 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    10987 > MPNN/PSI-Fdx Alt All surfaces front .png" width 1508 height 1200 supersample
    10988 > 3 transparentBackground true
    10989 
    10990 > hide #5.6 models
    10991 
    10992 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    10993 > MPNN/PSI-Fdx Alt no F surface front .png" width 1508 height 1200 supersample
    10994 > 3 transparentBackground true
    10995 
    10996 > show #5.6 models
    10997 
    10998 > hide #5.5 models
    10999 
    11000 > hide #5.4 models
    11001 
    11002 > hide #5.3 models
    11003 
    11004 > view back
    11005 
    11006 > show #5.3 models
    11007 
    11008 > hide #5.3 models
    11009 
    11010 > show #5.5 models
    11011 
    11012 > hide #5.5 models
    11013 
    11014 > trurn y 90
    11015 
    11016 Unknown command: trurn y 90 
    11017 
    11018 > turn y 90
    11019 
    11020 > show #5.3 models
    11021 
    11022 > turn y 30
    11023 
    11024 > view back
    11025 
    11026 [Repeated 1 time(s)]
    11027 
    11028 > turn y 30
    11029 
    11030 [Repeated 1 time(s)]
    11031 
    11032 > turn y 10
    11033 
    11034 > turn x 10
    11035 
    11036 [Repeated 1 time(s)]
    11037 
    11038 > turn y -10
    11039 
    11040 [Repeated 1 time(s)]
    11041 
    11042 > view back
    11043 
    11044 > turn x 10
    11045 
    11046 > turn y 30
    11047 
    11048 [Repeated 1 time(s)]
    11049 
    11050 > turn x 10
    11051 
    11052 > view back
    11053 
    11054 > turn x 60
    11055 
    11056 > turn y 60
    11057 
    11058 > turn y -30
    11059 
    11060 > view back
    11061 
    11062 > turn x 10
    11063 
    11064 > turn y 40
    11065 
    11066 > turn y 10
    11067 
    11068 > turn x 10
    11069 
    11070 > view back
    11071 
    11072 > turn y 50
    11073 
    11074 > turn x 20
    11075 
    11076 > show #5.4 models
    11077 
    11078 > show #5.5 models
    11079 
    11080 > view name side
    11081 
    11082 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11083 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11084 
    11085 > hide #5.6 models
    11086 
    11087 > hide #5.5 models
    11088 
    11089 > hide #5.4 models
    11090 
    11091 > hide #5.3 models
    11092 
    11093 > show #5.5 models
    11094 
    11095 > hide #5.5 models
    11096 
    11097 > show #5.5 models
    11098 
    11099 > show #5.6 models
    11100 
    11101 > show #5.4 models
    11102 
    11103 > show #5.3 models
    11104 
    11105 > view front
    11106 
    11107 > view side
    11108 
    11109 > view front
    11110 
    11111 > hide #5.5 models
    11112 
    11113 > show #5.5 models
    11114 
    11115 > view side
    11116 
    11117 > view front
    11118 
    11119 > hide #5.6 models
    11120 
    11121 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54
    11122 
    11123 167 atoms, 160 bonds, 9 residues, 1 model selected 
    11124 
    11125 > transparency (#!5 & sel) 80
    11126 
    11127 > select clear
    11128 
    11129 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54
    11130 
    11131 167 atoms, 160 bonds, 9 residues, 1 model selected 
    11132 
    11133 > transparency (#!5 & sel) 90
    11134 
    11135 > select clear
    11136 
    11137 > turn x 10
    11138 
    11139 > turn x -10
    11140 
    11141 > turn x 5
    11142 
    11143 > turn x -5
    11144 
    11145 > view side
    11146 
    11147 > view front
    11148 
    11149 [Repeated 1 time(s)]
    11150 
    11151 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11152 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11153 
    11154 > turn x 5
    11155 
    11156 > turn y 5
    11157 
    11158 > turn x 5
    11159 
    11160 [Repeated 1 time(s)]
    11161 
    11162 > turn y -5
    11163 
    11164 > view front
    11165 
    11166 > turn x 15
    11167 
    11168 > show #5.6 models
    11169 
    11170 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11171 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11172 
    11173 > select add #5.6
    11174 
    11175 844 atoms, 61 residues, 1 model selected 
    11176 
    11177 > select add #5.5
    11178 
    11179 1903 atoms, 127 residues, 2 models selected 
    11180 
    11181 > select add #5.4
    11182 
    11183 4180 atoms, 270 residues, 3 models selected 
    11184 
    11185 > select add #5.3
    11186 
    11187 5394 atoms, 350 residues, 4 models selected 
    11188 
    11189 > select add #5.2
    11190 
    11191 16909 atoms, 1083 residues, 5 models selected 
    11192 
    11193 > select add #5.1
    11194 
    11195 28490 atoms, 1826 residues, 6 models selected 
    11196 
    11197 > transparency (#!5 & sel) 20
    11198 
    11199 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11200 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11201 
    11202 > hide #5.7 models
    11203 
    11204 > show #5.7 models
    11205 
    11206 > hide #5.6 models
    11207 
    11208 > select clear
    11209 
    11210 > show #5.6 models
    11211 
    11212 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11213 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11214 
    11215 > view name front
    11216 
    11217 > turn y 50
    11218 
    11219 > hide #5.4 models
    11220 
    11221 > show #5.4 models
    11222 
    11223 > hide #5.5 models
    11224 
    11225 > show #5.5 models
    11226 
    11227 > view front
    11228 
    11229 > view side
    11230 
    11231 > hide #5.5 models
    11232 
    11233 > show #5.5 models
    11234 
    11235 > hide #5.4 models
    11236 
    11237 > show #5.4 models
    11238 
    11239 > view front
    11240 
    11241 > turn y 60
    11242 
    11243 > hide #5.4 models
    11244 
    11245 > show #5.4 models
    11246 
    11247 > view side
    11248 
    11249 > hide #5.4 models
    11250 
    11251 > view front
    11252 
    11253 > turn y 60
    11254 
    11255 > turn y -60
    11256 
    11257 [Repeated 1 time(s)]
    11258 
    11259 > show #5.4 models
    11260 
    11261 > view front
    11262 
    11263 > hide #5.5 models
    11264 
    11265 > show #5.5 models
    11266 
    11267 > view side
    11268 
    11269 > view front
    11270 
    11271 > view side
    11272 
    11273 > view front
    11274 
    11275 > turn y 90
    11276 
    11277 > hide #5.6 models
    11278 
    11279 > show #5.6 models
    11280 
    11281 > hide #5.6 models
    11282 
    11283 > show #5.6 models
    11284 
    11285 > hide #5.6 models
    11286 
    11287 > show #5.6 models
    11288 
    11289 > view front
    11290 
    11291 > turn x 90
    11292 
    11293 > hide #5.6 models
    11294 
    11295 > show #5.6 models
    11296 
    11297 > view front
    11298 
    11299 > turn 30
    11300 
    11301 Expected an axis vector or a keyword 
    11302 
    11303 > turn y 30
    11304 
    11305 > hide #5.6 models
    11306 
    11307 > show #5.6 models
    11308 
    11309 > hide #5.4 models
    11310 
    11311 > show #5.4 models
    11312 
    11313 > hide #5.5 models
    11314 
    11315 > show #5.5 models
    11316 
    11317 > turn y -30
    11318 
    11319 [Repeated 3 time(s)]
    11320 
    11321 > turn x 30
    11322 
    11323 > turn x 10
    11324 
    11325 > turn x 5
    11326 
    11327 > view front
    11328 
    11329 > turn x 45
    11330 
    11331 > turn x -45
    11332 
    11333 > turn y 30
    11334 
    11335 > view front
    11336 
    11337 > turn y 30
    11338 
    11339 > view front
    11340 
    11341 > turn y -30
    11342 
    11343 > turn x -45
    11344 
    11345 > turn x 45
    11346 
    11347 [Repeated 1 time(s)]
    11348 
    11349 > view front
    11350 
    11351 > turn y -45
    11352 
    11353 > view front
    11354 
    11355 > turn y -45
    11356 
    11357 > turn x 45
    11358 
    11359 > view front
    11360 
    11361 > turn y -50
    11362 
    11363 > turn x -45
    11364 
    11365 > view front
    11366 
    11367 > turn y -50
    11368 
    11369 > turn x 45
    11370 
    11371 > turn x -15
    11372 
    11373 > view front
    11374 
    11375 > turn y -50
    11376 
    11377 > turn x 30
    11378 
    11379 > view front
    11380 
    11381 > turn y -60
    11382 
    11383 > view front
    11384 
    11385 [Repeated 1 time(s)]
    11386 
    11387 > help help:user
    11388 
    11389 > trun 1,1,0 45
    11390 
    11391 Unknown command: trun 1,1,0 45 
    11392 
    11393 > turn 1,1,0 45
    11394 
    11395 > turn 1,1,0 -45
    11396 
    11397 > turn -1,1,0 45
    11398 
    11399 > view front
    11400 
    11401 > turn -1,1,0 -45
    11402 
    11403 > turn y 60
    11404 
    11405 > turn y -60
    11406 
    11407 [Repeated 1 time(s)]
    11408 
    11409 > view front
    11410 
    11411 > view back
    11412 
    11413 > view front
    11414 
    11415 > turn y 180
    11416 
    11417 > turn x 45
    11418 
    11419 > hide #5.4 models
    11420 
    11421 > show #5.4 models
    11422 
    11423 > view front
    11424 
    11425 > turn y 180
    11426 
    11427 > turn x 45
    11428 
    11429 [Repeated 1 time(s)]
    11430 
    11431 > turn x 15
    11432 
    11433 > view front
    11434 
    11435 > turn y 180
    11436 
    11437 > turn x 60
    11438 
    11439 > view front
    11440 
    11441 > turn y 180
    11442 
    11443 > turn x 60
    11444 
    11445 > turn x 30
    11446 
    11447 > view front
    11448 
    11449 > turn x 90
    11450 
    11451 > hide #5.6 models
    11452 
    11453 > show #5.6 models
    11454 
    11455 > view front
    11456 
    11457 > turn x 60
    11458 
    11459 > view front
    11460 
    11461 [Repeated 1 time(s)]
    11462 
    11463 > turn y 180
    11464 
    11465 > turn x 90
    11466 
    11467 > turn x 30
    11468 
    11469 > view front
    11470 
    11471 > turn y 180
    11472 
    11473 > turn x 120
    11474 
    11475 > view front
    11476 
    11477 > turn y 190
    11478 
    11479 > turn x 130
    11480 
    11481 > turn y 10
    11482 
    11483 [Repeated 2 time(s)]
    11484 
    11485 > view front
    11486 
    11487 > turn y 200
    11488 
    11489 > turn x 145
    11490 
    11491 > view front
    11492 
    11493 > turn x 145
    11494 
    11495 > turn y 200
    11496 
    11497 > view front
    11498 
    11499 > view name side
    11500 
    11501 > view front
    11502 
    11503 > hide #5.6 models
    11504 
    11505 > select add #8
    11506 
    11507 1 pseudobond, 2 models selected 
    11508 
    11509 > select subtract #8
    11510 
    11511 Nothing selected 
    11512 
    11513 > select add #8
    11514 
    11515 1 pseudobond, 2 models selected 
    11516 
    11517 > select subtract #8
    11518 
    11519 Nothing selected 
    11520 
    11521 > select add #8
    11522 
    11523 1 pseudobond, 2 models selected 
    11524 
    11525 > select subtract #8
    11526 
    11527 Nothing selected 
    11528 
    11529 > select add #8
    11530 
    11531 1 pseudobond, 2 models selected 
    11532 
    11533 > select subtract #8
    11534 
    11535 Nothing selected 
    11536 
    11537 > select add #8
    11538 
    11539 1 pseudobond, 2 models selected 
    11540 
    11541 > select subtract #8
    11542 
    11543 Nothing selected 
    11544 
    11545 > show #8.1 models
    11546 
    11547 > hide #8.1 models
    11548 
    11549 > select #5/A:27,28,31,34/C:18/D:109/E:43,53,54
    11550 
    11551 167 atoms, 160 bonds, 9 residues, 1 model selected 
    11552 
    11553 > transparency (#!5 & sel) 90
    11554 
    11555 > select clear
    11556 
    11557 > hide #7 models
    11558 
    11559 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11560 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11561 
    11562 > view name HbondsZoom
    11563 
    11564 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11565 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11566 
    11567 > view HbondsZoom
    11568 
    11569 > select #5/C:11,13-15,34-37,58
    11570 
    11571 146 atoms, 143 bonds, 9 residues, 1 model selected 
    11572 
    11573 > select #5/C:11,13-15
    11574 
    11575 61 atoms, 59 bonds, 4 residues, 1 model selected 
    11576 
    11577 > select #5/C:13-15
    11578 
    11579 42 atoms, 41 bonds, 3 residues, 1 model selected 
    11580 
    11581 > transparency (#!5 & sel) 90
    11582 
    11583 > view HbondsZoom
    11584 
    11585 > select #5/C:13-15
    11586 
    11587 42 atoms, 41 bonds, 3 residues, 1 model selected 
    11588 
    11589 > transparency (#!5 & sel) 20
    11590 
    11591 > select #5/C:11
    11592 
    11593 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11594 
    11595 > transparency (#!5 & sel) 90
    11596 
    11597 > select clear
    11598 
    11599 > graphics silhouettes false
    11600 
    11601 > graphics silhouettes true
    11602 
    11603 > view name HbondsZoom
    11604 
    11605 > view front
    11606 
    11607 > view side
    11608 
    11609 > view HbondsZoom
    11610 
    11611 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11612 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11613 
    11614 ——— End of log from Fri Oct 4 15:14:28 2024 ———
    11615 
    11616 opened ChimeraX session 
    11617 
    11618 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    11619 > MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3
    11620 > transparentBackground true
    11621 
    11622 > hide #!8 models
    11623 
    11624 > show #!8 models
    11625 
    11626 > select #6:1-2,8-24,30-47
    11627 
    11628 447 atoms, 448 bonds, 37 residues, 1 model selected 
    11629 
    11630 > select #3/B:1
    11631 
    11632 5 atoms, 4 bonds, 1 residue, 1 model selected 
    11633 
    11634 > select #3/B:1-2
    11635 
    11636 17 atoms, 17 bonds, 2 residues, 1 model selected 
    11637 
    11638 > select #6:1-2,8-24,30-47
    11639 
    11640 447 atoms, 448 bonds, 37 residues, 1 model selected 
    11641 
    11642 > select #3/B:1-2
    11643 
    11644 17 atoms, 17 bonds, 2 residues, 1 model selected 
    11645 
    11646 > select #6:1-2,8-24,30-47
    11647 
    11648 447 atoms, 448 bonds, 37 residues, 1 model selected 
    11649 
    11650 > select #6:1-2,8-24,30-47#5/F:1-2
    11651 
    11652 480 atoms, 481 bonds, 39 residues, 2 models selected 
    11653 
    11654 > select #6:1-2,8-24,30-47#5/F:1-2,8-24
    11655 
    11656 695 atoms, 697 bonds, 56 residues, 2 models selected 
    11657 
    11658 > ui tool show Matchmaker
    11659 
    11660 > matchmaker #!6 to #5/F pairing bs showAlignment true
    11661 
    11662 Parameters 
    11663 --- 
    11664 Chain pairing | bs 
    11665 Alignment algorithm | Needleman-Wunsch 
    11666 Similarity matrix | BLOSUM-62 
    11667 SS fraction | 0.3 
    11668 Gap open (HH/SS/other) | 18/18/6 
    11669 Gap extend | 1 
    11670 SS matrix |  |  | H | S | O 
    11671 ---|---|---|--- 
    11672 H | 6 | -9 | -6 
    11673 S |  | 6 | -6 
    11674 O |  |  | 4 
    11675 Iteration cutoff | 2 
    11676  
    11677 Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
    11678 sequence alignment score = 170.3 
    11679 Alignment identifier is 1 
    11680 Showing conservation header ("seq_conservation" residue attribute) for
    11681 alignment 1 
    11682 Hiding conservation header for alignment 1 
    11683 Chains used in RMSD evaluation for alignment 1: relaxed_structure.pdb #5/F,
    11684 2fdn #6/M 
    11685 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    11686 RMSD between 41 pruned atom pairs is 0.850 angstroms; (across all 54 pairs:
    11687 2.909) 
    11688  
    11689 
    11690 > sequence header 1 consensus show
    11691 
    11692 Showing consensus header ("seq_consensus" residue attribute) for alignment 1 
    11693 
    11694 > select #6:1-2,8-24,30-47#5/F:1-2,10-26
    11695 
    11696 696 atoms, 698 bonds, 56 residues, 2 models selected 
    11697 
    11698 > select #6:1-2,8-24,30-47#5/F:1-2,10-26,35-52
    11699 
    11700 925 atoms, 927 bonds, 74 residues, 2 models selected 
    11701 
    11702 > show sel cartoons
    11703 
    11704 > select #5
    11705 
    11706 28492 atoms, 28966 bonds, 19 pseudobonds, 1826 residues, 2 models selected 
    11707 
    11708 > hide sel cartoons
    11709 
    11710 > show sel cartoons
    11711 
    11712 > select #6
    11713 
    11714 762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected 
    11715 
    11716 > hide sel cartoons
    11717 
    11718 > select #5/F:1-2,10-26,35-52
    11719 
    11720 478 atoms, 479 bonds, 37 residues, 1 model selected 
    11721 
    11722 > color (#!5 & sel) orange
    11723 
    11724 > color sel byhetero
    11725 
    11726 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    11727 > MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3
    11728 > transparentBackground true
    11729 
    11730 > select clear
    11731 
    11732 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
    11733 > MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3
    11734 > transparentBackground true
    11735 
    11736 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11737 > Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
    11738 
    11739 ——— End of log from Sun Oct 6 13:38:31 2024 ———
    11740 
    11741 opened ChimeraX session 
    11742 
    11743 > hide #!1 models
    11744 
    11745 > close #20
    11746 
    11747 > close #8
    11748 
    11749 > close #7
    11750 
    11751 > hide #5.5 models
    11752 
    11753 > hide #5.3 models
    11754 
    11755 > hide #5.2 models
    11756 
    11757 > hide #5.1 models
    11758 
    11759 > hide #5.4 models
    11760 
    11761 > hide #2 models
    11762 
    11763 > show #2 models
    11764 
    11765 > select #2
    11766 
    11767 24 atoms, 36 bonds, 3 residues, 1 model selected 
    11768 
    11769 > select #2 :<3 &#5/A-C:Cys
    11770 
    11771 132 atoms, 120 bonds, 12 residues, 1 model selected 
    11772 
    11773 > show sel atoms
    11774 
    11775 > color sel byhetero
    11776 
    11777 > select #2 :<3 &#5/A-C:Cys &H
    11778 
    11779 60 atoms, 12 residues, 1 model selected 
    11780 
    11781 > hide sel atoms
    11782 
    11783 > select #2 :<3 &#5/A-C:Cys
    11784 
    11785 132 atoms, 120 bonds, 12 residues, 1 model selected 
    11786 
    11787 > style sel stick
    11788 
    11789 Changed 132 atom styles 
    11790 
    11791 > show #!1 models
    11792 
    11793 > hide #2 models
    11794 
    11795 > hide #!5 models
    11796 
    11797 > hide #!1 models
    11798 
    11799 > show #!1 models
    11800 
    11801 > select #1/B:549
    11802 
    11803 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11804 
    11805 > show sel cartoons
    11806 
    11807 > show #!5 models
    11808 
    11809 > hide #!5 models
    11810 
    11811 > select #1/A-B
    11812 
    11813 18021 atoms, 18789 bonds, 361 pseudobonds, 1592 residues, 2 models selected 
    11814 
    11815 > show sel cartoons
    11816 
    11817 > show #!5 models
    11818 
    11819 > hide #!1 models
    11820 
    11821 > hide #!5 models
    11822 
    11823 > show #!1 models
    11824 
    11825 > show #2 models
    11826 
    11827 > hide #2 models
    11828 
    11829 > show #2 models
    11830 
    11831 > hide #2 models
    11832 
    11833 > show #2 models
    11834 
    11835 > hide #2 models
    11836 
    11837 > show #2 models
    11838 
    11839 > hide #2 models
    11840 
    11841 > close #1
    11842 
    11843 > show #2 models
    11844 
    11845 > close #3-4
    11846 
    11847 > show #!5 models
    11848 
    11849 > ui mousemode right "translate selected atoms"
    11850 
    11851 > ui mousemode right "translate selected models"
    11852 
    11853 > rename #2 "PSI Fx Fa Fb clusters"
    11854 
    11855 > rename #5 id #1
    11856 
    11857 > rename #6 id #3
    11858 
    11859 > rename #1 "relaxed PsaABCDE BFd(F) complex"
    11860 
    11861 > show #1.1 models
    11862 
    11863 > show #1.2 models
    11864 
    11865 > show #1.3 models
    11866 
    11867 > show #1.4 models
    11868 
    11869 > show #1.5 models
    11870 
    11871 > show #1.6 models
    11872 
    11873 > hide #1.5 models
    11874 
    11875 > hide #1.4 models
    11876 
    11877 > hide #1.3 models
    11878 
    11879 > hide #1.2 models
    11880 
    11881 > hide #1.1 models
    11882 
    11883 > hide #1.6 models
    11884 
    11885 > rename #5/F
    11886 
    11887 No name or id option specified for renaming 
    11888 
    11889 > select #5/F
    11890 
    11891 Nothing selected 
    11892 
    11893 > select #1/F
    11894 
    11895 846 atoms, 853 bonds, 61 residues, 1 model selected 
    11896 
    11897 > color sel bychain
    11898 
    11899 > color sel byhetero
    11900 
    11901 > help help:user
    11902 
    11903 > color #1 chains pal sett3-9
    11904 
    11905 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    11906 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    11907 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    11908 
    11909 > color bychain #1 pal sett3-9
    11910 
    11911 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    11912 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    11913 
    11914 > color sequential #1 chains
    11915 
    11916 > color sequential #1 chains palette set3-9
    11917 
    11918 > color sel byhetero
    11919 
    11920 > ~select
    11921 
    11922 Nothing selected 
    11923 
    11924 > color byhetero
    11925 
    11926 > color sequential #1 chains palette pastel1
    11927 
    11928 > color byhetero
    11929 
    11930 > color sequential #1 chains palette accent
    11931 
    11932 > color byhetero
    11933 
    11934 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11935 > Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx
    11936 > dock/fdn_Alt/PSI BFd for minimization.cxs"
    11937 
    11938 > rename #3 "BFd (2fdn)"
    11939 
    11940 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11941 > Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx
    11942 > dock/fdn_Alt/PSI BFd for minimization.cxs"
    11943 
    11944 > close #1.1-7
    11945 
    11946 > save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
    11947 > Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx
    11948 > dock/fdn_Alt/PSI BFd for relaxation.cxs"
    11949 
    11950 ——— End of log from Tue Oct 8 17:54:27 2024 ———
    11951 
    11952 opened ChimeraX session 
    11953 
    11954 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    11955 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    11956 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb"
    11957 
    11958 Chain information for PSI_BFd.opt.pdb #4 
    11959 --- 
    11960 Chain | Description 
    11961 ? | No description available 
    11962  
    11963 
    11964 > split #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms
    11965 > :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828
    11966 
    11967 Split PSI_BFd.opt.pdb (#4) into 6 models 
    11968 Chain information for PSI_BFd.opt.pdb 1 #4.1 
    11969 --- 
    11970 Chain | Description 
    11971 ? | No description available 
    11972  
    11973 Chain information for PSI_BFd.opt.pdb 2 #4.2 
    11974 --- 
    11975 Chain | Description 
    11976 ? | No description available 
    11977  
    11978 Chain information for PSI_BFd.opt.pdb 3 #4.3 
    11979 --- 
    11980 Chain | Description 
    11981 ? | No description available 
    11982  
    11983 Chain information for PSI_BFd.opt.pdb 4 #4.4 
    11984 --- 
    11985 Chain | Description 
    11986 ? | No description available 
    11987  
    11988 Chain information for PSI_BFd.opt.pdb 5 #4.5 
    11989 --- 
    11990 Chain | Description 
    11991 ? | No description available 
    11992  
    11993 Chain information for PSI_BFd.opt.pdb 6 #4.6 
    11994 --- 
    11995 Chain | Description 
    11996 ? | No description available 
    11997  
    11998 
    11999 > combine #4.1#4.2#4.3#4.4#4.5#4.6
    12000 
    12001 Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A' 
    12002 Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'B' 
    12003 Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'C' 
    12004 Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'D' 
    12005 Remapping chain ID ' ' in PSI_BFd.opt.pdb 6 #4.6 to 'E' 
    12006 Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'F' 
    12007 Traceback (most recent call last): 
    12008 File
    12009 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12010 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12011 cmd.run(cmd_text) 
    12012 File
    12013 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12014 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12015 result = ci.function(session, **kw_args) 
    12016 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12017 File
    12018 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12019 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12020 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12021 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12022 File
    12023 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12024 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12025 cset(self._c_pointers, n, v) 
    12026 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12027 Chain 
    12028  
    12029 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12030 Chain 
    12031  
    12032 File
    12033 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12034 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12035 cset(self._c_pointers, n, v) 
    12036  
    12037 See log for complete Python traceback. 
    12038  
    12039 
    12040 > combine #4.1
    12041 
    12042 Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'A' 
    12043 Traceback (most recent call last): 
    12044 File
    12045 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12046 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12047 cmd.run(cmd_text) 
    12048 File
    12049 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12050 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12051 result = ci.function(session, **kw_args) 
    12052 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12053 File
    12054 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12055 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12056 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12057 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12058 File
    12059 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12060 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12061 cset(self._c_pointers, n, v) 
    12062 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12063 Chain 
    12064  
    12065 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12066 Chain 
    12067  
    12068 File
    12069 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12070 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12071 cset(self._c_pointers, n, v) 
    12072  
    12073 See log for complete Python traceback. 
    12074  
    12075 
    12076 > combine #4.2#4.3
    12077 
    12078 Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'A' 
    12079 Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B' 
    12080 Traceback (most recent call last): 
    12081 File
    12082 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12083 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12084 cmd.run(cmd_text) 
    12085 File
    12086 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12087 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12088 result = ci.function(session, **kw_args) 
    12089 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12090 File
    12091 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12092 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12093 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12094 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12095 File
    12096 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12097 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12098 cset(self._c_pointers, n, v) 
    12099 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12100 Chain 
    12101  
    12102 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12103 Chain 
    12104  
    12105 File
    12106 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12107 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12108 cset(self._c_pointers, n, v) 
    12109  
    12110 See log for complete Python traceback. 
    12111  
    12112 
    12113 > combine #4.2#4.4
    12114 
    12115 Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'A' 
    12116 Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B' 
    12117 Traceback (most recent call last): 
    12118 File
    12119 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12120 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12121 cmd.run(cmd_text) 
    12122 File
    12123 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12124 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12125 result = ci.function(session, **kw_args) 
    12126 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12127 File
    12128 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12129 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12130 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12131 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12132 File
    12133 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12134 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12135 cset(self._c_pointers, n, v) 
    12136 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12137 Chain 
    12138  
    12139 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12140 Chain 
    12141  
    12142 File
    12143 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12144 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12145 cset(self._c_pointers, n, v) 
    12146  
    12147 See log for complete Python traceback. 
    12148  
    12149 
    12150 > combine #4.2#4.5
    12151 
    12152 Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'A' 
    12153 Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B' 
    12154 Traceback (most recent call last): 
    12155 File
    12156 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12157 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12158 cmd.run(cmd_text) 
    12159 File
    12160 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12161 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12162 result = ci.function(session, **kw_args) 
    12163 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12164 File
    12165 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12166 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12167 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12168 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12169 File
    12170 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12171 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12172 cset(self._c_pointers, n, v) 
    12173 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12174 Chain 
    12175  
    12176 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12177 Chain 
    12178  
    12179 File
    12180 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12181 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12182 cset(self._c_pointers, n, v) 
    12183  
    12184 See log for complete Python traceback. 
    12185  
    12186 
    12187 > combine #4.2
    12188 
    12189 Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A' 
    12190 Traceback (most recent call last): 
    12191 File
    12192 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12193 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12194 cmd.run(cmd_text) 
    12195 File
    12196 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12197 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12198 result = ci.function(session, **kw_args) 
    12199 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12200 File
    12201 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12202 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12203 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12204 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12205 File
    12206 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12207 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12208 cset(self._c_pointers, n, v) 
    12209 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12210 Chain 
    12211  
    12212 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12213 Chain 
    12214  
    12215 File
    12216 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12217 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12218 cset(self._c_pointers, n, v) 
    12219  
    12220 See log for complete Python traceback. 
    12221  
    12222 
    12223 > combine #4
    12224 
    12225 Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A' 
    12226 Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'B' 
    12227 Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'C' 
    12228 Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'D' 
    12229 Remapping chain ID ' ' in PSI_BFd.opt.pdb 6 #4.6 to 'E' 
    12230 Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'F' 
    12231 Traceback (most recent call last): 
    12232 File
    12233 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12234 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12235 cmd.run(cmd_text) 
    12236 File
    12237 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12238 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12239 result = ci.function(session, **kw_args) 
    12240 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12241 File
    12242 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12243 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12244 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12245 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12246 File
    12247 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12248 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12249 cset(self._c_pointers, n, v) 
    12250 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12251 Chain 
    12252  
    12253 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12254 Chain 
    12255  
    12256 File
    12257 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12258 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12259 cset(self._c_pointers, n, v) 
    12260  
    12261 See log for complete Python traceback. 
    12262  
    12263 
    12264 > close #4
    12265 
    12266 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12267 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12268 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb"
    12269 
    12270 Chain information for PSI_BFd.opt.pdb #4 
    12271 --- 
    12272 Chain | Description 
    12273 ? | No description available 
    12274  
    12275 
    12276 > split #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms
    12277 > :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828
    12278 
    12279 Split PSI_BFd.opt.pdb (#4) into 6 models 
    12280 Chain information for PSI_BFd.opt.pdb 1 #4.1 
    12281 --- 
    12282 Chain | Description 
    12283 ? | No description available 
    12284  
    12285 Chain information for PSI_BFd.opt.pdb 2 #4.2 
    12286 --- 
    12287 Chain | Description 
    12288 ? | No description available 
    12289  
    12290 Chain information for PSI_BFd.opt.pdb 3 #4.3 
    12291 --- 
    12292 Chain | Description 
    12293 ? | No description available 
    12294  
    12295 Chain information for PSI_BFd.opt.pdb 4 #4.4 
    12296 --- 
    12297 Chain | Description 
    12298 ? | No description available 
    12299  
    12300 Chain information for PSI_BFd.opt.pdb 5 #4.5 
    12301 --- 
    12302 Chain | Description 
    12303 ? | No description available 
    12304  
    12305 Chain information for PSI_BFd.opt.pdb 6 #4.6 
    12306 --- 
    12307 Chain | Description 
    12308 ? | No description available 
    12309  
    12310 
    12311 > combine #4.2
    12312 
    12313 Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A' 
    12314 Traceback (most recent call last): 
    12315 File
    12316 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12317 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12318 cmd.run(cmd_text) 
    12319 File
    12320 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12321 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12322 result = ci.function(session, **kw_args) 
    12323 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12324 File
    12325 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12326 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12327 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12328 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12329 File
    12330 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12331 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12332 cset(self._c_pointers, n, v) 
    12333 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12334 Chain 
    12335  
    12336 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12337 Chain 
    12338  
    12339 File
    12340 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12341 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12342 cset(self._c_pointers, n, v) 
    12343  
    12344 See log for complete Python traceback. 
    12345  
    12346 
    12347 > combine #4
    12348 
    12349 Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A' 
    12350 Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'B' 
    12351 Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'C' 
    12352 Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'D' 
    12353 Remapping chain ID ' ' in PSI_BFd.opt.pdb 6 #4.6 to 'E' 
    12354 Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'F' 
    12355 Traceback (most recent call last): 
    12356 File
    12357 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12358 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12359 cmd.run(cmd_text) 
    12360 File
    12361 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12362 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12363 result = ci.function(session, **kw_args) 
    12364 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12365 File
    12366 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12367 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12368 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12369 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12370 File
    12371 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12372 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12373 cset(self._c_pointers, n, v) 
    12374 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12375 Chain 
    12376  
    12377 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12378 Chain 
    12379  
    12380 File
    12381 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12382 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12383 cset(self._c_pointers, n, v) 
    12384  
    12385 See log for complete Python traceback. 
    12386  
    12387 
    12388 > changechains #4.2 B
    12389 
    12390 Chain IDs of 733 residues changed 
    12391 
    12392 > changechains #4.3 C
    12393 
    12394 Chain IDs of 82 residues changed 
    12395 
    12396 > changechains #4.4 D
    12397 
    12398 Chain IDs of 143 residues changed 
    12399 
    12400 > changechains #4.5 E
    12401 
    12402 Chain IDs of 67 residues changed 
    12403 
    12404 > changechains #4.6 F
    12405 
    12406 Chain IDs of 62 residues changed 
    12407 
    12408 > renumber #4.1:1829 start 3001
    12409 
    12410 1 residues renumbered 
    12411 
    12412 > renumber #4.2 start 1
    12413 
    12414 733 residues renumbered 
    12415 
    12416 > renumber #4.3 start 1
    12417 
    12418 82 residues renumbered 
    12419 
    12420 > renumber #4.3:354-355 start 3002
    12421 
    12422 2 residues renumbered 
    12423 
    12424 > renumber #4.4 start 1
    12425 
    12426 143 residues renumbered 
    12427 
    12428 > renumber #4.5 start 1
    12429 
    12430 67 residues renumbered 
    12431 
    12432 > renumber #4.6 start 1
    12433 
    12434 62 residues renumbered 
    12435 
    12436 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12437 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12438 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb" models #4
    12439 
    12440 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12441 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12442 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb"
    12443 
    12444 Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-
    12445 Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI
    12446 interface/RFdiffusion with RoesttaDock H2ase BFdx
    12447 dock/fdn_Alt/PSI_BFd_SF4_opt.pdb 
    12448 --- 
    12449 warnings | Start residue of secondary structure not found: HELIX 1 1 THR 36 ALA 44 1 9 
    12450 Start residue of secondary structure not found: HELIX 2 2 PHE 49 HIE 52 1 4 
    12451 Start residue of secondary structure not found: HELIX 3 3 LEU 56 GLY 85 1 30 
    12452 Start residue of secondary structure not found: HELIX 4 4 TYR 91 ASN 96 1 6 
    12453 Start residue of secondary structure not found: HELIX 5 5 GLN 114 LEU 117 1 4 
    12454 180 messages similar to the above omitted 
    12455  
    12456 Chain information for PSI_BFd_SF4_opt.pdb 
    12457 --- 
    12458 Chain | Description 
    12459 5.1/? | No description available 
    12460 5.2/B | No description available 
    12461 5.3/C | No description available 
    12462 5.4/D | No description available 
    12463 5.5/E | No description available 
    12464 5.6/F | No description available 
    12465  
    12466 
    12467 > combine #5.1#5.2#5.3#5.4#5.5#5.6
    12468 
    12469 Remapping chain ID ' ' in PSI_BFd_SF4_opt.pdb #5.1 to 'A' 
    12470 Traceback (most recent call last): 
    12471 File
    12472 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12473 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12474 cmd.run(cmd_text) 
    12475 File
    12476 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12477 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12478 result = ci.function(session, **kw_args) 
    12479 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12480 File
    12481 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12482 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12483 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12484 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12485 File
    12486 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12487 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12488 cset(self._c_pointers, n, v) 
    12489 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12490 Chain 
    12491  
    12492 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12493 Chain 
    12494  
    12495 File
    12496 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12497 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12498 cset(self._c_pointers, n, v) 
    12499  
    12500 See log for complete Python traceback. 
    12501  
    12502 
    12503 > close #5
    12504 
    12505 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12506 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12507 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_[NUMBER].pdb" models #4
    12508 
    12509 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12510 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12511 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb" models #4.1
    12512 
    12513 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12514 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12515 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb" models #4.2
    12516 
    12517 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12518 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12519 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb"
    12520 > "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12521 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12522 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb"
    12523 
    12524 Chain information for PSI_BFd_SF4_opt_A.pdb #5 
    12525 --- 
    12526 Chain | Description 
    12527 ? | No description available 
    12528  
    12529 Chain information for PSI_BFd_SF4_opt_B.pdb #6 
    12530 --- 
    12531 Chain | Description 
    12532 B | No description available 
    12533  
    12534 
    12535 > combine #5#6
    12536 
    12537 Remapping chain ID ' ' in PSI_BFd_SF4_opt_A.pdb #5 to 'A' 
    12538 Traceback (most recent call last): 
    12539 File
    12540 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12541 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    12542 cmd.run(cmd_text) 
    12543 File
    12544 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12545 packages/chimerax/core/commands/cli.py", line 3213, in run 
    12546 result = ci.function(session, **kw_args) 
    12547 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12548 File
    12549 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12550 packages/chimerax/atomic/cmd.py", line 144, in combine_cmd 
    12551 residues[residues.chain_ids == chain_id].chain_ids = new_id 
    12552 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    12553 File
    12554 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12555 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12556 cset(self._c_pointers, n, v) 
    12557 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12558 Chain 
    12559  
    12560 ValueError: Cannot set polymeric chain ID directly from Residue; must use
    12561 Chain 
    12562  
    12563 File
    12564 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    12565 packages/chimerax/atomic/molc.py", line 234, in set_prop 
    12566 cset(self._c_pointers, n, v) 
    12567  
    12568 See log for complete Python traceback. 
    12569  
    12570 
    12571 > close #6#4-5
    12572 
    12573 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    12574 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    12575 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb"
    12576 
    12577 Chain information for PSI_BFd.opt.pdb #4 
    12578 --- 
    12579 Chain | Description 
    12580 ? | No description available 
    12581  
    12582 
    12583 > split #4 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699
    12584 > atoms :1700-1766 atoms :1767-1826
    12585 
    12586 Split PSI_BFd.opt.pdb (#4) into 7 models 
    12587 Chain information for PSI_BFd.opt.pdb 1 #4.1 
    12588 --- 
    12589 Chain | Description 
    12590 ? | No description available 
    12591  
    12592 Chain information for PSI_BFd.opt.pdb 2 #4.2 
    12593 --- 
    12594 Chain | Description 
    12595 ? | No description available 
    12596  
    12597 Chain information for PSI_BFd.opt.pdb 3 #4.3 
    12598 --- 
    12599 Chain | Description 
    12600 ? | No description available 
    12601  
    12602 Chain information for PSI_BFd.opt.pdb 4 #4.4 
    12603 --- 
    12604 Chain | Description 
    12605 ? | No description available 
    12606  
    12607 Chain information for PSI_BFd.opt.pdb 5 #4.5 
    12608 --- 
    12609 Chain | Description 
    12610 ? | No description available 
    12611  
    12612 Chain information for PSI_BFd.opt.pdb 6 #4.6 
    12613 --- 
    12614 Chain | Description 
    12615 ? | No description available 
    12616  
    12617 
    12618 > hide #!4.7 models
    12619 
    12620 > hide #1 models
    12621 
    12622 > hide #2 models
    12623 
    12624 > hide #!3 models
    12625 
    12626 > changechains #4.2 B
    12627 
    12628 Chain IDs of 733 residues changed 
    12629 
    12630 > changechains #4.3 C
    12631 
    12632 Chain IDs of 80 residues changed 
    12633 
    12634 > changechains #4.4 D
    12635 
    12636 Chain IDs of 143 residues changed 
    12637 
    12638 > changechains #4.5 E
    12639 
    12640 Chain IDs of 67 residues changed 
    12641 
    12642 > changechains #4.6 F
    12643 
    12644 Chain IDs of 60 residues changed 
    12645 
    12646 > renumber #4.2 start 1
    12647 
    12648 733 residues renumbered 
    12649 
    12650 > renumber #4.3 start 1
    12651 
    12652 80 residues renumbered 
    12653 
    12654 > renumber #4.4 start 1
    12655 
    12656 143 residues renumbered 
    12657 
    12658 > renumber #4.5 start 1
    12659 
    12660 67 residues renumbered 
    12661 
    12662 > renumber #4.6 start 1
    12663 
    12664 60 residues renumbered 
    12665 
    12666 > changechains #4.1 A
    12667 
    12668 Chain IDs of 743 residues changed 
    12669 
    12670 > changechains #4.7 X
    12671 
    12672 Chain IDs of 5 residues changed 
    12673 
    12674 > combine #4.1#4.2#4.3#4.4#4.5#4.6
    12675 
    12676 > hide #!4 models
    12677 
    12678 > show #!4 models
    12679 
    12680 > combine #4.7
    12681 
    12682 > combine #5#6
    12683 
    12684 > hide #!6 models
    12685 
    12686 > hide #5 models
    12687 
    12688 > hide #!4 models
    12689 
    12690 > color sequential #7 chains palette accent
    12691 
    12692 > show #1 models
    12693 
    12694 > hide #1 models
    12695 
    12696 > color #!7 byhetero
    12697 
    12698 > select #7/X:1827@F2
    12699 
    12700 1 atom, 1 residue, 1 model selected 
    12701 
    12702 > close #5#4,6
    12703 
    12704 > rename #7 PSI_BFD_SF4_opt.pdb
    12705 
    12706 > rename #7 id #4
    12707 
    12708 > show #1 models
    12709 
    12710 > hide #!4 models
    12711 
    12712 > show #!3 models
    12713 
    12714 > select add #3
    12715 
    12716 763 atoms, 681 bonds, 8 pseudobonds, 152 residues, 3 models selected 
    12717 
    12718 > select subtract #3
    12719 
    12720 1 atom, 1 residue, 1 model selected 
    12721 
    12722 > select #3
    12723 
    12724 762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected 
    12725 
    12726 > show sel cartoons
    12727 
    12728 > select #3:cys
    12729 
    12730 80 atoms, 72 bonds, 8 residues, 1 model selected 
    12731 
    12732 > show sel atoms
    12733 
    12734 > color sel byhetero
    12735 
    12736 > hide #!3 models
    12737 
    12738 > show #!4 models
    12739 
    12740 > hide #1 models
    12741 
    12742 > show #!3 models
    12743 
    12744 > align #3:SF4 toAtoms #4:1827-1828
    12745 
    12746 RMSD between 16 atom pairs is 0.346 angstroms 
    12747 
    12748 > hide #!3 models
    12749 
    12750 > show #1 models
    12751 
    12752 > hide #1 models
    12753 
    12754 > select #4/X:1831 @<9 &#4/X:1827
    12755 
    12756 Nothing selected 
    12757 
    12758 > select #4/X:1831 @<10 &#4/X:1827
    12759 
    12760 2 atoms, 1 pseudobond, 1 residue, 2 models selected 
    12761 
    12762 > select #4/X:1831 @<9.2 &#4/X:1827
    12763 
    12764 Nothing selected 
    12765 
    12766 > select #4/X:1831 @<9.5 &#4/X:1827
    12767 
    12768 Nothing selected 
    12769 
    12770 > select #4/X:1831 @<9.8 &#4/X:1827
    12771 
    12772 2 atoms, 1 pseudobond, 1 residue, 2 models selected 
    12773 
    12774 > select #4/X:1831 @<9.7 &#4/X:1827
    12775 
    12776 1 atom, 1 residue, 1 model selected 
    12777 
    12778 > select #4/X:1827 @<9.7 &#4/X:1831
    12779 
    12780 1 atom, 1 residue, 1 model selected 
    12781 
    12782 > select #4/X:1831 @<9.7 &#4/X:1827
    12783 
    12784 1 atom, 1 residue, 1 model selected 
    12785 
    12786 > select #4/X:1831@F2:1827@F1
    12787 
    12788 2 atoms, 2 residues, 1 model selected 
    12789 
    12790 > select #4/X:1831@F1:1827@F2
    12791 
    12792 2 atoms, 2 residues, 1 model selected 
    12793 
    12794 > ui tool show Distances
    12795 
    12796 > distance #4/X:1827@F2 #4/X:1831@F1
    12797 
    12798 Distance between PSI_BFD_SF4_opt.pdb #4/X SF4 1827 F2 and SF4 1831 F1: 9.521Å 
    12799 
    12800 > select #4/A-F
    12801 
    12802 28475 atoms, 28948 bonds, 1826 residues, 1 model selected 
    12803 
    12804 > select #4/A-F
    12805 
    12806 28475 atoms, 28948 bonds, 1826 residues, 1 model selected 
    12807 
    12808 > show sel surfaces
    12809 
    12810 > coulombic #4/A
    12811 
    12812 Using Amber 20 recommended default charges and atom types for standard
    12813 residues 
    12814 Assigning partial charges to residue CYF (net charge +1) with am1-bcc method 
    12815 Running ANTECHAMBER command:
    12816 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
    12817 qm_theory='AM1', -i
    12818 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.in.mol2 -fi
    12819 mol2 -o
    12820 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.out.mol2 -fo
    12821 mol2 -c bcc -nc 1 -j 5 -s 2 -dr n 
    12822 (CYF) `` 
    12823 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    12824 (CYF) `` 
    12825 (CYF) `Info: Finished reading file
    12826 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.in.mol2);
    12827 atoms read (22), bonds read (21).` 
    12828 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    12829 sensitive.` 
    12830 (CYF) `Running:
    12831 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
    12832 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    12833 (CYF) `` 
    12834 (CYF) `` 
    12835 (CYF) `Running:
    12836 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
    12837 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    12838 (CYF) `Info: Total number of electrons: 92; net charge: 1` 
    12839 (CYF) `` 
    12840 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
    12841 -i sqm.in -o sqm.out` 
    12842 (CYF) `` 
    12843 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
    12844 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    12845 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    12846 -s 2 -j 1` 
    12847 (CYF) `` 
    12848 (CYF) `Running:
    12849 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    12850 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    12851 (CYF) `` 
    12852 Charges for residue CYF determined 
    12853 Coulombic values for PSI_BFD_SF4_opt.pdb_A SES surface #4.2: minimum, -12.49,
    12854 mean 0.00, maximum 20.13 
    12855 
    12856 > coulombic #4/B
    12857 
    12858 Using Amber 20 recommended default charges and atom types for standard
    12859 residues 
    12860 Assigning partial charges to residue CYF (net charge -1) with am1-bcc method 
    12861 Running ANTECHAMBER command:
    12862 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
    12863 qm_theory='AM1', -i
    12864 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.in.mol2 -fi
    12865 mol2 -o
    12866 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.out.mol2 -fo
    12867 mol2 -c bcc -nc -1 -j 5 -s 2 -dr n 
    12868 (CYF) `` 
    12869 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    12870 (CYF) `` 
    12871 (CYF) `Info: Finished reading file
    12872 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.in.mol2);
    12873 atoms read (22), bonds read (21).` 
    12874 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    12875 sensitive.` 
    12876 (CYF) `Running:
    12877 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
    12878 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    12879 (CYF) `` 
    12880 (CYF) `` 
    12881 (CYF) `Running:
    12882 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
    12883 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    12884 (CYF) `Info: Total number of electrons: 94; net charge: -1` 
    12885 (CYF) `` 
    12886 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
    12887 -i sqm.in -o sqm.out` 
    12888 (CYF) `` 
    12889 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
    12890 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    12891 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    12892 -s 2 -j 1` 
    12893 (CYF) `` 
    12894 (CYF) `Running:
    12895 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    12896 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    12897 (CYF) `` 
    12898 Charges for residue CYF determined 
    12899 Coulombic values for PSI_BFD_SF4_opt.pdb_B SES surface #4.3: minimum, -15.85,
    12900 mean -0.16, maximum 13.13 
    12901 
    12902 > coulombic #4/C
    12903 
    12904 Using Amber 20 recommended default charges and atom types for standard
    12905 residues 
    12906 Assigning partial charges to residue CYF (net charge -1) with am1-bcc method 
    12907 Running ANTECHAMBER command:
    12908 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
    12909 qm_theory='AM1', -i
    12910 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.in.mol2 -fi
    12911 mol2 -o
    12912 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.out.mol2 -fo
    12913 mol2 -c bcc -nc -1 -j 5 -s 2 -dr n 
    12914 (CYF) `` 
    12915 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    12916 (CYF) `` 
    12917 (CYF) `Info: Finished reading file
    12918 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.in.mol2);
    12919 atoms read (22), bonds read (21).` 
    12920 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    12921 sensitive.` 
    12922 (CYF) `Running:
    12923 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
    12924 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    12925 (CYF) `` 
    12926 (CYF) `` 
    12927 (CYF) `Running:
    12928 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
    12929 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    12930 (CYF) `Info: Total number of electrons: 94; net charge: -1` 
    12931 (CYF) `` 
    12932 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
    12933 -i sqm.in -o sqm.out` 
    12934 (CYF) `` 
    12935 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
    12936 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    12937 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    12938 -s 2 -j 1` 
    12939 (CYF) `` 
    12940 (CYF) `Running:
    12941 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    12942 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    12943 (CYF) `` 
    12944 Charges for residue CYF determined 
    12945 Coulombic values for PSI_BFD_SF4_opt.pdb_C SES surface #4.4: minimum, -22.24,
    12946 mean -4.06, maximum 8.43 
    12947 
    12948 > coulombic #4/D
    12949 
    12950 Using Amber 20 recommended default charges and atom types for standard
    12951 residues 
    12952 Coulombic values for PSI_BFD_SF4_opt.pdb_D SES surface #4.5: minimum, -11.15,
    12953 mean 2.11, maximum 15.26 
    12954 
    12955 > coulombic #4/E
    12956 
    12957 Using Amber 20 recommended default charges and atom types for standard
    12958 residues 
    12959 Coulombic values for PSI_BFD_SF4_opt.pdb_E SES surface #4.6: minimum, -11.38,
    12960 mean 1.55, maximum 11.87 
    12961 
    12962 > coulombic #4/F
    12963 
    12964 Using Amber 20 recommended default charges and atom types for standard
    12965 residues 
    12966 Assigning partial charges to residue CYF (net charge +0) with am1-bcc method 
    12967 Running ANTECHAMBER command:
    12968 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
    12969 qm_theory='AM1', -i
    12970 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.in.mol2 -fi
    12971 mol2 -o
    12972 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.out.mol2 -fo
    12973 mol2 -c bcc -nc 0 -j 5 -s 2 -dr n 
    12974 (CYF) `` 
    12975 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    12976 (CYF) `` 
    12977 (CYF) `Info: Finished reading file
    12978 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.in.mol2);
    12979 atoms read (23), bonds read (22).` 
    12980 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    12981 sensitive.` 
    12982 (CYF) `Running:
    12983 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
    12984 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    12985 (CYF) `` 
    12986 (CYF) `` 
    12987 (CYF) `Running:
    12988 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
    12989 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    12990 (CYF) `Info: Total number of electrons: 94; net charge: 0` 
    12991 (CYF) `` 
    12992 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
    12993 -i sqm.in -o sqm.out` 
    12994 (CYF) `` 
    12995 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
    12996 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    12997 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    12998 -s 2 -j 1` 
    12999 (CYF) `` 
    13000 (CYF) `Running:
    13001 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    13002 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    13003 (CYF) `` 
    13004 Charges for residue CYF determined 
    13005 Coulombic values for PSI_BFD_SF4_opt.pdb_F SES surface #4.7: minimum, -16.02,
    13006 mean -3.74, maximum 7.04 
    13007 
    13008 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    13009 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    13010 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    13011 > relaxed.cxs"
    13012 
    13013 ——— End of log from Wed Oct 9 21:29:02 2024 ———
    13014 
    13015 opened ChimeraX session 
    13016 
    13017 > hide #4.7 models
    13018 
    13019 > hide #4.6 models
    13020 
    13021 > hide #4.5 models
    13022 
    13023 > hide #4.4 models
    13024 
    13025 > show #4.4 models
    13026 
    13027 > hide #4.4 models
    13028 
    13029 > hide #4.3 models
    13030 
    13031 > hide #4.2 models
    13032 
    13033 > select #4/F
    13034 
    13035 829 atoms, 836 bonds, 60 residues, 1 model selected 
    13036 
    13037 > ui tool show H-Bonds
    13038 
    13039 > hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false
    13040 > intraRes false reveal true log true
    13041 
    13042 Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt.pdb #4/A CYF 575
    13043 SG 
    13044 Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt.pdb #4/A
    13045 CYF 575 SG 
    13046  
    13047 [Repeated 1 time(s)]
    13048 
    13049 Skipped 2 atom(s) with bad connectivities; see log for details 
    13050 
    13051    
    13052    
    13053     Finding intramodel H-bonds
    13054     Constraints relaxed by 0.4 angstroms and 20 degrees
    13055     Models used:
    13056         4 PSI_BFD_SF4_opt.pdb
    13057    
    13058     21 H-bonds
    13059     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    13060     PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1  PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 HH11  2.760  1.842
    13061     PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2  PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 HH21  2.719  1.800
    13062     PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ   PSI_BFD_SF4_opt.pdb #4/F ASP 29 O    PSI_BFD_SF4_opt.pdb #4/A LYS 31 HZ1   3.148  2.456
    13063     PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ   PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2  PSI_BFD_SF4_opt.pdb #4/A LYS 31 HZ2   2.746  1.778
    13064     PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1  PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1  PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH11  2.812  1.825
    13065     PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1  PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH11  3.358  2.560
    13066     PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2  PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH22  2.780  1.765
    13067     PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ  PSI_BFD_SF4_opt.pdb #4/F PRO 17 O    PSI_BFD_SF4_opt.pdb #4/D LYS 109 HZ1  2.917  2.045
    13068     PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ  PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1  PSI_BFD_SF4_opt.pdb #4/D LYS 109 HZ2  2.737  1.813
    13069     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE   PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 HE    2.875  1.950
    13070     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1  PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH12  2.980  2.103
    13071     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2  PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH22  2.848  1.943
    13072     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2  PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH21  2.738  1.784
    13073     PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1  PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 HG1   2.666  1.685
    13074     PSI_BFD_SF4_opt.pdb #4/E ASN 56 ND2  PSI_BFD_SF4_opt.pdb #4/F PRO 52 O    PSI_BFD_SF4_opt.pdb #4/E ASN 56 HD22  3.598  2.755
    13075     PSI_BFD_SF4_opt.pdb #4/E ALA 67 N    PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD1  PSI_BFD_SF4_opt.pdb #4/E ALA 67 H1    3.484  2.798
    13076     PSI_BFD_SF4_opt.pdb #4/E ALA 67 N    PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 H1    2.745  1.804
    13077     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1  PSI_BFD_SF4_opt.pdb #4/F ARG 31 HE    2.902  1.898
    13078     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2  PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH12  2.894  1.970
    13079     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2  PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1  PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH21  3.324  2.539
    13080     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2  PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH22  2.784  1.818
    13081    
    13082 
    13083  
    13084 21 hydrogen bonds found 
    13085 
    13086 > ui tool show "Selection Inspector"
    13087 
    13088 > setattr sel r ribbon_hide_backbone false
    13089 
    13090 Assigning ribbon_hide_backbone attribute to 60 items 
    13091 
    13092 > select #4:SF4
    13093 
    13094 40 atoms, 91 pseudobonds, 5 residues, 3 models selected 
    13095 
    13096 > style sel sphere
    13097 
    13098 Changed 40 atom styles 
    13099 
    13100 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    13101 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    13102 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    13103 > relaxed.cxs"
    13104 
    13105 > select #4/F
    13106 
    13107 829 atoms, 836 bonds, 60 residues, 1 model selected 
    13108 
    13109 > ui tool show Contacts
    13110 
    13111 > select #4/F &~H
    13112 
    13113 430 atoms, 437 bonds, 60 residues, 1 model selected 
    13114 
    13115 > contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol
    13116 > false color #76d6ff radius 0.2 reveal true log true
    13117    
    13118    
    13119     Allowed overlap: -0.4
    13120     H-bond overlap reduction: 0.4
    13121     Ignore contacts between atoms separated by 4 bonds or less
    13122     Ignore contacts between atoms in residues less than 5 apart in sequence
    13123     Detect intra-residue contacts: False
    13124     Detect intra-molecule contacts: False
    13125    
    13126     88 contacts
    13127                    atom1                                atom2                 overlap  distance
    13128     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     2.060    1.340
    13129     PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA    PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.981    2.479
    13130     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    0.878    2.462
    13131     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.466    2.254
    13132     PSI_BFD_SF4_opt.pdb #4/F TYR 1 C     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.397    3.063
    13133     PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA    PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.361    2.819
    13134     PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.215    3.025
    13135     PSI_BFD_SF4_opt.pdb #4/F GLY 13 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   0.214    3.036
    13136     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG    0.203    3.197
    13137     PSI_BFD_SF4_opt.pdb #4/F TYR 1 C     PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.161    3.019
    13138     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 C     0.154    3.026
    13139     PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 C     0.095    3.085
    13140     PSI_BFD_SF4_opt.pdb #4/F GLU 18 CD   PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   0.059    3.266
    13141     PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1  PSI_BFD_SF4_opt.pdb #4/C PRO 58 CB    0.048    3.352
    13142     PSI_BFD_SF4_opt.pdb #4/F THR 7 CA    PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   0.005    3.320
    13143     PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 CZ    -0.006    3.186
    13144     PSI_BFD_SF4_opt.pdb #4/F ALA 38 O    PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    -0.013    3.193
    13145     PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.014    2.719
    13146     PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 O     -0.032    3.212
    13147     PSI_BFD_SF4_opt.pdb #4/F TYR 1 O     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     -0.032    3.272
    13148     PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1  PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   -0.032    2.737
    13149     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.033    2.738
    13150     PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.040    2.745
    13151     PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2  PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ    -0.041    2.746
    13152     PSI_BFD_SF4_opt.pdb #4/F THR 7 C     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.042    3.367
    13153     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.049    3.449
    13154     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 CG2   -0.052    3.232
    13155     PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 CB    -0.054    3.234
    13156     PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1   -0.055    2.760
    13157     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ    -0.060    3.240
    13158     PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.075    2.780
    13159     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.079    2.784
    13160     PSI_BFD_SF4_opt.pdb #4/F GLY 13 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.080    3.405
    13161     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1   -0.086    2.666
    13162     PSI_BFD_SF4_opt.pdb #4/F ALA 38 O    PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB    -0.088    3.268
    13163     PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1   -0.100    3.425
    13164     PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    -0.103    3.283
    13165     PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1  PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1   -0.107    2.812
    13166     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 CB    -0.122    3.302
    13167     PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 C     -0.130    3.530
    13168     PSI_BFD_SF4_opt.pdb #4/F GLY 13 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.134    3.459
    13169     PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ   PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.136    3.316
    13170     PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.143    2.848
    13171     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB    -0.146    3.486
    13172     PSI_BFD_SF4_opt.pdb #4/F GLY 13 O    PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ    -0.147    3.327
    13173     PSI_BFD_SF4_opt.pdb #4/F CYF 12 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.148    3.473
    13174     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG    -0.162    3.562
    13175     PSI_BFD_SF4_opt.pdb #4/F MET 53 SD   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1   -0.167    3.649
    13176     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE    -0.170    2.875
    13177     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1   -0.177    2.902
    13178     PSI_BFD_SF4_opt.pdb #4/F GLU 8 N     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.182    3.432
    13179     PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.182    3.507
    13180     PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ    -0.183    3.363
    13181     PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.187    3.512
    13182     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 CB    -0.188    3.368
    13183     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 CA    -0.188    3.368
    13184     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.189    2.894
    13185     PSI_BFD_SF4_opt.pdb #4/F ASP 43 CG   PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.197    3.522
    13186     PSI_BFD_SF4_opt.pdb #4/F PRO 17 O    PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   -0.212    2.917
    13187     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CG1   -0.215    3.615
    13188     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.219    3.619
    13189     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1   -0.225    3.625
    13190     PSI_BFD_SF4_opt.pdb #4/F PRO 17 CG   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.230    3.555
    13191     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.238    3.503
    13192     PSI_BFD_SF4_opt.pdb #4/F GLY 13 O    PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.254    2.959
    13193     PSI_BFD_SF4_opt.pdb #4/F ALA 14 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.256    3.506
    13194     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 N     -0.272    2.977
    13195     PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1   -0.275    2.980
    13196     PSI_BFD_SF4_opt.pdb #4/F TYR 1 CB    PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     -0.275    3.735
    13197     PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1  PSI_BFD_SF4_opt.pdb #4/C PRO 58 CG    -0.291    3.691
    13198     PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1   -0.299    3.499
    13199     PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1   -0.301    3.626
    13200     PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 CB    -0.316    3.716
    13201     PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD    PSI_BFD_SF4_opt.pdb #4/E SER 53 CB    -0.323    3.723
    13202     PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD    PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.332    3.657
    13203     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.337    3.662
    13204     PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1   -0.342    3.542
    13205     PSI_BFD_SF4_opt.pdb #4/F ASP 29 CA   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.346    3.671
    13206     PSI_BFD_SF4_opt.pdb #4/F CYF 12 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.353    3.753
    13207     PSI_BFD_SF4_opt.pdb #4/F GLY 13 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.355    3.680
    13208     PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ    -0.356    3.536
    13209     PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ    -0.363    3.688
    13210     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 O     -0.366    3.546
    13211     PSI_BFD_SF4_opt.pdb #4/F VAL 50 CA   PSI_BFD_SF4_opt.pdb #4/C ALA 35 CB    -0.371    3.771
    13212     PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 O     -0.372    3.332
    13213     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB    -0.376    3.776
    13214     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CG   PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB    -0.389    3.789
    13215     PSI_BFD_SF4_opt.pdb #4/F PRO 17 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.394    3.719
    13216    
    13217 
    13218  
    13219 88 contacts 
    13220 
    13221 > contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol
    13222 > false select true color #ff85ff radius 0.2 reveal true log true
    13223    
    13224    
    13225     Allowed overlap: -0.4
    13226     H-bond overlap reduction: 0.4
    13227     Ignore contacts between atoms separated by 4 bonds or less
    13228     Ignore contacts between atoms in residues less than 5 apart in sequence
    13229     Detect intra-residue contacts: False
    13230     Detect intra-molecule contacts: False
    13231    
    13232     88 contacts
    13233                    atom1                                atom2                 overlap  distance
    13234     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     2.060    1.340
    13235     PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA    PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.981    2.479
    13236     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    0.878    2.462
    13237     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.466    2.254
    13238     PSI_BFD_SF4_opt.pdb #4/F TYR 1 C     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.397    3.063
    13239     PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA    PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.361    2.819
    13240     PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.215    3.025
    13241     PSI_BFD_SF4_opt.pdb #4/F GLY 13 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   0.214    3.036
    13242     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG    0.203    3.197
    13243     PSI_BFD_SF4_opt.pdb #4/F TYR 1 C     PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.161    3.019
    13244     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 C     0.154    3.026
    13245     PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 C     0.095    3.085
    13246     PSI_BFD_SF4_opt.pdb #4/F GLU 18 CD   PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   0.059    3.266
    13247     PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1  PSI_BFD_SF4_opt.pdb #4/C PRO 58 CB    0.048    3.352
    13248     PSI_BFD_SF4_opt.pdb #4/F THR 7 CA    PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   0.005    3.320
    13249     PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 CZ    -0.006    3.186
    13250     PSI_BFD_SF4_opt.pdb #4/F ALA 38 O    PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    -0.013    3.193
    13251     PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.014    2.719
    13252     PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 O     -0.032    3.212
    13253     PSI_BFD_SF4_opt.pdb #4/F TYR 1 O     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     -0.032    3.272
    13254     PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1  PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   -0.032    2.737
    13255     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.033    2.738
    13256     PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.040    2.745
    13257     PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2  PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ    -0.041    2.746
    13258     PSI_BFD_SF4_opt.pdb #4/F THR 7 C     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.042    3.367
    13259     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.049    3.449
    13260     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 CG2   -0.052    3.232
    13261     PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 CB    -0.054    3.234
    13262     PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1   -0.055    2.760
    13263     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ    -0.060    3.240
    13264     PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.075    2.780
    13265     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.079    2.784
    13266     PSI_BFD_SF4_opt.pdb #4/F GLY 13 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.080    3.405
    13267     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1   -0.086    2.666
    13268     PSI_BFD_SF4_opt.pdb #4/F ALA 38 O    PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB    -0.088    3.268
    13269     PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1   -0.100    3.425
    13270     PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    -0.103    3.283
    13271     PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1  PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1   -0.107    2.812
    13272     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 CB    -0.122    3.302
    13273     PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 C     -0.130    3.530
    13274     PSI_BFD_SF4_opt.pdb #4/F GLY 13 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.134    3.459
    13275     PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ   PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.136    3.316
    13276     PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.143    2.848
    13277     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB    -0.146    3.486
    13278     PSI_BFD_SF4_opt.pdb #4/F GLY 13 O    PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ    -0.147    3.327
    13279     PSI_BFD_SF4_opt.pdb #4/F CYF 12 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.148    3.473
    13280     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG    -0.162    3.562
    13281     PSI_BFD_SF4_opt.pdb #4/F MET 53 SD   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1   -0.167    3.649
    13282     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE    -0.170    2.875
    13283     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1   -0.177    2.902
    13284     PSI_BFD_SF4_opt.pdb #4/F GLU 8 N     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.182    3.432
    13285     PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.182    3.507
    13286     PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ    -0.183    3.363
    13287     PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.187    3.512
    13288     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 CB    -0.188    3.368
    13289     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 CA    -0.188    3.368
    13290     PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.189    2.894
    13291     PSI_BFD_SF4_opt.pdb #4/F ASP 43 CG   PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.197    3.522
    13292     PSI_BFD_SF4_opt.pdb #4/F PRO 17 O    PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   -0.212    2.917
    13293     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CG1   -0.215    3.615
    13294     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.219    3.619
    13295     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1   -0.225    3.625
    13296     PSI_BFD_SF4_opt.pdb #4/F PRO 17 CG   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.230    3.555
    13297     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.238    3.503
    13298     PSI_BFD_SF4_opt.pdb #4/F GLY 13 O    PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.254    2.959
    13299     PSI_BFD_SF4_opt.pdb #4/F ALA 14 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.256    3.506
    13300     PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 N     -0.272    2.977
    13301     PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1   -0.275    2.980
    13302     PSI_BFD_SF4_opt.pdb #4/F TYR 1 CB    PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     -0.275    3.735
    13303     PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1  PSI_BFD_SF4_opt.pdb #4/C PRO 58 CG    -0.291    3.691
    13304     PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1   -0.299    3.499
    13305     PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1   -0.301    3.626
    13306     PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 CB    -0.316    3.716
    13307     PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD    PSI_BFD_SF4_opt.pdb #4/E SER 53 CB    -0.323    3.723
    13308     PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD    PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.332    3.657
    13309     PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.337    3.662
    13310     PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1   -0.342    3.542
    13311     PSI_BFD_SF4_opt.pdb #4/F ASP 29 CA   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.346    3.671
    13312     PSI_BFD_SF4_opt.pdb #4/F CYF 12 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.353    3.753
    13313     PSI_BFD_SF4_opt.pdb #4/F GLY 13 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.355    3.680
    13314     PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ    -0.356    3.536
    13315     PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ    -0.363    3.688
    13316     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 O     -0.366    3.546
    13317     PSI_BFD_SF4_opt.pdb #4/F VAL 50 CA   PSI_BFD_SF4_opt.pdb #4/C ALA 35 CB    -0.371    3.771
    13318     PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 O     -0.372    3.332
    13319     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB    -0.376    3.776
    13320     PSI_BFD_SF4_opt.pdb #4/F PRO 52 CG   PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB    -0.389    3.789
    13321     PSI_BFD_SF4_opt.pdb #4/F PRO 17 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.394    3.719
    13322    
    13323 
    13324  
    13325 88 contacts 
    13326 
    13327 > ui tool show "Selection Inspector"
    13328 
    13329 > setattr sel r ribbon_hide_backbone true
    13330 
    13331 Assigning ribbon_hide_backbone attribute to 35 items 
    13332 
    13333 > setattr sel r ribbon_hide_backbone false
    13334 
    13335 Assigning ribbon_hide_backbone attribute to 35 items 
    13336 
    13337 > hide #4.8 models
    13338 
    13339 > ui tool show Clashes
    13340 
    13341 > select #4/F
    13342 
    13343 829 atoms, 836 bonds, 60 residues, 1 model selected 
    13344 
    13345 > clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false
    13346 > color #fffb00 reveal true log true
    13347    
    13348    
    13349     Allowed overlap: 0.6
    13350     H-bond overlap reduction: 0.4
    13351     Ignore clashes between atoms separated by 4 bonds or less
    13352     Ignore clashes between atoms in residues less than 5 apart in sequence
    13353     Detect intra-residue clashes: False
    13354     Detect intra-molecule clashes: False
    13355    
    13356     4 clashes
    13357                   atom1                              atom2                 overlap  distance
    13358     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N   PSI_BFD_SF4_opt.pdb #4/E ALA 67 C    2.060    1.340
    13359     PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA  PSI_BFD_SF4_opt.pdb #4/E ALA 67 C    0.981    2.479
    13360     PSI_BFD_SF4_opt.pdb #4/F TYR 1 N   PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA   0.878    2.462
    13361     PSI_BFD_SF4_opt.pdb #4/F TYR 1 H   PSI_BFD_SF4_opt.pdb #4/E ALA 67 C    0.727    2.033
    13362    
    13363 
    13364  
    13365 4 clashes 
    13366 
    13367 > hide #4.9 models
    13368 
    13369 > select #4/E
    13370 
    13371 1071 atoms, 1082 bonds, 67 residues, 1 model selected 
    13372 
    13373 > show #1 models
    13374 
    13375 > hide #!4 models
    13376 
    13377 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    13378 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    13379 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb"
    13380 
    13381 Chain information for PSI_BFd.opt.pdb #6 
    13382 --- 
    13383 Chain | Description 
    13384 ? | No description available 
    13385  
    13386 
    13387 > split #6 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699
    13388 > atoms :1700-1765 atoms :1766-1826
    13389 
    13390 Split PSI_BFd.opt.pdb (#6) into 7 models 
    13391 Chain information for PSI_BFd.opt.pdb 1 #6.1 
    13392 --- 
    13393 Chain | Description 
    13394 ? | No description available 
    13395  
    13396 Chain information for PSI_BFd.opt.pdb 2 #6.2 
    13397 --- 
    13398 Chain | Description 
    13399 ? | No description available 
    13400  
    13401 Chain information for PSI_BFd.opt.pdb 3 #6.3 
    13402 --- 
    13403 Chain | Description 
    13404 ? | No description available 
    13405  
    13406 Chain information for PSI_BFd.opt.pdb 4 #6.4 
    13407 --- 
    13408 Chain | Description 
    13409 ? | No description available 
    13410  
    13411 Chain information for PSI_BFd.opt.pdb 5 #6.5 
    13412 --- 
    13413 Chain | Description 
    13414 ? | No description available 
    13415  
    13416 Chain information for PSI_BFd.opt.pdb 6 #6.6 
    13417 --- 
    13418 Chain | Description 
    13419 ? | No description available 
    13420  
    13421 
    13422 > changechains #6.1 A
    13423 
    13424 Chain IDs of 743 residues changed 
    13425 
    13426 > changechains #6.2 B
    13427 
    13428 Chain IDs of 733 residues changed 
    13429 
    13430 > changechains #6.3 C
    13431 
    13432 Chain IDs of 80 residues changed 
    13433 
    13434 > changechains #6.4 D
    13435 
    13436 Chain IDs of 143 residues changed 
    13437 
    13438 > changechains #6.5 E
    13439 
    13440 Chain IDs of 66 residues changed 
    13441 
    13442 > changechains #6.6 F
    13443 
    13444 Chain IDs of 61 residues changed 
    13445 
    13446 > changechains #6.7 X
    13447 
    13448 Chain IDs of 5 residues changed 
    13449 
    13450 > combine #6.1#6.2#6.3#6.4#6.5#6.6
    13451 
    13452 > combine #6.1#6.2#6.3#6.4#6.5#6.6#6.7
    13453 
    13454 > help help:user
    13455 
    13456 > renumber #8/A-E seqStart 1
    13457 
    13458 1022 residues renumbered 
    13459 
    13460 > hide #!6 models
    13461 
    13462 > hide #4.1 models
    13463 
    13464 > hide #1 models
    13465 
    13466 > hide #7 models
    13467 
    13468 > renumber #8/A start 1
    13469 
    13470 0 residues renumbered 
    13471 
    13472 > renumber #8/B start 1
    13473 
    13474 0 residues renumbered 
    13475 
    13476 > renumber #8/C start 1
    13477 
    13478 0 residues renumbered 
    13479 
    13480 > renumber #8/D start 1
    13481 
    13482 0 residues renumbered 
    13483 
    13484 > renumber #8/E start 1
    13485 
    13486 0 residues renumbered 
    13487 
    13488 > renumber #8/F start 1
    13489 
    13490 61 residues renumbered 
    13491 
    13492 > select #8/F
    13493 
    13494 841 atoms, 848 bonds, 61 residues, 1 model selected 
    13495 
    13496 > clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false
    13497 > color #fffb00 reveal true log true
    13498    
    13499    
    13500     Allowed overlap: 0.6
    13501     H-bond overlap reduction: 0.4
    13502     Ignore clashes between atoms separated by 4 bonds or less
    13503     Ignore clashes between atoms in residues less than 5 apart in sequence
    13504     Detect intra-residue clashes: False
    13505     Detect intra-molecule clashes: False
    13506    
    13507     0 clashes
    13508     atom1  atom2  overlap  distance
    13509    
    13510 
    13511  
    13512 No clashes 
    13513 
    13514 > clashes sel restrict #8/A-E resSeparation 5 interModel false intraMol false
    13515 > color #fffb00 reveal true log true
    13516    
    13517    
    13518     Allowed overlap: 0.6
    13519     H-bond overlap reduction: 0.4
    13520     Ignore clashes between atoms separated by 4 bonds or less
    13521     Ignore clashes between atoms in residues less than 5 apart in sequence
    13522     Detect intra-residue clashes: False
    13523     Detect intra-molecule clashes: False
    13524    
    13525     0 clashes
    13526     atom1  atom2  overlap  distance
    13527    
    13528 
    13529  
    13530 No clashes 
    13531 
    13532 > close #7#4-6
    13533 
    13534 > rename #8 id #4
    13535 
    13536 > close #9
    13537 
    13538 > select #4/F
    13539 
    13540 841 atoms, 848 bonds, 61 residues, 1 model selected 
    13541 
    13542 > clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false
    13543 > color #fffb00 reveal true log true
    13544    
    13545    
    13546     Allowed overlap: 0.6
    13547     H-bond overlap reduction: 0.4
    13548     Ignore clashes between atoms separated by 4 bonds or less
    13549     Ignore clashes between atoms in residues less than 5 apart in sequence
    13550     Detect intra-residue clashes: False
    13551     Detect intra-molecule clashes: False
    13552    
    13553     0 clashes
    13554     atom1  atom2  overlap  distance
    13555    
    13556 
    13557  
    13558 No clashes 
    13559 
    13560 > color sequential #4 chains palette accent
    13561 
    13562 > color sel byhetero
    13563 
    13564 > select #4/F
    13565 
    13566 841 atoms, 848 bonds, 61 residues, 1 model selected 
    13567 
    13568 > select #4/F &~H
    13569 
    13570 435 atoms, 442 bonds, 61 residues, 1 model selected 
    13571 
    13572 > contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol
    13573 > false color #ff85ff radius 0.2 reveal true log true
    13574    
    13575    
    13576     Allowed overlap: -0.4
    13577     H-bond overlap reduction: 0.4
    13578     Ignore contacts between atoms separated by 4 bonds or less
    13579     Ignore contacts between atoms in residues less than 5 apart in sequence
    13580     Detect intra-residue contacts: False
    13581     Detect intra-molecule contacts: False
    13582    
    13583     71 contacts
    13584                atom1                        atom2             overlap  distance
    13585     combination #4/F GLY 14 N    combination #4/C GLN 15 NE2   0.214    3.036
    13586     combination #4/F CYF 13 CB   combination #4/C GLN 15 CG    0.203    3.197
    13587     combination #4/F GLU 9 OE2   combination #4/E SER 53 C     0.154    3.026
    13588     combination #4/F GLY 50 O    combination #4/C LYS 34 C     0.095    3.085
    13589     combination #4/F GLU 19 CD   combination #4/D LYS 109 NZ   0.059    3.266
    13590     combination #4/F ILE 11 CD1  combination #4/C PRO 58 CB    0.048    3.352
    13591     combination #4/F THR 8 CA    combination #4/E ARG 43 NH2   0.005    3.320
    13592     combination #4/F ASP 30 OD1  combination #4/A ARG 27 CZ    -0.006    3.186
    13593     combination #4/F ASP 30 OD1  combination #4/A ARG 27 NH2   -0.014    2.719
    13594     combination #4/F MET 54 CE   combination #4/E THR 54 O     -0.032    3.212
    13595     combination #4/F GLU 19 OE1  combination #4/D LYS 109 NZ   -0.032    2.737
    13596     combination #4/F GLU 9 OE1   combination #4/E ARG 43 NH2   -0.033    2.738
    13597     combination #4/F ASP 30 OD2  combination #4/A LYS 31 NZ    -0.041    2.746
    13598     combination #4/F THR 8 C     combination #4/E ARG 43 NH2   -0.042    3.367
    13599     combination #4/F CYF 13 CA   combination #4/C GLN 15 CD    -0.049    3.449
    13600     combination #4/F GLU 9 OE2   combination #4/E THR 54 CG2   -0.052    3.232
    13601     combination #4/F GLY 50 O    combination #4/C LYS 34 CB    -0.054    3.234
    13602     combination #4/F ASP 30 OD1  combination #4/A ARG 27 NH1   -0.055    2.760
    13603     combination #4/F GLU 9 OE1   combination #4/E ARG 43 CZ    -0.060    3.240
    13604     combination #4/F GLU 17 OE2  combination #4/C ARG 18 NH2   -0.075    2.780
    13605     combination #4/F ARG 32 NH2  combination #4/A ASP 34 OD2   -0.079    2.784
    13606     combination #4/F GLY 14 N    combination #4/C GLN 15 CD    -0.080    3.405
    13607     combination #4/F GLU 9 OE2   combination #4/E THR 54 OG1   -0.086    2.666
    13608     combination #4/F GLU 17 CD   combination #4/C ARG 18 NH1   -0.100    3.425
    13609     combination #4/F GLU 17 OE1  combination #4/C ARG 18 NH1   -0.107    2.812
    13610     combination #4/F GLU 9 OE2   combination #4/E THR 54 CB    -0.122    3.302
    13611     combination #4/F MET 54 CE   combination #4/E THR 54 C     -0.130    3.530
    13612     combination #4/F GLY 14 C    combination #4/C GLN 15 NE2   -0.134    3.459
    13613     combination #4/F ARG 32 CZ   combination #4/A ASP 34 OD2   -0.136    3.316
    13614     combination #4/F ALA 7 O     combination #4/E ARG 43 NH2   -0.143    2.848
    13615     combination #4/F GLY 14 O    combination #4/C ARG 18 CZ    -0.147    3.327
    13616     combination #4/F CYF 13 C    combination #4/C GLN 15 NE2   -0.148    3.473
    13617     combination #4/F CYF 13 CA   combination #4/C GLN 15 CG    -0.162    3.562
    13618     combination #4/F MET 54 SD   combination #4/C ILE 11 CD1   -0.167    3.649
    13619     combination #4/F GLU 9 OE1   combination #4/E ARG 43 NE    -0.170    2.875
    13620     combination #4/F ARG 32 NE   combination #4/A THR 28 OG1   -0.177    2.902
    13621     combination #4/F GLU 9 N     combination #4/E ARG 43 NH2   -0.182    3.432
    13622     combination #4/F ASP 30 CG   combination #4/A ARG 27 NH2   -0.182    3.507
    13623     combination #4/F ALA 7 O     combination #4/E ARG 43 CZ    -0.183    3.363
    13624     combination #4/F GLU 17 CD   combination #4/C ARG 18 NH2   -0.187    3.512
    13625     combination #4/F GLU 9 OE2   combination #4/E SER 53 CB    -0.188    3.368
    13626     combination #4/F GLU 9 OE2   combination #4/E SER 53 CA    -0.188    3.368
    13627     combination #4/F ARG 32 NH1  combination #4/A ASP 34 OD2   -0.189    2.894
    13628     combination #4/F PRO 18 O    combination #4/D LYS 109 NZ   -0.212    2.917
    13629     combination #4/F PRO 53 CB   combination #4/C ILE 11 CG1   -0.215    3.615
    13630     combination #4/F CYF 13 CB   combination #4/C GLN 15 CD    -0.219    3.619
    13631     combination #4/F PRO 53 CB   combination #4/C ILE 11 CD1   -0.225    3.625
    13632     combination #4/F PRO 18 CG   combination #4/C ARG 18 NH2   -0.230    3.555
    13633     combination #4/F GLY 14 O    combination #4/C ARG 18 NH2   -0.254    2.959
    13634     combination #4/F ALA 15 N    combination #4/C GLN 15 NE2   -0.256    3.506
    13635     combination #4/F GLU 9 OE2   combination #4/E THR 54 N     -0.272    2.977
    13636     combination #4/F ALA 7 O     combination #4/E ARG 43 NH1   -0.275    2.980
    13637     combination #4/F ILE 11 CD1  combination #4/C PRO 58 CG    -0.291    3.691
    13638     combination #4/F MET 54 CE   combination #4/E THR 54 OG1   -0.299    3.499
    13639     combination #4/F ASP 30 CG   combination #4/A ARG 27 NH1   -0.301    3.626
    13640     combination #4/F MET 54 CE   combination #4/E THR 54 CB    -0.316    3.716
    13641     combination #4/F GLU 9 CD    combination #4/E SER 53 CB    -0.323    3.723
    13642     combination #4/F GLU 9 CD    combination #4/E ARG 43 NH2   -0.332    3.657
    13643     combination #4/F CYF 13 CA   combination #4/C GLN 15 NE2   -0.337    3.662
    13644     combination #4/F ARG 32 CZ   combination #4/A THR 28 OG1   -0.342    3.542
    13645     combination #4/F ASP 30 CA   combination #4/A ARG 27 NH2   -0.346    3.671
    13646     combination #4/F CYF 13 C    combination #4/C GLN 15 CD    -0.353    3.753
    13647     combination #4/F GLY 14 CA   combination #4/C GLN 15 NE2   -0.355    3.680
    13648     combination #4/F GLU 17 OE2  combination #4/C ARG 18 CZ    -0.356    3.536
    13649     combination #4/F ASP 30 CG   combination #4/A LYS 31 NZ    -0.363    3.688
    13650     combination #4/F PRO 53 CB   combination #4/C ILE 11 O     -0.366    3.546
    13651     combination #4/F VAL 51 CA   combination #4/C ALA 35 CB    -0.371    3.771
    13652     combination #4/F GLY 50 O    combination #4/C LYS 34 O     -0.372    3.332
    13653     combination #4/F PRO 53 CB   combination #4/C CYF 13 CB    -0.376    3.776
    13654     combination #4/F PRO 53 CG   combination #4/C CYF 13 CB    -0.389    3.789
    13655     combination #4/F PRO 18 CD   combination #4/C ARG 18 NH2   -0.394    3.719
    13656    
    13657 
    13658  
    13659 71 contacts 
    13660 
    13661 > select #4/F
    13662 
    13663 841 atoms, 848 bonds, 61 residues, 1 model selected 
    13664 
    13665 > hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false
    13666 > intraRes false reveal true log true
    13667 
    13668 Skipping possible acceptor with bad geometry: combination #4/A CYF 575 SG 
    13669 Wrong number of grandchild atoms for phi/psi acceptor combination #4/A CYF 575
    13670 SG 
    13671  
    13672 [Repeated 1 time(s)]
    13673 
    13674 Skipped 2 atom(s) with bad connectivities; see log for details 
    13675 
    13676    
    13677    
    13678     Finding intramodel H-bonds
    13679     Constraints relaxed by 0.4 angstroms and 20 degrees
    13680     Models used:
    13681         4 combination
    13682    
    13683     19 H-bonds
    13684     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    13685     combination #4/A ARG 27 NH1  combination #4/F ASP 30 OD1  combination #4/A ARG 27 HH11  2.760  1.842
    13686     combination #4/A ARG 27 NH2  combination #4/F ASP 30 OD1  combination #4/A ARG 27 HH21  2.719  1.800
    13687     combination #4/A LYS 31 NZ   combination #4/F ASP 30 O    combination #4/A LYS 31 HZ1   3.148  2.456
    13688     combination #4/A LYS 31 NZ   combination #4/F ASP 30 OD2  combination #4/A LYS 31 HZ2   2.746  1.778
    13689     combination #4/C ARG 18 NH1  combination #4/F GLU 17 OE1  combination #4/C ARG 18 HH11  2.812  1.825
    13690     combination #4/C ARG 18 NH1  combination #4/F GLU 17 OE2  combination #4/C ARG 18 HH11  3.358  2.560
    13691     combination #4/C ARG 18 NH2  combination #4/F GLU 17 OE2  combination #4/C ARG 18 HH22  2.780  1.765
    13692     combination #4/D LYS 109 NZ  combination #4/F PRO 18 O    combination #4/D LYS 109 HZ1  2.917  2.045
    13693     combination #4/D LYS 109 NZ  combination #4/F GLU 19 OE1  combination #4/D LYS 109 HZ2  2.737  1.813
    13694     combination #4/E ARG 43 NE   combination #4/F GLU 9 OE1   combination #4/E ARG 43 HE    2.875  1.950
    13695     combination #4/E ARG 43 NH1  combination #4/F ALA 7 O     combination #4/E ARG 43 HH12  2.980  2.103
    13696     combination #4/E ARG 43 NH2  combination #4/F ALA 7 O     combination #4/E ARG 43 HH22  2.848  1.943
    13697     combination #4/E ARG 43 NH2  combination #4/F GLU 9 OE1   combination #4/E ARG 43 HH21  2.738  1.784
    13698     combination #4/E THR 54 OG1  combination #4/F GLU 9 OE2   combination #4/E THR 54 HG1   2.666  1.685
    13699     combination #4/E ASN 56 ND2  combination #4/F PRO 53 O    combination #4/E ASN 56 HD22  3.598  2.755
    13700     combination #4/F ARG 32 NE   combination #4/A THR 28 OG1  combination #4/F ARG 32 HE    2.902  1.898
    13701     combination #4/F ARG 32 NH1  combination #4/A ASP 34 OD2  combination #4/F ARG 32 HH12  2.894  1.970
    13702     combination #4/F ARG 32 NH2  combination #4/A THR 28 OG1  combination #4/F ARG 32 HH21  3.324  2.539
    13703     combination #4/F ARG 32 NH2  combination #4/A ASP 34 OD2  combination #4/F ARG 32 HH22  2.784  1.818
    13704    
    13705 
    13706  
    13707 19 hydrogen bonds found 
    13708 
    13709 > select #4
    13710 
    13711 28515 atoms, 28949 bonds, 180 pseudobonds, 1831 residues, 4 models selected 
    13712 
    13713 > color sel byhetero
    13714 
    13715 > hide #4.3 models
    13716 
    13717 > rename #4 PSI_BFd_SF4_opt.pdb
    13718 
    13719 > select #4
    13720 
    13721 28515 atoms, 28949 bonds, 180 pseudobonds, 1831 residues, 4 models selected 
    13722 
    13723 > ui tool show "Selection Inspector"
    13724 
    13725 > setattr sel r ribbon_hide_backbone false
    13726 
    13727 Assigning ribbon_hide_backbone attribute to 1831 items 
    13728 
    13729 > coulombic #4/A
    13730 
    13731 Using Amber 20 recommended default charges and atom types for standard
    13732 residues 
    13733 Assigning partial charges to residue CYF (net charge +1) with am1-bcc method 
    13734 Running ANTECHAMBER command:
    13735 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
    13736 qm_theory='AM1', -i
    13737 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.in.mol2 -fi
    13738 mol2 -o
    13739 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.out.mol2 -fo
    13740 mol2 -c bcc -nc 1 -j 5 -s 2 -dr n 
    13741 (CYF) `` 
    13742 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    13743 (CYF) `` 
    13744 (CYF) `Info: Finished reading file
    13745 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.in.mol2);
    13746 atoms read (22), bonds read (21).` 
    13747 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    13748 sensitive.` 
    13749 (CYF) `Running:
    13750 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
    13751 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    13752 (CYF) `` 
    13753 (CYF) `` 
    13754 (CYF) `Running:
    13755 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
    13756 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    13757 (CYF) `Info: Total number of electrons: 92; net charge: 1` 
    13758 (CYF) `` 
    13759 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
    13760 -i sqm.in -o sqm.out` 
    13761 (CYF) `` 
    13762 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
    13763 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    13764 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    13765 -s 2 -j 1` 
    13766 (CYF) `` 
    13767 (CYF) `Running:
    13768 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    13769 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    13770 (CYF) `` 
    13771 Charges for residue CYF determined 
    13772 Coulombic values for PSI_BFd_SF4_opt.pdb_A SES surface #4.5: minimum, -12.49,
    13773 mean 0.00, maximum 20.13 
    13774 
    13775 > coulombic #4/B
    13776 
    13777 Using Amber 20 recommended default charges and atom types for standard
    13778 residues 
    13779 Assigning partial charges to residue CYF (net charge -1) with am1-bcc method 
    13780 Running ANTECHAMBER command:
    13781 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
    13782 qm_theory='AM1', -i
    13783 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.in.mol2 -fi
    13784 mol2 -o
    13785 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.out.mol2 -fo
    13786 mol2 -c bcc -nc -1 -j 5 -s 2 -dr n 
    13787 (CYF) `` 
    13788 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    13789 (CYF) `` 
    13790 (CYF) `Info: Finished reading file
    13791 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.in.mol2);
    13792 atoms read (22), bonds read (21).` 
    13793 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    13794 sensitive.` 
    13795 (CYF) `Running:
    13796 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
    13797 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    13798 (CYF) `` 
    13799 (CYF) `` 
    13800 (CYF) `Running:
    13801 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
    13802 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    13803 (CYF) `Info: Total number of electrons: 94; net charge: -1` 
    13804 (CYF) `` 
    13805 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
    13806 -i sqm.in -o sqm.out` 
    13807 (CYF) `` 
    13808 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
    13809 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    13810 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    13811 -s 2 -j 1` 
    13812 (CYF) `` 
    13813 (CYF) `Running:
    13814 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    13815 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    13816 (CYF) `` 
    13817 Charges for residue CYF determined 
    13818 Coulombic values for PSI_BFd_SF4_opt.pdb_B SES surface #4.6: minimum, -15.84,
    13819 mean -0.16, maximum 13.13 
    13820 
    13821 > coulombic #4/C
    13822 
    13823 Using Amber 20 recommended default charges and atom types for standard
    13824 residues 
    13825 Assigning partial charges to residue CYF (net charge -1) with am1-bcc method 
    13826 Running ANTECHAMBER command:
    13827 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
    13828 qm_theory='AM1', -i
    13829 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.in.mol2 -fi
    13830 mol2 -o
    13831 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.out.mol2 -fo
    13832 mol2 -c bcc -nc -1 -j 5 -s 2 -dr n 
    13833 (CYF) `` 
    13834 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    13835 (CYF) `` 
    13836 (CYF) `Info: Finished reading file
    13837 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.in.mol2);
    13838 atoms read (25), bonds read (24).` 
    13839 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    13840 sensitive.` 
    13841 (CYF) `Running:
    13842 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
    13843 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    13844 (CYF) `` 
    13845 (CYF) `` 
    13846 (CYF) `Running:
    13847 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
    13848 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    13849 (CYF) `Info: Total number of electrons: 102; net charge: -1` 
    13850 (CYF) `` 
    13851 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
    13852 -i sqm.in -o sqm.out` 
    13853 (CYF) `` 
    13854 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
    13855 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    13856 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    13857 -s 2 -j 1` 
    13858 (CYF) `` 
    13859 (CYF) `Running:
    13860 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    13861 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    13862 (CYF) `` 
    13863 Charges for residue CYF determined 
    13864 Coulombic values for PSI_BFd_SF4_opt.pdb_C SES surface #4.7: minimum, -21.93,
    13865 mean -4.05, maximum 8.44 
    13866 
    13867 > coulombic #4/D
    13868 
    13869 Using Amber 20 recommended default charges and atom types for standard
    13870 residues 
    13871 Coulombic values for PSI_BFd_SF4_opt.pdb_D SES surface #4.8: minimum, -11.15,
    13872 mean 2.11, maximum 15.26 
    13873 
    13874 > coulombic #4/E
    13875 
    13876 Using Amber 20 recommended default charges and atom types for standard
    13877 residues 
    13878 Coulombic values for PSI_BFd_SF4_opt.pdb_E SES surface #4.9: minimum, -11.38,
    13879 mean 1.55, maximum 11.87 
    13880 
    13881 > coulombic #4/F
    13882 
    13883 Using Amber 20 recommended default charges and atom types for standard
    13884 residues 
    13885 Assigning partial charges to residue CYF (net charge -1) with am1-bcc method 
    13886 Running ANTECHAMBER command:
    13887 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
    13888 qm_theory='AM1', -i
    13889 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.in.mol2 -fi
    13890 mol2 -o
    13891 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.out.mol2 -fo
    13892 mol2 -c bcc -nc -1 -j 5 -s 2 -dr n 
    13893 (CYF) `` 
    13894 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    13895 (CYF) `` 
    13896 (CYF) `Info: Finished reading file
    13897 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.in.mol2);
    13898 atoms read (22), bonds read (21).` 
    13899 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    13900 sensitive.` 
    13901 (CYF) `Running:
    13902 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
    13903 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    13904 (CYF) `` 
    13905 (CYF) `` 
    13906 (CYF) `Running:
    13907 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
    13908 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    13909 (CYF) `Info: Total number of electrons: 94; net charge: -1` 
    13910 (CYF) `` 
    13911 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
    13912 -i sqm.in -o sqm.out` 
    13913 (CYF) `` 
    13914 (CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
    13915 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    13916 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    13917 -s 2 -j 1` 
    13918 (CYF) `` 
    13919 (CYF) `Running:
    13920 /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    13921 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    13922 (CYF) `` 
    13923 Charges for residue CYF determined 
    13924 Coulombic values for PSI_BFd_SF4_opt.pdb_F SES surface #4.10: minimum, -24.55,
    13925 mean -9.44, maximum 5.59 
    13926 
    13927 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    13928 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    13929 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    13930 > relaxed.cxs"
    13931 
    13932 > hide #4.10 models
    13933 
    13934 > select #4/F
    13935 
    13936 841 atoms, 848 bonds, 61 residues, 1 model selected 
    13937 
    13938 > ui tool show "Color Actions"
    13939 
    13940 > color sel dark orange target acpf
    13941 
    13942 > color sel byhetero target acpf
    13943 
    13944 > select #4/X:1831@F1:1827@F2
    13945 
    13946 2 atoms, 2 residues, 1 model selected 
    13947 
    13948 > ui tool show Distances
    13949 
    13950 > distance #4/X:1827@F2 #4/X:1831@F1
    13951 
    13952 Distance between PSI_BFd_SF4_opt.pdb #4/X SF4 1827 F2 and SF4 1831 F1: 9.521Å 
    13953 
    13954 > distance style color #011993
    13955 
    13956 [Repeated 2 time(s)]
    13957 
    13958 > distance style decimalPlaces 4
    13959 
    13960 [Repeated 2 time(s)]
    13961 
    13962 > distance style decimalPlaces 5
    13963 
    13964 [Repeated 2 time(s)]
    13965 
    13966 > distance style decimalPlaces 6
    13967 
    13968 [Repeated 2 time(s)]
    13969 
    13970 > distance style decimalPlaces 5
    13971 
    13972 [Repeated 2 time(s)]
    13973 
    13974 > distance style decimalPlaces 4
    13975 
    13976 [Repeated 2 time(s)]
    13977 
    13978 > distance style decimalPlaces 3
    13979 
    13980 [Repeated 2 time(s)]
    13981 
    13982 > distance style decimalPlaces 2
    13983 
    13984 [Repeated 2 time(s)]
    13985 
    13986 > distance style decimalPlaces 1
    13987 
    13988 [Repeated 2 time(s)]
    13989 
    13990 > distance style radius 0.3
    13991 
    13992 [Repeated 2 time(s)]
    13993 
    13994 > distance style radius 0.2
    13995 
    13996 [Repeated 2 time(s)]
    13997 
    13998 > hide #!5 models
    13999 
    14000 > select #4/F:3-9,27-34,53-61
    14001 
    14002 368 atoms, 369 bonds, 24 residues, 1 model selected 
    14003 
    14004 > show #1 models
    14005 
    14006 > ui tool show Matchmaker
    14007 
    14008 > select #2:1-2,8-24,30-47 :<0.1 &#4/F
    14009 
    14010 Nothing selected 
    14011 
    14012 > select #3:1-2,8-24,30-47 :<0.1 &#4/F
    14013 
    14014 Nothing selected 
    14015 
    14016 > select #3:1-2,8-24,30-47
    14017 
    14018 447 atoms, 448 bonds, 37 residues, 1 model selected 
    14019 
    14020 > show #!3 models
    14021 
    14022 > select #3:1-2,8-24,30-47
    14023 
    14024 447 atoms, 448 bonds, 37 residues, 1 model selected 
    14025 
    14026 > select #3 &~:1-2,8-24,30-47
    14027 
    14028 315 atoms, 228 bonds, 114 residues, 1 model selected 
    14029 
    14030 > color sel cyan target acpf
    14031 
    14032 > hide #!3 models
    14033 
    14034 > show #!3 models
    14035 
    14036 > hide #1 models
    14037 
    14038 > hide #!3 models
    14039 
    14040 > show #!3 models
    14041 
    14042 > hide #!3 models
    14043 
    14044 > show #!3 models
    14045 
    14046 > hide #!3 models
    14047 
    14048 > ui tool show Matchmaker
    14049 
    14050 > matchmaker #!3 to #4/F pairing bs
    14051 
    14052 Parameters 
    14053 --- 
    14054 Chain pairing | bs 
    14055 Alignment algorithm | Needleman-Wunsch 
    14056 Similarity matrix | BLOSUM-62 
    14057 SS fraction | 0.3 
    14058 Gap open (HH/SS/other) | 18/18/6 
    14059 Gap extend | 1 
    14060 SS matrix |  |  | H | S | O 
    14061 ---|---|---|--- 
    14062 H | 6 | -9 | -6 
    14063 S |  | 6 | -6 
    14064 O |  |  | 4 
    14065 Iteration cutoff | 2 
    14066  
    14067 Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with BFd (2fdn), chain M (#3),
    14068 sequence alignment score = 115.9 
    14069 RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs:
    14070 3.340) 
    14071  
    14072 
    14073 > matchmaker #!3 to #4/F pairing bs showAlignment true
    14074 
    14075 Parameters 
    14076 --- 
    14077 Chain pairing | bs 
    14078 Alignment algorithm | Needleman-Wunsch 
    14079 Similarity matrix | BLOSUM-62 
    14080 SS fraction | 0.3 
    14081 Gap open (HH/SS/other) | 18/18/6 
    14082 Gap extend | 1 
    14083 SS matrix |  |  | H | S | O 
    14084 ---|---|---|--- 
    14085 H | 6 | -9 | -6 
    14086 S |  | 6 | -6 
    14087 O |  |  | 4 
    14088 Iteration cutoff | 2 
    14089  
    14090 Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with BFd (2fdn), chain M (#3),
    14091 sequence alignment score = 115.9 
    14092 Alignment identifier is 1 
    14093 Showing conservation header ("seq_conservation" residue attribute) for
    14094 alignment 1 
    14095 Hiding conservation header for alignment 1 
    14096 Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M,
    14097 PSI_BFd_SF4_opt.pdb #4/F 
    14098 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    14099 RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs:
    14100 3.340) 
    14101  
    14102 
    14103 > sequence header consensus show
    14104 
    14105 Showing consensus header ("seq_consensus" residue attribute) for alignment 1 
    14106 
    14107 > select #4:3-9,27-34,53-61
    14108 
    14109 2226 atoms, 2237 bonds, 35 pseudobonds, 144 residues, 3 models selected 
    14110 
    14111 > select #4/F:3-9,27-34,53-61
    14112 
    14113 368 atoms, 369 bonds, 24 residues, 1 model selected 
    14114 
    14115 > color sel cyan target acpf
    14116 
    14117 > color sel byhetero target acpf
    14118 
    14119 > show #4.10 models
    14120 
    14121 > hide #4.10 models
    14122 
    14123 > select #4/A:27,28,31,34
    14124 
    14125 72 atoms, 69 bonds, 4 residues, 1 model selected 
    14126 
    14127 > transparency (#!4 & sel) 20
    14128 
    14129 > transparency (#!4 & sel) 10
    14130 
    14131 > transparency (#!4 & sel) 90
    14132 
    14133 > select clear
    14134 
    14135 > select #4/C:18/D:109/E:43,54,56,67
    14136 
    14137 98 atoms, 93 bonds, 5 residues, 1 model selected 
    14138 
    14139 > transparency (#!4 & sel) 90
    14140 
    14141 > select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
    14142 
    14143 170 atoms, 162 bonds, 9 residues, 1 model selected 
    14144 
    14145 > transparency (#!4 & sel) 0
    14146 
    14147 > select #4/A-F
    14148 
    14149 28475 atoms, 28949 bonds, 90 pseudobonds, 1826 residues, 3 models selected 
    14150 
    14151 > show #4.10 models
    14152 
    14153 > transparency (#!4 & sel) 30
    14154 
    14155 > transparency (#!4 & sel) 20
    14156 
    14157 > transparency (#!4 & sel) 10
    14158 
    14159 > select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
    14160 
    14161 170 atoms, 162 bonds, 9 residues, 1 model selected 
    14162 
    14163 > transparency (#!4 & sel) 90
    14164 
    14165 > hide #4.10 models
    14166 
    14167 > select clear
    14168 
    14169 > transparency #4.1-2,4-9#!4 80
    14170 
    14171 > transparency #4.1-2,4-9#!4 10
    14172 
    14173 > select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
    14174 
    14175 170 atoms, 162 bonds, 9 residues, 1 model selected 
    14176 
    14177 > transparency (#!4 & sel) 80
    14178 
    14179 > select clear
    14180 
    14181 > hide #4.7 models
    14182 
    14183 > select #4/X
    14184 
    14185 40 atoms, 91 pseudobonds, 5 residues, 3 models selected 
    14186 
    14187 > style sel sphere
    14188 
    14189 Changed 40 atom styles 
    14190 
    14191 > style sel ball
    14192 
    14193 Changed 40 atom styles 
    14194 
    14195 > show #1 models
    14196 
    14197 > hide #!4 models
    14198 
    14199 > show #!4 models
    14200 
    14201 > show #!5 models
    14202 
    14203 > hide #1 models
    14204 
    14205 > style sel sphere
    14206 
    14207 Changed 40 atom styles 
    14208 
    14209 > select clear
    14210 
    14211 > show #4.10 models
    14212 
    14213 > hide #4.10 models
    14214 
    14215 > show #4.7 models
    14216 
    14217 > select #4/A-E
    14218 
    14219 27634 atoms, 28101 bonds, 1765 residues, 1 model selected 
    14220 
    14221 > transparency (#!4 & sel) 30
    14222 
    14223 > hide #4.9 models
    14224 
    14225 > hide #4.8 models
    14226 
    14227 > hide #4.7 models
    14228 
    14229 > hide #4.6 models
    14230 
    14231 > hide #4.5 models
    14232 
    14233 > show #4.5 models
    14234 
    14235 > show #4.6 models
    14236 
    14237 > show #4.7 models
    14238 
    14239 > show #4.8 models
    14240 
    14241 > show #4.9 models
    14242 
    14243 > show #4.10 models
    14244 
    14245 > select add #4.10
    14246 
    14247 28475 atoms, 28101 bonds, 1826 residues, 6 models selected 
    14248 
    14249 > select subtract #4.10
    14250 
    14251 27634 atoms, 28101 bonds, 1765 residues, 7 models selected 
    14252 
    14253 > select add #4.10
    14254 
    14255 28475 atoms, 28101 bonds, 1826 residues, 6 models selected 
    14256 
    14257 > select subtract #4.10
    14258 
    14259 27634 atoms, 28101 bonds, 1765 residues, 7 models selected 
    14260 
    14261 > select add #4.10
    14262 
    14263 28475 atoms, 28101 bonds, 1826 residues, 6 models selected 
    14264 
    14265 > select #4/F
    14266 
    14267 841 atoms, 848 bonds, 61 residues, 1 model selected 
    14268 
    14269 > transparency (#!4 & sel) 30
    14270 
    14271 > select clear
    14272 
    14273 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14274 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    14275 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    14276 > relaxed.cxs"
    14277 
    14278 > hide #4.10 models
    14279 
    14280 > show #4.10 models
    14281 
    14282 > hide #4.10 models
    14283 
    14284 > hide #4.7 models
    14285 
    14286 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14287 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    14288 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    14289 > relaxed.cxs"
    14290 
    14291 > hide #4.9 models
    14292 
    14293 > hide #4.8 models
    14294 
    14295 > hide #4.6 models
    14296 
    14297 > hide #4.5 models
    14298 
    14299 > select #4:SF4
    14300 
    14301 40 atoms, 91 pseudobonds, 5 residues, 3 models selected 
    14302 
    14303 > style sel stick
    14304 
    14305 Changed 40 atom styles 
    14306 
    14307 > style sel ball
    14308 
    14309 Changed 40 atom styles 
    14310 
    14311 > select #4/F:42@SG
    14312 
    14313 1 atom, 1 residue, 1 model selected 
    14314 
    14315 > select #4/X:1828@F1
    14316 
    14317 1 atom, 1 residue, 1 model selected 
    14318 
    14319 > ui tool show "Build Structure"
    14320 
    14321 > select clear
    14322 
    14323 [Repeated 1 time(s)]
    14324 
    14325 > help help:user
    14326 
    14327 > hide #4.1 models
    14328 
    14329 > show #4.1 models
    14330 
    14331 > hide #4.1 models
    14332 
    14333 > show #4.1 models
    14334 
    14335 > select #4:1828@F1
    14336 
    14337 1 atom, 1 residue, 1 model selected 
    14338 
    14339 > bond #4:1828@F1 reasonable true
    14340 
    14341 Must specify two or more atoms 
    14342 
    14343 > select #4:1828@F1,S2,S3,S4
    14344 
    14345 4 atoms, 3 pseudobonds, 1 residue, 2 models selected 
    14346 
    14347 > bond #4:1828@F1,S2,S3,S4
    14348 
    14349 Created 3 bonds 
    14350 
    14351 > bond #4:1828@F3,S1,S3,S2
    14352 
    14353 Created 2 bonds 
    14354 
    14355 > bond #4:1828@F3,S4
    14356 
    14357 Created 1 bond 
    14358 
    14359 > select #4:1828@F2,S4
    14360 
    14361 2 atoms, 1 pseudobond, 1 residue, 2 models selected 
    14362 
    14363 > select #4:1828@F2,S4,S1,S3
    14364 
    14365 4 atoms, 3 pseudobonds, 1 residue, 2 models selected 
    14366 
    14367 > bond #4:1828@F2,S4,S1,S3
    14368 
    14369 Created 3 bonds 
    14370 
    14371 > select #4:1828@F4,S2,S1,S3
    14372 
    14373 4 atoms, 3 pseudobonds, 1 residue, 2 models selected 
    14374 
    14375 > bond #4:1828@F4,S2,S1,S3
    14376 
    14377 Created 3 bonds 
    14378 
    14379 > bond #4:1828
    14380 
    14381 Created 6 bonds 
    14382 
    14383 > ~bond sel
    14384 
    14385 > bond #4:SF4
    14386 
    14387 Created 78 bonds 
    14388 
    14389 > ~bond #4:SF4@F1,F2,F3,F4
    14390 
    14391 > hide #4.1 models
    14392 
    14393 > select #4:SF4
    14394 
    14395 40 atoms, 60 bonds, 91 pseudobonds, 5 residues, 3 models selected 
    14396 
    14397 > style sel ball
    14398 
    14399 Changed 40 atom styles 
    14400 
    14401 > select clear
    14402 
    14403 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14404 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    14405 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    14406 > relaxed.cxs"
    14407 
    14408 > windowsize
    14409 
    14410 window size 806 684 
    14411 
    14412 > windowsize 750
    14413 
    14414 > windowsize 800
    14415 
    14416 > windowsize 800 600
    14417 
    14418 > windowsize 800 800
    14419 
    14420 > windowsize 800 700
    14421 
    14422 > windowsize 800 670
    14423 
    14424 > windowsize 800 675
    14425 
    14426 > show #4.10 models
    14427 
    14428 > show #4.9 models
    14429 
    14430 > show #4.8 models
    14431 
    14432 > show #4.7 models
    14433 
    14434 > show #4.6 models
    14435 
    14436 > show #4.5 models
    14437 
    14438 > view list
    14439 
    14440 Named views: HbondsZoom, back, front, side 
    14441 
    14442 > view front
    14443 
    14444 > view side
    14445 
    14446 > view HbondsZoom
    14447 
    14448 > hide #4.10 models
    14449 
    14450 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14451 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    14452 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    14453 > relaxed.cxs"
    14454 
    14455 > select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
    14456 
    14457 170 atoms, 162 bonds, 9 residues, 1 model selected 
    14458 
    14459 > transparency (#!4 & sel) 80
    14460 
    14461 > select clear
    14462 
    14463 > hide #4.9 models
    14464 
    14465 > show #4.3 models
    14466 
    14467 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14468 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    14469 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    14470 > relaxed.cxs"
    14471 
    14472 > ui tool show Contacts
    14473 
    14474 > select #4/F
    14475 
    14476 841 atoms, 848 bonds, 61 residues, 1 model selected 
    14477 
    14478 > select #4/F &~H
    14479 
    14480 435 atoms, 442 bonds, 61 residues, 1 model selected 
    14481 
    14482 > contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol
    14483 > false color #ff85ff radius 0.2 log true
    14484    
    14485    
    14486     Allowed overlap: -0.4
    14487     H-bond overlap reduction: 0.4
    14488     Ignore contacts between atoms separated by 4 bonds or less
    14489     Ignore contacts between atoms in residues less than 5 apart in sequence
    14490     Detect intra-residue contacts: False
    14491     Detect intra-molecule contacts: False
    14492    
    14493     71 contacts
    14494                    atom1                                atom2                 overlap  distance
    14495     PSI_BFd_SF4_opt.pdb #4/F GLY 14 N    PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   0.214    3.036
    14496     PSI_BFd_SF4_opt.pdb #4/F CYF 13 CB   PSI_BFd_SF4_opt.pdb #4/C GLN 15 CG    0.203    3.197
    14497     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E SER 53 C     0.154    3.026
    14498     PSI_BFd_SF4_opt.pdb #4/F GLY 50 O    PSI_BFd_SF4_opt.pdb #4/C LYS 34 C     0.095    3.085
    14499     PSI_BFd_SF4_opt.pdb #4/F GLU 19 CD   PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ   0.059    3.266
    14500     PSI_BFd_SF4_opt.pdb #4/F ILE 11 CD1  PSI_BFd_SF4_opt.pdb #4/C PRO 58 CB    0.048    3.352
    14501     PSI_BFd_SF4_opt.pdb #4/F THR 8 CA    PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   0.005    3.320
    14502     PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 CZ    -0.006    3.186
    14503     PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2   -0.014    2.719
    14504     PSI_BFd_SF4_opt.pdb #4/F MET 54 CE   PSI_BFd_SF4_opt.pdb #4/E THR 54 O     -0.032    3.212
    14505     PSI_BFd_SF4_opt.pdb #4/F GLU 19 OE1  PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ   -0.032    2.737
    14506     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.033    2.738
    14507     PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD2  PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ    -0.041    2.746
    14508     PSI_BFd_SF4_opt.pdb #4/F THR 8 C     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.042    3.367
    14509     PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA   PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD    -0.049    3.449
    14510     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 CG2   -0.052    3.232
    14511     PSI_BFd_SF4_opt.pdb #4/F GLY 50 O    PSI_BFd_SF4_opt.pdb #4/C LYS 34 CB    -0.054    3.234
    14512     PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1   -0.055    2.760
    14513     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 CZ    -0.060    3.240
    14514     PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2  PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.075    2.780
    14515     PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2  PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2   -0.079    2.784
    14516     PSI_BFd_SF4_opt.pdb #4/F GLY 14 N    PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD    -0.080    3.405
    14517     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1   -0.086    2.666
    14518     PSI_BFd_SF4_opt.pdb #4/F GLU 17 CD   PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1   -0.100    3.425
    14519     PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE1  PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1   -0.107    2.812
    14520     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 CB    -0.122    3.302
    14521     PSI_BFd_SF4_opt.pdb #4/F MET 54 CE   PSI_BFd_SF4_opt.pdb #4/E THR 54 C     -0.130    3.530
    14522     PSI_BFd_SF4_opt.pdb #4/F GLY 14 C    PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.134    3.459
    14523     PSI_BFd_SF4_opt.pdb #4/F ARG 32 CZ   PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2   -0.136    3.316
    14524     PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.143    2.848
    14525     PSI_BFd_SF4_opt.pdb #4/F GLY 14 O    PSI_BFd_SF4_opt.pdb #4/C ARG 18 CZ    -0.147    3.327
    14526     PSI_BFd_SF4_opt.pdb #4/F CYF 13 C    PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.148    3.473
    14527     PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA   PSI_BFd_SF4_opt.pdb #4/C GLN 15 CG    -0.162    3.562
    14528     PSI_BFd_SF4_opt.pdb #4/F MET 54 SD   PSI_BFd_SF4_opt.pdb #4/C ILE 11 CD1   -0.167    3.649
    14529     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 NE    -0.170    2.875
    14530     PSI_BFd_SF4_opt.pdb #4/F ARG 32 NE   PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1   -0.177    2.902
    14531     PSI_BFd_SF4_opt.pdb #4/F GLU 9 N     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.182    3.432
    14532     PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG   PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2   -0.182    3.507
    14533     PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 CZ    -0.183    3.363
    14534     PSI_BFd_SF4_opt.pdb #4/F GLU 17 CD   PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.187    3.512
    14535     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E SER 53 CB    -0.188    3.368
    14536     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E SER 53 CA    -0.188    3.368
    14537     PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH1  PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2   -0.189    2.894
    14538     PSI_BFd_SF4_opt.pdb #4/F PRO 18 O    PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ   -0.212    2.917
    14539     PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB   PSI_BFd_SF4_opt.pdb #4/C ILE 11 CG1   -0.215    3.615
    14540     PSI_BFd_SF4_opt.pdb #4/F CYF 13 CB   PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD    -0.219    3.619
    14541     PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB   PSI_BFd_SF4_opt.pdb #4/C ILE 11 CD1   -0.225    3.625
    14542     PSI_BFd_SF4_opt.pdb #4/F PRO 18 CG   PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.230    3.555
    14543     PSI_BFd_SF4_opt.pdb #4/F GLY 14 O    PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.254    2.959
    14544     PSI_BFd_SF4_opt.pdb #4/F ALA 15 N    PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.256    3.506
    14545     PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 N     -0.272    2.977
    14546     PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH1   -0.275    2.980
    14547     PSI_BFd_SF4_opt.pdb #4/F ILE 11 CD1  PSI_BFd_SF4_opt.pdb #4/C PRO 58 CG    -0.291    3.691
    14548     PSI_BFd_SF4_opt.pdb #4/F MET 54 CE   PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1   -0.299    3.499
    14549     PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG   PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1   -0.301    3.626
    14550     PSI_BFd_SF4_opt.pdb #4/F MET 54 CE   PSI_BFd_SF4_opt.pdb #4/E THR 54 CB    -0.316    3.716
    14551     PSI_BFd_SF4_opt.pdb #4/F GLU 9 CD    PSI_BFd_SF4_opt.pdb #4/E SER 53 CB    -0.323    3.723
    14552     PSI_BFd_SF4_opt.pdb #4/F GLU 9 CD    PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.332    3.657
    14553     PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA   PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.337    3.662
    14554     PSI_BFd_SF4_opt.pdb #4/F ARG 32 CZ   PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1   -0.342    3.542
    14555     PSI_BFd_SF4_opt.pdb #4/F ASP 30 CA   PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2   -0.346    3.671
    14556     PSI_BFd_SF4_opt.pdb #4/F CYF 13 C    PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD    -0.353    3.753
    14557     PSI_BFd_SF4_opt.pdb #4/F GLY 14 CA   PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.355    3.680
    14558     PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2  PSI_BFd_SF4_opt.pdb #4/C ARG 18 CZ    -0.356    3.536
    14559     PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG   PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ    -0.363    3.688
    14560     PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB   PSI_BFd_SF4_opt.pdb #4/C ILE 11 O     -0.366    3.546
    14561     PSI_BFd_SF4_opt.pdb #4/F VAL 51 CA   PSI_BFd_SF4_opt.pdb #4/C ALA 35 CB    -0.371    3.771
    14562     PSI_BFd_SF4_opt.pdb #4/F GLY 50 O    PSI_BFd_SF4_opt.pdb #4/C LYS 34 O     -0.372    3.332
    14563     PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB   PSI_BFd_SF4_opt.pdb #4/C CYF 13 CB    -0.376    3.776
    14564     PSI_BFd_SF4_opt.pdb #4/F PRO 53 CG   PSI_BFd_SF4_opt.pdb #4/C CYF 13 CB    -0.389    3.789
    14565     PSI_BFd_SF4_opt.pdb #4/F PRO 18 CD   PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.394    3.719
    14566    
    14567 
    14568  
    14569 71 contacts 
    14570 
    14571 > select #4/F:14,9,50,19,11,8,30,54,19,9,17,32,7,18,53,51
    14572 
    14573 199 atoms, 193 bonds, 14 residues, 1 model selected 
    14574 
    14575 > hide sel atoms
    14576 
    14577 > select #4/F
    14578 
    14579 841 atoms, 848 bonds, 61 residues, 1 model selected 
    14580 
    14581 > ui tool show "Selection Inspector"
    14582 
    14583 > setattr sel r ribbon_hide_backbone true
    14584 
    14585 Assigning ribbon_hide_backbone attribute to 61 items 
    14586 
    14587 > select #4/F &H
    14588 
    14589 406 atoms, 61 residues, 1 model selected 
    14590 
    14591 > hide sel atoms
    14592 
    14593 > ui tool show H-Bonds
    14594 
    14595 > select #4/F
    14596 
    14597 841 atoms, 848 bonds, 61 residues, 1 model selected 
    14598 
    14599 > hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false
    14600 > intraRes false select true reveal true log true
    14601 
    14602 Skipping possible acceptor with bad geometry: PSI_BFd_SF4_opt.pdb #4/A CYF 575
    14603 SG 
    14604 Wrong number of grandchild atoms for phi/psi acceptor PSI_BFd_SF4_opt.pdb #4/A
    14605 CYF 575 SG 
    14606  
    14607 [Repeated 1 time(s)]
    14608 
    14609 Skipped 2 atom(s) with bad connectivities; see log for details 
    14610 
    14611    
    14612    
    14613     Finding intramodel H-bonds
    14614     Constraints relaxed by 0.4 angstroms and 20 degrees
    14615     Models used:
    14616         4 PSI_BFd_SF4_opt.pdb
    14617    
    14618     19 H-bonds
    14619     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    14620     PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1  PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 HH11  2.760  1.842
    14621     PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2  PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 HH21  2.719  1.800
    14622     PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ   PSI_BFd_SF4_opt.pdb #4/F ASP 30 O    PSI_BFd_SF4_opt.pdb #4/A LYS 31 HZ1   3.148  2.456
    14623     PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ   PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD2  PSI_BFd_SF4_opt.pdb #4/A LYS 31 HZ2   2.746  1.778
    14624     PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1  PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE1  PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH11  2.812  1.825
    14625     PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1  PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2  PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH11  3.358  2.560
    14626     PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2  PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2  PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH22  2.780  1.765
    14627     PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ  PSI_BFd_SF4_opt.pdb #4/F PRO 18 O    PSI_BFd_SF4_opt.pdb #4/D LYS 109 HZ1  2.917  2.045
    14628     PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ  PSI_BFd_SF4_opt.pdb #4/F GLU 19 OE1  PSI_BFd_SF4_opt.pdb #4/D LYS 109 HZ2  2.737  1.813
    14629     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NE   PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 HE    2.875  1.950
    14630     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH1  PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH12  2.980  2.103
    14631     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2  PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH22  2.848  1.943
    14632     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2  PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH21  2.738  1.784
    14633     PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1  PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 HG1   2.666  1.685
    14634     PSI_BFd_SF4_opt.pdb #4/E ASN 56 ND2  PSI_BFd_SF4_opt.pdb #4/F PRO 53 O    PSI_BFd_SF4_opt.pdb #4/E ASN 56 HD22  3.598  2.755
    14635     PSI_BFd_SF4_opt.pdb #4/F ARG 32 NE   PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1  PSI_BFd_SF4_opt.pdb #4/F ARG 32 HE    2.902  1.898
    14636     PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH1  PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2  PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH12  2.894  1.970
    14637     PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2  PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1  PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH21  3.324  2.539
    14638     PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2  PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2  PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH22  2.784  1.818
    14639    
    14640 
    14641  
    14642 19 hydrogen bonds found 
    14643 
    14644 > ui tool show "Selection Inspector"
    14645 
    14646 > setattr sel r ribbon_hide_backbone true
    14647 
    14648 Assigning ribbon_hide_backbone attribute to 17 items 
    14649 
    14650 > setattr sel r ribbon_hide_backbone false
    14651 
    14652 Assigning ribbon_hide_backbone attribute to 17 items 
    14653 
    14654 > hide #4.3 models
    14655 
    14656 > show #4.9 models
    14657 
    14658 > show #4.10 models
    14659 
    14660 > hide #4.10 models
    14661 
    14662 > select clear
    14663 
    14664 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14665 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    14666 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    14667 > relaxed.cxs"
    14668 
    14669 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14670 > 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom
    14671 > hbonds.png" width 1600 height 1350 supersample 3 transparentBackground true
    14672 
    14673 > show #4.10 models
    14674 
    14675 > hide #5.1 models
    14676 
    14677 > select add #4.10
    14678 
    14679 841 atoms, 61 residues, 1 model selected 
    14680 
    14681 > select add #4.9
    14682 
    14683 1900 atoms, 127 residues, 2 models selected 
    14684 
    14685 > select add #4.8
    14686 
    14687 4177 atoms, 270 residues, 3 models selected 
    14688 
    14689 > select add #4.7
    14690 
    14691 5383 atoms, 350 residues, 4 models selected 
    14692 
    14693 > select add #4.6
    14694 
    14695 16896 atoms, 1083 residues, 5 models selected 
    14696 
    14697 > select add #4.5
    14698 
    14699 28475 atoms, 1826 residues, 6 models selected 
    14700 
    14701 > transparency (#!4 & sel) 20
    14702 
    14703 > view front
    14704 
    14705 > select clear
    14706 
    14707 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14708 > 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces
    14709 > front .png" width 1600 height 1350 supersample 3 transparentBackground true
    14710 
    14711 > view side
    14712 
    14713 > view front
    14714 
    14715 > ui tool show "Color Key"
    14716 
    14717 > ui mousemode right "color key"
    14718 
    14719 > key blue-white-red :min : :-
    14720 
    14721 > key blue-white-red :min :0 :-
    14722 
    14723 > key blue-white-red :+ :0 :-
    14724 
    14725 > key size 0.25000,0.02000
    14726 
    14727 > key size 0.25000,0.01000
    14728 
    14729 > key fontSize 23
    14730 
    14731 > key fontSize 22
    14732 
    14733 > key fontSize 21
    14734 
    14735 > key fontSize 20
    14736 
    14737 > key fontSize 19
    14738 
    14739 > key fontSize 18
    14740 
    14741 > key ticks true
    14742 
    14743 > key tickThickness 5.0
    14744 
    14745 > key tickThickness 4.0
    14746 
    14747 > key labelOffset -1.0
    14748 
    14749 > key labelOffset -2.0
    14750 
    14751 > key labelOffset -3.0
    14752 
    14753 > key labelOffset -4.0
    14754 
    14755 > key labelOffset -5.0
    14756 
    14757 > key labelOffset -6.0
    14758 
    14759 > key labelOffset -7.0
    14760 
    14761 > key labelOffset -8.0
    14762 
    14763 > key labelOffset -9.0
    14764 
    14765 > key labelOffset -10.0
    14766 
    14767 > key labelOffset -11.0
    14768 
    14769 > key labelOffset -12.0
    14770 
    14771 > key labelOffset -13.0
    14772 
    14773 > key labelOffset -14.0
    14774 
    14775 > key labelOffset -15.0
    14776 
    14777 > key labelOffset -16.0
    14778 
    14779 > key labelOffset -17.0
    14780 
    14781 > key labelOffset -16.0
    14782 
    14783 > key labelOffset -15.0
    14784 
    14785 > key fontSize 17
    14786 
    14787 > key bold true
    14788 
    14789 > key pos 0.1,0.08000
    14790 
    14791 > key pos 0.70000,0.08000
    14792 
    14793 > key pos 0.75000,0.08000
    14794 
    14795 > key pos 0.75000,0.8000
    14796 
    14797 > key pos 0.75000,0.9000
    14798 
    14799 > key pos 0.75000,0.95000
    14800 
    14801 > windowsize 800 675
    14802 
    14803 > key pos 0.75000,0.90000
    14804 
    14805 > key pos 0.75000,0.98000
    14806 
    14807 > key pos 0.75000,0.9000
    14808 
    14809 > key pos 0.75000,0.97000
    14810 
    14811 > key pos 0.72000,0.97000
    14812 
    14813 > ui mousemode right translate
    14814 
    14815 > windowsize 800 675
    14816 
    14817 > select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
    14818 
    14819 170 atoms, 162 bonds, 9 residues, 1 model selected 
    14820 
    14821 > select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
    14822 
    14823 170 atoms, 162 bonds, 9 residues, 1 model selected 
    14824 
    14825 > view HbondsZoom
    14826 
    14827 > hide #4.10 models
    14828 
    14829 > transparency (#!4 & sel) 80
    14830 
    14831 > select clear
    14832 
    14833 > hide #6 models
    14834 
    14835 > show #6 models
    14836 
    14837 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14838 > 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom
    14839 > hbonds.png" width 1600 height 1350 supersample 3 transparentBackground true
    14840 
    14841 > select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
    14842 
    14843 170 atoms, 162 bonds, 9 residues, 1 model selected 
    14844 
    14845 > transparency (#!4 & sel) 20
    14846 
    14847 > select clear
    14848 
    14849 > show #4.10 models
    14850 
    14851 > view front
    14852 
    14853 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14854 > 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces
    14855 > front .png" width 1600 height 1350 supersample 3 transparentBackground true
    14856 
    14857 > view side
    14858 
    14859 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14860 > 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png"
    14861 > width 1600 height 1350 supersample 3 transparentBackground true
    14862 
    14863 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14864 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    14865 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    14866 > relaxed.cxs"
    14867 
    14868 ——— End of log from Thu Oct 10 08:30:31 2024 ———
    14869 
    14870 opened ChimeraX session 
    14871 
    14872 > windowsize 900 675
    14873 
    14874 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14875 > 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png"
    14876 > width 1800 height 1350 supersample 3 transparentBackground true
    14877 
    14878 > view list
    14879 
    14880 Named views: HbondsZoom, back, front, side 
    14881 
    14882 > view front
    14883 
    14884 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14885 > 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces
    14886 > front .png" width 1800 height 1350 supersample 3 transparentBackground true
    14887 
    14888 > select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
    14889 
    14890 170 atoms, 162 bonds, 9 residues, 1 model selected 
    14891 
    14892 > transparency (#!4 & sel) 80
    14893 
    14894 > view HbondsZoom
    14895 
    14896 > hide #4.10 models
    14897 
    14898 > select clear
    14899 
    14900 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14901 > 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom
    14902 > hbonds.png" width 1800 height 1350 supersample 3 transparentBackground true
    14903 
    14904 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    14905 > 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with
    14906 > RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER
    14907 > relaxed.cxs"
    14908 
    14909 ——— End of log from Fri Oct 11 10:32:45 2024 ———
    14910 
    14911 opened ChimeraX session 
    14912 
    14913 > hide #4.9 models
    14914 
    14915 > hide #4.7 models
    14916 
    14917 > hide #4.8 models
    14918 
    14919 > hide #4.6 models
    14920 
    14921 > hide #4.5 models
    14922 
    14923 > hide #4.4 models
    14924 
    14925 > show #4.4 models
    14926 
    14927 > open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
    14928 > Migal/Dror Noy Group - General/@fromDROR-
    14929 > NAS/Prabir/PS1/PS1_dehydrogenase_docking/docking/Dock_PS1_Fd_test_output.pdb"
    14930 
    14931 Chain information for Dock_PS1_Fd_test_output.pdb #7 
    14932 --- 
    14933 Chain | Description 
    14934 Y | No description available 
    14935 Z | No description available 
    14936  
    14937 
    14938 > ui tool show Matchmaker
    14939 
    14940 > matchmaker #7/Z to #4/C pairing ss showAlignment true
    14941 
    14942 Parameters 
    14943 --- 
    14944 Chain pairing | ss 
    14945 Alignment algorithm | Needleman-Wunsch 
    14946 Similarity matrix | BLOSUM-62 
    14947 SS fraction | 0.3 
    14948 Gap open (HH/SS/other) | 18/18/6 
    14949 Gap extend | 1 
    14950 SS matrix |  |  | H | S | O 
    14951 ---|---|---|--- 
    14952 H | 6 | -9 | -6 
    14953 S |  | 6 | -6 
    14954 O |  |  | 4 
    14955 Iteration cutoff | 2 
    14956  
    14957 Matchmaker PSI_BFd_SF4_opt.pdb, chain C (#4) with Dock_PS1_Fd_test_output.pdb,
    14958 chain Z (#7), sequence alignment score = 342.4 
    14959 Alignment identifier is 2 
    14960 Showing conservation header ("seq_conservation" residue attribute) for
    14961 alignment 2 
    14962 Hiding conservation header for alignment 2 
    14963 Chains used in RMSD evaluation for alignment 2: PSI_BFd_SF4_opt.pdb #4/C,
    14964 Dock_PS1_Fd_test_output.pdb #7/Z 
    14965 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    14966 RMSD between 80 pruned atom pairs is 0.300 angstroms; (across all 80 pairs:
    14967 0.300) 
    14968  
    14969 
    14970 > select #9:1183@S4:1741@F1
    14971 
    14972 Nothing selected 
    14973 
    14974 > select #7:1183@S4:1741@F1
    14975 
    14976 2 atoms, 2 residues, 1 model selected 
    14977 
    14978 > hide #!7 models
    14979 
    14980 > show #!7 models
    14981 
    14982 > hide #!7 models
    14983 
    14984 > show #!7 models
    14985 
    14986 > ui tool show Distances
    14987 
    14988 > ~distance #4/X:1827@F2 #4/X:1831@F1
    14989 
    14990 > distance #7/Z:1741@F1 #7/Y:1183@S4
    14991 
    14992 Distance between Dock_PS1_Fd_test_output.pdb #7/Z SF4 1741 F1 and /Y SF4 1183
    14993 S4: 11.458Å 
    14994 
    14995 > select #7/Z
    14996 
    14997 13593 atoms, 13984 bonds, 54 pseudobonds, 1741 residues, 2 models selected 
    14998 
    14999 > ui tool show Clashes
    15000 
    15001 > clashes sel restrict #7/Y resSeparation 5 interModel false intraMol false
    15002 > color #fffb00 reveal true log true
    15003    
    15004    
    15005     Allowed overlap: 0.6
    15006     H-bond overlap reduction: 0.4
    15007     Ignore clashes between atoms separated by 4 bonds or less
    15008     Ignore clashes between atoms in residues less than 5 apart in sequence
    15009     Detect intra-residue clashes: False
    15010     Detect intra-molecule clashes: False
    15011    
    15012     9 clashes
    15013                        atom1                                         atom2                      overlap  distance
    15014     Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH2   Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 CB    1.695    1.825
    15015     Dock_PS1_Fd_test_output.pdb #7/Z LYS 189 CG   Dock_PS1_Fd_test_output.pdb #7/Y LYS 132 NZ    1.265    2.255
    15016     Dock_PS1_Fd_test_output.pdb #7/Z ILE 11 CD1   Dock_PS1_Fd_test_output.pdb #7/Y ASP 88 OD1    0.807    2.493
    15017     Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH1   Dock_PS1_Fd_test_output.pdb #7/Y ILE 111 CG2   0.798    2.722
    15018     Dock_PS1_Fd_test_output.pdb #7/Z ILE 11 CD1   Dock_PS1_Fd_test_output.pdb #7/Y ASP 88 CG     0.795    2.965
    15019     Dock_PS1_Fd_test_output.pdb #7/Z THR 277 CG2  Dock_PS1_Fd_test_output.pdb #7/Y GLU 90 OE1    0.792    2.508
    15020     Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH2   Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 CG    0.777    2.743
    15021     Dock_PS1_Fd_test_output.pdb #7/Z THR 277 CG2  Dock_PS1_Fd_test_output.pdb #7/Y GLU 90 CD     0.702    3.058
    15022     Dock_PS1_Fd_test_output.pdb #7/Z GLU 188 O    Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 OD1   0.639    2.201
    15023    
    15024 
    15025  
    15026 9 clashes 
    15027 
    15028 > hide #!4 models
    15029 
    15030 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single
    15031 > Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif"
    15032 
    15033 Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif
    15034 #8 
    15035 --- 
    15036 Chain | Description 
    15037 A | . 
    15038  
    15039 
    15040 > ui tool show Matchmaker
    15041 
    15042 > matchmaker #8/A to #7/Y pairing ss showAlignment true
    15043 
    15044 Parameters 
    15045 --- 
    15046 Chain pairing | ss 
    15047 Alignment algorithm | Needleman-Wunsch 
    15048 Similarity matrix | BLOSUM-62 
    15049 SS fraction | 0.3 
    15050 Gap open (HH/SS/other) | 18/18/6 
    15051 Gap extend | 1 
    15052 SS matrix |  |  | H | S | O 
    15053 ---|---|---|--- 
    15054 H | 6 | -9 | -6 
    15055 S |  | 6 | -6 
    15056 O |  |  | 4 
    15057 Iteration cutoff | 2 
    15058  
    15059 Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with
    15060 fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#8),
    15061 sequence alignment score = 139.8 
    15062 Alignment identifier is 3 
    15063 Showing conservation header ("seq_conservation" residue attribute) for
    15064 alignment 3 
    15065 Hiding conservation header for alignment 3 
    15066 Chains used in RMSD evaluation for alignment 3: Dock_PS1_Fd_test_output.pdb
    15067 #7/Y, fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8/A 
    15068 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3 
    15069 RMSD between 7 pruned atom pairs is 1.406 angstroms; (across all 441 pairs:
    15070 35.668) 
    15071  
    15072 
    15073 > hide #!7 models
    15074 
    15075 > close #8
    15076 
    15077 > show #!7 models
    15078 
    15079 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single
    15080 > Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif"
    15081 
    15082 Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif
    15083 #8 
    15084 --- 
    15085 Chain | Description 
    15086 A | . 
    15087  
    15088 Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to
    15089 fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 0
    15090 mismatches 
    15091 Chains used in RMSD evaluation for alignment 3: Dock_PS1_Fd_test_output.pdb
    15092 #7/Y, fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8/A 
    15093 
    15094 > view
    15095 
    15096 > hide #8 models
    15097 
    15098 > save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
    15099 
    15100 ——— End of log from Mon Oct 14 17:57:44 2024 ———
    15101 
    15102 opened ChimeraX session 
    15103 
    15104 > open 1hfe
    15105 
    15106 1hfe title: 
    15107 1.6 A resolution structure of the Fe-ONLY hydrogenase from desulfovibrio
    15108 desulfuricans [more info...] 
    15109  
    15110 Chain information for 1hfe #9 
    15111 --- 
    15112 Chain | Description | UniProt 
    15113 L M | PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) | PHFL_DESVH 1-421 
    15114 S T | PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) | PHFS_DESVH 1-123 
    15115  
    15116 Non-standard residues in 1hfe #9 
    15117 --- 
    15118 CMO — carbon monoxide 
    15119 CYN — cyanide ion 
    15120 CYS — cysteine 
    15121 FE2 — Fe (II) ion 
    15122 PDT — 1,3-propanedithiol 
    15123 SF4 — iron/sulfur cluster 
    15124 ZN — zinc ion 
    15125  
    15126 1hfe mmCIF Assemblies 
    15127 --- 
    15128 1| author_and_software_defined_assembly 
    15129 2| author_and_software_defined_assembly 
    15130 3| software_defined_assembly 
    15131  
    15132 351 atoms have alternate locations. Control/examine alternate locations with
    15133 Altloc Explorer [start tool...] or the altlocs command. 
    15134 Associated 1hfe chain L to
    15135 fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 25
    15136 mismatches 
    15137 Associated 1hfe chain M to
    15138 fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 25
    15139 mismatches 
    15140 
    15141 > view
    15142 
    15143 > show #8 models
    15144 
    15145 > open 6sdv
    15146 
    15147 Summary of feedback from opening 6sdv fetched from pdb 
    15148 --- 
    15149 note | Fetching compressed mmCIF 6sdv from http://files.rcsb.org/download/6sdv.cif 
    15150  
    15151 6sdv title: 
    15152 W-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced form
    15153 [more info...] 
    15154  
    15155 Chain information for 6sdv #10 
    15156 --- 
    15157 Chain | Description | UniProt 
    15158 A | Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit | Q72EJ1_DESVH 1-1005 
    15159 B | Formate dehydrogenase, beta subunit, putative | Q72EJ0_DESVH 1-236 
    15160  
    15161 Non-standard residues in 6sdv #10 
    15162 --- 
    15163 GOL — glycerol (glycerin; propane-1,2,3-triol) 
    15164 H2S — hydrosulfuric acid (hydrogen sulfide) 
    15165 MGD —
    15166 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-
    15167 anthracen-4-one guanosine dinucleotide (molybdopterin guanosine dinucleotide) 
    15168 NO3 — nitrate ion 
    15169 PEG — di(hydroxyethyl)ether 
    15170 SEC — selenocysteine 
    15171 SF4 — iron/sulfur cluster 
    15172 W — tungsten ion 
    15173  
    15174 
    15175 > hide #8 models
    15176 
    15177 > hide #!9 models
    15178 
    15179 > open "/Users/drornoy/Documents/Protein Designs/PSI H2ase/Prabir optimized
    15180 > structures/Dock_PS1_Fd_test_output.pdb"
    15181 
    15182 Chain information for Dock_PS1_Fd_test_output.pdb #11 
    15183 --- 
    15184 Chain | Description 
    15185 Y | No description available 
    15186 Z | No description available 
    15187  
    15188 Associated Dock_PS1_Fd_test_output.pdb chain Z to Dock_PS1_Fd_test_output.pdb,
    15189 chain Z with 0 mismatches 
    15190 Associated Dock_PS1_Fd_test_output.pdb chain Y to Dock_PS1_Fd_test_output.pdb,
    15191 chain Y with 0 mismatches 
    15192 
    15193 > show #!9 models
    15194 
    15195 > hide #!10 models
    15196 
    15197 > hide #!7 models
    15198 
    15199 > close #11
    15200 
    15201 > show #!10 models
    15202 
    15203 > save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
    15204 
    15205 ——— End of log from Mon Oct 14 18:11:28 2024 ———
    15206 
    15207 opened ChimeraX session 
    15208 
    15209 > show #!4 models
    15210 
    15211 > ui tool show Matchmaker
    15212 
    15213 > matchmaker #9/L to #4/F pairing ss
    15214 
    15215 Parameters 
    15216 --- 
    15217 Chain pairing | ss 
    15218 Alignment algorithm | Needleman-Wunsch 
    15219 Similarity matrix | BLOSUM-62 
    15220 SS fraction | 0.3 
    15221 Gap open (HH/SS/other) | 18/18/6 
    15222 Gap extend | 1 
    15223 SS matrix |  |  | H | S | O 
    15224 ---|---|---|--- 
    15225 H | 6 | -9 | -6 
    15226 S |  | 6 | -6 
    15227 O |  |  | 4 
    15228 Iteration cutoff | 2 
    15229  
    15230 Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with 1hfe, chain L (#9), sequence
    15231 alignment score = 28.8 
    15232 RMSD between 22 pruned atom pairs is 0.734 angstroms; (across all 52 pairs:
    15233 15.360) 
    15234  
    15235 
    15236 > select #9/M/T
    15237 
    15238 4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected 
    15239 
    15240 > hide #!4 models
    15241 
    15242 > hide sel cartoons
    15243 
    15244 > hide sel atoms
    15245 
    15246 > show #!4 models
    15247 
    15248 > hide #!4 models
    15249 
    15250 > show #1 models
    15251 
    15252 > hide #1 models
    15253 
    15254 > show #!4 models
    15255 
    15256 > hide #!4 models
    15257 
    15258 > show #!7 models
    15259 
    15260 > hide #!10 models
    15261 
    15262 > show #!10 models
    15263 
    15264 > hide #!9 models
    15265 
    15266 > hide #!10 models
    15267 
    15268 > show #!10 models
    15269 
    15270 No reference and/or match structure/chain chosen 
    15271 
    15272 > show #!4 models
    15273 
    15274 > hide #!10 models
    15275 
    15276 > hide #!7 models
    15277 
    15278 > show #!7 models
    15279 
    15280 > show #!10 models
    15281 
    15282 > hide #!7 models
    15283 
    15284 > show #!7 models
    15285 
    15286 > hide #!7 models
    15287 
    15288 > matchmaker #10/B to #7/Y pairing ss
    15289 
    15290 Parameters 
    15291 --- 
    15292 Chain pairing | ss 
    15293 Alignment algorithm | Needleman-Wunsch 
    15294 Similarity matrix | BLOSUM-62 
    15295 SS fraction | 0.3 
    15296 Gap open (HH/SS/other) | 18/18/6 
    15297 Gap extend | 1 
    15298 SS matrix |  |  | H | S | O 
    15299 ---|---|---|--- 
    15300 H | 6 | -9 | -6 
    15301 S |  | 6 | -6 
    15302 O |  |  | 4 
    15303 Iteration cutoff | 2 
    15304  
    15305 Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 6sdv, chain B (#10),
    15306 sequence alignment score = 1014 
    15307 RMSD between 123 pruned atom pairs is 1.190 angstroms; (across all 214 pairs:
    15308 3.455) 
    15309  
    15310 
    15311 > matchmaker #9/L to #10/B pairing ss
    15312 
    15313 Parameters 
    15314 --- 
    15315 Chain pairing | ss 
    15316 Alignment algorithm | Needleman-Wunsch 
    15317 Similarity matrix | BLOSUM-62 
    15318 SS fraction | 0.3 
    15319 Gap open (HH/SS/other) | 18/18/6 
    15320 Gap extend | 1 
    15321 SS matrix |  |  | H | S | O 
    15322 ---|---|---|--- 
    15323 H | 6 | -9 | -6 
    15324 S |  | 6 | -6 
    15325 O |  |  | 4 
    15326 Iteration cutoff | 2 
    15327  
    15328 Matchmaker 6sdv, chain B (#10) with 1hfe, chain L (#9), sequence alignment
    15329 score = 64.3 
    15330 RMSD between 6 pruned atom pairs is 1.458 angstroms; (across all 188 pairs:
    15331 28.430) 
    15332  
    15333 
    15334 > show #!9 models
    15335 
    15336 > hide #!10 models
    15337 
    15338 > hide #!9 models
    15339 
    15340 > show #!10 models
    15341 
    15342 > hide #!10 models
    15343 
    15344 > show #!7 models
    15345 
    15346 > hide #!4 models
    15347 
    15348 > select #7/Y:1-73
    15349 
    15350 585 atoms, 600 bonds, 73 residues, 1 model selected 
    15351 
    15352 > show #!9 models
    15353 
    15354 > hide #!7 models
    15355 
    15356 > select #9/Y:25-84
    15357 
    15358 Nothing selected 
    15359 
    15360 > select #9/S:25-84
    15361 
    15362 393 atoms, 400 bonds, 49 residues, 1 model selected 
    15363 
    15364 > select #9/L:25-84
    15365 
    15366 450 atoms, 461 bonds, 60 residues, 1 model selected 
    15367 
    15368 > select #7/Y:1-73#9/L:25-84
    15369 
    15370 1035 atoms, 1061 bonds, 133 residues, 2 models selected 
    15371 
    15372 > show #!10 models
    15373 
    15374 > hide #!10 models
    15375 
    15376 > show #!7 models
    15377 
    15378 > matchmaker #9/L & sel to #7/Y & sel pairing ss showAlignment true
    15379 
    15380 Parameters 
    15381 --- 
    15382 Chain pairing | ss 
    15383 Alignment algorithm | Needleman-Wunsch 
    15384 Similarity matrix | BLOSUM-62 
    15385 SS fraction | 0.3 
    15386 Gap open (HH/SS/other) | 18/18/6 
    15387 Gap extend | 1 
    15388 SS matrix |  |  | H | S | O 
    15389 ---|---|---|--- 
    15390 H | 6 | -9 | -6 
    15391 S |  | 6 | -6 
    15392 O |  |  | 4 
    15393 Iteration cutoff | 2 
    15394  
    15395 Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 1hfe, chain L (#9),
    15396 sequence alignment score = 34.8 
    15397 Alignment identifier is 2 
    15398 Showing conservation header ("seq_conservation" residue attribute) for
    15399 alignment 2 
    15400 Hiding conservation header for alignment 2 
    15401 Chains used in RMSD evaluation for alignment 2: Dock_PS1_Fd_test_output.pdb
    15402 #7/Y, 1hfe #9/L 
    15403 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    15404 RMSD between 8 pruned atom pairs is 1.316 angstroms; (across all 51 pairs:
    15405 12.843) 
    15406  
    15407 
    15408 > matchmaker #9/L & sel to #10/B pairing ss showAlignment true
    15409 
    15410 Parameters 
    15411 --- 
    15412 Chain pairing | ss 
    15413 Alignment algorithm | Needleman-Wunsch 
    15414 Similarity matrix | BLOSUM-62 
    15415 SS fraction | 0.3 
    15416 Gap open (HH/SS/other) | 18/18/6 
    15417 Gap extend | 1 
    15418 SS matrix |  |  | H | S | O 
    15419 ---|---|---|--- 
    15420 H | 6 | -9 | -6 
    15421 S |  | 6 | -6 
    15422 O |  |  | 4 
    15423 Iteration cutoff | 2 
    15424  
    15425 Matchmaker 6sdv, chain B (#10) with 1hfe, chain L (#9), sequence alignment
    15426 score = 34.1 
    15427 Alignment identifier is 3 
    15428 Showing conservation header ("seq_conservation" residue attribute) for
    15429 alignment 3 
    15430 Hiding conservation header for alignment 3 
    15431 Chains used in RMSD evaluation for alignment 3: 1hfe #9/L, 6sdv #10/B 
    15432 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3 
    15433 RMSD between 4 pruned atom pairs is 1.059 angstroms; (across all 59 pairs:
    15434 15.580) 
    15435  
    15436 
    15437 > hide #!7 models
    15438 
    15439 > show #!10 models
    15440 
    15441 > show #!7 models
    15442 
    15443 > hide #!10 models
    15444 
    15445 > hide #!9 models
    15446 
    15447 > show #!10 models
    15448 
    15449 > hide #!7 models
    15450 
    15451 > show #!7 models
    15452 
    15453 > select #7/Y:75-137#9/L:25-84
    15454 
    15455 910 atoms, 928 bonds, 123 residues, 2 models selected 
    15456 
    15457 > matchmaker #9/L & sel to #10/B & sel pairing ss showAlignment true
    15458 
    15459 No 'to' chains specified 
    15460 
    15461 > matchmaker #9/L & sel to #7/Y & sel pairing ss showAlignment true
    15462 
    15463 Parameters 
    15464 --- 
    15465 Chain pairing | ss 
    15466 Alignment algorithm | Needleman-Wunsch 
    15467 Similarity matrix | BLOSUM-62 
    15468 SS fraction | 0.3 
    15469 Gap open (HH/SS/other) | 18/18/6 
    15470 Gap extend | 1 
    15471 SS matrix |  |  | H | S | O 
    15472 ---|---|---|--- 
    15473 H | 6 | -9 | -6 
    15474 S |  | 6 | -6 
    15475 O |  |  | 4 
    15476 Iteration cutoff | 2 
    15477  
    15478 Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 1hfe, chain L (#9),
    15479 sequence alignment score = 52.2 
    15480 Alignment identifier is 4 
    15481 Showing conservation header ("seq_conservation" residue attribute) for
    15482 alignment 4 
    15483 Hiding conservation header for alignment 4 
    15484 Chains used in RMSD evaluation for alignment 4: Dock_PS1_Fd_test_output.pdb
    15485 #7/Y, 1hfe #9/L 
    15486 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4 
    15487 RMSD between 22 pruned atom pairs is 1.074 angstroms; (across all 46 pairs:
    15488 6.759) 
    15489  
    15490 
    15491 > hide #!10 models
    15492 
    15493 > show #!9 models
    15494 
    15495 > hide #!9 models
    15496 
    15497 > show #!3 models
    15498 
    15499 > hide #!3 models
    15500 
    15501 > select #7/Y
    15502 
    15503 9266 atoms, 9474 bonds, 90 pseudobonds, 1186 residues, 2 models selected 
    15504 
    15505 > color (#!7 & sel) gray
    15506 
    15507 > color sel byhetero
    15508 
    15509 > show #!3 models
    15510 
    15511 > hide #!3 models
    15512 
    15513 > show #!9 models
    15514 
    15515 > hide #!7 models
    15516 
    15517 > show #!3 models
    15518 
    15519 > hide #!3 models
    15520 
    15521 > hide #!9 models
    15522 
    15523 > show #!7 models
    15524 
    15525 > show #!9 models
    15526 
    15527 > hide #!7 models
    15528 
    15529 > hide #!9 models
    15530 
    15531 > show #!7 models
    15532 
    15533 > align #9/L:422-423 toAtoms #7/Y:1183-1184
    15534 
    15535 RMSD between 16 atom pairs is 1.724 angstroms 
    15536 
    15537 > show #!9 models
    15538 
    15539 > hide #!7 models
    15540 
    15541 > show #!7 models
    15542 
    15543 > hide #!9 models
    15544 
    15545 > show #!9 models
    15546 
    15547 > hide #!9 models
    15548 
    15549 > hide #!7 models
    15550 
    15551 > show #!9 models
    15552 
    15553 > select #9/L:35,38,41,76, 45,66,69,72#7/Y:73,76,81,120,85,110,113,116
    15554 
    15555 96 atoms, 80 bonds, 16 residues, 2 models selected 
    15556 
    15557 > hide #!9 models
    15558 
    15559 > show #!7 models
    15560 
    15561 > select #9/L:35-41 #7/Y:73-81
    15562 
    15563 114 atoms, 115 bonds, 16 residues, 2 models selected 
    15564 
    15565 > show #!9 models
    15566 
    15567 > hide #!7 models
    15568 
    15569 > show #!3 models
    15570 
    15571 > hide #!9 models
    15572 
    15573 > show #!9 models
    15574 
    15575 > select ~sel & ##selected
    15576 
    15577 31473 atoms, 31085 bonds, 193 pseudobonds, 5083 residues, 6 models selected 
    15578 
    15579 > align #9/L:422-423 toAtoms #3:61,62
    15580 
    15581 RMSD between 16 atom pairs is 2.679 angstroms 
    15582 
    15583 > select #9/S:25-84
    15584 
    15585 393 atoms, 400 bonds, 49 residues, 1 model selected 
    15586 
    15587 > hide #!3 models
    15588 
    15589 > select #9/L:25-84
    15590 
    15591 450 atoms, 461 bonds, 60 residues, 1 model selected 
    15592 
    15593 > select #9/L:27-84
    15594 
    15595 432 atoms, 442 bonds, 58 residues, 1 model selected 
    15596 
    15597 > select #9/L:27-84
    15598 
    15599 432 atoms, 442 bonds, 58 residues, 1 model selected 
    15600 
    15601 > color sel lime
    15602 
    15603 > color sel byhetero
    15604 
    15605 > hide #!9 models
    15606 
    15607 > show #!7 models
    15608 
    15609 > select #7/Y:63-121
    15610 
    15611 434 atoms, 443 bonds, 59 residues, 1 model selected 
    15612 
    15613 > select #7/Y:72-121
    15614 
    15615 354 atoms, 358 bonds, 50 residues, 1 model selected 
    15616 
    15617 > show #!9 models
    15618 
    15619 > hide #!9 models
    15620 
    15621 > combine #3
    15622 
    15623 Associated copy of BFd (2fdn) chain M to BFd (2fdn), chain M with 0 mismatches 
    15624 Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M,
    15625 PSI_BFd_SF4_opt.pdb #4/F, copy of BFd (2fdn) #11/M 
    15626 
    15627 > matchmaker #11/M to #7/Y & sel pairing ss
    15628 
    15629 Parameters 
    15630 --- 
    15631 Chain pairing | ss 
    15632 Alignment algorithm | Needleman-Wunsch 
    15633 Similarity matrix | BLOSUM-62 
    15634 SS fraction | 0.3 
    15635 Gap open (HH/SS/other) | 18/18/6 
    15636 Gap extend | 1 
    15637 SS matrix |  |  | H | S | O 
    15638 ---|---|---|--- 
    15639 H | 6 | -9 | -6 
    15640 S |  | 6 | -6 
    15641 O |  |  | 4 
    15642 Iteration cutoff | 2 
    15643  
    15644 Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with copy of BFd (2fdn),
    15645 chain M (#11), sequence alignment score = 86.5 
    15646 RMSD between 25 pruned atom pairs is 1.276 angstroms; (across all 42 pairs:
    15647 3.792) 
    15648  
    15649 
    15650 > hide #!7 models
    15651 
    15652 > show #!9 models
    15653 
    15654 > select #9/L:25-84
    15655 
    15656 450 atoms, 461 bonds, 60 residues, 1 model selected 
    15657 
    15658 > matchmaker #9/L & sel to #11/M pairing ss
    15659 
    15660 Parameters 
    15661 --- 
    15662 Chain pairing | ss 
    15663 Alignment algorithm | Needleman-Wunsch 
    15664 Similarity matrix | BLOSUM-62 
    15665 SS fraction | 0.3 
    15666 Gap open (HH/SS/other) | 18/18/6 
    15667 Gap extend | 1 
    15668 SS matrix |  |  | H | S | O 
    15669 ---|---|---|--- 
    15670 H | 6 | -9 | -6 
    15671 S |  | 6 | -6 
    15672 O |  |  | 4 
    15673 Iteration cutoff | 2 
    15674  
    15675 Matchmaker copy of BFd (2fdn), chain M (#11) with 1hfe, chain L (#9), sequence
    15676 alignment score = 104.3 
    15677 RMSD between 43 pruned atom pairs is 1.236 angstroms; (across all 55 pairs:
    15678 2.501) 
    15679  
    15680 
    15681 > show #!3 models
    15682 
    15683 > hide #!9 models
    15684 
    15685 > select #3:61/11:61
    15686 
    15687 8 atoms, 12 bonds, 1 residue, 1 model selected 
    15688 
    15689 > select #3:61#11:61
    15690 
    15691 16 atoms, 24 bonds, 2 residues, 2 models selected 
    15692 
    15693 > color sel cornflower blue
    15694 
    15695 > show #!9 models
    15696 
    15697 > hide #!9 models
    15698 
    15699 > select #9/L:25-84
    15700 
    15701 450 atoms, 461 bonds, 60 residues, 1 model selected 
    15702 
    15703 > hide #!11 models
    15704 
    15705 > show #!9 models
    15706 
    15707 > matchmaker #9/L & sel to #3/M pairing ss
    15708 
    15709 Parameters 
    15710 --- 
    15711 Chain pairing | ss 
    15712 Alignment algorithm | Needleman-Wunsch 
    15713 Similarity matrix | BLOSUM-62 
    15714 SS fraction | 0.3 
    15715 Gap open (HH/SS/other) | 18/18/6 
    15716 Gap extend | 1 
    15717 SS matrix |  |  | H | S | O 
    15718 ---|---|---|--- 
    15719 H | 6 | -9 | -6 
    15720 S |  | 6 | -6 
    15721 O |  |  | 4 
    15722 Iteration cutoff | 2 
    15723  
    15724 Matchmaker BFd (2fdn), chain M (#3) with 1hfe, chain L (#9), sequence
    15725 alignment score = 104.3 
    15726 RMSD between 43 pruned atom pairs is 1.232 angstroms; (across all 55 pairs:
    15727 2.484) 
    15728  
    15729 
    15730 > show #!4 models
    15731 
    15732 > show #8 models
    15733 
    15734 > matchmaker #8/A to #9/L pairing ss
    15735 
    15736 Parameters 
    15737 --- 
    15738 Chain pairing | ss 
    15739 Alignment algorithm | Needleman-Wunsch 
    15740 Similarity matrix | BLOSUM-62 
    15741 SS fraction | 0.3 
    15742 Gap open (HH/SS/other) | 18/18/6 
    15743 Gap extend | 1 
    15744 SS matrix |  |  | H | S | O 
    15745 ---|---|---|--- 
    15746 H | 6 | -9 | -6 
    15747 S |  | 6 | -6 
    15748 O |  |  | 4 
    15749 Iteration cutoff | 2 
    15750  
    15751 Matchmaker 1hfe, chain L (#9) with
    15752 fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#8),
    15753 sequence alignment score = 2066.5 
    15754 RMSD between 390 pruned atom pairs is 0.207 angstroms; (across all 396 pairs:
    15755 1.636) 
    15756  
    15757 
    15758 > hide #!9 models
    15759 
    15760 > show #!9 models
    15761 
    15762 > select #9/S
    15763 
    15764 860 atoms, 733 bonds, 1 pseudobond, 235 residues, 2 models selected 
    15765 
    15766 > color (#!9 & sel) cyan
    15767 
    15768 > hide #!9 models
    15769 
    15770 > select #8:467-477
    15771 
    15772 92 atoms, 96 bonds, 11 residues, 1 model selected 
    15773 
    15774 > hide sel cartoons
    15775 
    15776 > show #!9 models
    15777 
    15778 > select add #8
    15779 
    15780 3677 atoms, 3770 bonds, 477 residues, 1 model selected 
    15781 
    15782 > select subtract #8
    15783 
    15784 Nothing selected 
    15785 
    15786 > hide #8 models
    15787 
    15788 > hide #!9 models
    15789 
    15790 > show #8 models
    15791 
    15792 > close #9-10
    15793 
    15794 > save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
    15795 
    15796 > open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
    15797 > Migal/Dror Noy Group - General/FDH TUM/AF3 FdhF_HycB
    15798 > complex/fold_clj_fdhf_hycb_D8GNT2_ptm80_iptm_67/fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif"
    15799 
    15800 Chain information for fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif #9 
    15801 --- 
    15802 Chain | Description 
    15803 A | . 
    15804 B | . 
    15805  
    15806 
    15807 > hide #8 models
    15808 
    15809 > hide #!3 models
    15810 
    15811 > hide #!4 models
    15812 
    15813 > view
    15814 
    15815 > select #9:59-150 &:Cys
    15816 
    15817 78 atoms, 65 bonds, 13 residues, 1 model selected 
    15818 
    15819 > select #9:59-140 &:Cys
    15820 
    15821 66 atoms, 55 bonds, 11 residues, 1 model selected 
    15822 
    15823 > select #9/B:59-140 &:Cys
    15824 
    15825 48 atoms, 40 bonds, 8 residues, 1 model selected 
    15826 
    15827 > show #!11 models
    15828 
    15829 > matchmaker #9/B & sel to #11/M pairing ss
    15830 
    15831 Parameters 
    15832 --- 
    15833 Chain pairing | ss 
    15834 Alignment algorithm | Needleman-Wunsch 
    15835 Similarity matrix | BLOSUM-62 
    15836 SS fraction | 0.3 
    15837 Gap open (HH/SS/other) | 18/18/6 
    15838 Gap extend | 1 
    15839 SS matrix |  |  | H | S | O 
    15840 ---|---|---|--- 
    15841 H | 6 | -9 | -6 
    15842 S |  | 6 | -6 
    15843 O |  |  | 4 
    15844 Iteration cutoff | 2 
    15845  
    15846 Matchmaker copy of BFd (2fdn), chain M (#11) with
    15847 fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif, chain B (#9), sequence
    15848 alignment score = 46 
    15849 RMSD between 8 pruned atom pairs is 0.685 angstroms; (across all 8 pairs:
    15850 0.685) 
    15851  
    15852 
    15853 > view
    15854 
    15855 > show #!7 models
    15856 
    15857 > hide #!7 models
    15858 
    15859 > show #!4 models
    15860 
    15861 > hide #!11 models
    15862 
    15863 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
    15864 > PSI-BFd PSI-DdHyd.cxs"
    15865 
    15866 > select #9/B:112-137
    15867 
    15868 195 atoms, 196 bonds, 26 residues, 1 model selected 
    15869 
    15870 > show #!7 models
    15871 
    15872 > hide #!4 models
    15873 
    15874 > select #9/B:59-140 &:Cys
    15875 
    15876 48 atoms, 40 bonds, 8 residues, 1 model selected 
    15877 
    15878 > show sel atoms
    15879 
    15880 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
    15881 > PSI-BFd PSI-DdHyd.cxs"
    15882 
    15883 ——— End of log from Mon Oct 14 21:44:01 2024 ———
    15884 
    15885 opened ChimeraX session 
    15886 
    15887 > hide #!5 models
    15888 
    15889 > hide #5.1 models
    15890 
    15891 > hide #6 models
    15892 
    15893 > hide #!7 models
    15894 
    15895 > hide #9 models
    15896 
    15897 > show #!4 models
    15898 
    15899 > open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-
    15900 > DFG/DdHyd_PSI.opt.pdb
    15901 
    15902 Chain information for DdHyd_PSI.opt.pdb #10 
    15903 --- 
    15904 Chain | Description 
    15905 ? | No description available 
    15906  
    15907 
    15908 > ui tool show Matchmaker
    15909 
    15910 > matchmaker #!10 to #4 showAlignment true
    15911 
    15912 Parameters 
    15913 --- 
    15914 Chain pairing | bb 
    15915 Alignment algorithm | Needleman-Wunsch 
    15916 Similarity matrix | BLOSUM-62 
    15917 SS fraction | 0.3 
    15918 Gap open (HH/SS/other) | 18/18/6 
    15919 Gap extend | 1 
    15920 SS matrix |  |  | H | S | O 
    15921 ---|---|---|--- 
    15922 H | 6 | -9 | -6 
    15923 S |  | 6 | -6 
    15924 O |  |  | 4 
    15925 Iteration cutoff | 2 
    15926  
    15927 Matchmaker PSI_BFd_SF4_opt.pdb, chain A (#4) with DdHyd_PSI.opt.pdb, chain
    15928 (blank) (#10), sequence alignment score = 3958.5 
    15929 Alignment identifier is 2 
    15930 Showing conservation header ("seq_conservation" residue attribute) for
    15931 alignment 2 
    15932 Hiding conservation header for alignment 2 
    15933 Chains used in RMSD evaluation for alignment 2: PSI_BFd_SF4_opt.pdb #4/A,
    15934 DdHyd_PSI.opt.pdb #10/? 
    15935 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    15936 RMSD between 743 pruned atom pairs is 0.000 angstroms; (across all 743 pairs:
    15937 0.000) 
    15938  
    15939 
    15940 > hide #!4 models
    15941 
    15942 > split #10 atoms :1-743,2239 atoms :744-1476 atoms :1477-1556,2240-2241 atoms
    15943 > :1557-1699 atoms :1700-1765 atoms :1766-2238,2242-2244
    15944 
    15945 Split DdHyd_PSI.opt.pdb (#10) into 6 models 
    15946 Chain information for DdHyd_PSI.opt.pdb 1 #10.1 
    15947 --- 
    15948 Chain | Description 
    15949 ? | No description available 
    15950  
    15951 Chain information for DdHyd_PSI.opt.pdb 2 #10.2 
    15952 --- 
    15953 Chain | Description 
    15954 ? | No description available 
    15955  
    15956 Chain information for DdHyd_PSI.opt.pdb 3 #10.3 
    15957 --- 
    15958 Chain | Description 
    15959 ? | No description available 
    15960  
    15961 Chain information for DdHyd_PSI.opt.pdb 4 #10.4 
    15962 --- 
    15963 Chain | Description 
    15964 ? | No description available 
    15965  
    15966 Chain information for DdHyd_PSI.opt.pdb 5 #10.5 
    15967 --- 
    15968 Chain | Description 
    15969 ? | No description available 
    15970  
    15971 Chain information for DdHyd_PSI.opt.pdb 6 #10.6 
    15972 --- 
    15973 Chain | Description 
    15974 ? | No description available 
    15975  
    15976 Associated DdHyd_PSI.opt.pdb 1 (10.1) chain (blank) to PSI_BFd_SF4_opt.pdb,
    15977 chain A with 0 mismatches 
    15978 Associated DdHyd_PSI.opt.pdb 2 (10.2) chain (blank) to DdHyd_PSI.opt.pdb,
    15979 chain (blank) with 0 mismatches 
    15980 Associated DdHyd_PSI.opt.pdb 3 (10.3) chain (blank) to DdHyd_PSI.opt.pdb,
    15981 chain (blank) with 0 mismatches 
    15982 Associated DdHyd_PSI.opt.pdb 4 (10.4) chain (blank) to DdHyd_PSI.opt.pdb,
    15983 chain (blank) with 0 mismatches 
    15984 Associated DdHyd_PSI.opt.pdb 5 (10.5) chain (blank) to DdHyd_PSI.opt.pdb,
    15985 chain (blank) with 0 mismatches 
    15986 Associated DdHyd_PSI.opt.pdb 6 (10.6) chain (blank) to DdHyd_PSI.opt.pdb,
    15987 chain (blank) with 0 mismatches 
    15988 Traceback (most recent call last): 
    15989 File
    15990 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    15991 packages/chimerax/core/triggerset.py", line 149, in invoke 
    15992 return self._func(self._name, data) 
    15993 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    15994 File
    15995 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    15996 packages/chimerax/seqalign/alignment.py", line 427, in <lambda> 
    15997 self.associate([s for s in models if isinstance(s, AtomicStructure)],
    15998 force=False)) 
    15999 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    16000 File
    16001 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16002 packages/chimerax/seqalign/alignment.py", line 394, in associate 
    16003 self._notify_observers(note_name, note_data) 
    16004 File
    16005 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16006 packages/chimerax/seqalign/alignment.py", line 826, in _notify_observers 
    16007 self._notify_rmsd_change() 
    16008 File
    16009 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16010 packages/chimerax/seqalign/alignment.py", line 835, in _notify_rmsd_change 
    16011 self._notify_observers(self.NOTE_RMSD_UPDATE, None) 
    16012 File
    16013 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16014 packages/chimerax/seqalign/alignment.py", line 823, in _notify_observers 
    16015 recipient.alignment_notification(note_name, note_data) 
    16016 File
    16017 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16018 packages/chimerax/alignment_headers/rmsd.py", line 52, in
    16019 alignment_notification 
    16020 self.reevaluate() 
    16021 File
    16022 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16023 packages/chimerax/alignment_headers/rmsd.py", line 126, in reevaluate 
    16024 new_eval_chains = self.alignment.rmsd_chains 
    16025 ^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    16026 File
    16027 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16028 packages/chimerax/seqalign/alignment.py", line 670, in rmsd_chains 
    16029 rmsd = self._eval_rmsd([c1, c2]) 
    16030 ^^^^^^^^^^^^^^^^^^^^^^^^^ 
    16031 File
    16032 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16033 packages/chimerax/seqalign/alignment.py", line 769, in _eval_rmsd 
    16034 for coords in self._gather_coords(chains, pa_name): 
    16035 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    16036 File
    16037 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    16038 packages/chimerax/seqalign/alignment.py", line 794, in _gather_coords 
    16039 pa = r.find_atom(pa_name) 
    16040 ^^^^^^^^^^^^^^^^^^^^ 
    16041 File "atomic_cpp/cymol.pyx", line 1651, in
    16042 chimerax.atomic.cymol.CyResidue.find_atom 
    16043 RuntimeError: Residue already deleted 
    16044  
    16045 Error processing trigger "add models": 
    16046 RuntimeError: Residue already deleted 
    16047  
    16048 File "atomic_cpp/cymol.pyx", line 1651, in
    16049 chimerax.atomic.cymol.CyResidue.find_atom 
    16050  
    16051 See log for complete Python traceback. 
    16052  
    16053 
    16054 > hide #!10.1 models
    16055 
    16056 > hide #10.2 models
    16057 
    16058 > hide #!10.3 models
    16059 
    16060 > hide #10.4 models
    16061 
    16062 > hide #10.5 models
    16063 
    16064 > hide #!10.6 models
    16065 
    16066 > show #!10.1 models
    16067 
    16068 > hide #!10.1 models
    16069 
    16070 > show #10.2 models
    16071 
    16072 > show #!10.1 models
    16073 
    16074 > hide #10.2 models
    16075 
    16076 > hide #!10.1 models
    16077 
    16078 > show #!10.1 models
    16079 
    16080 > show #10.2 models
    16081 
    16082 > show #!10.3 models
    16083 
    16084 > show #10.4 models
    16085 
    16086 > hide #!10.3 models
    16087 
    16088 > hide #10.2 models
    16089 
    16090 > hide #!10.1 models
    16091 
    16092 > hide #10.4 models
    16093 
    16094 > show #10.5 models
    16095 
    16096 > hide #10.5 models
    16097 
    16098 > show #!10.6 models
    16099 
    16100 > show #10.2 models
    16101 
    16102 > show #!10.1 models
    16103 
    16104 > show #!10.3 models
    16105 
    16106 > show #10.4 models
    16107 
    16108 > show #10.5 models
    16109 
    16110 > ui tool show "Change Chain IDs"
    16111 
    16112 > select add #10.1
    16113 
    16114 11635 atoms, 11818 bonds, 18 pseudobonds, 752 residues, 3 models selected 
    16115 
    16116 > changechains sel A
    16117 
    16118 Cannot reassign chain ID to only part of polymeric chain
    16119 (fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif #9/B) 
    16120 
    16121 > select clear
    16122 
    16123 > select add #10.1
    16124 
    16125 11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected 
    16126 
    16127 > changechains sel A
    16128 
    16129 Chain IDs of 744 residues changed 
    16130 
    16131 > select subtract #10.1
    16132 
    16133 Nothing selected 
    16134 
    16135 > select add #10.2
    16136 
    16137 11513 atoms, 11725 bonds, 733 residues, 1 model selected 
    16138 
    16139 > changechains sel B
    16140 
    16141 Chain IDs of 733 residues changed 
    16142 
    16143 > select subtract #10.2
    16144 
    16145 Nothing selected 
    16146 
    16147 > select add #10.3
    16148 
    16149 1222 atoms, 1219 bonds, 36 pseudobonds, 82 residues, 2 models selected 
    16150 
    16151 > changechains sel C
    16152 
    16153 Chain IDs of 82 residues changed 
    16154 
    16155 > select subtract #10.3
    16156 
    16157 Nothing selected 
    16158 
    16159 > select add #10.4
    16160 
    16161 2277 atoms, 2308 bonds, 143 residues, 1 model selected 
    16162 
    16163 > changechains sel D
    16164 
    16165 Chain IDs of 143 residues changed 
    16166 
    16167 > select subtract #10.4
    16168 
    16169 Nothing selected 
    16170 
    16171 > select add #10.5
    16172 
    16173 1059 atoms, 1071 bonds, 66 residues, 1 model selected 
    16174 
    16175 > changechains sel E
    16176 
    16177 Chain IDs of 66 residues changed 
    16178 
    16179 > select add #10.6
    16180 
    16181 8232 atoms, 8313 bonds, 54 pseudobonds, 542 residues, 3 models selected 
    16182 
    16183 > select subtract #10.5
    16184 
    16185 7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected 
    16186 
    16187 > changechains sel F
    16188 
    16189 Chain IDs of 476 residues changed 
    16190 
    16191 > select add #10
    16192 
    16193 34831 atoms, 35343 bonds, 108 pseudobonds, 2244 residues, 10 models selected 
    16194 
    16195 > color sel bychain
    16196 
    16197 > color sel byhetero
    16198 
    16199 [Repeated 1 time(s)]
    16200 
    16201 > select clear
    16202 
    16203 > combine #10.1#10.2#10.3#10.4#10.5#10.6
    16204 
    16205 Associated combination chain A to PSI_BFd_SF4_opt.pdb, chain A with 0
    16206 mismatches 
    16207 Associated combination chain B to DdHyd_PSI.opt.pdb, chain (blank) with 0
    16208 mismatches 
    16209 Associated combination chain F to DdHyd_PSI.opt.pdb, chain (blank) with 0
    16210 mismatches 
    16211 Associated combination chain D to DdHyd_PSI.opt.pdb, chain (blank) with 0
    16212 mismatches 
    16213 Associated combination chain C to DdHyd_PSI.opt.pdb, chain (blank) with 0
    16214 mismatches 
    16215 Associated combination chain E to DdHyd_PSI.opt.pdb, chain (blank) with 0
    16216 mismatches 
    16217 
    16218 > hide #!10 models
    16219 
    16220 > show #!10 models
    16221 
    16222 > rename #12 "DdHyd_PSI.opt.pdb split to chains"
    16223 
    16224 > close #10
    16225 
    16226 > rename #12 id #10
    16227 
    16228 > select #10/A-E
    16229 
    16230 27658 atoms, 28101 bonds, 54 pseudobonds, 1768 residues, 2 models selected 
    16231 
    16232 > ui tool show Clashes
    16233 
    16234 > clashes sel restrict #10/F resSeparation 5 interModel false intraMol false
    16235 > color #fffb00 reveal true log true
    16236    
    16237    
    16238     Allowed overlap: 0.6
    16239     H-bond overlap reduction: 0.4
    16240     Ignore clashes between atoms separated by 4 bonds or less
    16241     Ignore clashes between atoms in residues less than 5 apart in sequence
    16242     Detect intra-residue clashes: False
    16243     Detect intra-molecule clashes: False
    16244    
    16245     0 clashes
    16246     atom1  atom2  overlap  distance
    16247    
    16248 
    16249  
    16250 No clashes 
    16251 
    16252 > ui tool show Contacts
    16253 
    16254 > select #10/A-E &~H
    16255 
    16256 14013 atoms, 14456 bonds, 54 pseudobonds, 1768 residues, 2 models selected 
    16257 
    16258 > contacts sel restrict "#10/F &~H" resSeparation 5 interModel false intraMol
    16259 > false color #ff85ff radius 0.2 reveal true log true
    16260    
    16261    
    16262     Allowed overlap: -0.4
    16263     H-bond overlap reduction: 0.4
    16264     Ignore contacts between atoms separated by 4 bonds or less
    16265     Ignore contacts between atoms in residues less than 5 apart in sequence
    16266     Detect intra-residue contacts: False
    16267     Detect intra-molecule contacts: False
    16268    
    16269     61 contacts
    16270                            atom1                                                 atom2                          overlap  distance
    16271     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 C     0.260    3.065
    16272     DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CA    0.258    2.922
    16273     DdHyd_PSI.opt.pdb split to chains #10/E ALA 1728 CB   DdHyd_PSI.opt.pdb split to chains #10/F THR 1767 CG2   0.154    3.246
    16274     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 N     0.146    3.104
    16275     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 OE1  DdHyd_PSI.opt.pdb split to chains #10/F PRO 1816 CB    0.120    3.060
    16276     DdHyd_PSI.opt.pdb split to chains #10/C ILE 1487 O    DdHyd_PSI.opt.pdb split to chains #10/F PRO 1841 CB    0.119    3.061
    16277     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 C     0.116    3.209
    16278     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 CG    0.093    3.232
    16279     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C     0.079    3.246
    16280     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CA    0.072    3.253
    16281     DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG   DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N     0.044    3.281
    16282     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ   DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N     0.010    3.315
    16283     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 O     -0.010    3.190
    16284     DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 C     -0.035    3.215
    16285     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CB    -0.041    3.366
    16286     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O     -0.057    2.762
    16287     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O     -0.077    3.257
    16288     DdHyd_PSI.opt.pdb split to chains #10/C ARG 1494 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 NE2   -0.098    3.348
    16289     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2   -0.100    2.805
    16290     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 CZ   DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2   -0.106    3.286
    16291     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 C     -0.107    3.507
    16292     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ   DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C     -0.117    3.517
    16293     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1   -0.124    2.829
    16294     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2   -0.130    2.835
    16295     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1   -0.134    2.839
    16296     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLY 1795 N     -0.145    3.395
    16297     DdHyd_PSI.opt.pdb split to chains #10/D VAL 1666 CG1  DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 O     -0.150    3.330
    16298     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CA    -0.155    3.555
    16299     DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N     -0.157    2.862
    16300     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CA    -0.160    3.485
    16301     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O     -0.161    2.866
    16302     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1512 CE   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2157 OH    -0.167    3.367
    16303     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O     -0.168    2.873
    16304     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 O     -0.177    2.882
    16305     DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N     -0.197    2.902
    16306     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N     -0.199    3.449
    16307     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 CB    -0.209    3.534
    16308     DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N    DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O     -0.210    2.915
    16309     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 OE1  DdHyd_PSI.opt.pdb split to chains #10/F PRO 1816 CG    -0.212    3.392
    16310     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CD    -0.217    3.542
    16311     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CB   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 ND2   -0.237    3.562
    16312     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 C     -0.249    3.574
    16313     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ   DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 CA    -0.265    3.665
    16314     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1512 CD   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2157 OH    -0.269    3.469
    16315     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1   -0.279    2.984
    16316     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NE   DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 CA    -0.285    3.610
    16317     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N     -0.292    3.542
    16318     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CG   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1   -0.295    3.475
    16319     DdHyd_PSI.opt.pdb split to chains #10/D VAL 1666 O    DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 O     -0.301    3.261
    16320     DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG   DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CA    -0.304    3.704
    16321     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2  DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C     -0.317    3.642
    16322     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ   DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O     -0.322    3.502
    16323     DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG   DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 C     -0.340    3.740
    16324     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 CD   DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CA    -0.345    3.745
    16325     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ   DdHyd_PSI.opt.pdb split to chains #10/F THR 1767 OG1   -0.349    3.074
    16326     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 N     -0.360    3.685
    16327     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CG    -0.363    3.688
    16328     DdHyd_PSI.opt.pdb split to chains #10/E GLN 1731 CB   DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 NZ    -0.363    3.688
    16329     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLY 1795 CA    -0.364    3.689
    16330     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CG   DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CG2   -0.368    3.768
    16331     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 C     -0.398    3.723
    16332    
    16333 
    16334  
    16335 61 contacts 
    16336 
    16337 > hide #10.3 models
    16338 
    16339 > ui tool show H-Bonds
    16340 
    16341 > hbonds sel color #0096ff restrict #10/F interModel false intraMol false
    16342 > intraRes false reveal true log true
    16343 
    16344 Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.pdb split to
    16345 chains #10/A CYF 575 SG 
    16346 Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.pdb split
    16347 to chains #10/A CYF 575 SG 
    16348  
    16349 [Repeated 1 time(s)]
    16350 
    16351 Skipped 2 atom(s) with bad connectivities; see log for details 
    16352 
    16353    
    16354    
    16355     Finding intramodel H-bonds
    16356     Constraints relaxed by 0.4 angstroms and 20 degrees
    16357     Models used:
    16358         10 DdHyd_PSI.opt.pdb split to chains
    16359    
    16360     13 H-bonds
    16361     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16362     DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 NH2    DdHyd_PSI.opt.pdb split to chains #10/F GLU 1814 OE1  DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 HH21    3.498  2.750
    16363     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O    DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 HE21  2.873  2.126
    16364     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1  DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 HZ2   2.829  1.880
    16365     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1  DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ2   2.839  1.911
    16366     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O    DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ1   2.762  1.871
    16367     DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N    DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O    DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 H3    2.915  1.906
    16368     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O    DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH11  2.866  1.886
    16369     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O    DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH21  3.207  2.381
    16370     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH12  2.805  1.855
    16371     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22  2.984  2.083
    16372     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22  2.835  1.934
    16373     DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N    DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1    2.862  2.132
    16374     DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N    DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1    2.902  1.907
    16375    
    16376 
    16377  
    16378 13 hydrogen bonds found 
    16379 
    16380 > select #10/A-E
    16381 
    16382 27658 atoms, 28101 bonds, 54 pseudobonds, 1768 residues, 2 models selected 
    16383 
    16384 > hbonds sel color #0096ff restrict #10/F interModel false intraMol false
    16385 > intraRes false reveal true log true
    16386 
    16387 Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.pdb split to
    16388 chains #10/A CYF 575 SG 
    16389 Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.pdb split
    16390 to chains #10/A CYF 575 SG 
    16391  
    16392 [Repeated 1 time(s)]
    16393 
    16394 Skipped 2 atom(s) with bad connectivities; see log for details 
    16395 
    16396    
    16397    
    16398     Finding intramodel H-bonds
    16399     Constraints relaxed by 0.4 angstroms and 20 degrees
    16400     Models used:
    16401         10 DdHyd_PSI.opt.pdb split to chains
    16402    
    16403     13 H-bonds
    16404     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16405     DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 NH2    DdHyd_PSI.opt.pdb split to chains #10/F GLU 1814 OE1  DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 HH21    3.498  2.750
    16406     DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O    DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 HE21  2.873  2.126
    16407     DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1  DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 HZ2   2.829  1.880
    16408     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1  DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ2   2.839  1.911
    16409     DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O    DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ1   2.762  1.871
    16410     DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N    DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O    DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 H3    2.915  1.906
    16411     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O    DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH11  2.866  1.886
    16412     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O    DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH21  3.207  2.381
    16413     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH12  2.805  1.855
    16414     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22  2.984  2.083
    16415     DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22  2.835  1.934
    16416     DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N    DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1    2.862  2.132
    16417     DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N    DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1    2.902  1.907
    16418    
    16419 
    16420  
    16421 13 hydrogen bonds found 
    16422 
    16423 > select #10/A-F
    16424 
    16425 34831 atoms, 35343 bonds, 182 pseudobonds, 2244 residues, 4 models selected 
    16426 
    16427 > hide sel cartoons
    16428 
    16429 > hide #10.1 models
    16430 
    16431 > help help:user
    16432 
    16433 > bonds #10:2239-2244@F4@F2
    16434 
    16435 Unknown command: bonds #10:2239-2244@F4@F2 
    16436 
    16437 > bond #10:2239-2244@F4@F2
    16438 
    16439 Created 6 bonds 
    16440 
    16441 > select #10:2239-2244
    16442 
    16443 48 atoms, 6 bonds, 108 pseudobonds, 6 residues, 2 models selected 
    16444 
    16445 > style sel stick
    16446 
    16447 Changed 48 atom styles 
    16448 
    16449 > ~bond #10:2239-2244@F4@F2
    16450 
    16451 > ~bond #10:2239-2244@F4@S1
    16452 
    16453 > bond #10:2239-2244@F4@S1
    16454 
    16455 Created 6 bonds 
    16456 
    16457 > bond #10:2239-2244@F3@S1
    16458 
    16459 Created 6 bonds 
    16460 
    16461 > bond #10:2239-2244@F3@S2
    16462 
    16463 Created 6 bonds 
    16464 
    16465 > bond #10:2239-2244@F4@S2
    16466 
    16467 Created 6 bonds 
    16468 
    16469 > bond #10:2239-2244@F3@S4
    16470 
    16471 Created 6 bonds 
    16472 
    16473 > bond #10:2239-2244@F2@S4
    16474 
    16475 Created 6 bonds 
    16476 
    16477 > bond #10:2239-2244@F2@S1
    16478 
    16479 Created 6 bonds 
    16480 
    16481 > bond #10:2239-2244@F2@S3
    16482 
    16483 Created 6 bonds 
    16484 
    16485 > bond #10:2239-2244@F4@S3
    16486 
    16487 Created 6 bonds 
    16488 
    16489 > bond #10:2239-2244@F1@S2
    16490 
    16491 Created 6 bonds 
    16492 
    16493 > bond #10:2239-2244@F1@S3
    16494 
    16495 Created 6 bonds 
    16496 
    16497 > bond #10:2239-2244@F1@S4
    16498 
    16499 Created 6 bonds 
    16500 
    16501 > select #10:SF4
    16502 
    16503 48 atoms, 72 bonds, 108 pseudobonds, 6 residues, 2 models selected 
    16504 
    16505 > style sel ball
    16506 
    16507 Changed 48 atom styles 
    16508 
    16509 > select #10:SF4 &Fe
    16510 
    16511 24 atoms, 36 pseudobonds, 6 residues, 2 models selected 
    16512 
    16513 > style sel sphere
    16514 
    16515 Changed 24 atom styles 
    16516 
    16517 > select #10
    16518 
    16519 34831 atoms, 35415 bonds, 183 pseudobonds, 2244 residues, 5 models selected 
    16520 
    16521 > show sel cartoons
    16522 
    16523 > show #!4 models
    16524 
    16525 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd
    16526 > PSI-BFd AMBER opt.cxs"
    16527 
    16528 ——— End of log from Mon Oct 21 23:18:11 2024 ———
    16529 
    16530 opened ChimeraX session 
    16531 
    16532 > hide #!4 models
    16533 
    16534 > show #!4 models
    16535 
    16536 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
    16537 > 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb" models #4
    16538 
    16539 > close session
    16540 
    16541 > open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-
    16542 > DFG/DdHyd_PSI.opt.chains.pdb "/Users/drornoy/Library/CloudStorage/OneDrive-
    16543 > Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb"
    16544 
    16545 Chain information for DdHyd_PSI.opt.chains.pdb #1 
    16546 --- 
    16547 Chain | Description 
    16548 A | No description available 
    16549 B | No description available 
    16550 C | No description available 
    16551 D | No description available 
    16552 E | No description available 
    16553 F | No description available 
    16554  
    16555 Chain information for PSI_BFD_SF4_opt_chains.pdb #2 
    16556 --- 
    16557 Chain | Description 
    16558 A | No description available 
    16559 B | No description available 
    16560 C | No description available 
    16561 D | No description available 
    16562 E | No description available 
    16563 F | No description available 
    16564  
    16565 
    16566 > select protein
    16567 
    16568 63258 atoms, 64292 bonds, 4064 residues, 2 models selected 
    16569 
    16570 > hide sel atoms
    16571 
    16572 > show sel cartoons
    16573 
    16574 > color sel bychain
    16575 
    16576 > color sel byhetero
    16577 
    16578 > ~select
    16579 
    16580 Nothing selected 
    16581 
    16582 > color byhetero
    16583 
    16584 > hide #!1 models
    16585 
    16586 > show #!1 models
    16587 
    16588 > hide #!1 models
    16589 
    16590 > show #!1 models
    16591 
    16592 > hide #!1 models
    16593 
    16594 > show #!1 models
    16595 
    16596 > hide #!1 models
    16597 
    16598 > show #!1 models
    16599 
    16600 > hide #!1 models
    16601 
    16602 > show #!1 models
    16603 
    16604 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
    16605 > PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs"
    16606 
    16607 ——— End of log from Tue Oct 22 09:43:01 2024 ———
    16608 
    16609 opened ChimeraX session 
    16610 
    16611 > hide #!2 models
    16612 
    16613 > show #!2 models
    16614 
    16615 > hide #!2 models
    16616 
    16617 > show #!2 models
    16618 
    16619 > hide #!1 models
    16620 
    16621 > show #!1 models
    16622 
    16623 > rename #1 id #3
    16624 
    16625 > rename #2 id #1
    16626 
    16627 > rename #3 id #2
    16628 
    16629 > open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-
    16630 > DFG/ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb
    16631 
    16632 Chain information for ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb #3 
    16633 --- 
    16634 Chain | Description 
    16635 A | No description available 
    16636 B | No description available 
    16637 C | No description available 
    16638 D | No description available 
    16639 E | No description available 
    16640 F | No description available 
    16641 G | No description available 
    16642  
    16643 
    16644 > select #3 &protein
    16645 
    16646 34578 atoms, 35179 bonds, 2662 residues, 1 model selected 
    16647 
    16648 > hide sel atoms
    16649 
    16650 > show sel cartoons
    16651 
    16652 > select #3/Y:1183-1187,1200
    16653 
    16654 41 atoms, 12 bonds, 72 pseudobonds, 6 residues, 2 models selected 
    16655 
    16656 > hide #!2 models
    16657 
    16658 > hide #!1 models
    16659 
    16660 > style sel sphere
    16661 
    16662 Changed 41 atom styles 
    16663 
    16664 > color sel byhetero
    16665 
    16666 > select #3/Z:SF4
    16667 
    16668 24 atoms, 54 pseudobonds, 3 residues, 2 models selected 
    16669 
    16670 > color sel byhetero
    16671 
    16672 > select #3
    16673 
    16674 34737 atoms, 35295 bonds, 130 pseudobonds, 2673 residues, 2 models selected 
    16675 
    16676 > color sel bychain
    16677 
    16678 > color sel byhetero
    16679 
    16680 > select #13/Y:1188-1189
    16681 
    16682 Nothing selected 
    16683 
    16684 > select #3/Y:1188-1189
    16685 
    16686 94 atoms, 104 bonds, 2 residues, 1 model selected 
    16687 
    16688 > color sel magenta
    16689 
    16690 > color sel byhetero
    16691 
    16692 > show #!2 models
    16693 
    16694 > show #!1 models
    16695 
    16696 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
    16697 > PSI-BFd PSI-DdHyd PSI-FdhF.cxs"
    16698 
    16699 ——— End of log from Tue Oct 22 11:39:31 2024 ———
    16700 
    16701 opened ChimeraX session 
    16702 
    16703 > select add #3
    16704 
    16705 34737 atoms, 35295 bonds, 130 pseudobonds, 2673 residues, 2 models selected 
    16706 
    16707 > select subtract #3
    16708 
    16709 Nothing selected 
    16710 
    16711 > hide #!3 models
    16712 
    16713 > hide #!2 models
    16714 
    16715 > show #!3 models
    16716 
    16717 > show #!2 models
    16718 
    16719 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
    16720 > PSI-BFd PSI-DdHyd PSI-FdhF.cxs"
    16721 
    16722 ——— End of log from Tue Oct 22 11:40:52 2024 ———
    16723 
    16724 > view name session-start
    16725 
    16726 opened ChimeraX session 
    16727 
    16728 > hide #!2 models
    16729 
    16730 > hide #!3 models
    16731 
    16732 > open 2fdn
    16733 
    16734 2fdn title: 
    16735 2[4FE-4S] ferredoxin from clostridium acidi-urici [more info...] 
    16736  
    16737 Chain information for 2fdn #4 
    16738 --- 
    16739 Chain | Description | UniProt 
    16740 A | FERREDOXIN | FER_CLOAC 1-55 
    16741  
    16742 Non-standard residues in 2fdn #4 
    16743 --- 
    16744 SF4 — iron/sulfur cluster 
    16745  
    16746 74 atoms have alternate locations. Control/examine alternate locations with
    16747 Altloc Explorer [start tool...] or the altlocs command. 
    16748 
    16749 > ui tool show Matchmaker
    16750 
    16751 > matchmaker #!4 to #1
    16752 
    16753 Parameters 
    16754 --- 
    16755 Chain pairing | bb 
    16756 Alignment algorithm | Needleman-Wunsch 
    16757 Similarity matrix | BLOSUM-62 
    16758 SS fraction | 0.3 
    16759 Gap open (HH/SS/other) | 18/18/6 
    16760 Gap extend | 1 
    16761 SS matrix |  |  | H | S | O 
    16762 ---|---|---|--- 
    16763 H | 6 | -9 | -6 
    16764 S |  | 6 | -6 
    16765 O |  |  | 4 
    16766 Iteration cutoff | 2 
    16767  
    16768 Matchmaker PSI_BFD_SF4_opt_chains.pdb, chain F (#1) with 2fdn, chain A (#4),
    16769 sequence alignment score = 115.9 
    16770 RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs:
    16771 3.340) 
    16772  
    16773 
    16774 > select #1/A-E
    16775 
    16776 27634 atoms, 28101 bonds, 1765 residues, 1 model selected 
    16777 
    16778 > hide sel cartoons
    16779 
    16780 > select #1/X
    16781 
    16782 40 atoms, 90 pseudobonds, 5 residues, 2 models selected 
    16783 
    16784 > hide sel atoms
    16785 
    16786 > undo
    16787 
    16788 > select #1/X:1829-1831
    16789 
    16790 24 atoms, 54 pseudobonds, 3 residues, 2 models selected 
    16791 
    16792 > hide sel atoms
    16793 
    16794 > select #1/X:1827-1828
    16795 
    16796 16 atoms, 36 pseudobonds, 2 residues, 2 models selected 
    16797 
    16798 > style sel stick
    16799 
    16800 Changed 16 atom styles 
    16801 
    16802 > hide #!4 models
    16803 
    16804 > select #1/F:Cys
    16805 
    16806 Nothing selected 
    16807 
    16808 > select #1/F:Cyf
    16809 
    16810 80 atoms, 72 bonds, 8 residues, 1 model selected 
    16811 
    16812 > show sel atoms
    16813 
    16814 > style sel stick
    16815 
    16816 Changed 80 atom styles 
    16817 
    16818 > select H
    16819 
    16820 45159 atoms, 5877 residues, 4 models selected 
    16821 
    16822 > hide sel & #!1 atoms
    16823 
    16824 > show #!4 models
    16825 
    16826 > select #1/X:1827-1828
    16827 
    16828 16 atoms, 36 pseudobonds, 2 residues, 2 models selected 
    16829 
    16830 > style sel sphere
    16831 
    16832 Changed 16 atom styles 
    16833 
    16834 > hide #!1 models
    16835 
    16836 > select #4:61-62
    16837 
    16838 16 atoms, 24 bonds, 2 residues, 1 model selected 
    16839 
    16840 > style sel sphere
    16841 
    16842 Changed 16 atom styles 
    16843 
    16844 > hide #4.1 models
    16845 
    16846 > show #!1 models
    16847 
    16848 > ui tool show Matchmaker
    16849 
    16850 > matchmaker #!4 to #1 showAlignment true
    16851 
    16852 Parameters 
    16853 --- 
    16854 Chain pairing | bb 
    16855 Alignment algorithm | Needleman-Wunsch 
    16856 Similarity matrix | BLOSUM-62 
    16857 SS fraction | 0.3 
    16858 Gap open (HH/SS/other) | 18/18/6 
    16859 Gap extend | 1 
    16860 SS matrix |  |  | H | S | O 
    16861 ---|---|---|--- 
    16862 H | 6 | -9 | -6 
    16863 S |  | 6 | -6 
    16864 O |  |  | 4 
    16865 Iteration cutoff | 2 
    16866  
    16867 Matchmaker PSI_BFD_SF4_opt_chains.pdb, chain F (#1) with 2fdn, chain A (#4),
    16868 sequence alignment score = 115.9 
    16869 Alignment identifier is 1 
    16870 Showing conservation header ("seq_conservation" residue attribute) for
    16871 alignment 1 
    16872 Hiding conservation header for alignment 1 
    16873 Chains used in RMSD evaluation for alignment 1: PSI_BFD_SF4_opt_chains.pdb
    16874 #1/F, 2fdn #4/A 
    16875 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    16876 RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs:
    16877 3.340) 
    16878  
    16879 
    16880 > select #1/F:3
    16881 
    16882 14 atoms, 14 bonds, 1 residue, 1 model selected 
    16883 
    16884 > select #1/F:3-8
    16885 
    16886 96 atoms, 96 bonds, 6 residues, 1 model selected 
    16887 
    16888 > select #1/F:3
    16889 
    16890 14 atoms, 14 bonds, 1 residue, 1 model selected 
    16891 
    16892 > select #1/F:3-8 #4/A:3-8
    16893 
    16894 168 atoms, 167 bonds, 12 residues, 2 models selected 
    16895 MatchMaker Alignment [ID: 1] region chain F..chain A [3-8] RMSD: 6.436 
    16896  
    16897 
    16898 > color sel cyan
    16899 
    16900 > select #1/F:9
    16901 
    16902 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16903 
    16904 > select #1/F:9
    16905 
    16906 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16907 
    16908 > color sel cyan
    16909 
    16910 > select #4/A:25
    16911 
    16912 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16913 
    16914 > select #1/F:27-34 #4/A:25-29
    16915 
    16916 160 atoms, 159 bonds, 13 residues, 2 models selected 
    16917 MatchMaker Alignment [ID: 1] region chain F..chain A [27-34] RMSD: 4.473 
    16918  
    16919 
    16920 > color sel cyan
    16921 
    16922 > select #4/A:48
    16923 
    16924 14 atoms, 14 bonds, 1 residue, 1 model selected 
    16925 
    16926 > select #1/F:53-61 #4/A:48-55
    16927 
    16928 240 atoms, 242 bonds, 17 residues, 2 models selected 
    16929 MatchMaker Alignment [ID: 1] region chain F..chain A [53-62] RMSD: 5.761 
    16930  
    16931 
    16932 > color sel cyan
    16933 
    16934 > hide #!4 models
    16935 
    16936 > show #!4 models
    16937 
    16938 > hide #!1 models
    16939 
    16940 > color sel & #!4 byhetero
    16941 
    16942 > select clear
    16943 
    16944 > color #!4 byhetero
    16945 
    16946 > select #1/F:3
    16947 
    16948 14 atoms, 14 bonds, 1 residue, 1 model selected 
    16949 
    16950 > select #1/F:3-9 #4/A:3-8
    16951 
    16952 183 atoms, 182 bonds, 13 residues, 2 models selected 
    16953 MatchMaker Alignment [ID: 1] region chain F..chain A [3-9] RMSD: 6.436 
    16954  
    16955 
    16956 > show sel & #!4 atoms
    16957 
    16958 > style sel & #!4 stick
    16959 
    16960 Changed 72 atom styles 
    16961 
    16962 > select #4/A:1-2,8-24,30-47
    16963 
    16964 447 atoms, 448 bonds, 37 residues, 1 model selected 
    16965 
    16966 > select #4/A:1-55 &~:1-2,8-24,30-47
    16967 
    16968 205 atoms, 204 bonds, 18 residues, 1 model selected 
    16969 
    16970 > show sel atoms
    16971 
    16972 > select H
    16973 
    16974 45159 atoms, 5877 residues, 4 models selected 
    16975 
    16976 > hide sel & #!4 atoms
    16977 
    16978 > select #4/A:1-55 &~:1-2,8-24,30-47
    16979 
    16980 205 atoms, 204 bonds, 18 residues, 1 model selected 
    16981 
    16982 > select #1/F:3
    16983 
    16984 14 atoms, 14 bonds, 1 residue, 1 model selected 
    16985 
    16986 > select #1/F:3-9
    16987 
    16988 111 atoms, 111 bonds, 7 residues, 1 model selected 
    16989 
    16990 > select #4/A:1-55 &~:1-2,8-24,30-47#1/F:3-9
    16991 
    16992 205 atoms, 204 bonds, 18 residues, 1 model selected 
    16993 
    16994 > select #4/A:1-55 &~:1-2,8-24,30-47 |#1/F:3-9
    16995 
    16996 205 atoms, 209 bonds, 18 residues, 1 model selected 
    16997 
    16998 > select #1/F:3-9,27-34,53-61
    16999 
    17000 368 atoms, 369 bonds, 24 residues, 1 model selected 
    17001 
    17002 > show #!1 models
    17003 
    17004 > show sel atoms
    17005 
    17006 > style sel stick
    17007 
    17008 Changed 368 atom styles 
    17009 
    17010 > color sel byhetero
    17011 
    17012 > select H
    17013 
    17014 45159 atoms, 5877 residues, 4 models selected 
    17015 
    17016 > hide sel & #!1,4 atoms
    17017 
    17018 > ui tool show "Selection Inspector"
    17019 
    17020 > setattr sel r ribbon_hide_backbone false
    17021 
    17022 Assigning ribbon_hide_backbone attribute to 5877 items 
    17023 
    17024 > select @N,O
    17025 
    17026 13656 atoms, 6875 residues, 4 models selected 
    17027 
    17028 > hide sel & #!1,4 atoms
    17029 
    17030 > hide #!4 models
    17031 
    17032 > select clear
    17033 
    17034 > show #!4 models
    17035 
    17036 > hide #!1 models
    17037 
    17038 > show #!1 models
    17039 
    17040 > hide #!4 models
    17041 
    17042 > show #!4 models
    17043 
    17044 > hide #!4 models
    17045 
    17046 > show #!4 models
    17047 
    17048 > hide #!1 models
    17049 
    17050 > show #!1 models
    17051 
    17052 > hide #!4 models
    17053 
    17054 > select #4/A:1-2,8-24,30-47
    17055 
    17056 447 atoms, 448 bonds, 37 residues, 1 model selected 
    17057 
    17058 > show #!4 models
    17059 
    17060 > hide #!1 models
    17061 
    17062 > ui tool show "Color Actions"
    17063 
    17064 > color sel light slate gray
    17065 
    17066 > color sel steel blue
    17067 
    17068 > color sel olive drab
    17069 
    17070 > color sel steel blue
    17071 
    17072 > select clear
    17073 
    17074 > show #!1 models
    17075 
    17076 > hide #!1 models
    17077 
    17078 > show #!1 models
    17079 
    17080 > hide #!1 models
    17081 
    17082 > show #!1 models
    17083 
    17084 > hide #!4 models
    17085 
    17086 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    17087 > sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs"
    17088 
    17089 ——— End of log from Sat Sep 13 22:23:04 2025 ———
    17090 
    17091 > view name session-start
    17092 
    17093 opened ChimeraX session 
    17094 
    17095 > select #1/A-E
    17096 
    17097 27634 atoms, 28101 bonds, 1765 residues, 1 model selected 
    17098 
    17099 > show sel cartoons
    17100 
    17101 > select #1/X:1827-1828
    17102 
    17103 16 atoms, 36 pseudobonds, 2 residues, 2 models selected 
    17104 
    17105 > select #1/X
    17106 
    17107 40 atoms, 90 pseudobonds, 5 residues, 2 models selected 
    17108 
    17109 > show sel atoms
    17110 
    17111 > select #1/F
    17112 
    17113 841 atoms, 848 bonds, 61 residues, 1 model selected 
    17114 
    17115 > ui tool show H-Bonds
    17116 
    17117 > hbonds sel color #0096ff showDist true interModel false intraMol false
    17118 > intraRes false select true log true
    17119 
    17120 Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A
    17121 CYF 575 SG 
    17122 Wrong number of grandchild atoms for phi/psi acceptor
    17123 PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG 
    17124  
    17125 [Repeated 1 time(s)]
    17126 
    17127 Skipped 2 atom(s) with bad connectivities; see log for details 
    17128 
    17129    
    17130    
    17131     Finding intramodel H-bonds
    17132     Constraints relaxed by 0.4 angstroms and 20 degrees
    17133     Models used:
    17134         1 PSI_BFD_SF4_opt_chains.pdb
    17135    
    17136     19 H-bonds
    17137     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    17138     PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11  2.760  1.842
    17139     PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21  2.719  1.800
    17140     PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O    PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1   3.148  2.456
    17141     PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2  PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2   2.746  1.778
    17142     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  2.812  1.825
    17143     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  3.358  2.560
    17144     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22  2.780  1.765
    17145     PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O    PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1  2.917  2.045
    17146     PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1  PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2  2.737  1.813
    17147     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE   PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE    2.875  1.950
    17148     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12  2.980  2.103
    17149     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22  2.848  1.943
    17150     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21  2.738  1.784
    17151     PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2   PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1   2.666  1.685
    17152     PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O    PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22  3.598  2.755
    17153     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE   PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE    2.902  1.898
    17154     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12  2.894  1.970
    17155     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21  3.324  2.539
    17156     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22  2.784  1.818
    17157    
    17158 
    17159  
    17160 19 hydrogen bonds found 
    17161 
    17162 > show sel atoms
    17163 
    17164 > style sel stick
    17165 
    17166 Changed 31 atom styles 
    17167 
    17168 > ui tool show H-Bonds
    17169 
    17170 > hbonds sel color #0096ff showDist true interModel false intraMol false
    17171 > intraRes false select true reveal true log true
    17172 
    17173 Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A
    17174 CYF 575 SG 
    17175 Wrong number of grandchild atoms for phi/psi acceptor
    17176 PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG 
    17177  
    17178 [Repeated 1 time(s)]
    17179 
    17180 Skipped 2 atom(s) with bad connectivities; see log for details 
    17181 
    17182    
    17183    
    17184     Finding intramodel H-bonds
    17185     Constraints relaxed by 0.4 angstroms and 20 degrees
    17186     Models used:
    17187         1 PSI_BFD_SF4_opt_chains.pdb
    17188    
    17189     19 H-bonds
    17190     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    17191     PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11  2.760  1.842
    17192     PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21  2.719  1.800
    17193     PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O    PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1   3.148  2.456
    17194     PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2  PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2   2.746  1.778
    17195     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  2.812  1.825
    17196     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  3.358  2.560
    17197     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22  2.780  1.765
    17198     PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O    PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1  2.917  2.045
    17199     PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1  PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2  2.737  1.813
    17200     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE   PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE    2.875  1.950
    17201     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12  2.980  2.103
    17202     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22  2.848  1.943
    17203     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21  2.738  1.784
    17204     PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2   PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1   2.666  1.685
    17205     PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O    PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22  3.598  2.755
    17206     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE   PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE    2.902  1.898
    17207     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12  2.894  1.970
    17208     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21  3.324  2.539
    17209     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22  2.784  1.818
    17210    
    17211 
    17212  
    17213 19 hydrogen bonds found 
    17214 
    17215 > select #1/F
    17216 
    17217 841 atoms, 848 bonds, 61 residues, 1 model selected 
    17218 
    17219 > hbonds sel color #0096ff showDist true interModel false intraMol false
    17220 > intraRes false select true reveal true log true
    17221 
    17222 Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A
    17223 CYF 575 SG 
    17224 Wrong number of grandchild atoms for phi/psi acceptor
    17225 PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG 
    17226  
    17227 [Repeated 1 time(s)]
    17228 
    17229 Skipped 2 atom(s) with bad connectivities; see log for details 
    17230 
    17231    
    17232    
    17233     Finding intramodel H-bonds
    17234     Constraints relaxed by 0.4 angstroms and 20 degrees
    17235     Models used:
    17236         1 PSI_BFD_SF4_opt_chains.pdb
    17237    
    17238     19 H-bonds
    17239     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    17240     PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11  2.760  1.842
    17241     PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21  2.719  1.800
    17242     PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O    PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1   3.148  2.456
    17243     PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2  PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2   2.746  1.778
    17244     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  2.812  1.825
    17245     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  3.358  2.560
    17246     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22  2.780  1.765
    17247     PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O    PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1  2.917  2.045
    17248     PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1  PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2  2.737  1.813
    17249     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE   PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE    2.875  1.950
    17250     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12  2.980  2.103
    17251     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22  2.848  1.943
    17252     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21  2.738  1.784
    17253     PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2   PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1   2.666  1.685
    17254     PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O    PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22  3.598  2.755
    17255     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE   PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE    2.902  1.898
    17256     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12  2.894  1.970
    17257     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21  3.324  2.539
    17258     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22  2.784  1.818
    17259    
    17260 
    17261  
    17262 19 hydrogen bonds found 
    17263 
    17264 > hbonds sel color #0096ff showDist true interModel false intraMol false
    17265 > intraRes false reveal true log true
    17266 
    17267 Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A
    17268 CYF 575 SG 
    17269 Wrong number of grandchild atoms for phi/psi acceptor
    17270 PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG 
    17271  
    17272 [Repeated 1 time(s)]
    17273 
    17274 Skipped 2 atom(s) with bad connectivities; see log for details 
    17275 
    17276    
    17277    
    17278     Finding intramodel H-bonds
    17279     Constraints relaxed by 0.4 angstroms and 20 degrees
    17280     Models used:
    17281         1 PSI_BFD_SF4_opt_chains.pdb
    17282    
    17283     19 H-bonds
    17284     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    17285     PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11  2.760  1.842
    17286     PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21  2.719  1.800
    17287     PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O    PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1   3.148  2.456
    17288     PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2  PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2   2.746  1.778
    17289     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  2.812  1.825
    17290     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  3.358  2.560
    17291     PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22  2.780  1.765
    17292     PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O    PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1  2.917  2.045
    17293     PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1  PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2  2.737  1.813
    17294     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE   PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE    2.875  1.950
    17295     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12  2.980  2.103
    17296     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22  2.848  1.943
    17297     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21  2.738  1.784
    17298     PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2   PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1   2.666  1.685
    17299     PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O    PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22  3.598  2.755
    17300     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE   PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE    2.902  1.898
    17301     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12  2.894  1.970
    17302     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21  3.324  2.539
    17303     PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22  2.784  1.818
    17304    
    17305 
    17306  
    17307 19 hydrogen bonds found 
    17308 
    17309 > select #1/A:27,28,31,34/C:18/D:109/E:43,54,56
    17310 
    17311 170 atoms, 162 bonds, 9 residues, 1 model selected 
    17312 
    17313 > select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &~H
    17314 
    17315 81 atoms, 73 bonds, 9 residues, 1 model selected 
    17316 
    17317 > show sel atoms
    17318 
    17319 > style sel stick
    17320 
    17321 Changed 81 atom styles 
    17322 
    17323 > hide #1.2.1 models
    17324 
    17325 > select clear
    17326 
    17327 > select #1/X:1829-1831
    17328 
    17329 24 atoms, 54 pseudobonds, 3 residues, 2 models selected 
    17330 
    17331 > style sel ball
    17332 
    17333 Changed 24 atom styles 
    17334 
    17335 > style sel sphere
    17336 
    17337 Changed 24 atom styles 
    17338 
    17339 > select #1/X:1829-1831 &S
    17340 
    17341 12 atoms, 3 residues, 1 model selected 
    17342 
    17343 > ui tool show "Color Actions"
    17344 
    17345 > color sel gold
    17346 
    17347 > color sel goldenrod
    17348 
    17349 > color sel gold
    17350 
    17351 > color sel green yellow
    17352 
    17353 > color sel yellow green
    17354 
    17355 > color sel green yellow
    17356 
    17357 > color sel pale goldenrod
    17358 
    17359 > color sel wheat
    17360 
    17361 [Repeated 1 time(s)]
    17362 
    17363 > color sel beige
    17364 
    17365 > color sel light goldenrod yellow
    17366 
    17367 > select clear
    17368 
    17369 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    17370 > sulfu/Resubmission2025/Graphics/Designs/BFD design on PSI H-bonds.png" width
    17371 > 1800 height 1355 supersample 3 transparentBackground true
    17372 
    17373 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    17374 > sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs"
    17375 
    17376 > view name zoom1
    17377 
    17378 > ui tool show "Color Actions"
    17379 
    17380 > select #1/A &protein
    17381 
    17382 11579 atoms, 11778 bonds, 743 residues, 1 model selected 
    17383 
    17384 > color sel thistle target c
    17385 
    17386 > color sel lavender target c
    17387 
    17388 > color sel light pink target c
    17389 
    17390 > color sel thistle target c
    17391 
    17392 > color sel plum target c
    17393 
    17394 > select #1/B &protein
    17395 
    17396 11513 atoms, 11725 bonds, 733 residues, 1 model selected 
    17397 
    17398 > color sel light pink target c
    17399 
    17400 > select #1/C &protein
    17401 
    17402 1206 atoms, 1219 bonds, 80 residues, 1 model selected 
    17403 
    17404 > color sel pale green target c
    17405 
    17406 > color sel dark sea green target c
    17407 
    17408 > select #1/C &protein
    17409 
    17410 1206 atoms, 1219 bonds, 80 residues, 1 model selected 
    17411 
    17412 > color sel dark gray target c
    17413 
    17414 > color sel gray target c
    17415 
    17416 > color sel teal target c
    17417 
    17418 > color sel green target c
    17419 
    17420 > color sel maroon target c
    17421 
    17422 > color sel dark salmon target c
    17423 
    17424 > color sel dark goldenrod target c
    17425 
    17426 > color sel brown target c
    17427 
    17428 > select #1/D &protein
    17429 
    17430 2277 atoms, 2308 bonds, 143 residues, 1 model selected 
    17431 
    17432 > color sel dark khaki target c
    17433 
    17434 > color sel wheat target c
    17435 
    17436 > color sel peach puff target c
    17437 
    17438 > color sel pale goldenrod target c
    17439 
    17440 > color sel light salmon target c
    17441 
    17442 > color sel burly wood target c
    17443 
    17444 > select #1/E &protein
    17445 
    17446 1059 atoms, 1071 bonds, 66 residues, 1 model selected 
    17447 
    17448 > view zoom1
    17449 
    17450 > view name zoom2
    17451 
    17452 > select #1/E &protein
    17453 
    17454 1059 atoms, 1071 bonds, 66 residues, 1 model selected 
    17455 
    17456 > color sel sandy brown target c
    17457 
    17458 > color sel peach puff target c
    17459 
    17460 > color sel light salmon target c
    17461 
    17462 [Repeated 1 time(s)]
    17463 
    17464 > color sel sandy brown target c
    17465 
    17466 > color sel light salmon target c
    17467 
    17468 > view name zoom2
    17469 
    17470 > select #1/F:17-18
    17471 
    17472 29 atoms, 29 bonds, 2 residues, 1 model selected 
    17473 
    17474 > select #1/F:17-18 &~H
    17475 
    17476 16 atoms, 16 bonds, 2 residues, 1 model selected 
    17477 
    17478 > show sel atoms
    17479 
    17480 > style sel stick
    17481 
    17482 Changed 16 atom styles 
    17483 
    17484 > select #1/F:17-19 &~H
    17485 
    17486 25 atoms, 25 bonds, 3 residues, 1 model selected 
    17487 
    17488 > show sel atoms
    17489 
    17490 > style sel stick
    17491 
    17492 Changed 25 atom styles 
    17493 
    17494 > select #1/C
    17495 
    17496 1206 atoms, 1219 bonds, 80 residues, 1 model selected 
    17497 
    17498 > select #1/C &protein
    17499 
    17500 1206 atoms, 1219 bonds, 80 residues, 1 model selected 
    17501 
    17502 > color sel brown target ac
    17503 
    17504 > color sel byhetero
    17505 
    17506 > color sel orange red target c
    17507 
    17508 > color sel dark orange target c
    17509 
    17510 > color sel coral target c
    17511 
    17512 > color sel chocolate target c
    17513 
    17514 > select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &~H
    17515 
    17516 81 atoms, 73 bonds, 9 residues, 1 model selected 
    17517 
    17518 > color sel steel blue target c
    17519 
    17520 > color sel steel blue target ac
    17521 
    17522 > color sel byhetero
    17523 
    17524 > color sel medium orchid target ac
    17525 
    17526 > color sel byhetero
    17527 
    17528 > color sel medium purple target ac
    17529 
    17530 > color sel byhetero
    17531 
    17532 > name frozen Hbonding sel
    17533 
    17534 > color sel medium violet red target ac
    17535 
    17536 > color sel deep pink target ac
    17537 
    17538 > color sel byhetero
    17539 
    17540 > select #1/E &protein
    17541 
    17542 1059 atoms, 1071 bonds, 66 residues, 1 model selected 
    17543 
    17544 > color sel bisque target c
    17545 
    17546 > color sel pink target c
    17547 
    17548 > color sel peach puff target c
    17549 
    17550 > select #1/C &protein
    17551 
    17552 1206 atoms, 1219 bonds, 80 residues, 1 model selected 
    17553 
    17554 > color sel wheat target c
    17555 
    17556 > color sel burly wood target c
    17557 
    17558 > color sel tan target c
    17559 
    17560 [Repeated 1 time(s)]
    17561 
    17562 > select #1/D &protein
    17563 
    17564 2277 atoms, 2308 bonds, 143 residues, 1 model selected 
    17565 
    17566 > color sel burly wood target c
    17567 
    17568 > select clear
    17569 
    17570 > select #1/F:9,17-19 &~H
    17571 
    17572 34 atoms, 33 bonds, 4 residues, 1 model selected 
    17573 
    17574 > show sel atoms
    17575 
    17576 > select clear
    17577 
    17578 > view name zoom2
    17579 
    17580 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    17581 > sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs"
    17582 
    17583 ——— End of log from Sun Sep 14 07:49:27 2025 ———
    17584 
    17585 > view name session-start
    17586 
    17587 opened ChimeraX session 
    17588 
    17589 > show #!2 models
    17590 
    17591 > hide #!1 models
    17592 
    17593 > show #!1 models
    17594 
    17595 > hide #!2 models
    17596 
    17597 > show #!2 models
    17598 
    17599 > hide #!2 models
    17600 
    17601 > ui tool show "Selection Inspector"
    17602 
    17603 > select #1/A:393
    17604 
    17605 16 atoms, 15 bonds, 1 residue, 1 model selected 
    17606 
    17607 > show #!2 models
    17608 
    17609 > select #2/A
    17610 
    17611 11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected 
    17612 
    17613 > help help:user
    17614 
    17615 > color #2/A DDA0DD target c
    17616 
    17617 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    17618 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    17619 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    17620 
    17621 > color #2/A #DDA0DD target c
    17622 
    17623 > select #1/B:393
    17624 
    17625 20 atoms, 20 bonds, 1 residue, 1 model selected 
    17626 
    17627 > color #2/B #FFB6C1 target c
    17628 
    17629 > select #1/C:40
    17630 
    17631 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17632 
    17633 > color #2/C #D2B48C target c
    17634 
    17635 > view session_start
    17636 
    17637 Expected an objects specifier or a view name or a keyword 
    17638 
    17639 > view list
    17640 
    17641 Named views: session-start, zoom1, zoom2 
    17642 
    17643 > view session-start
    17644 
    17645 > select #1/D:40
    17646 
    17647 14 atoms, 14 bonds, 1 residue, 1 model selected 
    17648 
    17649 > hide #!1 models
    17650 
    17651 > show #!1 models
    17652 
    17653 > hide #!1 models
    17654 
    17655 > show #!1 models
    17656 
    17657 > select #2/D:40
    17658 
    17659 Nothing selected 
    17660 
    17661 > hide #!1 models
    17662 
    17663 > view list
    17664 
    17665 Named views: session-start, zoom1, zoom2 
    17666 
    17667 > view session-start
    17668 
    17669 > select #1/D:40
    17670 
    17671 14 atoms, 14 bonds, 1 residue, 1 model selected 
    17672 
    17673 > color #2/D #DEB887 target c
    17674 
    17675 > select #1/E:40
    17676 
    17677 16 atoms, 15 bonds, 1 residue, 1 model selected 
    17678 
    17679 > show #!1 models
    17680 
    17681 > hide #!1 models
    17682 
    17683 > color #2/D #FFDAB9 target c
    17684 
    17685 > color #2/D #DEB887 target c
    17686 
    17687 > color #2/E #FFDAB9 target c
    17688 
    17689 > show #!1 models
    17690 
    17691 > hide #!1 models
    17692 
    17693 > show #!1 models
    17694 
    17695 > hide #!1 models
    17696 
    17697 > select #1/X:1829@S1
    17698 
    17699 1 atom, 1 residue, 1 model selected 
    17700 
    17701 > select #2:2239-2241
    17702 
    17703 24 atoms, 54 pseudobonds, 3 residues, 2 models selected 
    17704 
    17705 > select #2:2239-2241 &S
    17706 
    17707 12 atoms, 3 residues, 1 model selected 
    17708 
    17709 > select #1/X:1829@S1
    17710 
    17711 1 atom, 1 residue, 1 model selected 
    17712 
    17713 > select #2:2239-2241 &S
    17714 
    17715 12 atoms, 3 residues, 1 model selected 
    17716 
    17717 > color #2:2239-2241 &S #FAFAD2
    17718 
    17719 > view session-start
    17720 
    17721 > view name viewH2ase
    17722 
    17723 > open 1hfe
    17724 
    17725 1hfe title: 
    17726 1.6 A resolution structure of the Fe-ONLY hydrogenase from desulfovibrio
    17727 desulfuricans [more info...] 
    17728  
    17729 Chain information for 1hfe #5 
    17730 --- 
    17731 Chain | Description | UniProt 
    17732 L M | PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) | PHFL_DESVH 1-421 
    17733 S T | PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) | PHFS_DESVH 1-123 
    17734  
    17735 Non-standard residues in 1hfe #5 
    17736 --- 
    17737 CMO — carbon monoxide 
    17738 CYN — cyanide ion 
    17739 CYS — cysteine 
    17740 FE2 — Fe (II) ion 
    17741 PDT — 1,3-propanedithiol 
    17742 SF4 — iron/sulfur cluster 
    17743 ZN — zinc ion 
    17744  
    17745 1hfe mmCIF Assemblies 
    17746 --- 
    17747 1| author_and_software_defined_assembly 
    17748 2| author_and_software_defined_assembly 
    17749 3| software_defined_assembly 
    17750  
    17751 351 atoms have alternate locations. Control/examine alternate locations with
    17752 Altloc Explorer [start tool...] or the altlocs command. 
    17753 
    17754 > ui tool show Matchmaker
    17755 
    17756 > matchmaker #!5 to #2
    17757 
    17758 Parameters 
    17759 --- 
    17760 Chain pairing | bb 
    17761 Alignment algorithm | Needleman-Wunsch 
    17762 Similarity matrix | BLOSUM-62 
    17763 SS fraction | 0.3 
    17764 Gap open (HH/SS/other) | 18/18/6 
    17765 Gap extend | 1 
    17766 SS matrix |  |  | H | S | O 
    17767 ---|---|---|--- 
    17768 H | 6 | -9 | -6 
    17769 S |  | 6 | -6 
    17770 O |  |  | 4 
    17771 Iteration cutoff | 2 
    17772  
    17773 Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5),
    17774 sequence alignment score = 1795.1 
    17775 RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs:
    17776 2.105) 
    17777  
    17778 
    17779 > select #5/M/T
    17780 
    17781 4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected 
    17782 
    17783 > select #5/L/S
    17784 
    17785 4358 atoms, 3871 bonds, 19 pseudobonds, 1080 residues, 2 models selected 
    17786 
    17787 > select #5/M/T
    17788 
    17789 4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected 
    17790 
    17791 > hide sel cartoons
    17792 
    17793 > hide sel atoms
    17794 
    17795 > select #5/S
    17796 
    17797 860 atoms, 733 bonds, 1 pseudobond, 235 residues, 2 models selected 
    17798 
    17799 > color (#!5 & sel) orange
    17800 
    17801 > color sel byhetero
    17802 
    17803 > select #2/F:2157
    17804 
    17805 21 atoms, 21 bonds, 1 residue, 1 model selected 
    17806 
    17807 > select #2/F:2157-2238
    17808 
    17809 1309 atoms, 1329 bonds, 82 residues, 1 model selected 
    17810 
    17811 > ui tool show "Color Actions"
    17812 
    17813 > color sel steel blue
    17814 
    17815 > color sel slate gray
    17816 
    17817 > color sel light slate gray
    17818 
    17819 > color sel steel blue
    17820 
    17821 > color sel light steel blue
    17822 
    17823 > select #2/F:2150-2151
    17824 
    17825 14 atoms, 13 bonds, 2 residues, 1 model selected 
    17826 
    17827 > select #5:386
    17828 
    17829 8 atoms, 6 bonds, 2 residues, 1 model selected 
    17830 
    17831 > select #5:388
    17832 
    17833 18 atoms, 16 bonds, 2 residues, 1 model selected 
    17834 
    17835 > select #2/F:2152-2153
    17836 
    17837 22 atoms, 21 bonds, 2 residues, 1 model selected 
    17838 
    17839 > select #2/F:2152-2156
    17840 
    17841 65 atoms, 65 bonds, 5 residues, 1 model selected 
    17842 
    17843 > color sel cyan
    17844 
    17845 > select #2/F:388-390
    17846 
    17847 Nothing selected 
    17848 
    17849 > select #5/L:388-390
    17850 
    17851 23 atoms, 23 bonds, 3 residues, 1 model selected 
    17852 
    17853 > color sel orange
    17854 
    17855 > color sel orange red
    17856 
    17857 > select #5/L:388-397
    17858 
    17859 71 atoms, 72 bonds, 10 residues, 1 model selected 
    17860 
    17861 > color sel orange
    17862 
    17863 > color sel byhetero
    17864 
    17865 > select #5/M:43-123
    17866 
    17867 607 atoms, 624 bonds, 81 residues, 1 model selected 
    17868 
    17869 > color sel light steel blue
    17870 
    17871 > select #5/S:43-123
    17872 
    17873 651 atoms, 670 bonds, 81 residues, 1 model selected 
    17874 
    17875 > color sel light steel blue
    17876 
    17877 > select #5/:15-30,35-52,58-387,396-477
    17878 
    17879 Expected an objects specifier or a keyword 
    17880 
    17881 > select #5/L:15-30,35-52,58-387,396-477
    17882 
    17883 2866 atoms, 2890 bonds, 18 pseudobonds, 423 residues, 2 models selected 
    17884 
    17885 > hide #!2 models
    17886 
    17887 > show #!1 models
    17888 
    17889 > hide #!1 models
    17890 
    17891 > show #!2 models
    17892 
    17893 > select #5/L:1-400 &~15-30,35-52,58-387,396-477
    17894 
    17895 Expected a keyword 
    17896 
    17897 > select #5/L:1-400 &~:15-30,35-52,58-387,396-477
    17898 
    17899 240 atoms, 241 bonds, 30 residues, 1 model selected 
    17900 
    17901 > color sel cyan
    17902 
    17903 > color sel byhetero
    17904 
    17905 > select clear
    17906 
    17907 > hide #!5 models
    17908 
    17909 > view viewH2ase
    17910 
    17911 > show #!5 models
    17912 
    17913 > select #2/F:1766-1776
    17914 
    17915 160 atoms, 160 bonds, 11 residues, 1 model selected 
    17916 
    17917 > select #2/F:1766-1775
    17918 
    17919 146 atoms, 146 bonds, 10 residues, 1 model selected 
    17920 
    17921 > hide #!2 models
    17922 
    17923 > show #!2 models
    17924 
    17925 > select #2/F:1766-1775,1792-1795,1814-1821
    17926 
    17927 293 atoms, 293 bonds, 22 residues, 1 model selected 
    17928 
    17929 > color sel cyan
    17930 
    17931 > color sel byhetero
    17932 
    17933 > select clear
    17934 
    17935 > view viewH2ase
    17936 
    17937 > hide #!5 models
    17938 
    17939 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    17940 > sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
    17941 
    17942 > select #2/F &protein
    17943 
    17944 7149 atoms, 7242 bonds, 473 residues, 1 model selected 
    17945 
    17946 > ui tool show H-Bonds
    17947 
    17948 > hbonds sel color #0096ff showDist true interModel false intraMol false
    17949 > intraRes false reveal true log true
    17950 
    17951 Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A
    17952 CYF 575 SG 
    17953 Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb
    17954 #2/A CYF 575 SG 
    17955  
    17956 [Repeated 1 time(s)]
    17957 
    17958 Skipped 2 atom(s) with bad connectivities; see log for details 
    17959 
    17960    
    17961    
    17962     Finding intramodel H-bonds
    17963     Constraints relaxed by 0.4 angstroms and 20 degrees
    17964     Models used:
    17965         2 DdHyd_PSI.opt.chains.pdb
    17966    
    17967     13 H-bonds
    17968     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    17969     DdHyd_PSI.opt.chains.pdb #2/A ARG 27 NH2    DdHyd_PSI.opt.chains.pdb #2/F GLU 1814 OE1  DdHyd_PSI.opt.chains.pdb #2/A ARG 27 HH21    3.498  2.750
    17970     DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 NE2  DdHyd_PSI.opt.chains.pdb #2/F CYF 1799 O    DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 HE21  2.873  2.126
    17971     DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 NZ   DdHyd_PSI.opt.chains.pdb #2/F ASN 1843 OD1  DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 HZ2   2.829  1.880
    17972     DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ   DdHyd_PSI.opt.chains.pdb #2/F GLN 1804 OE1  DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ2   2.839  1.911
    17973     DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ   DdHyd_PSI.opt.chains.pdb #2/F PRO 2234 O    DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ1   2.762  1.871
    17974     DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 N    DdHyd_PSI.opt.chains.pdb #2/F LYS 2032 O    DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 H3    2.915  1.906
    17975     DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH1  DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O    DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH11  2.866  1.886
    17976     DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH2  DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O    DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH21  3.207  2.381
    17977     DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH1  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH12  2.805  1.855
    17978     DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD1  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22  2.984  2.083
    17979     DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22  2.835  1.934
    17980     DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N    DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD1  DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1    2.862  2.132
    17981     DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N    DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD2  DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1    2.902  1.907
    17982    
    17983 
    17984  
    17985 13 hydrogen bonds found 
    17986 
    17987 > select #2/F &protein
    17988 
    17989 7149 atoms, 7242 bonds, 473 residues, 1 model selected 
    17990 
    17991 > select #2 &protein
    17992 
    17993 34783 atoms, 35343 bonds, 13 pseudobonds, 2238 residues, 2 models selected 
    17994 
    17995 > style sel stick
    17996 
    17997 Changed 34783 atom styles 
    17998 
    17999 > select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730
    18000 
    18001 161 atoms, 154 bonds, 8 residues, 1 model selected 
    18002 
    18003 > ui tool show "Color Actions"
    18004 
    18005 > color sel deep pink
    18006 
    18007 > color sel byhetero
    18008 
    18009 > select #2 &H
    18010 
    18011 17179 atoms, 2238 residues, 1 model selected 
    18012 
    18013 > hide sel atoms
    18014 
    18015 > ui tool show H-Bonds
    18016 
    18017 > hbonds sel color #0096ff showDist true interModel false intraMol false
    18018 > intraRes false select true log true
    18019 
    18020 Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A
    18021 CYF 575 SG 
    18022 Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb
    18023 #2/A CYF 575 SG 
    18024  
    18025 [Repeated 1 time(s)]
    18026 
    18027 Skipped 2 atom(s) with bad connectivities; see log for details 
    18028 
    18029    
    18030    
    18031     Finding intramodel H-bonds
    18032     Constraints relaxed by 0.4 angstroms and 20 degrees
    18033     Models used:
    18034         2 DdHyd_PSI.opt.chains.pdb
    18035    
    18036     0 H-bonds
    18037     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    18038    
    18039 
    18040  
    18041 0 hydrogen bonds found 
    18042 
    18043 > select #2/F &protein
    18044 
    18045 7149 atoms, 7242 bonds, 473 residues, 1 model selected 
    18046 
    18047 > ui tool show H-Bonds
    18048 
    18049 > hbonds sel color #0096ff showDist true interModel false intraMol false
    18050 > intraRes false select true log true
    18051 
    18052 Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A
    18053 CYF 575 SG 
    18054 Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb
    18055 #2/A CYF 575 SG 
    18056  
    18057 [Repeated 1 time(s)]
    18058 
    18059 Skipped 2 atom(s) with bad connectivities; see log for details 
    18060 
    18061    
    18062    
    18063     Finding intramodel H-bonds
    18064     Constraints relaxed by 0.4 angstroms and 20 degrees
    18065     Models used:
    18066         2 DdHyd_PSI.opt.chains.pdb
    18067    
    18068     13 H-bonds
    18069     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    18070     DdHyd_PSI.opt.chains.pdb #2/A ARG 27 NH2    DdHyd_PSI.opt.chains.pdb #2/F GLU 1814 OE1  DdHyd_PSI.opt.chains.pdb #2/A ARG 27 HH21    3.498  2.750
    18071     DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 NE2  DdHyd_PSI.opt.chains.pdb #2/F CYF 1799 O    DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 HE21  2.873  2.126
    18072     DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 NZ   DdHyd_PSI.opt.chains.pdb #2/F ASN 1843 OD1  DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 HZ2   2.829  1.880
    18073     DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ   DdHyd_PSI.opt.chains.pdb #2/F GLN 1804 OE1  DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ2   2.839  1.911
    18074     DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ   DdHyd_PSI.opt.chains.pdb #2/F PRO 2234 O    DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ1   2.762  1.871
    18075     DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 N    DdHyd_PSI.opt.chains.pdb #2/F LYS 2032 O    DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 H3    2.915  1.906
    18076     DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH1  DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O    DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH11  2.866  1.886
    18077     DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH2  DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O    DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH21  3.207  2.381
    18078     DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH1  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH12  2.805  1.855
    18079     DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD1  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22  2.984  2.083
    18080     DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22  2.835  1.934
    18081     DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N    DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD1  DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1    2.862  2.132
    18082     DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N    DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD2  DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1    2.902  1.907
    18083    
    18084 
    18085  
    18086 13 hydrogen bonds found 
    18087 
    18088 > show sel atoms
    18089 
    18090 > hide #2.2.1 models
    18091 
    18092 > color #2/E #FFDAB9 target c
    18093 
    18094 > color #2/D #DEB887 target c
    18095 
    18096 > color #2/C #D2B48C target c
    18097 
    18098 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    18099 > sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
    18100 
    18101 > view list
    18102 
    18103 Named views: session-start, viewH2ase, zoom1, zoom2 
    18104 
    18105 > view session-start
    18106 
    18107 > color #2/A #DDA0DD target c
    18108 
    18109 > view name viewH2aseHbonds
    18110 
    18111 [Repeated 1 time(s)]
    18112 
    18113 > select clear
    18114 
    18115 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    18116 > sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
    18117 
    18118 ——— End of log from Mon Sep 15 19:12:58 2025 ———
    18119 
    18120 > view name session-start
    18121 
    18122 opened ChimeraX session 
    18123 
    18124 > view viewH2aseHbonds
    18125 
    18126 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    18127 > sulfu/Resubmission2025/Models and structures/PSI-DdHyd Hbonds.png" width
    18128 > 1800 height 1358 supersample 3 transparentBackground true
    18129 
    18130 > select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730
    18131 
    18132 161 atoms, 154 bonds, 8 residues, 1 model selected 
    18133 
    18134 > name frozen HbondingDdH sel
    18135 
    18136 > select clear
    18137 
    18138 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    18139 > sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
    18140 
    18141 ——— End of log from Mon Sep 15 20:51:36 2025 ———
    18142 
    18143 > view name session-start
    18144 
    18145 opened ChimeraX session 
    18146 
    18147 > select #2/F:1766-1775,1792-1795,1814-1821 &H
    18148 
    18149 139 atoms, 22 residues, 1 model selected 
    18150 
    18151 > select #2/F:1766-1775,1792-1795,1814-1821 &~H
    18152 
    18153 154 atoms, 154 bonds, 22 residues, 1 model selected 
    18154 
    18155 > show sel atoms
    18156 
    18157 > select #2/F:1766-1775,1792-1795,1814-1821,2151-2156 &~H
    18158 
    18159 196 atoms, 196 bonds, 28 residues, 1 model selected 
    18160 
    18161 > select #2/F:1766-1775,1792-1795,1814-1821,2152-2156 &~H
    18162 
    18163 192 atoms, 192 bonds, 27 residues, 1 model selected 
    18164 
    18165 > show sel atoms
    18166 
    18167 > color sel byhetero
    18168 
    18169 > view session-start
    18170 
    18171 > select clear
    18172 
    18173 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    18174 > sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
    18175 
    18176 ——— End of log from Mon Sep 15 21:24:55 2025 ———
    18177 
    18178 > view name session-start
    18179 
    18180 opened ChimeraX session 
    18181 
    18182 > select #2/C-F &protein
    18183 
    18184 11691 atoms, 11840 bonds, 12 pseudobonds, 762 residues, 2 models selected 
    18185 
    18186 > coulombic sel
    18187 
    18188 Using Amber 20 recommended default charges and atom types for standard
    18189 residues 
    18190 Assigning partial charges to residue CYF (net charge -1) with am1-bcc method 
    18191 Running ANTECHAMBER command:
    18192 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek
    18193 qm_theory='AM1', -i
    18194 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.in.mol2 -fi
    18195 mol2 -o
    18196 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.out.mol2 -fo
    18197 mol2 -c bcc -nc -1 -j 5 -s 2 -dr n 
    18198 (CYF) `` 
    18199 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    18200 (CYF) `` 
    18201 (CYF) `Info: Finished reading file
    18202 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.in.mol2);
    18203 atoms read (25), bonds read (24).` 
    18204 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    18205 sensitive.` 
    18206 (CYF) `Running:
    18207 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/bondtype -j part -i
    18208 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    18209 (CYF) `` 
    18210 (CYF) `` 
    18211 (CYF) `Running:
    18212 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -i
    18213 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    18214 (CYF) `Info: Total number of electrons: 102; net charge: -1` 
    18215 (CYF) `` 
    18216 (CYF) `Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm
    18217 -O -i sqm.in -o sqm.out` 
    18218 (CYF) `` 
    18219 (CYF) `Running:
    18220 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/am1bcc -i
    18221 ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    18222 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    18223 -s 2 -j 1` 
    18224 (CYF) `` 
    18225 (CYF) `Running:
    18226 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    18227 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    18228 (CYF) `` 
    18229 Charges for residue CYF determined 
    18230 Coulombic values for DdHyd_PSI.opt.chains.pdb_C SES surface #2.3: minimum,
    18231 -22.19, mean -4.05, maximum 8.43 
    18232 Coulombic values for DdHyd_PSI.opt.chains.pdb_D SES surface #2.4: minimum,
    18233 -10.22, mean 2.11, maximum 15.27 
    18234 Coulombic values for DdHyd_PSI.opt.chains.pdb_E SES surface #2.5: minimum,
    18235 -11.34, mean 1.57, maximum 12.31 
    18236 Coulombic values for DdHyd_PSI.opt.chains.pdb_F SES surface #2.6: minimum,
    18237 -23.25, mean -3.85, maximum 11.53 
    18238 To also show corresponding color key, enter the above coulombic command and
    18239 add key true 
    18240 
    18241 > view name coulSide
    18242 
    18243 > select #2/A-B &protein
    18244 
    18245 23092 atoms, 23503 bonds, 1476 residues, 1 model selected 
    18246 
    18247 > coulombic sel
    18248 
    18249 Using Amber 20 recommended default charges and atom types for standard
    18250 residues 
    18251 Assigning partial charges to residue CYF (net charge -1) with am1-bcc method 
    18252 Running ANTECHAMBER command:
    18253 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek
    18254 qm_theory='AM1', -i
    18255 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.in.mol2 -fi
    18256 mol2 -o
    18257 /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.out.mol2 -fo
    18258 mol2 -c bcc -nc -1 -j 5 -s 2 -dr n 
    18259 (CYF) `` 
    18260 (CYF) `Welcome to antechamber 20.0: molecular input file processor.` 
    18261 (CYF) `` 
    18262 (CYF) `Info: Finished reading file
    18263 (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.in.mol2);
    18264 atoms read (22), bonds read (21).` 
    18265 (CYF) `Info: Determining atomic numbers from atomic symbols which are case
    18266 sensitive.` 
    18267 (CYF) `Running:
    18268 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/bondtype -j part -i
    18269 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    18270 (CYF) `` 
    18271 (CYF) `` 
    18272 (CYF) `Running:
    18273 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -i
    18274 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    18275 (CYF) `Info: Total number of electrons: 94; net charge: -1` 
    18276 (CYF) `` 
    18277 (CYF) `Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm
    18278 -O -i sqm.in -o sqm.out` 
    18279 (CYF) `` 
    18280 (CYF) `Running:
    18281 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/am1bcc -i
    18282 ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    18283 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    18284 -s 2 -j 1` 
    18285 (CYF) `` 
    18286 (CYF) `Running:
    18287 /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    18288 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    18289 (CYF) `` 
    18290 Charges for residue CYF determined 
    18291 Coulombic values for DdHyd_PSI.opt.chains.pdb_A SES surface #2.7: minimum,
    18292 -12.58, mean -0.47, maximum 17.74 
    18293 Coulombic values for DdHyd_PSI.opt.chains.pdb_B SES surface #2.8: minimum,
    18294 -15.68, mean -0.16, maximum 13.13 
    18295 To also show corresponding color key, enter the above coulombic command and
    18296 add key true 
    18297 
    18298 > hide #2.6 models
    18299 
    18300 > combine #5
    18301 
    18302 > hide #!2 models
    18303 
    18304 > select #6/L:CMO,CYN,PDT,FE2:424
    18305 
    18306 23 atoms, 20 bonds, 4 pseudobonds, 8 residues, 2 models selected 
    18307 
    18308 > hide sel atoms
    18309 
    18310 > show sel atoms
    18311 
    18312 > select #6 &~/L:CMO,CYN,PDT,FE2:424
    18313 
    18314 8705 atoms, 7722 bonds, 29 pseudobonds, 2164 residues, 2 models selected 
    18315 
    18316 > hide sel cartoons
    18317 
    18318 > hide sel atoms
    18319 
    18320 > delete atoms (#!6 & sel)
    18321 
    18322 > delete bonds (#!6 & sel)
    18323 
    18324 > show #!2 models
    18325 
    18326 > align #6/L:424@FE4,S3,FE1,S2,S1,FE2,S4,FE3 toAtoms
    18327 > #2/F:2244@F4,S3,F1,S2,S1,F2,S4,F3
    18328 
    18329 RMSD between 8 atom pairs is 0.065 angstroms 
    18330 
    18331 > select #2/F:CYF
    18332 
    18333 120 atoms, 108 bonds, 12 residues, 1 model selected 
    18334 
    18335 > show sel atoms
    18336 
    18337 > select #2/F:CYF &H
    18338 
    18339 48 atoms, 12 residues, 1 model selected 
    18340 
    18341 > hide sel atoms
    18342 
    18343 > select #2/F:SF4
    18344 
    18345 24 atoms, 54 pseudobonds, 3 residues, 2 models selected 
    18346 
    18347 > style sel ball
    18348 
    18349 Changed 24 atom styles 
    18350 
    18351 > select #6:SF4
    18352 
    18353 8 atoms, 12 bonds, 1 residue, 1 model selected 
    18354 
    18355 > hide sel atoms
    18356 
    18357 > select #2/F:SF4
    18358 
    18359 24 atoms, 54 pseudobonds, 3 residues, 2 models selected 
    18360 
    18361 > style sel sphere
    18362 
    18363 Changed 24 atom styles 
    18364 
    18365 > select #6
    18366 
    18367 23 atoms, 20 bonds, 4 pseudobonds, 8 residues, 2 models selected 
    18368 
    18369 > ui tool show "Color Actions"
    18370 
    18371 > color sel maroon
    18372 
    18373 > color sel byhetero
    18374 
    18375 > style sel sphere
    18376 
    18377 Changed 23 atom styles 
    18378 
    18379 > show #2.6 models
    18380 
    18381 > hide #2.3 models
    18382 
    18383 > hide #2.4 models
    18384 
    18385 > hide #2.5 models
    18386 
    18387 > show #2.3 models
    18388 
    18389 > show #2.4 models
    18390 
    18391 > show #2.5 models
    18392 
    18393 > save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
    18394 > sulfu/Resubmission2025/Models and structures/PSI-DdHyd design coulombic
    18395 > surfs.cxs"
    18396 
    18397 > close #1
    18398 
    18399 > close #4
    18400 
    18401 > rename #6 "Catalytic Site"
    18402 
    18403 > ui tool show Matchmaker
    18404 
    18405 > close #3
    18406 
    18407 > matchmaker #5/L to #2/F pairing ss showAlignment true
    18408 
    18409 Parameters 
    18410 --- 
    18411 Chain pairing | ss 
    18412 Alignment algorithm | Needleman-Wunsch 
    18413 Similarity matrix | BLOSUM-62 
    18414 SS fraction | 0.3 
    18415 Gap open (HH/SS/other) | 18/18/6 
    18416 Gap extend | 1 
    18417 SS matrix |  |  | H | S | O 
    18418 ---|---|---|--- 
    18419 H | 6 | -9 | -6 
    18420 S |  | 6 | -6 
    18421 O |  |  | 4 
    18422 Iteration cutoff | 2 
    18423  
    18424 Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5),
    18425 sequence alignment score = 1795.1 
    18426 Alignment identifier is 1 
    18427 Showing conservation header ("seq_conservation" residue attribute) for
    18428 alignment 1 
    18429 Hiding conservation header for alignment 1 
    18430 Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #2/F,
    18431 1hfe #5/L 
    18432 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    18433 RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs:
    18434 2.105) 
    18435  
    18436 
    18437 > matchmaker #5/L to #2/F pairing ss showAlignment true
    18438 
    18439 Parameters 
    18440 --- 
    18441 Chain pairing | ss 
    18442 Alignment algorithm | Needleman-Wunsch 
    18443 Similarity matrix | BLOSUM-62 
    18444 SS fraction | 0.3 
    18445 Gap open (HH/SS/other) | 18/18/6 
    18446 Gap extend | 1 
    18447 SS matrix |  |  | H | S | O 
    18448 ---|---|---|--- 
    18449 H | 6 | -9 | -6 
    18450 S |  | 6 | -6 
    18451 O |  |  | 4 
    18452 Iteration cutoff | 2 
    18453  
    18454 Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5),
    18455 sequence alignment score = 1795.1 
    18456 Alignment identifier is 2 
    18457 Showing conservation header ("seq_conservation" residue attribute) for
    18458 alignment 2 
    18459 Hiding conservation header for alignment 2 
    18460 Chains used in RMSD evaluation for alignment 2: DdHyd_PSI.opt.chains.pdb #2/F,
    18461 1hfe #5/L 
    18462 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    18463 RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs:
    18464 2.105) 
    18465  
    18466 
    18467 > hide #2.3 models
    18468 
    18469 > show #2.3 models
    18470 
    18471 > hide #2.6 models
    18472 
    18473 > hide #2.7 models
    18474 
    18475 > hide #2.8 models
    18476 
    18477 > show #2.8 models
    18478 
    18479 > show #2.7 models
    18480 
    18481 > show #!5 models
    18482 
    18483 > select #2/F:1812
    18484 
    18485 20 atoms, 20 bonds, 1 residue, 1 model selected 
    18486 
    18487 > select #2/F:1812-1820 #5/L:51-56
    18488 
    18489 164 atoms, 166 bonds, 15 residues, 2 models selected 
    18490 MatchMaker Alignment [ID: 2] region chain F..chain L [51-59] RMSD: 2.042 
    18491  
    18492 
    18493 > select #2/F:1766
    18494 
    18495 21 atoms, 20 bonds, 1 residue, 1 model selected 
    18496 
    18497 > select #2/F:1766-1773 #5/L:3-12
    18498 
    18499 213 atoms, 212 bonds, 18 residues, 2 models selected 
    18500 MatchMaker Alignment [ID: 2] region chain F..chain L [3-12] RMSD: 8.370 
    18501  
    18502 
    18503 > hide #!5 models
    18504 
    18505 > show #2.6 models
    18506 
    18507 > hide #2.6 models
    18508 
    18509 > select clear
    18510 
    18511 > select #5/L:389
    18512 
    18513 7 atoms, 7 bonds, 1 residue, 1 model selected 
    18514 
    18515 > select #5/L:389-391
    18516 
    18517 22 atoms, 22 bonds, 3 residues, 1 model selected 
    18518 
    18519 > select #2/F:2149
    18520 
    18521 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18522 
    18523 > select #2/F:2149-2152
    18524 
    18525 28 atoms, 27 bonds, 4 residues, 1 model selected 
    18526 
    18527 > select #2/F:2152
    18528 
    18529 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18530 
    18531 > select #2/F:2152-2153
    18532 
    18533 22 atoms, 21 bonds, 2 residues, 1 model selected 
    18534 
    18535 > select #2/F:2152
    18536 
    18537 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18538 
    18539 > select #2/F:2152-2155
    18540 
    18541 50 atoms, 50 bonds, 4 residues, 1 model selected 
    18542 
    18543 > select #2/F:2152
    18544 
    18545 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18546 
    18547 > select #2/F:2152-2156
    18548 
    18549 65 atoms, 65 bonds, 5 residues, 1 model selected 
    18550 
    18551 > show #!5 models
    18552 
    18553 > ui tool show Matchmaker
    18554 
    18555 > matchmaker #5/L to #2/F pairing ss showAlignment true
    18556 
    18557 Parameters 
    18558 --- 
    18559 Chain pairing | ss 
    18560 Alignment algorithm | Needleman-Wunsch 
    18561 Similarity matrix | BLOSUM-62 
    18562 SS fraction | 0.3 
    18563 Gap open (HH/SS/other) | 18/18/6 
    18564 Gap extend | 1 
    18565 SS matrix |  |  | H | S | O 
    18566 ---|---|---|--- 
    18567 H | 6 | -9 | -6 
    18568 S |  | 6 | -6 
    18569 O |  |  | 4 
    18570 Iteration cutoff | 2 
    18571  
    18572 Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5),
    18573 sequence alignment score = 1795.1 
    18574 Alignment identifier is 1 
    18575 Showing conservation header ("seq_conservation" residue attribute) for
    18576 alignment 1 
    18577 Hiding conservation header for alignment 1 
    18578 Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #2/F,
    18579 1hfe #5/L 
    18580 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    18581 RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs:
    18582 2.105) 
    18583  
    18584 
    18585 > save "/Users/drornoy/OneDrive - Migal/ISF-DFG/PSI-DdHyd design.cxs"
    18586 
    18587 ——— End of log from Wed Sep 17 15:57:48 2025 ———
    18588 
    18589 > view name session-start
    18590 
    18591 opened ChimeraX session 
    18592 
    18593 > hide #!5 models
    18594 
    18595 > hide #!6 models
    18596 
    18597 > show #!5 models
    18598 
    18599 > hide #!5 models
    18600 
    18601 > show #!6 models
    18602 
    18603 > hide #!6 models
    18604 
    18605 > show #!5 models
    18606 
    18607 > hide #!5 models
    18608 
    18609 > show #!5 models
    18610 
    18611 > select clear
    18612 
    18613 > select #5/L:2-3
    18614 
    18615 17 atoms, 16 bonds, 2 residues, 1 model selected 
    18616 
    18617 > hide #!5 models
    18618 
    18619 > show #!5 models
    18620 
    18621 > hide #!5 models
    18622 
    18623 > show #!5 models
    18624 
    18625 > hide #!5 models
    18626 
    18627 > select #5/L:389
    18628 
    18629 7 atoms, 7 bonds, 1 residue, 1 model selected 
    18630 
    18631 > select #5/L:389-391
    18632 
    18633 22 atoms, 22 bonds, 3 residues, 1 model selected 
    18634 
    18635 > show #!5 models
    18636 
    18637 > select #2/F:2153
    18638 
    18639 15 atoms, 14 bonds, 1 residue, 1 model selected 
    18640 
    18641 > select #2/F:2153-2158
    18642 
    18643 96 atoms, 97 bonds, 6 residues, 1 model selected 
    18644 
    18645 > select #5/L:388-389
    18646 
    18647 16 atoms, 16 bonds, 2 residues, 1 model selected 
    18648 
    18649 > select #5/L:389-398
    18650 
    18651 63 atoms, 64 bonds, 10 residues, 1 model selected 
    18652 
    18653 > open 3lx4
    18654 
    18655 Summary of feedback from opening 3lx4 fetched from pdb 
    18656 --- 
    18657 note | Fetching compressed mmCIF 3lx4 from http://files.rcsb.org/download/3lx4.cif 
    18658  
    18659 3lx4 title: 
    18660 Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of
    18661 HydA(deltaEFG) [more info...] 
    18662  
    18663 Chain information for 3lx4 #1 
    18664 --- 
    18665 Chain | Description | UniProt 
    18666 A B | Fe-hydrogenase | Q9FYU1_CHLRE 17-457 
    18667  
    18668 Non-standard residues in 3lx4 #1 
    18669 --- 
    18670 ACT — acetate ion 
    18671 CL — chloride ion 
    18672 SF4 — iron/sulfur cluster 
    18673  
    18674 3lx4 mmCIF Assemblies 
    18675 --- 
    18676 1| author_and_software_defined_assembly 
    18677 2| author_and_software_defined_assembly 
    18678  
    18679 32 atoms have alternate locations. Control/examine alternate locations with
    18680 Altloc Explorer [start tool...] or the altlocs command. 
    18681 
    18682 > ui tool show Matchmaker
    18683 
    18684 > matchmaker #!1 to #2
    18685 
    18686 Parameters 
    18687 --- 
    18688 Chain pairing | bb 
    18689 Alignment algorithm | Needleman-Wunsch 
    18690 Similarity matrix | BLOSUM-62 
    18691 SS fraction | 0.3 
    18692 Gap open (HH/SS/other) | 18/18/6 
    18693 Gap extend | 1 
    18694 SS matrix |  |  | H | S | O 
    18695 ---|---|---|--- 
    18696 H | 6 | -9 | -6 
    18697 S |  | 6 | -6 
    18698 O |  |  | 4 
    18699 Iteration cutoff | 2 
    18700  
    18701 Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 3lx4, chain B (#1),
    18702 sequence alignment score = 861.9 
    18703 RMSD between 264 pruned atom pairs is 1.082 angstroms; (across all 356 pairs:
    18704 3.848) 
    18705  
    18706 
    18707 > hide #2.8 models
    18708 
    18709 > hide #2.7 models
    18710 
    18711 > show #2.6 models
    18712 
    18713 > hide #2.6 models
    18714 
    18715 > show #2.7 models
    18716 
    18717 > hide #2.7 models
    18718 
    18719 > hide #2.3 models
    18720 
    18721 > hide #2.4 models
    18722 
    18723 > hide #2.5 models
    18724 
    18725 > show #2.6 models
    18726 
    18727 > hide #2.6 models
    18728 
    18729 > show #2.5 models
    18730 
    18731 > show #2.4 models
    18732 
    18733 > show #2.3 models
    18734 
    18735 > hide #2.3 models
    18736 
    18737 > show #2.7 models
    18738 
    18739 > show #2.8 models
    18740 
    18741 > hide #!2 models
    18742 
    18743 > hide #!5 models
    18744 
    18745 > show #!2 models
    18746 
    18747 > hide #!2 models
    18748 
    18749 > select #1/A
    18750 
    18751 3460 atoms, 3157 bonds, 7 pseudobonds, 774 residues, 3 models selected 
    18752 
    18753 > hide sel cartoons
    18754 
    18755 > hide sel atoms
    18756 
    18757 > show #!2 models
    18758 
    18759 > ui tool show "Show Sequence Viewer"
    18760 
    18761 > sequence chain #5/S #5/T
    18762 
    18763 Alignment identifier is 2 
    18764 
    18765 > select clear
    18766 
    18767 [Repeated 1 time(s)]
    18768 
    18769 > show #!5 models
    18770 
    18771 > hide #!2 models
    18772 
    18773 > hide #!1 models
    18774 
    18775 > select clear
    18776 
    18777 [Repeated 1 time(s)]
    18778 
    18779 > select #5/S-T:38
    18780 
    18781 18 atoms, 16 bonds, 2 residues, 1 model selected 
    18782 
    18783 > select #5/S-T:38-45
    18784 
    18785 140 atoms, 140 bonds, 16 residues, 1 model selected 
    18786 
    18787 > select #5/S-T:46
    18788 
    18789 22 atoms, 20 bonds, 2 residues, 1 model selected 
    18790 
    18791 > select #5/S-T:46-51
    18792 
    18793 100 atoms, 100 bonds, 12 residues, 1 model selected 
    18794 
    18795 > select #5/S-T:38
    18796 
    18797 18 atoms, 16 bonds, 2 residues, 1 model selected 
    18798 
    18799 > select #5/S-T:38-45
    18800 
    18801 140 atoms, 140 bonds, 16 residues, 1 model selected 
    18802 
    18803 > select #5/L:2-14
    18804 
    18805 115 atoms, 116 bonds, 13 residues, 1 model selected 
    18806 
    18807 > select #5/L:2-14,31-34,53-57
    18808 
    18809 183 atoms, 183 bonds, 22 residues, 1 model selected 
    18810 
    18811 > select #5/L:2-14,31-34,53-57,388-397
    18812 
    18813 254 atoms, 255 bonds, 32 residues, 1 model selected 
    18814 
    18815 > ui tool show "Color Actions"
    18816 
    18817 > color sel alice blue
    18818 
    18819 > color sel sky blue
    18820 
    18821 > color sel light sky blue
    18822 
    18823 > color sel light blue
    18824 
    18825 > color sel pale turquoise
    18826 
    18827 > color sel light steel blue
    18828 
    18829 > color sel pale turquoise
    18830 
    18831 > color sel wheat
    18832 
    18833 > color sel gainsboro
    18834 
    18835 > color sel powder blue
    18836 
    18837 > color sel pale turquoise
    18838 
    18839 > color sel byhetero
    18840 
    18841 > show #!2 models
    18842 
    18843 > hide #!2 models
    18844 
    18845 > show #!2 models
    18846 
    18847 > select #5/L:2-14,31-34,53-57,388-397/S:36-42
    18848 
    18849 316 atoms, 317 bonds, 39 residues, 1 model selected 
    18850 
    18851 > select #5/L:2-14,31-34,53-57,388-397/S:36-41
    18852 
    18853 304 atoms, 304 bonds, 38 residues, 1 model selected 
    18854 
    18855 > hide #!5 models
    18856 
    18857 > save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking
    18858 > design.cxs"
    18859 
    18860 > close #1
    18861 
    18862 > rename #1 id 1
    18863 
    18864 > rename #2 id 1
    18865 
    18866 > rename #1 id 2
    18867 
    18868 > help help:user
    18869 
    18870 > rename #2#6 id #1
    18871 
    18872 > rename #1 DdHyd_PSI
    18873 
    18874 > rename #5 id #2
    18875 
    18876 > show #!1.2 models
    18877 
    18878 > combine #1 copy t
    18879 
    18880 Expected a keyword 
    18881 
    18882 > combine #1
    18883 
    18884 Associated combination chain F to chain F with 0 mismatches 
    18885 Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb
    18886 #1.1/F, 1hfe #2/L, combination #3/F 
    18887 
    18888 > hide #3.1 models
    18889 
    18890 > show #3.1 models
    18891 
    18892 > hide #!1 models
    18893 
    18894 > hide #!3 models
    18895 
    18896 > show #!3 models
    18897 
    18898 > hide #3.1 models
    18899 
    18900 > hide #3.2 models
    18901 
    18902 > help help:user
    18903 
    18904 [Repeated 1 time(s)]
    18905 
    18906 > split #3 chains
    18907 
    18908 Split combination (#3) into 7 models 
    18909 Chain information for combination A #3.1 
    18910 --- 
    18911 Chain | Description 
    18912 A | No description available 
    18913  
    18914 Chain information for combination B #3.2 
    18915 --- 
    18916 Chain | Description 
    18917 B | No description available 
    18918  
    18919 Chain information for combination C #3.3 
    18920 --- 
    18921 Chain | Description 
    18922 C | No description available 
    18923  
    18924 Chain information for combination D #3.4 
    18925 --- 
    18926 Chain | Description 
    18927 D | No description available 
    18928  
    18929 Chain information for combination E #3.5 
    18930 --- 
    18931 Chain | Description 
    18932 E | No description available 
    18933  
    18934 Chain information for combination F #3.6 
    18935 --- 
    18936 Chain | Description 
    18937 F | No description available 
    18938  
    18939 Associated combination F (3.6) chain F to chain F with 0 mismatches 
    18940 Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb
    18941 #1.1/F, 1hfe #2/L, combination F #3.6/F 
    18942 
    18943 > hide #!3.1 models
    18944 
    18945 > hide #3.2 models
    18946 
    18947 > hide #!3.3 models
    18948 
    18949 > hide #3.4 models
    18950 
    18951 > hide #3.5 models
    18952 
    18953 > show #!1 models
    18954 
    18955 > select #3.1-3.3
    18956 
    18957 Nothing selected 
    18958 
    18959 > select #3.1
    18960 
    18961 11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected 
    18962 
    18963 > select #3.1#3.2
    18964 
    18965 23100 atoms, 23503 bonds, 18 pseudobonds, 1477 residues, 3 models selected 
    18966 
    18967 > rename #3.1#3.2#3.3#3.4#3.5 id #4
    18968 
    18969 > show #1.1.3 models
    18970 
    18971 > hide #1.1.3 models
    18972 
    18973 > select #1/F
    18974 
    18975 7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected 
    18976 
    18977 > select #1.1/F
    18978 
    18979 7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected 
    18980 
    18981 > hide sel atoms
    18982 
    18983 > hide sel cartoons
    18984 
    18985 > hide #!1 models
    18986 
    18987 > hide #!3 models
    18988 
    18989 > show #!3 models
    18990 
    18991 > show #!1 models
    18992 
    18993 > hide #!1 models
    18994 
    18995 > show #!1 models
    18996 
    18997 > select #1.1/F
    18998 
    18999 7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected 
    19000 
    19001 > delete atoms (#!1.1 & sel)
    19002 
    19003 Chains used in RMSD evaluation for alignment 1: 1hfe #2/L, combination F
    19004 #3.6/F 
    19005 
    19006 > delete bonds (#!1.1 & sel)
    19007 
    19008 > hide #!1.1 models
    19009 
    19010 > show #!1.1 models
    19011 
    19012 > hide #!1.1 models
    19013 
    19014 > show #!1.1 models
    19015 
    19016 > close #1.2
    19017 
    19018 > rename #1.1 id #1
    19019 
    19020 > rename #1.1 id 1
    19021 
    19022 > combine #1.1
    19023 
    19024 > hide #!4 models
    19025 
    19026 > hide #!1 models
    19027 
    19028 > close #5
    19029 
    19030 > show #!1 models
    19031 
    19032 > hide #!1.1 models
    19033 
    19034 > show #!1.1 models
    19035 
    19036 > rename #1 PSI
    19037 
    19038 > rename #1.1 "DdHyd_PSI.opt.chains no DdHyd"
    19039 
    19040 > rename #2 id 6
    19041 
    19042 > show #!4 models
    19043 
    19044 > hide #!1 models
    19045 
    19046 > hide #!4 models
    19047 
    19048 > show #!4 models
    19049 
    19050 > show #!4.1 models
    19051 
    19052 > show #4.2 models
    19053 
    19054 > show #!4.3 models
    19055 
    19056 > show #4.4 models
    19057 
    19058 > show #4.5 models
    19059 
    19060 > close #4
    19061 
    19062 > show #!1 models
    19063 
    19064 > rename #3.6 DdHyd_PSI.opt.chains
    19065 
    19066 > rename #3.7 "Catalytic site"
    19067 
    19068 > rename #3 id 2
    19069 
    19070 > rename #6 id 3
    19071 
    19072 > rename #2 DdHyd_PSI
    19073 
    19074 > hide #!1 models
    19075 
    19076 > show #!3 models
    19077 
    19078 > open 9gbu 9gnk
    19079 
    19080 Summary of feedback from opening 9gbu fetched from pdb 
    19081 --- 
    19082 warnings | Atom HS2 is not in the residue template for 402 /A:505 
    19083 Atom HS2 is not in the residue template for 402 /B:504 
    19084 notes | Fetching compressed mmCIF 9gbu from http://files.rcsb.org/download/9gbu.cif 
    19085 Fetching CCD MPD from
    19086 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif 
    19087  
    19088 Summary of feedback from opening 9gnk fetched from pdb 
    19089 --- 
    19090 warnings | Atom HS2 is not in the residue template for 402 /A:502 
    19091 Atom H3 is not in the residue template for PG4 /A:512 
    19092 notes | Fetching compressed mmCIF 9gnk from http://files.rcsb.org/download/9gnk.cif 
    19093 Fetching CCD EPE from
    19094 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif 
    19095 Fetching CCD PG4 from
    19096 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PG4/PG4.cif 
    19097  
    19098 9gbu title: 
    19099 Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits
    19100 linked by a 13 amino acid linker peptide derived from a group A1 type
    19101 [FeFe]-hydrogenase of Solobacterium moorei [more info...] 
    19102  
    19103 Chain information for 9gbu #4 
    19104 --- 
    19105 Chain | Description | UniProt 
    19106 A B | Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit | PHFL_NITV2 1-389, PHFS_NITV2 403-480 
    19107  
    19108 Non-standard residues in 9gbu #4 
    19109 --- 
    19110 402 — dicarbonyl[bis(cyanide-
    19111 kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) 
    19112 MPD — (4S)-2-methyl-2,4-pentanediol 
    19113 SF4 — iron/sulfur cluster 
    19114  
    19115 9gbu mmCIF Assemblies 
    19116 --- 
    19117 1| author_defined_assembly 
    19118 2| author_defined_assembly 
    19119  
    19120 166 atoms have alternate locations. Control/examine alternate locations with
    19121 Altloc Explorer [start tool...] or the altlocs command. 
    19122 9gnk title: 
    19123 Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits
    19124 linked by a 13 amino acid linker peptide derived from CpI of Clostridium
    19125 pasteurianum [more info...] 
    19126  
    19127 Chain information for 9gnk #5 
    19128 --- 
    19129 Chain | Description | UniProt 
    19130 A | Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit | PHFL_NITV2 1-390, PHFS_NITV2 404-482 
    19131  
    19132 Non-standard residues in 9gnk #5 
    19133 --- 
    19134 402 — dicarbonyl[bis(cyanide-
    19135 kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) 
    19136 CMO — carbon monoxide 
    19137 EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) 
    19138 PEG — di(hydroxyethyl)ether 
    19139 PG4 — tetraethylene glycol 
    19140 SF4 — iron/sulfur cluster 
    19141  
    19142 9gnk mmCIF Assemblies 
    19143 --- 
    19144 1| author_defined_assembly 
    19145  
    19146 200 atoms have alternate locations. Control/examine alternate locations with
    19147 Altloc Explorer [start tool...] or the altlocs command. 
    19148 Associated 9gbu chain A to chain L with 31 mismatches 
    19149 Associated 9gbu chain B to chain L with 31 mismatches 
    19150 Associated 9gnk chain A to chain L with 29 mismatches 
    19151 Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains #2.6/F,
    19152 1hfe #3/L, 9gbu #4/B, 9gnk #5/A 
    19153 
    19154 > hide #!4 models
    19155 
    19156 > show #!4 models
    19157 
    19158 > hide #!5 models
    19159 
    19160 > select #4/B
    19161 
    19162 7543 atoms, 7548 bonds, 24 pseudobonds, 577 residues, 2 models selected 
    19163 
    19164 > hide sel cartoons
    19165 
    19166 > hide sel atoms
    19167 
    19168 > show #!5 models
    19169 
    19170 > matchmaker #!4-5 to #2.6
    19171 
    19172 Parameters 
    19173 --- 
    19174 Chain pairing | bb 
    19175 Alignment algorithm | Needleman-Wunsch 
    19176 Similarity matrix | BLOSUM-62 
    19177 SS fraction | 0.3 
    19178 Gap open (HH/SS/other) | 18/18/6 
    19179 Gap extend | 1 
    19180 SS matrix |  |  | H | S | O 
    19181 ---|---|---|--- 
    19182 H | 6 | -9 | -6 
    19183 S |  | 6 | -6 
    19184 O |  |  | 4 
    19185 Iteration cutoff | 2 
    19186  
    19187 Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 9gbu, chain A (#4),
    19188 sequence alignment score = 2182.6 
    19189 RMSD between 454 pruned atom pairs is 0.553 angstroms; (across all 469 pairs:
    19190 1.405) 
    19191  
    19192 Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 9gnk, chain A (#5),
    19193 sequence alignment score = 2184.3 
    19194 RMSD between 453 pruned atom pairs is 0.534 angstroms; (across all 470 pairs:
    19195 1.482) 
    19196  
    19197 Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains #2.6/F,
    19198 1hfe #3/L, 9gbu #4/A, 9gnk #5/A 
    19199 
    19200 > hide #!3 models
    19201 
    19202 > show #!3 models
    19203 
    19204 > hide #!3 models
    19205 
    19206 > show #!3 models
    19207 
    19208 > select add #3
    19209 
    19210 16271 atoms, 15290 bonds, 63 pseudobonds, 2749 residues, 4 models selected 
    19211 
    19212 > select add #4
    19213 
    19214 23871 atoms, 22854 bonds, 87 pseudobonds, 3365 residues, 4 models selected 
    19215 
    19216 > select subtract #4
    19217 
    19218 8728 atoms, 7742 bonds, 39 pseudobonds, 2172 residues, 2 models selected 
    19219 
    19220 > select subtract #3
    19221 
    19222 Nothing selected 
    19223 
    19224 > select add #5
    19225 
    19226 8157 atoms, 7706 bonds, 24 pseudobonds, 1040 residues, 2 models selected 
    19227 
    19228 > hide #!4 models
    19229 
    19230 > hide #!3 models
    19231 
    19232 > hide #!2 models
    19233 
    19234 > color sel sandy brown
    19235 
    19236 > color sel byhetero
    19237 
    19238 > show #!4 models
    19239 
    19240 > show #!3 models
    19241 
    19242 > show #!2 models
    19243 
    19244 > color sel dark khaki
    19245 
    19246 > color sel plum
    19247 
    19248 > color sel byhetero
    19249 
    19250 > select subtract #5
    19251 
    19252 Nothing selected 
    19253 
    19254 > hide #!4 models
    19255 
    19256 > hide #!3 models
    19257 
    19258 > hide #!2 models
    19259 
    19260 > select :4O2
    19261 
    19262 Nothing selected 
    19263 
    19264 > select :402
    19265 
    19266 64 atoms, 61 bonds, 4 residues, 3 models selected 
    19267 
    19268 > select #5:402
    19269 
    19270 22 atoms, 21 bonds, 1 residue, 1 model selected 
    19271 
    19272 > select ::name="402"
    19273 
    19274 72 atoms, 48 bonds, 33 pseudobonds, 3 residues, 4 models selected 
    19275 
    19276 > select :EPE,PEG,PG4,MPD
    19277 
    19278 290 atoms, 278 bonds, 13 residues, 2 models selected 
    19279 
    19280 > hide sel & #!5 atoms
    19281 
    19282 > select :EPE,PEG,PG4,MPD,HOH
    19283 
    19284 2233 atoms, 278 bonds, 1956 residues, 3 models selected 
    19285 
    19286 > hide sel & #!5 atoms
    19287 
    19288 > show #!4 models
    19289 
    19290 > show #!2 models
    19291 
    19292 > hide #!2 models
    19293 
    19294 > ui tool show "Show Sequence Viewer"
    19295 
    19296 > sequence chain #5/A
    19297 
    19298 Alignment identifier is 5/A 
    19299 
    19300 > sequence chain #4/A #4/B
    19301 
    19302 Alignment identifier is 3 
    19303 
    19304 > select #5/A:400
    19305 
    19306 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19307 
    19308 > select #5/A:388
    19309 
    19310 17 atoms, 16 bonds, 1 residue, 1 model selected 
    19311 
    19312 > select #5/A:388-400
    19313 
    19314 209 atoms, 210 bonds, 13 residues, 1 model selected 
    19315 
    19316 > select #5/A:390
    19317 
    19318 16 atoms, 15 bonds, 1 residue, 1 model selected 
    19319 
    19320 > select #5/A:390-399
    19321 
    19322 166 atoms, 166 bonds, 10 residues, 1 model selected 
    19323 
    19324 > select #4/A-B:402
    19325 
    19326 22 atoms, 20 bonds, 2 residues, 1 model selected 
    19327 
    19328 > select #4/A-B:390-402
    19329 
    19330 440 atoms, 442 bonds, 26 residues, 1 model selected 
    19331 
    19332 > select #5/A:404-405
    19333 
    19334 36 atoms, 35 bonds, 2 residues, 1 model selected 
    19335 
    19336 > select #5/A:390-405
    19337 
    19338 277 atoms, 277 bonds, 16 residues, 1 model selected 
    19339 
    19340 > select #5/A:390-391
    19341 
    19342 32 atoms, 31 bonds, 2 residues, 1 model selected 
    19343 
    19344 > select #5/A:390-404
    19345 
    19346 253 atoms, 253 bonds, 15 residues, 1 model selected 
    19347 
    19348 > select #5/A:390-404#4/A:390-402
    19349 
    19350 473 atoms, 474 bonds, 28 residues, 2 models selected 
    19351 
    19352 > show #!2 models
    19353 
    19354 > select #4/A:390-402
    19355 
    19356 220 atoms, 221 bonds, 13 residues, 1 model selected 
    19357 
    19358 > color sel sea green
    19359 
    19360 > select #5/A:390-404
    19361 
    19362 253 atoms, 253 bonds, 15 residues, 1 model selected 
    19363 
    19364 > color sel purple
    19365 
    19366 > show #!3 models
    19367 
    19368 > save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking
    19369 > design.cxs"
    19370 
    19371 ——— End of log from Wed Oct 22 18:27:07 2025 ———
    19372 
    19373 > view name session-start
    19374 
    19375 opened ChimeraX session 
    19376 
    19377 > open "/Users/drornoy/Google
    19378 > Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_model_0.cif"
    19379 
    19380 Chain information for fold_ddhyab_model_0.cif #6 
    19381 --- 
    19382 Chain | Description 
    19383 A | . 
    19384  
    19385 Associated fold_ddhyab_model_0.cif chain A to chain L with 27 mismatches 
    19386 Computing secondary structure 
    19387 
    19388 > hide #!5 models
    19389 
    19390 > hide #!4 models
    19391 
    19392 > hide #!2 models
    19393 
    19394 > ui tool show Matchmaker
    19395 
    19396 > matchmaker #6 to #2.6
    19397 
    19398 Parameters 
    19399 --- 
    19400 Chain pairing | bb 
    19401 Alignment algorithm | Needleman-Wunsch 
    19402 Similarity matrix | BLOSUM-62 
    19403 SS fraction | 0.3 
    19404 Gap open (HH/SS/other) | 18/18/6 
    19405 Gap extend | 1 
    19406 SS matrix |  |  | H | S | O 
    19407 ---|---|---|--- 
    19408 H | 6 | -9 | -6 
    19409 S |  | 6 | -6 
    19410 O |  |  | 4 
    19411 Iteration cutoff | 2 
    19412  
    19413 Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with fold_ddhyab_model_0.cif,
    19414 chain A (#6), sequence alignment score = 2224.5 
    19415 RMSD between 456 pruned atom pairs is 0.436 angstroms; (across all 470 pairs:
    19416 1.221) 
    19417  
    19418 
    19419 > ui tool show "AlphaFold Error Plot"
    19420 
    19421 > alphafold pae #6 file "/Users/drornoy/Google
    19422 > Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_full_data_0.json"
    19423 
    19424 > color bfactor #6 palette alphafold
    19425 
    19426 3649 atoms, 474 residues, atom bfactor range 50.4 to 99 
    19427 
    19428 > hide #!3 models
    19429 
    19430 > show #!5 models
    19431 
    19432 > show #!4 models
    19433 
    19434 > show #!2 models
    19435 
    19436 > show #!1 models
    19437 
    19438 > hide #!1 models
    19439 
    19440 > save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking
    19441 > design.cxs"
    19442 
    19443 ——— End of log from Wed Oct 22 19:01:49 2025 ———
    19444 
    19445 > view name session-start
    19446 
    19447 opened ChimeraX session 
    19448 
    19449 > hide #!5 models
    19450 
    19451 > hide #!4 models
    19452 
    19453 > hide #!2 models
    19454 
    19455 > show #!2 models
    19456 
    19457 > show #!1 models
    19458 
    19459 > hide #!2 models
    19460 
    19461 > show #!2 models
    19462 
    19463 > hide #!2 models
    19464 
    19465 > hide #!1 models
    19466 
    19467 > show #!3 models
    19468 
    19469 > hide #6 models
    19470 
    19471 > show #!1 models
    19472 
    19473 > show #!2 models
    19474 
    19475 > close #6
    19476 
    19477 > select add #5
    19478 
    19479 8157 atoms, 7706 bonds, 24 pseudobonds, 1040 residues, 2 models selected 
    19480 
    19481 > select subtract #5
    19482 
    19483 Nothing selected 
    19484 
    19485 > help help:user
    19486 
    19487 > rename #5 id 9
    19488 
    19489 > rename #4 id 8
    19490 
    19491 > rename #3 id 7
    19492 
    19493 > save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Structures and
    19494 > designs/PSI_DdH2ase dock design with all single chains variants.cxs"
    19495 
    19496 > open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase
    19497 > Single
    19498 > Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif"
    19499 
    19500 Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif
    19501 #3 
    19502 --- 
    19503 Chain | Description 
    19504 A | . 
    19505  
    19506 Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to
    19507 chain L with 25 mismatches 
    19508 Computing secondary structure 
    19509 
    19510 > hide #!1 models
    19511 
    19512 > hide #!7 models
    19513 
    19514 > ui tool show Matchmaker
    19515 
    19516 > matchmaker #3 to #2.6 showAlignment true
    19517 
    19518 Parameters 
    19519 --- 
    19520 Chain pairing | bb 
    19521 Alignment algorithm | Needleman-Wunsch 
    19522 Similarity matrix | BLOSUM-62 
    19523 SS fraction | 0.3 
    19524 Gap open (HH/SS/other) | 18/18/6 
    19525 Gap extend | 1 
    19526 SS matrix |  |  | H | S | O 
    19527 ---|---|---|--- 
    19528 H | 6 | -9 | -6 
    19529 S |  | 6 | -6 
    19530 O |  |  | 4 
    19531 Iteration cutoff | 2 
    19532  
    19533 Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with
    19534 fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3),
    19535 sequence alignment score = 2230.1 
    19536 Alignment identifier is 4 
    19537 Showing conservation header ("seq_conservation" residue attribute) for
    19538 alignment 4 
    19539 Hiding conservation header for alignment 4 
    19540 Chains used in RMSD evaluation for alignment 4: DdHyd_PSI.opt.chains #2.6/F,
    19541 fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A 
    19542 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4 
    19543 RMSD between 456 pruned atom pairs is 0.422 angstroms; (across all 470 pairs:
    19544 1.377) 
    19545  
    19546 
    19547 > ui tool show "AlphaFold Error Plot"
    19548 
    19549 > alphafold pae #3 file "/Users/drornoy/Library/CloudStorage/OneDrive-
    19550 > Migal/ISF-DFG/DdH2ase Single
    19551 > Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_full_data_0.json"
    19552 
    19553 > color bfactor #3 palette alphafold
    19554 
    19555 3677 atoms, 477 residues, atom bfactor range 44.8 to 99 
    19556 
    19557 > select add #3
    19558 
    19559 3677 atoms, 3770 bonds, 477 residues, 1 model selected 
    19560 
    19561 > color sel byhetero
    19562 
    19563 > select subtract #3
    19564 
    19565 Nothing selected 
    19566 
    19567 > show #!7 models
    19568 
    19569 > show #!8 models
    19570 
    19571 > hide #!7 models
    19572 
    19573 > hide #!8 models
    19574 
    19575 > open 3lx4
    19576 
    19577 3lx4 title: 
    19578 Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of
    19579 HydA(deltaEFG) [more info...] 
    19580  
    19581 Chain information for 3lx4 #4 
    19582 --- 
    19583 Chain | Description | UniProt 
    19584 A B | Fe-hydrogenase | Q9FYU1_CHLRE 17-457 
    19585  
    19586 Non-standard residues in 3lx4 #4 
    19587 --- 
    19588 ACT — acetate ion 
    19589 CL — chloride ion 
    19590 SF4 — iron/sulfur cluster 
    19591  
    19592 3lx4 mmCIF Assemblies 
    19593 --- 
    19594 1| author_and_software_defined_assembly 
    19595 2| author_and_software_defined_assembly 
    19596  
    19597 32 atoms have alternate locations. Control/examine alternate locations with
    19598 Altloc Explorer [start tool...] or the altlocs command. 
    19599 
    19600 > select :SF4
    19601 
    19602 192 atoms, 216 bonds, 108 pseudobonds, 24 residues, 9 models selected 
    19603 
    19604 > ui tool show Matchmaker
    19605 
    19606 > matchmaker #4/A to #2.6/F pairing ss showAlignment true
    19607 
    19608 Parameters 
    19609 --- 
    19610 Chain pairing | ss 
    19611 Alignment algorithm | Needleman-Wunsch 
    19612 Similarity matrix | BLOSUM-62 
    19613 SS fraction | 0.3 
    19614 Gap open (HH/SS/other) | 18/18/6 
    19615 Gap extend | 1 
    19616 SS matrix |  |  | H | S | O 
    19617 ---|---|---|--- 
    19618 H | 6 | -9 | -6 
    19619 S |  | 6 | -6 
    19620 O |  |  | 4 
    19621 Iteration cutoff | 2 
    19622  
    19623 Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 3lx4, chain A (#4),
    19624 sequence alignment score = 854.7 
    19625 Alignment identifier is 2 
    19626 Showing conservation header ("seq_conservation" residue attribute) for
    19627 alignment 2 
    19628 Hiding conservation header for alignment 2 
    19629 Chains used in RMSD evaluation for alignment 2: DdHyd_PSI.opt.chains #2.6/F,
    19630 3lx4 #4/A 
    19631 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    19632 RMSD between 265 pruned atom pairs is 1.087 angstroms; (across all 356 pairs:
    19633 3.844) 
    19634  
    19635 
    19636 > rename #4 "CrHydA1 3lx4"
    19637 
    19638 > rename #7 "DdHydAHydB 1hfe"
    19639 
    19640 > select #3/B
    19641 
    19642 Nothing selected 
    19643 
    19644 > select #4/B
    19645 
    19646 3507 atoms, 3157 bonds, 7 pseudobonds, 821 residues, 3 models selected 
    19647 
    19648 > hide sel cartoons
    19649 
    19650 > hide sel atoms
    19651 
    19652 > close #8
    19653 
    19654 > close #9
    19655 
    19656 > show #!7 models
    19657 
    19658 > hide #!7 models
    19659 
    19660 > rename #7 id 5
    19661 
    19662 > save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
    19663 > and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
    19664 
    19665 > open 8ru6
    19666 
    19667 Summary of feedback from opening 8ru6 fetched from pdb 
    19668 --- 
    19669 warning | Atom HS1 is not in the residue template for MHX /B:508 
    19670  
    19671 8ru6 title: 
    19672 Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits
    19673 linked by a 4 amino acid linker peptide derived from CpI of Clostridium
    19674 pasteurianum [more info...] 
    19675  
    19676 Chain information for 8ru6 #6 
    19677 --- 
    19678 Chain | Description | UniProt 
    19679 B | Periplasmic [Fe] hydrogenase large subunit,CpI,Periplasmic [Fe] hydrogenase small subunit | PHFL_DESVH 1-392, PHF1_CLOPA 393-396, PHFS_DESVH 397-481 
    19680  
    19681 Non-standard residues in 8ru6 #6 
    19682 --- 
    19683 MHX — Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster
    19684 (-CO form) 
    19685 PG4 — tetraethylene glycol 
    19686 SF4 — iron/sulfur cluster 
    19687  
    19688 147 atoms have alternate locations. Control/examine alternate locations with
    19689 Altloc Explorer [start tool...] or the altlocs command. 
    19690 Associated 8ru6 chain B to chain L with 25 mismatches 
    19691 
    19692 > hide #!4 models
    19693 
    19694 > hide #3 models
    19695 
    19696 > hide #!2 models
    19697 
    19698 > show #!2 models
    19699 
    19700 > show #3 models
    19701 
    19702 > show #!4 models
    19703 
    19704 > ui tool show Matchmaker
     4173[deleted to fit within ticket limits]
    197054174
    197064175> matchmaker #6/B to #3/A pairing ss showAlignment true