Changes between Initial Version and Version 1 of Ticket #18814


Ignore:
Timestamp:
Sep 18, 2025, 10:51:42 AM (4 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #18814

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

  • Ticket #18814 – Description

    initial v1  
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     73[deleted to fit within ticket limits]
     74
    167375],
    167476  "sharedCache" : {
    … …  
    4288269016 atoms, 16 residues, 16 models selected 
    42892691
    4290 > color sel blue
    4291 
    4292 > show #19 models
    4293 
    4294 > hide #19 models
    4295 
    4296 > show #19 models
    4297 
    4298 > hide #19 models
    4299 
    4300 > show #19 models
    4301 
    4302 > hide #19 models
    4303 
    4304 > show #19 models
    4305 
    4306 > hide #19 models
    4307 
    4308 > show #19 models
    4309 
    4310 > select #18/C:62@MG
    4311 
    4312 1 atom, 1 residue, 1 model selected 
    4313 
    4314 > select add #19/A:279
    4315 
    4316 21 atoms, 21 bonds, 2 residues, 2 models selected 
    4317 
    4318 > select #19/C:3
    4319 
    4320 23 atoms, 25 bonds, 1 residue, 1 model selected 
    4321 
    4322 > select #1-18/C:12
    4323 
    4324 17 atoms, 17 residues, 17 models selected 
    4325 
    4326 > color sel blue
    4327 
    4328 > select #18/C:62@MG
    4329 
    4330 1 atom, 1 residue, 1 model selected 
    4331 
    4332 > select add #19/C:3
    4333 
    4334 24 atoms, 25 bonds, 2 residues, 2 models selected 
    4335 
    4336 > select #19/C:3
    4337 
    4338 23 atoms, 25 bonds, 1 residue, 1 model selected 
    4339 
    4340 > show sel target ab
    4341 
    4342 > cartoon hide sel
    4343 
    4344 > select #19/C:3@C5'
    4345 
    4346 1 atom, 1 residue, 1 model selected 
    4347 
    4348 > select add #18/C:62@MG
    4349 
    4350 2 atoms, 2 residues, 2 models selected 
    4351 
    4352 > distance #19/C:3@C5' #18/C:62@MG
    4353 
    4354 Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
    4355 #19/C G 3 C5' and V25_holo-coot-2.pdb #18/C MG 62 MG: 7.071Å 
    4356 
    4357 > view matrix models
    4358 > #18,0.99985,0.00571,-0.016139,1.607,-0.0060653,0.99974,-0.02205,5.6923,0.016009,0.022145,0.99963,-5.4963,#19,-0.96809,0.078949,-0.23783,410.8,0.24041,0.024802,-0.97035,327.08,-0.070709,-0.99657,-0.042991,409.72
    4359 
    4360 > view matrix models
    4361 > #18,0.98188,-0.025202,-0.18781,39.726,0.0089682,0.99619,-0.086791,14.256,0.18928,0.083534,0.97836,-47.209,#19,-0.9475,0.24905,-0.20055,362.29,0.2289,0.090348,-0.96925,314.7,-0.22327,-0.96427,-0.14261,451.61
    4362 
    4363 > view matrix models
    4364 > #18,0.98928,0.0045084,-0.14599,25.485,-0.014636,0.99755,-0.068373,15.45,0.14533,0.069777,0.98692,-37.485,#19,-0.95027,0.20788,-0.2319,377.78,0.25102,0.070488,-0.96541,313.97,-0.18434,-0.97561,-0.11916,442
    4365 
    4366 > view matrix models
    4367 > #18,0.98454,-0.024891,-0.17338,36.644,0.017984,0.99899,-0.041293,4.3816,0.17423,0.037537,0.98399,-35.839,#19,-0.95088,0.23482,-0.20172,366.2,0.21806,0.045516,-0.97487,327.75,-0.21974,-0.97097,-0.094484,443.7
    4368 
    4369 > view matrix models
    4370 > #18,0.98484,0.054997,-0.16452,19.343,-0.062648,0.99717,-0.041676,20.275,0.16176,0.051351,0.98549,-36.422,#19,-0.93307,0.22625,-0.27964,379.17,0.29591,0.040826,-0.95434,309.51,-0.2045,-0.97321,-0.10504,443.16
    4371 
    4372 > matchmaker #!2-11 to #1 & sel matrix Nucleic
    4373 
    4374 No 'to' model specified 
    4375 
    4376 > select
    4377 > #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400
    4378 
    4379 3255 atoms, 3639 bonds, 151 residues, 1 model selected 
    4380 
    4381 > matchmaker #!2-11 to #1 & sel matrix Nucleic
    4382 
    4383 Computing secondary structure 
    4384 Parameters 
    4385 --- 
    4386 Chain pairing | bb 
    4387 Alignment algorithm | Needleman-Wunsch 
    4388 Similarity matrix | Nucleic 
    4389 SS fraction | 0.3 
    4390 Gap open (HH/SS/other) | 18/18/6 
    4391 Gap extend | 1 
    4392 SS matrix |  |  | H | S | O 
    4393 ---|---|---|--- 
    4394 H | 6 | -9 | -6 
    4395 S |  | 6 | -6 
    4396 O |  |  | 4 
    4397 Iteration cutoff | 2 
    4398  
    4399 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
    4400 (#2), sequence alignment score = 604 
    4401 RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
    4402 0.413) 
    4403  
    4404 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
    4405 (#3), sequence alignment score = 604 
    4406 RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
    4407 0.322) 
    4408  
    4409 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
    4410 (#4), sequence alignment score = 604 
    4411 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
    4412 0.445) 
    4413  
    4414 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
    4415 (#5), sequence alignment score = 604 
    4416 RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
    4417 0.365) 
    4418  
    4419 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
    4420 (#6), sequence alignment score = 604 
    4421 RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
    4422 0.323) 
    4423  
    4424 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
    4425 (#7), sequence alignment score = 604 
    4426 RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
    4427 0.325) 
    4428  
    4429 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
    4430 (#8), sequence alignment score = 604 
    4431 RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
    4432 0.364) 
    4433  
    4434 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
    4435 (#9), sequence alignment score = 604 
    4436 RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
    4437 0.374) 
    4438  
    4439 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
    4440 (#10), sequence alignment score = 604 
    4441 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
    4442 0.367) 
    4443  
    4444 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
    4445 (#11), sequence alignment score = 604 
    4446 RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
    4447 0.464) 
    4448  
    4449 
    4450 > matchmaker #19#!2-18 to #1 & sel matrix Nucleic
    4451 
    4452 Computing secondary structure 
    4453 Parameters 
    4454 --- 
    4455 Chain pairing | bb 
    4456 Alignment algorithm | Needleman-Wunsch 
    4457 Similarity matrix | Nucleic 
    4458 SS fraction | 0.3 
    4459 Gap open (HH/SS/other) | 18/18/6 
    4460 Gap extend | 1 
    4461 SS matrix |  |  | H | S | O 
    4462 ---|---|---|--- 
    4463 H | 6 | -9 | -6 
    4464 S |  | 6 | -6 
    4465 O |  |  | 4 
    4466 Iteration cutoff | 2 
    4467  
    4468 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
    4469 coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
    4470 604 
    4471 RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs:
    4472 0.766) 
    4473  
    4474 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
    4475 (#2), sequence alignment score = 604 
    4476 RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
    4477 0.413) 
    4478  
    4479 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
    4480 (#3), sequence alignment score = 604 
    4481 RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
    4482 0.322) 
    4483  
    4484 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
    4485 (#4), sequence alignment score = 604 
    4486 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
    4487 0.445) 
    4488  
    4489 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
    4490 (#5), sequence alignment score = 604 
    4491 RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
    4492 0.365) 
    4493  
    4494 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
    4495 (#6), sequence alignment score = 604 
    4496 RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
    4497 0.323) 
    4498  
    4499 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
    4500 (#7), sequence alignment score = 604 
    4501 RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
    4502 0.325) 
    4503  
    4504 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
    4505 (#8), sequence alignment score = 604 
    4506 RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
    4507 0.364) 
    4508  
    4509 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
    4510 (#9), sequence alignment score = 604 
    4511 RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
    4512 0.374) 
    4513  
    4514 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
    4515 (#10), sequence alignment score = 604 
    4516 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
    4517 0.367) 
    4518  
    4519 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
    4520 (#11), sequence alignment score = 604 
    4521 RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
    4522 0.464) 
    4523  
    4524 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A
    4525 (#12), sequence alignment score = 604 
    4526 RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs:
    4527 0.359) 
    4528  
    4529 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A
    4530 (#13), sequence alignment score = 604 
    4531 RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs:
    4532 0.441) 
    4533  
    4534 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A
    4535 (#14), sequence alignment score = 604 
    4536 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
    4537 0.367) 
    4538  
    4539 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A
    4540 (#15), sequence alignment score = 604 
    4541 RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs:
    4542 0.488) 
    4543  
    4544 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A
    4545 (#16), sequence alignment score = 604 
    4546 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
    4547 0.445) 
    4548  
    4549 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A
    4550 (#17), sequence alignment score = 604 
    4551 RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs:
    4552 0.368) 
    4553  
    4554 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A
    4555 (#18), sequence alignment score = 604 
    4556 RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs:
    4557 0.430) 
    4558  
    4559 
    4560 > ui mousemode right select
    4561 
    4562 > select clear
    4563 
    4564 Drag select of 6 residues 
    4565 
    4566 > select clear
    4567 
    4568 > hide #!1-18 target m
    4569 
    4570 > show #!1 models
    4571 
    4572 > hide #!1 models
    4573 
    4574 > show #!1 models
    4575 
    4576 > show #!1-18 target m
    4577 
    4578 Drag select of 17 residues 
    4579 
    4580 > select clear
    4581 
    4582 > select #1-18/C:10
    4583 
    4584 13 atoms, 13 residues, 13 models selected 
    4585 Drag select of 6 residues 
    4586 
    4587 > select #19/C:0
    4588 
    4589 20 atoms, 21 bonds, 1 residue, 1 model selected 
    4590 
    4591 > hide #19 models
    4592 
    4593 > select #14/C:80@MG
    4594 
    4595 1 atom, 1 residue, 1 model selected 
    4596 
    4597 > select subtract #14/C:80@MG
    4598 
    4599 Nothing selected 
    4600 
    4601 > select add #5/C:24@MG
    4602 
    4603 1 atom, 1 residue, 1 model selected 
    4604 
    4605 > select add #14/C:80@MG
    4606 
    4607 2 atoms, 2 residues, 2 models selected 
    4608 
    4609 > select #7/A:278
    4610 
    4611 20 atoms, 21 bonds, 1 residue, 1 model selected 
    4612 
    4613 > select #14/C:80@MG
    4614 
    4615 1 atom, 1 residue, 1 model selected 
    4616 
    4617 > select #1-18/A:50,389,390
    4618 
    4619 1188 atoms, 1314 bonds, 54 residues, 18 models selected 
    4620 
    4621 > select #1-18/A:49,50,51,389,390
    4622 
    4623 1998 atoms, 2232 bonds, 90 residues, 18 models selected 
    4624 
    4625 > select #7/A:391
    4626 
    4627 20 atoms, 21 bonds, 1 residue, 1 model selected 
    4628 
    4629 > select #1-18/A:49,50,51,389,390,391
    4630 
    4631 2358 atoms, 2628 bonds, 108 residues, 18 models selected 
    4632 
    4633 > select #1-18/A:49,50,51,52,388,389,390,391
    4634 
    4635 3132 atoms, 3492 bonds, 144 residues, 18 models selected 
    4636 
    4637 > show #19 models
    4638 
    4639 > hide #19 models
    4640 
    4641 > view sel
    4642 
    4643 > select #10/C:84@MG
    4644 
    4645 1 atom, 1 residue, 1 model selected 
    4646 
    4647 > select add #17/C:87@MG
    4648 
    4649 2 atoms, 2 residues, 2 models selected 
    4650 
    4651 > select add #1/C:4@MG
    4652 
    4653 3 atoms, 3 residues, 3 models selected 
    4654 
    4655 > select add #13/C:24@MG
    4656 
    4657 4 atoms, 4 residues, 4 models selected 
    4658 
    4659 > select add #11/A:390@OP2
    4660 
    4661 5 atoms, 5 residues, 5 models selected 
    4662 
    4663 > select add #12/C:7@MG
    4664 
    4665 6 atoms, 6 residues, 6 models selected 
    4666 
    4667 > select add #4/A:50@OP1
    4668 
    4669 7 atoms, 7 residues, 7 models selected 
    4670 
    4671 > view sel
    4672 
    4673 > show #19 models
    4674 
    4675 > hide #19 models
    4676 
    4677 > show #19 models
    4678 
    4679 > hide #19 models
    4680 
    4681 > select #7/A:390@O3'
    4682 
    4683 1 atom, 1 residue, 1 model selected 
    4684 
    4685 > select #7/A:390@O3'
    4686 
    4687 1 atom, 1 residue, 1 model selected 
    4688 
    4689 > select add #4/A:390@O2'
    4690 
    4691 2 atoms, 2 residues, 2 models selected 
    4692 
    4693 > select add #11/A:390@OP2
    4694 
    4695 3 atoms, 3 residues, 3 models selected 
    4696 
    4697 > select add #12/C:7@MG
    4698 
    4699 4 atoms, 4 residues, 4 models selected 
    4700 
    4701 > select add #13/C:7@MG
    4702 
    4703 5 atoms, 5 residues, 5 models selected 
    4704 
    4705 > select add #11/A:389@O5'
    4706 
    4707 6 atoms, 6 residues, 5 models selected 
    4708 
    4709 > select add #6/A:389@OP2
    4710 
    4711 7 atoms, 7 residues, 6 models selected 
    4712 
    4713 > select add #11/A:50@OP2
    4714 
    4715 8 atoms, 8 residues, 6 models selected 
    4716 
    4717 > select add #4/A:50@OP1
    4718 
    4719 9 atoms, 9 residues, 6 models selected 
    4720 
    4721 > select add #2/A:51
    4722 
    4723 32 atoms, 25 bonds, 10 residues, 7 models selected 
    4724 
    4725 > select add #17/A:49
    4726 
    4727 54 atoms, 49 bonds, 11 residues, 8 models selected 
    4728 
    4729 > select add #8/A:50@O2'
    4730 
    4731 55 atoms, 49 bonds, 12 residues, 9 models selected 
    4732 
    4733 > select add #11/A:50@O3'
    4734 
    4735 56 atoms, 49 bonds, 12 residues, 9 models selected 
    4736 
    4737 > select add #13/C:24@MG
    4738 
    4739 57 atoms, 49 bonds, 13 residues, 9 models selected 
    4740 
    4741 > select add #10/C:84@MG
    4742 
    4743 58 atoms, 49 bonds, 14 residues, 10 models selected 
    4744 
    4745 > select add #17/C:87@MG
    4746 
    4747 59 atoms, 49 bonds, 15 residues, 10 models selected 
    4748 
    4749 > select add #9/C:4@MG
    4750 
    4751 60 atoms, 49 bonds, 16 residues, 11 models selected 
    4752 
    4753 > view sel
    4754 
    4755 > show #19 models
    4756 
    4757 > hide #19 models
    4758 
    4759 > show #19 models
    4760 
    4761 > hide #19 models
    4762 
    4763 > show #19 models
    4764 
    4765 > hide #19 models
    4766 
    4767 > show #19 models
    4768 
    4769 > hide #19 models
    4770 
    4771 > show #19 models
    4772 
    4773 > hide #19 models
    4774 
    4775 > show #19 models
    4776 
    4777 > hide #19 models
    4778 
    4779 > show #19 models
    4780 
    4781 > hide #19 models
    4782 
    4783 > select #13/C:7@MG
    4784 
    4785 1 atom, 1 residue, 1 model selected 
    4786 
    4787 > select add #17/C:82@MG
    4788 
    4789 2 atoms, 2 residues, 2 models selected 
    4790 
    4791 > distance #13/C:7@MG #17/C:82@MG
    4792 
    4793 Distance between V17_holo-coot-3.pdb #13/C MG 7 MG and V23_holo-coot-2.pdb
    4794 #17/C MG 82 MG: 13.090Å 
    4795 
    4796 > distance #13/C:7@MG #17/C:82@MG
    4797 
    4798 Distance already exists; modify distance properties with 'distance style' 
    4799 
    4800 > ~distance #19/C:3@C5' #18/C:62@MG
    4801 
    4802 > ~distance #13/C:7@MG #17/C:82@MG
    4803 
    4804 > select clear
    4805 
    4806 > select #4/C:24@MG
    4807 
    4808 1 atom, 1 residue, 1 model selected 
    4809 
    4810 > select add #7/C:24@MG
    4811 
    4812 2 atoms, 2 residues, 2 models selected 
    4813 
    4814 > select add #18/C:24@MG
    4815 
    4816 3 atoms, 3 residues, 3 models selected 
    4817 
    4818 > select add #9/C:24@MG
    4819 
    4820 4 atoms, 4 residues, 4 models selected 
    4821 
    4822 > select add #3/C:24@MG
    4823 
    4824 5 atoms, 5 residues, 5 models selected 
    4825 
    4826 > select add #13/C:24@MG
    4827 
    4828 6 atoms, 6 residues, 6 models selected 
    4829 
    4830 > select add #6/C:24@MG
    4831 
    4832 7 atoms, 7 residues, 7 models selected 
    4833 
    4834 > select add #10/C:84@MG
    4835 
    4836 8 atoms, 8 residues, 8 models selected 
    4837 
    4838 > select add #17/C:87@MG
    4839 
    4840 9 atoms, 9 residues, 9 models selected 
    4841 
    4842 > select add #4/C:4@MG
    4843 
    4844 10 atoms, 10 residues, 9 models selected 
    4845 
    4846 > select add #8/C:4@MG
    4847 
    4848 11 atoms, 11 residues, 10 models selected 
    4849 
    4850 > select add #1/C:4@MG
    4851 
    4852 12 atoms, 12 residues, 11 models selected 
    4853 
    4854 > select add #9/C:4@MG
    4855 
    4856 13 atoms, 13 residues, 11 models selected 
    4857 
    4858 > select add #6/A:50@OP2
    4859 
    4860 14 atoms, 14 residues, 11 models selected 
    4861 
    4862 > select add #11/A:50@P
    4863 
    4864 15 atoms, 15 residues, 12 models selected 
    4865 
    4866 > select add #5/A:50@OP1
    4867 
    4868 16 atoms, 16 residues, 13 models selected 
    4869 
    4870 > select add #12/C:7@MG
    4871 
    4872 17 atoms, 17 residues, 14 models selected 
    4873 
    4874 > select add #13/C:7@MG
    4875 
    4876 18 atoms, 18 residues, 14 models selected 
    4877 
    4878 > select add #11/A:390@OP1
    4879 
    4880 19 atoms, 19 residues, 14 models selected 
    4881 
    4882 > select add #15/A:390@OP1
    4883 
    4884 20 atoms, 20 residues, 15 models selected 
    4885 
    4886 > select add #5/A:389@O2'
    4887 
    4888 21 atoms, 21 residues, 15 models selected 
    4889 
    4890 > select add #7/A:390@O2'
    4891 
    4892 22 atoms, 22 residues, 15 models selected 
    4893 
    4894 > select add #7/A:390@C5'
    4895 
    4896 23 atoms, 22 residues, 15 models selected 
    4897 
    4898 > select add #6/A:390@O5'
    4899 
    4900 24 atoms, 23 residues, 15 models selected 
    4901 
    4902 > select add #17/A:389@O5'
    4903 
    4904 25 atoms, 24 residues, 15 models selected 
    4905 
    4906 > select add #11/A:389@C4'
    4907 
    4908 26 atoms, 25 residues, 15 models selected 
    4909 
    4910 > select add #11/A:389@OP2
    4911 
    4912 27 atoms, 25 residues, 15 models selected 
    4913 
    4914 > select add #17/A:388
    4915 
    4916 50 atoms, 25 bonds, 26 residues, 15 models selected 
    4917 
    4918 > select add #4/A:51
    4919 
    4920 73 atoms, 50 bonds, 27 residues, 15 models selected 
    4921 
    4922 > select add #2/A:50@C5'
    4923 
    4924 74 atoms, 50 bonds, 28 residues, 16 models selected 
    4925 
    4926 > select add #4/A:50@O5'
    4927 
    4928 75 atoms, 50 bonds, 29 residues, 16 models selected 
    4929 
    4930 > select add #14/A:52
    4931 
    4932 95 atoms, 71 bonds, 30 residues, 17 models selected 
    4933 
    4934 > select add #17/A:49
    4935 
    4936 117 atoms, 95 bonds, 31 residues, 17 models selected 
    4937 
    4938 > view sel
    4939 
    4940 > show #19 models
    4941 
    4942 > hide #19 models
    4943 
    4944 > show #19 models
    4945 
    4946 > hide #19 models
    4947 
    4948 > show #19 models
    4949 
    4950 > hide #19 models
    4951 
    4952 > show #19 models
    4953 
    4954 > hide #19 models
    4955 
    4956 > select #3/C:68@MG
    4957 
    4958 1 atom, 1 residue, 1 model selected 
    4959 
    4960 > select add #13/C:7@MG
    4961 
    4962 2 atoms, 2 residues, 2 models selected 
    4963 
    4964 > show #19 models
    4965 
    4966 > select #3/C:68@MG
    4967 
    4968 1 atom, 1 residue, 1 model selected 
    4969 
    4970 > select add #19/C:-1
    4971 
    4972 21 atoms, 21 bonds, 2 residues, 2 models selected 
    4973 Exactly two atoms must be selected! 
    4974 
    4975 > select #3/C:68@MG
    4976 
    4977 1 atom, 1 residue, 1 model selected 
    4978 
    4979 > hide sel target a
    4980 
    4981 > hide #!18 models
    4982 
    4983 > show #!18 models
    4984 
    4985 > hide #19 models
    4986 
    4987 > select #10/C:84@MG
    4988 
    4989 1 atom, 1 residue, 1 model selected 
    4990 
    4991 > select #17/C:87@MG
    4992 
    4993 1 atom, 1 residue, 1 model selected 
    4994 
    4995 > show #19 models
    4996 
    4997 > hide #19 models
    4998 
    4999 > select clear
    5000 
    5001 > select #10/C:84@MG
    5002 
    5003 1 atom, 1 residue, 1 model selected 
    5004 
    5005 > select add #17/C:87@MG
    5006 
    5007 2 atoms, 2 residues, 2 models selected 
    5008 
    5009 > select add #13/C:7@MG
    5010 
    5011 3 atoms, 3 residues, 3 models selected 
    5012 
    5013 > view sel
    5014 
    5015 > select add #13/C:24@MG
    5016 
    5017 4 atoms, 4 residues, 3 models selected 
    5018 
    5019 > select add #18/C:62@MG
    5020 
    5021 5 atoms, 5 residues, 4 models selected 
    5022 
    5023 > view sel
    5024 
    5025 > show #19 models
    5026 
    5027 > hide #19 models
    5028 
    5029 > show #19 models
    5030 
    5031 > hide #19 models
    5032 
    5033 > select #6/A:50@OP2
    5034 
    5035 1 atom, 1 residue, 1 model selected 
    5036 
    5037 > select add #13/C:7@MG
    5038 
    5039 2 atoms, 2 residues, 2 models selected 
    5040 
    5041 > select add #11/A:390@OP1
    5042 
    5043 3 atoms, 3 residues, 3 models selected 
    5044 
    5045 > select add #10/C:84@MG
    5046 
    5047 4 atoms, 4 residues, 4 models selected 
    5048 
    5049 > select add #18/C:24@MG
    5050 
    5051 5 atoms, 5 residues, 5 models selected 
    5052 
    5053 > select add #9/C:4@MG
    5054 
    5055 6 atoms, 6 residues, 6 models selected 
    5056 
    5057 > select add #4/C:4@MG
    5058 
    5059 7 atoms, 7 residues, 7 models selected 
    5060 
    5061 > select add #1/C:4@MG
    5062 
    5063 8 atoms, 8 residues, 8 models selected 
    5064 
    5065 > select add #17/C:87@MG
    5066 
    5067 9 atoms, 9 residues, 9 models selected 
    5068 
    5069 > select add #13/C:24@MG
    5070 
    5071 10 atoms, 10 residues, 9 models selected 
    5072 
    5073 > select add #6/C:24@MG
    5074 
    5075 11 atoms, 11 residues, 9 models selected 
    5076 
    5077 > select add #12/C:7@MG
    5078 
    5079 12 atoms, 12 residues, 10 models selected 
    5080 
    5081 > select add #3/C:7@MG
    5082 
    5083 13 atoms, 13 residues, 11 models selected 
    5084 
    5085 > select add #5/A:50@OP1
    5086 
    5087 14 atoms, 14 residues, 12 models selected 
    5088 
    5089 > select add #17/A:389@OP2
    5090 
    5091 15 atoms, 15 residues, 12 models selected 
    5092 
    5093 > select add #6/A:389@OP2
    5094 
    5095 16 atoms, 16 residues, 12 models selected 
    5096 
    5097 > select add #15/A:390@OP1
    5098 
    5099 17 atoms, 17 residues, 13 models selected 
    5100 
    5101 > select add #9/A:390@OP2
    5102 
    5103 18 atoms, 18 residues, 13 models selected 
    5104 
    5105 > view sel
    5106 
    5107 > select #17/C:87@MG
    5108 
    5109 1 atom, 1 residue, 1 model selected 
    5110 
    5111 > view sel
    5112 
    5113 > select #1-18/A:49,50,51,52,388,389,390,391
    5114 
    5115 3132 atoms, 3492 bonds, 144 residues, 18 models selected 
    5116 
    5117 > view sel
    5118 
    5119 > select #10/C:84@MG
    5120 
    5121 1 atom, 1 residue, 1 model selected 
    5122 
    5123 > select add #3/C:24@MG
    5124 
    5125 2 atoms, 2 residues, 2 models selected 
    5126 
    5127 > select add #13/C:24@MG
    5128 
    5129 3 atoms, 3 residues, 3 models selected 
    5130 
    5131 > select add #18/C:24@MG
    5132 
    5133 4 atoms, 4 residues, 4 models selected 
    5134 
    5135 > select add #9/A:390@OP2
    5136 
    5137 5 atoms, 5 residues, 5 models selected 
    5138 
    5139 > select add #13/C:7@MG
    5140 
    5141 6 atoms, 6 residues, 5 models selected 
    5142 
    5143 > select add #17/C:87@MG
    5144 
    5145 7 atoms, 7 residues, 6 models selected 
    5146 
    5147 > select add #1/C:4@MG
    5148 
    5149 8 atoms, 8 residues, 7 models selected 
    5150 
    5151 > select #1-18/A:49,50,51,52,388,389,390,391
    5152 
    5153 3132 atoms, 3492 bonds, 144 residues, 18 models selected 
    5154 
    5155 > select add #10/C:84@MG
    5156 
    5157 3133 atoms, 3492 bonds, 145 residues, 18 models selected 
    5158 
    5159 > select add #17/C:87@MG
    5160 
    5161 3134 atoms, 3492 bonds, 146 residues, 18 models selected 
    5162 
    5163 > select add #3/C:24@MG
    5164 
    5165 3135 atoms, 3492 bonds, 147 residues, 18 models selected 
    5166 
    5167 > select add #6/C:24@MG
    5168 
    5169 3136 atoms, 3492 bonds, 148 residues, 18 models selected 
    5170 
    5171 > select add #9/C:24@MG
    5172 
    5173 3137 atoms, 3492 bonds, 149 residues, 18 models selected 
    5174 
    5175 > select add #18/C:24@MG
    5176 
    5177 3138 atoms, 3492 bonds, 150 residues, 18 models selected 
    5178 
    5179 > select add #1/C:4@MG
    5180 
    5181 3139 atoms, 3492 bonds, 151 residues, 18 models selected 
    5182 
    5183 > select add #4/C:4@MG
    5184 
    5185 3140 atoms, 3492 bonds, 152 residues, 18 models selected 
    5186 
    5187 > select add #9/C:4@MG
    5188 
    5189 3141 atoms, 3492 bonds, 153 residues, 18 models selected 
    5190 
    5191 > select add #18/C:4@MG
    5192 
    5193 3142 atoms, 3492 bonds, 154 residues, 18 models selected 
    5194 
    5195 > select add #12/C:7@MG
    5196 
    5197 3143 atoms, 3492 bonds, 155 residues, 18 models selected 
    5198 
    5199 > select add #13/C:7@MG
    5200 
    5201 3144 atoms, 3492 bonds, 156 residues, 18 models selected 
    5202 
    5203 > select add #3/C:7@MG
    5204 
    5205 3145 atoms, 3492 bonds, 157 residues, 18 models selected 
    5206 
    5207 > view sel
    5208 
    5209 > show #19 models
    5210 
    5211 > hide #19 models
    5212 
    5213 > select clear
    5214 
    5215 > select #10/C:84@MG
    5216 
    5217 1 atom, 1 residue, 1 model selected 
    5218 
    5219 > select clear
    5220 
    5221 > select #10/C:84@MG
    5222 
    5223 1 atom, 1 residue, 1 model selected 
    5224 
    5225 > select add #17/C:87@MG
    5226 
    5227 2 atoms, 2 residues, 2 models selected 
    5228 
    5229 > color sel magenta
    5230 
    5231 > select clear
    5232 
    5233 No map chosen to save 
    5234 
    5235 > save
    5236 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs
    5237 
    5238 > show #19 models
    5239 
    5240 > select #19/C:4
    5241 
    5242 23 atoms, 25 bonds, 1 residue, 1 model selected 
    5243 
    5244 > hide sel target a
    5245 
    5246 > cartoon hide sel
    5247 
    5248 > select #19/C:2
    5249 
    5250 20 atoms, 21 bonds, 1 residue, 1 model selected 
    5251 
    5252 > select add #19/C:1
    5253 
    5254 43 atoms, 46 bonds, 2 residues, 1 model selected 
    5255 
    5256 > select add #19/C:0
    5257 
    5258 63 atoms, 67 bonds, 3 residues, 1 model selected 
    5259 
    5260 > select #19/C:2
    5261 
    5262 20 atoms, 21 bonds, 1 residue, 1 model selected 
    5263 
    5264 > select add #19/C:1
    5265 
    5266 43 atoms, 46 bonds, 2 residues, 1 model selected 
    5267 
    5268 > select add #19/C:0
    5269 
    5270 63 atoms, 67 bonds, 3 residues, 1 model selected 
    5271 
    5272 > show sel target ab
    5273 
    5274 > cartoon hide sel
    5275 
    5276 > nucleotides sel atoms
    5277 
    5278 > style nucleic & sel stick
    5279 
    5280 Changed 63 atom styles 
    5281 
    5282 > select #1/A:49,50,51,52,388,389,390,391
    5283 
    5284 174 atoms, 194 bonds, 8 residues, 1 model selected 
    5285 
    5286 > matchmaker #19 to #1 & sel matrix Nucleic
    5287 
    5288 Computing secondary structure 
    5289 Parameters 
    5290 --- 
    5291 Chain pairing | bb 
    5292 Alignment algorithm | Needleman-Wunsch 
    5293 Similarity matrix | Nucleic 
    5294 SS fraction | 0.3 
    5295 Gap open (HH/SS/other) | 18/18/6 
    5296 Gap extend | 1 
    5297 SS matrix |  |  | H | S | O 
    5298 ---|---|---|--- 
    5299 H | 6 | -9 | -6 
    5300 S |  | 6 | -6 
    5301 O |  |  | 4 
    5302 Iteration cutoff | 2 
    5303  
    5304 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
    5305 coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
    5306 32 
    5307 RMSD between 8 pruned atom pairs is 0.305 angstroms; (across all 8 pairs:
    5308 0.305) 
    5309  
    5310 
    5311 > select #19/A
    5312 
    5313 8962 atoms, 10038 bonds, 417 residues, 1 model selected 
    5314 
    5315 > hide sel target a
    5316 
    5317 > cartoon hide sel
    5318 
    5319 > select #19/C:2
    5320 
    5321 20 atoms, 21 bonds, 1 residue, 1 model selected 
    5322 
    5323 > hide sel target a
    5324 
    5325 > select #19/C
    5326 
    5327 1889 atoms, 2107 bonds, 89 residues, 1 model selected 
    5328 
    5329 > nucleotides sel tube/slab shape ellipsoid
    5330 
    5331 > nucleotides sel atoms
    5332 
    5333 > style nucleic & sel stick
    5334 
    5335 Changed 1889 atom styles 
    5336 
    5337 > hide (sel-residues & (protein|nucleic)) target a
    5338 
    5339 > cartoon hide sel-residues
    5340 
    5341 > show (sel-residues & backbone) target ab
    5342 
    5343 > select #19/C:2-40
    5344 
    5345 835 atoms, 934 bonds, 39 residues, 1 model selected 
    5346 
    5347 > hide sel target a
    5348 
    5349 > select #19/C
    5350 
    5351 1889 atoms, 2107 bonds, 89 residues, 1 model selected 
    5352 
    5353 > cartoon sel
    5354 
    5355 > cartoon hide sel
    5356 
    5357 > color sel gray
    5358 
    5359 > ui tool show "Color Actions"
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    5925 > color sel #5e5e5ee7
    5926 
    5927 > color sel #5e5e5ee8
    5928 
    5929 > color sel #5e5e5ee9
    5930 
    5931 > color sel #5e5e5eeb
    5932 
    5933 > color sel #5e5e5eed
    5934 
    5935 > color sel #5e5e5ef0
    5936 
    5937 > color sel #5e5e5ef4
    5938 
    5939 > color sel #5e5e5ef8
    5940 
    5941 > color sel #5e5e5efb
    5942 
    5943 > color sel #5e5e5efd
    5944 
    5945 > color sel #5e5e5eff
    5946 
    5947 > color sel #4c4c4cff
    5948 
    5949 > color sel #4d4d4dff
    5950 
    5951 > color sel #4e4e4eff
    5952 
    5953 > color sel #4f4f4fff
    5954 
    5955 > color sel #505050ff
    5956 
    5957 > color sel #515151ff
    5958 
    5959 > color sel #525252ff
    5960 
    5961 > color sel #535353ff
    5962 
    5963 > color sel #545454ff
    5964 
    5965 > color sel #555555ff
    5966 
    5967 > color sel #565656ff
    5968 
    5969 > color sel #575757ff
    5970 
    5971 > color sel #595959ff
    5972 
    5973 > color sel #5a5a5aff
    5974 
    5975 > color sel #5b5b5bff
    5976 
    5977 > color sel #5c5c5cff
    5978 
    5979 > color sel #5d5d5dff
    5980 
    5981 > color sel #5e5e5eff
    5982 
    5983 > color sel #5f5f5fff
    5984 
    5985 > color sel #616161ff
    5986 
    5987 > color sel #636363ff
    5988 
    5989 > color sel #656565ff
    5990 
    5991 > color sel #696969ff
    5992 
    5993 > color sel #6b6b6bff
    5994 
    5995 > color sel #717171ff
    5996 
    5997 > color sel #767676ff
    5998 
    5999 > color sel #7a7a7aff
    6000 
    6001 > color sel #7d7d7dff
    6002 
    6003 > color sel #808080ff
    6004 
    6005 > color sel #848484ff
    6006 
    6007 > color sel #868686ff
    6008 
    6009 > color sel #878787ff
    6010 
    6011 > color sel #898989ff
    6012 
    6013 > color sel #8b8b8bff
    6014 
    6015 > color sel #8c8c8cff
    6016 
    6017 > color sel #8f8f8fff
    6018 
    6019 > color sel #909090ff
    6020 
    6021 > color sel #929292ff
    6022 
    6023 > color sel #939393ff
    6024 
    6025 > color sel #949494ff
    6026 
    6027 > color sel #959595ff
    6028 
    6029 > color sel #969696ff
    6030 
    6031 > color sel #979797ff
    6032 
    6033 > color sel #989898ff
    6034 
    6035 > color sel #999999ff
    6036 
    6037 > color sel #9a9a9aff
    6038 
    6039 > color sel #9b9b9bff
    6040 
    6041 > color sel #9c9c9cff
    6042 
    6043 > color sel #9d9d9dff
    6044 
    6045 > color sel #9e9e9eff
    6046 
    6047 > color sel #9f9f9fff
    6048 
    6049 > color sel #a0a0a0ff
    6050 
    6051 > color sel #a1a1a1ff
    6052 
    6053 > color sel #a3a3a3ff
    6054 
    6055 > color sel #a4a4a4ff
    6056 
    6057 > color sel #a6a6a6ff
    6058 
    6059 > color sel #a7a7a7ff
    6060 
    6061 > color sel #a8a8a8ff
    6062 
    6063 > color sel #aaaaaaff
    6064 
    6065 > color sel #abababff
    6066 
    6067 > color sel #acacacff
    6068 
    6069 > color sel #aeaeaeff
    6070 
    6071 > color sel #b0b0b0ff
    6072 
    6073 > color sel #b1b1b1ff
    6074 
    6075 > color sel #b2b2b2ff
    6076 
    6077 > color sel #b3b3b3ff
    6078 
    6079 > color sel #b4b4b4ff
    6080 
    6081 > color sel #b5b5b5ff
    6082 
    6083 > color sel #b6b6b6ff
    6084 
    6085 > color sel #b7b7b7ff
    6086 
    6087 > color sel #b8b8b8ff
    6088 
    6089 > color sel #b7b7b7ff
    6090 
    6091 > color sel #b6b6b6ff
    6092 
    6093 > color sel #b5b5b5ff
    6094 
    6095 > color sel #b3b3b3ff
    6096 
    6097 > color sel #afafafff
    6098 
    6099 > color sel #a4a4a4ff
    6100 
    6101 > color sel #989898ff
    6102 
    6103 > color sel #8f8f8fff
    6104 
    6105 > color sel #878787ff
    6106 
    6107 > color sel #828282ff
    6108 
    6109 > color sel #7c7c7cff
    6110 
    6111 > color sel #767676ff
    6112 
    6113 > color sel #727272ff
    6114 
    6115 > color sel #6d6d6dff
    6116 
    6117 > color sel #686868ff
    6118 
    6119 > color sel #646464ff
    6120 
    6121 > color sel #606060ff
    6122 
    6123 > color sel #5b5b5bff
    6124 
    6125 > color sel #585858ff
    6126 
    6127 > color sel #535353ff
    6128 
    6129 > color sel #4f4f4fff
    6130 
    6131 > color sel #4c4c4cff
    6132 
    6133 > color sel #4a4a4aff
    6134 
    6135 > color sel #474747ff
    6136 
    6137 > color sel #454545ff
    6138 
    6139 > color sel #444444ff
    6140 
    6141 > color sel #424242ff
    6142 
    6143 > color sel #404040ff
    6144 
    6145 > color sel #3f3f3fff
    6146 
    6147 > color sel #3d3d3dff
    6148 
    6149 > color sel #3b3b3bff
    6150 
    6151 > color sel #3a3a3aff
    6152 
    6153 > color sel #383838ff
    6154 
    6155 > color sel #373737ff
    6156 
    6157 > color sel #363636ff
    6158 
    6159 > color sel #353535ff
    6160 
    6161 > color sel #343434ff
    6162 
    6163 > color sel #333333ff
    6164 
    6165 > color sel #313131ff
    6166 
    6167 > color sel #303030ff
    6168 
    6169 > color sel #2f2f2fff
    6170 
    6171 > color sel #2e2e2eff
    6172 
    6173 > color sel #2d2d2dff
    6174 
    6175 > color sel #2e2e2eff
    6176 
    6177 > color sel #303030ff
    6178 
    6179 > color sel #343434ff
    6180 
    6181 > color sel #393939ff
    6182 
    6183 > color sel #3d3d3dff
    6184 
    6185 > color sel #434343ff
    6186 
    6187 > color sel #4a4a4aff
    6188 
    6189 > color sel #4d4d4dff
    6190 
    6191 > color sel #515151ff
    6192 
    6193 > color sel #525252ff
    6194 
    6195 > color sel #535353ff
    6196 
    6197 > color sel #545454ff
    6198 
    6199 > color sel #555555ff
    6200 
    6201 > color sel #565656ff
    6202 
    6203 > color sel #575757ff
    6204 
    6205 > color sel #585858ff
    6206 
    6207 > color sel #595959ff
    6208 
    6209 > color sel #5a5a5aff
    6210 
    6211 > color sel #5c5c5cff
    6212 
    6213 > color sel #5e5e5eff
    6214 
    6215 > color sel #5f5f5fff
    6216 
    6217 > color sel #606060ff
    6218 
    6219 > color sel #616161ff
    6220 
    6221 > color sel #626262ff
    6222 
    6223 > color sel #636363ff
    6224 
    6225 > color sel #646464ff
    6226 
    6227 > color sel #656565ff
    6228 
    6229 > color sel #666666ff
    6230 
    6231 > color sel #676767ff
    6232 
    6233 > color sel #686868ff
    6234 
    6235 > color sel #696969ff
    6236 
    6237 > color sel #6a6a6aff
    6238 
    6239 > color sel #6b6b6bff
    6240 
    6241 > color sel #6a6a6aff
    6242 
    6243 > color sel #686868ff
    6244 
    6245 > color sel #676767ff
    6246 
    6247 > color sel #666666ff
    6248 
    6249 > color sel #646464ff
    6250 
    6251 > color sel #626262ff
    6252 
    6253 > color sel #616161ff
    6254 
    6255 > color sel #5f5f5fff
    6256 
    6257 > color sel #5e5e5eff
    6258 
    6259 > color sel #5d5d5dff
    6260 
    6261 > color sel #5c5c5cff
    6262 
    6263 > color sel #5b5b5bff
    6264 
    6265 > color sel #5a5a5aff
    6266 
    6267 > color sel #595959ff
    6268 
    6269 > color sel #585858ff
    6270 
    6271 > color sel #575757ff
    6272 
    6273 > color sel #565656ff
    6274 
    6275 > color sel #555555ff
    6276 
    6277 > color sel #545454ff
    6278 
    6279 > color sel #535353ff
    6280 
    6281 > color sel #525252ff
    6282 
    6283 > color sel #515151ff
    6284 
    6285 > color sel #505050ff
    6286 
    6287 > color sel #4f4f4fff
    6288 
    6289 > color sel #4e4e4eff
    6290 
    6291 > color sel #4d4d4dff
    6292 
    6293 > color sel #4c4c4cff
    6294 
    6295 > color sel #4b4b4bff
    6296 
    6297 > color sel #4a4a4aff
    6298 
    6299 > color sel #494949ff
    6300 
    6301 > color sel #484848ff
    6302 
    6303 > color sel #474747ff
    6304 
    6305 > color sel #464646ff
    6306 
    6307 > color sel #454545ff
    6308 
    6309 > color sel #464646ff
    6310 
    6311 > color sel #474747ff
    6312 
    6313 > color sel #494949ff
    6314 
    6315 > color sel #4b4b4bff
    6316 
    6317 > color sel #4c4c4cff
    6318 
    6319 > color sel #4d4d4dff
    6320 
    6321 > color sel #4e4e4eff
    6322 
    6323 > color sel #505050ff
    6324 
    6325 > color sel #515151ff
    6326 
    6327 > color sel #525252ff
    6328 
    6329 > color sel #535353ff
    6330 
    6331 > color sel #545454ff
    6332 
    6333 > color sel #555555ff
    6334 
    6335 > color sel #565656ff
    6336 
    6337 > color sel #575757ff
    6338 
    6339 > color sel #585858ff
    6340 
    6341 > color sel #595959ff
    6342 
    6343 > color sel #5a5a5aff
    6344 
    6345 > color sel #5b5b5bff
    6346 
    6347 > color sel #5c5c5cff
    6348 
    6349 > color sel #5f5f5fff
    6350 
    6351 > color sel #606060ff
    6352 
    6353 > color sel #626262ff
    6354 
    6355 > color sel #646464ff
    6356 
    6357 > color sel #656565ff
    6358 
    6359 > color sel #676767ff
    6360 
    6361 > color sel #696969ff
    6362 
    6363 > color sel #6a6a6aff
    6364 
    6365 > color sel #6c6c6cff
    6366 
    6367 > color sel #6e6e6eff
    6368 
    6369 > color sel #6f6f6fff
    6370 
    6371 > color sel #717171ff
    6372 
    6373 > color sel #737373ff
    6374 
    6375 > color sel #757575ff
    6376 
    6377 > color sel #767676ff
    6378 
    6379 > color sel #787878ff
    6380 
    6381 > color sel #797979ff
    6382 
    6383 > color sel #7a7a7aff
    6384 
    6385 > color sel #7b7b7bff
    6386 
    6387 > color sel #7c7c7cff
    6388 
    6389 > color sel #7d7d7dff
    6390 
    6391 > color sel #7f7f7fff
    6392 
    6393 > color sel #808080ff
    6394 
    6395 > color sel #848484ff
    6396 
    6397 > color sel #858585ff
    6398 
    6399 > color sel #878787ff
    6400 
    6401 > color sel #898989ff
    6402 
    6403 > color sel #8a8a8aff
    6404 
    6405 > color sel #8c8c8cff
    6406 
    6407 > color sel #8e8e8eff
    6408 
    6409 > color sel #8f8f8fff
    6410 
    6411 > color sel #919191ff
    6412 
    6413 > color sel #929292ff
    6414 
    6415 > color sel #949494ff
    6416 
    6417 > color sel #969696ff
    6418 
    6419 > color sel #979797ff
    6420 
    6421 > color sel #989898ff
    6422 
    6423 > color sel #999999ff
    6424 
    6425 > color sel #989898ff
    6426 
    6427 > color sel #949494ff
    6428 
    6429 > color sel #8a8a8aff
    6430 
    6431 > color sel #838383ff
    6432 
    6433 > color sel #7d7d7dff
    6434 
    6435 > color sel #7a7a7aff
    6436 
    6437 > color sel #777777ff
    6438 
    6439 > color sel #747474ff
    6440 
    6441 > color sel #717171ff
    6442 
    6443 > color sel #6f6f6fff
    6444 
    6445 > color sel #6d6d6dff
    6446 
    6447 > color sel #6b6b6bff
    6448 
    6449 > color sel #696969ff
    6450 
    6451 > color sel #676767ff
    6452 
    6453 > color sel #666666ff
    6454 
    6455 > color sel #646464ff
    6456 
    6457 > color sel #636363ff
    6458 
    6459 > color sel #616161ff
    6460 
    6461 > color sel #606060ff
    6462 
    6463 > color sel #5f5f5fff
    6464 
    6465 > color sel #5e5e5eff
    6466 
    6467 > color sel #5d5d5dff
    6468 
    6469 > color sel #5c5c5cff
    6470 
    6471 > color sel #5b5b5bff
    6472 
    6473 > color sel #5a5a5aff
    6474 
    6475 > color sel #595959ff
    6476 
    6477 > color sel #585858ff
    6478 
    6479 > color sel #575757ff
    6480 
    6481 > color sel #565656ff
    6482 
    6483 > color sel #555555ff
    6484 
    6485 > color sel #565656ff
    6486 
    6487 > color sel #575757ff
    6488 
    6489 > color sel #585858ff
    6490 
    6491 > color sel #5a5a5aff
    6492 
    6493 > color sel #5b5b5bff
    6494 
    6495 > color sel #5c5c5cff
    6496 
    6497 > color sel #5d5d5dff
    6498 
    6499 > color sel #5e5e5eff
    6500 
    6501 > color sel #5f5f5fff
    6502 
    6503 > select #10/C:84@MG
    6504 
    6505 1 atom, 1 residue, 1 model selected 
    6506 
    6507 > select add #17/C:87@MG
    6508 
    6509 2 atoms, 2 residues, 2 models selected 
    6510 
    6511 > distance #10/C:84@MG #17/C:87@MG
    6512 
    6513 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V23_holo-coot-2.pdb
    6514 #17/C MG 87 MG: 3.390Å 
    6515 
    6516 > select #10/C:84@MG
    6517 
    6518 1 atom, 1 residue, 1 model selected 
    6519 
    6520 > select add #19/C:1@O3'
    6521 
    6522 2 atoms, 2 residues, 2 models selected 
    6523 
    6524 > distance #10/C:84@MG #19/C:1@O3'
    6525 
    6526 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
    6527 Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 7.687Å 
    6528 
    6529 > select #10/C:84@MG
    6530 
    6531 1 atom, 1 residue, 1 model selected 
    6532 
    6533 > select add #19/D:5@CA
    6534 
    6535 2 atoms, 2 residues, 2 models selected 
    6536 
    6537 > select #19/D:5@CA
    6538 
    6539 1 atom, 1 residue, 1 model selected 
    6540 
    6541 > select add #10/C:84@MG
    6542 
    6543 2 atoms, 2 residues, 2 models selected 
    6544 
    6545 > distance #19/D:5@CA #10/C:84@MG
    6546 
    6547 Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
    6548 #19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.681Å 
    6549 
    6550 > select #10/C:84@MG
    6551 
    6552 1 atom, 1 residue, 1 model selected 
    6553 
    6554 > select add #19/D:6@CA
    6555 
    6556 2 atoms, 2 residues, 2 models selected 
    6557 
    6558 > distance #10/C:84@MG #19/D:6@CA
    6559 
    6560 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
    6561 Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 2.783Å 
    6562 
    6563 > select #10/C:84@MG
    6564 
    6565 1 atom, 1 residue, 1 model selected 
    6566 
    6567 > select add #3/C:24@MG
    6568 
    6569 2 atoms, 2 residues, 2 models selected 
    6570 
    6571 > distance #10/C:84@MG #3/C:24@MG
    6572 
    6573 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V4_holo-coot-3.pdb
    6574 #3/C MG 24 MG: 3.250Å 
    6575 
    6576 > select #17/C:87@MG
    6577 
    6578 1 atom, 1 residue, 1 model selected 
    6579 
    6580 > select add #19/D:6@CA
    6581 
    6582 2 atoms, 2 residues, 2 models selected 
    6583 
    6584 > distance #17/C:87@MG #19/D:6@CA
    6585 
    6586 Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
    6587 Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 5.916Å 
    6588 
    6589 > select #17/C:87@MG
    6590 
    6591 1 atom, 1 residue, 1 model selected 
    6592 
    6593 > select add #19/C:1@O3'
    6594 
    6595 2 atoms, 2 residues, 2 models selected 
    6596 
    6597 > distance #17/C:87@MG #19/C:1@O3'
    6598 
    6599 Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
    6600 Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 4.880Å 
    6601 
    6602 > select #17/C:87@MG
    6603 
    6604 1 atom, 1 residue, 1 model selected 
    6605 
    6606 > select add #19/D:5@CA
    6607 
    6608 2 atoms, 2 residues, 2 models selected 
    6609 
    6610 > distance #17/C:87@MG #19/D:5@CA
    6611 
    6612 Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
    6613 Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 5 CA: 6.174Å 
    6614 
    6615 > select #17/C:87@MG
    6616 
    6617 1 atom, 1 residue, 1 model selected 
    6618 
    6619 > select add #19/C:1@OP1
    6620 
    6621 2 atoms, 2 residues, 2 models selected 
    6622 
    6623 > distance #17/C:87@MG #19/C:1@OP1
    6624 
    6625 Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
    6626 Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 OP1: 6.874Å 
    6627 
    6628 > select #19/D:5@CA
    6629 
    6630 1 atom, 1 residue, 1 model selected 
    6631 
    6632 > select add #19/C:1@OP1
    6633 
    6634 2 atoms, 2 residues, 1 model selected 
    6635 
    6636 > distance #19/D:5@CA #19/C:1@OP1
    6637 
    6638 Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
    6639 #19/D CA 5 CA and /C G 1 OP1: 2.234Å 
    6640 
    6641 > select #19/D:7@CA
    6642 
    6643 1 atom, 1 residue, 1 model selected 
    6644 
    6645 > select add #19/C:1@OP2
    6646 
    6647 2 atoms, 2 residues, 1 model selected 
    6648 
    6649 > distance #19/D:7@CA #19/C:1@OP2
    6650 
    6651 Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
    6652 #19/D CA 7 CA and /C G 1 OP2: 2.625Å 
    6653 
    6654 > ~distance #10/C:84@MG #17/C:87@MG
    6655 
    6656 > ~distance #19/D:5@CA #10/C:84@MG
    6657 
    6658 > ~distance #10/C:84@MG #19/C:1@O3'
    6659 
    6660 > ~distance #19/D:7@CA #19/C:1@OP2
    6661 
    6662 > ~distance #17/C:87@MG #19/C:1@O3'
    6663 
    6664 > ~distance #19/D:5@CA #19/C:1@OP1
    6665 
    6666 > ~distance #17/C:87@MG #19/C:1@OP1
    6667 
    6668 > ~distance #10/C:84@MG #19/D:6@CA
    6669 
    6670 > ~distance #17/C:87@MG #19/D:5@CA
    6671 
    6672 > ~distance #10/C:84@MG #3/C:24@MG
    6673 
    6674 > ~distance #17/C:87@MG #19/D:6@CA
    6675 
    6676 > color sel #5f5f5fff
    6677 
    6678 > color sel #5f5f5ffe
    6679 
    6680 > color sel #5f5f5ffd
    6681 
    6682 > color sel #5f5f5ffc
    6683 
    6684 > color sel #5f5f5ffb
    6685 
    6686 > color sel #5f5f5ffa
    6687 
    6688 > color sel #5f5f5ff9
    6689 
    6690 > color sel #5f5f5ff8
    6691 
    6692 > color sel #5f5f5ff7
    6693 
    6694 > color sel #5f5f5ff6
    6695 
    6696 > color sel #5f5f5ff5
    6697 
    6698 > color sel #5f5f5ff3
    6699 
    6700 > color sel #5f5f5ff2
    6701 
    6702 > color sel #5f5f5ff1
    6703 
    6704 > color sel #5f5f5ff0
    6705 
    6706 > color sel #5f5f5fee
    6707 
    6708 > color sel #5f5f5fec
    6709 
    6710 > color sel #5f5f5feb
    6711 
    6712 > color sel #5f5f5fea
    6713 
    6714 > color sel #5f5f5fe9
    6715 
    6716 > color sel #5f5f5fe8
    6717 
    6718 > color sel #5f5f5fe7
    6719 
    6720 > select #19/C
    6721 
    6722 1889 atoms, 2107 bonds, 89 residues, 1 model selected 
    6723 
    6724 > lighting simple
    6725 
    6726 > lighting soft
    6727 
    6728 > lighting full
    6729 
    6730 > lighting soft
    6731 
    6732 > lighting simple
    6733 
    6734 > lighting soft
    6735 
    6736 > lighting simple
    6737 
    6738 > color sel #5f5f5fe7
    6739 
    6740 > color sel #5f5f5fe6
    6741 
    6742 > color sel #5f5f5fe3
    6743 
    6744 > color sel #5f5f5fe2
    6745 
    6746 > color sel #5f5f5fe1
    6747 
    6748 > color sel #5f5f5fe0
    6749 
    6750 > color sel #5f5f5fdf
    6751 
    6752 > color sel #5f5f5fde
    6753 
    6754 > color sel #5f5f5fdd
    6755 
    6756 > color sel #5f5f5fdc
    6757 
    6758 > color sel #5f5f5fda
    6759 
    6760 > color sel #5f5f5fd8
    6761 
    6762 > color sel #5f5f5fd6
    6763 
    6764 > color sel #5f5f5fd4
    6765 
    6766 > color sel #5f5f5fd2
    6767 
    6768 > color sel #5f5f5fd1
    6769 
    6770 > color sel #5f5f5fd0
    6771 
    6772 > color sel #5f5f5fcf
    6773 
    6774 > color sel #5f5f5fcd
    6775 
    6776 > color sel #5f5f5fcc
    6777 
    6778 > color sel #5f5f5fca
    6779 
    6780 > color sel #5f5f5fc9
    6781 
    6782 > color sel #5f5f5fc7
    6783 
    6784 > color sel #5f5f5fc5
    6785 
    6786 > color sel #5f5f5fc1
    6787 
    6788 > color sel #5f5f5fbf
    6789 
    6790 > color sel #5f5f5fbd
    6791 
    6792 > color sel #5f5f5fbb
    6793 
    6794 > color sel #5f5f5fba
    6795 
    6796 > color sel #5f5f5fb8
    6797 
    6798 > color sel #5f5f5fb5
    6799 
    6800 > color sel #5f5f5fb4
    6801 
    6802 > color sel #5f5f5fb1
    6803 
    6804 > color sel #5f5f5fb0
    6805 
    6806 > color sel #5f5f5fae
    6807 
    6808 > color sel #5f5f5fad
    6809 
    6810 > color sel #5f5f5fac
    6811 
    6812 > color sel #5f5f5fab
    6813 
    6814 > color sel #5f5f5fa9
    6815 
    6816 > color sel #5f5f5fa7
    6817 
    6818 > color sel #5f5f5fa3
    6819 
    6820 > color sel #5f5f5f9f
    6821 
    6822 > color sel #5f5f5f9b
    6823 
    6824 > color sel #5f5f5f99
    6825 
    6826 > color sel #5f5f5f96
    6827 
    6828 > color sel #5f5f5f95
    6829 
    6830 > color sel #5f5f5f94
    6831 
    6832 > color sel #5f5f5f93
    6833 
    6834 > color sel #5f5f5f92
    6835 
    6836 > color sel #5f5f5f90
    6837 
    6838 > color sel #5f5f5f8f
    6839 
    6840 > color sel #5f5f5f8e
    6841 
    6842 > color sel #5f5f5f8d
    6843 
    6844 > color sel #5f5f5f8c
    6845 
    6846 > color sel #5f5f5f8b
    6847 
    6848 > color sel #5f5f5f89
    6849 
    6850 > color sel #5f5f5f88
    6851 
    6852 > color sel #5f5f5f87
    6853 
    6854 > color sel #5f5f5f85
    6855 
    6856 > color sel #5f5f5f84
    6857 
    6858 > color sel #5f5f5f83
    6859 
    6860 > color sel #5f5f5f84
    6861 
    6862 > color sel #5f5f5f87
    6863 
    6864 > color sel #5f5f5f8d
    6865 
    6866 > color sel #5f5f5f95
    6867 
    6868 > color sel #5f5f5f99
    6869 
    6870 > color sel #5f5f5f9d
    6871 
    6872 > color sel #5f5f5f9f
    6873 
    6874 > color sel #5f5f5fa1
    6875 
    6876 > color sel #5f5f5fa3
    6877 
    6878 > color sel #5f5f5fa4
    6879 
    6880 > color sel #5f5f5fa5
    6881 
    6882 > color sel #5f5f5fa6
    6883 
    6884 > color sel #5f5f5fa8
    6885 
    6886 > color sel #5f5f5fab
    6887 
    6888 > color sel #5f5f5fad
    6889 
    6890 > color sel #5f5f5fae
    6891 
    6892 > color sel #5f5f5faf
    6893 
    6894 > color sel #5f5f5fb1
    6895 
    6896 > color sel #5f5f5fb2
    6897 
    6898 > color sel #5f5f5fb5
    6899 
    6900 > color sel #5f5f5fb6
    6901 
    6902 > color sel #5f5f5fb7
    6903 
    6904 > color sel #5f5f5fb8
    6905 
    6906 > color sel #5f5f5fb9
    6907 
    6908 > color sel #5f5f5fbb
    6909 
    6910 > color sel #5f5f5fbd
    6911 
    6912 > color sel #5f5f5fc1
    6913 
    6914 > color sel #5f5f5fc7
    6915 
    6916 > color sel #5f5f5fcc
    6917 
    6918 > color sel #5f5f5fcf
    6919 
    6920 > color sel #5f5f5fd0
    6921 
    6922 > color sel #5f5f5fce
    6923 
    6924 > color sel #5f5f5fc2
    6925 
    6926 > color sel #5f5f5fb8
    6927 
    6928 > color sel #5f5f5fb2
    6929 
    6930 > color sel #5f5f5fb1
    6931 
    6932 > color sel #5f5f5fb0
    6933 
    6934 > color sel #5f5f5fad
    6935 
    6936 > color sel #5f5f5fab
    6937 
    6938 > color sel #5f5f5fa9
    6939 
    6940 > color sel #5f5f5fa5
    6941 
    6942 > color sel #5f5f5fa3
    6943 
    6944 > select #19/D:30@CA
    6945 
    6946 1 atom, 1 residue, 1 model selected 
    6947 
    6948 > select add #19/D:5@CA
    6949 
    6950 2 atoms, 2 residues, 1 model selected 
    6951 
    6952 > color sel #404040ff
    6953 
    6954 > select #19/D:7@CA
    6955 
    6956 1 atom, 1 residue, 1 model selected 
    6957 
    6958 > select #19/D:7@CA
    6959 
    6960 1 atom, 1 residue, 1 model selected 
    6961 
    6962 > color sel #404040ff
    6963 
    6964 > color sel #3f3f3fff
    6965 
    6966 > color sel #3e3e3eff
    6967 
    6968 > color sel #3d3d3dff
    6969 
    6970 > color sel #3c3c3cff
    6971 
    6972 > color sel #3d3d3dff
    6973 
    6974 > select #19/D:6@CA
    6975 
    6976 1 atom, 1 residue, 1 model selected 
    6977 
    6978 > select add #19/D:1@CA
    6979 
    6980 2 atoms, 2 residues, 1 model selected 
    6981 
    6982 > select add #19/D:3@CA
    6983 
    6984 3 atoms, 3 residues, 1 model selected 
    6985 
    6986 > color sel #4f8f00ff
    6987 
    6988 > color sel #005493ff
    6989 
    6990 > select clear
    6991 
    6992 > save
    6993 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models_ternary_comp.cxs
    6994 
    6995 > hide #19 models
    6996 
    6997 > save ions_core_holo.png supersample 3 transparentBackground true
    6998 
    6999 > lighting simple
    7000 
    7001 > lighting soft
    7002 
    7003 > lighting simple
    7004 
    7005 > graphics silhouettes true
    7006 
    7007 > graphics silhouettes false
    7008 
    7009 > graphics silhouettes true
    7010 
    7011 > graphics silhouettes false
    7012 
    7013 > graphics silhouettes true
    7014 
    7015 > graphics silhouettes false
    7016 
    7017 > graphics silhouettes true
    7018 
    7019 > graphics silhouettes false
    7020 
    7021 > graphics silhouettes true
    7022 
    7023 > graphics silhouettes false
    7024 
    7025 > ui tool show "Side View"
    7026 
    7027 > lighting soft
    7028 
    7029 > lighting simple
    7030 
    7031 > lighting soft
    7032 
    7033 > save ions_core_holo_2.png supersample 3 transparentBackground true
    7034 
    7035 > select #10/C:84@MG
    7036 
    7037 1 atom, 1 residue, 1 model selected 
    7038 
    7039 > select add #11/A:390@OP2
    7040 
    7041 2 atoms, 2 residues, 2 models selected 
    7042 
    7043 > distance #10/C:84@MG #11/A:390@OP2
    7044 
    7045 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb
    7046 #11/A A 390 OP2: 3.278Å 
    7047 
    7048 > select #6/C:24@MG
    7049 
    7050 1 atom, 1 residue, 1 model selected 
    7051 
    7052 > select add #6/A:390@OP2
    7053 
    7054 2 atoms, 2 residues, 1 model selected 
    7055 
    7056 > distance #6/C:24@MG #6/A:390@OP2
    7057 
    7058 Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and /A A 390 OP2: 4.213Å 
    7059 
    7060 > select #6/C:24@MG
    7061 
    7062 1 atom, 1 residue, 1 model selected 
    7063 
    7064 > select #10/C:84@MG
    7065 
    7066 1 atom, 1 residue, 1 model selected 
    7067 
    7068 > select clear
    7069 
    7070 > select #17/C:87@MG
    7071 
    7072 1 atom, 1 residue, 1 model selected 
    7073 
    7074 > select add #11/A:390@OP2
    7075 
    7076 2 atoms, 2 residues, 2 models selected 
    7077 
    7078 > distance #17/C:87@MG #11/A:390@OP2
    7079 
    7080 Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V14_holo-coot-1.pdb
    7081 #11/A A 390 OP2: 4.350Å 
    7082 
    7083 > ~distance #6/C:24@MG #6/A:390@OP2
    7084 
    7085 > ~distance #10/C:84@MG #11/A:390@OP2
    7086 
    7087 > ~distance #17/C:87@MG #11/A:390@OP2
    7088 
    7089 > select clear
    7090 
    7091 > lighting simple
    7092 
    7093 > toolshed show
    7094 
    7095 > select #18/C:24@MG
    7096 
    7097 1 atom, 1 residue, 1 model selected 
    7098 
    7099 > select add #11/A:390@OP2
    7100 
    7101 2 atoms, 2 residues, 2 models selected 
    7102 
    7103 > distance #18/C:24@MG #11/A:390@OP2
    7104 
    7105 Distance between V25_holo-coot-2.pdb #18/C MG 24 MG and V14_holo-coot-1.pdb
    7106 #11/A A 390 OP2: 4.140Å 
    7107 
    7108 > select #17/A:50@OP2
    7109 
    7110 1 atom, 1 residue, 1 model selected 
    7111 
    7112 > select add #9/C:4@MG
    7113 
    7114 2 atoms, 2 residues, 2 models selected 
    7115 
    7116 > distance #17/A:50@OP2 #9/C:4@MG
    7117 
    7118 Distance between V23_holo-coot-2.pdb #17/A A 50 OP2 and V11_holo-coot-1.pdb
    7119 #9/C MG 4 MG: 5.979Å 
    7120 
    7121 > select #11/A:390@OP2
    7122 
    7123 1 atom, 1 residue, 1 model selected 
    7124 
    7125 > select add #10/C:84@MG
    7126 
    7127 2 atoms, 2 residues, 2 models selected 
    7128 
    7129 > distance #11/A:390@OP2 #10/C:84@MG
    7130 
    7131 Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V12_holo-coot-3.pdb
    7132 #10/C MG 84 MG: 3.278Å 
    7133 
    7134 > select #17/C:87@MG
    7135 
    7136 1 atom, 1 residue, 1 model selected 
    7137 
    7138 > select add #10/C:84@MG
    7139 
    7140 2 atoms, 2 residues, 2 models selected 
    7141 
    7142 > distance #17/C:87@MG #10/C:84@MG
    7143 
    7144 Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V12_holo-coot-3.pdb
    7145 #10/C MG 84 MG: 3.390Å 
    7146 
    7147 > select #10/C:84@MG
    7148 
    7149 1 atom, 1 residue, 1 model selected 
    7150 
    7151 > select add #17/C:87@MG
    7152 
    7153 2 atoms, 2 residues, 2 models selected 
    7154 
    7155 > select #10/C:84@MG
    7156 
    7157 1 atom, 1 residue, 1 model selected 
    7158 
    7159 > select #10/C:84@MG
    7160 
    7161 1 atom, 1 residue, 1 model selected 
    7162 
    7163 > color sel lime
    7164 
    7165 > color sel purple
    7166 
    7167 > ~distance #11/A:390@OP2 #10/C:84@MG
    7168 
    7169 > ~distance #17/A:50@OP2 #9/C:4@MG
    7170 
    7171 > ~distance #17/C:87@MG #10/C:84@MG
    7172 
    7173 > ~distance #18/C:24@MG #11/A:390@OP2
    7174 
    7175 > select clear
    7176 
    7177 > select #7/C:24@MG
    7178 
    7179 1 atom, 1 residue, 1 model selected 
    7180 
    7181 > select add #7/A:390@C5'
    7182 
    7183 2 atoms, 2 residues, 1 model selected 
    7184 
    7185 > distance #7/C:24@MG #7/A:390@C5'
    7186 
    7187 Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and /A A 390 C5': 5.156Å 
    7188 
    7189 > select clear
    7190 
    7191 > select #7/C:24@MG
    7192 
    7193 1 atom, 1 residue, 1 model selected 
    7194 
    7195 > select add #11/A:390@OP2
    7196 
    7197 2 atoms, 2 residues, 2 models selected 
    7198 
    7199 > distance #7/C:24@MG #11/A:390@OP2
    7200 
    7201 Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and V14_holo-coot-1.pdb
    7202 #11/A A 390 OP2: 4.308Å 
    7203 
    7204 > select #3/C:24@MG
    7205 
    7206 1 atom, 1 residue, 1 model selected 
    7207 
    7208 > select add #11/A:390@OP2
    7209 
    7210 2 atoms, 2 residues, 2 models selected 
    7211 
    7212 > distance #3/C:24@MG #11/A:390@OP2
    7213 
    7214 Distance between V4_holo-coot-3.pdb #3/C MG 24 MG and V14_holo-coot-1.pdb
    7215 #11/A A 390 OP2: 4.180Å 
    7216 
    7217 > select #13/C:24@MG
    7218 
    7219 1 atom, 1 residue, 1 model selected 
    7220 
    7221 > select #11/A:390@OP2
    7222 
    7223 1 atom, 1 residue, 1 model selected 
    7224 
    7225 > select add #13/C:24@MG
    7226 
    7227 2 atoms, 2 residues, 2 models selected 
    7228 
    7229 > distance #11/A:390@OP2 #13/C:24@MG
    7230 
    7231 Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V17_holo-coot-3.pdb
    7232 #13/C MG 24 MG: 4.168Å 
    7233 
    7234 > select #4/C:24@MG
    7235 
    7236 1 atom, 1 residue, 1 model selected 
    7237 
    7238 > select add #11/A:390@OP2
    7239 
    7240 2 atoms, 2 residues, 2 models selected 
    7241 
    7242 > distance #4/C:24@MG #11/A:390@OP2
    7243 
    7244 Distance between V5_holo-coot-1.pdb #4/C MG 24 MG and V14_holo-coot-1.pdb
    7245 #11/A A 390 OP2: 4.683Å 
    7246 
    7247 > ~distance #7/C:24@MG #7/A:390@C5'
    7248 
    7249 > ~distance #4/C:24@MG #11/A:390@OP2
    7250 
    7251 > ~distance #3/C:24@MG #11/A:390@OP2
    7252 
    7253 > ~distance #7/C:24@MG #11/A:390@OP2
    7254 
    7255 > ~distance #11/A:390@OP2 #13/C:24@MG
    7256 
    7257 > select clear
    7258 
    7259 > save ions_core_holo_2.png supersample 3 transparentBackground true
    7260 
    7261 > save
    7262 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs
    7263 
    7264 > open
    7265 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V1_Mg-
    7266 > coot-1.pdb
    7267 
    7268 Chain information for V1_Mg-coot-1.pdb #20 
    7269 --- 
    7270 Chain | Description 
    7271 A | No description available 
    7272  
    7273 
    7274 > open
    7275 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V2_Mg-
    7276 > coot-1.pdb
    7277 
    7278 Chain information for V2_Mg-coot-1.pdb #21 
    7279 --- 
    7280 Chain | Description 
    7281 A | No description available 
    7282  
    7283 
    7284 > open
    7285 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V3_Mg-
    7286 > coot-2.pdb
    7287 
    7288 Chain information for V3_Mg-coot-2.pdb #22 
    7289 --- 
    7290 Chain | Description 
    7291 A | No description available 
    7292  
    7293 
    7294 > open
    7295 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V4_Mg-
    7296 > coot-2.pdb
    7297 
    7298 Chain information for V4_Mg-coot-2.pdb #23 
    7299 --- 
    7300 Chain | Description 
    7301 A | No description available 
    7302  
    7303 
    7304 > open
    7305 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V5_Mg-
    7306 > coot-1.pdb
    7307 
    7308 Chain information for V5_Mg-coot-1.pdb #24 
    7309 --- 
    7310 Chain | Description 
    7311 A | No description available 
    7312  
    7313 
    7314 > open
    7315 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V6_Mg-
    7316 > coot-1.pdb
    7317 
    7318 Chain information for V6_Mg-coot-1.pdb #25 
    7319 --- 
    7320 Chain | Description 
    7321 A | No description available 
    7322  
    7323 
    7324 > open
    7325 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V7_Mg-
    7326 > coot-2.pdb
    7327 
    7328 Chain information for V7_Mg-coot-2.pdb #26 
    7329 --- 
    7330 Chain | Description 
    7331 A | No description available 
    7332  
    7333 
    7334 > open
    7335 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V8_Mg-
    7336 > coot-2.pdb
    7337 
    7338 Chain information for V8_Mg-coot-2.pdb #27 
    7339 --- 
    7340 Chain | Description 
    7341 A | No description available 
    7342  
    7343 
    7344 > open
    7345 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V9_Mg-
    7346 > coot-3.pdb
    7347 
    7348 Chain information for V9_Mg-coot-3.pdb #28 
    7349 --- 
    7350 Chain | Description 
    7351 A | No description available 
    7352  
    7353 
    7354 > open
    7355 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V10_Mg-
    7356 > coot-3.pdb
    7357 
    7358 Chain information for V10_Mg-coot-3.pdb #29 
    7359 --- 
    7360 Chain | Description 
    7361 A | No description available 
    7362  
    7363 
    7364 > open
    7365 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V11_Mg-
    7366 > coot-2.pdb
    7367 
    7368 Chain information for V11_Mg-coot-2.pdb #30 
    7369 --- 
    7370 Chain | Description 
    7371 A | No description available 
    7372  
    7373 
    7374 > open
    7375 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V12_real_space_refined_011-coot-0.pdb
    7376 
    7377 Chain information for V12_real_space_refined_011-coot-0.pdb #31 
    7378 --- 
    7379 Chain | Description 
    7380 A | No description available 
    7381  
    7382 
    7383 > open
    7384 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg-
    7385 > coot-2.pdb
    7386 
    7387 Chain information for V13_Mg-coot-2.pdb #32 
    7388 --- 
    7389 Chain | Description 
    7390 A | No description available 
    7391  
    7392 
    7393 > open
    7394 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg-
    7395 > coot-3_6.pdb
    7396 
    7397 Chain information for V13_Mg-coot-3_6.pdb #33 
    7398 --- 
    7399 Chain | Description 
    7400 A | No description available 
    7401  
    7402 
    7403 > open
    7404 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V14_Mg-
    7405 > coot-1.pdb
    7406 
    7407 Chain information for V14_Mg-coot-1.pdb #34 
    7408 --- 
    7409 Chain | Description 
    7410 A | No description available 
    7411  
    7412 
    7413 > open
    7414 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V15_Mg-
    7415 > coot-2.pdb
    7416 
    7417 Chain information for V15_Mg-coot-2.pdb #35 
    7418 --- 
    7419 Chain | Description 
    7420 A | No description available 
    7421  
    7422 
    7423 > open
    7424 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V16_Mg-
    7425 > coot-1.pdb
    7426 
    7427 Chain information for V16_Mg-coot-1.pdb #36 
    7428 --- 
    7429 Chain | Description 
    7430 A | No description available 
    7431  
    7432 
    7433 > open
    7434 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V17_Mg-
    7435 > coot-2.pdb
    7436 
    7437 Chain information for V17_Mg-coot-2.pdb #37 
    7438 --- 
    7439 Chain | Description 
    7440 A | No description available 
    7441  
    7442 
    7443 > open
    7444 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V18_Mg-
    7445 > coot-1.pdb
    7446 
    7447 Chain information for V18_Mg-coot-1.pdb #38 
    7448 --- 
    7449 Chain | Description 
    7450 A | No description available 
    7451  
    7452 
    7453 > open
    7454 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V19_Mg-
    7455 > coot-3.pdb
    7456 
    7457 Chain information for V19_Mg-coot-3.pdb #39 
    7458 --- 
    7459 Chain | Description 
    7460 A | No description available 
    7461  
    7462 
    7463 > open
    7464 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V20_Mg-
    7465 > coot-2.pdb
    7466 
    7467 Chain information for V20_Mg-coot-2.pdb #40 
    7468 --- 
    7469 Chain | Description 
    7470 A | No description available 
    7471  
    7472 
    7473 > open
    7474 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V21_Mg_real_space_refined_002-coot-1.pdb
    7475 
    7476 Chain information for V21_Mg_real_space_refined_002-coot-1.pdb #41 
    7477 --- 
    7478 Chain | Description 
    7479 A | No description available 
    7480  
    7481 
    7482 > open
    7483 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_6sig.pdb
    7484 
    7485 Chain information for V22_Mg_6sig.pdb #42 
    7486 --- 
    7487 Chain | Description 
    7488 A | No description available 
    7489  
    7490 
    7491 > open
    7492 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_real_space_refined_002-coot-1.pdb
    7493 
    7494 Chain information for V22_Mg_real_space_refined_002-coot-1.pdb #43 
    7495 --- 
    7496 Chain | Description 
    7497 A | No description available 
    7498  
    7499 
    7500 > open
    7501 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg_6sig.pdb
    7502 
    7503 Chain information for V23_Mg_6sig.pdb #44 
    7504 --- 
    7505 Chain | Description 
    7506 A | No description available 
    7507  
    7508 
    7509 > open
    7510 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg-
    7511 > coot-1.pdb
    7512 
    7513 Chain information for V23_Mg-coot-1.pdb #45 
    7514 --- 
    7515 Chain | Description 
    7516 A | No description available 
    7517  
    7518 
    7519 > open
    7520 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_6sig.pdb
    7521 
    7522 Chain information for V24_6sig.pdb #46 
    7523 --- 
    7524 Chain | Description 
    7525 A | No description available 
    7526  
    7527 
    7528 > open
    7529 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_Mg-
    7530 > coot-6.pdb
    7531 
    7532 Chain information for V24_Mg-coot-6.pdb #47 
    7533 --- 
    7534 Chain | Description 
    7535 A | No description available 
    7536  
    7537 
    7538 > open
    7539 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V25_Mg-
    7540 > coot-1.pdb
    7541 
    7542 Chain information for V25_Mg-coot-1.pdb #48 
    7543 --- 
    7544 Chain | Description 
    7545 A | No description available 
    7546  
    7547 
    7548 > open
    7549 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V26_Mg-
    7550 > coot-1.pdb
    7551 
    7552 Chain information for V26_Mg-coot-1.pdb #49 
    7553 --- 
    7554 Chain | Description 
    7555 A | No description available 
    7556  
    7557 
    7558 > open
    7559 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V27_Mg-
    7560 > coot-2.pdb
    7561 
    7562 Chain information for V27_Mg-coot-2.pdb #50 
    7563 --- 
    7564 Chain | Description 
    7565 A | No description available 
    7566  
    7567 
    7568 > open
    7569 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V28_Mg-
    7570 > coot-1.pdb
    7571 
    7572 Chain information for V28_Mg-coot-1.pdb #51 
    7573 --- 
    7574 Chain | Description 
    7575 A | No description available 
    7576  
    7577 
    7578 > open
    7579 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V29_Mg-
    7580 > coot-2.pdb
    7581 
    7582 Chain information for V29_Mg-coot-2.pdb #52 
    7583 --- 
    7584 Chain | Description 
    7585 A | No description available 
    7586  
    7587 
    7588 > open
    7589 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V30_Mg-
    7590 > coot-3.pdb
    7591 
    7592 Chain information for V30_Mg-coot-3.pdb #53 
    7593 --- 
    7594 Chain | Description 
    7595 A | No description available 
    7596  
    7597 
    7598 > open
    7599 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V31_Mg-
    7600 > coot-3.pdb
    7601 
    7602 Chain information for V31_Mg-coot-3.pdb #54 
    7603 --- 
    7604 Chain | Description 
    7605 A | No description available 
    7606  
    7607 
    7608 > open
    7609 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V32_Mg-
    7610 > coot-2.pdb
    7611 
    7612 Chain information for V32_Mg-coot-2.pdb #55 
    7613 --- 
    7614 Chain | Description 
    7615 A | No description available 
    7616  
    7617 
    7618 > open
    7619 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V33_Mg-
    7620 > coot-2.pdb
    7621 
    7622 Chain information for V33_Mg-coot-2.pdb #56 
    7623 --- 
    7624 Chain | Description 
    7625 A | No description available 
    7626  
    7627 
    7628 > open
    7629 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V34_Mg-
    7630 > coot-3.pdb
    7631 
    7632 Chain information for V34_Mg-coot-3.pdb #57 
    7633 --- 
    7634 Chain | Description 
    7635 A | No description available 
    7636  
    7637 
    7638 > open
    7639 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V35_Mg-
    7640 > coot-2.pdb
    7641 
    7642 Chain information for V35_Mg-coot-2.pdb #58 
    7643 --- 
    7644 Chain | Description 
    7645 A | No description available 
    7646  
    7647 
    7648 > open
    7649 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V36_Mg-
    7650 > coot-1.pdb
    7651 
    7652 Chain information for V36_Mg-coot-1.pdb #59 
    7653 --- 
    7654 Chain | Description 
    7655 A | No description available 
    7656  
    7657 
    7658 > open
    7659 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V37_Mg-
    7660 > coot-1.pdb
    7661 
    7662 Chain information for V37_Mg-coot-1.pdb #60 
    7663 --- 
    7664 Chain | Description 
    7665 A | No description available 
    7666  
    7667 
    7668 > open
    7669 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V38_Mg-
    7670 > coot-1.pdb
    7671 
    7672 Chain information for V38_Mg-coot-1.pdb #61 
    7673 --- 
    7674 Chain | Description 
    7675 A | No description available 
    7676  
    7677 
    7678 > open
    7679 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V39_Mg_real_space_refined_002-coot-0.pdb
    7680 
    7681 Chain information for V39_Mg_real_space_refined_002-coot-0.pdb #62 
    7682 --- 
    7683 Chain | Description 
    7684 A | No description available 
    7685  
    7686 
    7687 > open
    7688 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0_aligned.pdb
    7689 
    7690 Chain information for V40_Mg_real_space_refined_003-coot-0_aligned.pdb #63 
    7691 --- 
    7692 Chain | Description 
    7693 A | No description available 
    7694  
    7695 
    7696 > open
    7697 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0.pdb
    7698 
    7699 Chain information for V40_Mg_real_space_refined_003-coot-0.pdb #64 
    7700 --- 
    7701 Chain | Description 
    7702 A | No description available 
    7703  
    7704 
    7705 > open
    7706 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V41_Mg_real_space_refined_003-coot-0.pdb
    7707 
    7708 Chain information for V41_Mg_real_space_refined_003-coot-0.pdb #65 
    7709 --- 
    7710 Chain | Description 
    7711 A | No description available 
    7712  
    7713 
    7714 > open
    7715 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V42_Mg_real_space_refined_003-coot-0.pdb
    7716 
    7717 Chain information for V42_Mg_real_space_refined_003-coot-0.pdb #66 
    7718 --- 
    7719 Chain | Description 
    7720 A | No description available 
    7721  
    7722 
    7723 > open
    7724 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V43_Mg_real_space_refined_001-coot-0.pdb
    7725 
    7726 Chain information for V43_Mg_real_space_refined_001-coot-0.pdb #67 
    7727 --- 
    7728 Chain | Description 
    7729 A | No description available 
    7730  
    7731 
    7732 > open
    7733 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V44_Mg_real_space_refined_003-coot-0.pdb
    7734 
    7735 Chain information for V44_Mg_real_space_refined_003-coot-0.pdb #68 
    7736 --- 
    7737 Chain | Description 
    7738 A | No description available 
    7739  
    7740 
    7741 > open
    7742 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V45_Mg-
    7743 > coot-3.pdb
    7744 
    7745 Chain information for V45_Mg-coot-3.pdb #69 
    7746 --- 
    7747 Chain | Description 
    7748 A | No description available 
    7749  
    7750 
    7751 > open
    7752 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V46_Mg-
    7753 > coot-2.pdb
    7754 
    7755 Chain information for V46_Mg-coot-2.pdb #70 
    7756 --- 
    7757 Chain | Description 
    7758 A | No description available 
    7759  
    7760 
    7761 > open
    7762 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V47_Mg-
    7763 > coot-4.pdb
    7764 
    7765 Chain information for V47_Mg-coot-4.pdb #71 
    7766 --- 
    7767 Chain | Description 
    7768 A | No description available 
    7769  
    7770 
    7771 > open
    7772 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V48_Mg-
    7773 > coot-1.pdb
    7774 
    7775 Chain information for V48_Mg-coot-1.pdb #72 
    7776 --- 
    7777 Chain | Description 
    7778 A | No description available 
    7779  
    7780 
    7781 > open
    7782 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V49_Mg-
    7783 > coot-2.pdb
    7784 
    7785 Chain information for V49_Mg-coot-2.pdb #73 
    7786 --- 
    7787 Chain | Description 
    7788 A | No description available 
    7789  
    7790 Computing secondary structure 
    7791 
    7792 > open
    7793 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V1_holo_set_noprot-
    7794 > coot-2.pdb
    7795 
    7796 Chain information for V1_holo_set_noprot-coot-2.pdb #74 
    7797 --- 
    7798 Chain | Description 
    7799 A | No description available 
    7800  
    7801 
    7802 > open
    7803 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a-
    7804 > coot-4.pdb
    7805 
    7806 Summary of feedback from opening
    7807 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a-
    7808 coot-4.pdb 
    7809 --- 
    7810 warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10 
    7811 Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1
    7812 17 
    7813 Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1
    7814 3 
    7815 Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1
    7816 14 
    7817 Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34
    7818 0 
    7819 2 messages similar to the above omitted 
    7820  
    7821 Chain information for V8_holo_no_prot_a-coot-4.pdb #75 
    7822 --- 
    7823 Chain | Description 
    7824 A | No description available 
    7825  
    7826 
    7827 > open
    7828 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo-
    7829 > coot-3.pdb
    7830 
    7831 Summary of feedback from opening
    7832 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo-
    7833 coot-3.pdb 
    7834 --- 
    7835 warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10 
    7836 Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1
    7837 17 
    7838 Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1
    7839 3 
    7840 Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1
    7841 14 
    7842 Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34
    7843 0 
    7844 2 messages similar to the above omitted 
    7845  
    7846 Chain information for V13_holo_set_noapo-coot-3.pdb #76 
    7847 --- 
    7848 Chain | Description 
    7849 A | No description available 
    7850  
    7851 
    7852 > open
    7853 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V20_holo_no_prot-
    7854 > coot-1.pdb
    7855 
    7856 Chain information for V20_holo_no_prot-coot-1.pdb #77 
    7857 --- 
    7858 Chain | Description 
    7859 A | No description available 
    7860  
    7861 
    7862 > open
    7863 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V22_holo_no_prot-
    7864 > coot-1.pdb
    7865 
    7866 Chain information for V22_holo_no_prot-coot-1.pdb #78 
    7867 --- 
    7868 Chain | Description 
    7869 A | No description available 
    7870  
    7871 
    7872 > open
    7873 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V24_holo_no_prot-
    7874 > coot-3.pdb
    7875 
    7876 Chain information for V24_holo_no_prot-coot-3.pdb #79 
    7877 --- 
    7878 Chain | Description 
    7879 A | No description available 
    7880  
    7881 Computing secondary structure 
    7882 
    7883 > select
    7884 > #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400
    7885 
    7886 3255 atoms, 3639 bonds, 151 residues, 1 model selected 
    7887 
    7888 > ui tool show Matchmaker
    7889 
    7890 > matchmaker #20-49,51-79#!50 to #1 & sel matrix Nucleic
    7891 
    7892 Computing secondary structure 
    7893 Parameters 
    7894 --- 
    7895 Chain pairing | bb 
    7896 Alignment algorithm | Needleman-Wunsch 
    7897 Similarity matrix | Nucleic 
    7898 SS fraction | 0.3 
    7899 Gap open (HH/SS/other) | 18/18/6 
    7900 Gap extend | 1 
    7901 SS matrix |  |  | H | S | O 
    7902 ---|---|---|--- 
    7903 H | 6 | -9 | -6 
    7904 S |  | 6 | -6 
    7905 O |  |  | 4 
    7906 Iteration cutoff | 2 
    7907  
    7908 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_Mg-coot-1.pdb, chain A
    7909 (#20), sequence alignment score = 604 
    7910 RMSD between 150 pruned atom pairs is 0.460 angstroms; (across all 151 pairs:
    7911 0.510) 
    7912  
    7913 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V2_Mg-coot-1.pdb, chain A
    7914 (#21), sequence alignment score = 604 
    7915 RMSD between 150 pruned atom pairs is 0.443 angstroms; (across all 151 pairs:
    7916 0.490) 
    7917  
    7918 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_Mg-coot-2.pdb, chain A
    7919 (#22), sequence alignment score = 604 
    7920 RMSD between 150 pruned atom pairs is 0.478 angstroms; (across all 151 pairs:
    7921 0.530) 
    7922  
    7923 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_Mg-coot-2.pdb, chain A
    7924 (#23), sequence alignment score = 604 
    7925 RMSD between 150 pruned atom pairs is 0.470 angstroms; (across all 151 pairs:
    7926 0.515) 
    7927  
    7928 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_Mg-coot-1.pdb, chain A
    7929 (#24), sequence alignment score = 604 
    7930 RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs:
    7931 0.521) 
    7932  
    7933 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_Mg-coot-1.pdb, chain A
    7934 (#25), sequence alignment score = 604 
    7935 RMSD between 150 pruned atom pairs is 0.469 angstroms; (across all 151 pairs:
    7936 0.519) 
    7937  
    7938 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_Mg-coot-2.pdb, chain A
    7939 (#26), sequence alignment score = 604 
    7940 RMSD between 148 pruned atom pairs is 0.517 angstroms; (across all 151 pairs:
    7941 0.622) 
    7942  
    7943 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_Mg-coot-2.pdb, chain A
    7944 (#27), sequence alignment score = 604 
    7945 RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs:
    7946 0.504) 
    7947  
    7948 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_Mg-coot-3.pdb, chain A
    7949 (#28), sequence alignment score = 604 
    7950 RMSD between 150 pruned atom pairs is 0.490 angstroms; (across all 151 pairs:
    7951 0.523) 
    7952  
    7953 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_Mg-coot-3.pdb, chain A
    7954 (#29), sequence alignment score = 604 
    7955 RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
    7956 0.532) 
    7957  
    7958 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_Mg-coot-2.pdb, chain A
    7959 (#30), sequence alignment score = 604 
    7960 RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs:
    7961 0.536) 
    7962  
    7963 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    7964 V12_real_space_refined_011-coot-0.pdb, chain A (#31), sequence alignment score
    7965 = 604 
    7966 RMSD between 150 pruned atom pairs is 0.523 angstroms; (across all 151 pairs:
    7967 0.559) 
    7968  
    7969 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-2.pdb, chain A
    7970 (#32), sequence alignment score = 604 
    7971 RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs:
    7972 0.540) 
    7973  
    7974 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-3_6.pdb, chain A
    7975 (#33), sequence alignment score = 604 
    7976 RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs:
    7977 0.540) 
    7978  
    7979 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_Mg-coot-1.pdb, chain A
    7980 (#34), sequence alignment score = 604 
    7981 RMSD between 150 pruned atom pairs is 0.477 angstroms; (across all 151 pairs:
    7982 0.534) 
    7983  
    7984 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_Mg-coot-2.pdb, chain A
    7985 (#35), sequence alignment score = 604 
    7986 RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
    7987 0.518) 
    7988  
    7989 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V16_Mg-coot-1.pdb, chain A
    7990 (#36), sequence alignment score = 604 
    7991 RMSD between 150 pruned atom pairs is 0.452 angstroms; (across all 151 pairs:
    7992 0.506) 
    7993  
    7994 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_Mg-coot-2.pdb, chain A
    7995 (#37), sequence alignment score = 604 
    7996 RMSD between 150 pruned atom pairs is 0.439 angstroms; (across all 151 pairs:
    7997 0.502) 
    7998  
    7999 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_Mg-coot-1.pdb, chain A
    8000 (#38), sequence alignment score = 604 
    8001 RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
    8002 0.498) 
    8003  
    8004 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_Mg-coot-3.pdb, chain A
    8005 (#39), sequence alignment score = 604 
    8006 RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs:
    8007 0.496) 
    8008  
    8009 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_Mg-coot-2.pdb, chain A
    8010 (#40), sequence alignment score = 604 
    8011 RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs:
    8012 0.520) 
    8013  
    8014 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8015 V21_Mg_real_space_refined_002-coot-1.pdb, chain A (#41), sequence alignment
    8016 score = 604 
    8017 RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs:
    8018 0.525) 
    8019  
    8020 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_Mg_6sig.pdb, chain A
    8021 (#42), sequence alignment score = 604 
    8022 RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs:
    8023 0.508) 
    8024  
    8025 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8026 V22_Mg_real_space_refined_002-coot-1.pdb, chain A (#43), sequence alignment
    8027 score = 604 
    8028 RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs:
    8029 0.508) 
    8030  
    8031 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg_6sig.pdb, chain A
    8032 (#44), sequence alignment score = 604 
    8033 RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
    8034 0.534) 
    8035  
    8036 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg-coot-1.pdb, chain A
    8037 (#45), sequence alignment score = 604 
    8038 RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
    8039 0.534) 
    8040  
    8041 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_6sig.pdb, chain A (#46),
    8042 sequence alignment score = 604 
    8043 RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs:
    8044 0.552) 
    8045  
    8046 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_Mg-coot-6.pdb, chain A
    8047 (#47), sequence alignment score = 604 
    8048 RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs:
    8049 0.552) 
    8050  
    8051 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_Mg-coot-1.pdb, chain A
    8052 (#48), sequence alignment score = 604 
    8053 RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs:
    8054 0.518) 
    8055  
    8056 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V26_Mg-coot-1.pdb, chain A
    8057 (#49), sequence alignment score = 604 
    8058 RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
    8059 0.546) 
    8060  
    8061 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V28_Mg-coot-1.pdb, chain A
    8062 (#51), sequence alignment score = 604 
    8063 RMSD between 150 pruned atom pairs is 0.514 angstroms; (across all 151 pairs:
    8064 0.557) 
    8065  
    8066 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V29_Mg-coot-2.pdb, chain A
    8067 (#52), sequence alignment score = 604 
    8068 RMSD between 150 pruned atom pairs is 0.486 angstroms; (across all 151 pairs:
    8069 0.512) 
    8070  
    8071 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V30_Mg-coot-3.pdb, chain A
    8072 (#53), sequence alignment score = 604 
    8073 RMSD between 150 pruned atom pairs is 0.427 angstroms; (across all 151 pairs:
    8074 0.470) 
    8075  
    8076 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V31_Mg-coot-3.pdb, chain A
    8077 (#54), sequence alignment score = 604 
    8078 RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs:
    8079 0.524) 
    8080  
    8081 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V32_Mg-coot-2.pdb, chain A
    8082 (#55), sequence alignment score = 604 
    8083 RMSD between 149 pruned atom pairs is 0.454 angstroms; (across all 151 pairs:
    8084 0.624) 
    8085  
    8086 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V33_Mg-coot-2.pdb, chain A
    8087 (#56), sequence alignment score = 604 
    8088 RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs:
    8089 0.515) 
    8090  
    8091 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V34_Mg-coot-3.pdb, chain A
    8092 (#57), sequence alignment score = 604 
    8093 RMSD between 149 pruned atom pairs is 0.539 angstroms; (across all 151 pairs:
    8094 0.609) 
    8095  
    8096 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V35_Mg-coot-2.pdb, chain A
    8097 (#58), sequence alignment score = 604 
    8098 RMSD between 150 pruned atom pairs is 0.538 angstroms; (across all 151 pairs:
    8099 0.577) 
    8100  
    8101 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V36_Mg-coot-1.pdb, chain A
    8102 (#59), sequence alignment score = 604 
    8103 RMSD between 149 pruned atom pairs is 0.505 angstroms; (across all 151 pairs:
    8104 0.589) 
    8105  
    8106 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V37_Mg-coot-1.pdb, chain A
    8107 (#60), sequence alignment score = 604 
    8108 RMSD between 150 pruned atom pairs is 0.476 angstroms; (across all 151 pairs:
    8109 0.520) 
    8110  
    8111 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V38_Mg-coot-1.pdb, chain A
    8112 (#61), sequence alignment score = 604 
    8113 RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs:
    8114 0.509) 
    8115  
    8116 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8117 V39_Mg_real_space_refined_002-coot-0.pdb, chain A (#62), sequence alignment
    8118 score = 604 
    8119 RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
    8120 0.539) 
    8121  
    8122 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8123 V40_Mg_real_space_refined_003-coot-0_aligned.pdb, chain A (#63), sequence
    8124 alignment score = 604 
    8125 RMSD between 149 pruned atom pairs is 0.522 angstroms; (across all 151 pairs:
    8126 0.591) 
    8127  
    8128 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8129 V40_Mg_real_space_refined_003-coot-0.pdb, chain A (#64), sequence alignment
    8130 score = 604 
    8131 RMSD between 149 pruned atom pairs is 0.526 angstroms; (across all 151 pairs:
    8132 0.595) 
    8133  
    8134 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8135 V41_Mg_real_space_refined_003-coot-0.pdb, chain A (#65), sequence alignment
    8136 score = 604 
    8137 RMSD between 150 pruned atom pairs is 0.484 angstroms; (across all 151 pairs:
    8138 0.540) 
    8139  
    8140 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8141 V42_Mg_real_space_refined_003-coot-0.pdb, chain A (#66), sequence alignment
    8142 score = 604 
    8143 RMSD between 150 pruned atom pairs is 0.482 angstroms; (across all 151 pairs:
    8144 0.526) 
    8145  
    8146 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8147 V43_Mg_real_space_refined_001-coot-0.pdb, chain A (#67), sequence alignment
    8148 score = 604 
    8149 RMSD between 149 pruned atom pairs is 0.513 angstroms; (across all 151 pairs:
    8150 0.602) 
    8151  
    8152 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
    8153 V44_Mg_real_space_refined_003-coot-0.pdb, chain A (#68), sequence alignment
    8154 score = 604 
    8155 RMSD between 150 pruned atom pairs is 0.507 angstroms; (across all 151 pairs:
    8156 0.549) 
    8157  
    8158 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V45_Mg-coot-3.pdb, chain A
    8159 (#69), sequence alignment score = 604 
    8160 RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs:
    8161 0.546) 
    8162  
    8163 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V46_Mg-coot-2.pdb, chain A
    8164 (#70), sequence alignment score = 604 
    8165 RMSD between 150 pruned atom pairs is 0.436 angstroms; (across all 151 pairs:
    8166 0.490) 
    8167  
    8168 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V47_Mg-coot-4.pdb, chain A
    8169 (#71), sequence alignment score = 604 
    8170 RMSD between 150 pruned atom pairs is 0.564 angstroms; (across all 151 pairs:
    8171 0.596) 
    8172  
    8173 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V48_Mg-coot-1.pdb, chain A
    8174 (#72), sequence alignment score = 604 
    8175 RMSD between 150 pruned atom pairs is 0.468 angstroms; (across all 151 pairs:
    8176 0.523) 
    8177  
    8178 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V49_Mg-coot-2.pdb, chain A
    8179 (#73), sequence alignment score = 604 
    8180 RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
    8181 0.529) 
    8182  
    8183 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_holo_set_noprot-
    8184 coot-2.pdb, chain A (#74), sequence alignment score = 604 
    8185 RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
    8186 0.464) 
    8187  
    8188 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_holo_no_prot_a-coot-4.pdb,
    8189 chain A (#75), sequence alignment score = 604 
    8190 RMSD between 149 pruned atom pairs is 0.486 angstroms; (across all 151 pairs:
    8191 0.562) 
    8192  
    8193 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_holo_set_noapo-
    8194 coot-3.pdb, chain A (#76), sequence alignment score = 604 
    8195 RMSD between 151 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
    8196 0.491) 
    8197  
    8198 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_holo_no_prot-coot-1.pdb,
    8199 chain A (#77), sequence alignment score = 604 
    8200 RMSD between 151 pruned atom pairs is 0.442 angstroms; (across all 151 pairs:
    8201 0.442) 
    8202  
    8203 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_holo_no_prot-coot-1.pdb,
    8204 chain A (#78), sequence alignment score = 604 
    8205 RMSD between 149 pruned atom pairs is 0.357 angstroms; (across all 151 pairs:
    8206 0.438) 
    8207  
    8208 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_holo_no_prot-coot-3.pdb,
    8209 chain A (#79), sequence alignment score = 604 
    8210 RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs:
    8211 0.557) 
    8212  
    8213 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V27_Mg-coot-2.pdb, chain A
    8214 (#50), sequence alignment score = 604 
    8215 RMSD between 150 pruned atom pairs is 0.544 angstroms; (across all 151 pairs:
    8216 0.594) 
    8217  
    8218 
    8219 > select #20-79/A
    8220 
    8221 537720 atoms, 602280 bonds, 25020 residues, 60 models selected 
    8222 
    8223 > color sel dim gray
    8224 
    8225 > hide sel target a
    8226 
    8227 > select #20-79/A:50,389,390
    8228 
    8229 3960 atoms, 4380 bonds, 180 residues, 60 models selected 
    8230 
    8231 > cartoon hide sel
    8232 
    8233 > show sel target ab
    8234 
    8235 > nucleotides sel atoms
    8236 
    8237 > style nucleic & sel stick
    8238 
    8239 Changed 3960 atom styles 
    8240 
    8241 > hide (sel-residues & (protein|nucleic)) target a
    8242 
    8243 > cartoon hide sel-residues
    8244 
    8245 > show (sel-residues & backbone) target ab
    8246 
    8247 > ui tool show "Color Actions"
    8248 
    8249 > color sel cornflower blue
    8250 
    8251 > hide #19#!1-18 target m
    8252 
    8253 > select #20/C:1@O
    8254 
    8255 1 atom, 1 residue, 1 model selected 
    8256 
    8257 > select add #42/B:67@MG
    8258 
    8259 2 atoms, 2 residues, 2 models selected 
    8260 
    8261 > select add #61/B:65@MG
    8262 
    8263 3 atoms, 3 residues, 3 models selected 
    8264 
    8265 > select add #65/B:44@MG
    8266 
    8267 4 atoms, 4 residues, 4 models selected 
    8268 
    8269 > hide sel target a
    8270 
    8271 > select #30/B:61@MG
    8272 
    8273 1 atom, 1 residue, 1 model selected 
    8274 
    8275 > select add #69/B:62@MG
    8276 
    8277 2 atoms, 2 residues, 2 models selected 
    8278 
    8279 > hide sel target a
    8280 
    8281 > select #20-79/B
    8282 
    8283 2199 atoms, 1 pseudobond, 2199 residues, 56 models selected 
    8284 
    8285 > ui tool show "Selection Inspector"
    8286 
    8287 > size sel atomRadius 0.7
    8288 
    8289 Changed 2199 atom radii 
    8290 
    8291 > select clear
    8292 
    8293 > select #46/B:66@MG
    8294 
    8295 1 atom, 1 residue, 1 model selected 
    8296 
    8297 > select add #75/A:390@O3'
    8298 
    8299 2 atoms, 2 residues, 2 models selected 
    8300 
    8301 > distance #46/B:66@MG #75/A:390@O3'
    8302 
    8303 Distance between V24_6sig.pdb #46/B MG 66 MG and V8_holo_no_prot_a-coot-4.pdb
    8304 #75/A A 390 O3': 5.502Å 
    8305 
    8306 > close #42
    8307 
    8308 > close #44
    8309 
    8310 > close #46
    8311 
    8312 > select #20-79/B
    8313 
    8314 2062 atoms, 1 pseudobond, 2062 residues, 53 models selected 
    8315 
    8316 > close #33
    8317 
    8318 > close #63
    8319 
    8320 > select #20-79/B:7
    8321 
    8322 50 atoms, 50 residues, 50 models selected 
    8323 
    8324 > select #75/C:7@MG
    8325 
    8326 1 atom, 1 residue, 1 model selected 
    8327 
    8328 > select add #69/B:7@MG
    8329 
    8330 2 atoms, 2 residues, 2 models selected 
    8331 
    8332 > select add #68/B:7@MG
    8333 
    8334 3 atoms, 3 residues, 3 models selected 
    8335 
    8336 > select add #55/B:7@MG
    8337 
    8338 4 atoms, 4 residues, 4 models selected 
    8339 
    8340 > select #20-79/B
    8341 
    8342 1987 atoms, 1 pseudobond, 1987 residues, 51 models selected 
    8343 
    8344 > select #20-79/C
    8345 
    8346 187 atoms, 187 residues, 6 models selected 
    8347 
    8348 > ui tool show "Selection Inspector"
    8349 
    8350 > size sel atomRadius 0.7
    8351 
    8352 Changed 187 atom radii 
    8353 
    8354 > select #20-79/B:7
    8355 
    8356 50 atoms, 50 residues, 50 models selected 
    8357 
    8358 > ui tool show "Color Actions"
    8359 
    8360 > color sel #941100ff
    8361 
    8362 > select #20-79/C:7
    8363 
    8364 5 atoms, 5 residues, 5 models selected 
    8365 
    8366 > ui tool show "Color Actions"
    8367 
    8368 > select #20-79/C:7
    8369 
    8370 5 atoms, 5 residues, 5 models selected 
    8371 
    8372 > ui tool show "Color Actions"
    8373 
    8374 > color sel #4f8f00ff
    8375 
    8376 > color sel #941100ff
    8377 
    8378 > select #20-79/B
    8379 
    8380 1987 atoms, 1 pseudobond, 1987 residues, 51 models selected 
    8381 
    8382 > ui tool show "Color Actions"
    8383 
    8384 > color sel forest green
    8385 
    8386 > select #20-79/C
    8387 
    8388 187 atoms, 187 residues, 6 models selected 
    8389 
    8390 > ui tool show "Color Actions"
    8391 
    8392 > color sel forest green
    8393 
    8394 > select #20-79/C:7
    8395 
    8396 5 atoms, 5 residues, 5 models selected 
    8397 
    8398 > ui tool show "Color Actions"
    8399 
    8400 > select #20-79/B:7
    8401 
    8402 50 atoms, 50 residues, 50 models selected 
    8403 
    8404 > ui tool show "Color Actions"
    8405 
    8406 > color sel #945200ff
    8407 
    8408 > color sel #941100ff
    8409 
    8410 > select #20-79/C:7
    8411 
    8412 5 atoms, 5 residues, 5 models selected 
    8413 
    8414 > ui tool show "Color Actions"
    8415 
    8416 > color sel #945200ff
    8417 
    8418 > color sel #941100ff
    8419 
    8420 > select clear
    8421 
    8422 > select #20-79/B:57
    8423 
    8424 21 atoms, 21 residues, 21 models selected 
    8425 
    8426 > select #20-79/B:57,66
    8427 
    8428 35 atoms, 35 residues, 25 models selected 
    8429 
    8430 > select clear
    8431 
    8432 > select #65/B:41@MG
    8433 
    8434 1 atom, 1 residue, 1 model selected 
    8435 
    8436 > select add #39/B:64@MG
    8437 
    8438 2 atoms, 2 residues, 2 models selected 
    8439 
    8440 > select add #41/B:62@MG
    8441 
    8442 3 atoms, 3 residues, 3 models selected 
    8443 
    8444 > select add #43/B:63@MG
    8445 
    8446 4 atoms, 4 residues, 4 models selected 
    8447 
    8448 > select subtract #43/B:63@MG
    8449 
    8450 3 atoms, 3 residues, 3 models selected 
    8451 
    8452 > select add #43/B:63@MG
    8453 
    8454 4 atoms, 4 residues, 4 models selected 
    8455 
    8456 > select subtract #41/B:62@MG
    8457 
    8458 3 atoms, 3 residues, 3 models selected 
    8459 
    8460 > select add #31/B:58@MG
    8461 
    8462 4 atoms, 4 residues, 4 models selected 
    8463 
    8464 > select add #30/B:57@MG
    8465 
    8466 5 atoms, 5 residues, 5 models selected 
    8467 
    8468 > select subtract #31/B:58@MG
    8469 
    8470 4 atoms, 4 residues, 4 models selected 
    8471 
    8472 > select subtract #65/B:41@MG
    8473 
    8474 3 atoms, 3 residues, 3 models selected 
    8475 
    8476 > select add #65/B:41@MG
    8477 
    8478 4 atoms, 4 residues, 4 models selected 
    8479 
    8480 > select add #31/B:58@MG
    8481 
    8482 5 atoms, 5 residues, 5 models selected 
    8483 
    8484 > select subtract #31/B:58@MG
    8485 
    8486 4 atoms, 4 residues, 4 models selected 
    8487 
    8488 > select subtract #39/B:64@MG
    8489 
    8490 3 atoms, 3 residues, 3 models selected 
    8491 
    8492 > select add #39/B:64@MG
    8493 
    8494 4 atoms, 4 residues, 4 models selected 
    8495 
    8496 > select add #38/B:61@MG
    8497 
    8498 5 atoms, 5 residues, 5 models selected 
    8499 
    8500 > select add #36/B:60@MG
    8501 
    8502 6 atoms, 6 residues, 6 models selected 
    8503 
    8504 > select subtract #43/B:63@MG
    8505 
    8506 5 atoms, 5 residues, 5 models selected 
    8507 
    8508 > select add #43/B:63@MG
    8509 
    8510 6 atoms, 6 residues, 6 models selected 
    8511 
    8512 > hide sel target a
    8513 
    8514 > select #26/B:49@MG
    8515 
    8516 1 atom, 1 residue, 1 model selected 
    8517 
    8518 > select add #31/B:58@MG
    8519 
    8520 2 atoms, 2 residues, 2 models selected 
    8521 
    8522 > select add #41/B:62@MG
    8523 
    8524 3 atoms, 3 residues, 3 models selected 
    8525 
    8526 > select add #34/B:59@MG
    8527 
    8528 4 atoms, 4 residues, 4 models selected 
    8529 
    8530 > hide sel target a
    8531 
    8532 > select #43/B:65@MG
    8533 
    8534 1 atom, 1 residue, 1 model selected 
    8535 
    8536 > select add #30/B:60@MG
    8537 
    8538 2 atoms, 2 residues, 2 models selected 
    8539 
    8540 > show #19 models
    8541 
    8542 > hide #19 models
    8543 
    8544 > show #19 models
    8545 
    8546 > hide #19 models
    8547 
    8548 > show #19 models
    8549 
    8550 > hide #19 models
    8551 
    8552 > show #19 models
    8553 
    8554 > hide #19 models
    8555 
    8556 > show #19 models
    8557 
    8558 > hide #19 models
    8559 
    8560 > show #19 models
    8561 
    8562 > hide #19 models
    8563 
    8564 > show #19 models
    8565 
    8566 > hide #19 models
    8567 
    8568 > show #19 models
    8569 
    8570 > hide #19 models
    8571 
    8572 > select #50/B:64@MG
    8573 
    8574 1 atom, 1 residue, 1 model selected 
    8575 
    8576 > select add #35/B:62@MG
    8577 
    8578 2 atoms, 2 residues, 2 models selected 
    8579 
    8580 > select add #51/B:68@MG
    8581 
    8582 3 atoms, 3 residues, 3 models selected 
    8583 
    8584 > select add #69/B:57@MG
    8585 
    8586 4 atoms, 4 residues, 4 models selected 
    8587 
    8588 > select add #62/B:45@MG
    8589 
    8590 5 atoms, 5 residues, 5 models selected 
    8591 
    8592 > select add #64/B:42@MG
    8593 
    8594 6 atoms, 6 residues, 6 models selected 
    8595 
    8596 > select add #27/B:54@MG
    8597 
    8598 7 atoms, 7 residues, 7 models selected 
    8599 
    8600 > select add #59/B:66@MG
    8601 
    8602 8 atoms, 8 residues, 8 models selected 
    8603 
    8604 > hide sel target a
    8605 
    8606 > show sel target ab
    8607 
    8608 > show #19 models
    8609 
    8610 > hide #19 models
    8611 
    8612 > show #19 models
    8613 
    8614 > hide #19 models
    8615 
    8616 > show #19 models
    8617 
    8618 > hide #19 models
    8619 
    8620 > show #19 models
    8621 
    8622 > hide #19 models
    8623 
    8624 > show #19 models
    8625 
    8626 > hide #19 models
    8627 
    8628 > show #19 models
    8629 
    8630 > hide #19 models
    8631 
    8632 > select #21/B:38@MG
    8633 
    8634 1 atom, 1 residue, 1 model selected 
    8635 
    8636 > select add #30/B:38@MG
    8637 
    8638 2 atoms, 2 residues, 2 models selected 
    8639 
    8640 > select add #26/B:38@MG
    8641 
    8642 3 atoms, 3 residues, 3 models selected 
    8643 
    8644 > select #26/B:38@MG
    8645 
    8646 1 atom, 1 residue, 1 model selected 
    8647 
    8648 > select add #59/B:64@MG
    8649 
    8650 2 atoms, 2 residues, 2 models selected 
    8651 
    8652 > distance #26/B:38@MG #59/B:64@MG
    8653 
    8654 Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V36_Mg-coot-1.pdb #59/B
    8655 MG 64 MG: 9.452Å 
    8656 
    8657 > select #26/B:38@MG
    8658 
    8659 1 atom, 1 residue, 1 model selected 
    8660 
    8661 > select add #23/B:7@MG
    8662 
    8663 2 atoms, 2 residues, 2 models selected 
    8664 
    8665 > distance #26/B:38@MG #23/B:7@MG
    8666 
    8667 Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V4_Mg-coot-2.pdb #23/B MG
    8668 7 MG: 8.150Å 
    8669 
    8670 > select #26/B:38@MG
    8671 
    8672 1 atom, 1 residue, 1 model selected 
    8673 
    8674 > select add #21/B:38@MG
    8675 
    8676 2 atoms, 2 residues, 2 models selected 
    8677 
    8678 > select add #30/B:38@MG
    8679 
    8680 3 atoms, 3 residues, 3 models selected 
    8681 
    8682 > hide sel target a
    8683 
    8684 > select #36/B:38@MG
    8685 
    8686 1 atom, 1 residue, 1 model selected 
    8687 
    8688 > select add #59/B:38@MG
    8689 
    8690 2 atoms, 2 residues, 2 models selected 
    8691 
    8692 > hide sel target a
    8693 
    8694 > select add #62/B:30@MG
    8695 
    8696 3 atoms, 3 residues, 3 models selected 
    8697 
    8698 > select #53/B:65@MG
    8699 
    8700 1 atom, 1 residue, 1 model selected 
    8701 
    8702 > select #75/A:390@O3'
    8703 
    8704 1 atom, 1 residue, 1 model selected 
    8705 
    8706 > select add #24/B:50@MG
    8707 
    8708 2 atoms, 2 residues, 2 models selected 
    8709 
    8710 > distance #75/A:390@O3' #24/B:50@MG
    8711 
    8712 Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V5_Mg-
    8713 coot-1.pdb #24/B MG 50 MG: 5.771Å 
    8714 
    8715 > select #24/B:50@MG
    8716 
    8717 1 atom, 1 residue, 1 model selected 
    8718 
    8719 > select #47/B:66@MG
    8720 
    8721 1 atom, 1 residue, 1 model selected 
    8722 
    8723 > select add #34/B:61@MG
    8724 
    8725 2 atoms, 2 residues, 2 models selected 
    8726 
    8727 > select add #32/B:60@MG
    8728 
    8729 3 atoms, 3 residues, 3 models selected 
    8730 
    8731 > select add #24/B:50@MG
    8732 
    8733 4 atoms, 4 residues, 4 models selected 
    8734 
    8735 > select add #53/B:65@MG
    8736 
    8737 5 atoms, 5 residues, 5 models selected 
    8738 
    8739 > select add #48/B:69@MG
    8740 
    8741 6 atoms, 6 residues, 6 models selected 
    8742 
    8743 > select add #36/B:61@MG
    8744 
    8745 7 atoms, 7 residues, 7 models selected 
    8746 
    8747 > select #47/B:66@MG
    8748 
    8749 1 atom, 1 residue, 1 model selected 
    8750 
    8751 > select add #55/B:62@MG
    8752 
    8753 2 atoms, 2 residues, 2 models selected 
    8754 
    8755 > distance #47/B:66@MG #55/B:62@MG
    8756 
    8757 Distance between V24_Mg-coot-6.pdb #47/B MG 66 MG and V32_Mg-coot-2.pdb #55/B
    8758 MG 62 MG: 5.257Å 
    8759 
    8760 > save
    8761 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs
    8762 
    8763 > select #43/B:65@MG
    8764 
    8765 1 atom, 1 residue, 1 model selected 
    8766 
    8767 > select add #58/B:4@MG
    8768 
    8769 2 atoms, 2 residues, 2 models selected 
    8770 
    8771 > distance #43/B:65@MG #58/B:4@MG
    8772 
    8773 Distance between V22_Mg_real_space_refined_002-coot-1.pdb #43/B MG 65 MG and
    8774 V35_Mg-coot-2.pdb #58/B MG 4 MG: 9.512Å 
    8775 
    8776 > select #43/B:65@MG
    8777 
    8778 1 atom, 1 residue, 1 model selected 
    8779 
    8780 > select add #30/B:60@MG
    8781 
    8782 2 atoms, 2 residues, 2 models selected 
    8783 
    8784 > hide sel target a
    8785 
    8786 > save
    8787 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs
    8788 
    8789 > select #59/B:64@MG
    8790 
    8791 1 atom, 1 residue, 1 model selected 
    8792 
    8793 > select clear
    8794 
    8795 > select #48/B:30@MG
    8796 
    8797 1 atom, 1 residue, 1 model selected 
    8798 
    8799 > select add #75/C:7@MG
    8800 
    8801 2 atoms, 2 residues, 2 models selected 
    8802 
    8803 > distance #48/B:30@MG #75/C:7@MG
    8804 
    8805 Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V8_holo_no_prot_a-
    8806 coot-4.pdb #75/C MG 7 MG: 7.041Å 
    8807 
    8808 > select #48/B:30@MG
    8809 
    8810 1 atom, 1 residue, 1 model selected 
    8811 
    8812 > select add #58/A:389@OP1
    8813 
    8814 2 atoms, 2 residues, 2 models selected 
    8815 
    8816 > distance #48/B:30@MG #58/A:389@OP1
    8817 
    8818 Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V35_Mg-coot-2.pdb #58/A
    8819 A 389 OP1: 2.362Å 
    8820 
    8821 > select #69/B:30@MG
    8822 
    8823 1 atom, 1 residue, 1 model selected 
    8824 
    8825 > select add #65/B:30@MG
    8826 
    8827 2 atoms, 2 residues, 2 models selected 
    8828 
    8829 > select add #48/B:30@MG
    8830 
    8831 3 atoms, 3 residues, 3 models selected 
    8832 
    8833 > select add #41/B:30@MG
    8834 
    8835 4 atoms, 4 residues, 4 models selected 
    8836 
    8837 > select add #55/B:66@MG
    8838 
    8839 5 atoms, 5 residues, 5 models selected 
    8840 
    8841 > select add #50/B:30@MG
    8842 
    8843 6 atoms, 6 residues, 6 models selected 
    8844 
    8845 > color sel blue
    8846 
    8847 > select clear
    8848 
    8849 > select #39/B:65@MG
    8850 
    8851 1 atom, 1 residue, 1 model selected 
    8852 
    8853 > select add #75/A:390@O3'
    8854 
    8855 2 atoms, 2 residues, 2 models selected 
    8856 
    8857 > distance #39/B:65@MG #75/A:390@O3'
    8858 
    8859 Distance between V19_Mg-coot-3.pdb #39/B MG 65 MG and V8_holo_no_prot_a-
    8860 coot-4.pdb #75/A A 390 O3': 4.560Å 
    8861 
    8862 > select #28/B:40@MG
    8863 
    8864 1 atom, 1 residue, 1 model selected 
    8865 
    8866 > select #75/A:390@O3'
    8867 
    8868 1 atom, 1 residue, 1 model selected 
    8869 
    8870 > select add #72/B:40@MG
    8871 
    8872 2 atoms, 2 residues, 2 models selected 
    8873 
    8874 > distance #75/A:390@O3' #72/B:40@MG
    8875 
    8876 Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V48_Mg-
    8877 coot-1.pdb #72/B MG 40 MG: 5.512Å 
    8878 
    8879 > select #20-79/B:40
    8880 
    8881 33 atoms, 33 residues, 33 models selected 
    8882 
    8883 > save
    8884 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs
    8885 
    8886 
    8887 ===== Log before crash end =====
    8888 
    8889 Log:
    8890 UCSF ChimeraX version: 1.9 (2024-12-11) 
    8891 © 2016-2024 Regents of the University of California. All rights reserved. 
    8892 
    8893 > open
    8894 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs
    8895 
    8896 Log from Wed Sep 17 17:35:30 2025 Startup Messages 
    8897 --- 
    8898 note | available bundle cache has not been initialized yet 
    8899  
    8900 UCSF ChimeraX version: 1.9 (2024-12-11) 
    8901 © 2016-2024 Regents of the University of California. All rights reserved. 
    8902 How to cite UCSF ChimeraX 
    8903 
    8904 > open
    8905 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume.mrc
    8906 
    8907 Opened J3985_class_01_00049_volume.mrc as #1, grid size 128,128,128, pixel
    8908 2.74, shown at level 0.0714, step 1, values float32 
    8909 
    8910 > open
    8911 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_00_00049_volume.mrc
    8912 
    8913 Opened J3985_class_00_00049_volume.mrc as #2, grid size 128,128,128, pixel
    8914 2.74, shown at level 0.0704, step 1, values float32 
    8915 
    8916 > volume #2 level 0.1464
    8917 
    8918 > volume #2 level 0.1878
    8919 
    8920 > volume #1 level 0.1749
    8921 
    8922 > volume #1 level 0.2362
    8923 
    8924 > volume #2 level 0.2672
    8925 
    8926 > volume #1 level 0.2324
    8927 
    8928 > volume #1 level 0.2937
    8929 
    8930 > volume #1 level 0.1634
    8931 
    8932 > volume #1 level 0.1979
    8933 
    8934 > volume #2 level 0.2879
    8935 
    8936 > volume #1 level 0.2247
    8937 
    8938 > volume #1 level 0.2055
    8939 
    8940 > volume #2 level 0.3432
    8941 
    8942 > volume #1 level 0.3014
    8943 
    8944 > volume #1 level 0.1557
    8945 
    8946 [Repeated 1 time(s)]
    8947 
    8948 > ui tool show "Segment Map"
    8949 
    8950 Select a density map in the Segment map field 
    8951 Segmenting J3985_class_01_00049_volume.mrc, density threshold 0.155709 
    8952 Showing 1 region surfaces 
    8953 187 watershed regions, grouped to 1 regions 
    8954 Showing J3985_class_01_00049_volume.seg - 1 regions, 1 surfaces 
    8955 Ungrouped to 3 regions 
    8956 
    8957 > select #3.3
    8958 
    8959 1 model selected 
    8960 Ungrouped to 8 regions 
    8961 
    8962 > select #3.6
    8963 
    8964 1 model selected 
    8965 Ungrouped to 5 regions 
    8966 
    8967 > select #3.3
    8968 
    8969 1 model selected 
    8970 
    8971 > select add #3.14
    8972 
    8973 2 models selected 
    8974 
    8975 > select add #3.9
    8976 
    8977 3 models selected 
    8978 Grouped 3 regions 
    8979 Ungrouped to 3 regions 
    8980 
    8981 > select #3.6
    8982 
    8983 1 model selected 
    8984 Ungrouped to 3 regions 
    8985 
    8986 > select #3.3
    8987 
    8988 1 model selected 
    8989 Ungrouped to 15 regions 
    8990 
    8991 > select #3.31
    8992 
    8993 1 model selected 
    8994 
    8995 > select add #3.9
    8996 
    8997 2 models selected 
    8998 
    8999 > select add #3.14
    9000 
    9001 3 models selected 
    9002 Grouped 3 regions 
    9003 Saving 1 regions to mrc file... 
    9004 Opened J3985_class_01_00049_volume_region_234.mrc as #4, grid size 21,17,18,
    9005 pixel 2.74, shown at step 1, values float32 
    9006 Wrote J3985_class_01_00049_volume_region_234.mrc 
    9007 
    9008 > volume resample #4 onGrid 1
    9009 
    9010 Invalid "onGrid" argument: invalid density maps specifier 
    9011 
    9012 > volume resample #4 onGrid #1
    9013 
    9014 Opened J3985_class_01_00049_volume_region_234.mrc resampled as #5, grid size
    9015 128,128,128, pixel 2.74, shown at step 1, values float32 
    9016 
    9017 > hide #!3 models
    9018 
    9019 > volume #5 level 0.2124
    9020 
    9021 > volume #5 level 0.1251
    9022 
    9023 > save
    9024 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume_region_p.mrc
    9025 > models #5
    9026 
    9027 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3986_006_volume_map.mrc
    9028 
    9029 Opened cryosparc_P9_J3986_006_volume_map.mrc as #6, grid size 480,480,480,
    9030 pixel 0.732, shown at level 0.0101, step 2, values float32 
    9031 
    9032 > volume #6 level 0.0249
    9033 
    9034 > volume #6 level 0.01868
    9035 
    9036 > volume #6 level 0.03345
    9037 
    9038 > volume #!5-6 hide
    9039 
    9040 > volume #1 level 0.2702
    9041 
    9042 > volume #2 level 0.1264
    9043 
    9044 > volume #1 level 0.1478
    9045 
    9046 > volume #1 level 0.1123
    9047 
    9048 > volume #2 level 0.1797
    9049 
    9050 > volume #1 level 0.2623
    9051 
    9052 > volume #2 level 0.3574
    9053 
    9054 > volume #1 level 0.3294
    9055 
    9056 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3984_007_volume_map.mrc
    9057 
    9058 Opened cryosparc_P9_J3984_007_volume_map.mrc as #7, grid size 480,480,480,
    9059 pixel 0.732, shown at level 0.0104, step 2, values float32 
    9060 
    9061 > volume #!1,7 hide
    9062 
    9063 > volume #7 level 0.02771
    9064 
    9065 > volume #7 level 0.04405
    9066 
    9067 > volume #7 level 0.03924
    9068 
    9069 > volume #7 level 0.04789
    9070 
    9071 > volume #7 level 0.0575
    9072 
    9073 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3983_007_volume_map.mrc
    9074 
    9075 Opened cryosparc_P9_J3983_007_volume_map.mrc as #8, grid size 480,480,480,
    9076 pixel 0.732, shown at level 0.0105, step 2, values float32 
    9077 
    9078 > volume #8 level 0.0575
    9079 
    9080 > volume #8 level 0.04195
    9081 
    9082 > volume #7 level 0.03636
    9083 
    9084 > select add #7
    9085 
    9086 3 models selected 
    9087 
    9088 > ui mousemode right "rotate selected models"
    9089 
    9090 > view matrix models
    9091 > #3.3,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795,#7,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795
    9092 
    9093 > view matrix models
    9094 > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93,#7,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
    9095 
    9096 > fitmap #7 inMap #8
    9097 
    9098 Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
    9099 cryosparc_P9_J3983_007_volume_map.mrc using 49963 points 
    9100 correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7 
    9101 steps = 380, shift = 16.1, angle = 34.3 degrees 
    9102  
    9103 Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
    9104 cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates: 
    9105 Matrix rotation and translation 
    9106 -0.72583440 0.68279829 -0.08337219 201.41842056 
    9107 -0.29586248 -0.41930957 -0.85828018 446.74544623 
    9108 -0.62099100 -0.59830258 0.50636370 306.03816839 
    9109 Axis 0.22676305 0.46893301 -0.85362776 
    9110 Axis point 224.32984314 270.00684921 0.00000000 
    9111 Rotation angle (degrees) 145.02379031 
    9112 Shift along axis -6.07473264 
    9113  
    9114 
    9115 > fitmap #7 inMap #8
    9116 
    9117 Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
    9118 cryosparc_P9_J3983_007_volume_map.mrc using 49963 points 
    9119 correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7 
    9120 steps = 64, shift = 0.012, angle = 0.00824 degrees 
    9121  
    9122 Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
    9123 cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates: 
    9124 Matrix rotation and translation 
    9125 -0.72583244 0.68280184 -0.08336017 201.41856784 
    9126 -0.29596038 -0.41938679 -0.85820870 446.76271306 
    9127 -0.62094664 -0.59824441 0.50648682 306.00978970 
    9128 Axis 0.22673791 0.46887682 -0.85366530 
    9129 Axis point 224.32617617 269.99245085 0.00000000 
    9130 Rotation angle (degrees) 145.02139829 
    9131 Shift along axis -6.08403693 
    9132  
    9133 
    9134 > fitmap #7 inMap #8
    9135 
    9136 Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
    9137 cryosparc_P9_J3983_007_volume_map.mrc using 49963 points 
    9138 correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7 
    9139 steps = 44, shift = 0.0118, angle = 0.00629 degrees 
    9140  
    9141 Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
    9142 cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates: 
    9143 Matrix rotation and translation 
    9144 -0.72584163 0.68278694 -0.08340211 201.42434440 
    9145 -0.29586571 -0.41935773 -0.85825554 446.75301724 
    9146 -0.62098100 -0.59828178 0.50640054 306.02837341 
    9147 Axis 0.22676494 0.46890903 -0.85364043 
    9148 Axis point 224.32912008 270.00287478 0.00000000 
    9149 Rotation angle (degrees) 145.02471726 
    9150 Shift along axis -6.07568669 
    9151  
    9152 
    9153 > fitmap #7 inMap #8
    9154 
    9155 Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
    9156 cryosparc_P9_J3983_007_volume_map.mrc using 49963 points 
    9157 correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7 
    9158 steps = 100, shift = 0.0117, angle = 0.00919 degrees 
    9159  
    9160 Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
    9161 cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates: 
    9162 Matrix rotation and translation 
    9163 -0.72585579 0.68276216 -0.08348176 201.44447216 
    9164 -0.29589017 -0.41949591 -0.85817958 446.76049346 
    9165 -0.62095280 -0.59821318 0.50651615 305.99878042 
    9166 Axis 0.22676890 0.46883644 -0.85367925 
    9167 Axis point 224.32788267 269.98130269 0.00000000 
    9168 Rotation angle (degrees) 145.02655337 
    9169 Shift along axis -6.08586737 
    9170  
    9171 
    9172 > volume #8 level 0.0364
    9173 
    9174 > select subtract #7
    9175 
    9176 1 model selected 
    9177 
    9178 > view matrix models
    9179 > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
    9180 
    9181 > volume #7 level 0.06423
    9182 
    9183 > view matrix models
    9184 > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
    9185 
    9186 > volume #7 level 0.02003
    9187 
    9188 > volume #8 level 0.02571
    9189 
    9190 > volume #8 level 0.04417
    9191 
    9192 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3969_006_volume_map.mrc
    9193 
    9194 Opened cryosparc_P9_J3969_006_volume_map.mrc as #9, grid size 480,480,480,
    9195 pixel 0.732, shown at level 0.0103, step 2, values float32 
    9196 
    9197 > volume #9 level 0.03176
    9198 
    9199 > volume #9 level 0.01519
    9200 
    9201 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3951_008_volume_map.mrc
    9202 
    9203 Opened cryosparc_P9_J3951_008_volume_map.mrc as #10, grid size 480,480,480,
    9204 pixel 0.732, shown at level 0.0114, step 2, values float32 
    9205 
    9206 > volume #!8,10 hide
    9207 
    9208 > volume #10 level 0.03828
    9209 
    9210 > volume #10 level 0.02869
    9211 
    9212 > volume #10 level 0.04979
    9213 
    9214 > fitmap #1 inMap #10
    9215 
    9216 Fit map J3985_class_01_00049_volume.mrc in map
    9217 cryosparc_P9_J3951_008_volume_map.mrc using 6629 points 
    9218 correlation = 0.8689, correlation about mean = 0.602, overlap = 377 
    9219 steps = 96, shift = 1.6, angle = 4.19 degrees 
    9220  
    9221 Position of J3985_class_01_00049_volume.mrc (#1) relative to
    9222 cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates: 
    9223 Matrix rotation and translation 
    9224 0.99743315 -0.00176327 -0.07158214 11.61334330 
    9225 0.00282388 0.99988770 0.01471808 -3.39292521 
    9226 0.07154815 -0.01488244 0.99732611 -10.23271671 
    9227 Axis -0.20242295 -0.97879565 0.03136921 
    9228 Axis point 149.23497483 0.00000000 158.72238428 
    9229 Rotation angle (degrees) 4.19295196 
    9230 Shift along axis 0.64918094 
    9231  
    9232 
    9233 > fitmap #1 inMap #10
    9234 
    9235 Fit map J3985_class_01_00049_volume.mrc in map
    9236 cryosparc_P9_J3951_008_volume_map.mrc using 6629 points 
    9237 correlation = 0.8688, correlation about mean = 0.6019, overlap = 377 
    9238 steps = 40, shift = 0.0111, angle = 0.00583 degrees 
    9239  
    9240 Position of J3985_class_01_00049_volume.mrc (#1) relative to
    9241 cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates: 
    9242 Matrix rotation and translation 
    9243 0.99743292 -0.00175838 -0.07158540 11.60987325 
    9244 0.00281177 0.99988921 0.01461711 -3.38346500 
    9245 0.07155176 -0.01478087 0.99732736 -10.24684374 
    9246 Axis -0.20108561 -0.97907475 0.03126035 
    9247 Axis point 149.42296601 0.00000000 158.67147531 
    9248 Rotation angle (degrees) 4.19195597 
    9249 Shift along axis 0.65776684 
    9250  
    9251 
    9252 > fitmap #1 inMap #10
    9253 
    9254 Fit map J3985_class_01_00049_volume.mrc in map
    9255 cryosparc_P9_J3951_008_volume_map.mrc using 6629 points 
    9256 correlation = 0.8688, correlation about mean = 0.6019, overlap = 377 
    9257 steps = 60, shift = 0.00202, angle = 0.00304 degrees 
    9258  
    9259 Position of J3985_class_01_00049_volume.mrc (#1) relative to
    9260 cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates: 
    9261 Matrix rotation and translation 
    9262 0.99743293 -0.00175093 -0.07158545 11.60870841 
    9263 0.00280811 0.99988844 0.01467011 -3.38985788 
    9264 0.07155178 -0.01483347 0.99732658 -10.23757914 
    9265 Axis -0.20177899 -0.97893465 0.03117985 
    9266 Axis point 149.29375605 0.00000000 158.66352892 
    9267 Rotation angle (degrees) 4.19255884 
    9268 Shift along axis 0.65684980 
    9269  
    9270 
    9271 > fitmap #1 inMap #10
    9272 
    9273 Fit map J3985_class_01_00049_volume.mrc in map
    9274 cryosparc_P9_J3951_008_volume_map.mrc using 6629 points 
    9275 correlation = 0.8688, correlation about mean = 0.6019, overlap = 377 
    9276 steps = 96, shift = 0.002, angle = 0.00324 degrees 
    9277  
    9278 Position of J3985_class_01_00049_volume.mrc (#1) relative to
    9279 cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates: 
    9280 Matrix rotation and translation 
    9281 0.99743159 -0.00171901 -0.07160488 11.60617014 
    9282 0.00277352 0.99988913 0.01463001 -3.37850973 
    9283 0.07157180 -0.01479103 0.99732578 -10.24880751 
    9284 Axis -0.20118700 -0.97907100 0.03072081 
    9285 Axis point 149.40364660 0.00000000 158.57590880 
    9286 Rotation angle (degrees) 4.19313151 
    9287 Shift along axis 0.65793867 
    9288  
    9289 
    9290 > open
    9291 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_01_00048_volume.mrc
    9292 
    9293 Opened J3989_class_01_00048_volume.mrc as #11, grid size 128,128,128, pixel
    9294 2.74, shown at level 0.0696, step 1, values float32 
    9295 
    9296 > open
    9297 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_00_00048_volume.mrc
    9298 
    9299 Opened J3989_class_00_00048_volume.mrc as #12, grid size 128,128,128, pixel
    9300 2.74, shown at level 0.0695, step 1, values float32 
    9301 
    9302 > volume #!1,10-12 hide
    9303 
    9304 > volume #12 level 0.1515
    9305 
    9306 > volume #11 level 0.1326
    9307 
    9308 > volume #11 level 0.1548
    9309 
    9310 > volume #1 level 0.211
    9311 
    9312 > volume #2 level 0.1832
    9313 
    9314 > volume #!2 hide
    9315 
    9316 > open
    9317 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_01_00116_volume.mrc
    9318 
    9319 Opened J3968_class_01_00116_volume.mrc as #13, grid size 144,144,144, pixel
    9320 2.75, shown at level 0.0545, step 1, values float32 
    9321 
    9322 > open
    9323 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_00_00116_volume.mrc
    9324 
    9325 Opened J3968_class_00_00116_volume.mrc as #14, grid size 144,144,144, pixel
    9326 2.75, shown at level 0.0495, step 1, values float32 
    9327 
    9328 > volume #14 level 0.115
    9329 
    9330 > volume #13 level 0.1179
    9331 
    9332 > select add #13
    9333 
    9334 3 models selected 
    9335 
    9336 > hide #!14 models
    9337 
    9338 > fitmap #13 inMap #11
    9339 
    9340 Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc
    9341 using 15819 points 
    9342 correlation = 0.8706, correlation about mean = 0.722, overlap = 2919 
    9343 steps = 140, shift = 37.7, angle = 1.37 degrees 
    9344  
    9345 Position of J3968_class_01_00116_volume.mrc (#13) relative to
    9346 J3989_class_01_00048_volume.mrc (#11) coordinates: 
    9347 Matrix rotation and translation 
    9348 0.99971437 0.01959626 0.01368115 -28.66197852 
    9349 -0.01958627 0.99980780 -0.00086396 -16.84931847 
    9350 -0.01369545 0.00059576 0.99990604 -19.58306288 
    9351 Axis 0.03052447 0.57247681 -0.81935252 
    9352 Axis point -1036.02962297 1456.12966984 0.00000000 
    9353 Rotation angle (degrees) 1.37011058 
    9354 Shift along axis 5.52469615 
    9355  
    9356 
    9357 > fitmap #13 inMap #11
    9358 
    9359 Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc
    9360 using 15819 points 
    9361 correlation = 0.8705, correlation about mean = 0.7217, overlap = 2919 
    9362 steps = 56, shift = 0.023, angle = 0.0138 degrees 
    9363  
    9364 Position of J3968_class_01_00116_volume.mrc (#13) relative to
    9365 J3989_class_01_00048_volume.mrc (#11) coordinates: 
    9366 Matrix rotation and translation 
    9367 0.99971346 0.01976263 0.01350659 -28.68065746 
    9368 -0.01975270 0.99980452 -0.00086839 -16.82188386 
    9369 -0.01352112 0.00060135 0.99990840 -19.61515682 
    9370 Axis 0.03068551 0.56428859 -0.82500714 
    9371 Axis point -1031.91078715 1445.31671200 0.00000000 
    9372 Rotation angle (degrees) 1.37227811 
    9373 Shift along axis 5.81016679 
    9374  
    9375 
    9376 > fitmap #11 inMap #14
    9377 
    9378 Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
    9379 using 11649 points 
    9380 correlation = 0.8966, correlation about mean = 0.7157, overlap = 2894 
    9381 steps = 124, shift = 38, angle = 1.45 degrees 
    9382  
    9383 Position of J3989_class_01_00048_volume.mrc (#11) relative to
    9384 J3968_class_00_00116_volume.mrc (#14) coordinates: 
    9385 Matrix rotation and translation 
    9386 0.99969266 -0.02253533 -0.01033133 28.08037343 
    9387 0.02259070 0.99973088 0.00527456 16.14208619 
    9388 0.01020969 -0.00550634 0.99993272 21.38876177 
    9389 Axis -0.21247458 -0.40483111 0.88936287 
    9390 Axis point -815.69812369 1318.66977759 0.00000000 
    9391 Rotation angle (degrees) 1.45374188 
    9392 Shift along axis 6.52118636 
    9393  
    9394 
    9395 > fitmap #11 inMap #14
    9396 
    9397 Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
    9398 using 11649 points 
    9399 correlation = 0.8967, correlation about mean = 0.7151, overlap = 2889 
    9400 steps = 80, shift = 0.042, angle = 0.00904 degrees 
    9401  
    9402 Position of J3989_class_01_00048_volume.mrc (#11) relative to
    9403 J3968_class_00_00116_volume.mrc (#14) coordinates: 
    9404 Matrix rotation and translation 
    9405 0.99969400 -0.02251644 -0.01024267 28.07371662 
    9406 0.02257002 0.99973202 0.00514573 16.13692320 
    9407 0.01012406 -0.00537533 0.99993430 21.40764237 
    9408 Axis -0.20801043 -0.40266782 0.89139794 
    9409 Axis point -819.63745883 1320.26275326 0.00000000 
    9410 Rotation angle (degrees) 1.44915013 
    9411 Shift along axis 6.74528284 
    9412  
    9413 
    9414 > fitmap #11 inMap #14
    9415 
    9416 Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
    9417 using 11649 points 
    9418 correlation = 0.8965, correlation about mean = 0.7152, overlap = 2893 
    9419 steps = 80, shift = 0.0478, angle = 0.0308 degrees 
    9420  
    9421 Position of J3989_class_01_00048_volume.mrc (#11) relative to
    9422 J3968_class_00_00116_volume.mrc (#14) coordinates: 
    9423 Matrix rotation and translation 
    9424 0.99968804 -0.02285456 -0.01007459 28.12280975 
    9425 0.02291102 0.99972224 0.00552539 16.05278061 
    9426 0.00994551 -0.00575449 0.99993398 21.48943495 
    9427 Axis -0.22026445 -0.39093637 0.89367350 
    9428 Axis point -799.73209073 1306.33286302 0.00000000 
    9429 Rotation angle (degrees) 1.46723678 
    9430 Shift along axis 6.73446774 
    9431  
    9432 
    9433 > fitmap #11 inMap #14
    9434 
    9435 Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
    9436 using 11649 points 
    9437 correlation = 0.8965, correlation about mean = 0.7151, overlap = 2893 
    9438 steps = 64, shift = 0.00592, angle = 0.0116 degrees 
    9439  
    9440 Position of J3989_class_01_00048_volume.mrc (#11) relative to
    9441 J3968_class_00_00116_volume.mrc (#14) coordinates: 
    9442 Matrix rotation and translation 
    9443 0.99969172 -0.02267013 -0.01012540 28.09508155 
    9444 0.02272756 0.99972605 0.00559283 16.07389740 
    9445 0.00999584 -0.00582123 0.99993310 21.49281283 
    9446 Axis -0.22401656 -0.39490657 0.89099123 
    9447 Axis point -804.48634434 1314.55289352 0.00000000 
    9448 Rotation angle (degrees) 1.45982216 
    9449 Shift along axis 6.50845650 
    9450  
    9451 
    9452 > hide #!11 models
    9453 
    9454 > select subtract #13
    9455 
    9456 1 model selected 
    9457 
    9458 > volume #14 level 0.2241
    9459 
    9460 > volume #14 level 0.06262
    9461 
    9462 > volume #14 level 0.2241
    9463 
    9464 > volume #14 level 0.4248
    9465 
    9466 > volume #14 level 0.115
    9467 
    9468 > volume #14 level 0.1717
    9469 
    9470 > volume #14 level 0.211
    9471 
    9472 > volume #14 level 0.1237
    9473 
    9474 > volume #14 level 0.06698
    9475 
    9476 > volume #14 level 0.2764
    9477 
    9478 > volume #14 level 0.2241
    9479 
    9480 > volume #14 level 0.2197
    9481 
    9482 > volume #14 level 0.2808
    9483 
    9484 > view matrix models
    9485 > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
    9486 
    9487 > volume #14 level 0.1673
    9488 
    9489 > volume #14 level 0.211
    9490 
    9491 > view matrix models
    9492 > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
    9493 
    9494 [Repeated 2 time(s)]
    9495 
    9496 > volume #14 level 0.09752
    9497 
    9498 > volume #14 level 0.1804
    9499 
    9500 > volume #14 level 0.307
    9501 
    9502 > volume #14 level 0.08007
    9503 
    9504 > volume #14 level 0.1062
    9505 
    9506 > view matrix models
    9507 > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
    9508 
    9509 [Repeated 1 time(s)]
    9510 
    9511 > volume #14 level 0.1542
    9512 
    9513 > volume #14 level 0.1979
    9514 
    9515 > view matrix models
    9516 > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
    9517 
    9518 > volume #14 level 0.1499
    9519 
    9520 > volume #14 level 0.2066
    9521 
    9522 > volume #14 level 0.1019
    9523 
    9524 > volume #14 level 0.1542
    9525 
    9526 > volume #14 level 0.2022
    9527 
    9528 > view matrix models
    9529 > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
    9530 
    9531 > volume #14 level 0.115
    9532 
    9533 > volume #14 level 0.403
    9534 
    9535 > volume #14 level 0.1019
    9536 
    9537 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map.mrc
    9538 
    9539 Opened cryosparc_P9_J3967_007_volume_map.mrc as #15, grid size 324,324,324,
    9540 pixel 1.22, shown at level 0.0302, step 2, values float32 
    9541 
    9542 > volume #15 level 0.08332
    9543 
    9544 > volume #15 level 0.101
    9545 
    9546 > volume #15 level 0.08996
    9547 
    9548 > volume #15 level 0.07669
    9549 
    9550 > volume #15 level 0.09438
    9551 
    9552 > volume #15 level 0.163
    9553 
    9554 > volume #15 level 0.1696
    9555 
    9556 [Repeated 1 time(s)]Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density
    9557 threshold 0.169599 
    9558 Showing 17 region surfaces 
    9559 1009 watershed regions, grouped to 17 regions 
    9560 Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces 
    9561 Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density threshold 0.169599 
    9562 Showing 17 region surfaces 
    9563 1009 watershed regions, grouped to 17 regions 
    9564 Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces 
    9565 
    9566 > select #3.17
    9567 
    9568 1 model selected 
    9569 Deleted 1 regions 
    9570 
    9571 > select #3.3
    9572 
    9573 1 model selected 
    9574 
    9575 > select clear
    9576 
    9577 > select #3.1
    9578 
    9579 1 model selected 
    9580 
    9581 > select add #3.7
    9582 
    9583 2 models selected 
    9584 
    9585 > select add #3.8
    9586 
    9587 3 models selected 
    9588 
    9589 > select add #3.12
    9590 
    9591 4 models selected 
    9592 
    9593 > select add #3.10
    9594 
    9595 5 models selected 
    9596 
    9597 > select add #3.16
    9598 
    9599 6 models selected 
    9600 
    9601 > select add #3.2
    9602 
    9603 7 models selected 
    9604 
    9605 > select add #3.3
    9606 
    9607 8 models selected 
    9608 
    9609 > select add #3.11
    9610 
    9611 9 models selected 
    9612 
    9613 > select add #3.6
    9614 
    9615 10 models selected 
    9616 
    9617 > select add #3.4
    9618 
    9619 11 models selected 
    9620 
    9621 > select add #3.5
    9622 
    9623 12 models selected 
    9624 
    9625 > select subtract #3.2
    9626 
    9627 11 models selected 
    9628 
    9629 > select add #3.9
    9630 
    9631 12 models selected 
    9632 
    9633 > select clear
    9634 
    9635 Drag select of 1359, 48002 of 48056 triangles, 1356, 1362, 1341, 1360, 1345,
    9636 1335, 1339, 1350, 1357, 1358, 1344, 1347, 1281, 1361, 1338, 15
    9637 cryosparc_P9_J3967_007_volume_map.mrc 
    9638 
    9639 > view matrix models
    9640 > #15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.1,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.2,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.3,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.4,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.5,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.6,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.7,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.8,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.9,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.10,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.11,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.12,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.13,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.14,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.16,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796
    9641 
    9642 Saving 16 regions to mrc file... 
    9643 Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc as #16, grid size
    9644 73,125,114, pixel 1.22, shown at step 1, values float32 
    9645 Wrote cryosparc_P9_J3967_007_volume_map_16_regions.mrc 
    9646 
    9647 > volume resample #16 onGrid #15
    9648 
    9649 Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc resampled as #17, grid
    9650 size 324,324,324, pixel 1.22, shown at step 1, values float32 
    9651 
    9652 > hide #!3 models
    9653 
    9654 > volume #17 level 0.09743
    9655 
    9656 > save
    9657 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map_16_regions.mrc
    9658 > models #17
    9659 
    9660 > volume #16 level 0.296
    9661 
    9662 > volume #16 level 0.2176
    9663 
    9664 > volume #16 level 0.2393
    9665 
    9666 > close #16
    9667 
    9668 > close #17
    9669 
    9670 > volume #15 level 0.06784
    9671 
    9672 > volume #15 level 0.03687
    9673 
    9674 > volume #15 level 0.0966
    9675 
    9676 > volume #15 level 0.08111
    9677 
    9678 > volume #15 level 0.1254
    9679 
    9680 > view matrix models
    9681 > #15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.1,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.2,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.3,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.4,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.5,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.6,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.7,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.8,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.9,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.10,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.11,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.12,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.13,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.14,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.16,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69
    9682 
    9683 > close session
    9684 
    9685 > open
    9686 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_03_00142_volume.mrc
    9687 
    9688 Opened J3977_class_03_00142_volume.mrc as #1, grid size 128,128,128, pixel
    9689 3.09, shown at level 0.0569, step 1, values float32 
    9690 
    9691 > open
    9692 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_02_00142_volume.mrc
    9693 
    9694 Opened J3977_class_02_00142_volume.mrc as #2, grid size 128,128,128, pixel
    9695 3.09, shown at level 0.0652, step 1, values float32 
    9696 
    9697 > open
    9698 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_01_00142_volume.mrc
    9699 
    9700 Opened J3977_class_01_00142_volume.mrc as #3, grid size 128,128,128, pixel
    9701 3.09, shown at level 0.0644, step 1, values float32 
    9702 
    9703 > open
    9704 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_00_00142_volume.mrc
    9705 
    9706 Opened J3977_class_00_00142_volume.mrc as #4, grid size 128,128,128, pixel
    9707 3.09, shown at level 0.0511, step 1, values float32 
    9708 
    9709 > surface dust #1 size 30.9
    9710 
    9711 > surface dust #2 size 30.9
    9712 
    9713 > surface dust #3 size 30.9
    9714 
    9715 > surface dust #4 size 30.9
    9716 
    9717 > volume #!1-2,4 hide
    9718 
    9719 > select add #4
    9720 
    9721 2 models selected 
    9722 
    9723 > view matrix models
    9724 > #4,0.94781,0.16804,0.27096,-68.241,-0.31283,0.32602,0.8921,34.283,0.061569,-0.93031,0.36157,273.55
    9725 
    9726 > view matrix models
    9727 > #4,0.95967,0.13122,0.24861,-59.846,-0.27903,0.33713,0.89916,24.083,0.034174,-0.93227,0.36015,279.75
    9728 
    9729 > view matrix models
    9730 > #4,0.81403,-0.58022,0.026318,142.13,0.23948,0.37658,0.89489,-88.181,-0.52915,-0.72217,0.4455,340.15
    9731 
    9732 > volume #3 level 0.08997
    9733 
    9734 > volume #3 level 0.1412
    9735 
    9736 > volume #4 level 0.1357
    9737 
    9738 > view matrix models
    9739 > #4,-0.98182,-0.15393,0.11102,400.77,-0.16014,0.98586,-0.049341,48.503,-0.10186,-0.066224,-0.99259,395.11
    9740 
    9741 > view matrix models
    9742 > #4,-0.88503,0.34552,0.312,251.01,0.33497,0.93805,-0.088657,-33.002,-0.3233,0.026046,-0.94594,412.92
    9743 
    9744 > volume #4 level 0.3894
    9745 
    9746 > volume #4 z flip
    9747 
    9748 Expected a keyword 
    9749 
    9750 > volume #4 zflip
    9751 
    9752 Expected a keyword 
    9753 
    9754 > volume #4 flipNormals
    9755 
    9756 Missing "flipNormals" keyword's argument 
    9757 
    9758 > volume flip #4
    9759 
    9760 Opened J3977_class_00_00142_volume.mrc z flip as #5, grid size 128,128,128,
    9761 pixel 3.09, shown at step 1, values float32 
    9762 
    9763 > select #5
    9764 
    9765 2 models selected 
    9766 
    9767 > view matrix models
    9768 > #5,-0.85933,0.30635,0.40953,234.55,-0.2375,0.47014,-0.85004,313.88,-0.45294,-0.82772,-0.33125,480.43
    9769 
    9770 > fitmap #5 inMap #3
    9771 
    9772 Fit map J3977_class_00_00142_volume.mrc z flip in map
    9773 J3977_class_01_00142_volume.mrc using 4563 points 
    9774 correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457 
    9775 steps = 132, shift = 31.6, angle = 38.4 degrees 
    9776  
    9777 Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
    9778 J3977_class_01_00142_volume.mrc (#3) coordinates: 
    9779 Matrix rotation and translation 
    9780 -0.99116610 0.00155516 -0.13261718 420.28508914 
    9781 0.12896783 0.24454249 -0.96102354 304.65893499 
    9782 0.03093599 -0.96963731 -0.24258280 429.65932782 
    9783 Axis -0.04151142 -0.78819365 0.61402571 
    9784 Axis point 188.06887356 0.00000000 347.37550767 
    9785 Rotation angle (degrees) 174.04473730 
    9786 Shift along axis 6.24500964 
    9787  
    9788 
    9789 > fitmap #5 inMap #3
    9790 
    9791 Fit map J3977_class_00_00142_volume.mrc z flip in map
    9792 J3977_class_01_00142_volume.mrc using 4563 points 
    9793 correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457 
    9794 steps = 48, shift = 0.0213, angle = 0.0281 degrees 
    9795  
    9796 Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
    9797 J3977_class_01_00142_volume.mrc (#3) coordinates: 
    9798 Matrix rotation and translation 
    9799 -0.99117083 0.00165958 -0.13258052 420.24478315 
    9800 0.12894289 0.24500496 -0.96090909 304.53529817 
    9801 0.03088818 -0.96952039 -0.24305576 429.72894017 
    9802 Axis -0.04152874 -0.78834163 0.61383453 
    9803 Axis point 188.06053369 0.00000000 347.28922017 
    9804 Rotation angle (degrees) 174.04894559 
    9805 Shift along axis 6.25237502 
    9806  
    9807 
    9808 > volume #3 level 0.6852
    9809 
    9810 > volume #5 level 0.188
    9811 
    9812 > volume #3 level 0.1028
    9813 
    9814 > volume #3 level 0.138
    9815 
    9816 > volume #5 level 0.1598
    9817 
    9818 > volume #5 level 0.1679
    9819 
    9820 > volume #3 level 0.07077
    9821 
    9822 > volume #3 level 0.1988
    9823 
    9824 > volume #5 level 0.2806
    9825 
    9826 > volume #1 level 0.2265
    9827 
    9828 > fitmap #5 inMap #1
    9829 
    9830 Fit map J3977_class_00_00142_volume.mrc z flip in map
    9831 J3977_class_03_00142_volume.mrc using 6115 points 
    9832 correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909 
    9833 steps = 84, shift = 2.02, angle = 4.3 degrees 
    9834  
    9835 Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
    9836 J3977_class_03_00142_volume.mrc (#1) coordinates: 
    9837 Matrix rotation and translation 
    9838 -0.99754203 0.02498920 -0.06546303 405.36740821 
    9839 0.06977180 0.26807185 -0.96086906 311.85792420 
    9840 -0.00646256 -0.96307476 -0.26915648 438.89272991 
    9841 Axis -0.02976493 -0.79618479 0.60432096 
    9842 Axis point 191.78070263 0.00000000 342.51916349 
    9843 Rotation angle (degrees) 177.87659093 
    9844 Shift along axis 4.86980674 
    9845  
    9846 
    9847 > fitmap #5 inMap #1
    9848 
    9849 Fit map J3977_class_00_00142_volume.mrc z flip in map
    9850 J3977_class_03_00142_volume.mrc using 6115 points 
    9851 correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909 
    9852 steps = 44, shift = 0.0143, angle = 0.0162 degrees 
    9853  
    9854 Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
    9855 J3977_class_03_00142_volume.mrc (#1) coordinates: 
    9856 Matrix rotation and translation 
    9857 -0.99754942 0.02519611 -0.06527087 405.29719322 
    9858 0.06964248 0.26808225 -0.96087554 311.87541512 
    9859 -0.00671237 -0.96306647 -0.26918001 438.93275976 
    9860 Axis -0.02978898 -0.79618924 0.60431392 
    9861 Axis point 191.77820368 0.00000000 342.50753611 
    9862 Rotation angle (degrees) 177.89251633 
    9863 Shift along axis 4.86793646 
    9864  
    9865 
    9866 > volume #1 level 0.3043
    9867 
    9868 > volume #1 level 0.2513
    9869 
    9870 > volume sel hide
    9871 
    9872 > volume #1 level 0.1453
    9873 
    9874 > volume #4 level 0.1961
    9875 
    9876 > close #4
    9877 
    9878 > volume #5 level 0.2122
    9879 
    9880 > volume #1 level 0.2053
    9881 
    9882 > fitmap #5 inMap #1
    9883 
    9884 Fit map J3977_class_00_00142_volume.mrc z flip in map
    9885 J3977_class_03_00142_volume.mrc using 7583 points 
    9886 correlation = 0.9685, correlation about mean = 0.8754, overlap = 2994 
    9887 steps = 48, shift = 0.038, angle = 0.0347 degrees 
    9888  
    9889 Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
    9890 J3977_class_03_00142_volume.mrc (#1) coordinates: 
    9891 Matrix rotation and translation 
    9892 -0.99750974 0.02523858 -0.06585823 405.37295159 
    9893 0.07022047 0.26819842 -0.96080105 311.75529366 
    9894 -0.00658618 -0.96303302 -0.26930280 438.93804803 
    9895 Axis -0.02998281 -0.79622383 0.60425876 
    9896 Axis point 191.71948602 0.00000000 342.50624022 
    9897 Rotation angle (degrees) 177.86691692 
    9898 Shift along axis 4.85094606 
    9899  
    9900 
    9901 > fitmap #5 inMap #1
    9902 
    9903 Fit map J3977_class_00_00142_volume.mrc z flip in map
    9904 J3977_class_03_00142_volume.mrc using 7583 points 
    9905 correlation = 0.9684, correlation about mean = 0.8752, overlap = 2994 
    9906 steps = 44, shift = 0.0584, angle = 0.026 degrees 
    9907  
    9908 Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
    9909 J3977_class_03_00142_volume.mrc (#1) coordinates: 
    9910 Matrix rotation and translation 
    9911 -0.99752439 0.02490787 -0.06576214 405.45522347 
    9912 0.07003701 0.26791788 -0.96089271 311.91208460 
    9913 -0.00631494 -0.96311971 -0.26899910 438.84730228 
    9914 Axis -0.02982470 -0.79613522 0.60438332 
    9915 Axis point 191.77259653 0.00000000 342.57395662 
    9916 Rotation angle (degrees) 177.86037271 
    9917 Shift along axis 4.81521528 
    9918  
    9919 
    9920 > select subtract #5
    9921 
    9922 Nothing selected 
    9923 
    9924 > show #!5 models
    9925 
    9926 > volume #5 level 0.2525
    9927 
    9928 > hide #!5 models
    9929 
    9930 > show #!1 models
    9931 
    9932 > volume #1 level 0.2795
    9933 
    9934 > volume #1 level 0.276
    9935 
    9936 > volume #1 level 0.08519
    9937 
    9938 > volume #1 level 0.1665
    9939 
    9940 > volume #2 level 0.1703
    9941 
    9942 > volume #2 level 0.1327
    9943 
    9944 > volume #2 level 0.1928
    9945 
    9946 > volume #1 level 0.223
    9947 
    9948 > fitmap #1 inMap #2
    9949 
    9950 Fit map J3977_class_03_00142_volume.mrc in map J3977_class_02_00142_volume.mrc
    9951 using 7452 points 
    9952 correlation = 0.9571, correlation about mean = 0.8286, overlap = 2948 
    9953 steps = 84, shift = 1.2, angle = 2.65 degrees 
    9954  
    9955 Position of J3977_class_03_00142_volume.mrc (#1) relative to
    9956 J3977_class_02_00142_volume.mrc (#2) coordinates: 
    9957 Matrix rotation and translation 
    9958 0.99892948 -0.04344038 -0.01590040 11.73510950 
    9959 0.04345212 0.99905543 0.00039400 -9.71668965 
    9960 0.01586826 -0.00108448 0.99987350 -3.49169470 
    9961 Axis -0.01597843 -0.34333482 0.93907715 
    9962 Axis point 230.39658326 264.41720009 0.00000000 
    9963 Rotation angle (degrees) 2.65172634 
    9964 Shift along axis -0.13040143 
    9965  
    9966 
    9967 > hide #!1 models
    9968 
    9969 > volume #2 level 0.08769
    9970 
    9971 > volume #2 level 0.0539
    9972 
    9973 > volume #2 level 0.03889
    9974 
    9975 > volume #3 level 0.03877
    9976 
    9977 > volume #3 level 0.08037
    9978 
    9979 > volume #2 level 0.0539
    9980 
    9981 > volume #2 level 0.06517
    9982 
    9983 > volume #2 level 0.07267
    9984 
    9985 > volume #2 level 0.07643
    9986 
    9987 > volume #2 level 0.08018
    9988 
    9989 > volume #!2 hide
    9990 
    9991 > volume #5 level 0.06724
    9992 
    9993 > volume #5 level 0.1156
    9994 
    9995 > volume #5 level 0.5102
    9996 
    9997 > volume #5 level 0.3088
    9998 
    9999 > volume #5 level 0.2364
    10000 
    10001 > volume #5 level 0.2202
    10002 
    10003 > volume #5 level 0.2162
    10004 
    10005 > volume #5 level 0.2122
    10006 
    10007 [Repeated 1 time(s)]
    10008 
    10009 > volume #5 level 0.2082
    10010 
    10011 > volume #5 level 0.2041
    10012 
    10013 [Repeated 1 time(s)]
    10014 
    10015 > volume #5 level 0.2001
    10016 
    10017 > volume #5 level 0.1961
    10018 
    10019 [Repeated 1 time(s)]
    10020 
    10021 > volume #5 level 0.1921
    10022 
    10023 > volume #5 level 0.188
    10024 
    10025 > volume #5 level 0.184
    10026 
    10027 > volume #5 level 0.18
    10028 
    10029 > volume #5 level 0.176
    10030 
    10031 > volume #5 level 0.1719
    10032 
    10033 > volume #5 level 0.1679
    10034 
    10035 > volume #5 level 0.1639
    10036 
    10037 > volume #5 level 0.1598
    10038 
    10039 > volume #5 level 0.1558
    10040 
    10041 > volume #5 level 0.1518
    10042 
    10043 [Repeated 1 time(s)]
    10044 
    10045 > volume #5 level 0.1478
    10046 
    10047 > volume #5 level 0.1437
    10048 
    10049 > volume #5 level 0.1397
    10050 
    10051 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc
    10052 
    10053 Opened cryosparc_P9_J3954_006_volume_map.mrc as #4, grid size 324,324,324,
    10054 pixel 1.22, shown at level 0.0183, step 2, values float32 
    10055 
    10056 > volume #!4-5 hide
    10057 
    10058 > volume #4 level 0.06737
    10059 
    10060 > volume #4 level 0.08168
    10061 
    10062 > volume #4 level 0.03262
    10063 
    10064 > volume #4 level 0.0551
    10065 
    10066 > volume #4 level 0.0735
    10067 
    10068 > ui tool show Segmentations
    10069 
    10070 > ui view fourup
    10071 
    10072 Traceback (most recent call last): 
    10073 File
    10074 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10075 packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
    10076 _surfaceChosen 
    10077 self._update_position_label_text() 
    10078 File
    10079 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10080 packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
    10081 _update_position_label_text 
    10082 dicom_data = self.view.drawing.parent.data.dicom_data 
    10083 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    10084 AttributeError: 'MRCGrid' object has no attribute 'dicom_data' 
    10085  
    10086 AttributeError: 'MRCGrid' object has no attribute 'dicom_data' 
    10087  
    10088 File
    10089 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10090 packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
    10091 _update_position_label_text 
    10092 dicom_data = self.view.drawing.parent.data.dicom_data 
    10093 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    10094  
    10095 See log for complete Python traceback. 
    10096  
    10097 Traceback (most recent call last): 
    10098 File
    10099 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10100 packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
    10101 _surfaceChosen 
    10102 self._update_position_label_text() 
    10103 File
    10104 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10105 packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
    10106 _update_position_label_text 
    10107 dicom_data = self.view.drawing.parent.data.dicom_data 
    10108 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    10109 AttributeError: 'MRCGrid' object has no attribute 'dicom_data' 
    10110  
    10111 AttributeError: 'MRCGrid' object has no attribute 'dicom_data' 
    10112  
    10113 File
    10114 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10115 packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
    10116 _update_position_label_text 
    10117 dicom_data = self.view.drawing.parent.data.dicom_data 
    10118 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    10119  
    10120 See log for complete Python traceback. 
    10121  
    10122 Traceback (most recent call last): 
    10123 File
    10124 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10125 packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
    10126 _surfaceChosen 
    10127 self._update_position_label_text() 
    10128 File
    10129 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10130 packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
    10131 _update_position_label_text 
    10132 dicom_data = self.view.drawing.parent.data.dicom_data 
    10133 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    10134 AttributeError: 'MRCGrid' object has no attribute 'dicom_data' 
    10135  
    10136 AttributeError: 'MRCGrid' object has no attribute 'dicom_data' 
    10137  
    10138 File
    10139 "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    10140 packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
    10141 _update_position_label_text 
    10142 dicom_data = self.view.drawing.parent.data.dicom_data 
    10143 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    10144  
    10145 See log for complete Python traceback. 
    10146  
    10147 
    10148 > close session
    10149 
    10150 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc
    10151 
    10152 Opened cryosparc_P9_J3954_006_volume_map.mrc as #1, grid size 324,324,324,
    10153 pixel 1.22, shown at level 0.0183, step 2, values float32 
    10154 
    10155 > volume #1 level 0.03022
    10156 
    10157 > ui tool show "Segment Map"
    10158 
    10159 > volume #1 level 0.06089
    10160 
    10161 Segmenting cryosparc_P9_J3954_006_volume_map.mrc, density threshold 0.060885 
    10162 Showing 17 region surfaces 
    10163 1782 watershed regions, grouped to 17 regions 
    10164 Showing cryosparc_P9_J3954_006_volume_map.seg - 17 regions, 17 surfaces 
    10165 
    10166 > select #2.4
    10167 
    10168 1 model selected 
    10169 Saving 1 regions to mrc file... 
    10170 Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc as #3, grid size
    10171 42,45,72, pixel 1.22, shown at step 1, values float32 
    10172 Wrote cryosparc_P9_J3954_006_volume_map_region_2128.mrc 
    10173 
    10174 > volume resample #3 onGrid #1
    10175 
    10176 Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc resampled as #4, grid
    10177 size 324,324,324, pixel 1.22, shown at step 1, values float32 
    10178 
    10179 > save
    10180 > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map_region_2128.mrc
    10181 > models #4
    10182 
    10183 > volume #1 level 0.07315
    10184 
    10185 > close session
    10186 
    10187 > open
    10188 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo-
    10189 > coot-2.pdb
    10190 
    10191 Summary of feedback from opening
    10192 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo-
    10193 coot-2.pdb 
    10194 --- 
    10195 warnings | Duplicate atom serial number found: 8964 
    10196 Duplicate atom serial number found: 8965 
    10197 Duplicate atom serial number found: 8966 
    10198 Duplicate atom serial number found: 8967 
    10199 Duplicate atom serial number found: 8968 
    10200 26 messages similar to the above omitted 
    10201  
    10202 Chain information for V2_holo-coot-2.pdb #1 
    10203 --- 
    10204 Chain | Description 
    10205 A | No description available 
    10206 B | No description available 
    10207  
    10208 
    10209 > open
    10210 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo-
    10211 > coot-2.pdb
    10212 
    10213 Summary of feedback from opening
    10214 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo-
    10215 coot-2.pdb 
    10216 --- 
    10217 warnings | Duplicate atom serial number found: 8964 
    10218 Duplicate atom serial number found: 8965 
    10219 Duplicate atom serial number found: 8966 
    10220 Duplicate atom serial number found: 8967 
    10221 Duplicate atom serial number found: 8968 
    10222 26 messages similar to the above omitted 
    10223  
    10224 Chain information for V3_holo-coot-2.pdb #2 
    10225 --- 
    10226 Chain | Description 
    10227 A | No description available 
    10228 B | No description available 
    10229  
    10230 
    10231 > open
    10232 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo-
    10233 > coot-3.pdb
    10234 
    10235 Summary of feedback from opening
    10236 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo-
    10237 coot-3.pdb 
    10238 --- 
    10239 warnings | Duplicate atom serial number found: 8965 
    10240 Duplicate atom serial number found: 8966 
    10241 Duplicate atom serial number found: 8967 
    10242 Duplicate atom serial number found: 8968 
    10243 Duplicate atom serial number found: 8969 
    10244 30 messages similar to the above omitted 
    10245  
    10246 Chain information for V4_holo-coot-3.pdb #3 
    10247 --- 
    10248 Chain | Description 
    10249 A | No description available 
    10250 B | No description available 
    10251  
    10252 
    10253 > open
    10254 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo-
    10255 > coot-1.pdb
    10256 
    10257 Summary of feedback from opening
    10258 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo-
    10259 coot-1.pdb 
    10260 --- 
    10261 warnings | Duplicate atom serial number found: 8965 
    10262 Duplicate atom serial number found: 8966 
    10263 Duplicate atom serial number found: 8967 
    10264 Duplicate atom serial number found: 8968 
    10265 Duplicate atom serial number found: 8969 
    10266 17 messages similar to the above omitted 
    10267  
    10268 Chain information for V5_holo-coot-1.pdb #4 
    10269 --- 
    10270 Chain | Description 
    10271 A | No description available 
    10272 B | No description available 
    10273  
    10274 
    10275 > open
    10276 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo-
    10277 > coot-1.pdb
    10278 
    10279 Summary of feedback from opening
    10280 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo-
    10281 coot-1.pdb 
    10282 --- 
    10283 warnings | Duplicate atom serial number found: 8965 
    10284 Duplicate atom serial number found: 8966 
    10285 Duplicate atom serial number found: 8967 
    10286 Duplicate atom serial number found: 8968 
    10287 Duplicate atom serial number found: 8969 
    10288 20 messages similar to the above omitted 
    10289  
    10290 Chain information for V6_holo-coot-1.pdb #5 
    10291 --- 
    10292 Chain | Description 
    10293 A | No description available 
    10294 B | No description available 
    10295  
    10296 
    10297 > open
    10298 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V7_holo-
    10299 > coot-2.pdb
    10300 
    10301 Chain information for V7_holo-coot-2.pdb #6 
    10302 --- 
    10303 Chain | Description 
    10304 A | No description available 
    10305 B | No description available 
    10306  
    10307 
    10308 > open
    10309 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo-
    10310 > coot-0.pdb
    10311 
    10312 Summary of feedback from opening
    10313 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo-
    10314 coot-0.pdb 
    10315 --- 
    10316 warnings | Duplicate atom serial number found: 8965 
    10317 Duplicate atom serial number found: 8966 
    10318 Duplicate atom serial number found: 8967 
    10319 Duplicate atom serial number found: 8968 
    10320 Duplicate atom serial number found: 8969 
    10321 24 messages similar to the above omitted 
    10322  
    10323 Chain information for V9_holo-coot-0.pdb #7 
    10324 --- 
    10325 Chain | Description 
    10326 A | No description available 
    10327 B | No description available 
    10328  
    10329 
    10330 > open
    10331 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V10_holo-
    10332 > coot-1.pdb
    10333 
    10334 Chain information for V10_holo-coot-1.pdb #8 
    10335 --- 
    10336 Chain | Description 
    10337 A | No description available 
    10338 B | No description available 
    10339  
    10340 
    10341 > open
    10342 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo-
    10343 > coot-1.pdb
    10344 
    10345 Summary of feedback from opening
    10346 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo-
    10347 coot-1.pdb 
    10348 --- 
    10349 warnings | Duplicate atom serial number found: 8965 
    10350 Duplicate atom serial number found: 8966 
    10351 Duplicate atom serial number found: 8967 
    10352 Duplicate atom serial number found: 8968 
    10353 Duplicate atom serial number found: 8969 
    10354 29 messages similar to the above omitted 
    10355  
    10356 Chain information for V11_holo-coot-1.pdb #9 
    10357 --- 
    10358 Chain | Description 
    10359 A | No description available 
    10360 B | No description available 
    10361  
    10362 
    10363 > open
    10364 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V12_holo-
    10365 > coot-3.pdb
    10366 
    10367 Chain information for V12_holo-coot-3.pdb #10 
    10368 --- 
    10369 Chain | Description 
    10370 A | No description available 
    10371 B | No description available 
    10372  
    10373 
    10374 > open
    10375 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo-
    10376 > coot-1.pdb
    10377 
    10378 Summary of feedback from opening
    10379 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo-
    10380 coot-1.pdb 
    10381 --- 
    10382 warnings | Duplicate atom serial number found: 8964 
    10383 Duplicate atom serial number found: 8965 
    10384 Duplicate atom serial number found: 8966 
    10385 Duplicate atom serial number found: 8967 
    10386 Duplicate atom serial number found: 8968 
    10387 28 messages similar to the above omitted 
    10388  
    10389 Chain information for V14_holo-coot-1.pdb #11 
    10390 --- 
    10391 Chain | Description 
    10392 A | No description available 
    10393 B | No description available 
    10394  
    10395 
    10396 > open
    10397 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo-
    10398 > coot-1.pdb
    10399 
    10400 Summary of feedback from opening
    10401 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo-
    10402 coot-1.pdb 
    10403 --- 
    10404 warnings | Duplicate atom serial number found: 8965 
    10405 Duplicate atom serial number found: 8966 
    10406 Duplicate atom serial number found: 8968 
    10407 Duplicate atom serial number found: 8969 
    10408 Duplicate atom serial number found: 8970 
    10409 20 messages similar to the above omitted 
    10410  
    10411 Chain information for V15_holo-coot-1.pdb #12 
    10412 --- 
    10413 Chain | Description 
    10414 A | No description available 
    10415 B | No description available 
    10416  
    10417 
    10418 > open
    10419 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo-
    10420 > coot-3.pdb
    10421 
    10422 Summary of feedback from opening
    10423 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo-
    10424 coot-3.pdb 
    10425 --- 
    10426 warnings | Duplicate atom serial number found: 8965 
    10427 Duplicate atom serial number found: 8966 
    10428 Duplicate atom serial number found: 8967 
    10429 Duplicate atom serial number found: 8968 
    10430 Duplicate atom serial number found: 8969 
    10431 22 messages similar to the above omitted 
    10432  
    10433 Chain information for V17_holo-coot-3.pdb #13 
    10434 --- 
    10435 Chain | Description 
    10436 A | No description available 
    10437 B | No description available 
    10438  
    10439 
    10440 > open
    10441 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo-
    10442 > coot-1.pdb
    10443 
    10444 Summary of feedback from opening
    10445 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo-
    10446 coot-1.pdb 
    10447 --- 
    10448 warnings | Duplicate atom serial number found: 8965 
    10449 Duplicate atom serial number found: 8966 
    10450 Duplicate atom serial number found: 8967 
    10451 Duplicate atom serial number found: 8968 
    10452 Duplicate atom serial number found: 8969 
    10453 24 messages similar to the above omitted 
    10454  
    10455 Chain information for V18_holo-coot-1.pdb #14 
    10456 --- 
    10457 Chain | Description 
    10458 A | No description available 
    10459 B | No description available 
    10460  
    10461 
    10462 > open
    10463 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo-
    10464 > coot-6.pdb
    10465 
    10466 Summary of feedback from opening
    10467 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo-
    10468 coot-6.pdb 
    10469 --- 
    10470 warnings | Duplicate atom serial number found: 8965 
    10471 Duplicate atom serial number found: 8966 
    10472 Duplicate atom serial number found: 8967 
    10473 Duplicate atom serial number found: 8968 
    10474 Duplicate atom serial number found: 8969 
    10475 26 messages similar to the above omitted 
    10476  
    10477 Chain information for V19_holo-coot-6.pdb #15 
    10478 --- 
    10479 Chain | Description 
    10480 A | No description available 
    10481 B | No description available 
    10482  
    10483 
    10484 > open
    10485 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo-
    10486 > coot-2.pdb
    10487 
    10488 Summary of feedback from opening
    10489 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo-
    10490 coot-2.pdb 
    10491 --- 
    10492 warnings | Duplicate atom serial number found: 8964 
    10493 Duplicate atom serial number found: 8965 
    10494 Duplicate atom serial number found: 8966 
    10495 Duplicate atom serial number found: 8967 
    10496 Duplicate atom serial number found: 8968 
    10497 23 messages similar to the above omitted 
    10498  
    10499 Chain information for V21_holo-coot-2.pdb #16 
    10500 --- 
    10501 Chain | Description 
    10502 A | No description available 
    10503 B | No description available 
    10504  
    10505 
    10506 > open
    10507 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V23_holo-
    10508 > coot-2.pdb
    10509 
    10510 Chain information for V23_holo-coot-2.pdb #17 
    10511 --- 
    10512 Chain | Description 
    10513 A | No description available 
    10514 B | No description available 
    10515  
    10516 
    10517 > open
    10518 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo-
    10519 > coot-2.pdb
    10520 
    10521 Summary of feedback from opening
    10522 /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo-
    10523 coot-2.pdb 
    10524 --- 
    10525 warnings | Duplicate atom serial number found: 8964 
    10526 Duplicate atom serial number found: 8965 
    10527 Duplicate atom serial number found: 8966 
    10528 Duplicate atom serial number found: 8967 
    10529 Duplicate atom serial number found: 8968 
    10530 30 messages similar to the above omitted 
    10531  
    10532 Chain information for V25_holo-coot-2.pdb #18 
    10533 --- 
    10534 Chain | Description 
    10535 A | No description available 
    10536 B | No description available 
    10537  
    10538 Computing secondary structure 
    10539 [Repeated 2 time(s)]
    10540 
    10541 > select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274,
    10542 > 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257,
    10543 > 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293,
    10544 > 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81
    10545 
    10546 983 atoms, 1091 bonds, 45 residues, 1 model selected 
    10547 
    10548 > hide #2-18 target m
    10549 
    10550 > select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274,
    10551 > 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257,
    10552 > 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293,
    10553 > 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81
    10554 
    10555 983 atoms, 1091 bonds, 45 residues, 1 model selected 
    10556 
    10557 > select #8/A:100, 101, 102, 103,256, 257, 258,261, 271, 272, 273,26, 27, 28,
    10558 > 41,275, 276, 332, 333,275, 276, 333,49, 50, 51, 388, 389, 390,48, 50, 386,
    10559 > 387, 399,385, 386, 387,291, 292, 293, 294,277, 278, 329, 330, 331,275, 276,
    10560 > 333,113, 114, 136,15, 16, 17,25, 26, 274, 332,25, 26, 332,26, 274, 332,272,
    10561 > 273, 274,272, 273, 274, 275,273, 333,337, 338, 388,337, 388,382, 383,
    10562 > 384,49, 389, 390, 392, 393,49, 394, 395,49, 51, 394, 395,56, 57, 254,59, 60,
    10563 > 78, 79,61, 81, 250,80, 81
    10564 
    10565 1459 atoms, 1618 bonds, 67 residues, 1 model selected 
    10566 
    10567 > show #8 models
    10568 
    10569 > hide #1 models
    10570 
    10571 > select
    10572 > #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400
    10573 
    10574 3255 atoms, 3639 bonds, 151 residues, 1 model selected 
    10575 
    10576 > hide #8 models
    10577 
    10578 > show #1 models
    10579 
    10580 > show #2-18 target m
    10581 
    10582 > ui tool show Matchmaker
    10583 
    10584 > matchmaker #2-18 to #1 & sel matrix Nucleic
    10585 
    10586 Computing secondary structure 
    10587 [Repeated 17 time(s)]  Parameters 
    10588 --- 
    10589 Chain pairing | bb 
    10590 Alignment algorithm | Needleman-Wunsch 
    10591 Similarity matrix | Nucleic 
    10592 SS fraction | 0.3 
    10593 Gap open (HH/SS/other) | 18/18/6 
    10594 Gap extend | 1 
    10595 SS matrix |  |  | H | S | O 
    10596 ---|---|---|--- 
    10597 H | 6 | -9 | -6 
    10598 S |  | 6 | -6 
    10599 O |  |  | 4 
    10600 Iteration cutoff | 2 
    10601  
    10602 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
    10603 (#2), sequence alignment score = 604 
    10604 RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
    10605 0.413) 
    10606  
    10607 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
    10608 (#3), sequence alignment score = 604 
    10609 RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
    10610 0.322) 
    10611  
    10612 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
    10613 (#4), sequence alignment score = 604 
    10614 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
    10615 0.445) 
    10616  
    10617 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
    10618 (#5), sequence alignment score = 604 
    10619 RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
    10620 0.365) 
    10621  
    10622 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
    10623 (#6), sequence alignment score = 604 
    10624 RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
    10625 0.323) 
    10626  
    10627 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
    10628 (#7), sequence alignment score = 604 
    10629 RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
    10630 0.325) 
    10631  
    10632 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
    10633 (#8), sequence alignment score = 604 
    10634 RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
    10635 0.364) 
    10636  
    10637 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
    10638 (#9), sequence alignment score = 604 
    10639 RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
    10640 0.374) 
    10641  
    10642 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
    10643 (#10), sequence alignment score = 604 
    10644 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
    10645 0.367) 
    10646  
    10647 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
    10648 (#11), sequence alignment score = 604 
    10649 RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
    10650 0.464) 
    10651  
    10652 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A
    10653 (#12), sequence alignment score = 604 
    10654 RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs:
    10655 0.359) 
    10656  
    10657 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A
    10658 (#13), sequence alignment score = 604 
    10659 RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs:
    10660 0.441) 
    10661  
    10662 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A
    10663 (#14), sequence alignment score = 604 
    10664 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
    10665 0.367) 
    10666  
    10667 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A
    10668 (#15), sequence alignment score = 604 
    10669 RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs:
    10670 0.488) 
    10671  
    10672 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A
    10673 (#16), sequence alignment score = 604 
    10674 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
    10675 0.445) 
    10676  
    10677 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A
    10678 (#17), sequence alignment score = 604 
    10679 RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs:
    10680 0.368) 
    10681  
    10682 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A
    10683 (#18), sequence alignment score = 604 
    10684 RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs:
    10685 0.430) 
    10686  
    10687 
    10688 > select
    10689 
    10690 178904 atoms, 198000 bonds, 10136 residues, 18 models selected 
    10691 
    10692 > hide sel target a
    10693 
    10694 > select #1/C
    10695 
    10696 31 atoms, 31 residues, 1 model selected 
    10697 
    10698 > select #1-18/C
    10699 
    10700 542 atoms, 542 residues, 18 models selected 
    10701 
    10702 > show sel target ab
    10703 
    10704 > style sel sphere
    10705 
    10706 Changed 542 atom styles 
    10707 
    10708 > hide #2-18 target m
    10709 
    10710 > hide #1 models
    10711 
    10712 > show #1 models
    10713 
    10714 > show #2 models
    10715 
    10716 > hide #1 models
    10717 
    10718 > show #1 models
    10719 
    10720 > hide #1 models
    10721 
    10722 > show #3 models
    10723 
    10724 > hide #3 models
    10725 
    10726 > show #4 models
    10727 
    10728 > hide #4 models
    10729 
    10730 > show #5 models
    10731 
    10732 > hide #5 models
    10733 
    10734 > show #6 models
    10735 
    10736 > hide #6 models
    10737 
    10738 > show #7 models
    10739 
    10740 > hide #7 models
    10741 
    10742 > show #8 models
    10743 
    10744 > hide #8 models
    10745 
    10746 > show #9 models
    10747 
    10748 > hide #9 models
    10749 
    10750 > show #10 models
    10751 
    10752 > hide #10 models
    10753 
    10754 > show #11 models
    10755 
    10756 > show #12 models
    10757 
    10758 > show #13 models
    10759 
    10760 > hide #13 models
    10761 
    10762 > show #13 models
    10763 
    10764 > hide #13 models
    10765 
    10766 > show #14 models
    10767 
    10768 > hide #14 models
    10769 
    10770 > show #15 models
    10771 
    10772 > show #16 models
    10773 
    10774 > show #17 models
    10775 
    10776 > hide #17 models
    10777 
    10778 > show #18 models
    10779 
    10780 > select #1-18/C/7
    10781 
    10782 542 atoms, 542 residues, 18 models selected 
    10783 
    10784 > select #1-18/C:7
    10785 
    10786 18 atoms, 18 residues, 18 models selected 
    10787 
    10788 > select #1-18/C:4
    10789 
    10790 18 atoms, 18 residues, 18 models selected 
    10791 
    10792 > select #1-18/C:24
    10793 
    10794 12 atoms, 12 residues, 12 models selected 
    10795 
    10796 > select clear
    10797 
    10798 > hide #2 models
    10799 
    10800 > hide #11 models
    10801 
    10802 > hide #12 models
    10803 
    10804 > hide #15 models
    10805 
    10806 > hide #16 models
    10807 
    10808 > hide #18 models
    10809 
    10810 > show #1 models
    10811 
    10812 > show #2 models
    10813 
    10814 > hide #2 models
    10815 
    10816 > show #2 models
    10817 
    10818 > hide #2 models
    10819 
    10820 > show #3 models
    10821 
    10822 > show #2 models
    10823 
    10824 > show #4 models
    10825 
    10826 > show #5 models
    10827 
    10828 > hide #5 models
    10829 
    10830 > show #5 models
    10831 
    10832 > show #6 models
    10833 
    10834 > show #7 models
    10835 
    10836 > show #8 models
    10837 
    10838 > show #9 models
    10839 
    10840 > show #10 models
    10841 
    10842 > show #11 models
    10843 
    10844 > show #12 models
    10845 
    10846 > show #13 models
    10847 
    10848 > show #14 models
    10849 
    10850 > show #15 models
    10851 
    10852 > show #16 models
    10853 
    10854 > show #17 models
    10855 
    10856 > show #18 models
    10857 
    10858 > set bgColor white
    10859 
    10860 > select #1-18/A
    10861 
    10862 161316 atoms, 180684 bonds, 7506 residues, 18 models selected 
    10863 
    10864 > ui tool show "Color Actions"
    10865 
    10866 > color sel light slate gray
    10867 
    10868 > select #1-18/B
    10869 
    10870 17046 atoms, 17316 bonds, 2088 residues, 18 models selected 
    10871 
    10872 > ui tool show "Color Actions"
    10873 
    10874 > color sel plum
    10875 
    10876 > surface sel
    10877 
    10878 > surface hidePatches (#!1-18 & sel)
    10879 
    10880 > select #1/B
    10881 
    10882 947 atoms, 962 bonds, 116 residues, 1 model selected 
    10883 
    10884 > surface (#!1 & sel)
    10885 
    10886 > surface hidePatches (#!1 & sel)
    10887 
    10888 > surface (#!1 & sel)
    10889 
    10890 > coulombic sel
    10891 
    10892 Using Amber 20 recommended default charges and atom types for standard
    10893 residues 
    10894 Coulombic values for V2_holo-coot-2.pdb_B SES surface #1.1: minimum, -9.82,
    10895 mean 5.09, maximum 22.28 
    10896 To also show corresponding color key, enter the above coulombic command and
    10897 add key true 
    10898 
    10899 > hide #!1 models
    10900 
    10901 > show #!1 models
    10902 
    10903 > hide #!1 models
    10904 
    10905 > show #!1 models
    10906 
    10907 > surface hidePatches (#!1 & sel)
    10908 
    10909 > select #1-18/C:1
    10910 
    10911 7 atoms, 7 residues, 7 models selected 
    10912 
    10913 > select #1-18/A:50,389,390
    10914 
    10915 1188 atoms, 1314 bonds, 54 residues, 18 models selected 
    10916 
    10917 > cartoon hide sel
    10918 
    10919 > show sel target ab
    10920 
    10921 > hide (sel-residues & (protein|nucleic)) target a
    10922 
    10923 > cartoon hide sel-residues
    10924 
    10925 > show (sel-residues & backbone) target ab
    10926 
    10927 > hide sel target a
    10928 
    10929 > hide (sel-residues & (protein|nucleic)) target a
    10930 
    10931 > cartoon hide sel-residues
    10932 
    10933 > show (sel-residues & backbone) target ab
    10934 
    10935 > hide (sel-residues & (protein|nucleic)) target a
    10936 
    10937 > cartoon hide sel-residues
    10938 
    10939 > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
    10940 
    10941 > show (sel-residues & sidechain) target ab
    10942 
    10943 > hide (sel-residues & (protein|nucleic)) target a
    10944 
    10945 > cartoon hide sel-residues
    10946 
    10947 > show (sel-residues & backbone) target ab
    10948 
    10949 > hide sel target a
    10950 
    10951 > hide (sel-residues & (protein|nucleic)) target a
    10952 
    10953 > cartoon hide sel-residues
    10954 
    10955 > show (sel-residues & backbone) target ab
    10956 
    10957 > nucleotides sel atoms
    10958 
    10959 > style nucleic & sel stick
    10960 
    10961 Changed 1188 atom styles 
    10962 
    10963 > select #1-18/A:7
    10964 
    10965 360 atoms, 378 bonds, 18 residues, 18 models selected 
    10966 
    10967 > select #1-18/A:50,389,390
    10968 
    10969 1188 atoms, 1314 bonds, 54 residues, 18 models selected 
    10970 
    10971 > color sel red
    10972 
    10973 > select #6/A:392
    10974 
    10975 22 atoms, 24 bonds, 1 residue, 1 model selected 
    10976 
    10977 > select #15/A:393
    10978 
    10979 20 atoms, 21 bonds, 1 residue, 1 model selected 
    10980 
    10981 > select #3/C:68@MG
    10982 
    10983 1 atom, 1 residue, 1 model selected 
    10984 
    10985 > select up
    10986 
    10987 35 atoms, 35 residues, 1 model selected 
    10988 
    10989 > select #1-18/C:7
    10990 
    10991 18 atoms, 18 residues, 18 models selected 
    10992 
    10993 > ui tool show "Selection Inspector"
    10994 
    10995 > size sel atomRadius 0.7
    10996 
    10997 Changed 18 atom radii 
    10998 
    10999 > color sel red
    11000 
    11001 > select #1-18/A:50,389,390
    11002 
    11003 1188 atoms, 1314 bonds, 54 residues, 18 models selected 
    11004 
    11005 > ui tool show "Color Actions"
    11006 
    11007 > color sel brown
    11008 
    11009 > color sel coral
    11010 
    11011 > color sel orange
    11012 
    11013 > color sel coral
    11014 
    11015 > color sel tomato
    11016 
    11017 > color sel coral
    11018 
    11019 > select #14/C:80@MG
    11020 
    11021 1 atom, 1 residue, 1 model selected 
    11022 
    11023 > select add #13/C:7@MG
    11024 
    11025 2 atoms, 2 residues, 2 models selected 
    11026 
    11027 > ui tool show Distances
    11028 
    11029 > distance #14/C:80@MG #13/C:7@MG
    11030 
    11031 Distance between V18_holo-coot-1.pdb #14/C MG 80 MG and V17_holo-coot-3.pdb
    11032 #13/C MG 7 MG: 14.313Å 
    11033 
    11034 > select #10/C:80@MG
    11035 
    11036 1 atom, 1 residue, 1 model selected 
    11037 
    11038 > select add #12/C:7@MG
    11039 
    11040 2 atoms, 2 residues, 2 models selected 
    11041 
    11042 > distance #10/C:80@MG #12/C:7@MG
    11043 
    11044 Distance between V12_holo-coot-3.pdb #10/C MG 80 MG and V15_holo-coot-1.pdb
    11045 #12/C MG 7 MG: 12.866Å 
    11046 
    11047 > hide #!1-18 target m
    11048 
    11049 > show #!1 models
    11050 
    11051 > show #!2 models
    11052 
    11053 > show #!3 models
    11054 
    11055 > show #!4 models
    11056 
    11057 > show #!5 models
    11058 
    11059 > show #!6 models
    11060 
    11061 > hide #!6 models
    11062 
    11063 > show #!6 models
    11064 
    11065 > show #!7 models
    11066 
    11067 > show #!8 models
    11068 
    11069 > show #!9 models
    11070 
    11071 > show #!10 models
    11072 
    11073 > hide #!10 models
    11074 
    11075 > show #!10 models
    11076 
    11077 > show #!11 models
    11078 
    11079 > show #!12 models
    11080 
    11081 > hide #!12 models
    11082 
    11083 > show #!12 models
    11084 
    11085 > show #!13 models
    11086 
    11087 > show #!14 models
    11088 
    11089 > hide #!6 models
    11090 
    11091 > show #!6 models
    11092 
    11093 > hide #!6 models
    11094 
    11095 > show #!6 models
    11096 
    11097 > hide #!6 models
    11098 
    11099 > show #!6 models
    11100 
    11101 > select #6/C:24@MG
    11102 
    11103 1 atom, 1 residue, 1 model selected 
    11104 
    11105 > select add #6/C:75@MG
    11106 
    11107 2 atoms, 2 residues, 1 model selected 
    11108 
    11109 > distance #6/C:24@MG #6/C:75@MG
    11110 
    11111 Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and MG 75 MG: 6.929Å 
    11112 
    11113 > select #10/C:84@MG
    11114 
    11115 1 atom, 1 residue, 1 model selected 
    11116 
    11117 > select add #6/C:24@MG
    11118 
    11119 2 atoms, 2 residues, 2 models selected 
    11120 
    11121 > distance #10/C:84@MG #6/C:24@MG
    11122 
    11123 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V7_holo-coot-2.pdb
    11124 #6/C MG 24 MG: 3.368Å 
    11125 
    11126 > select #6/C:24@MG
    11127 
    11128 1 atom, 1 residue, 1 model selected 
    11129 
    11130 > select add #5/C:7@MG
    11131 
    11132 2 atoms, 2 residues, 2 models selected 
    11133 
    11134 > distance #6/C:24@MG #5/C:7@MG
    11135 
    11136 Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and V6_holo-coot-1.pdb #5/C
    11137 MG 7 MG: 7.527Å 
    11138 
    11139 > select #9/C:4@MG
    11140 
    11141 1 atom, 1 residue, 1 model selected 
    11142 
    11143 > select add #12/C:7@MG
    11144 
    11145 2 atoms, 2 residues, 2 models selected 
    11146 
    11147 > distance #9/C:4@MG #12/C:7@MG
    11148 
    11149 Distance between V11_holo-coot-1.pdb #9/C MG 4 MG and V15_holo-coot-1.pdb
    11150 #12/C MG 7 MG: 9.036Å 
    11151 
    11152 > ~distance #6/C:24@MG #6/C:75@MG
    11153 
    11154 > ~distance #9/C:4@MG #12/C:7@MG
    11155 
    11156 > ~distance #14/C:80@MG #13/C:7@MG
    11157 
    11158 > ~distance #10/C:84@MG #6/C:24@MG
    11159 
    11160 > ~distance #6/C:24@MG #5/C:7@MG
    11161 
    11162 > ~distance #10/C:80@MG #12/C:7@MG
    11163 
    11164 > select #1-18/A:50,389,390
    11165 
    11166 1188 atoms, 1314 bonds, 54 residues, 18 models selected 
    11167 
    11168 > ui tool show "Color Actions"
    11169 
    11170 > color sel tomato
    11171 
    11172 > color sel chocolate
    11173 
    11174 > color sel fire brick
    11175 
    11176 > color sel coral
    11177 
    11178 > color sel goldenrod
    11179 
    11180 > color (#!1-14 & sel) #ff2600ff
    11181 
    11182 > color sel sienna
    11183 
    11184 > color sel cyan
    11185 
    11186 > color sel medium blue
    11187 
    11188 > color sel cornflower blue
    11189 
    11190 > select #1-18/C:7
    11191 
    11192 18 atoms, 18 residues, 18 models selected 
    11193 
    11194 > color (#!1-14 & sel) blue
    11195 
    11196 > color sel red
    11197 
    11198 > open
    11199 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/pdb_models_YTZ/holoES-
    11200 > pretRNA-5mM-Ca/Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
    11201 
    11202 Chain information for Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
    11203 #19 
    11204 --- 
    11205 Chain | Description 
    11206 A | No description available 
    11207 B | No description available 
    11208 C | No description available 
    11209 E | No description available 
    11210  
    11211 Computing secondary structure 
    11212 
    11213 > select up
    11214 
    11215 542 atoms, 542 residues, 18 models selected 
    11216 
    11217 > select up
    11218 
    11219 178904 atoms, 198000 bonds, 10136 residues, 18 models selected 
    11220 
    11221 > select
    11222 > #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400
    11223 
    11224 3255 atoms, 3639 bonds, 151 residues, 1 model selected 
    11225 
    11226 > ui tool show Matchmaker
    11227 
    11228 > matchmaker #19 to #1 & sel matrix Nucleic
    11229 
    11230 Computing secondary structure 
    11231 [Repeated 1 time(s)]  Parameters 
    11232 --- 
    11233 Chain pairing | bb 
    11234 Alignment algorithm | Needleman-Wunsch 
    11235 Similarity matrix | Nucleic 
    11236 SS fraction | 0.3 
    11237 Gap open (HH/SS/other) | 18/18/6 
    11238 Gap extend | 1 
    11239 SS matrix |  |  | H | S | O 
    11240 ---|---|---|--- 
    11241 H | 6 | -9 | -6 
    11242 S |  | 6 | -6 
    11243 O |  |  | 4 
    11244 Iteration cutoff | 2 
    11245  
    11246 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
    11247 coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
    11248 604 
    11249 RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs:
    11250 0.766) 
    11251  
    11252 
    11253 > select #19
    11254 
    11255 12016 atoms, 13315 bonds, 661 residues, 1 model selected 
    11256 
    11257 > hide sel target a
    11258 
    11259 > select #19/C
    11260 
    11261 1889 atoms, 2107 bonds, 89 residues, 1 model selected 
    11262 
    11263 > hide #19 models
    11264 
    11265 > show #19 models
    11266 
    11267 > hide #19 models
    11268 
    11269 > show #19 models
    11270 
    11271 > color sel yellow
    11272 
    11273 > select #19/D
    11274 
    11275 30 atoms, 30 residues, 1 model selected 
    11276 
    11277 > show sel target ab
    11278 
    11279 > hide #19 models
    11280 
    11281 > show #19 models
    11282 
    11283 > hide #19 models
    11284 
    11285 > show #19 models
    11286 
    11287 > select #10/C:84@MG
    11288 
    11289 1 atom, 1 residue, 1 model selected 
    11290 
    11291 > select clear
    11292 
    11293 > select #10/C:84@MG
    11294 
    11295 1 atom, 1 residue, 1 model selected 
    11296 
    11297 > select add #11/A:390@OP2
    11298 
    11299 2 atoms, 2 residues, 2 models selected 
    11300 
    11301 > distance #10/C:84@MG #11/A:390@OP2
    11302 
    11303 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb
    11304 #11/A A 390 OP2: 3.278Å 
    11305 
    11306 > select #10/C:84@MG
    11307 
    11308 1 atom, 1 residue, 1 model selected 
    11309 
    11310 > select #19/D:5@CA
    11311 
    11312 1 atom, 1 residue, 1 model selected 
    11313 
    11314 > select add #10/C:84@MG
    11315 
    11316 2 atoms, 2 residues, 2 models selected 
    11317 
    11318 > distance #19/D:5@CA #10/C:84@MG
    11319 
    11320 Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
    11321 #19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.302Å 
    11322 
    11323 > select #10/C:84@MG
    11324 
    11325 1 atom, 1 residue, 1 model selected 
    11326 
    11327 > select add #19/D:30@CA
    11328 
    11329 2 atoms, 2 residues, 2 models selected 
    11330 
    11331 > distance #10/C:84@MG #19/D:30@CA
    11332 
    11333 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
    11334 Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 30 CA:
    11335 7.802Å 
    11336 
    11337 > hide #19 models
    11338 
    11339 > hide #!10 models
    11340 
    11341 > show #!10 models
    11342 
    11343 > hide #!10 models
    11344 
    11345 > show #!10 models
    11346 
    11347 > hide #!10 models
    11348 
    11349 > show #!10 models
    11350 
    11351 > hide #!10 models
    11352 
    11353 > show #!10 models
    11354 
    11355 > select #13/C:24@MG
    11356 
    11357 1 atom, 1 residue, 1 model selected 
    11358 
    11359 > select #9/C:24@MG
    11360 
    11361 1 atom, 1 residue, 1 model selected 
    11362 
    11363 > select add #10/C:84@MG
    11364 
    11365 2 atoms, 2 residues, 2 models selected 
    11366 
    11367 > distance #9/C:24@MG #10/C:84@MG
    11368 
    11369 Distance between V11_holo-coot-1.pdb #9/C MG 24 MG and V12_holo-coot-3.pdb
    11370 #10/C MG 84 MG: 3.570Å 
    11371 
    11372 > select #10/C:84@MG
    11373 
    11374 1 atom, 1 residue, 1 model selected 
    11375 
    11376 > hide #!1-14 target m
    11377 
    11378 > show #!12 models
    11379 
    11380 > show #19 models
    11381 
    11382 > hide #19 models
    11383 
    11384 > show #19 models
    11385 
    11386 > hide #19 models
    11387 
    11388 > hide #!12 models
    11389 
    11390 > show #!10 models
    11391 
    11392 > show #19 models
    11393 
    11394 > select #19/C:0
    11395 
    11396 20 atoms, 21 bonds, 1 residue, 1 model selected 
    11397 
    11398 > select #19/C:1
    11399 
    11400 23 atoms, 25 bonds, 1 residue, 1 model selected 
    11401 
    11402 > select add #19/C:0
    11403 
    11404 43 atoms, 46 bonds, 2 residues, 1 model selected 
    11405 
    11406 > hide #19 models
    11407 
    11408 > show #!1-18 target m
    11409 
    11410 > select #10/C:80@MG
    11411 
    11412 1 atom, 1 residue, 1 model selected 
    11413 
    11414 > select clear
    11415 
    11416 > show #19 models
    11417 
    11418 > hide #19 models
    11419 
    11420 > show #19 models
    11421 
    11422 > hide #19 models
    11423 
    11424 > show #19 models
    11425 
    11426 > hide #19 models
    11427 
    11428 > select #1-18/
    11429 
    11430 Expected an objects specifier or a keyword 
    11431 
    11432 > select #1-18
    11433 
    11434 178904 atoms, 198000 bonds, 2 pseudobonds, 10136 residues, 19 models selected 
    11435 
    11436 > select #1-18/C
    11437 
    11438 542 atoms, 1 pseudobond, 542 residues, 19 models selected 
    11439 
    11440 > ui tool show "Color Actions"
    11441 
    11442 > color sel forest green
    11443 
    11444 > select #1-18/C:7
    11445 
    11446 18 atoms, 18 residues, 18 models selected 
    11447 
    11448 > ui tool show "Color Actions"
    11449 
    11450 > color sel dark red
    11451 
    11452 [Repeated 1 time(s)]
    11453 
    11454 > color sel maroon
    11455 
    11456 > color sel dark red
    11457 
    11458 > ui tool show "Selection Inspector"
    11459 
    11460 > ~distance #10/C:84@MG #11/A:390@OP2
    11461 
    11462 > ~distance #19/D:5@CA #10/C:84@MG
    11463 
    11464 > ~distance #9/C:24@MG #10/C:84@MG
    11465 
    11466 > ~distance #10/C:84@MG #19/D:30@CA
    11467 
    11468 > select #10/C:84@MG
    11469 
    11470 1 atom, 1 residue, 1 model selected 
    11471 
    11472 > select add #17/C:87@MG
    11473 
    11474 2 atoms, 2 residues, 2 models selected 
    11475 
    11476 > select #1-18/C
    11477 
    11478 542 atoms, 542 residues, 18 models selected 
    11479 
    11480 > ui tool show "Selection Inspector"
    11481 
    11482 > size sel atomRadius 0.7
    11483 
    11484 Changed 542 atom radii 
    11485 
    11486 > select #13/C:22@MG
    11487 
    11488 1 atom, 1 residue, 1 model selected 
    11489 
    11490 > select #1-18/C:9
    11491 
    11492 16 atoms, 16 residues, 16 models selected 
    11493 
    11494 > color sel blue
    11495 
    11496 > show #19 models
    11497 
    11498 > hide #19 models
    11499 
    11500 > show #19 models
    11501 
    11502 > hide #19 models
    11503 
    11504 > show #19 models
    11505 
    11506 > hide #19 models
    11507 
    11508 > show #19 models
    11509 
    11510 > hide #19 models
    11511 
    11512 > show #19 models
    11513 
    11514 > select #18/C:62@MG
    11515 
    11516 1 atom, 1 residue, 1 model selected 
    11517 
    11518 > select add #19/A:279
    11519 
    11520 21 atoms, 21 bonds, 2 residues, 2 models selected 
    11521 
    11522 > select #19/C:3
    11523 
    11524 23 atoms, 25 bonds, 1 residue, 1 model selected 
    11525 
    11526 > select #1-18/C:12
    11527 
    11528 17 atoms, 17 residues, 17 models selected 
    11529 
    11530 > color sel blue
    11531 
    11532 > select #18/C:62@MG
    11533 
    11534 1 atom, 1 residue, 1 model selected 
    11535 
    11536 > select add #19/C:3
    11537 
    11538 24 atoms, 25 bonds, 2 residues, 2 models selected 
    11539 
    11540 > select #19/C:3
    11541 
    11542 23 atoms, 25 bonds, 1 residue, 1 model selected 
    11543 
    11544 > show sel target ab
    11545 
    11546 > cartoon hide sel
    11547 
    11548 > select #19/C:3@C5'
    11549 
    11550 1 atom, 1 residue, 1 model selected 
    11551 
    11552 > select add #18/C:62@MG
    11553 
    11554 2 atoms, 2 residues, 2 models selected 
    11555 
    11556 > distance #19/C:3@C5' #18/C:62@MG
    11557 
    11558 Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
    11559 #19/C G 3 C5' and V25_holo-coot-2.pdb #18/C MG 62 MG: 7.071Å 
    11560 
    11561 > view matrix models
    11562 > #18,0.99985,0.00571,-0.016139,1.607,-0.0060653,0.99974,-0.02205,5.6923,0.016009,0.022145,0.99963,-5.4963,#19,-0.96809,0.078949,-0.23783,410.8,0.24041,0.024802,-0.97035,327.08,-0.070709,-0.99657,-0.042991,409.72
    11563 
    11564 > view matrix models
    11565 > #18,0.98188,-0.025202,-0.18781,39.726,0.0089682,0.99619,-0.086791,14.256,0.18928,0.083534,0.97836,-47.209,#19,-0.9475,0.24905,-0.20055,362.29,0.2289,0.090348,-0.96925,314.7,-0.22327,-0.96427,-0.14261,451.61
    11566 
    11567 > view matrix models
    11568 > #18,0.98928,0.0045084,-0.14599,25.485,-0.014636,0.99755,-0.068373,15.45,0.14533,0.069777,0.98692,-37.485,#19,-0.95027,0.20788,-0.2319,377.78,0.25102,0.070488,-0.96541,313.97,-0.18434,-0.97561,-0.11916,442
    11569 
    11570 > view matrix models
    11571 > #18,0.98454,-0.024891,-0.17338,36.644,0.017984,0.99899,-0.041293,4.3816,0.17423,0.037537,0.98399,-35.839,#19,-0.95088,0.23482,-0.20172,366.2,0.21806,0.045516,-0.97487,327.75,-0.21974,-0.97097,-0.094484,443.7
    11572 
    11573 > view matrix models
    11574 > #18,0.98484,0.054997,-0.16452,19.343,-0.062648,0.99717,-0.041676,20.275,0.16176,0.051351,0.98549,-36.422,#19,-0.93307,0.22625,-0.27964,379.17,0.29591,0.040826,-0.95434,309.51,-0.2045,-0.97321,-0.10504,443.16
    11575 
    11576 > matchmaker #!2-11 to #1 & sel matrix Nucleic
    11577 
    11578 No 'to' model specified 
    11579 
    11580 > select
    11581 > #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400
    11582 
    11583 3255 atoms, 3639 bonds, 151 residues, 1 model selected 
    11584 
    11585 > matchmaker #!2-11 to #1 & sel matrix Nucleic
    11586 
    11587 Computing secondary structure 
    11588 [Repeated 10 time(s)]  Parameters 
    11589 --- 
    11590 Chain pairing | bb 
    11591 Alignment algorithm | Needleman-Wunsch 
    11592 Similarity matrix | Nucleic 
    11593 SS fraction | 0.3 
    11594 Gap open (HH/SS/other) | 18/18/6 
    11595 Gap extend | 1 
    11596 SS matrix |  |  | H | S | O 
    11597 ---|---|---|--- 
    11598 H | 6 | -9 | -6 
    11599 S |  | 6 | -6 
    11600 O |  |  | 4 
    11601 Iteration cutoff | 2 
    11602  
    11603 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
    11604 (#2), sequence alignment score = 604 
    11605 RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
    11606 0.413) 
    11607  
    11608 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
    11609 (#3), sequence alignment score = 604 
    11610 RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
    11611 0.322) 
    11612  
    11613 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
    11614 (#4), sequence alignment score = 604 
    11615 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
    11616 0.445) 
    11617  
    11618 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
    11619 (#5), sequence alignment score = 604 
    11620 RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
    11621 0.365) 
    11622  
    11623 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
    11624 (#6), sequence alignment score = 604 
    11625 RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
    11626 0.323) 
    11627  
    11628 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
    11629 (#7), sequence alignment score = 604 
    11630 RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
    11631 0.325) 
    11632  
    11633 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
    11634 (#8), sequence alignment score = 604 
    11635 RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
    11636 0.364) 
    11637  
    11638 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
    11639 (#9), sequence alignment score = 604 
    11640 RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
    11641 0.374) 
    11642  
    11643 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
    11644 (#10), sequence alignment score = 604 
    11645 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
    11646 0.367) 
    11647  
    11648 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
    11649 (#11), sequence alignment score = 604 
    11650 RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
    11651 0.464) 
    11652  
    11653 
    11654 > matchmaker #19#!2-18 to #1 & sel matrix Nucleic
    11655 
    11656 Computing secondary structure 
    11657 [Repeated 18 time(s)]  Parameters 
    11658 --- 
    11659 Chain pairing | bb 
    11660 Alignment algorithm | Needleman-Wunsch 
    11661 Similarity matrix | Nucleic 
    11662 SS fraction | 0.3 
    11663 Gap open (HH/SS/other) | 18/18/6 
    11664 Gap extend | 1 
    11665 SS matrix |  |  | H | S | O 
    11666 ---|---|---|--- 
    11667 H | 6 | -9 | -6 
    11668 S |  | 6 | -6 
    11669 O |  |  | 4 
    11670 Iteration cutoff | 2 
    11671  
    11672 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
    11673 coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
    11674 604 
    11675 RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs:
    11676 0.766) 
    11677  
    11678 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
    11679 (#2), sequence alignment score = 604 
    11680 RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
    11681 0.413) 
    11682  
    11683 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
    11684 (#3), sequence alignment score = 604 
    11685 RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
    11686 0.322) 
    11687  
    11688 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
    11689 (#4), sequence alignment score = 604 
    11690 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
    11691 0.445) 
    11692  
    11693 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
    11694 (#5), sequence alignment score = 604 
    11695 RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
    11696 0.365) 
    11697  
    11698 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
    11699 (#6), sequence alignment score = 604 
    11700 RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
    11701 0.323) 
    11702  
    11703 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
    11704 (#7), sequence alignment score = 604 
    11705 RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
    11706 0.325) 
    11707  
    11708 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
    11709 (#8), sequence alignment score = 604 
    11710 RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
    11711 0.364) 
    11712  
    11713 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
    11714 (#9), sequence alignment score = 604 
    11715 RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
    11716 0.374) 
    11717  
    11718 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
    11719 (#10), sequence alignment score = 604 
    11720 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
    11721 0.367) 
    11722  
    11723 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
    11724 (#11), sequence alignment score = 604 
    11725 RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
    11726 0.464) 
    11727  
    11728 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A
    11729 (#12), sequence alignment score = 604 
    11730 RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs:
    11731 0.359) 
    11732  
    11733 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A
    11734 (#13), sequence alignment score = 604 
    11735 RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs:
    11736 0.441) 
    11737  
    11738 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A
    11739 (#14), sequence alignment score = 604 
    11740 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
    11741 0.367) 
    11742  
    11743 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A
    11744 (#15), sequence alignment score = 604 
    11745 RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs:
    11746 0.488) 
    11747  
    11748 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A
    11749 (#16), sequence alignment score = 604 
    11750 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
    11751 0.445) 
    11752  
    11753 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A
    11754 (#17), sequence alignment score = 604 
    11755 RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs:
    11756 0.368) 
    11757  
    11758 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A
    11759 (#18), sequence alignment score = 604 
    11760 RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs:
    11761 0.430) 
    11762  
    11763 
    11764 > ui mousemode right select
    11765 
    11766 > select clear
    11767 
    11768 Drag select of 6 residues 
    11769 
    11770 > select clear
    11771 
    11772 > hide #!1-18 target m
    11773 
    11774 > show #!1 models
    11775 
    11776 > hide #!1 models
    11777 
    11778 > show #!1 models
    11779 
    11780 > show #!1-18 target m
    11781 
    11782 Drag select of 17 residues 
    11783 
    11784 > select clear
    11785 
    11786 > select #1-18/C:10
    11787 
    11788 13 atoms, 13 residues, 13 models selected 
    11789 Drag select of 6 residues 
    11790 
    11791 > select #19/C:0
    11792 
    11793 20 atoms, 21 bonds, 1 residue, 1 model selected 
    11794 
    11795 > hide #19 models
    11796 
    11797 > select #14/C:80@MG
    11798 
    11799 1 atom, 1 residue, 1 model selected 
    11800 
    11801 > select subtract #14/C:80@MG
    11802 
    11803 Nothing selected 
    11804 
    11805 > select add #5/C:24@MG
    11806 
    11807 1 atom, 1 residue, 1 model selected 
    11808 
    11809 > select add #14/C:80@MG
    11810 
    11811 2 atoms, 2 residues, 2 models selected 
    11812 
    11813 > select #7/A:278
    11814 
    11815 20 atoms, 21 bonds, 1 residue, 1 model selected 
    11816 
    11817 > select #14/C:80@MG
    11818 
    11819 1 atom, 1 residue, 1 model selected 
    11820 
    11821 > select #1-18/A:50,389,390
    11822 
    11823 1188 atoms, 1314 bonds, 54 residues, 18 models selected 
    11824 
    11825 > select #1-18/A:49,50,51,389,390
    11826 
    11827 1998 atoms, 2232 bonds, 90 residues, 18 models selected 
    11828 
    11829 > select #7/A:391
    11830 
    11831 20 atoms, 21 bonds, 1 residue, 1 model selected 
    11832 
    11833 > select #1-18/A:49,50,51,389,390,391
    11834 
    11835 2358 atoms, 2628 bonds, 108 residues, 18 models selected 
    11836 
    11837 > select #1-18/A:49,50,51,52,388,389,390,391
    11838 
    11839 3132 atoms, 3492 bonds, 144 residues, 18 models selected 
    11840 
    11841 > show #19 models
    11842 
    11843 > hide #19 models
    11844 
    11845 > view sel
    11846 
    11847 > select #10/C:84@MG
    11848 
    11849 1 atom, 1 residue, 1 model selected 
    11850 
    11851 > select add #17/C:87@MG
    11852 
    11853 2 atoms, 2 residues, 2 models selected 
    11854 
    11855 > select add #1/C:4@MG
    11856 
    11857 3 atoms, 3 residues, 3 models selected 
    11858 
    11859 > select add #13/C:24@MG
    11860 
    11861 4 atoms, 4 residues, 4 models selected 
    11862 
    11863 > select add #11/A:390@OP2
    11864 
    11865 5 atoms, 5 residues, 5 models selected 
    11866 
    11867 > select add #12/C:7@MG
    11868 
    11869 6 atoms, 6 residues, 6 models selected 
    11870 
    11871 > select add #4/A:50@OP1
    11872 
    11873 7 atoms, 7 residues, 7 models selected 
    11874 
    11875 > view sel
    11876 
    11877 > show #19 models
    11878 
    11879 > hide #19 models
    11880 
    11881 > show #19 models
    11882 
    11883 > hide #19 models
    11884 
    11885 > select #7/A:390@O3'
    11886 
    11887 1 atom, 1 residue, 1 model selected 
    11888 
    11889 > select #7/A:390@O3'
    11890 
    11891 1 atom, 1 residue, 1 model selected 
    11892 
    11893 > select add #4/A:390@O2'
    11894 
    11895 2 atoms, 2 residues, 2 models selected 
    11896 
    11897 > select add #11/A:390@OP2
    11898 
    11899 3 atoms, 3 residues, 3 models selected 
    11900 
    11901 > select add #12/C:7@MG
    11902 
    11903 4 atoms, 4 residues, 4 models selected 
    11904 
    11905 > select add #13/C:7@MG
    11906 
    11907 5 atoms, 5 residues, 5 models selected 
    11908 
    11909 > select add #11/A:389@O5'
    11910 
    11911 6 atoms, 6 residues, 5 models selected 
    11912 
    11913 > select add #6/A:389@OP2
    11914 
    11915 7 atoms, 7 residues, 6 models selected 
    11916 
    11917 > select add #11/A:50@OP2
    11918 
    11919 8 atoms, 8 residues, 6 models selected 
    11920 
    11921 > select add #4/A:50@OP1
    11922 
    11923 9 atoms, 9 residues, 6 models selected 
    11924 
    11925 > select add #2/A:51
    11926 
    11927 32 atoms, 25 bonds, 10 residues, 7 models selected 
    11928 
    11929 > select add #17/A:49
    11930 
    11931 54 atoms, 49 bonds, 11 residues, 8 models selected 
    11932 
    11933 > select add #8/A:50@O2'
    11934 
    11935 55 atoms, 49 bonds, 12 residues, 9 models selected 
    11936 
    11937 > select add #11/A:50@O3'
    11938 
    11939 56 atoms, 49 bonds, 12 residues, 9 models selected 
    11940 
    11941 > select add #13/C:24@MG
    11942 
    11943 57 atoms, 49 bonds, 13 residues, 9 models selected 
    11944 
    11945 > select add #10/C:84@MG
    11946 
    11947 58 atoms, 49 bonds, 14 residues, 10 models selected 
    11948 
    11949 > select add #17/C:87@MG
    11950 
    11951 59 atoms, 49 bonds, 15 residues, 10 models selected 
    11952 
    11953 > select add #9/C:4@MG
    11954 
    11955 60 atoms, 49 bonds, 16 residues, 11 models selected 
    11956 
    11957 > view sel
    11958 
    11959 > show #19 models
    11960 
    11961 > hide #19 models
    11962 
    11963 > show #19 models
    11964 
    11965 > hide #19 models
    11966 
    11967 > show #19 models
    11968 
    11969 > hide #19 models
    11970 
    11971 > show #19 models
    11972 
    11973 > hide #19 models
    11974 
    11975 > show #19 models
    11976 
    11977 > hide #19 models
    11978 
    11979 > show #19 models
    11980 
    11981 > hide #19 models
    11982 
    11983 > show #19 models
    11984 
    11985 > hide #19 models
    11986 
    11987 > select #13/C:7@MG
    11988 
    11989 1 atom, 1 residue, 1 model selected 
    11990 
    11991 > select add #17/C:82@MG
    11992 
    11993 2 atoms, 2 residues, 2 models selected 
    11994 
    11995 > distance #13/C:7@MG #17/C:82@MG
    11996 
    11997 Distance between V17_holo-coot-3.pdb #13/C MG 7 MG and V23_holo-coot-2.pdb
    11998 #17/C MG 82 MG: 13.090Å 
    11999 
    12000 > distance #13/C:7@MG #17/C:82@MG
    12001 
    12002 Distance already exists; modify distance properties with 'distance style' 
    12003 
    12004 > ~distance #19/C:3@C5' #18/C:62@MG
    12005 
    12006 > ~distance #13/C:7@MG #17/C:82@MG
    12007 
    12008 > select clear
    12009 
    12010 > select #4/C:24@MG
    12011 
    12012 1 atom, 1 residue, 1 model selected 
    12013 
    12014 > select add #7/C:24@MG
    12015 
    12016 2 atoms, 2 residues, 2 models selected 
    12017 
    12018 > select add #18/C:24@MG
    12019 
    12020 3 atoms, 3 residues, 3 models selected 
    12021 
    12022 > select add #9/C:24@MG
    12023 
    12024 4 atoms, 4 residues, 4 models selected 
    12025 
    12026 > select add #3/C:24@MG
    12027 
    12028 5 atoms, 5 residues, 5 models selected 
    12029 
    12030 > select add #13/C:24@MG
    12031 
    12032 6 atoms, 6 residues, 6 models selected 
    12033 
    12034 > select add #6/C:24@MG
    12035 
    12036 7 atoms, 7 residues, 7 models selected 
    12037 
    12038 > select add #10/C:84@MG
    12039 
    12040 8 atoms, 8 residues, 8 models selected 
    12041 
    12042 > select add #17/C:87@MG
    12043 
    12044 9 atoms, 9 residues, 9 models selected 
    12045 
    12046 > select add #4/C:4@MG
    12047 
    12048 10 atoms, 10 residues, 9 models selected 
    12049 
    12050 > select add #8/C:4@MG
    12051 
    12052 11 atoms, 11 residues, 10 models selected 
    12053 
    12054 > select add #1/C:4@MG
    12055 
    12056 12 atoms, 12 residues, 11 models selected 
    12057 
    12058 > select add #9/C:4@MG
    12059 
    12060 13 atoms, 13 residues, 11 models selected 
    12061 
    12062 > select add #6/A:50@OP2
    12063 
    12064 14 atoms, 14 residues, 11 models selected 
    12065 
    12066 > select add #11/A:50@P
    12067 
    12068 15 atoms, 15 residues, 12 models selected 
    12069 
    12070 > select add #5/A:50@OP1
    12071 
    12072 16 atoms, 16 residues, 13 models selected 
    12073 
    12074 > select add #12/C:7@MG
    12075 
    12076 17 atoms, 17 residues, 14 models selected 
    12077 
    12078 > select add #13/C:7@MG
    12079 
    12080 18 atoms, 18 residues, 14 models selected 
    12081 
    12082 > select add #11/A:390@OP1
    12083 
    12084 19 atoms, 19 residues, 14 models selected 
    12085 
    12086 > select add #15/A:390@OP1
    12087 
    12088 20 atoms, 20 residues, 15 models selected 
    12089 
    12090 > select add #5/A:389@O2'
    12091 
    12092 21 atoms, 21 residues, 15 models selected 
    12093 
    12094 > select add #7/A:390@O2'
    12095 
    12096 22 atoms, 22 residues, 15 models selected 
    12097 
    12098 > select add #7/A:390@C5'
    12099 
    12100 23 atoms, 22 residues, 15 models selected 
    12101 
    12102 > select add #6/A:390@O5'
    12103 
    12104 24 atoms, 23 residues, 15 models selected 
    12105 
    12106 > select add #17/A:389@O5'
    12107 
    12108 25 atoms, 24 residues, 15 models selected 
    12109 
    12110 > select add #11/A:389@C4'
    12111 
    12112 26 atoms, 25 residues, 15 models selected 
    12113 
    12114 > select add #11/A:389@OP2
    12115 
    12116 27 atoms, 25 residues, 15 models selected 
    12117 
    12118 > select add #17/A:388
    12119 
    12120 50 atoms, 25 bonds, 26 residues, 15 models selected 
    12121 
    12122 > select add #4/A:51
    12123 
    12124 73 atoms, 50 bonds, 27 residues, 15 models selected 
    12125 
    12126 > select add #2/A:50@C5'
    12127 
    12128 74 atoms, 50 bonds, 28 residues, 16 models selected 
    12129 
    12130 > select add #4/A:50@O5'
    12131 
    12132 75 atoms, 50 bonds, 29 residues, 16 models selected 
    12133 
    12134 > select add #14/A:52
    12135 
    12136 95 atoms, 71 bonds, 30 residues, 17 models selected 
    12137 
    12138 > select add #17/A:49
    12139 
    12140 117 atoms, 95 bonds, 31 residues, 17 models selected 
    12141 
    12142 > view sel
    12143 
    12144 > show #19 models
    12145 
    12146 > hide #19 models
    12147 
    12148 > show #19 models
    12149 
    12150 > hide #19 models
    12151 
    12152 > show #19 models
    12153 
    12154 > hide #19 models
    12155 
    12156 > show #19 models
    12157 
    12158 > hide #19 models
    12159 
    12160 > select #3/C:68@MG
    12161 
    12162 1 atom, 1 residue, 1 model selected 
    12163 
    12164 > select add #13/C:7@MG
    12165 
    12166 2 atoms, 2 residues, 2 models selected 
    12167 
    12168 > show #19 models
    12169 
    12170 > select #3/C:68@MG
    12171 
    12172 1 atom, 1 residue, 1 model selected 
    12173 
    12174 > select add #19/C:-1
    12175 
    12176 21 atoms, 21 bonds, 2 residues, 2 models selected 
    12177 Exactly two atoms must be selected! 
    12178 
    12179 > select #3/C:68@MG
    12180 
    12181 1 atom, 1 residue, 1 model selected 
    12182 
    12183 > hide sel target a
    12184 
    12185 > hide #!18 models
    12186 
    12187 > show #!18 models
    12188 
    12189 > hide #19 models
    12190 
    12191 > select #10/C:84@MG
    12192 
    12193 1 atom, 1 residue, 1 model selected 
    12194 
    12195 > select #17/C:87@MG
    12196 
    12197 1 atom, 1 residue, 1 model selected 
    12198 
    12199 > show #19 models
    12200 
    12201 > hide #19 models
    12202 
    12203 > select clear
    12204 
    12205 > select #10/C:84@MG
    12206 
    12207 1 atom, 1 residue, 1 model selected 
    12208 
    12209 > select add #17/C:87@MG
    12210 
    12211 2 atoms, 2 residues, 2 models selected 
    12212 
    12213 > select add #13/C:7@MG
    12214 
    12215 3 atoms, 3 residues, 3 models selected 
    12216 
    12217 > view sel
    12218 
    12219 > select add #13/C:24@MG
    12220 
    12221 4 atoms, 4 residues, 3 models selected 
    12222 
    12223 > select add #18/C:62@MG
    12224 
    12225 5 atoms, 5 residues, 4 models selected 
    12226 
    12227 > view sel
    12228 
    12229 > show #19 models
    12230 
    12231 > hide #19 models
    12232 
    12233 > show #19 models
    12234 
    12235 > hide #19 models
    12236 
    12237 > select #6/A:50@OP2
    12238 
    12239 1 atom, 1 residue, 1 model selected 
    12240 
    12241 > select add #13/C:7@MG
    12242 
    12243 2 atoms, 2 residues, 2 models selected 
    12244 
    12245 > select add #11/A:390@OP1
    12246 
    12247 3 atoms, 3 residues, 3 models selected 
    12248 
    12249 > select add #10/C:84@MG
    12250 
    12251 4 atoms, 4 residues, 4 models selected 
    12252 
    12253 > select add #18/C:24@MG
    12254 
    12255 5 atoms, 5 residues, 5 models selected 
    12256 
    12257 > select add #9/C:4@MG
    12258 
    12259 6 atoms, 6 residues, 6 models selected 
    12260 
    12261 > select add #4/C:4@MG
    12262 
    12263 7 atoms, 7 residues, 7 models selected 
    12264 
    12265 > select add #1/C:4@MG
    12266 
    12267 8 atoms, 8 residues, 8 models selected 
    12268 
    12269 > select add #17/C:87@MG
    12270 
    12271 9 atoms, 9 residues, 9 models selected 
    12272 
    12273 > select add #13/C:24@MG
    12274 
    12275 10 atoms, 10 residues, 9 models selected 
    12276 
    12277 > select add #6/C:24@MG
    12278 
    12279 11 atoms, 11 residues, 9 models selected 
    12280 
    12281 > select add #12/C:7@MG
    12282 
    12283 12 atoms, 12 residues, 10 models selected 
    12284 
    12285 > select add #3/C:7@MG
    12286 
    12287 13 atoms, 13 residues, 11 models selected 
    12288 
    12289 > select add #5/A:50@OP1
    12290 
    12291 14 atoms, 14 residues, 12 models selected 
    12292 
    12293 > select add #17/A:389@OP2
    12294 
    12295 15 atoms, 15 residues, 12 models selected 
    12296 
    12297 > select add #6/A:389@OP2
    12298 
    12299 16 atoms, 16 residues, 12 models selected 
    12300 
    12301 > select add #15/A:390@OP1
    12302 
    12303 17 atoms, 17 residues, 13 models selected 
    12304 
    12305 > select add #9/A:390@OP2
    12306 
    12307 18 atoms, 18 residues, 13 models selected 
    12308 
    12309 > view sel
    12310 
    12311 > select #17/C:87@MG
    12312 
    12313 1 atom, 1 residue, 1 model selected 
    12314 
    12315 > view sel
    12316 
    12317 > select #1-18/A:49,50,51,52,388,389,390,391
    12318 
    12319 3132 atoms, 3492 bonds, 144 residues, 18 models selected 
    12320 
    12321 > view sel
    12322 
    12323 > select #10/C:84@MG
    12324 
    12325 1 atom, 1 residue, 1 model selected 
    12326 
    12327 > select add #3/C:24@MG
    12328 
    12329 2 atoms, 2 residues, 2 models selected 
    12330 
    12331 > select add #13/C:24@MG
    12332 
    12333 3 atoms, 3 residues, 3 models selected 
    12334 
    12335 > select add #18/C:24@MG
    12336 
    12337 4 atoms, 4 residues, 4 models selected 
    12338 
    12339 > select add #9/A:390@OP2
    12340 
    12341 5 atoms, 5 residues, 5 models selected 
    12342 
    12343 > select add #13/C:7@MG
    12344 
    12345 6 atoms, 6 residues, 5 models selected 
    12346 
    12347 > select add #17/C:87@MG
    12348 
    12349 7 atoms, 7 residues, 6 models selected 
    12350 
    12351 > select add #1/C:4@MG
    12352 
    12353 8 atoms, 8 residues, 7 models selected 
    12354 
    12355 > select #1-18/A:49,50,51,52,388,389,390,391
    12356 
    12357 3132 atoms, 3492 bonds, 144 residues, 18 models selected 
    12358 
    12359 > select add #10/C:84@MG
    12360 
    12361 3133 atoms, 3492 bonds, 145 residues, 18 models selected 
    12362 
    12363 > select add #17/C:87@MG
    12364 
    12365 3134 atoms, 3492 bonds, 146 residues, 18 models selected 
    12366 
    12367 > select add #3/C:24@MG
    12368 
    12369 3135 atoms, 3492 bonds, 147 residues, 18 models selected 
    12370 
    12371 > select add #6/C:24@MG
    12372 
    12373 3136 atoms, 3492 bonds, 148 residues, 18 models selected 
    12374 
    12375 > select add #9/C:24@MG
    12376 
    12377 3137 atoms, 3492 bonds, 149 residues, 18 models selected 
    12378 
    12379 > select add #18/C:24@MG
    12380 
    12381 3138 atoms, 3492 bonds, 150 residues, 18 models selected 
    12382 
    12383 > select add #1/C:4@MG
    12384 
    12385 3139 atoms, 3492 bonds, 151 residues, 18 models selected 
    12386 
    12387 > select add #4/C:4@MG
    12388 
    12389 3140 atoms, 3492 bonds, 152 residues, 18 models selected 
    12390 
    12391 > select add #9/C:4@MG
    12392 
    12393 3141 atoms, 3492 bonds, 153 residues, 18 models selected 
    12394 
    12395 > select add #18/C:4@MG
    12396 
    12397 3142 atoms, 3492 bonds, 154 residues, 18 models selected 
    12398 
    12399 > select add #12/C:7@MG
    12400 
    12401 3143 atoms, 3492 bonds, 155 residues, 18 models selected 
    12402 
    12403 > select add #13/C:7@MG
    12404 
    12405 3144 atoms, 3492 bonds, 156 residues, 18 models selected 
    12406 
    12407 > select add #3/C:7@MG
    12408 
    12409 3145 atoms, 3492 bonds, 157 residues, 18 models selected 
    12410 
    12411 > view sel
    12412 
    12413 > show #19 models
    12414 
    12415 > hide #19 models
    12416 
    12417 > select clear
    12418 
    12419 > select #10/C:84@MG
    12420 
    12421 1 atom, 1 residue, 1 model selected 
    12422 
    12423 > select clear
    12424 
    12425 > select #10/C:84@MG
    12426 
    12427 1 atom, 1 residue, 1 model selected 
    12428 
    12429 > select add #17/C:87@MG
    12430 
    12431 2 atoms, 2 residues, 2 models selected 
    12432 
    12433 > color sel magenta
    12434 
    12435 > select clear
    12436 
    12437 No map chosen to save 
    12438 
    12439 > save
    12440 > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs
    12441 
    12442 > show #19 models
    12443 
    12444 > select #19/C:4
    12445 
    12446 23 atoms, 25 bonds, 1 residue, 1 model selected 
    12447 
    12448 > hide sel target a
    12449 
    12450 > cartoon hide sel
    12451 
    12452 > select #19/C:2
    12453 
    12454 20 atoms, 21 bonds, 1 residue, 1 model selected 
    12455 
    12456 > select add #19/C:1
    12457 
    12458 43 atoms, 46 bonds, 2 residues, 1 model selected 
    12459 
    12460 > select add #19/C:0
    12461 
    12462 63 atoms, 67 bonds, 3 residues, 1 model selected 
    12463 
    12464 > select #19/C:2
    12465 
    12466 20 atoms, 21 bonds, 1 residue, 1 model selected 
    12467 
    12468 > select add #19/C:1
    12469 
    12470 43 atoms, 46 bonds, 2 residues, 1 model selected 
    12471 
    12472 > select add #19/C:0
    12473 
    12474 63 atoms, 67 bonds, 3 residues, 1 model selected 
    12475 
    12476 > show sel target ab
    12477 
    12478 > cartoon hide sel
    12479 
    12480 > nucleotides sel atoms
    12481 
    12482 > style nucleic & sel stick
    12483 
    12484 Changed 63 atom styles 
    12485 
    12486 > select #1/A:49,50,51,52,388,389,390,391
    12487 
    12488 174 atoms, 194 bonds, 8 residues, 1 model selected 
    12489 
    12490 > matchmaker #19 to #1 & sel matrix Nucleic
    12491 
    12492 Computing secondary structure 
    12493 [Repeated 1 time(s)]  Parameters 
    12494 --- 
    12495 Chain pairing | bb 
    12496 Alignment algorithm | Needleman-Wunsch 
    12497 Similarity matrix | Nucleic 
    12498 SS fraction | 0.3 
    12499 Gap open (HH/SS/other) | 18/18/6 
    12500 Gap extend | 1 
    12501 SS matrix |  |  | H | S | O 
    12502 ---|---|---|--- 
    12503 H | 6 | -9 | -6 
    12504 S |  | 6 | -6 
    12505 O |  |  | 4 
    12506 Iteration cutoff | 2 
    12507  
    12508 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
    12509 coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
    12510 32 
    12511 RMSD between 8 pruned atom pairs is 0.305 angstroms; (across all 8 pairs:
    12512 0.305) 
    12513  
    12514 
    12515 > select #19/A
    12516 
    12517 8962 atoms, 10038 bonds, 417 residues, 1 model selected 
    12518 
    12519 > hide sel target a
    12520 
    12521 > cartoon hide sel
    12522 
    12523 > select #19/C:2
    12524 
    12525 20 atoms, 21 bonds, 1 residue, 1 model selected 
    12526 
    12527 > hide sel target a
    12528 
    12529 > select #19/C
    12530 
    12531 1889 atoms, 2107 bonds, 89 residues, 1 model selected 
    12532 
    12533 > nucleotides sel tube/slab shape ellipsoid
    12534 
    12535 > nucleotides sel atoms
    12536 
    12537 > style nucleic & sel stick
    12538 
    12539 Changed 1889 atom styles 
    12540 
    12541 > hide (sel-residues & (protein|nucleic)) target a
    12542 
    12543 > cartoon hide sel-residues
    12544 
    12545 > show (sel-residues & backbone) target ab
    12546 
    12547 > select #19/C:2-40
    12548 
    12549 835 atoms, 934 bonds, 39 residues, 1 model selected 
    12550 
    12551 > hide sel target a
    12552 
    12553 > select #19/C
    12554 
    12555 1889 atoms, 2107 bonds, 89 residues, 1 model selected 
    12556 
    12557 > cartoon sel
    12558 
    12559 > cartoon hide sel
    12560 
    12561 > color sel gray
    12562 
    12563 > ui tool show "Color Actions"
    12564 
    12565 > color sel dim gray
    12566 
    12567 > color sel #75fbf2ff
    12568 
    12569 > color sel #75fbf4ff
    12570 
    12571 [Repeated 1 time(s)]
    12572 
    12573 > color sel #75fbf5ff
    12574 
    12575 [Repeated 1 time(s)]
    12576 
    12577 > color sel #75fbf7ff
    12578 
    12579 > color sel #74fafaff
    12580 
    12581 [Repeated 4 time(s)]
    12582 
    12583 > color sel #74fafbff
    12584 
    12585 [Repeated 3 time(s)]
    12586 
    12587 > color sel #74f9fcff
    12588 
    12589 > color sel #72f5fcff
    12590 
    12591 > color sel #6eedfbff
    12592 
    12593 > color sel #6ce9fbff
    12594 
    12595 > color sel #69e3fbff
    12596 
    12597 > color sel #68e1faff
    12598 
    12599 > color sel #64d9faff
    12600 
    12601 > color sel #63d6faff
    12602 
    12603 > color sel #5ecdf9ff
    12604 
    12605 > color sel #5dcbf9ff
    12606 
    12607 > color sel #5cc9f9ff
    12608 
    12609 > color sel #58c1f9ff
    12610 
    12611 > color sel #56bdf8ff
    12612 
    12613 > color sel #52b5f8ff
    12614 
    12615 > color sel #50b1f8ff
    12616 
    12617 > color sel #4ca7f7ff
    12618 
    12619 > color sel #469cf7ff
    12620 
    12621 > color sel #4397f7ff
    12622 
    12623 > color sel #3e8bf6ff
    12624 
    12625 > color sel #3981f6ff
    12626 
    12627 > color sel #3477f5ff
    12628 
    12629 > color sel #3274f5ff
    12630 
    12631 > color sel #3171f5ff
    12632 
    12633 > color sel #2e6cf5ff
    12634 
    12635 > color sel #2c67f5ff
    12636 
    12637 > color sel #2b66f5ff
    12638 
    12639 > color sel #2a64f5ff
    12640 
    12641 > color sel #2860f5ff
    12642 
    12643 > color sel #275df5ff
    12644 
    12645 > color sel #255af5ff
    12646 
    12647 > color sel #2559f5ff
    12648 
    12649 > color sel #2355f5ff
    12650 
    12651 > color sel #1f4ef4ff
    12652 
    12653 > color sel #1e4bf4ff
    12654 
    12655 > color sel #1d49f4ff
    12656 
    12657 > color sel #1b46f4ff
    12658 
    12659 > color sel #1a43f3ff
    12660 
    12661 > color sel #1941f3ff
    12662 
    12663 [Repeated 1 time(s)]
    12664 
    12665 > color sel #1940f3ff
    12666 
    12667 > color sel #183ff3ff
    12668 
    12669 > color sel #183df2ff
    12670 
    12671 > color sel #1639f2ff
    12672 
    12673 > color sel #1536f1ff
    12674 
    12675 [Repeated 3 time(s)]
    12676 
    12677 > color sel #1536f0ff
    12678 
    12679 > color sel #1535efff
    12680 
    12681 [Repeated 2 time(s)]
    12682 
    12683 > color sel #1434efff
    12684 
    12685 > color sel #1535f0ff
    12686 
    12687 > color sel #1330edff
    12688 
    12689 > color sel #132eecff
    12690 
    12691 > color sel #142ee7ff
    12692 
    12693 > color sel #162edfff
    12694 
    12695 > color sel #1529d9ff
    12696 
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    12698 
    12699 [Repeated 2 time(s)]
    12700 
    12701 > color sel #1628d5ff
    12702 
    12703 > color sel #1629d3ff
    12704 
    12705 [Repeated 1 time(s)]
    12706 
    12707 > color sel #1628d3ff
    12708 
    12709 > color sel #172ad1ff
    12710 
    12711 > color sel #1729cfff
    12712 
    12713 > color sel #1829c9ff
    12714 
    12715 > color sel #192ac5ff
    12716 
    12717 > color sel #1a29baff
    12718 
    12719 > color sel #1b29b3ff
    12720 
    12721 > color sel #1b28a7ff
    12722 
    12723 > color sel #1c28a1ff
    12724 
    12725 > color sel #1b279cff
    12726 
    12727 > color sel #1b2794ff
    12728 
    12729 > color sel #1b268fff
    12730 
    12731 > color sel #1b268aff
    12732 
    12733 > color sel #1a2482ff
    12734 
    12735 > color sel #1a237dff
    12736 
    12737 > color sel #1a2277ff
    12738 
    12739 > color sel #192070ff
    12740 
    12741 > color sel #19206bff
    12742 
    12743 > color sel #192069ff
    12744 
    12745 > color sel #181f65ff
    12746 
    12747 > color sel #181e62ff
    12748 
    12749 > color sel #181d60ff
    12750 
    12751 > color sel #181e5fff
    12752 
    12753 > color sel #171d5cff
    12754 
    12755 > color sel #171e59ff
    12756 
    12757 > color sel #161c52ff
    12758 
    12759 > color sel #161c50ff
    12760 
    12761 > color sel #151b4aff
    12762 
    12763 > color sel #151b48ff
    12764 
    12765 > color sel #151a46ff
    12766 
    12767 [Repeated 1 time(s)]
    12768 
    12769 > color sel #141a45ff
    12770 
    12771 > color sel #141b43ff
    12772 
    12773 > color sel #141c43ff
    12774 
    12775 [Repeated 3 time(s)]
    12776 
    12777 > color sel #141d43ff
    12778 
    12779 [Repeated 1 time(s)]
    12780 
    12781 > color sel #151d43ff
    12782 
    12783 [Repeated 2 time(s)]
    12784 
    12785 > color sel #151e44ff
    12786 
    12787 [Repeated 1 time(s)]
    12788 
    12789 > color sel #161f47ff
    12790 
    12791 > color sel #17214cff
    12792 
    12793 > color sel #172151ff
    12794 
    12795 > color sel #182252ff
    12796 
    12797 > color sel #182254ff
    12798 
    12799 > color sel #182257ff
    12800 
    12801 > color sel #18215aff
    12802 
    12803 > color sel #18215dff
    12804 
    12805 > color sel #182060ff
    12806 
    12807 > color sel #181f63ff
    12808 
    12809 > color sel #191f67ff
    12810 
    12811 > color sel #192068ff
    12812 
    12813 > color sel #191f6bff
    12814 
    12815 > color sel #191f6eff
    12816 
    12817 > color sel #191f6fff
    12818 
    12819 > color sel #192176ff
    12820 
    12821 > color sel #1a237bff
    12822 
    12823 > color sel #1b2580ff
    12824 
    12825 > color sel #1b2688ff
    12826 
    12827 > color sel #1e3198ff
    12828 
    12829 > color sel #20379eff
    12830 
    12831 > color sel #274cafff
    12832 
    12833 > color sel #2a56b5ff
    12834 
    12835 > color sel #3065bdff
    12836 
    12837 > color sel #3570c2ff
    12838 
    12839 > color sel #3d83c9ff
    12840 
    12841 > color sel #3f87ccff
    12842 
    12843 > color sel #4492cfff
    12844 
    12845 > color sel #4696d2ff
    12846 
    12847 > color sel #4a9fd4ff
    12848 
    12849 > color sel #4fabd8ff
    12850 
    12851 > color sel #51aedbff
    12852 
    12853 > color sel #54b5deff
    12854 
    12855 [Repeated 1 time(s)]
    12856 
    12857 > color sel #54b6deff
    12858 
    12859 > color sel #55b8dfff
    12860 
    12861 > color sel #56bbe1ff
    12862 
    12863 > color sel #59c0e6ff
    12864 
    12865 > color sel #5fcdecff
    12866 
    12867 > color sel #65d9f1ff
    12868 
    12869 > color sel #69e2f3ff
    12870 
    12871 > color sel #6decf7ff
    12872 
    12873 > color sel #6eedf8ff
    12874 
    12875 > color sel #70f0f9ff
    12876 
    12877 > color sel #70f1faff
    12878 
    12879 [Repeated 1 time(s)]
    12880 
    12881 > color sel #70f2faff
    12882 
    12883 > color sel #71f2fbff
    12884 
    12885 > color sel #71f3fcff
    12886 
    12887 > color sel #70f2fcff
    12888 
    12889 > color sel #70f1fcff
    12890 
    12891 > color sel #6feffaff
    12892 
    12893 > color sel #6eedf9ff
    12894 
    12895 > color sel #6deaf9ff
    12896 
    12897 > color sel #6deaf8ff
    12898 
    12899 > color sel #6deaf7ff
    12900 
    12901 > color sel #5e5e5eff
    12902 
    12903 > color sel #424242ff
    12904 
    12905 > color sel #5e5e5eff
    12906 
    12907 [Repeated 2 time(s)]
    12908 
    12909 > color sel #5e5e5efe
    12910 
    12911 > color sel #5e5e5efa
    12912 
    12913 > color sel #5e5e5ef8
    12914 
    12915 > color sel #5e5e5ef5
    12916 
    12917 > color sel #5e5e5ef3
    12918 
    12919 > color sel #5e5e5ef1
    12920 
    12921 > color sel #5e5e5eef
    12922 
    12923 > color sel #5e5e5eee
    12924 
    12925 > color sel #5e5e5eeb
    12926 
    12927 > color sel #5e5e5ee8
    12928 
    12929 > color sel #5e5e5ee5
    12930 
    12931 > color sel #5e5e5ee3
    12932 
    12933 > color sel #5e5e5ed2
    12934 
    12935 > color sel #5e5e5ecb
    12936 
    12937 > color sel #5e5e5ec0
    12938 
    12939 > color sel #5e5e5eb8
    12940 
    12941 > color sel #5e5e5eb1
    12942 
    12943 > color sel #5e5e5eaa
    12944 
    12945 > color sel #5e5e5ea6
    12946 
    12947 > color sel #5e5e5ea3
    12948 
    12949 > color sel #5e5e5ea1
     2692[deleted to fit within ticket limits]
     2693
    129502694
    129512695> color sel #5e5e5e9f