Changes between Initial Version and Version 1 of Ticket #19990


Ignore:
Timestamp:
Mar 18, 2026, 9:50:18 AM (3 weeks ago)
Author:
Eric Pettersen
Comment:

Reported by Emily Tai

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19990

    • 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 #19990 – Description

    initial v1  
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    2178     "arch" : "arm64e",
    2179     "base" : 6681264128,
    2180     "CFBundleShortVersionString" : "2.1.1",
    2181     "CFBundleIdentifier" : "com.apple.HIToolbox",
    2182     "size" : 3174368,
    2183     "uuid" : "1a037942-11e0-3fc8-aad2-20b11e7ae1a4",
    2184     "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    2185     "name" : "HIToolbox"
    2186   },
    2187   {
    2188     "source" : "P",
    2189     "arch" : "arm64e",
    2190     "base" : 6481575936,
    2191     "size" : 636280,
    2192     "uuid" : "3247e185-ced2-36ff-9e29-47a77c23e004",
    2193     "path" : "\/usr\/lib\/dyld",
    2194     "name" : "dyld"
    2195   },
    2196   {
    2197     "size" : 0,
    2198     "source" : "A",
    2199     "base" : 0,
    2200     "uuid" : "00000000-0000-0000-0000-000000000000"
    2201   },
    2202   {
    2203     "source" : "P",
    2204     "arch" : "arm64e",
    2205     "base" : 6508867584,
    2206     "CFBundleShortVersionString" : "6.9",
    2207     "CFBundleIdentifier" : "com.apple.Foundation",
    2208     "size" : 14587296,
    2209     "uuid" : "b9a92060-f21e-3ecf-9ded-94a65c68a6f4",
    2210     "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    2211     "name" : "Foundation",
    2212     "CFBundleVersion" : "3603"
    2213   },
    2214   {
    2215     "source" : "P",
    2216     "arch" : "arm64e",
    2217     "base" : 6481231872,
    2218     "size" : 342164,
    2219     "uuid" : "8ca52e4d-f699-3d14-8061-eea9d4366538",
    2220     "path" : "\/usr\/lib\/libobjc.A.dylib",
    2221     "name" : "libobjc.A.dylib"
    2222   },
    2223   {
    2224     "source" : "P",
    2225     "arch" : "arm64e",
    2226     "base" : 6482231296,
    2227     "size" : 305408,
    2228     "uuid" : "1b8951eb-68db-37ba-9581-240b796aa872",
    2229     "path" : "\/usr\/lib\/system\/libxpc.dylib",
    2230     "name" : "libxpc.dylib"
    2231   }
     74[deleted to fit within ticket limits]
     75
    223276],
    223377  "sharedCache" : {
    … …  
    44992343> ui tool show Matchmaker
    45002344
    4501 > matchmaker #8 to #14 & sel
    4502 
    4503 Parameters 
    4504 --- 
    4505 Chain pairing | bb 
    4506 Alignment algorithm | Needleman-Wunsch 
    4507 Similarity matrix | BLOSUM-62 
    4508 SS fraction | 0.3 
    4509 Gap open (HH/SS/other) | 18/18/6 
    4510 Gap extend | 1 
    4511 SS matrix |  |  | H | S | O 
    4512 ---|---|---|--- 
    4513 H | 6 | -9 | -6 
    4514 S |  | 6 | -6 
    4515 O |  |  | 4 
    4516 Iteration cutoff | 2 
    4517  
    4518 Matchmaker 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    4519 A (#8), sequence alignment score = 2066.9 
    4520 RMSD between 239 pruned atom pairs is 0.651 angstroms; (across all 412 pairs:
    4521 31.465) 
    4522  
    4523 
    4524 > select #14/E#8/E
    4525 
    4526 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    4527 
    4528 > matchmaker #8 & sel to #14 & sel
    4529 
    4530 Parameters 
    4531 --- 
    4532 Chain pairing | bb 
    4533 Alignment algorithm | Needleman-Wunsch 
    4534 Similarity matrix | BLOSUM-62 
    4535 SS fraction | 0.3 
    4536 Gap open (HH/SS/other) | 18/18/6 
    4537 Gap extend | 1 
    4538 SS matrix |  |  | H | S | O 
    4539 ---|---|---|--- 
    4540 H | 6 | -9 | -6 
    4541 S |  | 6 | -6 
    4542 O |  |  | 4 
    4543 Iteration cutoff | 2 
    4544  
    4545 Matchmaker 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    4546 E (#8), sequence alignment score = 2066.9 
    4547 RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
    4548 31.537) 
    4549  
    4550 
    4551 > select clear
    4552 
    4553 > select #14
    4554 
    4555 22743 atoms, 23408 bonds, 7 pseudobonds, 2884 residues, 2 models selected 
    4556 
    4557 > show sel cartoons
    4558 
    4559 > undo
    4560 
    4561 [Repeated 1 time(s)]
    4562 
    4563 > select clear
    4564 
    4565 > save "/Users/taic/OneDrive - National Institutes of
    4566 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.vs.AF3.unit.png"
    4567 > width 800 height 565 supersample 4 transparentBackground true
    4568 
    4569 > hide #8 models
    4570 
    4571 > select #14
    4572 
    4573 22743 atoms, 23408 bonds, 7 pseudobonds, 2884 residues, 2 models selected 
    4574 
    4575 > show sel cartoons
    4576 
    4577 > color sel bychain
    4578 
    4579 > select #14/E
    4580 
    4581 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    4582 
    4583 > rainbow sel
    4584 
    4585 > undo
    4586 
    4587 > select clear
    4588 
    4589 > show #8 models
    4590 
    4591 > hide #!14 models
    4592 
    4593 > select #8
    4594 
    4595 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    4596 
    4597 > show sel cartoons
    4598 
    4599 > color sel bychain
    4600 
    4601 > select #8/E
    4602 
    4603 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    4604 
    4605 > rainbow sel
    4606 
    4607 > select clear
    4608 
    4609 > show #!14 models
    4610 
    4611 > hide #8 models
    4612 
    4613 > show #8 models
    4614 
    4615 > hide #!14 models
    4616 
    4617 > show #!14 models
    4618 
    4619 > hide #8 models
    4620 
    4621 > show #8 models
    4622 
    4623 > hide #8 models
    4624 
    4625 > show #8 models
    4626 
    4627 > hide #8 models
    4628 
    4629 > open /Users/taic/Library/CloudStorage/OneDrive-
    4630 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_0.cif
    4631 
    4632 Chain information for fold_aerolysin_wt_9fm6_model_0.cif #9 
    4633 --- 
    4634 Chain | Description 
    4635 A B C D E F G | . 
    4636  
    4637 
    4638 > hide #!14 models
    4639 
    4640 > show #9 cartoons
    4641 
    4642 Computing secondary structure 
    4643 
    4644 > hide #9 atoms
    4645 
    4646 > show #!14 models
    4647 
    4648 > show #8 models
    4649 
    4650 > select #8/E
    4651 
    4652 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    4653 
    4654 > matchmaker #9 to #8 & sel
    4655 
    4656 Computing secondary structure 
    4657 Parameters 
    4658 --- 
    4659 Chain pairing | bb 
    4660 Alignment algorithm | Needleman-Wunsch 
    4661 Similarity matrix | BLOSUM-62 
    4662 SS fraction | 0.3 
    4663 Gap open (HH/SS/other) | 18/18/6 
    4664 Gap extend | 1 
    4665 SS matrix |  |  | H | S | O 
    4666 ---|---|---|--- 
    4667 H | 6 | -9 | -6 
    4668 S |  | 6 | -6 
    4669 O |  |  | 4 
    4670 Iteration cutoff | 2 
    4671  
    4672 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with
    4673 fold_aerolysin_wt_9fm6_model_0.cif, chain A (#9), sequence alignment score =
    4674 2272.4 
    4675 RMSD between 424 pruned atom pairs is 0.245 angstroms; (across all 424 pairs:
    4676 0.245) 
    4677  
    4678 
    4679 > hide #8 models
    4680 
    4681 > hide #!14 models
    4682 
    4683 > select #9/E
    4684 
    4685 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    4686 
    4687 > show #8 models
    4688 
    4689 > hide #8 models
    4690 
    4691 > rainbow sel
    4692 
    4693 > show #!14 models
    4694 
    4695 > undo
    4696 
    4697 > hide #9 models
    4698 
    4699 > select #9/E
    4700 
    4701 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    4702 
    4703 > select #14/E
    4704 
    4705 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    4706 
    4707 > select clear
    4708 
    4709 > show #9 models
    4710 
    4711 > show #8 models
    4712 
    4713 > hide #9 models
    4714 
    4715 > hide #!14 models
    4716 
    4717 > show #!14 models
    4718 
    4719 > hide #8 models
    4720 
    4721 > show #9 models
    4722 
    4723 > hide #!14 models
    4724 
    4725 > show #!14 models
    4726 
    4727 > hide #!14 models
    4728 
    4729 > show #!14 models
    4730 
    4731 > hide #9 models
    4732 
    4733 > show #9 models
    4734 
    4735 > hide #9 models
    4736 
    4737 > show #9 models
    4738 
    4739 > show #8 models
    4740 
    4741 > hide #9 models
    4742 
    4743 > hide #!14 models
    4744 
    4745 > select #9
    4746 
    4747 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    4748 
    4749 > show #9 models
    4750 
    4751 > hide #9 models
    4752 
    4753 > show #!14 models
    4754 
    4755 > hide #8 models
    4756 
    4757 > show #9 models
    4758 
    4759 > ui mousemode right "rotate selected models"
    4760 
    4761 > view matrix models
    4762 > #9,-0.46445,-0.79953,-0.38084,163.55,-0.1926,-0.32855,0.92464,178.17,-0.8644,0.5028,-0.0013961,187.23
    4763 
    4764 > view matrix models
    4765 > #9,-0.43901,-0.71339,-0.54622,158.66,0.21806,-0.67435,0.70548,145.23,-0.87162,0.1906,0.4516,196.26
    4766 
    4767 > view matrix models
    4768 > #9,-0.4878,-0.22692,-0.84295,177.56,-0.14029,-0.9327,0.33226,70.026,-0.86161,0.28033,0.42314,202.97
    4769 
    4770 > view matrix models
    4771 > #9,-0.48207,-0.25635,-0.83779,175.43,-0.05356,-0.94583,0.32023,71.895,-0.8745,0.19924,0.44222,196.14
    4772 
    4773 > view matrix models
    4774 > #9,-0.47677,-0.19158,-0.8579,180.22,-0.087854,-0.96069,0.26336,63.801,-0.87462,0.20093,0.4412,196.2
    4775 
    4776 > ui mousemode right "move picked models"
    4777 
    4778 > view matrix models
    4779 > #9,-0.47677,-0.19158,-0.8579,168.63,-0.087854,-0.96069,0.26336,65.177,-0.87462,0.20093,0.4412,196.79
    4780 
    4781 > view matrix models
    4782 > #9,-0.47677,-0.19158,-0.8579,159.22,-0.087854,-0.96069,0.26336,66.148,-0.87462,0.20093,0.4412,210.7
    4783 
    4784 > select #9
    4785 
    4786 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    4787 
    4788 > ui mousemode right "move picked models"
    4789 
    4790 > hide #9 models
    4791 
    4792 > view matrix models #14,1,0,0,-8.678,0,1,0,5.1742,0,0,1,-33.825
    4793 
    4794 > show #9 models
    4795 
    4796 > hide #!14 models
    4797 
    4798 > show #!14 models
    4799 
    4800 > select #9
    4801 
    4802 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    4803 
    4804 > ui mousemode right "move picked models"
    4805 
    4806 > ui mousemode right "translate selected atoms"
    4807 
    4808 > ui mousemode right "rotate selected models"
    4809 
    4810 > view matrix models
    4811 > #9,-0.31221,-0.22529,-0.92291,161.06,-0.040688,-0.96741,0.24992,67.842,-0.94914,0.11558,0.29287,169.98
    4812 
    4813 > view matrix models
    4814 > #9,-0.27389,0.026902,-0.96138,208.98,-0.14067,-0.98998,0.012374,26.513,-0.95142,0.13863,0.27493,172.15
    4815 
    4816 > view matrix models
    4817 > #9,-0.27566,0.018044,-0.96109,207.13,-0.13736,-0.9903,0.020806,27.74,-0.95139,0.13775,0.27547,172.04
    4818 
    4819 > view matrix models
    4820 > #9,-0.25847,0.014987,-0.9659,207.64,-0.13281,-0.99094,0.020164,27.981,-0.95685,0.13349,0.25812,168.7
    4821 
    4822 > view matrix models
    4823 > #9,-0.25597,0.027767,-0.96629,210.3,-0.13736,-0.99049,0.0079238,26.22,-0.95688,0.13475,0.25735,168.85
    4824 
    4825 > select clear
    4826 
    4827 > select #9
    4828 
    4829 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    4830 
    4831 > view matrix models
    4832 > #9,-0.33257,0.047672,-0.94187,209.58,-0.16132,-0.98688,0.007013,24.506,-0.92918,0.15428,0.3359,184.33
    4833 
    4834 > view matrix models
    4835 > #9,-0.36676,0.027073,-0.92992,203.7,-0.046556,-0.99886,-0.010718,31.198,-0.92915,0.039362,0.3676,165.81
    4836 
    4837 > view matrix models
    4838 > #9,-0.39529,0.031452,-0.91802,203.17,-0.055674,-0.9984,-0.010233,30.465,-0.91687,0.047064,0.39641,171.79
    4839 
    4840 > ui mousemode right "translate selected atoms"
    4841 
    4842 > show #8 models
    4843 
    4844 > hide #!14 models
    4845 
    4846 > select clear
    4847 
    4848 > hide #9 models
    4849 
    4850 > show #!14 models
    4851 
    4852 > show #9 models
    4853 
    4854 > hide #9 models
    4855 
    4856 > hide #8 models
    4857 
    4858 > show #9 models
    4859 
    4860 > select clear
    4861 
    4862 > select #14/E:209-288
    4863 
    4864 618 atoms, 631 bonds, 80 residues, 1 model selected 
    4865 
    4866 > select #14/E
    4867 
    4868 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    4869 
    4870 > ui tool show Matchmaker
    4871 
    4872 > matchmaker #8 to #14 & sel
    4873 
    4874 Parameters 
    4875 --- 
    4876 Chain pairing | bb 
    4877 Alignment algorithm | Needleman-Wunsch 
    4878 Similarity matrix | BLOSUM-62 
    4879 SS fraction | 0.3 
    4880 Gap open (HH/SS/other) | 18/18/6 
    4881 Gap extend | 1 
    4882 SS matrix |  |  | H | S | O 
    4883 ---|---|---|--- 
    4884 H | 6 | -9 | -6 
    4885 S |  | 6 | -6 
    4886 O |  |  | 4 
    4887 Iteration cutoff | 2 
    4888  
    4889 Matchmaker 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    4890 A (#8), sequence alignment score = 2066.9 
    4891 RMSD between 239 pruned atom pairs is 0.651 angstroms; (across all 412 pairs:
    4892 31.465) 
    4893  
    4894 
    4895 > select add #9
    4896 
    4897 26587 atoms, 27354 bonds, 1 pseudobond, 3380 residues, 3 models selected 
    4898 
    4899 > show #8 models
    4900 
    4901 > select subtract #9
    4902 
    4903 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    4904 
    4905 > select clear
    4906 
    4907 > select #14/E#8/E
    4908 
    4909 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    4910 
    4911 > ui tool show Matchmaker
    4912 
    4913 > matchmaker #8 & sel to #14 & sel
    4914 
    4915 Parameters 
    4916 --- 
    4917 Chain pairing | bb 
    4918 Alignment algorithm | Needleman-Wunsch 
    4919 Similarity matrix | BLOSUM-62 
    4920 SS fraction | 0.3 
    4921 Gap open (HH/SS/other) | 18/18/6 
    4922 Gap extend | 1 
    4923 SS matrix |  |  | H | S | O 
    4924 ---|---|---|--- 
    4925 H | 6 | -9 | -6 
    4926 S |  | 6 | -6 
    4927 O |  |  | 4 
    4928 Iteration cutoff | 2 
    4929  
    4930 Matchmaker 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    4931 E (#8), sequence alignment score = 2066.9 
    4932 RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
    4933 31.537) 
    4934  
    4935 
    4936 > hide #9 models
    4937 
    4938 > select clear
    4939 
    4940 > hide #8 models
    4941 
    4942 > select clear
    4943 
    4944 [Repeated 1 time(s)]
    4945 
    4946 > show #8 models
    4947 
    4948 > hide #!14 models
    4949 
    4950 > show #9 models
    4951 
    4952 > select #14/E#9/E
    4953 
    4954 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    4955 
    4956 > matchmaker #9 & sel to #14 & sel
    4957 
    4958 Computing secondary structure 
    4959 Parameters 
    4960 --- 
    4961 Chain pairing | bb 
    4962 Alignment algorithm | Needleman-Wunsch 
    4963 Similarity matrix | BLOSUM-62 
    4964 SS fraction | 0.3 
    4965 Gap open (HH/SS/other) | 18/18/6 
    4966 Gap extend | 1 
    4967 SS matrix |  |  | H | S | O 
    4968 ---|---|---|--- 
    4969 H | 6 | -9 | -6 
    4970 S |  | 6 | -6 
    4971 O |  |  | 4 
    4972 Iteration cutoff | 2 
    4973  
    4974 Matchmaker 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    4975 E (#9), sequence alignment score = 2066.9 
    4976 RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
    4977 31.537) 
    4978  
    4979 
    4980 > select #9
    4981 
    4982 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    4983 
    4984 > ui mousemode right "rotate selected models"
    4985 
    4986 > view matrix models
    4987 > #9,0.33584,0.18461,0.92365,338.65,0.21649,0.93922,-0.26644,340.25,-0.9167,0.28944,0.27546,142.37
    4988 
    4989 > view matrix models
    4990 > #9,0.33894,0.21011,0.91705,343.19,0.21958,0.93015,-0.29427,339.6,-0.91482,0.30111,0.26913,144.55
    4991 
    4992 > view matrix models
    4993 > #9,0.38644,0.19886,0.90062,343.55,0.21939,0.92863,-0.29919,339.46,-0.89584,0.31321,0.31523,146.06
    4994 
    4995 > view matrix models
    4996 > #9,0.38577,0.19903,0.90087,343.54,0.2194,0.92865,-0.29912,339.47,-0.89613,0.31304,0.31458,146.03
    4997 
    4998 > view matrix models
    4999 > #9,0.38662,0.20248,0.89974,344.18,0.20679,0.93173,-0.29854,339.49,-0.89876,0.30148,0.31835,143.91
    5000 
    5001 > select clear
    5002 
    5003 > show #!14 models
    5004 
    5005 > hide #9 models
    5006 
    5007 > hide #8 models
    5008 
    5009 > show #8 models
    5010 
    5011 > hide #!14 models
    5012 
    5013 > show #9 models
    5014 
    5015 > ui mousemode right "rotate selected models"
    5016 
    5017 > select #9
    5018 
    5019 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    5020 
    5021 > view matrix models
    5022 > #9,0.54495,0.14749,0.8254,342.97,0.1938,0.9356,-0.29513,339.55,-0.81577,0.32079,0.48127,145.94
    5023 
    5024 > view matrix models
    5025 > #9,0.57833,0.1368,0.80425,343.01,0.17749,0.94112,-0.28772,339.66,-0.79626,0.30914,0.52,143.71
    5026 
    5027 > hide #8 models
    5028 
    5029 > show #8 models
    5030 
    5031 > select clear
    5032 
    5033 > select #9
    5034 
    5035 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    5036 
    5037 > ui mousemode right "rotate selected models"
    5038 
    5039 > view matrix models
    5040 > #9,-0.33945,-0.19129,-0.92097,299.46,0.018945,-0.9803,0.19663,0.97332,-0.94043,0.049297,0.33638,99.879
    5041 
    5042 > view matrix models
    5043 > #9,-0.2355,-0.20469,-0.95008,301.93,0.041259,-0.97879,0.20065,1.9587,-0.971,0.0080519,0.23895,94.44
    5044 
    5045 > ui mousemode right "move picked models"
    5046 
    5047 > ui mousemode right "translate selected atoms"
    5048 
    5049 > select clear
    5050 
    5051 > select #9
    5052 
    5053 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    5054 
    5055 > ui mousemode right "rotate selected models"
    5056 
    5057 > view matrix models
    5058 > #9,-0.40302,-0.19785,-0.89355,295.32,0.044691,-0.97944,0.19672,2.0829,-0.9141,0.039349,0.40358,97.424
    5059 
    5060 > view matrix models
    5061 > #9,-0.40723,-0.20807,-0.88931,293.39,-0.064428,-0.96473,0.25522,-1.1123,-0.91105,0.16123,0.37947,117.95
    5062 
    5063 > view matrix models
    5064 > #9,-0.44183,-0.20119,-0.87425,292.83,-0.063787,-0.96501,0.25432,-1.1107,-0.89483,0.16813,0.41354,118.8
    5065 
    5066 > view matrix models
    5067 > #9,-0.44244,-0.21887,-0.86968,289.82,-0.038117,-0.9643,0.26207,-0.23275,-0.89599,0.1491,0.4183,115.54
    5068 
    5069 > select clear
    5070 
    5071 > show #!14 models
    5072 
    5073 > hide #8 models
    5074 
    5075 > open /Users/taic/Library/CloudStorage/OneDrive-
    5076 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_1.cif
    5077 > /Users/taic/Library/CloudStorage/OneDrive-
    5078 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_2.cif
    5079 > /Users/taic/Library/CloudStorage/OneDrive-
    5080 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_3.cif
    5081 > /Users/taic/Library/CloudStorage/OneDrive-
    5082 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_4.cif
    5083 
    5084 Chain information for fold_aerolysin_wt_9fm6_model_1.cif #10 
    5085 --- 
    5086 Chain | Description 
    5087 A B C D E F G | . 
    5088  
    5089 Chain information for fold_aerolysin_wt_9fm6_model_2.cif #11 
    5090 --- 
    5091 Chain | Description 
    5092 A B C D E F G | . 
    5093  
    5094 Chain information for fold_aerolysin_wt_9fm6_model_3.cif #13 
    5095 --- 
    5096 Chain | Description 
    5097 A B C D E F G | . 
    5098  
    5099 Chain information for fold_aerolysin_wt_9fm6_model_4.cif #15 
    5100 --- 
    5101 Chain | Description 
    5102 A B C D E F G | . 
    5103  
    5104 
    5105 > ui tool show Matchmaker
    5106 
    5107 > matchmaker #10-11,13,15 to #14
    5108 
    5109 Computing secondary structure 
    5110 [Repeated 7 time(s)]  Parameters 
    5111 --- 
    5112 Chain pairing | bb 
    5113 Alignment algorithm | Needleman-Wunsch 
    5114 Similarity matrix | BLOSUM-62 
    5115 SS fraction | 0.3 
    5116 Gap open (HH/SS/other) | 18/18/6 
    5117 Gap extend | 1 
    5118 SS matrix |  |  | H | S | O 
    5119 ---|---|---|--- 
    5120 H | 6 | -9 | -6 
    5121 S |  | 6 | -6 
    5122 O |  |  | 4 
    5123 Iteration cutoff | 2 
    5124  
    5125 Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_1.cif, chain
    5126 A (#10), sequence alignment score = 2074.7 
    5127 RMSD between 240 pruned atom pairs is 0.637 angstroms; (across all 412 pairs:
    5128 31.072) 
    5129  
    5130 Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_2.cif, chain
    5131 A (#11), sequence alignment score = 2077.7 
    5132 RMSD between 238 pruned atom pairs is 0.626 angstroms; (across all 412 pairs:
    5133 31.112) 
    5134  
    5135 Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_3.cif, chain
    5136 A (#13), sequence alignment score = 2077.7 
    5137 RMSD between 239 pruned atom pairs is 0.770 angstroms; (across all 412 pairs:
    5138 30.864) 
    5139  
    5140 Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_4.cif, chain
    5141 A (#15), sequence alignment score = 2070.5 
    5142 RMSD between 237 pruned atom pairs is 0.727 angstroms; (across all 412 pairs:
    5143 31.238) 
    5144  
    5145 
    5146 > hide #9 models
    5147 
    5148 > hide #10 models
    5149 
    5150 > hide #13 models
    5151 
    5152 > hide #!14 models
    5153 
    5154 > show #13 models
    5155 
    5156 > show #10 models
    5157 
    5158 > show #9 models
    5159 
    5160 > hide #9 models
    5161 
    5162 > show #9 models
    5163 
    5164 > show #8 models
    5165 
    5166 > show #!12 models
    5167 
    5168 > hide #8 models
    5169 
    5170 > show #8 models
    5171 
    5172 > hide #8 models
    5173 
    5174 > hide #9 models
    5175 
    5176 > hide #13 models
    5177 
    5178 > show #13 models
    5179 
    5180 > hide #!12 models
    5181 
    5182 > delete atoms #10-11,13,15
    5183 
    5184 > delete bonds #10-11,13,15
    5185 
    5186 > show #8 models
    5187 
    5188 > show #!14 models
    5189 
    5190 > hide #8 models
    5191 
    5192 > show #!14 atoms
    5193 
    5194 > show #8 models
    5195 
    5196 > hide #8 models
    5197 
    5198 > show #9 models
    5199 
    5200 > hide #!14 models
    5201 
    5202 > show #9 atoms
    5203 
    5204 > show #!14 models
    5205 
    5206 > hide #9 models
    5207 
    5208 > show #9 models
    5209 
    5210 > show #8 models
    5211 
    5212 > hide #9 models
    5213 
    5214 > hide #!14 models
    5215 
    5216 > show #8 atoms
    5217 
    5218 > show #9 models
    5219 
    5220 > hide #9 models
    5221 
    5222 > show #9 models
    5223 
    5224 > hide #8-9 atoms
    5225 
    5226 > show #!14 models
    5227 
    5228 > hide #9 models
    5229 
    5230 > hide #8 models
    5231 
    5232 > show #9 models
    5233 
    5234 > hide #9#!14 atoms
    5235 
    5236 > select #14/E:209-288
    5237 
    5238 618 atoms, 631 bonds, 80 residues, 1 model selected 
    5239 
    5240 > ui tool show "Color Actions"
    5241 
    5242 > select #14/E:209-288
    5243 
    5244 618 atoms, 631 bonds, 80 residues, 1 model selected 
    5245 
    5246 > select :209-288
    5247 
    5248 21819 atoms, 22292 bonds, 1 pseudobond, 2842 residues, 12 models selected 
    5249 
    5250 > select /E:209-288
    5251 
    5252 1854 atoms, 1893 bonds, 240 residues, 3 models selected 
    5253 
    5254 > show #8 models
    5255 
    5256 > hide #8 models
    5257 
    5258 > show #8 models
    5259 
    5260 > hide #9 models
    5261 
    5262 > show #9 models
    5263 
    5264 > hide #9 models
    5265 
    5266 > hide #8 models
    5267 
    5268 > lighting simple
    5269 
    5270 > lighting full
    5271 
    5272 > lighting gentle
    5273 
    5274 > lighting full
    5275 
    5276 > lighting soft
    5277 
    5278 > lighting default
    5279 
    5280 > select clear
    5281 
    5282 > show #8 models
    5283 
    5284 > ui tool show Matchmaker
    5285 
    5286 > matchmaker #8 to #14
    5287 
    5288 Parameters 
    5289 --- 
    5290 Chain pairing | bb 
    5291 Alignment algorithm | Needleman-Wunsch 
    5292 Similarity matrix | BLOSUM-62 
    5293 SS fraction | 0.3 
    5294 Gap open (HH/SS/other) | 18/18/6 
    5295 Gap extend | 1 
    5296 SS matrix |  |  | H | S | O 
    5297 ---|---|---|--- 
    5298 H | 6 | -9 | -6 
    5299 S |  | 6 | -6 
    5300 O |  |  | 4 
    5301 Iteration cutoff | 2 
    5302  
    5303 Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    5304 A (#8), sequence alignment score = 2066.9 
    5305 RMSD between 239 pruned atom pairs is 0.651 angstroms; (across all 412 pairs:
    5306 31.465) 
    5307  
    5308 
    5309 > hide #!14 models
    5310 
    5311 > show #!14 models
    5312 
    5313 > hide #8 models
    5314 
    5315 > show #8 models
    5316 
    5317 > hide #!14 models
    5318 
    5319 > show #9 models
    5320 
    5321 > hide #9 models
    5322 
    5323 > show #!14 models
    5324 
    5325 > hide #8 models
    5326 
    5327 > save /Users/taic/Library/CloudStorage/OneDrive-
    5328 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.png
    5329 > width 600 height 614 supersample 4 transparentBackground true
    5330 
    5331 > show #8 models
    5332 
    5333 > hide #!14 models
    5334 
    5335 > save /Users/taic/Library/CloudStorage/OneDrive-
    5336 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.png
    5337 > width 600 height 614 supersample 4 transparentBackground true
    5338 
    5339 > save /Users/taic/Library/CloudStorage/OneDrive-
    5340 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.side.png
    5341 > width 600 height 614 supersample 4 transparentBackground true
    5342 
    5343 > show #!14 models
    5344 
    5345 > hide #8 models
    5346 
    5347 > save /Users/taic/Library/CloudStorage/OneDrive-
    5348 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.side.png
    5349 > width 600 height 614 supersample 4 transparentBackground true
    5350 
    5351 > select /E
    5352 
    5353 16121 atoms, 16490 bonds, 1 pseudobond, 2037 residues, 10 models selected 
    5354 
    5355 > select ~sel & ##selected
    5356 
    5357 192837 atoms, 201894 bonds, 427 pseudobonds, 21431 residues, 12 models
    5358 selected 
    5359 
    5360 > hide sel & #!14 cartoons
    5361 
    5362 > show #8 models
    5363 
    5364 > hide #8 models
    5365 
    5366 > hide #!14 models
    5367 
    5368 > show #9 models
    5369 
    5370 > select clear
    5371 
    5372 > select #9
    5373 
    5374 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    5375 
    5376 > select clear
    5377 
    5378 > select #9
    5379 
    5380 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    5381 
    5382 > ui mousemode right "rotate selected models"
    5383 
    5384 [Repeated 1 time(s)]
    5385 
    5386 > select clear
    5387 
    5388 > save /Users/taic/Library/CloudStorage/OneDrive-
    5389 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.side-2.png
    5390 > width 600 height 614 supersample 4 transparentBackground true
    5391 
    5392 > select #9
    5393 
    5394 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    5395 
    5396 > ui mousemode right "rotate selected models"
    5397 
    5398 > select clear
    5399 
    5400 > save /Users/taic/Library/CloudStorage/OneDrive-
    5401 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.top-2.png
    5402 > width 600 height 614 supersample 4 transparentBackground true
    5403 
    5404 > select #9
    5405 
    5406 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    5407 
    5408 > select #9/E
    5409 
    5410 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    5411 
    5412 > select ~sel & ##selected
    5413 
    5414 20004 atoms, 20580 bonds, 2544 residues, 1 model selected 
    5415 
    5416 > hide sel atoms
    5417 
    5418 [Repeated 1 time(s)]
    5419 
    5420 > hide sel cartoons
    5421 
    5422 > show #8 models
    5423 
    5424 > show #!14 models
    5425 
    5426 > select #8/E#14/E
    5427 
    5428 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    5429 
    5430 > select ~sel & ##selected
    5431 
    5432 39498 atoms, 40644 bonds, 6 pseudobonds, 5016 residues, 3 models selected 
    5433 
    5434 > hide sel cartoons
    5435 
    5436 > select #8/E#14/E
    5437 
    5438 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    5439 
    5440 > matchmaker #8 & sel to #14 & sel
    5441 
    5442 Parameters 
    5443 --- 
    5444 Chain pairing | bb 
    5445 Alignment algorithm | Needleman-Wunsch 
    5446 Similarity matrix | BLOSUM-62 
    5447 SS fraction | 0.3 
    5448 Gap open (HH/SS/other) | 18/18/6 
    5449 Gap extend | 1 
    5450 SS matrix |  |  | H | S | O 
    5451 ---|---|---|--- 
    5452 H | 6 | -9 | -6 
    5453 S |  | 6 | -6 
    5454 O |  |  | 4 
    5455 Iteration cutoff | 2 
    5456  
    5457 Matchmaker 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    5458 E (#8), sequence alignment score = 2066.9 
    5459 RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
    5460 31.537) 
    5461  
    5462 
    5463 > select clear
    5464 
    5465 > hide #9 models
    5466 
    5467 > show #9 models
    5468 
    5469 > hide #8 models
    5470 
    5471 > show #8 models
    5472 
    5473 > hide #8 models
    5474 
    5475 > show #8 models
    5476 
    5477 > hide #!14 models
    5478 
    5479 > show #!14 models
    5480 
    5481 > hide #8 models
    5482 
    5483 > hide #9 models
    5484 
    5485 > save /Users/taic/Library/CloudStorage/OneDrive-
    5486 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.png
    5487 > width 600 height 614 supersample 4 transparentBackground true
    5488 
    5489 > show #8 models
    5490 
    5491 > hide #!14 models
    5492 
    5493 > save /Users/taic/Library/CloudStorage/OneDrive-
    5494 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one.png
    5495 > width 600 height 614 supersample 4 transparentBackground true
    5496 
    5497 > show #!14 models
    5498 
    5499 > save /Users/taic/Library/CloudStorage/OneDrive-
    5500 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.vs.AF3.unit.png
    5501 > width 600 height 614 supersample 4 transparentBackground true
    5502 
    5503 > show #9 models
    5504 
    5505 > save /Users/taic/Library/CloudStorage/OneDrive-
    5506 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one-2.png
    5507 > width 600 height 614 supersample 4 transparentBackground true
    5508 
    5509 > select #8/E#14/E#9/E:209-288
    5510 
    5511 7201 atoms, 7405 bonds, 1 pseudobond, 916 residues, 4 models selected 
    5512 
    5513 > select clear
    5514 
    5515 > hide #9 models
    5516 
    5517 > hide #8 models
    5518 
    5519 > show #8 models
    5520 
    5521 > hide #!14 models
    5522 
    5523 > show #!14 models
    5524 
    5525 > hide #8 models
    5526 
    5527 > show #8 models
    5528 
    5529 > hide #8 models
    5530 
    5531 > show #8 models
    5532 
    5533 > hide #8 models
    5534 
    5535 > show #8 models
    5536 
    5537 > hide #8 models
    5538 
    5539 > select #14/E:179-190
    5540 
    5541 93 atoms, 95 bonds, 12 residues, 1 model selected 
    5542 
    5543 > color sel medium slate blue target acs
    5544 
    5545 > select #14/E
    5546 
    5547 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    5548 
    5549 > rainbow sel
    5550 
    5551 > select #14/E:180-190
    5552 
    5553 85 atoms, 87 bonds, 11 residues, 1 model selected 
    5554 
    5555 > select #14/E:180-189
    5556 
    5557 78 atoms, 80 bonds, 10 residues, 1 model selected 
    5558 
    5559 > color sel medium slate blue target acs
    5560 
    5561 > select clear
    5562 
    5563 > show #8 models
    5564 
    5565 > select #8/E:180-189
    5566 
    5567 78 atoms, 80 bonds, 10 residues, 1 model selected 
    5568 
    5569 > color sel medium slate blue target acs
    5570 
    5571 > select clear
    5572 
    5573 > select #8/E:180-189
    5574 
    5575 78 atoms, 80 bonds, 10 residues, 1 model selected 
    5576 
    5577 > hide #8 models
    5578 
    5579 > show #8 models
    5580 
    5581 > hide #!14 models
    5582 
    5583 > show #!14 models
    5584 
    5585 > select #8/E:180-194
    5586 
    5587 119 atoms, 121 bonds, 15 residues, 1 model selected 
    5588 
    5589 > color sel medium slate blue target acs
    5590 
    5591 > select #14/E:180-194
    5592 
    5593 119 atoms, 121 bonds, 15 residues, 1 model selected 
    5594 
    5595 > color sel medium slate blue target acs
    5596 
    5597 > hide #8 models
    5598 
    5599 > show #8 models
    5600 
    5601 > hide #8 models
    5602 
    5603 > show #8 models
    5604 
    5605 > hide #!14 models
    5606 
    5607 > show #!14 models
    5608 
    5609 > hide #8 models
    5610 
    5611 > show #8 models
    5612 
    5613 > hide #!14 models
    5614 
    5615 > select #8/E:230-270
    5616 
    5617 320 atoms, 326 bonds, 41 residues, 1 model selected 
    5618 
    5619 > color sel medium slate blue target acs
    5620 
    5621 > select clear
    5622 
    5623 > select #8/E:180
    5624 
    5625 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5626 
    5627 > color sel lime target acs
    5628 
    5629 > select clear
    5630 
    5631 > show #!14 models
    5632 
    5633 > select #14/E:230-270
    5634 
    5635 320 atoms, 326 bonds, 41 residues, 1 model selected 
    5636 
    5637 > color sel medium slate blue target acs
    5638 
    5639 > hide #8 models
    5640 
    5641 > select clear
    5642 
    5643 > show #7 models
    5644 
    5645 > hide #7 models
    5646 
    5647 > show #8 models
    5648 
    5649 > hide #!14 models
    5650 
    5651 > show #!14 models
    5652 
    5653 > hide #8 models
    5654 
    5655 > select #14/E:180-194
    5656 
    5657 119 atoms, 121 bonds, 15 residues, 1 model selected 
    5658 
    5659 > color sel magenta target acs
    5660 
    5661 > color sel hot pink target acs
    5662 
    5663 > color sel magenta target acs
    5664 
    5665 > color sel dark gray target acs
    5666 
    5667 > color sel dim gray target acs
    5668 
    5669 > color sel magenta target acs
    5670 
    5671 > select clear
    5672 
    5673 > select #8/E:180-194
    5674 
    5675 119 atoms, 121 bonds, 15 residues, 1 model selected 
    5676 
    5677 > color sel magenta target acs
    5678 
    5679 > show #8 models
    5680 
    5681 > hide #!14 models
    5682 
    5683 > select clear
    5684 
    5685 > show #!14 models
    5686 
    5687 > hide #!14 models
    5688 
    5689 > show #!14 models
    5690 
    5691 > hide #8 models
    5692 
    5693 > show #8 models
    5694 
    5695 > hide #!14 models
    5696 
    5697 > show #!14 models
    5698 
    5699 > hide #8 models
    5700 
    5701 > show #8 models
    5702 
    5703 > hide #8 models
    5704 
    5705 > show #8 models
    5706 
    5707 > hide #!14 models
    5708 
    5709 > show #!14 models
    5710 
    5711 > show #9 models
    5712 
    5713 > hide #9 models
    5714 
    5715 > show #9 models
    5716 
    5717 > hide #9 models
    5718 
    5719 > hide #8 models
    5720 
    5721 > show #8 models
    5722 
    5723 > hide #8 models
    5724 
    5725 > show #8 models
    5726 
    5727 > hide #!14 models
    5728 
    5729 > show #!14 models
    5730 
    5731 > hide #8 models
    5732 
    5733 > show #!14 atoms
    5734 
    5735 > hide #!14 atoms
    5736 
    5737 > show #!14 atoms
    5738 
    5739 > hide #!14 atoms
    5740 
    5741 > show #!14 atoms
    5742 
    5743 > hide #!14 atoms
    5744 
    5745 > show #8 models
    5746 
    5747 > hide #8 models
    5748 
    5749 > show #!14 atoms
    5750 
    5751 > hide #!14 atoms
    5752 
    5753 > show #!14 atoms
    5754 
    5755 > hide #!14 atoms
    5756 
    5757 > show #!14 atoms
    5758 
    5759 > hide #!14 atoms
    5760 
    5761 > show #9 models
    5762 
    5763 > hide #9 models
    5764 
    5765 > show #8 models
    5766 
    5767 > hide #!14 models
    5768 
    5769 > show #!14 models
    5770 
    5771 > hide #8 models
    5772 
    5773 > show #8 models
    5774 
    5775 > hide #!14 models
    5776 
    5777 > show #!14 models
    5778 
    5779 > hide #8 models
    5780 
    5781 > select #14/E:180-194
    5782 
    5783 119 atoms, 121 bonds, 15 residues, 1 model selected 
    5784 
    5785 > ui tool show "Color Actions"
    5786 
    5787 > color sel violet target acs
    5788 
    5789 > color sel plum target acs
    5790 
    5791 > select clear
    5792 
    5793 > select #14/E:180-194
    5794 
    5795 119 atoms, 121 bonds, 15 residues, 1 model selected 
    5796 
    5797 > color sel violet target acs
    5798 
    5799 > select clear
    5800 
    5801 > select #8/E:180-194
    5802 
    5803 119 atoms, 121 bonds, 15 residues, 1 model selected 
    5804 
    5805 > show #8 models
    5806 
    5807 > color sel violet target acs
    5808 
    5809 > select clear
    5810 
    5811 > hide #!14 models
    5812 
    5813 > show #!14 models
    5814 
    5815 > hide #8 models
    5816 
    5817 > show #8 models
    5818 
    5819 > hide #!14 models
    5820 
    5821 > show #!14 models
    5822 
    5823 > hide #8 models
    5824 
    5825 > save /Users/taic/Library/CloudStorage/OneDrive-
    5826 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.side.png
    5827 > width 600 height 614 supersample 4 transparentBackground true
    5828 
    5829 > show #8 models
    5830 
    5831 > hide #!14 models
    5832 
    5833 > show #!14 models
    5834 
    5835 > hide #!14 models
    5836 
    5837 > show #!14 models
    5838 
    5839 > hide #!14 models
    5840 
    5841 > show #!14 models
    5842 
    5843 > hide #!14 models
    5844 
    5845 > show #!14 models
    5846 
    5847 > hide #8 models
    5848 
    5849 > save /Users/taic/Library/CloudStorage/OneDrive-
    5850 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.side.png
    5851 > width 600 height 614 supersample 4 transparentBackground true
    5852 
    5853 > show #8 models
    5854 
    5855 > hide #!14 models
    5856 
    5857 > save /Users/taic/Library/CloudStorage/OneDrive-
    5858 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one.side.png
    5859 > width 600 height 614 supersample 3 transparentBackground true
    5860 
    5861 > show #9 models
    5862 
    5863 > hide #8 models
    5864 
    5865 > show #8 models
    5866 
    5867 > hide #8 models
    5868 
    5869 > select #/E:180-194
    5870 
    5871 Expected an objects specifier or a keyword 
    5872 
    5873 > select #9/E:180-194
    5874 
    5875 119 atoms, 121 bonds, 15 residues, 1 model selected 
    5876 
    5877 > color sel violet target acs
    5878 
    5879 > show #!14 models
    5880 
    5881 > select #9/E:230-270
    5882 
    5883 320 atoms, 326 bonds, 41 residues, 1 model selected 
    5884 
    5885 > color sel medium slate blue target acs
    5886 
    5887 > select clear
    5888 
    5889 > show #8 models
    5890 
    5891 > hide #!14 models
    5892 
    5893 > hide #9 models
    5894 
    5895 > show #9 models
    5896 
    5897 > hide #8 models
    5898 
    5899 > show #9 atoms
    5900 
    5901 > hide #9 atoms
    5902 
    5903 > show #9 atoms
    5904 
    5905 > hide #9 atoms
    5906 
    5907 > show #!14 models
    5908 
    5909 > hide #9 models
    5910 
    5911 > show #!14 atoms
    5912 
    5913 > show #9 models
    5914 
    5915 > show #9#!14 atoms
    5916 
    5917 > hide #!14 models
    5918 
    5919 > show #!14 models
    5920 
    5921 > hide #!14 models
    5922 
    5923 > hide #9 atoms
    5924 
    5925 [Repeated 1 time(s)]
    5926 
    5927 > show #9 atoms
    5928 
    5929 > hide #9 atoms
    5930 
    5931 > matchmaker #8 to #14
    5932 
    5933 Parameters 
    5934 --- 
    5935 Chain pairing | bb 
    5936 Alignment algorithm | Needleman-Wunsch 
    5937 Similarity matrix | BLOSUM-62 
    5938 SS fraction | 0.3 
    5939 Gap open (HH/SS/other) | 18/18/6 
    5940 Gap extend | 1 
    5941 SS matrix |  |  | H | S | O 
    5942 ---|---|---|--- 
    5943 H | 6 | -9 | -6 
    5944 S |  | 6 | -6 
    5945 O |  |  | 4 
    5946 Iteration cutoff | 2 
    5947  
    5948 Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    5949 A (#8), sequence alignment score = 2066.9 
    5950 RMSD between 239 pruned atom pairs is 0.651 angstroms; (across all 412 pairs:
    5951 31.465) 
    5952  
    5953 
    5954 > show #8 models
    5955 
    5956 > hide #9 models
    5957 
    5958 > show #9 models
    5959 
    5960 > hide #9 models
    5961 
    5962 > show #8 atoms
    5963 
    5964 > hide #8 atoms
    5965 
    5966 > show #8 atoms
    5967 
    5968 > hide #8 atoms
    5969 
    5970 > save /Users/taic/Library/CloudStorage/OneDrive-
    5971 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one.side-2.png
    5972 > width 600 height 614 supersample 4 transparentBackground true
    5973 
    5974 > select #9/E#14/E
    5975 
    5976 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    5977 
    5978 > select #8/E#14/E
    5979 
    5980 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    5981 
    5982 > rainbow sel & #8
    5983 
    5984 > select #9/E:230-270#14/E:230-270
    5985 
    5986 640 atoms, 652 bonds, 82 residues, 2 models selected 
    5987 
    5988 > ui tool show "Color Actions"
    5989 
    5990 > color sel medium slate blue target acs
    5991 
    5992 > select #8/E:230-270#14/E:230-270
    5993 
    5994 640 atoms, 652 bonds, 82 residues, 2 models selected 
    5995 
    5996 > color sel medium slate blue target acs
    5997 
    5998 > select clear
    5999 
    6000 > show #!14 models
    6001 
    6002 > hide #8#!14 atoms
    6003 
    6004 > show #8#!14 cartoons
    6005 
    6006 > hide #8 models
    6007 
    6008 > select #8/E#14/E
    6009 
    6010 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    6011 
    6012 > select ~sel & ##selected
    6013 
    6014 39498 atoms, 40644 bonds, 6 pseudobonds, 5016 residues, 3 models selected 
    6015 
    6016 > hide sel & #!14 cartoons
    6017 
    6018 > show #8 models
    6019 
    6020 > select #9/E
    6021 
    6022 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    6023 
    6024 > select #9/E
    6025 
    6026 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    6027 
    6028 > select #8/E
    6029 
    6030 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    6031 
    6032 > select ~sel & ##selected
    6033 
    6034 20004 atoms, 20580 bonds, 2544 residues, 1 model selected 
    6035 
    6036 > hide sel cartoons
    6037 
    6038 > select #14/E
    6039 
    6040 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    6041 
    6042 > rainbow sel
    6043 
    6044 > select #8/E:230-270#14/E:230-270
    6045 
    6046 640 atoms, 652 bonds, 82 residues, 2 models selected 
    6047 
    6048 > ui tool show "Color Actions"
    6049 
    6050 > color sel medium slate blue target acs
    6051 
    6052 > select clear
    6053 
    6054 [Repeated 1 time(s)]
    6055 
    6056 > hide #8 models
    6057 
    6058 > show #8 models
    6059 
    6060 > hide #!14 models
    6061 
    6062 > show #!14 models
    6063 
    6064 > show #7 models
    6065 
    6066 > hide #7 models
    6067 
    6068 > hide #8 models
    6069 
    6070 > show #8 models
    6071 
    6072 > hide #8 models
    6073 
    6074 > show #8 models
    6075 
    6076 > hide #!14 models
    6077 
    6078 > show #!14 models
    6079 
    6080 > hide #8 models
    6081 
    6082 > show #8 models
    6083 
    6084 > hide #8 models
    6085 
    6086 > save /Users/taic/Library/CloudStorage/OneDrive-
    6087 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.side.png
    6088 > width 600 height 614 supersample 4 transparentBackground true
    6089 
    6090 > show #8 models
    6091 
    6092 > hide #!14 models
    6093 
    6094 > save /Users/taic/Library/CloudStorage/OneDrive-
    6095 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one.side.png
    6096 > width 600 height 614 supersample 4 transparentBackground true
    6097 
    6098 > show #!14 models
    6099 
    6100 > select #8/E
    6101 
    6102 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    6103 
    6104 > select #14/E
    6105 
    6106 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    6107 
    6108 > matchmaker #8 to #14 & sel
    6109 
    6110 Parameters 
    6111 --- 
    6112 Chain pairing | bb 
    6113 Alignment algorithm | Needleman-Wunsch 
    6114 Similarity matrix | BLOSUM-62 
    6115 SS fraction | 0.3 
    6116 Gap open (HH/SS/other) | 18/18/6 
    6117 Gap extend | 1 
    6118 SS matrix |  |  | H | S | O 
    6119 ---|---|---|--- 
    6120 H | 6 | -9 | -6 
    6121 S |  | 6 | -6 
    6122 O |  |  | 4 
    6123 Iteration cutoff | 2 
    6124  
    6125 Matchmaker 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    6126 A (#8), sequence alignment score = 2066.9 
    6127 RMSD between 239 pruned atom pairs is 0.651 angstroms; (across all 412 pairs:
    6128 31.465) 
    6129  
    6130 
    6131 > select /E
    6132 
    6133 16121 atoms, 16490 bonds, 1 pseudobond, 2037 residues, 10 models selected 
    6134 
    6135 > matchmaker #8 & sel to #14 & sel
    6136 
    6137 Parameters 
    6138 --- 
    6139 Chain pairing | bb 
    6140 Alignment algorithm | Needleman-Wunsch 
    6141 Similarity matrix | BLOSUM-62 
    6142 SS fraction | 0.3 
    6143 Gap open (HH/SS/other) | 18/18/6 
    6144 Gap extend | 1 
    6145 SS matrix |  |  | H | S | O 
    6146 ---|---|---|--- 
    6147 H | 6 | -9 | -6 
    6148 S |  | 6 | -6 
    6149 O |  |  | 4 
    6150 Iteration cutoff | 2 
    6151  
    6152 Matchmaker 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
    6153 E (#8), sequence alignment score = 2066.9 
    6154 RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
    6155 31.537) 
    6156  
    6157 
    6158 > hide #8 models
    6159 
    6160 > show #8 models
    6161 
    6162 > hide #!14 models
    6163 
    6164 > show #!14 models
    6165 
    6166 > view matrix models
    6167 > #6,-0.93309,0.34317,0.1076,228.65,-0.35255,-0.81364,-0.46228,428.09,-0.071098,-0.46928,0.88018,97.064,#1,0.10137,-0.47898,-0.87195,135.58,-0.7169,-0.64285,0.26979,167.95,-0.68976,0.59776,-0.40855,143,#2,0.66978,0.72663,-0.15297,163.19,-0.19254,0.3689,0.90931,169.03,0.71716,-0.57959,0.38699,161.31,#3,0.92751,-0.35868,0.10525,145.16,0.37372,0.89551,-0.24166,167.73,-0.0075712,0.26347,0.96464,148.17,#4,0.97266,-0.085236,0.21601,146.04,-0.20296,0.13997,0.96913,171.62,-0.11284,-0.98648,0.11885,149.2,#5,0.9921,0.11709,0.045065,165.23,-0.067586,0.80137,-0.59434,161.78,-0.10571,0.5866,0.80295,144.96,#8,0.46652,0.56007,0.6846,142.53,0.29416,-0.82817,0.47708,160.76,0.83417,-0.021183,-0.55111,132.7,#14,0.9112,-0.40973,0.042858,51.919,0.38133,0.87822,0.28866,-88.748,-0.15591,-0.24668,0.95647,30.601,#9,-0.42594,0.20206,-0.8819,332.53,-0.46082,-0.88728,0.019271,63.445,-0.7786,0.41461,0.47104,128.26
    6168 
    6169 > view matrix models
    6170 > #6,-0.73769,0.37453,-0.56173,291.79,0.036448,-0.80872,-0.58707,378.2,-0.67416,-0.45355,0.58293,239.92,#1,0.34863,-0.86979,-0.34918,137.08,-0.59863,-0.4933,0.63111,168.23,-0.72118,-0.010996,-0.69266,137.85,#2,0.022216,0.98699,-0.15925,146.88,-0.5277,0.14687,0.83664,156.32,0.84914,0.06545,0.5241,167.18,#3,0.78662,-0.24152,-0.56825,141.09,-0.00395,0.91834,-0.39578,163.72,0.61743,0.31357,0.72142,146.91,#4,0.76181,0.57501,0.29836,141.95,-0.53471,0.29814,0.7907,166.8,0.36571,-0.76189,0.53459,149.49,#5,0.80121,-0.10149,-0.58972,156.97,-0.41891,0.6086,-0.67388,151.19,0.4273,0.78696,0.4451,153.19,#8,-0.099169,0.25866,0.96086,147.15,-0.021814,-0.96596,0.25778,160.48,0.99483,0.0046033,0.10144,131.18,#14,0.86755,0.031287,-0.49637,88.033,0.029869,0.99294,0.11479,-19.983,0.49645,-0.11441,0.86049,-80.548,#9,0.059707,-0.29406,-0.95392,272.68,-0.15391,-0.94691,0.28226,0.70996,-0.98628,0.12997,-0.1018,196.79
    6171 
    6172 > hide #8 models
    6173 
    6174 > show #8 models
    6175 
    6176 > hide #8 models
    6177 
    6178 > show #8 models
    6179 
    6180 > hide #!14 models
    6181 
    6182 > show #!14 models
    6183 
    6184 > hide #!14 models
    6185 
    6186 > show #!14 models
    6187 
    6188 > select ~sel & ##selected
    6189 
    6190 192837 atoms, 201894 bonds, 427 pseudobonds, 21431 residues, 12 models
    6191 selected 
    6192 
    6193 > show sel & #8#!14 cartoons
    6194 
    6195 > hide #8 models
    6196 
    6197 > mlp sel & #!14
    6198 
    6199 Map values for surface "9fm6_A SES surface": minimum -28.49, mean -5.274,
    6200 maximum 23.57 
    6201 Map values for surface "9fm6_B SES surface": minimum -28.44, mean -5.228,
    6202 maximum 23.49 
    6203 Map values for surface "9fm6_C SES surface": minimum -30.11, mean -5.256,
    6204 maximum 23.45 
    6205 Map values for surface "9fm6_D SES surface": minimum -30.01, mean -5.292,
    6206 maximum 23.07 
    6207 Map values for surface "9fm6_F SES surface": minimum -27.85, mean -5.245,
    6208 maximum 23.29 
    6209 Map values for surface "9fm6_G SES surface": minimum -28.1, mean -5.267,
    6210 maximum 23.18 
    6211 To also show corresponding color key, enter the above mlp command and add key
    6212 true 
    6213 
    6214 > select clear
    6215 
    6216 > mlp #!14
    6217 
    6218 Map values for surface "9fm6_A SES surface": minimum -28.49, mean -5.274,
    6219 maximum 23.57 
    6220 Map values for surface "9fm6_B SES surface": minimum -28.44, mean -5.228,
    6221 maximum 23.49 
    6222 Map values for surface "9fm6_C SES surface": minimum -30.11, mean -5.256,
    6223 maximum 23.45 
    6224 Map values for surface "9fm6_D SES surface": minimum -30.01, mean -5.292,
    6225 maximum 23.07 
    6226 Map values for surface "9fm6_E SES surface": minimum -28.89, mean -5.236,
    6227 maximum 22.96 
    6228 Map values for surface "9fm6_F SES surface": minimum -27.85, mean -5.245,
    6229 maximum 23.29 
    6230 Map values for surface "9fm6_G SES surface": minimum -28.1, mean -5.267,
    6231 maximum 23.18 
    6232 To also show corresponding color key, enter the above mlp command and add key
    6233 true 
    6234 
    6235 > coulombic #!14
    6236 
    6237 Using Amber 20 recommended default charges and atom types for standard
    6238 residues 
    6239 Coulombic values for 9fm6_A SES surface #14.2: minimum, -19.39, mean -1.41,
    6240 maximum 9.89 
    6241 Coulombic values for 9fm6_B SES surface #14.3: minimum, -18.64, mean -1.42,
    6242 maximum 9.90 
    6243 Coulombic values for 9fm6_C SES surface #14.4: minimum, -19.09, mean -1.41,
    6244 maximum 9.79 
    6245 Coulombic values for 9fm6_D SES surface #14.5: minimum, -19.53, mean -1.54,
    6246 maximum 11.33 
    6247 Coulombic values for 9fm6_E SES surface #14.8: minimum, -19.66, mean -1.68,
    6248 maximum 11.91 
    6249 Coulombic values for 9fm6_F SES surface #14.6: minimum, -19.14, mean -1.55,
    6250 maximum 9.44 
    6251 Coulombic values for 9fm6_G SES surface #14.7: minimum, -18.97, mean -1.42,
    6252 maximum 10.20 
    6253 To also show corresponding color key, enter the above coulombic command and
    6254 add key true 
    6255 
    6256 > show #9 models
    6257 
    6258 > hide #!14 models
    6259 
    6260 > show #8 models
    6261 
    6262 > hide #9 models
    6263 
    6264 > coulombic #8
    6265 
    6266 Using Amber 20 recommended default charges and atom types for standard
    6267 residues 
    6268 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_A SES surface #8.1:
    6269 minimum, -16.74, mean -1.45, maximum 9.96 
    6270 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_B SES surface #8.2:
    6271 minimum, -22.14, mean -1.45, maximum 9.94 
    6272 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_C SES surface #8.3:
    6273 minimum, -17.79, mean -1.41, maximum 9.97 
    6274 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_D SES surface #8.4:
    6275 minimum, -20.47, mean -1.44, maximum 9.74 
    6276 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_E SES surface #8.5:
    6277 minimum, -15.80, mean -1.43, maximum 9.90 
    6278 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_F SES surface #8.6:
    6279 minimum, -16.14, mean -1.45, maximum 9.61 
    6280 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_G SES surface #8.7:
    6281 minimum, -15.60, mean -1.42, maximum 10.22 
    6282 To also show corresponding color key, enter the above coulombic command and
    6283 add key true 
    6284 
    6285 > coulombic #!8
    6286 
    6287 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_A SES surface #8.1:
    6288 minimum, -16.74, mean -1.45, maximum 9.96 
    6289 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_B SES surface #8.2:
    6290 minimum, -22.14, mean -1.45, maximum 9.94 
    6291 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_C SES surface #8.3:
    6292 minimum, -17.79, mean -1.41, maximum 9.97 
    6293 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_D SES surface #8.4:
    6294 minimum, -20.47, mean -1.44, maximum 9.74 
    6295 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_E SES surface #8.5:
    6296 minimum, -15.80, mean -1.43, maximum 9.90 
    6297 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_F SES surface #8.6:
    6298 minimum, -16.14, mean -1.45, maximum 9.61 
    6299 Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_G SES surface #8.7:
    6300 minimum, -15.60, mean -1.42, maximum 10.22 
    6301 To also show corresponding color key, enter the above coulombic command and
    6302 add key true 
    6303 
    6304 > hide #!8 surfaces
    6305 
    6306 > open 1PRE fromDatabase pdb format mmcif
    6307 
    6308 Summary of feedback from opening 1PRE fetched from pdb 
    6309 --- 
    6310 note | Fetching compressed mmCIF 1pre from http://files.rcsb.org/download/1pre.cif 
    6311  
    6312 1pre title: 
    6313 Proaerolysin [more info...] 
    6314  
    6315 Chain information for 1pre #10 
    6316 --- 
    6317 Chain | Description | UniProt 
    6318 A B | PROAEROLYSIN | AERA_AERHY 1-470 
    6319  
    6320 
    6321 > select ~sel & ##selected
    6322 
    6323 Nothing selected 
    6324 
    6325 > select down
    6326 
    6327 Nothing selected 
    6328 
    6329 > select #14/E
    6330 
    6331 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    6332 
    6333 > select #14/E
    6334 
    6335 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    6336 
    6337 > show #!14 models
    6338 
    6339 > show #7 models
    6340 
    6341 > hide #7 models
    6342 
    6343 > hide sel surfaces
    6344 
    6345 > matchmaker #!10 to #14 & sel
    6346 
    6347 Computing secondary structure 
    6348 Parameters 
    6349 --- 
    6350 Chain pairing | bb 
    6351 Alignment algorithm | Needleman-Wunsch 
    6352 Similarity matrix | BLOSUM-62 
    6353 SS fraction | 0.3 
    6354 Gap open (HH/SS/other) | 18/18/6 
    6355 Gap extend | 1 
    6356 SS matrix |  |  | H | S | O 
    6357 ---|---|---|--- 
    6358 H | 6 | -9 | -6 
    6359 S |  | 6 | -6 
    6360 O |  |  | 4 
    6361 Iteration cutoff | 2 
    6362  
    6363 Matchmaker 9fm6, chain E (#14) with 1pre, chain B (#10), sequence alignment
    6364 score = 2033.3 
    6365 RMSD between 136 pruned atom pairs is 0.493 angstroms; (across all 411 pairs:
    6366 35.144) 
    6367  
    6368 
    6369 > hide #!8 models
    6370 
    6371 > hide #!14 models
    6372 
    6373 > color #!10 bychain
    6374 
    6375 > select #8/E
    6376 
    6377 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    6378 
    6379 > matchmaker #!10 to #8 & sel
    6380 
    6381 Computing secondary structure 
    6382 Parameters 
    6383 --- 
    6384 Chain pairing | bb 
    6385 Alignment algorithm | Needleman-Wunsch 
    6386 Similarity matrix | BLOSUM-62 
    6387 SS fraction | 0.3 
    6388 Gap open (HH/SS/other) | 18/18/6 
    6389 Gap extend | 1 
    6390 SS matrix |  |  | H | S | O 
    6391 ---|---|---|--- 
    6392 H | 6 | -9 | -6 
    6393 S |  | 6 | -6 
    6394 O |  |  | 4 
    6395 Iteration cutoff | 2 
    6396  
    6397 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 1pre, chain B
    6398 (#10), sequence alignment score = 2199.2 
    6399 RMSD between 256 pruned atom pairs is 0.714 angstroms; (across all 423 pairs:
    6400 17.434) 
    6401  
    6402 
    6403 > show #!8 models
    6404 
    6405 > hide #!8 models
    6406 
    6407 > select #10/A
    6408 
    6409 3541 atoms, 3622 bonds, 2 pseudobonds, 467 residues, 2 models selected 
    6410 
    6411 > hide sel cartoons
    6412 
    6413 > show #!8 models
    6414 
    6415 > select #8/E
    6416 
    6417 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    6418 
    6419 > select ~sel & ##selected
    6420 
    6421 20004 atoms, 20580 bonds, 2544 residues, 1 model selected 
    6422 
    6423 > hide sel cartoons
    6424 
    6425 > select #10
    6426 
    6427 7089 atoms, 7255 bonds, 3 pseudobonds, 933 residues, 3 models selected 
    6428 
    6429 > color sel dark gray target acs
    6430 
    6431 > select clear
    6432 
    6433 > select #8/E
    6434 
    6435 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    6436 
    6437 > select #8/E#10/B
    6438 
    6439 6882 atoms, 7063 bonds, 1 pseudobond, 890 residues, 3 models selected 
    6440 
    6441 > matchmaker #!10 & sel to #8 & sel
    6442 
    6443 Computing secondary structure 
    6444 Parameters 
    6445 --- 
    6446 Chain pairing | bb 
    6447 Alignment algorithm | Needleman-Wunsch 
    6448 Similarity matrix | BLOSUM-62 
    6449 SS fraction | 0.3 
    6450 Gap open (HH/SS/other) | 18/18/6 
    6451 Gap extend | 1 
    6452 SS matrix |  |  | H | S | O 
    6453 ---|---|---|--- 
    6454 H | 6 | -9 | -6 
    6455 S |  | 6 | -6 
    6456 O |  |  | 4 
    6457 Iteration cutoff | 2 
    6458  
    6459 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 1pre, chain B
    6460 (#10), sequence alignment score = 2199.2 
    6461 RMSD between 256 pruned atom pairs is 0.714 angstroms; (across all 423 pairs:
    6462 17.434) 
    6463  
    6464 
    6465 > select clear
    6466 
    6467 > hide #!10 models
    6468 
    6469 > show #!10 models
    6470 
    6471 > hide #!8 models
    6472 
    6473 > show #!8 models
    6474 
    6475 > show #!14 models
    6476 
    6477 > hide #!8 models
    6478 
    6479 > select #14/E
    6480 
    6481 3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected 
    6482 
    6483 > select ~sel & ##selected
    6484 
    6485 19494 atoms, 20064 bonds, 6 pseudobonds, 2472 residues, 2 models selected 
    6486 
    6487 > hide sel surfaces
    6488 
    6489 > hide sel cartoons
    6490 
    6491 > show #!8 models
    6492 
    6493 > hide #!10 models
    6494 
    6495 > show #!10 models
    6496 
    6497 > hide #!8 models
    6498 
    6499 > show #!8 models
    6500 
    6501 > hide #!14 models
    6502 
    6503 > show #!14 models
    6504 
    6505 > hide #!10 models
    6506 
    6507 > show #!10 models
    6508 
    6509 > hide #!14 models
    6510 
    6511 > show #!14 models
    6512 
    6513 > hide #!10 models
    6514 
    6515 > save /Users/taic/Library/CloudStorage/OneDrive-
    6516 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.vs.AF3.one.png
    6517 > width 600 height 614 supersample 4 transparentBackground true
    6518 
    6519 > show #!10 models
    6520 
    6521 > hide #!14 models
    6522 
    6523 > save /Users/taic/Library/CloudStorage/OneDrive-
    6524 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/1PRE.vs.AF3.one.png
    6525 > width 600 height 614 supersample 4 transparentBackground true
    6526 
    6527 > show #!14 models
    6528 
    6529 > hide #!10 models
    6530 
    6531 > hide #!8 models
    6532 
    6533 > save /Users/taic/Library/CloudStorage/OneDrive-
    6534 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.side.png
    6535 > width 600 height 614 supersample 4 transparentBackground true
    6536 
    6537 > show #!8 models
    6538 
    6539 > select #14/E#8/E
    6540 
    6541 6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected 
    6542 
    6543 > matchmaker #!10 & sel to #8 & sel
    6544 
    6545 No molecules/chains to match specified 
    6546 
    6547 > matchmaker #!14 & sel to #8 & sel
    6548 
    6549 Parameters 
    6550 --- 
    6551 Chain pairing | bb 
    6552 Alignment algorithm | Needleman-Wunsch 
    6553 Similarity matrix | BLOSUM-62 
    6554 SS fraction | 0.3 
    6555 Gap open (HH/SS/other) | 18/18/6 
    6556 Gap extend | 1 
    6557 SS matrix |  |  | H | S | O 
    6558 ---|---|---|--- 
    6559 H | 6 | -9 | -6 
    6560 S |  | 6 | -6 
    6561 O |  |  | 4 
    6562 Iteration cutoff | 2 
    6563  
    6564 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 9fm6, chain E
    6565 (#14), sequence alignment score = 2066.9 
    6566 RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
    6567 31.537) 
    6568  
    6569 
    6570 > show #!10 models
    6571 
    6572 > hide #!14 models
    6573 
    6574 > matchmaker #!10 & sel to #8 & sel
    6575 
    6576 No molecules/chains to match specified 
    6577 
    6578 > select #8/E#10/B
    6579 
    6580 6882 atoms, 7063 bonds, 1 pseudobond, 890 residues, 3 models selected 
    6581 
    6582 > matchmaker #!10 & sel to #8 & sel
    6583 
    6584 Computing secondary structure 
    6585 Parameters 
    6586 --- 
    6587 Chain pairing | bb 
    6588 Alignment algorithm | Needleman-Wunsch 
    6589 Similarity matrix | BLOSUM-62 
    6590 SS fraction | 0.3 
    6591 Gap open (HH/SS/other) | 18/18/6 
    6592 Gap extend | 1 
    6593 SS matrix |  |  | H | S | O 
    6594 ---|---|---|--- 
    6595 H | 6 | -9 | -6 
    6596 S |  | 6 | -6 
    6597 O |  |  | 4 
    6598 Iteration cutoff | 2 
    6599  
    6600 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 1pre, chain B
    6601 (#10), sequence alignment score = 2199.2 
    6602 RMSD between 256 pruned atom pairs is 0.714 angstroms; (across all 423 pairs:
    6603 17.434) 
    6604  
    6605 
    6606 > hide #!8 models
    6607 
    6608 > show #!8 models
    6609 
    6610 > hide #!10 models
    6611 
    6612 > show #9 models
    6613 
    6614 > hide #9 models
    6615 
    6616 > show #!14 models
    6617 
    6618 > select #8#10
    6619 
    6620 30427 atoms, 31265 bonds, 3 pseudobonds, 3901 residues, 4 models selected 
    6621 
    6622 > show sel & #!8 cartoons
    6623 
    6624 > select #8#14
    6625 
    6626 46081 atoms, 47418 bonds, 7 pseudobonds, 5852 residues, 3 models selected 
    6627 
    6628 > show sel cartoons
    6629 
    6630 > hide #!8 models
    6631 
    6632 > show #!8 models
    6633 
    6634 > hide #!14 models
    6635 
    6636 > show #!14 models
    6637 
    6638 > hide #!14 models
    6639 
    6640 > select clear
    6641 
    6642 > open 5JZH fromDatabase pdb format mmcif
    6643 
    6644 Summary of feedback from opening 5JZH fetched from pdb 
    6645 --- 
    6646 note | Fetching compressed mmCIF 5jzh from http://files.rcsb.org/download/5jzh.cif 
    6647  
    6648 5jzh title: 
    6649 Cryo-EM structure of aerolysin prepore [more info...] 
    6650  
    6651 Chain information for 5jzh #11 
    6652 --- 
    6653 Chain | Description | UniProt 
    6654 A B C D E F G H I J K L M N | Aerolysin | AERA_AERHY 1-424 
    6655  
    6656 5jzh mmCIF Assemblies 
    6657 --- 
    6658 1| author_defined_assembly 
    6659 2| author_defined_assembly 
    6660  
    6661 
    6662 > hide #11#!8 atoms
    6663 
    6664 > show #11#!8 cartoons
    6665 
    6666 > matchmaker #11 to #8
    6667 
    6668 Computing secondary structure 
    6669 Parameters 
    6670 --- 
    6671 Chain pairing | bb 
    6672 Alignment algorithm | Needleman-Wunsch 
    6673 Similarity matrix | BLOSUM-62 
    6674 SS fraction | 0.3 
    6675 Gap open (HH/SS/other) | 18/18/6 
    6676 Gap extend | 1 
    6677 SS matrix |  |  | H | S | O 
    6678 ---|---|---|--- 
    6679 H | 6 | -9 | -6 
    6680 S |  | 6 | -6 
    6681 O |  |  | 4 
    6682 Iteration cutoff | 2 
    6683  
    6684 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 5jzh, chain A
    6685 (#11), sequence alignment score = 2122.9 
    6686 RMSD between 396 pruned atom pairs is 0.870 angstroms; (across all 424 pairs:
    6687 1.173) 
    6688  
    6689 
    6690 > select #8/E
    6691 
    6692 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    6693 
    6694 > matchmaker #11 to #8 & sel
    6695 
    6696 Computing secondary structure 
    6697 Parameters 
    6698 --- 
    6699 Chain pairing | bb 
    6700 Alignment algorithm | Needleman-Wunsch 
    6701 Similarity matrix | BLOSUM-62 
    6702 SS fraction | 0.3 
    6703 Gap open (HH/SS/other) | 18/18/6 
    6704 Gap extend | 1 
    6705 SS matrix |  |  | H | S | O 
    6706 ---|---|---|--- 
    6707 H | 6 | -9 | -6 
    6708 S |  | 6 | -6 
    6709 O |  |  | 4 
    6710 Iteration cutoff | 2 
    6711  
    6712 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 5jzh, chain A
    6713 (#11), sequence alignment score = 2122.9 
    6714 RMSD between 365 pruned atom pairs is 0.790 angstroms; (across all 424 pairs:
    6715 1.323) 
    6716  
    6717 
    6718 > matchmaker #11 to #14
    6719 
    6720 Computing secondary structure 
    6721 Parameters 
    6722 --- 
    6723 Chain pairing | bb 
    6724 Alignment algorithm | Needleman-Wunsch 
    6725 Similarity matrix | BLOSUM-62 
    6726 SS fraction | 0.3 
    6727 Gap open (HH/SS/other) | 18/18/6 
    6728 Gap extend | 1 
    6729 SS matrix |  |  | H | S | O 
    6730 ---|---|---|--- 
    6731 H | 6 | -9 | -6 
    6732 S |  | 6 | -6 
    6733 O |  |  | 4 
    6734 Iteration cutoff | 2 
    6735  
    6736 Matchmaker 9fm6, chain A (#14) with 5jzh, chain A (#11), sequence alignment
    6737 score = 1957.6 
    6738 RMSD between 240 pruned atom pairs is 0.671 angstroms; (across all 412 pairs:
    6739 30.764) 
    6740  
    6741 
    6742 > show #!14 models
    6743 
    6744 > hide #!8 models
    6745 
    6746 > show #!8 models
    6747 
    6748 > hide #!8 models
    6749 
    6750 > show #!8 models
    6751 
    6752 > hide #!8 models
    6753 
    6754 > show #!8 models
    6755 
    6756 > hide #!14 models
    6757 
    6758 > hide #!8 models
    6759 
    6760 > show #!8 models
    6761 
    6762 > hide #!8 models
    6763 
    6764 > show #!8 models
    6765 
    6766 > hide #!8 models
    6767 
    6768 > select #11/A/B/C/D/E
    6769 
    6770 32425 atoms, 32910 bonds, 2120 residues, 1 model selected 
    6771 
    6772 > select ~sel & ##selected
    6773 
    6774 58365 atoms, 59238 bonds, 3816 residues, 1 model selected 
    6775 
    6776 > select #11/A/B/C/D/E/F/G
    6777 
    6778 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6779 
    6780 > select ~sel
    6781 
    6782 309759 atoms, 321009 bonds, 451 pseudobonds, 33583 residues, 20 models
    6783 selected 
    6784 
    6785 > select #11/A/B/C/D/E/F/G
    6786 
    6787 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6788 
    6789 > select ~sel & ##selected
    6790 
    6791 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6792 
    6793 > hide sel cartoons
    6794 
    6795 > show #!8 models
    6796 
    6797 > hide #!8 models
    6798 
    6799 > show #!8 models
    6800 
    6801 > hide #!8 models
    6802 
    6803 > show #!14 models
    6804 
    6805 > show #!10 models
    6806 
    6807 > hide #!10 models
    6808 
    6809 > hide #!14 models
    6810 
    6811 > show #!10 models
    6812 
    6813 > hide #!10 models
    6814 
    6815 > show #!10 models
    6816 
    6817 > hide #!10 models
    6818 
    6819 > show #!8 models
    6820 
    6821 > select #11/A/B/C/D/E/F/G
    6822 
    6823 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6824 
    6825 > matchmaker #11 & sel to #8
    6826 
    6827 Computing secondary structure 
    6828 Parameters 
    6829 --- 
    6830 Chain pairing | bb 
    6831 Alignment algorithm | Needleman-Wunsch 
    6832 Similarity matrix | BLOSUM-62 
    6833 SS fraction | 0.3 
    6834 Gap open (HH/SS/other) | 18/18/6 
    6835 Gap extend | 1 
    6836 SS matrix |  |  | H | S | O 
    6837 ---|---|---|--- 
    6838 H | 6 | -9 | -6 
    6839 S |  | 6 | -6 
    6840 O |  |  | 4 
    6841 Iteration cutoff | 2 
    6842  
    6843 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 5jzh, chain A
    6844 (#11), sequence alignment score = 2122.9 
    6845 RMSD between 396 pruned atom pairs is 0.870 angstroms; (across all 424 pairs:
    6846 1.173) 
    6847  
    6848 
    6849 > select clear
    6850 
    6851 > hide #!8 models
    6852 
    6853 > color #11 bychain
    6854 
    6855 > show #!8 models
    6856 
    6857 > hide #11 models
    6858 
    6859 > show #11 models
    6860 
    6861 > hide #!8 models
    6862 
    6863 > show #!8 models
    6864 
    6865 > select #11/A/B/C/D/E/F/G
    6866 
    6867 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6868 
    6869 > color sel tan target acs
    6870 
    6871 > select clear
    6872 
    6873 > select #11/A/B/C/D/E/F/G
    6874 
    6875 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6876 
    6877 > hide #11 models
    6878 
    6879 > show #11 models
    6880 
    6881 > select #11/A/B/C/D/E/F/G
    6882 
    6883 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6884 
    6885 > color sel sky blue target acs
    6886 
    6887 > select clear
    6888 
    6889 > select #11/A/B/C/D/E/F/G
    6890 
    6891 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6892 
    6893 > color sel cornflower blue target acs
    6894 
    6895 > select #11/A/B/C/D/E/F/G
    6896 
    6897 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6898 
    6899 > select clear
    6900 
    6901 > select #11/A/B/C/D/E/F/G
    6902 
    6903 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6904 
    6905 > color sel royal blue target acs
    6906 
    6907 > color sel powder blue target acs
    6908 
    6909 > select clear
    6910 
    6911 > select #11/A/B/C/D/E/F/G
    6912 
    6913 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6914 
    6915 > color sel pale violet red target acs
    6916 
    6917 > select clear
    6918 
    6919 > select #11/A/B/C/D/E/F/G
    6920 
    6921 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6922 
    6923 > color sel pink target acs
    6924 
    6925 > color sel plum target acs
    6926 
    6927 > color sel peach puff target acs
    6928 
    6929 > color sel pink target acs
    6930 
    6931 > color sel light pink target acs
    6932 
    6933 > select clear
    6934 
    6935 > select #11/A/B/C/D/E/F/G
    6936 
    6937 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6938 
    6939 > color sel bychain
    6940 
    6941 > select clear
    6942 
    6943 [Repeated 1 time(s)]
    6944 
    6945 > select #11/A/B/C/D/E/F/G
    6946 
    6947 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6948 
    6949 > color sel tan target acs
    6950 
    6951 > select clear
    6952 
    6953 > hide #11 models
    6954 
    6955 > select #11/A/B/C/D/E/F/G
    6956 
    6957 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6958 
    6959 > color sel sky blue target acs
    6960 
    6961 > select add #8
    6962 
    6963 68733 atoms, 70084 bonds, 5936 residues, 2 models selected 
    6964 
    6965 > select add #11
    6966 
    6967 114128 atoms, 116158 bonds, 8904 residues, 9 models selected 
    6968 
    6969 > select subtract #11
    6970 
    6971 23338 atoms, 24010 bonds, 2968 residues, 8 models selected 
    6972 
    6973 > color sel sky blue target acs
    6974 
    6975 > select clear
    6976 
    6977 > show #!10 models
    6978 
    6979 > hide #!10 models
    6980 
    6981 > show #11 models
    6982 
    6983 > hide #!8 models
    6984 
    6985 > select #11/A/B/C/D/E/F/G
    6986 
    6987 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6988 
    6989 > color sel tan target acs
    6990 
    6991 > select clear
    6992 
    6993 > show #!8 models
    6994 
    6995 > select #11/A/B/C/D/E/F/G
    6996 
    6997 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    6998 
    6999 > hide #!8 models
    7000 
    7001 > hide #11 models
    7002 
    7003 > show #!8 models
    7004 
    7005 > select add #8
    7006 
    7007 68733 atoms, 70084 bonds, 5936 residues, 2 models selected 
    7008 
    7009 > select add #11
    7010 
    7011 114128 atoms, 116158 bonds, 8904 residues, 9 models selected 
    7012 
    7013 > select subtract #11
    7014 
    7015 23338 atoms, 24010 bonds, 2968 residues, 8 models selected 
    7016 
    7017 > color sel plum target acs
    7018 
    7019 > select clear
    7020 
    7021 > show #11 models
    7022 
    7023 > select #11/A/B/C/D/E/F/G
    7024 
    7025 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    7026 
    7027 > color sel dodger blue target acs
    7028 
    7029 > color sel cornflower blue target acs
    7030 
    7031 > select clear
    7032 
    7033 > hide #11 models
    7034 
    7035 > select add #8
    7036 
    7037 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    7038 
    7039 > color sel tan target acs
    7040 
    7041 > select clear
    7042 
    7043 > show #11 models
    7044 
    7045 > hide #!8 models
    7046 
    7047 > hide #11 models
    7048 
    7049 > show #!8 models
    7050 
    7051 > select add #8
    7052 
    7053 23338 atoms, 24010 bonds, 2968 residues, 1 model selected 
    7054 
    7055 > color sel lime target acs
    7056 
    7057 > select clear
    7058 
    7059 > show #11 models
    7060 
    7061 > hide #11 models
    7062 
    7063 > color #!8 bychain
    7064 
    7065 > select #8/A
    7066 
    7067 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    7068 
    7069 > rainbow sel
    7070 
    7071 > select clear
    7072 
    7073 > color #!8 bychain
    7074 
    7075 > select #8/E
    7076 
    7077 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    7078 
    7079 > rainbow sel
    7080 
    7081 > show #11 models
    7082 
    7083 > hide #!8 models
    7084 
    7085 > show #!8 models
    7086 
    7087 > hide #11 models
    7088 
    7089 > show #11 models
    7090 
    7091 > select clear
    7092 
    7093 > save /Users/taic/Library/CloudStorage/OneDrive-
    7094 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/5JZHvsAF3.top.png
    7095 > width 600 height 614 supersample 4 transparentBackground true
    7096 
    7097 > save /Users/taic/Library/CloudStorage/OneDrive-
    7098 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/5JZHvsAF3.side.png
    7099 > width 600 height 614 supersample 4 transparentBackground true
    7100 
    7101 > show #!14 models
    7102 
    7103 > hide #11 models
    7104 
    7105 > hide #!8 models
    7106 
    7107 > show #11 models
    7108 
    7109 > hide #!14 models
    7110 
    7111 > open 9FMX fromDatabase pdb format mmcif
    7112 
    7113 Summary of feedback from opening 9FMX fetched from pdb 
    7114 --- 
    7115 note | Fetching compressed mmCIF 9fmx from http://files.rcsb.org/download/9fmx.cif 
    7116  
    7117 9fmx title: 
    7118 Aerolysin Y221G - prepore [more info...] 
    7119  
    7120 Chain information for 9fmx #13 
    7121 --- 
    7122 Chain | Description | UniProt 
    7123 A B C D E F G H I J K L M N | Aerolysin | AERA_AERHY 1-470 
    7124  
    7125 
    7126 > show #11,13 cartoons
    7127 
    7128 > hide #11,13 atoms
    7129 
    7130 > hide #11 models
    7131 
    7132 > matchmaker #!14 & sel to #11
    7133 
    7134 No molecules/chains to match specified 
    7135 
    7136 > matchmaker #!14 to #11
    7137 
    7138 Computing secondary structure 
    7139 Parameters 
    7140 --- 
    7141 Chain pairing | bb 
    7142 Alignment algorithm | Needleman-Wunsch 
    7143 Similarity matrix | BLOSUM-62 
    7144 SS fraction | 0.3 
    7145 Gap open (HH/SS/other) | 18/18/6 
    7146 Gap extend | 1 
    7147 SS matrix |  |  | H | S | O 
    7148 ---|---|---|--- 
    7149 H | 6 | -9 | -6 
    7150 S |  | 6 | -6 
    7151 O |  |  | 4 
    7152 Iteration cutoff | 2 
    7153  
    7154 Matchmaker 5jzh, chain A (#11) with 9fm6, chain A (#14), sequence alignment
    7155 score = 1957.6 
    7156 RMSD between 240 pruned atom pairs is 0.671 angstroms; (across all 412 pairs:
    7157 30.764) 
    7158  
    7159 
    7160 > matchmaker #13 to #11
    7161 
    7162 Computing secondary structure 
    7163 [Repeated 1 time(s)]  Parameters 
    7164 --- 
    7165 Chain pairing | bb 
    7166 Alignment algorithm | Needleman-Wunsch 
    7167 Similarity matrix | BLOSUM-62 
    7168 SS fraction | 0.3 
    7169 Gap open (HH/SS/other) | 18/18/6 
    7170 Gap extend | 1 
    7171 SS matrix |  |  | H | S | O 
    7172 ---|---|---|--- 
    7173 H | 6 | -9 | -6 
    7174 S |  | 6 | -6 
    7175 O |  |  | 4 
    7176 Iteration cutoff | 2 
    7177  
    7178 Matchmaker 5jzh, chain A (#11) with 9fmx, chain A (#13), sequence alignment
    7179 score = 2135.5 
    7180 RMSD between 418 pruned atom pairs is 0.578 angstroms; (across all 424 pairs:
    7181 0.683) 
    7182  
    7183 
    7184 > show #!14 models
    7185 
    7186 > select #13/H#13/I#13/J#13/L#13/M#13/N#13/K
    7187 
    7188 45388 atoms, 46067 bonds, 2968 residues, 1 model selected 
    7189 
    7190 > hide sel cartoons
    7191 
    7192 > hide #!14 models
    7193 
    7194 > show #7 models
    7195 
    7196 > hide #7 models
    7197 
    7198 > show #!8 models
    7199 
    7200 > select #13/H#13/I#13/J#13/L#13/M#13/N#13/K
    7201 
    7202 45388 atoms, 46067 bonds, 2968 residues, 1 model selected 
    7203 
    7204 > select ~sel & ##selected
    7205 
    7206 45388 atoms, 46067 bonds, 2968 residues, 1 model selected 
    7207 
    7208 > matchmaker #13 & sel to #8
    7209 
    7210 Computing secondary structure 
    7211 Parameters 
    7212 --- 
    7213 Chain pairing | bb 
    7214 Alignment algorithm | Needleman-Wunsch 
    7215 Similarity matrix | BLOSUM-62 
    7216 SS fraction | 0.3 
    7217 Gap open (HH/SS/other) | 18/18/6 
    7218 Gap extend | 1 
    7219 SS matrix |  |  | H | S | O 
    7220 ---|---|---|--- 
    7221 H | 6 | -9 | -6 
    7222 S |  | 6 | -6 
    7223 O |  |  | 4 
    7224 Iteration cutoff | 2 
    7225  
    7226 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
    7227 (#13), sequence alignment score = 2181.4 
    7228 RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
    7229 0.985) 
    7230  
    7231 
    7232 > select clear
    7233 
    7234 > select #13:221
    7235 
    7236 98 atoms, 84 bonds, 14 residues, 1 model selected 
    7237 
    7238 > show #!14 models
    7239 
    7240 > hide #!8 models
    7241 
    7242 > select #13:221#14:221
    7243 
    7244 182 atoms, 168 bonds, 21 residues, 2 models selected 
    7245 
    7246 > show sel atoms
    7247 
    7248 > hide sel atoms
    7249 
    7250 > hide #13 models
    7251 
    7252 > show #13 models
    7253 
    7254 > hide #!14 models
    7255 
    7256 > show #!14 models
    7257 
    7258 > hide #13 models
    7259 
    7260 > show #13 models
    7261 
    7262 > select #13:/D
    7263 
    7264 Expected an objects specifier or a keyword 
    7265 
    7266 > select #13/D
    7267 
    7268 6484 atoms, 6581 bonds, 424 residues, 1 model selected 
    7269 
    7270 > hide #!14 models
    7271 
    7272 > rainbow sel
    7273 
    7274 > open /Users/taic/Library/CloudStorage/OneDrive-
    7275 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_0.cif
    7276 
    7277 Chain information for fold_aerolysin_9fmx_model_0.cif #15 
    7278 --- 
    7279 Chain | Description 
    7280 A B C D E F G | . 
    7281  
    7282 
    7283 > open /Users/taic/Library/CloudStorage/OneDrive-
    7284 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_1.cif
    7285 
    7286 Chain information for fold_aerolysin_9fmx_model_1.cif #16 
    7287 --- 
    7288 Chain | Description 
    7289 A B C D E F G | . 
    7290  
    7291 
    7292 > open /Users/taic/Library/CloudStorage/OneDrive-
    7293 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_2.cif
    7294 
    7295 Chain information for fold_aerolysin_9fmx_model_2.cif #17 
    7296 --- 
    7297 Chain | Description 
    7298 A B C D E F G | . 
    7299  
    7300 
    7301 > open /Users/taic/Library/CloudStorage/OneDrive-
    7302 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_3.cif
    7303 
    7304 Chain information for fold_aerolysin_9fmx_model_3.cif #18 
    7305 --- 
    7306 Chain | Description 
    7307 A B C D E F G | . 
    7308  
    7309 
    7310 > open /Users/taic/Library/CloudStorage/OneDrive-
    7311 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_4.cif
    7312 
    7313 Chain information for fold_aerolysin_9fmx_model_4.cif #19 
    7314 --- 
    7315 Chain | Description 
    7316 A B C D E F G | . 
    7317  
    7318 
    7319 > hide #13 models
    7320 
    7321 > select add #13
    7322 
    7323 90776 atoms, 92134 bonds, 5936 residues, 1 model selected 
    7324 
    7325 > select subtract #13
    7326 
    7327 Nothing selected 
    7328 
    7329 > show #15-19 cartoons
    7330 
    7331 Computing secondary structure 
    7332 [Repeated 4 time(s)]
    7333 
    7334 > show #15-19 cartoons
    7335 
    7336 > hide #15-19 atoms
    7337 
    7338 > select #13/D
    7339 
    7340 6484 atoms, 6581 bonds, 424 residues, 1 model selected 
    7341 
    7342 > matchmaker #15-19 to #13 & sel
    7343 
    7344 Computing secondary structure 
    7345 [Repeated 5 time(s)]  Parameters 
    7346 --- 
    7347 Chain pairing | bb 
    7348 Alignment algorithm | Needleman-Wunsch 
    7349 Similarity matrix | BLOSUM-62 
    7350 SS fraction | 0.3 
    7351 Gap open (HH/SS/other) | 18/18/6 
    7352 Gap extend | 1 
    7353 SS matrix |  |  | H | S | O 
    7354 ---|---|---|--- 
    7355 H | 6 | -9 | -6 
    7356 S |  | 6 | -6 
    7357 O |  |  | 4 
    7358 Iteration cutoff | 2 
    7359  
    7360 Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_0.cif, chain A
    7361 (#15), sequence alignment score = 2333.5 
    7362 RMSD between 255 pruned atom pairs is 0.655 angstroms; (across all 424 pairs:
    7363 17.845) 
    7364  
    7365 Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_1.cif, chain A
    7366 (#16), sequence alignment score = 2336.5 
    7367 RMSD between 257 pruned atom pairs is 0.672 angstroms; (across all 424 pairs:
    7368 17.898) 
    7369  
    7370 Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_2.cif, chain A
    7371 (#17), sequence alignment score = 2336.5 
    7372 RMSD between 258 pruned atom pairs is 0.687 angstroms; (across all 424 pairs:
    7373 17.841) 
    7374  
    7375 Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_3.cif, chain A
    7376 (#18), sequence alignment score = 2336.5 
    7377 RMSD between 255 pruned atom pairs is 0.654 angstroms; (across all 424 pairs:
    7378 17.922) 
    7379  
    7380 Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_4.cif, chain A
    7381 (#19), sequence alignment score = 2322.7 
    7382 RMSD between 254 pruned atom pairs is 0.752 angstroms; (across all 424 pairs:
    7383 17.875) 
    7384  
    7385 
    7386 > hide #16 models
    7387 
    7388 > hide #17 models
    7389 
    7390 > hide #18 models
    7391 
    7392 > hide #19 models
    7393 
    7394 > show #!10 models
    7395 
    7396 > hide #!10 models
    7397 
    7398 > show #16 models
    7399 
    7400 > show #17 models
    7401 
    7402 > show #18 models
    7403 
    7404 > hide #15 models
    7405 
    7406 > hide #17 models
    7407 
    7408 > hide #18 models
    7409 
    7410 > show #15 models
    7411 
    7412 > hide #16 models
    7413 
    7414 > show #16 models
    7415 
    7416 > show #17 models
    7417 
    7418 > hide #15 models
    7419 
    7420 > hide #16 models
    7421 
    7422 > show #18 models
    7423 
    7424 > hide #17 models
    7425 
    7426 > show #19 models
    7427 
    7428 > hide #18 models
    7429 
    7430 > show #15 models
    7431 
    7432 > hide #19 models
    7433 
    7434 > show #!10 models
    7435 
    7436 > select #15/A
    7437 
    7438 3680 atoms, 3778 bonds, 472 residues, 1 model selected 
    7439 
    7440 > rainbow sel
    7441 
    7442 > select #15/F:201
    7443 
    7444 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7445 
    7446 > select clear
    7447 
    7448 > hide #!10 models
    7449 
    7450 > color #15 bychain
    7451 
    7452 > save /Users/taic/Library/CloudStorage/OneDrive-
    7453 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FMX.AF3.png
    7454 > width 600 height 614 supersample 4 transparentBackground true
    7455 
    7456 > show #!10 models
    7457 
    7458 > select #15/A
    7459 
    7460 3680 atoms, 3778 bonds, 472 residues, 1 model selected 
    7461 
    7462 > select ~sel & ##selected
    7463 
    7464 22080 atoms, 22668 bonds, 2832 residues, 1 model selected 
    7465 
    7466 > hide sel cartoons
    7467 
    7468 > select #15/A
    7469 
    7470 3680 atoms, 3778 bonds, 472 residues, 1 model selected 
    7471 
    7472 > matchmaker #15 to #10
    7473 
    7474 Computing secondary structure 
    7475 [Repeated 1 time(s)]  Parameters 
    7476 --- 
    7477 Chain pairing | bb 
    7478 Alignment algorithm | Needleman-Wunsch 
    7479 Similarity matrix | BLOSUM-62 
    7480 SS fraction | 0.3 
    7481 Gap open (HH/SS/other) | 18/18/6 
    7482 Gap extend | 1 
    7483 SS matrix |  |  | H | S | O 
    7484 ---|---|---|--- 
    7485 H | 6 | -9 | -6 
    7486 S |  | 6 | -6 
    7487 O |  |  | 4 
    7488 Iteration cutoff | 2 
    7489  
    7490 Matchmaker 1pre, chain B (#10) with fold_aerolysin_9fmx_model_0.cif, chain A
    7491 (#15), sequence alignment score = 2407.9 
    7492 RMSD between 448 pruned atom pairs is 0.805 angstroms; (across all 451 pairs:
    7493 0.831) 
    7494  
    7495 
    7496 > select clear
    7497 
    7498 [Repeated 1 time(s)]
    7499 
    7500 > save /Users/taic/Library/CloudStorage/OneDrive-
    7501 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/1PRE.vs.9FMX_A.AF3.png
    7502 > width 600 height 614 supersample 4 transparentBackground true
    7503 
    7504 [Repeated 1 time(s)]
    7505 
    7506 > hide #15 models
    7507 
    7508 > hide #!10 models
    7509 
    7510 > show #13 models
    7511 
    7512 > show #11 models
    7513 
    7514 > select #11/A/B/C/D/E/F/G
    7515 
    7516 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    7517 
    7518 > select ~sel & ##selected
    7519 
    7520 45395 atoms, 46074 bonds, 2968 residues, 1 model selected 
    7521 
    7522 > hide sel cartoons
    7523 
    7524 > hide #13 models
    7525 
    7526 > show #13 models
    7527 
    7528 > hide #11 models
    7529 
    7530 > show #11 models
    7531 
    7532 > hide #11 models
    7533 
    7534 > color #13 bychain
    7535 
    7536 > select #9/E
    7537 
    7538 3334 atoms, 3430 bonds, 424 residues, 1 model selected 
    7539 
    7540 > select #13/E
    7541 
    7542 6484 atoms, 6581 bonds, 424 residues, 1 model selected 
    7543 
    7544 > rainbow sel
    7545 
    7546 > select clear
    7547 
    7548 Drag select of 25 residues 
    7549 Drag select of 2 residues 
    7550 
    7551 > select #13/E:214
    7552 
    7553 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7554 
    7555 > show #!8 models
    7556 
    7557 > hide #13 models
    7558 
    7559 > show #13 models
    7560 
    7561 > hide #!8 models
    7562 
    7563 > show #!8 models
    7564 
    7565 > hide #!8 models
    7566 
    7567 > show #!8 models
    7568 
    7569 > matchmaker #13 to #8
    7570 
    7571 Computing secondary structure 
    7572 Parameters 
    7573 --- 
    7574 Chain pairing | bb 
    7575 Alignment algorithm | Needleman-Wunsch 
    7576 Similarity matrix | BLOSUM-62 
    7577 SS fraction | 0.3 
    7578 Gap open (HH/SS/other) | 18/18/6 
    7579 Gap extend | 1 
    7580 SS matrix |  |  | H | S | O 
    7581 ---|---|---|--- 
    7582 H | 6 | -9 | -6 
    7583 S |  | 6 | -6 
    7584 O |  |  | 4 
    7585 Iteration cutoff | 2 
    7586  
    7587 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
    7588 (#13), sequence alignment score = 2181.4 
    7589 RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
    7590 0.985) 
    7591  
    7592 
    7593 > matchmaker #13 to #8
    7594 
    7595 Computing secondary structure 
    7596 Parameters 
    7597 --- 
    7598 Chain pairing | bb 
    7599 Alignment algorithm | Needleman-Wunsch 
    7600 Similarity matrix | BLOSUM-62 
    7601 SS fraction | 0.3 
    7602 Gap open (HH/SS/other) | 18/18/6 
    7603 Gap extend | 1 
    7604 SS matrix |  |  | H | S | O 
    7605 ---|---|---|--- 
    7606 H | 6 | -9 | -6 
    7607 S |  | 6 | -6 
    7608 O |  |  | 4 
    7609 Iteration cutoff | 2 
    7610  
    7611 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
    7612 (#13), sequence alignment score = 2181.4 
    7613 RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
    7614 0.985) 
    7615  
    7616 
    7617 > hide #13 models
    7618 
    7619 > show #13 models
    7620 
    7621 > hide #!8 models
    7622 
    7623 > select #13
    7624 
    7625 90776 atoms, 92134 bonds, 5936 residues, 1 model selected 
    7626 
    7627 > color sel thistle target acs
    7628 
    7629 > color sel pink target acs
    7630 
    7631 > color sel plum target acs
    7632 
    7633 > select clear
    7634 
    7635 > show #!8 models
    7636 
    7637 > select #13
    7638 
    7639 90776 atoms, 92134 bonds, 5936 residues, 1 model selected 
    7640 
    7641 > color sel gray target acs
    7642 
    7643 > select clear
    7644 
    7645 > select #13
    7646 
    7647 90776 atoms, 92134 bonds, 5936 residues, 1 model selected 
    7648 
    7649 > color sel burly wood target acs
    7650 
    7651 > select clear
    7652 
    7653 > hide #!8 models
    7654 
    7655 > show #!8 models
    7656 
    7657 > hide #13 models
    7658 
    7659 > show #13 models
    7660 
    7661 > select #13
    7662 
    7663 90776 atoms, 92134 bonds, 5936 residues, 1 model selected 
    7664 
    7665 > color sel gainsboro target acs
    7666 
    7667 > color sel light cyan target acs
    7668 
    7669 > color sel pale green target acs
    7670 
    7671 > select clear
    7672 
    7673 > select #13
    7674 
    7675 90776 atoms, 92134 bonds, 5936 residues, 1 model selected 
    7676 
    7677 > select clear
    7678 
    7679 > hide #13 models
    7680 
    7681 > show #13 models
    7682 
    7683 > save /Users/taic/Library/CloudStorage/OneDrive-
    7684 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FMXvsAF3.png
    7685 > width 600 height 614 supersample 4 transparentBackground true
    7686 
    7687 > save /Users/taic/Library/CloudStorage/OneDrive-
    7688 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FMXvsAF3.side.png
    7689 > width 600 height 614 supersample 4 transparentBackground true
    7690 
    7691 > matchmaker #13 to #8
    7692 
    7693 Computing secondary structure 
    7694 Parameters 
    7695 --- 
    7696 Chain pairing | bb 
    7697 Alignment algorithm | Needleman-Wunsch 
    7698 Similarity matrix | BLOSUM-62 
    7699 SS fraction | 0.3 
    7700 Gap open (HH/SS/other) | 18/18/6 
    7701 Gap extend | 1 
    7702 SS matrix |  |  | H | S | O 
    7703 ---|---|---|--- 
    7704 H | 6 | -9 | -6 
    7705 S |  | 6 | -6 
    7706 O |  |  | 4 
    7707 Iteration cutoff | 2 
    7708  
    7709 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
    7710 (#13), sequence alignment score = 2181.4 
    7711 RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
    7712 0.985) 
    7713  
    7714 
    7715 > matchmaker #13 to #8
    7716 
    7717 Computing secondary structure 
    7718 Parameters 
    7719 --- 
    7720 Chain pairing | bb 
    7721 Alignment algorithm | Needleman-Wunsch 
    7722 Similarity matrix | BLOSUM-62 
    7723 SS fraction | 0.3 
    7724 Gap open (HH/SS/other) | 18/18/6 
    7725 Gap extend | 1 
    7726 SS matrix |  |  | H | S | O 
    7727 ---|---|---|--- 
    7728 H | 6 | -9 | -6 
    7729 S |  | 6 | -6 
    7730 O |  |  | 4 
    7731 Iteration cutoff | 2 
    7732  
    7733 Matchmaker fold_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
    7734 (#13), sequence alignment score = 2181.4 
    7735 RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
    7736 0.985) 
    7737  
    7738 
    7739 > show #!10 models
    7740 
    7741 > hide #!8 models
    7742 
    7743 > hide #13 models
    7744 
    7745 > rainbow #!10
    7746 
    7747 > show #!14 models
    7748 
    7749 > hide #!10 models
    7750 
    7751 > show #13 models
    7752 
    7753 > hide #!14 models
    7754 
    7755 > show #!8 models
    7756 
    7757 > hide #!8 models
    7758 
    7759 > show #11 models
    7760 
    7761 > hide #11 models
    7762 
    7763 > show #11 models
    7764 
    7765 > hide #13 models
    7766 
    7767 > show #13 models
    7768 
    7769 > hide #11 models
    7770 
    7771 > show #!14 models
    7772 
    7773 > hide #13 models
    7774 
    7775 > show #!8 models
    7776 
    7777 > hide #!8 models
    7778 
    7779 > show #!8 models
    7780 
    7781 > hide #!14 models
    7782 
    7783 > show #!14 models
    7784 
    7785 > show #13 models
    7786 
    7787 > hide #!14 models
    7788 
    7789 > hide #!8 models
    7790 
    7791 > show #15 models
    7792 
    7793 > hide #13 models
    7794 
    7795 > show #16 models
    7796 
    7797 > hide #15 models
    7798 
    7799 > show #17 models
    7800 
    7801 > hide #16 models
    7802 
    7803 > show #18 models
    7804 
    7805 > hide #17 models
    7806 
    7807 > show #19 models
    7808 
    7809 > hide #18 models
    7810 
    7811 > show #!14 models
    7812 
    7813 > hide #19 models
    7814 
    7815 > save /Users/taic/Library/CloudStorage/OneDrive-
    7816 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/GATA4_8vg1.aerolysin_9FMM6.cxs
    7817 
    7818 ——— End of log from Mon Jun 23 17:09:27 2025 ———
    7819 
    7820 opened ChimeraX session 
    7821 
    7822 > hide #!14 models
    7823 
    7824 > show #!6 models
    7825 
    7826 > open 3aze fromDatabase pdb format mmcif
    7827 
    7828 Summary of feedback from opening 3aze fetched from pdb 
    7829 --- 
    7830 notes | Fetching compressed mmCIF 3aze from http://files.rcsb.org/download/3aze.cif 
    7831 Fetching CCD MN from
    7832 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif 
    7833  
    7834 3aze title: 
    7835 Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation
    7836 [more info...] 
    7837  
    7838 Chain information for 3aze #20 
    7839 --- 
    7840 Chain | Description | UniProt 
    7841 A E | Histone H3.1 | H31_HUMAN 0-135 
    7842 B F | Histone H4 | H4_HUMAN 0-102 
    7843 C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129 
    7844 D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125 
    7845 I J | 146-MER DNA |   
    7846  
    7847 Non-standard residues in 3aze #20 
    7848 --- 
    7849 CL — chloride ion 
    7850 MN — manganese (II) ion 
    7851  
    7852 
    7853 > show #!6,20 cartoons
    7854 
    7855 > hide #!6,20 atoms
    7856 
    7857 > ui tool show Matchmaker
    7858 
    7859 > select #6/A
    7860 
    7861 799 atoms, 811 bonds, 97 residues, 1 model selected 
    7862 
    7863 > matchmaker #!20 to #6 & sel
    7864 
    7865 Computing secondary structure 
    7866 Parameters 
    7867 --- 
    7868 Chain pairing | bb 
    7869 Alignment algorithm | Needleman-Wunsch 
    7870 Similarity matrix | BLOSUM-62 
    7871 SS fraction | 0.3 
    7872 Gap open (HH/SS/other) | 18/18/6 
    7873 Gap extend | 1 
    7874 SS matrix |  |  | H | S | O 
    7875 ---|---|---|--- 
    7876 H | 6 | -9 | -6 
    7877 S |  | 6 | -6 
    7878 O |  |  | 4 
    7879 Iteration cutoff | 2 
    7880  
    7881 Matchmaker 8vg1, chain A (#6) with 3aze, chain A (#20), sequence alignment
    7882 score = 623.8 
    7883 RMSD between 96 pruned atom pairs is 0.318 angstroms; (across all 96 pairs:
    7884 0.318) 
    7885  
    7886 
    7887 > hide #!6 models
    7888 
    7889 > show #!6 models
    7890 
    7891 > hide #!6 models
    7892 
    7893 > show #!6 models
    7894 
    7895 > hide #!6 models
    7896 
    7897 > show #!6 models
    7898 
    7899 > hide #!6 models
    7900 
    7901 > show #!6 models
    7902 
    7903 > hide #!6 models
    7904 
    7905 > show #!6 models
    7906 
    7907 > hide #!6 models
    7908 
    7909 > show #!6 models
    7910 
    7911 > matchmaker #!20 to #6 & sel
    7912 
    7913 Computing secondary structure 
    7914 Parameters 
    7915 --- 
    7916 Chain pairing | bb 
    7917 Alignment algorithm | Needleman-Wunsch 
    7918 Similarity matrix | BLOSUM-62 
    7919 SS fraction | 0.3 
    7920 Gap open (HH/SS/other) | 18/18/6 
    7921 Gap extend | 1 
    7922 SS matrix |  |  | H | S | O 
    7923 ---|---|---|--- 
    7924 H | 6 | -9 | -6 
    7925 S |  | 6 | -6 
    7926 O |  |  | 4 
    7927 Iteration cutoff | 2 
    7928  
    7929 Matchmaker 8vg1, chain A (#6) with 3aze, chain A (#20), sequence alignment
    7930 score = 623.8 
    7931 RMSD between 96 pruned atom pairs is 0.318 angstroms; (across all 96 pairs:
    7932 0.318) 
    7933  
    7934 
    7935 > select #6
    7936 
    7937 14434 atoms, 15401 bonds, 421 pseudobonds, 1273 residues, 3 models selected 
    7938 
    7939 > matchmaker #!20 to #6 & sel
    7940 
    7941 Computing secondary structure 
    7942 Parameters 
    7943 --- 
    7944 Chain pairing | bb 
    7945 Alignment algorithm | Needleman-Wunsch 
    7946 Similarity matrix | BLOSUM-62 
    7947 SS fraction | 0.3 
    7948 Gap open (HH/SS/other) | 18/18/6 
    7949 Gap extend | 1 
    7950 SS matrix |  |  | H | S | O 
    7951 ---|---|---|--- 
    7952 H | 6 | -9 | -6 
    7953 S |  | 6 | -6 
    7954 O |  |  | 4 
    7955 Iteration cutoff | 2 
    7956  
    7957 Matchmaker 8vg1, chain E (#6) with 3aze, chain E (#20), sequence alignment
    7958 score = 625.6 
    7959 RMSD between 96 pruned atom pairs is 0.335 angstroms; (across all 97 pairs:
    7960 0.414) 
    7961  
    7962 
    7963 > select clear
    7964 
    7965 > hide #!6 models
    7966 
    7967 > show #!6 models
    7968 
    7969 > hide #!6 models
    7970 
    7971 > show #!6 models
    7972 
    7973 > hide #!6 models
    7974 
    7975 > show #!6 models
    7976 
    7977 > hide #!6 models
    7978 
    7979 > show #1 models
    7980 
    7981 > hide #!20 models
    7982 
    7983 > show #2 models
    7984 
    7985 > hide #1 models
    7986 
    7987 > show #3 models
    7988 
    7989 > hide #2 models
    7990 
    7991 > show #4 models
    7992 
    7993 > hide #3 models
    7994 
    7995 > show #5 models
    7996 
    7997 > hide #4 models
    7998 
    7999 > show #1 models
    8000 
    8001 > hide #5 models
    8002 
    8003 > show #!6 models
    8004 
    8005 > hide #1 models
    8006 
    8007 > select #6/B/F
    8008 
    8009 1324 atoms, 1338 bonds, 166 residues, 1 model selected 
    8010 
    8011 > ui tool show "Color Actions"
    8012 
    8013 > color sel plum
    8014 
    8015 > color sel pale violet red
    8016 
    8017 > color sel burly wood
    8018 
    8019 > color sel rosy brown
    8020 
    8021 > color sel light pink
    8022 
    8023 > color sel thistle
    8024 
    8025 > select #6/C/G
    8026 
    8027 1740 atoms, 1762 bonds, 225 residues, 1 model selected 
    8028 
    8029 > color sel sky blue
    8030 
    8031 > color sel deep sky blue
    8032 
    8033 > color sel powder blue
    8034 
    8035 > color sel light steel blue
    8036 
    8037 > color sel sky blue
    8038 
    8039 > color sel light sky blue
    8040 
    8041 > color sel deep sky blue
    8042 
    8043 > color sel sky blue
    8044 
    8045 > select #6/C/G
    8046 
    8047 1740 atoms, 1762 bonds, 225 residues, 1 model selected 
    8048 
    8049 > color sel medium slate blue
    8050 
    8051 > color sel medium purple
    8052 
    8053 > color sel thistle
    8054 
    8055 > color sel gray
    8056 
    8057 > color sel silver
    8058 
    8059 > color sel light steel blue
    8060 
    8061 > color sel sky blue
    8062 
    8063 > select #6/D/H
    8064 
    8065 1490 atoms, 1512 bonds, 190 residues, 1 model selected 
    8066 
    8067 > color sel dark sea green
    8068 
    8069 > select #6/A/E
    8070 
    8071 1598 atoms, 1622 bonds, 194 residues, 1 model selected 
    8072 
    8073 > color sel light coral
    8074 
    8075 > select #6/B/F
    8076 
    8077 1324 atoms, 1338 bonds, 166 residues, 1 model selected 
    8078 
    8079 > color sel tan
    8080 
    8081 > color sel khaki
    8082 
    8083 > select clear
    8084 
    8085 > select #6/I
    8086 
    8087 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    8088 
    8089 > color sel silver
    8090 
    8091 > select #6/J
    8092 
    8093 3510 atoms, 3942 bonds, 171 residues, 1 model selected 
    8094 
    8095 > color sel light steel blue
    8096 
    8097 > select clear
    8098 
    8099 > select #6/T
    8100 
    8101 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8102 
    8103 > color sel deep sky blue
    8104 
    8105 > color sel royal blue
    8106 
    8107 > select #6/O
    8108 
    8109 856 atoms, 883 bonds, 102 residues, 1 model selected 
    8110 
    8111 > select clear
    8112 
    8113 > select #6/O
    8114 
    8115 856 atoms, 883 bonds, 102 residues, 1 model selected 
    8116 
    8117 > color sel hot pink
    8118 
    8119 > select clear
    8120 
    8121 > select #6/I
    8122 
    8123 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    8124 
    8125 > color sel aquamarine
    8126 
    8127 > select clear
    8128 
    8129 > select #6/I
    8130 
    8131 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    8132 
    8133 > color sel light pink
    8134 
    8135 > select clear
    8136 
    8137 > select #6/I
    8138 
    8139 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    8140 
    8141 > color sel wheat
    8142 
    8143 > select clear
    8144 
    8145 > select #6/T
    8146 
    8147 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8148 
    8149 > color sel olive drab
    8150 
    8151 > color sel forest green
    8152 
    8153 > select clear
    8154 
    8155 > select #6/T
    8156 
    8157 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8158 
    8159 > color sel dodger blue
    8160 
    8161 > select clear
    8162 
    8163 > select #6/T
    8164 
    8165 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8166 
    8167 > color sel medium purple
    8168 
    8169 > select clear
    8170 
    8171 > select #6/D
    8172 
    8173 745 atoms, 756 bonds, 95 residues, 1 model selected 
    8174 
    8175 > color sel pale green
    8176 
    8177 > select clear
    8178 
    8179 > select #6/C
    8180 
    8181 840 atoms, 850 bonds, 109 residues, 1 model selected 
    8182 
    8183 > color sel pale turquoise
    8184 
    8185 > select clear
    8186 
    8187 > select #6/A
    8188 
    8189 799 atoms, 811 bonds, 97 residues, 1 model selected 
    8190 
    8191 > color sel light pink
    8192 
    8193 > color sel light coral
    8194 
    8195 > select clear
    8196 
    8197 > select #6/B
    8198 
    8199 662 atoms, 669 bonds, 83 residues, 1 model selected 
    8200 
    8201 > color sel pale goldenrod
    8202 
    8203 > select clear
    8204 
    8205 > select #6/I
    8206 
    8207 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    8208 
    8209 > color sel lavender
    8210 
    8211 [Repeated 1 time(s)]
    8212 
    8213 > color sel thistle
    8214 
    8215 > select clear
    8216 
    8217 > select #6/T
    8218 
    8219 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8220 
    8221 > color sel royal blue
    8222 
    8223 > select clear
    8224 
    8225 > select #6/O
    8226 
    8227 856 atoms, 883 bonds, 102 residues, 1 model selected 
    8228 
    8229 > color sel medium violet red
    8230 
    8231 > select clear
    8232 
    8233 > select #6/J
    8234 
    8235 3510 atoms, 3942 bonds, 171 residues, 1 model selected 
    8236 
    8237 > color sel light steel blue
    8238 
    8239 > color sel pale turquoise
    8240 
    8241 > color sel powder blue
    8242 
    8243 > select clear
    8244 
    8245 > select #6/J
    8246 
    8247 3510 atoms, 3942 bonds, 171 residues, 1 model selected 
    8248 
    8249 > color sel pale turquoise
    8250 
    8251 > select clear
    8252 
    8253 > select #6/J
    8254 
    8255 3510 atoms, 3942 bonds, 171 residues, 1 model selected 
    8256 
    8257 > color sel light steel blue
    8258 
    8259 > select clear
    8260 
    8261 > show #1 models
    8262 
    8263 > hide #!6 models
    8264 
    8265 > show #!6 models
    8266 
    8267 > hide #!6 models
    8268 
    8269 > show #7 models
    8270 
    8271 > hide #7 models
    8272 
    8273 > show #!6 models
    8274 
    8275 > hide #1 models
    8276 
    8277 > show #1 models
    8278 
    8279 > hide #!6 models
    8280 
    8281 > show #!6 models
    8282 
    8283 > hide #1 models
    8284 
    8285 > show #1 models
    8286 
    8287 > hide #!6 models
    8288 
    8289 > show #!6 models
    8290 
    8291 > hide #1 models
    8292 
    8293 > show #1 models
    8294 
    8295 > hide #!6 models
    8296 
    8297 > select #6/I
    8298 
    8299 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    8300 
    8301 > color sel medium violet red
    8302 
    8303 > show #!6 models
    8304 
    8305 > color sel thistle
    8306 
    8307 > select clear
    8308 
    8309 > hide #!6 models
    8310 
    8311 > select #1/I
    8312 
    8313 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    8314 
    8315 > color sel medium violet red
    8316 
    8317 > select clear
    8318 
    8319 > select #1/I/J
    8320 
    8321 9685 atoms, 9949 bonds, 1313 residues, 1 model selected 
    8322 
    8323 > hide sel cartoons
    8324 
    8325 > show #7 models
    8326 
    8327 > hide #7 models
    8328 
    8329 > show #!6 models
    8330 
    8331 > hide #!6 models
    8332 
    8333 > show #!6 models
    8334 
    8335 > select #1/A:1-38
    8336 
    8337 274 atoms, 275 bonds, 38 residues, 1 model selected 
    8338 
    8339 > select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
    8340 
    8341 2280 atoms, 2296 bonds, 304 residues, 1 model selected 
    8342 
    8343 > hide #1 models
    8344 
    8345 > show #1 models
    8346 
    8347 > color sel ivory
    8348 
    8349 > select clear
    8350 
    8351 > select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
    8352 
    8353 2280 atoms, 2296 bonds, 304 residues, 1 model selected 
    8354 
    8355 > hide sel cartoons
    8356 
    8357 > hide #!6 models
    8358 
    8359 > show #!6 models
    8360 
    8361 > hide #!6 models
    8362 
    8363 > show #7 models
    8364 
    8365 > hide #7 models
    8366 
    8367 > show #!6 models
    8368 
    8369 > hide #!6 models
    8370 
    8371 > select #1/L
    8372 
    8373 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    8374 
    8375 > show #!6 models
    8376 
    8377 > hide #!6 models
    8378 
    8379 > show #!6 models
    8380 
    8381 > hide #!6 models
    8382 
    8383 > color sel deep sky blue
    8384 
    8385 > select #1/K
    8386 
    8387 3811 atoms, 4270 bonds, 186 residues, 1 model selected 
    8388 
    8389 > show #!6 models
    8390 
    8391 > hide #!6 models
    8392 
    8393 > color sel violet
    8394 
    8395 > select clear
    8396 
    8397 > show #!6 models
    8398 
    8399 > hide #!6 models
    8400 
    8401 > show #!6 models
    8402 
    8403 > hide #1 models
    8404 
    8405 > select #6/I
    8406 
    8407 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    8408 
    8409 > rainbow sel
    8410 
    8411 > select clear
    8412 
    8413 > show #1 models
    8414 
    8415 > hide #!6 models
    8416 
    8417 > show #!6 models
    8418 
    8419 > hide #1 models
    8420 
    8421 > undo
    8422 
    8423 [Repeated 6 time(s)]
    8424 
    8425 > select #6/J
    8426 
    8427 3510 atoms, 3942 bonds, 171 residues, 1 model selected 
    8428 
    8429 > rainbow sel
    8430 
    8431 > select clear
    8432 
    8433 > undo
    8434 
    8435 [Repeated 2 time(s)]
    8436 
    8437 > show #1 models
    8438 
    8439 > select clear
    8440 
    8441 > hide #1 models
    8442 
    8443 > show #1 models
    8444 
    8445 > hide #!6 models
    8446 
    8447 > show #!6 models
    8448 
    8449 > hide #1 models
    8450 
    8451 > select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
    8452 
    8453 2280 atoms, 2296 bonds, 304 residues, 1 model selected 
    8454 
    8455 > show #!6 cartoons
    8456 
    8457 > show #1 models
    8458 
    8459 > select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
    8460 
    8461 2280 atoms, 2296 bonds, 304 residues, 1 model selected 
    8462 
    8463 > select clear
    8464 
    8465 > hide #1 models
    8466 
    8467 > show #1 models
    8468 
    8469 > select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
    8470 
    8471 2280 atoms, 2296 bonds, 304 residues, 1 model selected 
    8472 
    8473 > show sel cartoons
    8474 
    8475 > select clear
    8476 
    8477 > select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-30
    8478 
    8479 2207 atoms, 2222 bonds, 296 residues, 1 model selected 
    8480 
    8481 > select #1/A:1-30/B:1-30/C:1-30/D:1-30/E:1-30/F:1-30/G:1-30/H:1-30
    8482 
    8483 1762 atoms, 1770 bonds, 240 residues, 1 model selected 
    8484 
    8485 > hide sel cartoons
    8486 
    8487 > select clear
    8488 
    8489 > hide #1 models
    8490 
    8491 > show #1 models
    8492 
    8493 > hide #!6 models
    8494 
    8495 > show #!6 models
    8496 
    8497 > hide #1 models
    8498 
    8499 > show #1 models
    8500 
    8501 > hide #!6 models
    8502 
    8503 > hide #1 models
    8504 
    8505 > show #1 models
    8506 
    8507 > show #!6 models
    8508 
    8509 > hide #1 models
    8510 
    8511 > show #1 models
    8512 
    8513 > hide #!6 models
    8514 
    8515 > show #!6 models
    8516 
    8517 > hide #1 models
    8518 
    8519 > show #1 models
    8520 
    8521 > hide #!6 models
    8522 
    8523 > show #!6 models
    8524 
    8525 > hide #1 models
    8526 
    8527 > show #1 models
    8528 
    8529 > hide #1 models
    8530 
    8531 > show #1 models
    8532 
    8533 > hide #!6 models
    8534 
    8535 > show #!6 models
    8536 
    8537 > select #6/T30
    8538 
    8539 Nothing selected 
    8540 
    8541 > select #6/T
    8542 
    8543 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8544 
    8545 > color sel royal blue
    8546 
    8547 > select clear
    8548 
    8549 > select #6/T
    8550 
    8551 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8552 
    8553 > color sel medium blue
    8554 
    8555 > select clear
    8556 
    8557 > hide #1 models
    8558 
    8559 > select #6/T
    8560 
    8561 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8562 
    8563 > color sel dark turquoise
    8564 
    8565 > color sel dark cyan
    8566 
    8567 > select clear
    8568 
    8569 > select #6/T
    8570 
    8571 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    8572 
    8573 > color sel deep sky blue
    8574 
    8575 > color sel dodger blue
    8576 
    8577 > color sel blue
    8578 
    8579 > select clear
    8580 
    8581 > show #1 models
    8582 
    8583 > hide #!6 models
    8584 
    8585 > show #!6 models
    8586 
    8587 > hide #1 models
    8588 
    8589 > show #1 models
    8590 
    8591 > hide #1 models
    8592 
    8593 > show #1 models
    8594 
    8595 > hide #1 models
    8596 
    8597 > show #1 models
    8598 
    8599 > hide #1 models
    8600 
    8601 > show #1 models
    8602 
    8603 > hide #1 models
    8604 
    8605 > show #1 models
    8606 
    8607 > hide #!6 models
    8608 
    8609 > select
    8610 > #1/A:120-126/B:120-126/C:120-126/D:120-126/E:120-126/F:120-126/G:120-126/H:120-126
    8611 
    8612 346 atoms, 348 bonds, 42 residues, 1 model selected 
    8613 
    8614 > select
    8615 > #1/A:120-126/B:120-126/C:120-126/D:120-126/E:120-126/F:120-126/G:120-126/H:120-130
    8616 
    8617 346 atoms, 348 bonds, 42 residues, 1 model selected 
    8618 
    8619 > select
    8620 > #1/A:120-130/B:120-130/C:120-130/D:120-130/E:120-130/F:1120-130/G:120-130/H:120-130
    8621 
    8622 472 atoms, 474 bonds, 58 residues, 1 model selected 
    8623 
    8624 > show #!6 models
    8625 
    8626 > hide #!6 models
    8627 
    8628 > show #!6 models
    8629 
    8630 > hide #1 models
    8631 
    8632 > show #1 models
    8633 
    8634 > hide #1 models
    8635 
    8636 > show #1 models
    8637 
    8638 > color sel white
    8639 
    8640 > select clear
    8641 
    8642 [Repeated 1 time(s)]
    8643 
    8644 > hide #!6 models
    8645 
    8646 > select clear
    8647 
    8648 > show #!6 models
    8649 
    8650 > hide #!6 models
    8651 
    8652 > select #1/I/J
    8653 
    8654 9685 atoms, 9949 bonds, 1313 residues, 1 model selected 
    8655 
    8656 > show sel cartoons
    8657 
    8658 > select clear
    8659 
    8660 > select #1/I/J
    8661 
    8662 9685 atoms, 9949 bonds, 1313 residues, 1 model selected 
    8663 
    8664 > hide sel cartoons
    8665 
    8666 > show sel cartoons
    8667 
    8668 [Repeated 1 time(s)]
    8669 
    8670 > hide sel cartoons
    8671 
    8672 > show #!6 models
    8673 
    8674 > hide #1 models
    8675 
    8676 > show #1 models
    8677 
    8678 > select #1/I/J
    8679 
    8680 9685 atoms, 9949 bonds, 1313 residues, 1 model selected 
    8681 
    8682 > show sel cartoons
    8683 
    8684 > select clear
    8685 
    8686 > select #1/J
    8687 
    8688 6183 atoms, 6345 bonds, 835 residues, 1 model selected 
    8689 
    8690 > color sel blue
    8691 
    8692 > select clear
    8693 
    8694 > hide #!6 models
    8695 
    8696 > select clear
    8697 
    8698 > save "/Users/taic/OneDrive - National Institutes of
    8699 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-2.png" width 740
    8700 > height 627 supersample 4 transparentBackground true
    8701 
    8702 > select #1/J
    8703 
    8704 6183 atoms, 6345 bonds, 835 residues, 1 model selected 
    8705 
    8706 > hide sel cartoons
    8707 
    8708 > select #1/J/J
    8709 
    8710 6183 atoms, 6345 bonds, 835 residues, 1 model selected 
    8711 
    8712 > select #1/J/I
    8713 
    8714 9685 atoms, 9949 bonds, 1313 residues, 1 model selected 
    8715 
    8716 > hide sel cartoons
    8717 
    8718 > save "/Users/taic/OneDrive - National Institutes of
    8719 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-2.noTFs.png"
    8720 > width 740 height 627 supersample 4 transparentBackground true
    8721 
    8722 > show #!6 models
    8723 
    8724 > hide #1 models
    8725 
    8726 > show #1 models
    8727 
    8728 > hide #!6 models
    8729 
    8730 > select #1/J/I
    8731 
    8732 9685 atoms, 9949 bonds, 1313 residues, 1 model selected 
    8733 
    8734 > show sel cartoons
    8735 
    8736 > select #1/J:1-268/J:321-900/I:1-167/I:270-478
    8737 
    8738 8445 atoms, 8673 bonds, 1159 residues, 1 model selected 
    8739 
    8740 > hide sel cartoons
    8741 
    8742 > show #!6 models
    8743 
    8744 > hide #!6 models
    8745 
    8746 > show #!6 models
    8747 
    8748 > hide #!6 models
    8749 
    8750 > save "/Users/taic/OneDrive - National Institutes of
    8751 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-2.png" width 740
    8752 > height 627 supersample 4 transparentBackground true
    8753 
    8754 > show #!6 models
    8755 
    8756 > hide #!6 models
    8757 
    8758 > select
    8759 > #1/A:120-130/B:120-130/C:120-130/D:120-130/E:120-130/F:1120-130/G:120-130/H:120-130
    8760 
    8761 472 atoms, 474 bonds, 58 residues, 1 model selected 
    8762 
    8763 > show #!6 models
    8764 
    8765 > hide #!6 models
    8766 
    8767 > show #!6 models
    8768 
    8769 > hide #!6 models
    8770 
    8771 > show #!6 models
    8772 
    8773 > hide #!6 models
    8774 
    8775 > show #!6 models
    8776 
    8777 > hide #!6 models
    8778 
    8779 > show #!6 models
    8780 
    8781 > hide #!6 models
    8782 
    8783 > show #!6 models
    8784 
    8785 > hide #!6 models
    8786 
    8787 > select
    8788 > #1/A:120-130/B:120-130/C:120-130/D:120-130/E:120-130/F:1120-130/G:120-130/H:120-130
    8789 
    8790 472 atoms, 474 bonds, 58 residues, 1 model selected 
    8791 
    8792 > hide sel cartoons
    8793 
    8794 > select #1/I/J/K/L
    8795 
    8796 17313 atoms, 18505 bonds, 1685 residues, 1 model selected 
    8797 
    8798 > hide sel cartoons
    8799 
    8800 > show #!6 models
    8801 
    8802 > select #6/I/J/O/T
    8803 
    8804 8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected 
    8805 
    8806 > hide sel cartoons
    8807 
    8808 Drag select of 7 residues 
    8809 
    8810 > hide sel cartoons
    8811 
    8812 Drag select of 8 residues 
    8813 
    8814 > hide sel cartoons
    8815 
    8816 > select clear
    8817 
    8818 > select #1/A:38
    8819 
    8820 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8821 
    8822 > ui tool show "Color Actions"
    8823 
    8824 > color sel salmon
    8825 
    8826 > select clear
    8827 
    8828 > hide #1 models
    8829 
    8830 > show #1 models
    8831 
    8832 > hide #1 models
    8833 
    8834 > show #1 models
    8835 
    8836 > hide #1 models
    8837 
    8838 > show #1 models
    8839 
    8840 > hide #1 models
    8841 
    8842 > show #1 models
    8843 
    8844 > hide #1 models
    8845 
    8846 > select #6/D
    8847 
    8848 745 atoms, 756 bonds, 95 residues, 1 model selected 
    8849 
    8850 > color sel pale green
    8851 
    8852 > color sel thistle
    8853 
    8854 > color sel honeydew
    8855 
    8856 > color sel azure
    8857 
    8858 > color sel honeydew
    8859 
    8860 > select clear
    8861 
    8862 > select #6/D
    8863 
    8864 745 atoms, 756 bonds, 95 residues, 1 model selected 
    8865 
    8866 > color sel pale green
    8867 
    8868 > select #6/H
    8869 
    8870 745 atoms, 756 bonds, 95 residues, 1 model selected 
    8871 
    8872 > color sel medium sea green
    8873 
    8874 > select clear
    8875 
    8876 > select #6/G
    8877 
    8878 900 atoms, 912 bonds, 116 residues, 1 model selected 
    8879 
    8880 > color sel dark turquoise
    8881 
    8882 > select clear
    8883 
    8884 > select #6/E
    8885 
    8886 799 atoms, 811 bonds, 97 residues, 1 model selected 
    8887 
    8888 > show #1 models
    8889 
    8890 > hide #!6 models
    8891 
    8892 > show #!6 models
    8893 
    8894 > hide #1 models
    8895 
    8896 > show #1 models
    8897 
    8898 > hide #1 models
    8899 
    8900 > show #1 models
    8901 
    8902 > hide #!6 models
    8903 
    8904 > show #!6 models
    8905 
    8906 > hide #!6 models
    8907 
    8908 > show #!6 models
    8909 
    8910 > hide #!6 models
    8911 
    8912 > select #1/B
    8913 
    8914 800 atoms, 808 bonds, 103 residues, 1 model selected 
    8915 
    8916 > color sel saddle brown
    8917 
    8918 > select clear
    8919 
    8920 > show #!6 models
    8921 
    8922 > hide #!6 models
    8923 
    8924 > show #!6 models
    8925 
    8926 > hide #!6 models
    8927 
    8928 > show #!6 models
    8929 
    8930 > hide #!6 models
    8931 
    8932 > show #!6 models
    8933 
    8934 > hide #1 models
    8935 
    8936 > show #1 models
    8937 
    8938 > hide #1 models
    8939 
    8940 > select #6/E
    8941 
    8942 799 atoms, 811 bonds, 97 residues, 1 model selected 
    8943 
    8944 > color sel tomato
    8945 
    8946 > select clear
    8947 
    8948 > show #1 models
    8949 
    8950 > hide #!6 models
    8951 
    8952 > select #1/E
    8953 
    8954 1081 atoms, 1095 bonds, 136 residues, 1 model selected 
    8955 
    8956 > color sel dark goldenrod
    8957 
    8958 > show #!6 models
    8959 
    8960 > select clear
    8961 
    8962 > hide #!6 models
    8963 
    8964 > show #!6 models
    8965 
    8966 > hide #1 models
    8967 
    8968 > show #1 models
    8969 
    8970 > hide #1 models
    8971 
    8972 > show #1 models
    8973 
    8974 > hide #!6 models
    8975 
    8976 > show #!6 models
    8977 
    8978 > hide #1 models
    8979 
    8980 > show #1 models
    8981 
    8982 > hide #!6 models
    8983 
    8984 > show #!6 models
    8985 
    8986 > hide #!6 models
    8987 
    8988 > show #!6 models
    8989 
    8990 > hide #!6 models
    8991 
    8992 > select #1/C:10-26
    8993 
    8994 131 atoms, 131 bonds, 17 residues, 1 model selected 
    8995 
    8996 > show sel cartoons
    8997 
    8998 > select #1/C:10-40
    8999 
    9000 248 atoms, 251 bonds, 31 residues, 1 model selected 
    9001 
    9002 > show sel cartoons
    9003 
    9004 > color sel pale green
    9005 
    9006 > select clear
    9007 
    9008 > show #!6 models
    9009 
    9010 > hide #!6 models
    9011 
    9012 > show #!6 models
    9013 
    9014 > hide #!6 models
    9015 
    9016 > show #!6 models
    9017 
    9018 > hide #1 models
    9019 
    9020 > select #1/C
    9021 
    9022 996 atoms, 1008 bonds, 130 residues, 1 model selected 
    9023 
    9024 > select #6/C
    9025 
    9026 840 atoms, 850 bonds, 109 residues, 1 model selected 
    9027 
    9028 > color sel sky blue
    9029 
    9030 > color sel light sky blue
    9031 
    9032 > select clear
    9033 
    9034 > show #1 models
    9035 
    9036 > hide #1 models
    9037 
    9038 > show #1 models
    9039 
    9040 > hide #!6 models
    9041 
    9042 > select #1/D:31-39
    9043 
    9044 79 atoms, 79 bonds, 9 residues, 1 model selected 
    9045 
    9046 > color sel tan
    9047 
    9048 > select clear
    9049 
    9050 > show #!6 models
    9051 
    9052 > select clear
    9053 
    9054 > hide #1 models
    9055 
    9056 > show #1 models
    9057 
    9058 > hide #1 models
    9059 
    9060 > show #1 models
    9061 
    9062 > select clear
    9063 
    9064 > save "/Users/taic/OneDrive - National Institutes of
    9065 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.vs.AF3.histones.png"
    9066 > width 740 height 627 supersample 4 transparentBackground true
    9067 
    9068 > select #6
    9069 
    9070 14434 atoms, 15401 bonds, 421 pseudobonds, 1273 residues, 3 models selected 
    9071 
    9072 > hide #1 models
    9073 
    9074 > show sel cartoons
    9075 
    9076 > select clear
    9077 
    9078 > save "/Users/taic/OneDrive - National Institutes of
    9079 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1-2.png" width 740
    9080 > height 627 supersample 3
    9081 
    9082 > show #1 models
    9083 
    9084 > hide #!6 models
    9085 
    9086 > select #1
    9087 
    9088 25021 atoms, 26311 bonds, 2675 residues, 1 model selected 
    9089 
    9090 > show sel cartoons
    9091 
    9092 > select clear
    9093 
    9094 > select #1/J:1-268/J:321-900/I:1-167/I:270-478
    9095 
    9096 8445 atoms, 8673 bonds, 1159 residues, 1 model selected 
    9097 
    9098 > hide sel cartoons
    9099 
    9100 > show #!6 models
    9101 
    9102 > select #6/O
    9103 
    9104 856 atoms, 883 bonds, 102 residues, 1 model selected 
    9105 
    9106 > hide #!6 models
    9107 
    9108 > show #!6 models
    9109 
    9110 > select #6/O#1/I:168-269
    9111 
    9112 1712 atoms, 1766 bonds, 204 residues, 2 models selected 
    9113 
    9114 > matchmaker #1 & sel to #6 & sel
    9115 
    9116 Parameters 
    9117 --- 
    9118 Chain pairing | bb 
    9119 Alignment algorithm | Needleman-Wunsch 
    9120 Similarity matrix | BLOSUM-62 
    9121 SS fraction | 0.3 
    9122 Gap open (HH/SS/other) | 18/18/6 
    9123 Gap extend | 1 
    9124 SS matrix |  |  | H | S | O 
    9125 ---|---|---|--- 
    9126 H | 6 | -9 | -6 
    9127 S |  | 6 | -6 
    9128 O |  |  | 4 
    9129 Iteration cutoff | 2 
    9130  
    9131 Matchmaker 8vg1, chain O (#6) with fold_nucleosome_foxa1_gata4_model_0.cif,
    9132 chain I (#1), sequence alignment score = 540.2 
    9133 RMSD between 85 pruned atom pairs is 0.884 angstroms; (across all 102 pairs:
    9134 1.802) 
    9135  
    9136 
    9137 > hide #!6 models
    9138 
    9139 > select clear
    9140 
    9141 > show #!6 models
    9142 
    9143 > hide #!6 models
    9144 
    9145 > show #!6 models
    9146 
    9147 > hide #1 models
    9148 
    9149 > show #1 models
    9150 
    9151 > ui tool show "Side View"
    9152 
    9153 > hide #1 models
    9154 
    9155 > select #6/O
    9156 
    9157 856 atoms, 883 bonds, 102 residues, 1 model selected 
    9158 
    9159 > show sel surfaces
    9160 
    9161 > transparency (#!6 & sel) 70
    9162 
    9163 > select clear
    9164 
    9165 > select #6/I
    9166 
    9167 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    9168 
    9169 > select #6/I/J
    9170 
    9171 7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected 
    9172 
    9173 > show sel atoms
    9174 
    9175 > nucleotides sel atoms
    9176 
    9177 > style nucleic & sel stick
    9178 
    9179 Changed 7011 atom styles 
    9180 
    9181 > select clear
    9182 
    9183 > select #6/I/J
    9184 
    9185 7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected 
    9186 
    9187 > select clear
    9188 
    9189 > select #6/I/J
    9190 
    9191 7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected 
    9192 
    9193 > color sel bynucleotide
    9194 
    9195 > select clear
    9196 
    9197 > undo
    9198 
    9199 [Repeated 2 time(s)]
    9200 
    9201 > select clear
    9202 
    9203 > undo
    9204 
    9205 [Repeated 5 time(s)]
    9206 
    9207 > hide #!6 atoms
    9208 
    9209 > nucleotides #!6 atoms
    9210 
    9211 > style nucleic & #!6 stick
    9212 
    9213 Changed 7011 atom styles 
    9214 
    9215 > show #!6 atoms
    9216 
    9217 > hide #!6 atoms
    9218 
    9219 > select #6/I/J
    9220 
    9221 7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected 
    9222 
    9223 > nucleotides sel atoms
    9224 
    9225 > style nucleic & sel stick
    9226 
    9227 Changed 7011 atom styles 
    9228 
    9229 > show sel atoms
    9230 
    9231 > color sel bynucleotide
    9232 
    9233 > select clear
    9234 
    9235 > transparency #6 60
    9236 
    9237 > transparency #6 30
    9238 
    9239 > transparency #6 40
    9240 
    9241 > save "/Users/taic/OneDrive - National Institutes of
    9242 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.s.png" width
    9243 > 740 height 627 supersample 4 transparentBackground true
    9244 
    9245 > hide #!6 surfaces
    9246 
    9247 > save "/Users/taic/OneDrive - National Institutes of
    9248 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.png" width 740
    9249 > height 627 supersample 4 transparentBackground true
    9250 
    9251 > select #6/T
    9252 
    9253 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    9254 
    9255 > show sel surfaces
    9256 
    9257 > hide sel surfaces
    9258 
    9259 > select clear
    9260 
    9261 > show #1 models
    9262 
    9263 > hide #!6 models
    9264 
    9265 > show #!6 models
    9266 
    9267 > hide #1 models
    9268 
    9269 > show #1 models
    9270 
    9271 > hide #1 models
    9272 
    9273 > save "/Users/taic/OneDrive - National Institutes of
    9274 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.png" width 740
    9275 > height 627 supersample 4 transparentBackground true
    9276 
    9277 > show #1 models
    9278 
    9279 > hide #!6 models
    9280 
    9281 > select #1/I
    9282 
    9283 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    9284 
    9285 > color sel dark orchid
    9286 
    9287 > color sel medium violet red
    9288 
    9289 > color sel deep pink
    9290 
    9291 > color sel medium orchid
    9292 
    9293 [Repeated 1 time(s)]
    9294 
    9295 > select clear
    9296 
    9297 > show #!6 models
    9298 
    9299 > hide #!6 models
    9300 
    9301 > select #1/L/K
    9302 
    9303 7628 atoms, 8556 bonds, 372 residues, 1 model selected 
    9304 
    9305 > color sel bynucleotide
    9306 
    9307 > show #!6 models
    9308 
    9309 > hide #!6 models
    9310 
    9311 > select #1/L/K
    9312 
    9313 7628 atoms, 8556 bonds, 372 residues, 1 model selected 
    9314 
    9315 > color sel bynucleotide
    9316 
    9317 > show sel atoms
    9318 
    9319 > nucleotides sel atoms
    9320 
    9321 > style nucleic & sel stick
    9322 
    9323 Changed 7628 atom styles 
    9324 
    9325 > select clear
    9326 
    9327 > save "/Users/taic/OneDrive - National Institutes of
    9328 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.AF3.png" width
    9329 > 740 height 627 supersample 4 transparentBackground true
    9330 
    9331 > show #!6 models
    9332 
    9333 > hide #!6 models
    9334 
    9335 > show #!6 models
    9336 
    9337 > hide #!6 models
    9338 
    9339 > show #!6 models
    9340 
    9341 > hide #!6 models
    9342 
    9343 > show #!6 models
    9344 
    9345 > save "/Users/taic/OneDrive - National Institutes of
    9346 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.vs.AF3.png"
    9347 > width 740 height 627 supersample 4 transparentBackground true
    9348 
    9349 > hide #1 models
    9350 
    9351 > select #6/T
    9352 
    9353 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    9354 
    9355 > show #1 models
    9356 
    9357 > select #6/T#1/J
    9358 
    9359 6598 atoms, 6765 bonds, 4 pseudobonds, 889 residues, 3 models selected 
    9360 
    9361 > matchmaker #1 & sel to #6 & sel
    9362 
    9363 Parameters 
    9364 --- 
    9365 Chain pairing | bb 
    9366 Alignment algorithm | Needleman-Wunsch 
    9367 Similarity matrix | BLOSUM-62 
    9368 SS fraction | 0.3 
    9369 Gap open (HH/SS/other) | 18/18/6 
    9370 Gap extend | 1 
    9371 SS matrix |  |  | H | S | O 
    9372 ---|---|---|--- 
    9373 H | 6 | -9 | -6 
    9374 S |  | 6 | -6 
    9375 O |  |  | 4 
    9376 Iteration cutoff | 2 
    9377  
    9378 Matchmaker 8vg1, chain T (#6) with fold_nucleosome_foxa1_gata4_model_0.cif,
    9379 chain J (#1), sequence alignment score = 3142.7 
    9380 RMSD between 45 pruned atom pairs is 0.548 angstroms; (across all 53 pairs:
    9381 7.623) 
    9382  
    9383 
    9384 > hide #!6 models
    9385 
    9386 > show #!6 models
    9387 
    9388 > hide #1 models
    9389 
    9390 > show #1 models
    9391 
    9392 > hide #1 models
    9393 
    9394 > show #1 models
    9395 
    9396 > hide #1 models
    9397 
    9398 > select #6/I
    9399 
    9400 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    9401 
    9402 > color sel thistle
    9403 
    9404 > select #6/J
    9405 
    9406 3510 atoms, 3942 bonds, 171 residues, 1 model selected 
    9407 
    9408 > color sel lavender
    9409 
    9410 > color sel pale turquoise
    9411 
    9412 > select #6/J/I
    9413 
    9414 7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected 
    9415 
    9416 > style sel stick
    9417 
    9418 Changed 7011 atom styles 
    9419 
    9420 > hide sel atoms
    9421 
    9422 > show sel atoms
    9423 
    9424 > nucleotides sel atoms
    9425 
    9426 > style nucleic & sel stick
    9427 
    9428 Changed 7011 atom styles 
    9429 
    9430 > select clear
    9431 
    9432 > save "/Users/taic/OneDrive - National Institutes of
    9433 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.GATA3.png" width 740
    9434 > height 627 supersample 4 transparentBackground true
    9435 
    9436 > show #1 models
    9437 
    9438 > hide #!6 models
    9439 
    9440 > show #!6 models
    9441 
    9442 > hide #1 models
    9443 
    9444 > select clear
    9445 
    9446 > show #1 models
    9447 
    9448 > hide #!6 models
    9449 
    9450 > select #1/L
    9451 
    9452 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    9453 
    9454 > color sel plum
    9455 
    9456 > select #1/K
    9457 
    9458 3811 atoms, 4270 bonds, 186 residues, 1 model selected 
    9459 
    9460 > color sel deep sky blue
    9461 
    9462 > select #1/L:158
    9463 
    9464 21 atoms, 23 bonds, 1 residue, 1 model selected 
    9465 
    9466 > select #1/L
    9467 
    9468 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    9469 
    9470 > color sel violet
    9471 
    9472 > select clear
    9473 
    9474 > select #1/L/K
    9475 
    9476 7628 atoms, 8556 bonds, 372 residues, 1 model selected 
    9477 
    9478 > hide sel atoms
    9479 
    9480 > select clear
    9481 
    9482 > select #1/I
    9483 
    9484 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    9485 
    9486 > color sel deep pink
    9487 
    9488 > select clear
    9489 
    9490 > show #!6 models
    9491 
    9492 > hide #!6 models
    9493 
    9494 > save "/Users/taic/OneDrive - National Institutes of
    9495 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.GATA3.AF3.png" width
    9496 > 740 height 627 supersample 4 transparentBackground true
    9497 
    9498 > hide #1 models
    9499 
    9500 > show #2 models
    9501 
    9502 > show #3 models
    9503 
    9504 > show #4 models
    9505 
    9506 > show #5 models
    9507 
    9508 > delete atoms #2-5
    9509 
    9510 > delete bonds #2-5
    9511 
    9512 > show #15 models
    9513 
    9514 > show #16 models
    9515 
    9516 > hide #15 models
    9517 
    9518 > show #17 models
    9519 
    9520 > show #18 models
    9521 
    9522 > show #19 models
    9523 
    9524 > delete atoms #16-19
    9525 
    9526 > delete bonds #16-19
    9527 
    9528 > show #!14 models
    9529 
    9530 > show #15 models
    9531 
    9532 > save "/Users/taic/OneDrive - National Institutes of
    9533 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/GATA4_8vg1.aerolysin_9FMM6.cxs"
    9534 
    9535 ——— End of log from Wed Jul 16 09:52:26 2025 ———
    9536 
    9537 opened ChimeraX session 
    9538 
    9539 > hide #!14 models
    9540 
    9541 > hide #15 models
    9542 
    9543 > show #!6 models
    9544 
    9545 > show #1 models
    9546 
    9547 > show #7 models
    9548 
    9549 > hide #7 models
    9550 
    9551 > show #!20 models
    9552 
    9553 > show #!12 models
    9554 
    9555 > show #11 models
    9556 
    9557 > hide #11 models
    9558 
    9559 > save "/Users/taic/OneDrive - National Institutes of
    9560 > Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs"
    9561 
    9562 > hide #1 models
    9563 
    9564 > hide #!6 models
    9565 
    9566 > hide #!12 models
    9567 
    9568 > hide #!20 models
    9569 
    9570 > show #7 models
    9571 
    9572 > hide #7 models
    9573 
    9574 > show #!8 models
    9575 
    9576 > show #9 models
    9577 
    9578 > show #!10 models
    9579 
    9580 > show #11 models
    9581 
    9582 > show #!12 models
    9583 
    9584 > show #7 models
    9585 
    9586 > show #13 models
    9587 
    9588 > show #!14 models
    9589 
    9590 > show #15 models
    9591 
    9592 > show #!20 models
    9593 
    9594 > hide #!20 models
    9595 
    9596 > show #!20 models
    9597 
    9598 > hide #!20 models
    9599 
    9600 > delete atoms #7-15
    9601 
    9602 > delete bonds #7-15
    9603 
    9604 > show #1 models
    9605 
    9606 > show #!6 models
    9607 
    9608 > show #!20 models
    9609 
    9610 > save "/Users/taic/OneDrive - National Institutes of
    9611 > Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs"
    9612 
    9613 ——— End of log from Tue Aug 26 11:16:07 2025 ———
    9614 
    9615 opened ChimeraX session 
    9616 
    9617 > hide #1 models
    9618 
    9619 > hide #!20 models
    9620 
    9621 > hide #!6 models
    9622 
    9623 > show #!20 models
    9624 
    9625 > hide #!20 models
    9626 
    9627 > show #!6 models
    9628 
    9629 > show #1 models
    9630 
    9631 > hide #!6 models
    9632 
    9633 > select #1/J
    9634 
    9635 6183 atoms, 6345 bonds, 835 residues, 1 model selected 
    9636 
    9637 > show sel cartoons
    9638 
    9639 > show #!6 models
    9640 
    9641 > hide #1 models
    9642 
    9643 > view matrix models
    9644 > #1,-0.92427,0.28609,-0.25274,96.671,-0.20231,0.19434,0.95984,231.94,0.32372,0.93829,-0.12175,145.04
    9645 
    9646 > view matrix models
    9647 > #1,-0.92427,0.28609,-0.25274,107.63,-0.20231,0.19434,0.95984,235.09,0.32372,0.93829,-0.12175,125.75
    9648 
    9649 > hide #!6 atoms
    9650 
    9651 > select ::name="CYS"
    9652 
    9653 186 atoms, 155 bonds, 31 residues, 3 models selected 
    9654 
    9655 > show sel & #!6 atoms
    9656 
    9657 > style sel & #!6 ball
    9658 
    9659 Changed 66 atom styles 
    9660 
    9661 > color (#!6 & sel) yellow
    9662 
    9663 > select clear
    9664 
    9665 > show #1 models
    9666 
    9667 > hide #!6 models
    9668 
    9669 > select #1/J:269-320
    9670 
    9671 384 atoms, 389 bonds, 52 residues, 1 model selected 
    9672 
    9673 > color sel cyan
    9674 
    9675 > select ::name="CYS"
    9676 
    9677 186 atoms, 155 bonds, 31 residues, 3 models selected 
    9678 
    9679 > show sel & #1 atoms
    9680 
    9681 > style sel & #1 ball
    9682 
    9683 Changed 96 atom styles 
    9684 
    9685 > color (#1 & sel) yellow
    9686 
    9687 > show #!6 models
    9688 
    9689 > hide #1 models
    9690 
    9691 > show #1 models
    9692 
    9693 > hide #!6 models
    9694 
    9695 > select #1/J:269-320
    9696 
    9697 384 atoms, 389 bonds, 52 residues, 1 model selected 
    9698 
    9699 > show #!6 models
    9700 
    9701 > hide #1 models
    9702 
    9703 > show #1 models
    9704 
    9705 > hide #!6 models
    9706 
    9707 > select #1/J:394
    9708 
    9709 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9710 
    9711 > show sel atoms
    9712 
    9713 [Repeated 2 time(s)]
    9714 
    9715 > hide sel atoms
    9716 
    9717 > select #1/J:1-393
    9718 
    9719 3055 atoms, 3132 bonds, 393 residues, 1 model selected 
    9720 
    9721 > select #1/J:1-393
    9722 
    9723 3055 atoms, 3132 bonds, 393 residues, 1 model selected 
    9724 
    9725 > hide sel cartoons
    9726 
    9727 > hide sel atoms
    9728 
    9729 > select #1/J:1-393
    9730 
    9731 3055 atoms, 3132 bonds, 393 residues, 1 model selected 
    9732 
    9733 > hide sel atoms
    9734 
    9735 [Repeated 2 time(s)]
    9736 
    9737 > show #!6 models
    9738 
    9739 > hide #1 models
    9740 
    9741 > select Zn
    9742 
    9743 1 atom, 1 residue, 1 model selected 
    9744 
    9745 > show sel atoms
    9746 
    9747 > color sel dark gray
    9748 
    9749 > select clear
    9750 
    9751 > open /Users/taic/Library/CloudStorage/OneDrive-
    9752 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif
    9753 
    9754 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif #2 
    9755 --- 
    9756 Chain | Description 
    9757 A E | . 
    9758 B F | . 
    9759 C G | . 
    9760 D H | . 
    9761 I | . 
    9762 J | . 
    9763 L | . 
    9764 M | . 
    9765  
    9766 
    9767 > open /Users/taic/Library/CloudStorage/OneDrive-
    9768 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif
    9769 
    9770 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif #3 
    9771 --- 
    9772 Chain | Description 
    9773 A E | . 
    9774 B F | . 
    9775 C G | . 
    9776 D H | . 
    9777 I | . 
    9778 J | . 
    9779 L | . 
    9780 M | . 
    9781  
    9782 
    9783 > open /Users/taic/Library/CloudStorage/OneDrive-
    9784 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif
    9785 
    9786 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif #4 
    9787 --- 
    9788 Chain | Description 
    9789 A E | . 
    9790 B F | . 
    9791 C G | . 
    9792 D H | . 
    9793 I | . 
    9794 J | . 
    9795 L | . 
    9796 M | . 
    9797  
    9798 
    9799 > open /Users/taic/Library/CloudStorage/OneDrive-
    9800 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif
    9801 
    9802 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif #5 
    9803 --- 
    9804 Chain | Description 
    9805 A E | . 
    9806 B F | . 
    9807 C G | . 
    9808 D H | . 
    9809 I | . 
    9810 J | . 
    9811 L | . 
    9812 M | . 
    9813  
    9814 
    9815 > open /Users/taic/Library/CloudStorage/OneDrive-
    9816 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif
    9817 
    9818 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif #7 
    9819 --- 
    9820 Chain | Description 
    9821 A E | . 
    9822 B F | . 
    9823 C G | . 
    9824 D H | . 
    9825 I | . 
    9826 J | . 
    9827 L | . 
    9828 M | . 
    9829  
    9830 
    9831 > open /Users/taic/Library/CloudStorage/OneDrive-
    9832 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif
    9833 
    9834 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif #8 
    9835 --- 
    9836 Chain | Description 
    9837 A E | . 
    9838 B F | . 
    9839 C G | . 
    9840 D H | . 
    9841 I | . 
    9842 J | . 
    9843 L | . 
    9844 M | . 
    9845  
    9846 
    9847 > open /Users/taic/Library/CloudStorage/OneDrive-
    9848 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif
    9849 
    9850 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif #9 
    9851 --- 
    9852 Chain | Description 
    9853 A E | . 
    9854 B F | . 
    9855 C G | . 
    9856 D H | . 
    9857 I | . 
    9858 J | . 
    9859 L | . 
    9860 M | . 
    9861  
    9862 
    9863 > open /Users/taic/Library/CloudStorage/OneDrive-
    9864 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif
    9865 
    9866 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif #10 
    9867 --- 
    9868 Chain | Description 
    9869 A E | . 
    9870 B F | . 
    9871 C G | . 
    9872 D H | . 
    9873 I | . 
    9874 J | . 
    9875 L | . 
    9876 M | . 
    9877  
    9878 
    9879 > open /Users/taic/Library/CloudStorage/OneDrive-
    9880 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif
    9881 
    9882 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif #11 
    9883 --- 
    9884 Chain | Description 
    9885 A E | . 
    9886 B F | . 
    9887 C G | . 
    9888 D H | . 
    9889 I | . 
    9890 J | . 
    9891 L | . 
    9892 M | . 
    9893  
    9894 
    9895 > open /Users/taic/Library/CloudStorage/OneDrive-
    9896 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif
    9897 
    9898 Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif #12 
    9899 --- 
    9900 Chain | Description 
    9901 A E | . 
    9902 B F | . 
    9903 C G | . 
    9904 D H | . 
    9905 I | . 
    9906 J | . 
    9907 L | . 
    9908 M | . 
    9909  
    9910 
    9911 > open /Users/taic/Library/CloudStorage/OneDrive-
    9912 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif
    9913 
    9914 Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif #13 
    9915 --- 
    9916 Chain | Description 
    9917 A E | . 
    9918 B F | . 
    9919 C G | . 
    9920 D H | . 
    9921 I | . 
    9922 J | . 
    9923 L | . 
    9924 M | . 
    9925  
    9926 
    9927 > open /Users/taic/Library/CloudStorage/OneDrive-
    9928 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif
    9929 
    9930 Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif #14 
    9931 --- 
    9932 Chain | Description 
    9933 A E | . 
    9934 B F | . 
    9935 C G | . 
    9936 D H | . 
    9937 I | . 
    9938 J | . 
    9939 L | . 
    9940 M | . 
    9941  
    9942 
    9943 > open /Users/taic/Library/CloudStorage/OneDrive-
    9944 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif
    9945 
    9946 Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif #15 
    9947 --- 
    9948 Chain | Description 
    9949 A E | . 
    9950 B F | . 
    9951 C G | . 
    9952 D H | . 
    9953 I | . 
    9954 J | . 
    9955 L | . 
    9956 M | . 
    9957  
    9958 
    9959 > open /Users/taic/Library/CloudStorage/OneDrive-
    9960 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif
    9961 
    9962 Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif #16 
    9963 --- 
    9964 Chain | Description 
    9965 A E | . 
    9966 B F | . 
    9967 C G | . 
    9968 D H | . 
    9969 I | . 
    9970 J | . 
    9971 L | . 
    9972 M | . 
    9973  
    9974 
    9975 > open /Users/taic/Library/CloudStorage/OneDrive-
    9976 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif
    9977 
    9978 Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif #17 
    9979 --- 
    9980 Chain | Description 
    9981 A E | . 
    9982 B F | . 
    9983 C G | . 
    9984 D H | . 
    9985 I | . 
    9986 J | . 
    9987 L | . 
    9988 M | . 
    9989  
    9990 
    9991 > ui tool show Matchmaker
    9992 
    9993 > matchmaker #1-5,7-17#!20 to #6
    9994 
    9995 Computing secondary structure 
    9996 [Repeated 29 time(s)]  Parameters 
    9997 --- 
    9998 Chain pairing | bb 
    9999 Alignment algorithm | Needleman-Wunsch 
    10000 Similarity matrix | BLOSUM-62 
    10001 SS fraction | 0.3 
    10002 Gap open (HH/SS/other) | 18/18/6 
    10003 Gap extend | 1 
    10004 SS matrix |  |  | H | S | O 
    10005 ---|---|---|--- 
    10006 H | 6 | -9 | -6 
    10007 S |  | 6 | -6 
    10008 O |  |  | 4 
    10009 Iteration cutoff | 2 
    10010  
    10011 Matchmaker 8vg1, chain T (#6) with fold_nucleosome_foxa1_gata4_model_0.cif,
    10012 chain J (#1), sequence alignment score = 3142.7 
    10013 RMSD between 45 pruned atom pairs is 0.548 angstroms; (across all 53 pairs:
    10014 7.623) 
    10015  
    10016 Matchmaker 8vg1, chain T (#6) with
    10017 fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain J (#2), sequence
    10018 alignment score = 3151.7 
    10019 RMSD between 43 pruned atom pairs is 0.482 angstroms; (across all 53 pairs:
    10020 7.477) 
    10021  
    10022 Matchmaker 8vg1, chain T (#6) with
    10023 fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain J (#3), sequence
    10024 alignment score = 3142.7 
    10025 RMSD between 45 pruned atom pairs is 0.604 angstroms; (across all 53 pairs:
    10026 7.758) 
    10027  
    10028 Matchmaker 8vg1, chain T (#6) with
    10029 fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain J (#4), sequence
    10030 alignment score = 3139.7 
    10031 RMSD between 45 pruned atom pairs is 0.494 angstroms; (across all 53 pairs:
    10032 7.946) 
    10033  
    10034 Matchmaker 8vg1, chain T (#6) with
    10035 fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain J (#5), sequence
    10036 alignment score = 3109.7 
    10037 RMSD between 44 pruned atom pairs is 0.520 angstroms; (across all 53 pairs:
    10038 6.394) 
    10039  
    10040 Matchmaker 8vg1, chain T (#6) with
    10041 fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain J (#7), sequence
    10042 alignment score = 3139.7 
    10043 RMSD between 44 pruned atom pairs is 0.558 angstroms; (across all 53 pairs:
    10044 7.840) 
    10045  
    10046 Matchmaker 8vg1, chain T (#6) with
    10047 fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain J (#8), sequence
    10048 alignment score = 3151.7 
    10049 RMSD between 43 pruned atom pairs is 0.482 angstroms; (across all 53 pairs:
    10050 7.477) 
    10051  
    10052 Matchmaker 8vg1, chain T (#6) with
    10053 fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain J (#9), sequence
    10054 alignment score = 3142.7 
    10055 RMSD between 45 pruned atom pairs is 0.604 angstroms; (across all 53 pairs:
    10056 7.758) 
    10057  
    10058 Matchmaker 8vg1, chain T (#6) with
    10059 fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain J (#10), sequence
    10060 alignment score = 3139.7 
    10061 RMSD between 45 pruned atom pairs is 0.494 angstroms; (across all 53 pairs:
    10062 7.946) 
    10063  
    10064 Matchmaker 8vg1, chain T (#6) with
    10065 fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain J (#11), sequence
    10066 alignment score = 3109.7 
    10067 RMSD between 44 pruned atom pairs is 0.520 angstroms; (across all 53 pairs:
    10068 6.394) 
    10069  
    10070 Matchmaker 8vg1, chain T (#6) with
    10071 fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain J (#12), sequence
    10072 alignment score = 3139.7 
    10073 RMSD between 44 pruned atom pairs is 0.558 angstroms; (across all 53 pairs:
    10074 7.840) 
    10075  
    10076 Matchmaker 8vg1, chain O (#6) with
    10077 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
    10078 alignment score = 1915.2 
    10079 RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
    10080 1.960) 
    10081  
    10082 Matchmaker 8vg1, chain O (#6) with
    10083 fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain I (#14), sequence
    10084 alignment score = 1927.2 
    10085 RMSD between 82 pruned atom pairs is 0.853 angstroms; (across all 102 pairs:
    10086 1.776) 
    10087  
    10088 Matchmaker 8vg1, chain O (#6) with
    10089 fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain I (#15), sequence
    10090 alignment score = 1924.2 
    10091 RMSD between 78 pruned atom pairs is 0.751 angstroms; (across all 102 pairs:
    10092 2.144) 
    10093  
    10094 Matchmaker 8vg1, chain O (#6) with
    10095 fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain I (#16), sequence
    10096 alignment score = 1901.4 
    10097 RMSD between 80 pruned atom pairs is 0.855 angstroms; (across all 102 pairs:
    10098 3.778) 
    10099  
    10100 Matchmaker 8vg1, chain O (#6) with
    10101 fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain I (#17), sequence
    10102 alignment score = 1909.2 
    10103 RMSD between 82 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
    10104 1.994) 
    10105  
    10106 Matchmaker 8vg1, chain E (#6) with 3aze, chain E (#20), sequence alignment
    10107 score = 625.6 
    10108 RMSD between 96 pruned atom pairs is 0.335 angstroms; (across all 97 pairs:
    10109 0.414) 
    10110  
    10111 
    10112 > hide #2-5,7-17#!6 surfaces
    10113 
    10114 > hide #2-5,7-17#!6 atoms
    10115 
    10116 > show #2-5,7-17#!6 cartoons
    10117 
    10118 > hide #7 models
    10119 
    10120 > hide #8 models
    10121 
    10122 > hide #9 models
    10123 
    10124 > hide #10 models
    10125 
    10126 > hide #11 models
    10127 
    10128 > hide #12 models
    10129 
    10130 > hide #13 models
    10131 
    10132 > hide #14 models
    10133 
    10134 > hide #15 models
    10135 
    10136 > hide #16 models
    10137 
    10138 > hide #17 models
    10139 
    10140 > hide #!6 models
    10141 
    10142 > show #7 models
    10143 
    10144 > hide #2 models
    10145 
    10146 > hide #3 models
    10147 
    10148 > hide #4 models
    10149 
    10150 > hide #5 models
    10151 
    10152 > hide #7 models
    10153 
    10154 > show #8 models
    10155 
    10156 > show #9 models
    10157 
    10158 > show #10 models
    10159 
    10160 > show #11 models
    10161 
    10162 > show #12 models
    10163 
    10164 > delete atoms #8-12
    10165 
    10166 > delete bonds #8-12
    10167 
    10168 > open /Users/taic/Library/CloudStorage/OneDrive-
    10169 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_0.cif
    10170 
    10171 Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_0.cif #8 
    10172 --- 
    10173 Chain | Description 
    10174 A | . 
    10175 B | . 
    10176 D | . 
    10177 E | . 
    10178  
    10179 
    10180 > open /Users/taic/Library/CloudStorage/OneDrive-
    10181 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_1.cif
    10182 
    10183 Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_1.cif #9 
    10184 --- 
    10185 Chain | Description 
    10186 A | . 
    10187 B | . 
    10188 D | . 
    10189 E | . 
    10190  
    10191 
    10192 > open /Users/taic/Library/CloudStorage/OneDrive-
    10193 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_2.cif
    10194 
    10195 Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_2.cif #10 
    10196 --- 
    10197 Chain | Description 
    10198 A | . 
    10199 B | . 
    10200 D | . 
    10201 E | . 
    10202  
    10203 
    10204 > open /Users/taic/Library/CloudStorage/OneDrive-
    10205 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_3.cif
    10206 
    10207 Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_3.cif #11 
    10208 --- 
    10209 Chain | Description 
    10210 A | . 
    10211 B | . 
    10212 D | . 
    10213 E | . 
    10214  
    10215 
    10216 > open /Users/taic/Library/CloudStorage/OneDrive-
    10217 > NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_4.cif
    10218 
    10219 Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_4.cif #12 
    10220 --- 
    10221 Chain | Description 
    10222 A | . 
    10223 B | . 
    10224 D | . 
    10225 E | . 
    10226  
    10227 Computing secondary structure 
    10228 [Repeated 4 time(s)]
    10229 
    10230 > ui tool show Matchmaker
    10231 
    10232 > matchmaker #8-12 to #6
    10233 
    10234 Computing secondary structure 
    10235 [Repeated 4 time(s)]  Parameters 
    10236 --- 
    10237 Chain pairing | bb 
    10238 Alignment algorithm | Needleman-Wunsch 
    10239 Similarity matrix | BLOSUM-62 
    10240 SS fraction | 0.3 
    10241 Gap open (HH/SS/other) | 18/18/6 
    10242 Gap extend | 1 
    10243 SS matrix |  |  | H | S | O 
    10244 ---|---|---|--- 
    10245 H | 6 | -9 | -6 
    10246 S |  | 6 | -6 
    10247 O |  |  | 4 
    10248 Iteration cutoff | 2 
    10249  
    10250 Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_0.cif,
    10251 chain B (#8), sequence alignment score = 3142.7 
    10252 RMSD between 44 pruned atom pairs is 0.526 angstroms; (across all 53 pairs:
    10253 8.378) 
    10254  
    10255 Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_1.cif,
    10256 chain B (#9), sequence alignment score = 3139.7 
    10257 RMSD between 44 pruned atom pairs is 0.562 angstroms; (across all 53 pairs:
    10258 8.220) 
    10259  
    10260 Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_2.cif,
    10261 chain B (#10), sequence alignment score = 3142.7 
    10262 RMSD between 44 pruned atom pairs is 0.525 angstroms; (across all 53 pairs:
    10263 8.352) 
    10264  
    10265 Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_3.cif,
    10266 chain B (#11), sequence alignment score = 3142.7 
    10267 RMSD between 44 pruned atom pairs is 0.484 angstroms; (across all 53 pairs:
    10268 8.451) 
    10269  
    10270 Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_4.cif,
    10271 chain B (#12), sequence alignment score = 3142.7 
    10272 RMSD between 44 pruned atom pairs is 0.546 angstroms; (across all 53 pairs:
    10273 8.252) 
    10274  
    10275 
    10276 > hide #9 models
    10277 
    10278 > hide #10 models
    10279 
    10280 > hide #11 models
    10281 
    10282 > hide #12 models
    10283 
    10284 > color #8 bychain
    10285 
    10286 > undo
    10287 
    10288 > show #9 models
    10289 
    10290 > hide #9 models
    10291 
    10292 > show #9 models
    10293 
    10294 > hide #8 models
    10295 
    10296 > show #8 models
    10297 
    10298 > hide #8 models
    10299 
    10300 > show #8 models
    10301 
    10302 > hide #9 models
    10303 
    10304 > show #10 models
    10305 
    10306 > hide #8 models
    10307 
    10308 > show #11 models
    10309 
    10310 > hide #10 models
    10311 
    10312 > color #11 bychain
    10313 
    10314 > show #12 models
    10315 
    10316 > hide #11 models
    10317 
    10318 > color #12 bychain
    10319 
    10320 > show #!6 models
    10321 
    10322 > hide #12 models
    10323 
    10324 > select #6/J:129
    10325 
    10326 20 atoms, 21 bonds, 1 residue, 1 model selected 
    10327 
    10328 > select #6/J:130
    10329 
    10330 21 atoms, 23 bonds, 1 residue, 1 model selected 
    10331 
    10332 > select add #6/J:129
    10333 
    10334 41 atoms, 44 bonds, 2 residues, 1 model selected 
    10335 
    10336 > select add #6/J:127
    10337 
    10338 63 atoms, 68 bonds, 3 residues, 1 model selected 
    10339 
    10340 > select add #6/J:128
    10341 
    10342 85 atoms, 92 bonds, 4 residues, 1 model selected 
    10343 
    10344 > show #8 models
    10345 
    10346 > hide #!6 models
    10347 
    10348 > select #8/D:127-130/E:127-130
    10349 
    10350 167 atoms, 186 bonds, 8 residues, 1 model selected 
    10351 
    10352 > show sel surfaces
    10353 
    10354 > hide sel surfaces
    10355 
    10356 > view matrix models
    10357 > #8,-0.46108,0.5647,0.68448,84.162,0.54831,-0.42517,0.72012,195.51,0.69768,0.70735,-0.11359,198.18
    10358 
    10359 > show #!6 models
    10360 
    10361 > hide #!8 models
    10362 
    10363 > ui tool show "Show Sequence Viewer"
    10364 
    10365 > sequence chain #6/I
    10366 
    10367 Alignment identifier is 6/I 
    10368 
    10369 > sequence chain #6/J
    10370 
    10371 Alignment identifier is 6/J 
    10372 
    10373 > select #6/J:129
    10374 
    10375 20 atoms, 21 bonds, 1 residue, 1 model selected 
    10376 
    10377 > select add #6/J:130
    10378 
    10379 41 atoms, 44 bonds, 2 residues, 1 model selected 
    10380 Drag select of 69 residues 
    10381 
    10382 > select #6/I:55
    10383 
    10384 22 atoms, 24 bonds, 1 residue, 1 model selected 
    10385 
    10386 > select #6/I:55-58
    10387 
    10388 84 atoms, 94 bonds, 4 residues, 1 model selected 
    10389 
    10390 > show sel atoms
    10391 
    10392 > color sel bynucleotide
    10393 
    10394 > select clear
    10395 
    10396 > show #!8 models
    10397 
    10398 > hide #!6 models
    10399 
    10400 > select #8/D:55-58/E:55-58
    10401 
    10402 165 atoms, 183 bonds, 8 residues, 1 model selected 
    10403 
    10404 > select #8/D:55-58
    10405 
    10406 84 atoms, 94 bonds, 4 residues, 1 model selected 
    10407 
    10408 > color sel bynucleotide
    10409 
    10410 > select #6/I:74-75
    10411 
    10412 39 atoms, 42 bonds, 2 residues, 1 model selected 
    10413 
    10414 > select #6/I:74-85
    10415 
    10416 242 atoms, 270 bonds, 12 residues, 1 model selected 
    10417 
    10418 > hide #!8 models
    10419 
    10420 > show #!8 models
    10421 
    10422 > show #!6 models
    10423 
    10424 > hide #!8 models
    10425 
    10426 > view matrix models
    10427 > #6,-0.73769,0.37453,-0.56173,264.58,0.036448,-0.80872,-0.58707,415.46,-0.67416,-0.45355,0.58293,241.01
    10428 
    10429 > select #6/I:74
    10430 
    10431 20 atoms, 21 bonds, 1 residue, 1 model selected 
    10432 
    10433 > select #6/I:74-85
    10434 
    10435 242 atoms, 270 bonds, 12 residues, 1 model selected 
    10436 
    10437 > select #6/I:29-30
    10438 
    10439 39 atoms, 42 bonds, 2 residues, 1 model selected 
    10440 
    10441 > select #6/I:29-41
    10442 
    10443 269 atoms, 301 bonds, 13 residues, 1 model selected 
    10444 
    10445 > show #!8 models
    10446 
    10447 > hide #!6 models
    10448 
    10449 > select #8/B
    10450 
    10451 6183 atoms, 6345 bonds, 835 residues, 1 model selected 
    10452 
    10453 > rainbow sel
    10454 
    10455 > select clear
    10456 
    10457 > show #9 models
    10458 
    10459 > hide #!8 models
    10460 
    10461 > select #8/D:55-58
    10462 
    10463 84 atoms, 94 bonds, 4 residues, 1 model selected 
    10464 
    10465 > select #9/D:55-58
    10466 
    10467 84 atoms, 94 bonds, 4 residues, 1 model selected 
    10468 
    10469 > color sel bynucleotide
    10470 
    10471 > show #10 models
    10472 
    10473 > show #11 models
    10474 
    10475 > show #12 models
    10476 
    10477 > delete atoms sel
    10478 
    10479 > delete bonds sel
    10480 
    10481 > delete atoms #9-12
    10482 
    10483 > delete bonds #9-12
    10484 
    10485 > show #13 models
    10486 
    10487 > hide #13 models
    10488 
    10489 > show #2 models
    10490 
    10491 > select #2/D:55-58
    10492 
    10493 29 atoms, 28 bonds, 4 residues, 1 model selected 
    10494 
    10495 > select #2/L:55-58
    10496 
    10497 84 atoms, 94 bonds, 4 residues, 1 model selected 
    10498 
    10499 > color sel bynucleotide
    10500 
    10501 > show sel atoms
    10502 
    10503 > nucleotides sel atoms
    10504 
    10505 > style nucleic & sel stick
    10506 
    10507 Changed 84 atom styles 
    10508 
    10509 > select ::name="CYS"
    10510 
    10511 1218 atoms, 1015 bonds, 203 residues, 14 models selected 
    10512 
    10513 > view matrix models
    10514 > #6,-0.73769,0.37453,-0.56173,269.6,0.036448,-0.80872,-0.58707,432.04,-0.67416,-0.45355,0.58293,254.02,#1,-0.92427,0.28609,-0.25274,101.56,-0.20231,0.19434,0.95984,246.06,0.32372,0.93829,-0.12175,156.74,#20,0.14776,-0.82411,0.54682,108.45,-0.98901,-0.12627,0.076949,151.2,0.0056323,-0.55218,-0.83371,190.92,#2,0.024733,0.99955,-0.016702,116.88,0.86184,-0.012853,0.50702,233.63,0.50658,-0.026935,-0.86177,141.05,#3,-0.83981,0.54288,-0.0021306,112.92,0.53652,0.83055,0.14943,240.58,0.082892,0.12435,-0.98877,143.99,#4,-0.63125,0.75845,-0.1621,122.48,0.26879,0.40999,0.87158,218.47,0.72752,0.50661,-0.46267,137.12,#5,0.63307,-0.70266,-0.32479,124.8,-0.16013,0.29162,-0.94304,229.07,0.75735,0.64902,0.072096,143.22,#7,0.62567,0.033784,-0.77936,119.07,0.72551,-0.39233,0.56543,209.05,-0.28666,-0.9192,-0.26998,149.03,#13,0.0038706,-0.86688,-0.49851,188.37,0.53647,-0.4189,0.73261,202.94,-0.84391,-0.27027,0.46343,99.492,#14,-0.26132,0.8822,0.39171,219.83,-0.81884,-0.41748,0.39396,236.82,0.51108,-0.21779,0.83148,168.82,#15,-0.24072,0.6086,-0.75608,210.52,-0.8187,0.29109,0.49497,247.97,0.52133,0.73815,0.42819,157.81,#16,0.85782,0.51132,-0.051848,180.55,-0.18642,0.40358,0.89575,169.72,0.47894,-0.75873,0.44152,125.75,#17,-0.42368,-0.0075666,-0.90578,204.22,-0.89534,-0.14814,0.42003,190.96,-0.13736,0.98894,0.05599,104.17,#8,-0.46108,0.5647,0.68448,89.185,0.54831,-0.42517,0.72012,212.08,0.69768,0.70735,-0.11359,211.19
    10515 
    10516 > select #2/J:610
    10517 
    10518 6 atoms, 5 bonds, 1 residue, 1 model selected 
    10519 
    10520 > select add #2/J:631
    10521 
    10522 12 atoms, 10 bonds, 2 residues, 1 model selected 
    10523 
    10524 > select add #2/J:634
    10525 
    10526 18 atoms, 15 bonds, 3 residues, 1 model selected 
    10527 
    10528 > select clear
    10529 
    10530 > select cys
    10531 
    10532 Expected an objects specifier or a keyword 
    10533 
    10534 > show #!6 models
    10535 
    10536 > hide #2 models
    10537 
    10538 > select #6/T:274
    10539 
    10540 6 atoms, 5 bonds, 1 residue, 1 model selected 
    10541 
    10542 > select add #6/T:292
    10543 
    10544 12 atoms, 10 bonds, 2 residues, 2 models selected 
    10545 
    10546 > select add #6/T:271
    10547 
    10548 18 atoms, 15 bonds, 3 residues, 2 models selected 
    10549 
    10550 > select add #6/T:295
    10551 
    10552 24 atoms, 20 bonds, 4 residues, 2 models selected 
    10553 
    10554 > show sel atoms
    10555 
    10556 > select #6/T:289
    10557 
    10558 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10559 
    10560 > select clear
    10561 
    10562 > show #13 models
    10563 
    10564 > hide #!6 models
    10565 
    10566 > show #14 models
    10567 
    10568 > hide #13 models
    10569 
    10570 > show #15 models
    10571 
    10572 > hide #14 models
    10573 
    10574 > show #16 models
    10575 
    10576 > hide #15 models
    10577 
    10578 > show #!6 models
    10579 
    10580 > hide #16 models
    10581 
    10582 > select #6/A/B/C/D/E/F/G/H
    10583 
    10584 6152 atoms, 6234 bonds, 775 residues, 1 model selected 
    10585 
    10586 > ui tool show Matchmaker
    10587 
    10588 > matchmaker #3-5,7,13-17 to #6 & sel
    10589 
    10590 Computing secondary structure 
    10591 [Repeated 8 time(s)]  Parameters 
    10592 --- 
    10593 Chain pairing | bb 
    10594 Alignment algorithm | Needleman-Wunsch 
    10595 Similarity matrix | BLOSUM-62 
    10596 SS fraction | 0.3 
    10597 Gap open (HH/SS/other) | 18/18/6 
    10598 Gap extend | 1 
    10599 SS matrix |  |  | H | S | O 
    10600 ---|---|---|--- 
    10601 H | 6 | -9 | -6 
    10602 S |  | 6 | -6 
    10603 O |  |  | 4 
    10604 Iteration cutoff | 2 
    10605  
    10606 Matchmaker 8vg1, chain E (#6) with
    10607 fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain A (#3), sequence
    10608 alignment score = 628.4 
    10609 RMSD between 96 pruned atom pairs is 0.333 angstroms; (across all 97 pairs:
    10610 0.536) 
    10611  
    10612 Matchmaker 8vg1, chain E (#6) with
    10613 fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain A (#4), sequence
    10614 alignment score = 628.4 
    10615 RMSD between 96 pruned atom pairs is 0.280 angstroms; (across all 97 pairs:
    10616 0.445) 
    10617  
    10618 Matchmaker 8vg1, chain E (#6) with
    10619 fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain A (#5), sequence
    10620 alignment score = 628.4 
    10621 RMSD between 96 pruned atom pairs is 0.270 angstroms; (across all 97 pairs:
    10622 0.580) 
    10623  
    10624 Matchmaker 8vg1, chain E (#6) with
    10625 fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain A (#7), sequence
    10626 alignment score = 628.4 
    10627 RMSD between 96 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
    10628 0.719) 
    10629  
    10630 Matchmaker 8vg1, chain E (#6) with
    10631 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
    10632 alignment score = 628.4 
    10633 RMSD between 97 pruned atom pairs is 0.330 angstroms; (across all 97 pairs:
    10634 0.330) 
    10635  
    10636 Matchmaker 8vg1, chain E (#6) with
    10637 fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
    10638 alignment score = 628.4 
    10639 RMSD between 96 pruned atom pairs is 0.313 angstroms; (across all 97 pairs:
    10640 0.576) 
    10641  
    10642 Matchmaker 8vg1, chain E (#6) with
    10643 fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
    10644 alignment score = 628.4 
    10645 RMSD between 96 pruned atom pairs is 0.271 angstroms; (across all 97 pairs:
    10646 0.518) 
    10647  
    10648 Matchmaker 8vg1, chain E (#6) with
    10649 fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
    10650 alignment score = 628.4 
    10651 RMSD between 96 pruned atom pairs is 0.327 angstroms; (across all 97 pairs:
    10652 0.530) 
    10653  
    10654 Matchmaker 8vg1, chain E (#6) with
    10655 fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
    10656 alignment score = 628.4 
    10657 RMSD between 93 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
    10658 0.994) 
    10659  
    10660 
    10661 > matchmaker #3-5,7,13-17 to #6 & sel
    10662 
    10663 Computing secondary structure 
    10664 [Repeated 8 time(s)]  Parameters 
    10665 --- 
    10666 Chain pairing | bb 
    10667 Alignment algorithm | Needleman-Wunsch 
    10668 Similarity matrix | BLOSUM-62 
    10669 SS fraction | 0.3 
    10670 Gap open (HH/SS/other) | 18/18/6 
    10671 Gap extend | 1 
    10672 SS matrix |  |  | H | S | O 
    10673 ---|---|---|--- 
    10674 H | 6 | -9 | -6 
    10675 S |  | 6 | -6 
    10676 O |  |  | 4 
    10677 Iteration cutoff | 2 
    10678  
    10679 Matchmaker 8vg1, chain E (#6) with
    10680 fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain A (#3), sequence
    10681 alignment score = 628.4 
    10682 RMSD between 96 pruned atom pairs is 0.333 angstroms; (across all 97 pairs:
    10683 0.536) 
    10684  
    10685 Matchmaker 8vg1, chain E (#6) with
    10686 fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain A (#4), sequence
    10687 alignment score = 628.4 
    10688 RMSD between 96 pruned atom pairs is 0.280 angstroms; (across all 97 pairs:
    10689 0.445) 
    10690  
    10691 Matchmaker 8vg1, chain E (#6) with
    10692 fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain A (#5), sequence
    10693 alignment score = 628.4 
    10694 RMSD between 96 pruned atom pairs is 0.270 angstroms; (across all 97 pairs:
    10695 0.580) 
    10696  
    10697 Matchmaker 8vg1, chain E (#6) with
    10698 fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain A (#7), sequence
    10699 alignment score = 628.4 
    10700 RMSD between 96 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
    10701 0.719) 
    10702  
    10703 Matchmaker 8vg1, chain E (#6) with
    10704 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
    10705 alignment score = 628.4 
    10706 RMSD between 97 pruned atom pairs is 0.330 angstroms; (across all 97 pairs:
    10707 0.330) 
    10708  
    10709 Matchmaker 8vg1, chain E (#6) with
    10710 fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
    10711 alignment score = 628.4 
    10712 RMSD between 96 pruned atom pairs is 0.313 angstroms; (across all 97 pairs:
    10713 0.576) 
    10714  
    10715 Matchmaker 8vg1, chain E (#6) with
    10716 fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
    10717 alignment score = 628.4 
    10718 RMSD between 96 pruned atom pairs is 0.271 angstroms; (across all 97 pairs:
    10719 0.518) 
    10720  
    10721 Matchmaker 8vg1, chain E (#6) with
    10722 fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
    10723 alignment score = 628.4 
    10724 RMSD between 96 pruned atom pairs is 0.327 angstroms; (across all 97 pairs:
    10725 0.530) 
    10726  
    10727 Matchmaker 8vg1, chain E (#6) with
    10728 fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
    10729 alignment score = 628.4 
    10730 RMSD between 93 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
    10731 0.994) 
    10732  
    10733 
    10734 > view matrix models
    10735 > #6,-0.73769,0.37453,-0.56173,278.96,0.036448,-0.80872,-0.58707,433.15,-0.67416,-0.45355,0.58293,242.88
    10736 
    10737 > show #2 models
    10738 
    10739 > hide #!6 models
    10740 
    10741 > hide #2 models
    10742 
    10743 > show #!6 models
    10744 
    10745 > hide #!6 models
    10746 
    10747 > show #13 models
    10748 
    10749 > show #!6 models
    10750 
    10751 > hide #!6 models
    10752 
    10753 > select #13/A/B/C/D/E/F/G/H
    10754 
    10755 7708 atoms, 7806 bonds, 990 residues, 1 model selected 
    10756 
    10757 > select ~sel & ##selected
    10758 
    10759 14259 atoms, 15372 bonds, 1293 residues, 1 model selected 
    10760 
    10761 > hide sel cartoons
    10762 
    10763 > view matrix models
    10764 > #13,0.35348,0.24328,-0.90325,108.78,-0.42269,-0.81985,-0.38623,247.75,-0.8345,0.51832,-0.18697,212.23
    10765 
    10766 > show #!6 models
    10767 
    10768 > hide #13 models
    10769 
    10770 > select #6/A/B/C/D/E/F/G/H
    10771 
    10772 6152 atoms, 6234 bonds, 775 residues, 1 model selected 
    10773 
    10774 > select ~sel & ##selected
    10775 
    10776 8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected 
    10777 
    10778 > hide sel cartoons
    10779 
    10780 > show #13 models
    10781 
    10782 > select #6/A/B/C/D/E/F/G/H
    10783 
    10784 6152 atoms, 6234 bonds, 775 residues, 1 model selected 
    10785 
    10786 > ui tool show Matchmaker
    10787 
    10788 > matchmaker #13 to #6 & sel
    10789 
    10790 Computing secondary structure 
    10791 Parameters 
    10792 --- 
    10793 Chain pairing | bb 
    10794 Alignment algorithm | Needleman-Wunsch 
    10795 Similarity matrix | BLOSUM-62 
    10796 SS fraction | 0.3 
    10797 Gap open (HH/SS/other) | 18/18/6 
    10798 Gap extend | 1 
    10799 SS matrix |  |  | H | S | O 
    10800 ---|---|---|--- 
    10801 H | 6 | -9 | -6 
    10802 S |  | 6 | -6 
    10803 O |  |  | 4 
    10804 Iteration cutoff | 2 
    10805  
    10806 Matchmaker 8vg1, chain E (#6) with
    10807 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
    10808 alignment score = 628.4 
    10809 RMSD between 97 pruned atom pairs is 0.330 angstroms; (across all 97 pairs:
    10810 0.330) 
    10811  
    10812 
    10813 > matchmaker #1-5,7 to #6 & sel
    10814 
    10815 Computing secondary structure 
    10816 [Repeated 4 time(s)]  Parameters 
    10817 --- 
    10818 Chain pairing | bb 
    10819 Alignment algorithm | Needleman-Wunsch 
    10820 Similarity matrix | BLOSUM-62 
    10821 SS fraction | 0.3 
    10822 Gap open (HH/SS/other) | 18/18/6 
    10823 Gap extend | 1 
    10824 SS matrix |  |  | H | S | O 
    10825 ---|---|---|--- 
    10826 H | 6 | -9 | -6 
    10827 S |  | 6 | -6 
    10828 O |  |  | 4 
    10829 Iteration cutoff | 2 
    10830  
    10831 Matchmaker 8vg1, chain E (#6) with fold_nucleosome_foxa1_gata4_model_0.cif,
    10832 chain A (#1), sequence alignment score = 628.4 
    10833 RMSD between 97 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
    10834 0.283) 
    10835  
    10836 Matchmaker 8vg1, chain E (#6) with
    10837 fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain A (#2), sequence
    10838 alignment score = 628.4 
    10839 RMSD between 97 pruned atom pairs is 0.242 angstroms; (across all 97 pairs:
    10840 0.242) 
    10841  
    10842 Matchmaker 8vg1, chain E (#6) with
    10843 fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain A (#3), sequence
    10844 alignment score = 628.4 
    10845 RMSD between 96 pruned atom pairs is 0.333 angstroms; (across all 97 pairs:
    10846 0.536) 
    10847  
    10848 Matchmaker 8vg1, chain E (#6) with
    10849 fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain A (#4), sequence
    10850 alignment score = 628.4 
    10851 RMSD between 96 pruned atom pairs is 0.280 angstroms; (across all 97 pairs:
    10852 0.445) 
    10853  
    10854 Matchmaker 8vg1, chain E (#6) with
    10855 fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain A (#5), sequence
    10856 alignment score = 628.4 
    10857 RMSD between 96 pruned atom pairs is 0.270 angstroms; (across all 97 pairs:
    10858 0.580) 
    10859  
    10860 Matchmaker 8vg1, chain E (#6) with
    10861 fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain A (#7), sequence
    10862 alignment score = 628.4 
    10863 RMSD between 96 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
    10864 0.719) 
    10865  
    10866 
    10867 > matchmaker #14-17#!20 to #6 & sel
    10868 
    10869 Computing secondary structure 
    10870 [Repeated 3 time(s)]  Parameters 
    10871 --- 
    10872 Chain pairing | bb 
    10873 Alignment algorithm | Needleman-Wunsch 
    10874 Similarity matrix | BLOSUM-62 
    10875 SS fraction | 0.3 
    10876 Gap open (HH/SS/other) | 18/18/6 
    10877 Gap extend | 1 
    10878 SS matrix |  |  | H | S | O 
    10879 ---|---|---|--- 
    10880 H | 6 | -9 | -6 
    10881 S |  | 6 | -6 
    10882 O |  |  | 4 
    10883 Iteration cutoff | 2 
    10884  
    10885 Matchmaker 8vg1, chain E (#6) with
    10886 fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
    10887 alignment score = 628.4 
    10888 RMSD between 96 pruned atom pairs is 0.313 angstroms; (across all 97 pairs:
    10889 0.576) 
    10890  
    10891 Matchmaker 8vg1, chain E (#6) with
    10892 fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
    10893 alignment score = 628.4 
    10894 RMSD between 96 pruned atom pairs is 0.271 angstroms; (across all 97 pairs:
    10895 0.518) 
    10896  
    10897 Matchmaker 8vg1, chain E (#6) with
    10898 fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
    10899 alignment score = 628.4 
    10900 RMSD between 96 pruned atom pairs is 0.327 angstroms; (across all 97 pairs:
    10901 0.530) 
    10902  
    10903 Matchmaker 8vg1, chain E (#6) with
    10904 fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
    10905 alignment score = 628.4 
    10906 RMSD between 93 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
    10907 0.994) 
    10908  
    10909 Matchmaker 8vg1, chain E (#6) with 3aze, chain E (#20), sequence alignment
    10910 score = 625.6 
    10911 RMSD between 96 pruned atom pairs is 0.335 angstroms; (across all 97 pairs:
    10912 0.414) 
    10913  
    10914 
    10915 > select clear
    10916 
    10917 > show #14 models
    10918 
    10919 > hide #13 models
    10920 
    10921 > hide #!6 models
    10922 
    10923 > show #!6 models
    10924 
    10925 > hide #!6 models
    10926 
    10927 > show #15 models
    10928 
    10929 > show #16 models
    10930 
    10931 > show #17 models
    10932 
    10933 > hide #15 models
    10934 
    10935 > hide #16 models
    10936 
    10937 > hide #17 models
    10938 
    10939 > show #13 models
    10940 
    10941 > hide #14 models
    10942 
    10943 > show #14 models
    10944 
    10945 > select #13#14/I/J
    10946 
    10947 28597 atoms, 29994 bonds, 3203 residues, 2 models selected 
    10948 
    10949 > hide sel cartoons
    10950 
    10951 > show #15 models
    10952 
    10953 > show #16 models
    10954 
    10955 > show #17 models
    10956 
    10957 > select #13#14#15#16#17/I/J
    10958 
    10959 94498 atoms, 99528 bonds, 10052 residues, 5 models selected 
    10960 
    10961 > select #13#14#15/I/J#16/I/J#17/I/J
    10962 
    10963 63824 atoms, 66804 bonds, 7326 residues, 5 models selected 
    10964 
    10965 > hide sel cartoons
    10966 
    10967 > view matrix models
    10968 > #13,0.35348,0.24328,-0.90325,123.72,-0.42269,-0.81985,-0.38623,236.68,-0.8345,0.51832,-0.18697,157.55,#14,0.19712,0.42197,-0.88492,137.55,0.12928,-0.90594,-0.4032,235.57,-0.97182,-0.034925,-0.23313,158.82,#15,0.60279,-0.17833,-0.77771,136.5,0.36617,-0.80418,0.46821,238.71,-0.70892,-0.56701,-0.41945,151.78,#16,-0.74187,0.17181,0.64815,134.72,0.59305,-0.28296,0.75381,234.63,0.31291,0.94362,0.10802,161.92,#17,0.44598,-0.29411,-0.84534,122.34,-0.61903,0.5808,-0.52865,242.51,0.64646,0.75906,0.076956,154.59
    10969 
    10970 > show #!6 models
    10971 
    10972 > select #13#14/K/L#15/K/L#16/K/L#17/K/L
    10973 
    10974 37215 atoms, 40258 bonds, 3031 residues, 5 models selected 
    10975 
    10976 > hide sel cartoons
    10977 
    10978 > select #13#14/K/L#15/M#16/K/L#17/K/L
    10979 
    10980 37220 atoms, 40274 bonds, 3030 residues, 5 models selected 
    10981 
    10982 > hide sel cartoons
    10983 
    10984 > select #13#14/K/L#15/M#16/K/L#17/M/L
    10985 
    10986 41036 atoms, 44560 bonds, 3215 residues, 5 models selected 
    10987 
    10988 > hide sel cartoons
    10989 
    10990 > select #13#14/K/L#15/M#16/M/L#17/M/L
    10991 
    10992 44852 atoms, 48846 bonds, 3400 residues, 5 models selected 
    10993 
    10994 > hide sel cartoons
    10995 
    10996 > hide #14 models
    10997 
    10998 > hide #!6 models
    10999 
    11000 > show #14 models
    11001 
    11002 > show #!6 models
    11003 
    11004 > hide #14 models
    11005 
    11006 > hide #15 models
    11007 
    11008 > hide #16 models
    11009 
    11010 > hide #17 models
    11011 
    11012 > hide #13 models
    11013 
    11014 > show #13 models
    11015 
    11016 > select #13
    11017 
    11018 21967 atoms, 23178 bonds, 2283 residues, 1 model selected 
    11019 
    11020 > show sel cartoons
    11021 
    11022 > select #13/I/J/K/L/M/N
    11023 
    11024 14259 atoms, 15372 bonds, 1293 residues, 1 model selected 
    11025 
    11026 > hide sel cartoons
    11027 
    11028 > hide #13 models
    11029 
    11030 > show #13 models
    11031 
    11032 > hide #13 models
    11033 
    11034 > show #13 models
    11035 
    11036 > ui tool show Matchmaker
    11037 
    11038 > select #13/I/J/K/L/M/N
    11039 
    11040 14259 atoms, 15372 bonds, 1293 residues, 1 model selected 
    11041 
    11042 > select ~sel & ##selected
    11043 
    11044 7708 atoms, 7806 bonds, 990 residues, 1 model selected 
    11045 
    11046 > matchmaker #13-17 to #6 & sel
    11047 
    11048 No 'to' model specified 
    11049 
    11050 > ui tool show Matchmaker
    11051 
    11052 > select #13/A/B/C/D/E/F/G/H
    11053 
    11054 7708 atoms, 7806 bonds, 990 residues, 1 model selected 
    11055 
    11056 > matchmaker #13-17 to #1
    11057 
    11058 Computing secondary structure 
    11059 [Repeated 4 time(s)]  Parameters 
    11060 --- 
    11061 Chain pairing | bb 
    11062 Alignment algorithm | Needleman-Wunsch 
    11063 Similarity matrix | BLOSUM-62 
    11064 SS fraction | 0.3 
    11065 Gap open (HH/SS/other) | 18/18/6 
    11066 Gap extend | 1 
    11067 SS matrix |  |  | H | S | O 
    11068 ---|---|---|--- 
    11069 H | 6 | -9 | -6 
    11070 S |  | 6 | -6 
    11071 O |  |  | 4 
    11072 Iteration cutoff | 2 
    11073  
    11074 Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
    11075 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
    11076 alignment score = 2350.2 
    11077 RMSD between 18 pruned atom pairs is 1.472 angstroms; (across all 478 pairs:
    11078 37.002) 
    11079  
    11080 Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
    11081 fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain I (#14), sequence
    11082 alignment score = 2302.8 
    11083 RMSD between 88 pruned atom pairs is 0.556 angstroms; (across all 478 pairs:
    11084 31.892) 
    11085  
    11086 Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
    11087 fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain I (#15), sequence
    11088 alignment score = 2288.4 
    11089 RMSD between 93 pruned atom pairs is 0.653 angstroms; (across all 478 pairs:
    11090 33.966) 
    11091  
    11092 Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
    11093 fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain I (#16), sequence
    11094 alignment score = 2262.6 
    11095 RMSD between 60 pruned atom pairs is 0.381 angstroms; (across all 478 pairs:
    11096 51.446) 
    11097  
    11098 Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
    11099 fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain I (#17), sequence
    11100 alignment score = 2265 
    11101 RMSD between 5 pruned atom pairs is 1.237 angstroms; (across all 478 pairs:
    11102 30.443) 
    11103  
    11104 
    11105 > select #6/A/B/C/D/E/F/G/H
    11106 
    11107 6152 atoms, 6234 bonds, 775 residues, 1 model selected 
    11108 
    11109 > matchmaker #13-17 to #6 & sel
    11110 
    11111 Computing secondary structure 
    11112 [Repeated 4 time(s)]  Parameters 
    11113 --- 
    11114 Chain pairing | bb 
    11115 Alignment algorithm | Needleman-Wunsch 
    11116 Similarity matrix | BLOSUM-62 
    11117 SS fraction | 0.3 
    11118 Gap open (HH/SS/other) | 18/18/6 
    11119 Gap extend | 1 
    11120 SS matrix |  |  | H | S | O 
    11121 ---|---|---|--- 
    11122 H | 6 | -9 | -6 
    11123 S |  | 6 | -6 
    11124 O |  |  | 4 
    11125 Iteration cutoff | 2 
    11126  
    11127 Matchmaker 8vg1, chain E (#6) with
    11128 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
    11129 alignment score = 628.4 
    11130 RMSD between 97 pruned atom pairs is 0.330 angstroms; (across all 97 pairs:
    11131 0.330) 
    11132  
    11133 Matchmaker 8vg1, chain E (#6) with
    11134 fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
    11135 alignment score = 628.4 
    11136 RMSD between 96 pruned atom pairs is 0.313 angstroms; (across all 97 pairs:
    11137 0.576) 
    11138  
    11139 Matchmaker 8vg1, chain E (#6) with
    11140 fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
    11141 alignment score = 628.4 
    11142 RMSD between 96 pruned atom pairs is 0.271 angstroms; (across all 97 pairs:
    11143 0.518) 
    11144  
    11145 Matchmaker 8vg1, chain E (#6) with
    11146 fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
    11147 alignment score = 628.4 
    11148 RMSD between 96 pruned atom pairs is 0.327 angstroms; (across all 97 pairs:
    11149 0.530) 
    11150  
    11151 Matchmaker 8vg1, chain E (#6) with
    11152 fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
    11153 alignment score = 628.4 
    11154 RMSD between 93 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
    11155 0.994) 
    11156  
    11157 
    11158 > show #14 models
    11159 
    11160 > show #16 models
    11161 
    11162 > hide #13 models
    11163 
    11164 > hide #16 models
    11165 
    11166 > select clear
    11167 
    11168 > select #14/A/B/C/D/E/F/G/H
    11169 
    11170 7708 atoms, 7806 bonds, 990 residues, 1 model selected 
    11171 
    11172 > show sel cartoons
    11173 
    11174 > select clear
    11175 
    11176 > show #13 models
    11177 
    11178 > hide #14 models
    11179 
    11180 > hide #!6 models
    11181 
    11182 > show #!6 models
    11183 
    11184 > show #14 models
    11185 
    11186 > show #15 models
    11187 
    11188 > show #16 models
    11189 
    11190 > show #17 models
    11191 
    11192 > hide #13 models
    11193 
    11194 > hide #14 models
    11195 
    11196 > hide #15 models
    11197 
    11198 > hide #16 models
    11199 
    11200 > hide #17 models
    11201 
    11202 > show #17 models
    11203 
    11204 > show #16 models
    11205 
    11206 > show #15 models
    11207 
    11208 > show #14 models
    11209 
    11210 > show #13 models
    11211 
    11212 > hide #13 models
    11213 
    11214 > hide #14 models
    11215 
    11216 > hide #15 models
    11217 
    11218 > hide #16 models
    11219 
    11220 > hide #17 models
    11221 
    11222 > select #6
    11223 
    11224 14434 atoms, 15401 bonds, 421 pseudobonds, 1273 residues, 3 models selected 
    11225 
    11226 > show sel cartoons
    11227 
    11228 > select clear
    11229 
    11230 > show #13 models
    11231 
    11232 > hide #!6 models
    11233 
    11234 > show #!6 models
    11235 
    11236 > hide #13 models
    11237 
    11238 > show #13 models
    11239 
    11240 > hide #!6 models
    11241 
    11242 > show #!6 models
    11243 
    11244 > hide #!6 models
    11245 
    11246 > show #!6 models
    11247 
    11248 > hide #!6 models
    11249 
    11250 > show #14 models
    11251 
    11252 > show #15 models
    11253 
    11254 > show #16 models
    11255 
    11256 > show #!6 models
    11257 
    11258 > hide #!6 models
    11259 
    11260 > show #!6 models
    11261 
    11262 > hide #!6 models
    11263 
    11264 > hide #14 models
    11265 
    11266 > hide #15 models
    11267 
    11268 > hide #16 models
    11269 
    11270 > show #!6 models
    11271 
    11272 > select /A
    11273 
    11274 16994 atoms, 17273 bonds, 2169 residues, 14 models selected 
    11275 
    11276 > hide #!6 models
    11277 
    11278 > show #!6 models
    11279 
    11280 > select /A
    11281 
    11282 16994 atoms, 17273 bonds, 2169 residues, 14 models selected 
    11283 
    11284 > matchmaker #13-17 & sel to #6 & sel
    11285 
    11286 Computing secondary structure 
    11287 [Repeated 4 time(s)]  Parameters 
    11288 --- 
    11289 Chain pairing | bb 
    11290 Alignment algorithm | Needleman-Wunsch 
    11291 Similarity matrix | BLOSUM-62 
    11292 SS fraction | 0.3 
    11293 Gap open (HH/SS/other) | 18/18/6 
    11294 Gap extend | 1 
    11295 SS matrix |  |  | H | S | O 
    11296 ---|---|---|--- 
    11297 H | 6 | -9 | -6 
    11298 S |  | 6 | -6 
    11299 O |  |  | 4 
    11300 Iteration cutoff | 2 
    11301  
    11302 Matchmaker 8vg1, chain A (#6) with
    11303 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
    11304 alignment score = 627.8 
    11305 RMSD between 97 pruned atom pairs is 0.335 angstroms; (across all 97 pairs:
    11306 0.335) 
    11307  
    11308 Matchmaker 8vg1, chain A (#6) with
    11309 fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
    11310 alignment score = 627.8 
    11311 RMSD between 96 pruned atom pairs is 0.286 angstroms; (across all 97 pairs:
    11312 0.591) 
    11313  
    11314 Matchmaker 8vg1, chain A (#6) with
    11315 fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
    11316 alignment score = 627.8 
    11317 RMSD between 96 pruned atom pairs is 0.257 angstroms; (across all 97 pairs:
    11318 0.549) 
    11319  
    11320 Matchmaker 8vg1, chain A (#6) with
    11321 fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
    11322 alignment score = 627.8 
    11323 RMSD between 96 pruned atom pairs is 0.292 angstroms; (across all 97 pairs:
    11324 0.549) 
    11325  
    11326 Matchmaker 8vg1, chain A (#6) with
    11327 fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
    11328 alignment score = 627.8 
    11329 RMSD between 93 pruned atom pairs is 0.307 angstroms; (across all 97 pairs:
    11330 0.978) 
    11331  
    11332 
    11333 > show #14 models
    11334 
    11335 > show #15 models
    11336 
    11337 > show #16 models
    11338 
    11339 > show #17 models
    11340 
    11341 > hide #13 models
    11342 
    11343 > hide #14 models
    11344 
    11345 > hide #15 models
    11346 
    11347 > hide #16 models
    11348 
    11349 > hide #17 models
    11350 
    11351 > color sel & #!6 bychain
    11352 
    11353 > select clear
    11354 
    11355 > color #!6 bychain
    11356 
    11357 > undo
    11358 
    11359 [Repeated 3 time(s)]
    11360 
    11361 > view matrix models
    11362 > #6,-0.73769,0.37453,-0.56173,282.99,0.036448,-0.80872,-0.58707,434.38,-0.67416,-0.45355,0.58293,234.8,#1,0.34863,-0.86979,-0.34918,128.28,-0.59863,-0.4933,0.63111,224.41,-0.72118,-0.010996,-0.69266,132.73,#20,0.14776,-0.82411,0.54682,94.626,-0.98901,-0.12627,0.076949,190.8,0.0056323,-0.55218,-0.83371,172.79,#2,-0.78547,-0.55054,0.28274,136.79,-0.049609,0.51138,0.85792,225.98,-0.61691,0.65985,-0.42898,142.62,#3,0.86327,0.50474,-0.0016107,141.97,0.44874,-0.76894,-0.45538,211.84,-0.23109,0.39239,-0.8903,138.27,#4,-0.29416,-0.93822,-0.18224,142.42,-0.72095,0.092643,0.68677,229.03,-0.62746,0.33341,-0.70366,155.96,#5,-0.73977,0.075381,0.66862,129.67,-0.44258,-0.80299,-0.39915,231.15,0.50681,-0.5912,0.6274,149.58,#7,0.13642,-0.011203,0.99059,138.93,-0.88638,-0.44793,0.117,206.62,0.4424,-0.894,-0.071036,150.01,#13,0.5006,-0.78154,0.37228,134.44,0.80193,0.58063,0.1406,208.91,-0.32604,0.22816,0.91741,154.17,#14,0.83547,-0.37468,0.40201,128.15,0.33015,0.92702,0.17787,213.49,-0.43931,-0.015884,0.89819,142.59,#15,0.52676,0.33889,0.77954,135.69,0.1418,0.8692,-0.47369,213.23,-0.8381,0.36006,0.4098,140.7,#16,0.14896,-0.98297,-0.10763,126.11,-0.8605,-0.075231,-0.50386,212.24,0.48718,0.16767,-0.85705,146.16,#17,-0.90964,-0.40837,0.076035,139.24,0.41536,-0.89211,0.17782,204.61,-0.0047835,0.19333,0.98112,152.39,#8,-0.46108,0.5647,0.68448,93.212,0.54831,-0.42517,0.72012,213.31,0.69768,0.70735,-0.11359,203.11
    11363 
    11364 > show #13 models
    11365 
    11366 > show #14 models
    11367 
    11368 > show #15 models
    11369 
    11370 > show #16 models
    11371 
    11372 > show #17 models
    11373 
    11374 > ui tool show "Color Actions"
    11375 
    11376 > select /A/E
    11377 
    11378 34318 atoms, 35243 bonds, 4048 residues, 14 models selected 
    11379 
    11380 > color sel cornflower blue
    11381 
    11382 > select /B/F
    11383 
    11384 26404 atoms, 26771 bonds, 3429 residues, 14 models selected 
    11385 
    11386 > color sel medium turquoise
    11387 
    11388 > color sel yellow green
    11389 
    11390 > color sel olive drab
    11391 
    11392 > color sel dark sea green
    11393 
    11394 > select /C/G
    11395 
    11396 25294 atoms, 25598 bonds, 3299 residues, 14 models selected 
    11397 
    11398 > color sel tan
    11399 
    11400 > select /D/H
    11401 
    11402 28252 atoms, 29083 bonds, 1 pseudobond, 3336 residues, 15 models selected 
    11403 
    11404 > color sel plum
    11405 
    11406 > select clear
    11407 
    11408 > hide #!6 models
    11409 
    11410 > show #!6 models
    11411 
    11412 > hide #!6 models
    11413 
    11414 > select #13/I/J
    11415 
    11416 6630 atoms, 6816 bonds, 920 residues, 1 model selected 
    11417 
    11418 > show sel cartoons
    11419 
    11420 > hide sel cartoons
    11421 
    11422 > select #13/L/M
    11423 
    11424 7628 atoms, 8556 bonds, 372 residues, 1 model selected 
    11425 
    11426 > show sel cartoons
    11427 
    11428 > select clear
    11429 
    11430 > select /I
    11431 
    11432 45018 atoms, 46920 bonds, 4 pseudobonds, 5580 residues, 14 models selected 
    11433 
    11434 > show #7 models
    11435 
    11436 > hide #7 models
    11437 
    11438 > show #7 models
    11439 
    11440 > hide #7 models
    11441 
    11442 > show #!6 models
    11443 
    11444 > color sel dim gray
    11445 
    11446 > select /J
    11447 
    11448 59201 atoms, 61380 bonds, 1 pseudobond, 7539 residues, 14 models selected 
    11449 
    11450 > color sel dark gray
    11451 
    11452 > color sel gray
    11453 
    11454 > color sel light gray
    11455 
    11456 > select clear
    11457 
    11458 > hide #!6 models
    11459 
    11460 > select #13/L#14/L#15/L#16/L#17/L
    11461 
    11462 19055 atoms, 21350 bonds, 930 residues, 5 models selected 
    11463 
    11464 > color sel dim gray
    11465 
    11466 > save "/Users/taic/OneDrive - National Institutes of
    11467 > Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs"
    11468 
    11469 > hide #13 models
    11470 
    11471 > show #13 models
    11472 
    11473 > hide #14 models
    11474 
    11475 > show #14 models
    11476 
    11477 > hide #14 models
    11478 
    11479 > hide #13 models
    11480 
    11481 > show #13 models
    11482 
    11483 > hide #15 models
    11484 
    11485 > hide #16 models
    11486 
    11487 > hide #17 models
    11488 
    11489 > hide #13 models
    11490 
    11491 > show #14 models
    11492 
    11493 > show #15 models
    11494 
    11495 > hide #15 models
    11496 
    11497 > show #15 models
    11498 
    11499 > hide #15 models
    11500 
    11501 > show #15 models
    11502 
    11503 > show #16 models
    11504 
    11505 > show #17 models
    11506 
    11507 > show #13 models
    11508 
    11509 > select /L/M
    11510 
    11511 80097 atoms, 89846 bonds, 3906 residues, 11 models selected 
    11512 
    11513 > hide sel & #13-17 cartoons
    11514 
    11515 [Repeated 1 time(s)]
    11516 
    11517 > show sel & #13-17 cartoons
    11518 
    11519 > hide sel & #13-17 cartoons
    11520 
    11521 > show #!6 models
    11522 
    11523 > hide #13 models
    11524 
    11525 > hide #14 models
    11526 
    11527 > hide #15 models
    11528 
    11529 > hide #16 models
    11530 
    11531 > hide #17 models
    11532 
    11533 > show #13 models
    11534 
    11535 > hide #13 models
    11536 
    11537 > show #13 models
    11538 
    11539 > hide #13 models
    11540 
    11541 > select /#6/I#6/J#6/O#6/T
    11542 
    11543 Expected an objects specifier or a keyword 
    11544 
    11545 > select #6/I#6/J#6/O#6/T
    11546 
    11547 8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected 
    11548 
    11549 > hide sel cartoons
    11550 
    11551 > hide sel atoms
    11552 
    11553 > show #13 models
    11554 
    11555 > show #14 models
    11556 
    11557 > show #15 models
    11558 
    11559 > show #16 models
    11560 
    11561 > show #17 models
    11562 
    11563 > hide #17 models
    11564 
    11565 > hide #16 models
    11566 
    11567 > hide #14 models
    11568 
    11569 > hide #15 models
    11570 
    11571 > hide #13 models
    11572 
    11573 > select #6/A#6/E
    11574 
    11575 1598 atoms, 1622 bonds, 194 residues, 1 model selected 
    11576 
    11577 > ui tool show "Color Actions"
    11578 
    11579 > color sel royal blue
    11580 
    11581 > show #13 models
    11582 
    11583 > hide #13 models
    11584 
    11585 > color sel medium blue
    11586 
    11587 > show #13 models
    11588 
    11589 > select clear
    11590 
    11591 > hide #13 models
    11592 
    11593 > select #6/C#6/G
    11594 
    11595 1740 atoms, 1762 bonds, 225 residues, 1 model selected 
    11596 
    11597 > color sel dark goldenrod
    11598 
    11599 > show #13 models
    11600 
    11601 > select clear
    11602 
    11603 > show #14 models
    11604 
    11605 > show #15 models
    11606 
    11607 > show #16 models
    11608 
    11609 > hide #16 models
    11610 
    11611 > show #16 models
    11612 
    11613 > hide #16 models
    11614 
    11615 > show #16 models
    11616 
    11617 > show #17 models
    11618 
    11619 > hide #17 models
    11620 
    11621 > hide #16 models
    11622 
    11623 > hide #15 models
    11624 
    11625 > hide #14 models
    11626 
    11627 > hide #13 models
    11628 
    11629 > select #6/D#6/H
    11630 
    11631 1490 atoms, 1512 bonds, 190 residues, 1 model selected 
    11632 
    11633 > color sel magenta
    11634 
    11635 > show #13 models
    11636 
    11637 > hide #13 models
    11638 
    11639 > select #6/D#6/H
    11640 
    11641 1490 atoms, 1512 bonds, 190 residues, 1 model selected 
    11642 
    11643 > color sel orchid
    11644 
    11645 > show #13 models
    11646 
    11647 > color sel magenta
    11648 
    11649 > select clear
    11650 
    11651 > select #6/B#6/F
    11652 
    11653 1324 atoms, 1338 bonds, 166 residues, 1 model selected 
    11654 
    11655 > color sel forest green
    11656 
    11657 > color sel green
    11658 
    11659 > select clear
    11660 
    11661 > hide #13 models
    11662 
    11663 > select #6/I#6/J#6/O#6/T
    11664 
    11665 8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected 
    11666 
    11667 > show sel cartoons
    11668 
    11669 > select clear
    11670 
    11671 > select #6/I#6/J#6/O#6/T
    11672 
    11673 8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected 
    11674 
    11675 > select #6/O
    11676 
    11677 856 atoms, 883 bonds, 102 residues, 1 model selected 
    11678 
    11679 > show #13 models
    11680 
    11681 > color sel deep sky blue
    11682 
    11683 > select clear
    11684 
    11685 > hide #13 models
    11686 
    11687 > select #6/T
    11688 
    11689 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    11690 
    11691 > color sel medium purple
    11692 
    11693 > color sel deep sky blue
    11694 
    11695 > select clear
    11696 
    11697 > select #6/O
    11698 
    11699 856 atoms, 883 bonds, 102 residues, 1 model selected 
    11700 
    11701 > color sel medium purple
    11702 
    11703 > select clear
    11704 
    11705 > select ::name="CYS"
    11706 
    11707 1218 atoms, 1015 bonds, 203 residues, 14 models selected 
    11708 
    11709 > select #6/T:295
    11710 
    11711 6 atoms, 5 bonds, 1 residue, 1 model selected 
    11712 
    11713 > select add #6/T:271
    11714 
    11715 12 atoms, 10 bonds, 2 residues, 2 models selected 
    11716 
    11717 > color sel gold
    11718 
    11719 > show sel atoms
    11720 
    11721 > select ::name="CYS"
    11722 
    11723 1218 atoms, 1015 bonds, 203 residues, 14 models selected 
    11724 
    11725 > select clear
    11726 
    11727 > select add #6/T:292
    11728 
    11729 6 atoms, 5 bonds, 1 residue, 1 model selected 
    11730 
    11731 > select add #6/T:274
    11732 
    11733 12 atoms, 10 bonds, 2 residues, 2 models selected 
    11734 
    11735 > color sel gold
    11736 
    11737 > show sel atoms
    11738 
    11739 > select #6/I:56
    11740 
    11741 21 atoms, 23 bonds, 1 residue, 1 model selected 
    11742 
    11743 > select #6
    11744 
    11745 14434 atoms, 15401 bonds, 421 pseudobonds, 1273 residues, 3 models selected 
    11746 
    11747 > show sel atoms
    11748 
    11749 > hide sel atoms
    11750 
    11751 > undo
    11752 
    11753 [Repeated 2 time(s)]
    11754 
    11755 > select clear
    11756 
    11757 > save "/Users/taic/OneDrive - National Institutes of
    11758 > Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs"
    11759 
    11760 > select ::name="ZN"
    11761 
    11762 12 atoms, 12 residues, 12 models selected 
    11763 
    11764 > show sel & #!6 atoms
    11765 
    11766 > color sel dim gray
    11767 
    11768 > select #6/I
    11769 
    11770 3501 atoms, 3922 bonds, 171 residues, 1 model selected 
    11771 
    11772 > ui tool show "Color Actions"
    11773 
    11774 > color sel silver
    11775 
    11776 > color sel dark sea green
    11777 
    11778 > color sel dark olive green
    11779 
    11780 > color sel steel blue
    11781 
    11782 > color sel cadet blue
    11783 
    11784 > color sel light slate gray
    11785 
    11786 > color sel slate gray
    11787 
    11788 > color sel light slate gray
    11789 
    11790 > select clear
    11791 
    11792 > select #6/J
    11793 
    11794 3510 atoms, 3942 bonds, 171 residues, 1 model selected 
    11795 
    11796 > color sel light steel blue
    11797 
    11798 > color sel light blue
    11799 
    11800 > select clear
    11801 
    11802 > show #13 models
    11803 
    11804 > hide #13 models
    11805 
    11806 > select #6/I#6/J#6/O#6/T
    11807 
    11808 8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected 
    11809 
    11810 > hide sel cartoons
    11811 
    11812 > hide sel atoms
    11813 
    11814 > show sel cartoons
    11815 
    11816 > hide sel cartoons
    11817 
    11818 > show #13 models
    11819 
    11820 > show #14 models
    11821 
    11822 > show #15 models
    11823 
    11824 > show #16 models
    11825 
    11826 > show #17 models
    11827 
    11828 > show #1 models
    11829 
    11830 > hide #1 models
    11831 
    11832 > hide #13 models
    11833 
    11834 > hide #14 models
    11835 
    11836 > hide #15 models
    11837 
    11838 > hide #16 models
    11839 
    11840 > hide #17 models
    11841 
    11842 > show #13 models
    11843 
    11844 > hide #13 models
    11845 
    11846 > show #13 models
    11847 
    11848 > hide #13 models
    11849 
    11850 > show #13 models
    11851 
    11852 > hide #!6 models
    11853 
    11854 > show #14 models
    11855 
    11856 > show #15 models
    11857 
    11858 > show #16 models
    11859 
    11860 > show #17 models
    11861 
    11862 > save "/Users/taic/OneDrive - National Institutes of
    11863 > Health/MacBookPro021/project/CASP16/yet2solve/AF3_0-4.8VG1_nucleosome.png"
    11864 > width 900 height 712 supersample 4 transparentBackground true
    11865 
    11866 > show #!6 models
    11867 
    11868 > save "/Users/taic/OneDrive - National Institutes of
    11869 > Health/MacBookPro021/project/CASP16/yet2solve/8VG1.vs.AF3.nucleosome.png"
    11870 > width 900 height 712 supersample 4 transparentBackground true
    11871 
    11872 > hide #14 models
    11873 
    11874 > hide #15 models
    11875 
    11876 > hide #16 models
    11877 
    11878 > hide #17 models
    11879 
    11880 > show #14 models
    11881 
    11882 > show #15 models
    11883 
    11884 > hide #14 models
    11885 
    11886 > hide #15 models
    11887 
    11888 > show #14 models
    11889 
    11890 > hide #14 models
    11891 
    11892 > show #14 models
    11893 
    11894 > hide #14 models
    11895 
    11896 > save "/Users/taic/OneDrive - National Institutes of
    11897 > Health/MacBookPro021/project/CASP16/yet2solve/8VG1.vs.AF3-0.nucleosome.png"
    11898 > width 900 height 712 supersample 4 transparentBackground true
    11899 
    11900 > show sel cartoons
    11901 
    11902 > hide #13 models
    11903 
    11904 > hide sel cartoons
    11905 
    11906 > show #2 models
    11907 
    11908 > hide #2 models
    11909 
    11910 > show sel cartoons
    11911 
    11912 > select #13#14#15#16#17
    11913 
    11914 109835 atoms, 115890 bonds, 11415 residues, 5 models selected 
    11915 
    11916 > show #13 models
    11917 
    11918 > show #14 models
    11919 
    11920 > show #15 models
    11921 
    11922 > show #16 models
    11923 
    11924 > show #17 models
    11925 
    11926 > show sel cartoons
    11927 
    11928 > hide #14 models
    11929 
    11930 > hide #15 models
    11931 
    11932 > hide #16 models
    11933 
    11934 > hide #17 models
    11935 
    11936 > hide #13 models
    11937 
    11938 > show #13 models
    11939 
    11940 > hide #!6 models
    11941 
    11942 > select clear
    11943 
    11944 > show #!6 models
    11945 
    11946 > hide #!6 models
    11947 
    11948 > show #!6 models
    11949 
    11950 > hide #!6 models
    11951 
    11952 > show #14 models
    11953 
    11954 > hide #14 models
    11955 
    11956 > show #14 models
    11957 
    11958 > hide #14 models
    11959 
    11960 > show #14 models
    11961 
    11962 > hide #14 models
    11963 
    11964 > show #!6 models
    11965 
    11966 > hide #!6 models
    11967 
    11968 > show #!6 models
    11969 
    11970 > hide #13 models
    11971 
    11972 > show #13 models
    11973 
    11974 > hide #!6 models
    11975 
    11976 > show #!6 models
    11977 
    11978 > hide #13 models
    11979 
    11980 > show #13 models
    11981 
    11982 > hide #!6 models
    11983 
    11984 > select #13/L#14/L#15/L#16/L#17/L
    11985 
    11986 19055 atoms, 21350 bonds, 930 residues, 5 models selected 
    11987 
    11988 > ui tool show "Color Actions"
    11989 
    11990 > color sel light slate gray
    11991 
    11992 > show #!6 models
    11993 
    11994 > hide #!6 models
    11995 
    11996 > select #13/M#14/M#15/M#16/M#17/M
    11997 
    11998 19085 atoms, 21430 bonds, 930 residues, 5 models selected 
    11999 
    12000 > select #6/J:134
    12001 
    12002 22 atoms, 24 bonds, 1 residue, 1 model selected 
    12003 
    12004 > select #6/J:134
    12005 
    12006 22 atoms, 24 bonds, 1 residue, 1 model selected 
    12007 
    12008 > ui tool show "Color Actions"
    12009 
    12010 > color sel light steel blue
    12011 
    12012 > select #13/M#14/M#15/M#16/M#17/M
    12013 
    12014 19085 atoms, 21430 bonds, 930 residues, 5 models selected 
    12015 
    12016 > color sel light steel blue
    12017 
    12018 > select clear
    12019 
    12020 > show #!6 models
    12021 
    12022 > hide #!6 models
    12023 
    12024 > show #!6 models
    12025 
    12026 > hide #!6 models
    12027 
    12028 > show #!6 models
    12029 
    12030 > hide #!6 models
    12031 
    12032 > select #13/I#14/I#15/I#16/I#17/I
    12033 
    12034 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12035 
    12036 > select ::name="CYS"
    12037 
    12038 1218 atoms, 1015 bonds, 203 residues, 14 models selected 
    12039 
    12040 > show #!6 models
    12041 
    12042 > hide #13 models
    12043 
    12044 > show #13 models
    12045 
    12046 > hide #!6 models
    12047 
    12048 > select #13/I#14/I#15/I#16/I#17/I
    12049 
    12050 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12051 
    12052 > select #13/I#14/I#15/I#16/I#17/I
    12053 
    12054 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12055 
    12056 > color sel medium slate blue
    12057 
    12058 > color sel medium purple
    12059 
    12060 > show #!6 models
    12061 
    12062 > hide #13 models
    12063 
    12064 > select #6/o
    12065 
    12066 856 atoms, 883 bonds, 102 residues, 1 model selected 
    12067 
    12068 > color sel purple
    12069 
    12070 > color sel medium slate blue
    12071 
    12072 > color sel slate blue
    12073 
    12074 > select clear
    12075 
    12076 > show #13 models
    12077 
    12078 > hide #!6 models
    12079 
    12080 > select #13/J#14/J#15/J#16/J#17/J
    12081 
    12082 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12083 
    12084 > color sel violet
    12085 
    12086 > color sel pale violet red
    12087 
    12088 > color sel hot pink
    12089 
    12090 [Repeated 1 time(s)]
    12091 
    12092 > select clear
    12093 
    12094 > show #!6 models
    12095 
    12096 > hide #!6 models
    12097 
    12098 > select #13/J#14/J#15/J#16/J#17/J
    12099 
    12100 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12101 
    12102 > color sel aquamarine
    12103 
    12104 > color sel light sky blue
    12105 
    12106 > select clear
    12107 
    12108 > select #13/J#14/J#15/J#16/J#17/J
    12109 
    12110 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12111 
    12112 > color sel aquamarine
    12113 
    12114 > color sel light sky blue
    12115 
    12116 > select clear
    12117 
    12118 > select #13/J#14/J#15/J#16/J#17/J
    12119 
    12120 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12121 
    12122 > color sel light sky blue
    12123 
    12124 > color sel aquamarine
    12125 
    12126 > select clear
    12127 
    12128 [Repeated 1 time(s)]
    12129 
    12130 > select #13/J#14/J#15/J#16/J#17/J
    12131 
    12132 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12133 
    12134 > color sel dark turquoise
    12135 
    12136 > color sel light sky blue
    12137 
    12138 > select clear
    12139 
    12140 > select #13/J#14/J#15/J#16/J#17/J
    12141 
    12142 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12143 
    12144 > color sel aquamarine
    12145 
    12146 > select clear
    12147 
    12148 [Repeated 2 time(s)]
    12149 
    12150 > select #13/I#14/I#15/I#16/I#17/I
    12151 
    12152 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12153 
    12154 > color sel thistle
    12155 
    12156 > color sel plum
    12157 
    12158 > color sel orchid
    12159 
    12160 > color sel medium orchid
    12161 
    12162 > color sel medium purple
    12163 
    12164 > select clear
    12165 
    12166 > show #!6 models
    12167 
    12168 > hide #!6 models
    12169 
    12170 > select #13/I#14/I#15/I#16/I#17/I
    12171 
    12172 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12173 
    12174 > color sel thistle
    12175 
    12176 > select #13/I#14/I#15/I#16/I#17/I
    12177 
    12178 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12179 
    12180 > select clear
    12181 
    12182 > select #13/I#14/I#15/I#16/I#17/I
    12183 
    12184 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12185 
    12186 > select #13/J#14/J#15/J#16/J#17/J
    12187 
    12188 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12189 
    12190 > color sel powder blue
    12191 
    12192 > color sel pale turquoise
    12193 
    12194 > select clear
    12195 
    12196 > select #13/J#14/J#15/J#16/J#17/J
    12197 
    12198 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12199 
    12200 > color sel light cyan
    12201 
    12202 > select clear
    12203 
    12204 > select #13/I#14/I#15/I#16/I#17/I
    12205 
    12206 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12207 
    12208 > color sel lavender
    12209 
    12210 > select clear
    12211 
    12212 > select #13/I#14/I#15/I#16/I#17/I
    12213 
    12214 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12215 
    12216 > color sel thistle
    12217 
    12218 > select clear
    12219 
    12220 > show #!6 models
    12221 
    12222 > hide #13 models
    12223 
    12224 > show #13 models
    12225 
    12226 > hide #!6 models
    12227 
    12228 > select #13/I#14/I#15/I#16/I#17/I:168-269
    12229 
    12230 14864 atoms, 15299 bonds, 2014 residues, 5 models selected 
    12231 
    12232 > show #!6 models
    12233 
    12234 > hide #13 models
    12235 
    12236 > show #13 models
    12237 
    12238 [Repeated 1 time(s)]
    12239 
    12240 > select #13/I:168-269#14/I:168-269#15/I:168-269#16/I:168-269#17/I:168-269
    12241 
    12242 4280 atoms, 4415 bonds, 510 residues, 5 models selected 
    12243 
    12244 > select #13/I#14/I#15/I#16/I#17/I
    12245 
    12246 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12247 
    12248 > color sel lavender blush
    12249 
    12250 > select clear
    12251 
    12252 > select #13/I:168-269#14/I:168-269#15/I:168-269#16/I:168-269#17/I:168-269
    12253 
    12254 4280 atoms, 4415 bonds, 510 residues, 5 models selected 
    12255 
    12256 > color sel medium purple
    12257 
    12258 > hide #13 models
    12259 
    12260 > show #13 models
    12261 
    12262 > hide #!6 models
    12263 
    12264 > show #!6 models
    12265 
    12266 > hide #13 models
    12267 
    12268 > show #13 models
    12269 
    12270 > hide #!6 models
    12271 
    12272 > select #13/J:269-321
    12273 
    12274 414 atoms, 420 bonds, 53 residues, 1 model selected 
    12275 
    12276 > show #!6 models
    12277 
    12278 > hide #13 models
    12279 
    12280 > show #13 models
    12281 
    12282 > hide #!6 models
    12283 
    12284 > ui tool show "Color Actions"
    12285 
    12286 > color sel dark turquoise
    12287 
    12288 > select clear
    12289 
    12290 > select ::name="CYS"
    12291 
    12292 1218 atoms, 1015 bonds, 203 residues, 14 models selected 
    12293 
    12294 > select #13/L:67
    12295 
    12296 20 atoms, 21 bonds, 1 residue, 1 model selected 
    12297 
    12298 > select #13/J:274
    12299 
    12300 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12301 
    12302 > select add #13/J:294
    12303 
    12304 11 atoms, 9 bonds, 2 residues, 1 model selected 
    12305 
    12306 > select add #13/J:295
    12307 
    12308 17 atoms, 14 bonds, 3 residues, 1 model selected 
    12309 
    12310 > select subtract #13/J:294
    12311 
    12312 12 atoms, 10 bonds, 2 residues, 1 model selected 
    12313 
    12314 > select add #13/J:271
    12315 
    12316 18 atoms, 15 bonds, 3 residues, 1 model selected 
    12317 
    12318 > select add #13/J:292
    12319 
    12320 24 atoms, 20 bonds, 4 residues, 1 model selected 
    12321 
    12322 > color sel gold
    12323 
    12324 > show sel atoms
    12325 
    12326 > nucleotides sel atoms
    12327 
    12328 > style nucleic & sel stick
    12329 
    12330 Changed 0 atom styles 
    12331 
    12332 > style sel ball
    12333 
    12334 Changed 24 atom styles 
    12335 
    12336 > select clear
    12337 
    12338 > select #14/J:269-321
    12339 
    12340 414 atoms, 420 bonds, 53 residues, 1 model selected 
    12341 
    12342 > select #14/J:269-321#15/J:269-321#16/J:269-321#17/J:269-321
    12343 
    12344 1656 atoms, 1680 bonds, 212 residues, 4 models selected 
    12345 
    12346 > color sel dark turquoise
    12347 
    12348 > show #14 models
    12349 
    12350 > hide #13 models
    12351 
    12352 > show #15 models
    12353 
    12354 > hide #14 models
    12355 
    12356 > select clear
    12357 
    12358 > show #13 models
    12359 
    12360 > select #13/I#14/I#15/I#16/I#17/I
    12361 
    12362 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12363 
    12364 > hide sel & #13,15 cartoons
    12365 
    12366 > select #13/J#14/J#15/J#16/J#17/J
    12367 
    12368 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12369 
    12370 > hide sel & #13,15 cartoons
    12371 
    12372 > show #!6 models
    12373 
    12374 > hide #13 models
    12375 
    12376 > hide #15 models
    12377 
    12378 > show #13 models
    12379 
    12380 > hide #!6 models
    12381 
    12382 > show #!6 models
    12383 
    12384 > hide #13 models
    12385 
    12386 > show #13 models
    12387 
    12388 > hide #!6 models
    12389 
    12390 > show #!6 models
    12391 
    12392 > hide #!6 models
    12393 
    12394 > show #!6 models
    12395 
    12396 > hide #!6 models
    12397 
    12398 > show #!6 models
    12399 
    12400 > hide #!6 models
    12401 
    12402 > show #!6 models
    12403 
    12404 > hide #13 models
    12405 
    12406 > show #13 models
    12407 
    12408 > hide #!6 models
    12409 
    12410 > show #!6 models
    12411 
    12412 > hide #!6 models
    12413 
    12414 > show #14 models
    12415 
    12416 > hide #13 models
    12417 
    12418 > show #15 models
    12419 
    12420 > hide #14 models
    12421 
    12422 > show #14 models
    12423 
    12424 > hide #15 models
    12425 
    12426 > hide sel & #14 cartoons
    12427 
    12428 > select #13/I#14/I#15/I#16/I#17/I
    12429 
    12430 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12431 
    12432 > hide sel & #14 cartoons
    12433 
    12434 > show #15 models
    12435 
    12436 > hide #14 models
    12437 
    12438 > show #14 models
    12439 
    12440 > hide #14 models
    12441 
    12442 > show #16 models
    12443 
    12444 > hide #15 models
    12445 
    12446 > show #17 models
    12447 
    12448 > hide sel & #16-17 cartoons
    12449 
    12450 > select #13/J#14/J#15/J#16/J#17/J
    12451 
    12452 15640 atoms, 16060 bonds, 2210 residues, 5 models selected 
    12453 
    12454 > hide sel & #16-17 cartoons
    12455 
    12456 > show #15 models
    12457 
    12458 > show #14 models
    12459 
    12460 > show #13 models
    12461 
    12462 > show #!6 models
    12463 
    12464 > hide #!6 models
    12465 
    12466 > hide #13 models
    12467 
    12468 > hide #14 models
    12469 
    12470 > hide #15 models
    12471 
    12472 > hide #16 models
    12473 
    12474 > hide #17 models
    12475 
    12476 > show #!6 models
    12477 
    12478 > select #6/T:298
    12479 
    12480 12 atoms, 12 bonds, 1 residue, 1 model selected 
    12481 
    12482 > color sel dodger blue
    12483 
    12484 > color sel deep sky blue
    12485 
    12486 > select clear
    12487 
    12488 > show #13 models
    12489 
    12490 > hide #!6 models
    12491 
    12492 > show #14 models
    12493 
    12494 > hide #13 models
    12495 
    12496 > show #13 models
    12497 
    12498 > hide #14 models
    12499 
    12500 > show #15 models
    12501 
    12502 > hide #13 models
    12503 
    12504 > show #16 models
    12505 
    12506 > hide #15 models
    12507 
    12508 > show #17 models
    12509 
    12510 > hide #16 models
    12511 
    12512 > show #!6 models
    12513 
    12514 > hide #17 models
    12515 
    12516 > show #13 models
    12517 
    12518 > hide #!6 models
    12519 
    12520 > hide #13 models
    12521 
    12522 > show #13 models
    12523 
    12524 > show #17 models
    12525 
    12526 > hide #17 models
    12527 
    12528 > show #!6 models
    12529 
    12530 > hide #13 models
    12531 
    12532 > show #13 models
    12533 
    12534 > hide #!6 models
    12535 
    12536 > show #!6 models
    12537 
    12538 > hide #13 models
    12539 
    12540 > show #13 models
    12541 
    12542 > hide #!6 models
    12543 
    12544 > rainbow #13
    12545 
    12546 > undo
    12547 
    12548 > select #13/J
    12549 
    12550 3128 atoms, 3212 bonds, 442 residues, 1 model selected 
    12551 
    12552 > show #14 models
    12553 
    12554 > hide #13 models
    12555 
    12556 > show #15 models
    12557 
    12558 > hide #14 models
    12559 
    12560 > show #!6 models
    12561 
    12562 > hide #15 models
    12563 
    12564 > show #13 models
    12565 
    12566 > hide #!6 models
    12567 
    12568 > show #!6 models
    12569 
    12570 > hide #13 models
    12571 
    12572 > show #13 models
    12573 
    12574 > hide #!6 models
    12575 
    12576 > hide sel atoms
    12577 
    12578 > show #!6 models
    12579 
    12580 > show #!8 models
    12581 
    12582 > hide #!8 models
    12583 
    12584 > hide #13 models
    12585 
    12586 > show #13 models
    12587 
    12588 > hide #!6 models
    12589 
    12590 > show #14 models
    12591 
    12592 > hide #13 models
    12593 
    12594 > show #15 models
    12595 
    12596 > hide #14 models
    12597 
    12598 > show #16 models
    12599 
    12600 > hide #15 models
    12601 
    12602 > show #17 models
    12603 
    12604 > hide #16 models
    12605 
    12606 > show #!6 models
    12607 
    12608 > hide #17 models
    12609 
    12610 > save "/Users/taic/OneDrive - National Institutes of
    12611 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.DNA.png" width 900
    12612 > height 712 supersample 4 transparentBackground true
    12613 
    12614 > show #13 models
    12615 
    12616 > hide #!6 models
    12617 
    12618 > save "/Users/taic/OneDrive - National Institutes of
    12619 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-0.DNA.png" width
    12620 > 900 height 712 supersample 4 transparentBackground true
    12621 
    12622 > show #14 models
    12623 
    12624 > hide #13 models
    12625 
    12626 > save "/Users/taic/OneDrive - National Institutes of
    12627 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-.DNA.png" width
    12628 > 900 height 712 supersample 4 transparentBackground true
    12629 
    12630 > show #15 models
    12631 
    12632 > hide #14 models
    12633 
    12634 > save "/Users/taic/OneDrive - National Institutes of
    12635 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-2.DNA.png" width
    12636 > 900 height 712 supersample 4 transparentBackground true
    12637 
    12638 > show #16 models
    12639 
    12640 > hide #15 models
    12641 
    12642 > save "/Users/taic/OneDrive - National Institutes of
    12643 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-3.DNA.png" width
    12644 > 900 height 712 supersample 4 transparentBackground true
    12645 
    12646 > show #17 models
    12647 
    12648 > hide #16 models
    12649 
    12650 > save "/Users/taic/OneDrive - National Institutes of
    12651 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-4.DNA.png" width
    12652 > 900 height 712 supersample 4 transparentBackground true
    12653 
    12654 > show #!6 models
    12655 
    12656 > hide #17 models
    12657 
    12658 > view matrix models
    12659 > #13,0.5006,-0.78154,0.37228,131.9,0.80193,0.58063,0.1406,208.59,-0.32604,0.22816,0.91741,156.99
    12660 
    12661 > view matrix models
    12662 > #13,0.5006,-0.78154,0.37228,129.59,0.80193,0.58063,0.1406,208.48,-0.32604,0.22816,0.91741,156.57
    12663 
    12664 > select #6/I:33
    12665 
    12666 20 atoms, 21 bonds, 1 residue, 1 model selected 
    12667 
    12668 > select add #6/I:34
    12669 
    12670 39 atoms, 41 bonds, 2 residues, 1 model selected 
    12671 
    12672 > select add #6/I:35
    12673 
    12674 60 atoms, 64 bonds, 3 residues, 1 model selected 
    12675 
    12676 > select add #6/I:37
    12677 
    12678 79 atoms, 84 bonds, 4 residues, 1 model selected 
    12679 
    12680 > select add #6/I:36
    12681 
    12682 101 atoms, 108 bonds, 5 residues, 1 model selected 
    12683 
    12684 > select add #6/I:38
    12685 
    12686 122 atoms, 131 bonds, 6 residues, 1 model selected 
    12687 
    12688 > select add #6/I:39
    12689 
    12690 144 atoms, 155 bonds, 7 residues, 1 model selected 
    12691 
    12692 > ui tool show "Show Sequence Viewer"
    12693 
    12694 > sequence chain #6/I
    12695 
    12696 Alignment identifier is 6/I 
    12697 
    12698 > select #6/I:31
    12699 
    12700 20 atoms, 21 bonds, 1 residue, 1 model selected 
    12701 
    12702 > select #6/I:31-37
    12703 
    12704 143 atoms, 159 bonds, 7 residues, 1 model selected 
    12705 
    12706 > color sel bynucleotide
    12707 
    12708 > show sel atoms
    12709 
    12710 > label sel attribute label_one_letter_code
    12711 
    12712 > label height 2
    12713 
    12714 > label height 3
    12715 
    12716 > view matrix models
    12717 > #6,-0.73769,0.37453,-0.56173,277.08,0.036448,-0.80872,-0.58707,433.88,-0.67416,-0.45355,0.58293,237.79
    12718 
    12719 > select clear
    12720 
    12721 > select #6/J:156
    12722 
    12723 21 atoms, 23 bonds, 1 residue, 1 model selected 
    12724 
    12725 > show sel atoms
    12726 
    12727 > select add #6/J:155
    12728 
    12729 40 atoms, 43 bonds, 2 residues, 1 model selected 
    12730 
    12731 > select add #6/J:154
    12732 
    12733 61 atoms, 66 bonds, 3 residues, 1 model selected 
    12734 
    12735 > select add #6/J:153
    12736 
    12737 83 atoms, 90 bonds, 4 residues, 1 model selected 
    12738 
    12739 > select add #6/J:152
    12740 
    12741 103 atoms, 111 bonds, 5 residues, 1 model selected 
    12742 
    12743 > select add #6/J:151
    12744 
    12745 122 atoms, 131 bonds, 6 residues, 1 model selected 
    12746 
    12747 > select add #6/J:150
    12748 
    12749 144 atoms, 155 bonds, 7 residues, 1 model selected 
    12750 
    12751 > show sel atoms
    12752 
    12753 > select clear
    12754 
    12755 > save "/Users/taic/OneDrive - National Institutes of
    12756 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.png" width 900
    12757 > height 712 supersample 4 transparentBackground true
    12758 
    12759 [Repeated 1 time(s)]
    12760 
    12761 > show #13 models
    12762 
    12763 > hide #!6 models
    12764 
    12765 > select #13/I#14/I#15/I#16/I#17/I
    12766 
    12767 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12768 
    12769 > show sel & #13 cartoons
    12770 
    12771 > select clear
    12772 
    12773 > select #13/I:31-37#14/I:31-37#15/I:31-37#16/I:31-37#17/I:31-37
    12774 
    12775 235 atoms, 230 bonds, 35 residues, 5 models selected 
    12776 
    12777 > select #13/L:31-37#14/L:31-37#15/L:31-37#16/L:31-37#17/L:31-37
    12778 
    12779 715 atoms, 795 bonds, 35 residues, 5 models selected 
    12780 
    12781 > rainbow sel & #13
    12782 
    12783 > show #14 models
    12784 
    12785 > hide #13 models
    12786 
    12787 > rainbow sel & #14
    12788 
    12789 > color sel & #14 bynucleotide
    12790 
    12791 > show #13 models
    12792 
    12793 > color sel & #13-14 bynucleotide
    12794 
    12795 > hide #13 models
    12796 
    12797 > hide #14 models
    12798 
    12799 > show #15 models
    12800 
    12801 > color sel & #15 bynucleotide
    12802 
    12803 > show #16 models
    12804 
    12805 > hide #15 models
    12806 
    12807 > color sel & #16 bynucleotide
    12808 
    12809 > show #17 models
    12810 
    12811 > hide #16 models
    12812 
    12813 > color sel & #17 bynucleotide
    12814 
    12815 > show #14 models
    12816 
    12817 > show #15 models
    12818 
    12819 > show #16 models
    12820 
    12821 > select #13/I#14/I#15/I#16/I#17/I
    12822 
    12823 17510 atoms, 18020 bonds, 2390 residues, 5 models selected 
    12824 
    12825 > show #13 models
    12826 
    12827 > show sel cartoons
    12828 
    12829 > hide #14 models
    12830 
    12831 > hide #15 models
    12832 
    12833 > hide #16 models
    12834 
    12835 > hide #17 models
    12836 
    12837 > select clear
    12838 
    12839 > show #14 models
    12840 
    12841 > hide #13 models
    12842 
    12843 > show #15 models
    12844 
    12845 > hide #14 models
    12846 
    12847 > show #16 models
    12848 
    12849 > hide #15 models
    12850 
    12851 > show #17 models
    12852 
    12853 > hide #16 models
    12854 
    12855 > show #!6 models
    12856 
    12857 > hide #17 models
    12858 
    12859 > show #13 models
    12860 
    12861 > hide #!6 models
    12862 
    12863 > show #13 cartoons
    12864 
    12865 > show #!6 models
    12866 
    12867 > hide #13 models
    12868 
    12869 > select #6/J:130
    12870 
    12871 21 atoms, 23 bonds, 1 residue, 1 model selected 
    12872 
    12873 > select #6/I:55
    12874 
    12875 22 atoms, 24 bonds, 1 residue, 1 model selected 
    12876 
    12877 > select add #6/I:56
    12878 
    12879 43 atoms, 47 bonds, 2 residues, 1 model selected 
    12880 
    12881 > select add #6/I:57
    12882 
    12883 63 atoms, 68 bonds, 3 residues, 1 model selected 
    12884 
    12885 > select add #6/I:58
    12886 
    12887 84 atoms, 91 bonds, 4 residues, 1 model selected 
    12888 
    12889 > color sel bynucleotide
    12890 
    12891 > label sel attribute label_one_letter_code
    12892 
    12893 > label height 3
    12894 
    12895 > show sel atoms
    12896 
    12897 > show #13 models
    12898 
    12899 > hide #!6 models
    12900 
    12901 > color #13 bynucleotide
    12902 
    12903 > undo
    12904 
    12905 > select #13/L:55-58#14/L:55-58#15/L:55-58#16/L:55-58#17/L:55-58
    12906 
    12907 420 atoms, 470 bonds, 20 residues, 5 models selected 
    12908 
    12909 > color sel & #13 bynucleotide
    12910 
    12911 > show #14 models
    12912 
    12913 > hide #13 models
    12914 
    12915 > select clear
    12916 
    12917 > show #14 cartoons
    12918 
    12919 > show #15 models
    12920 
    12921 > hide #14 models
    12922 
    12923 > show #15 cartoons
    12924 
    12925 > show #16 models
    12926 
    12927 > hide #15 models
    12928 
    12929 > show #16 cartoons
    12930 
    12931 > show #17 models
    12932 
    12933 > hide #16 models
    12934 
    12935 > show #17 cartoons
    12936 
    12937 > show #16 models
    12938 
    12939 > show #15 models
    12940 
    12941 > show #14 models
    12942 
    12943 > show #13 models
    12944 
    12945 > select #13/L:55-58#14/L:55-58#15/L:55-58#16/L:55-58#17/L:55-58
    12946 
    12947 420 atoms, 470 bonds, 20 residues, 5 models selected 
    12948 
    12949 > color sel bynucleotide
    12950 
    12951 > hide #13 models
    12952 
    12953 > show #13 models
    12954 
    12955 > hide #14 models
    12956 
    12957 > hide #15 models
    12958 
    12959 > hide #16 models
    12960 
    12961 > hide #17 models
    12962 
    12963 > show #!6 models
    12964 
    12965 > hide #13 models
    12966 
    12967 Drag select of 19 residues 
    12968 
    12969 > select #6/H:48
    12970 
    12971 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12972 
    12973 > select #6/T
    12974 
    12975 415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected 
    12976 
    12977 > show sel surfaces
    12978 
    12979 > hide sel surfaces
    12980 
    12981 > show #13 models
    12982 
    12983 > hide #!6 models
    12984 
    12985 > show #!6 models
    12986 
    12987 > hide #!6 models
    12988 
    12989 > show #14 models
    12990 
    12991 > hide #13 models
    12992 
    12993 > show #14 cartoons
    12994 
    12995 [Repeated 1 time(s)]
    12996 
    12997 > select #14
    12998 
    12999 21967 atoms, 23178 bonds, 2283 residues, 1 model selected 
    13000 
    13001 > show sel cartoons
    13002 
    13003 > select clear
    13004 
    13005 > show #15 models
    13006 
    13007 > hide #14 models
    13008 
    13009 > show #16 models
    13010 
    13011 > hide #15 models
    13012 
    13013 > show #17 models
    13014 
    13015 > hide #16 models
    13016 
    13017 > show #!6 models
    13018 
    13019 > hide #17 models
    13020 
    13021 > show #13 models
    13022 
    13023 > hide #!6 models
    13024 
    13025 > select #13/J
    13026 
    13027 3128 atoms, 3212 bonds, 442 residues, 1 model selected 
    13028 
    13029 > select #13/I
    13030 
    13031 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    13032 
    13033 > hide sel cartoons
    13034 
    13035 > show #!6 models
    13036 
    13037 > hide #13 models
    13038 
    13039 Drag select of 165 residues 
    13040 
    13041 > select clear
    13042 
    13043 > show #2 models
    13044 
    13045 > hide #!6 models
    13046 
    13047 > show #3 models
    13048 
    13049 > hide #2 models
    13050 
    13051 > show #4 models
    13052 
    13053 > hide #3 models
    13054 
    13055 > show #5 models
    13056 
    13057 > hide #4 models
    13058 
    13059 > show #7 models
    13060 
    13061 > hide #5 models
    13062 
    13063 > show #!8 models
    13064 
    13065 > hide #!8 models
    13066 
    13067 > show #!8 models
    13068 
    13069 > hide #7 models
    13070 
    13071 > show #1 models
    13072 
    13073 > hide #1 models
    13074 
    13075 > show #2 models
    13076 
    13077 > hide #!8 models
    13078 
    13079 > show #!6 models
    13080 
    13081 > hide #2 models
    13082 
    13083 > show #13 models
    13084 
    13085 > hide #!6 models
    13086 
    13087 > show #!6 models
    13088 
    13089 > hide #13 models
    13090 
    13091 > show #13 models
    13092 
    13093 > hide #13 models
    13094 
    13095 > show #13 models
    13096 
    13097 > hide #!6 models
    13098 
    13099 > select #13/I
    13100 
    13101 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    13102 
    13103 > show sel cartoons
    13104 
    13105 > select clear
    13106 
    13107 > show #!6 models
    13108 
    13109 > hide #13 models
    13110 
    13111 > show #13 models
    13112 
    13113 > select #6/O
    13114 
    13115 856 atoms, 883 bonds, 102 residues, 1 model selected 
    13116 
    13117 > ui tool show Matchmaker
    13118 
    13119 > select #6/O#13/I#14/I#15/I#16/I#17/I
    13120 
    13121 18366 atoms, 18903 bonds, 2492 residues, 6 models selected 
    13122 
    13123 > show #14 models
    13124 
    13125 > show #15 models
    13126 
    13127 > show #16 models
    13128 
    13129 > show #17 models
    13130 
    13131 > matchmaker #13-17 & sel to #6 & sel
    13132 
    13133 Computing secondary structure 
    13134 [Repeated 4 time(s)]  Parameters 
    13135 --- 
    13136 Chain pairing | bb 
    13137 Alignment algorithm | Needleman-Wunsch 
    13138 Similarity matrix | BLOSUM-62 
    13139 SS fraction | 0.3 
    13140 Gap open (HH/SS/other) | 18/18/6 
    13141 Gap extend | 1 
    13142 SS matrix |  |  | H | S | O 
    13143 ---|---|---|--- 
    13144 H | 6 | -9 | -6 
    13145 S |  | 6 | -6 
    13146 O |  |  | 4 
    13147 Iteration cutoff | 2 
    13148  
    13149 Matchmaker 8vg1, chain O (#6) with
    13150 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
    13151 alignment score = 1915.2 
    13152 RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
    13153 1.960) 
    13154  
    13155 Matchmaker 8vg1, chain O (#6) with
    13156 fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain I (#14), sequence
    13157 alignment score = 1927.2 
    13158 RMSD between 82 pruned atom pairs is 0.853 angstroms; (across all 102 pairs:
    13159 1.776) 
    13160  
    13161 Matchmaker 8vg1, chain O (#6) with
    13162 fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain I (#15), sequence
    13163 alignment score = 1924.2 
    13164 RMSD between 78 pruned atom pairs is 0.751 angstroms; (across all 102 pairs:
    13165 2.144) 
    13166  
    13167 Matchmaker 8vg1, chain O (#6) with
    13168 fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain I (#16), sequence
    13169 alignment score = 1901.4 
    13170 RMSD between 80 pruned atom pairs is 0.855 angstroms; (across all 102 pairs:
    13171 3.778) 
    13172  
    13173 Matchmaker 8vg1, chain O (#6) with
    13174 fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain I (#17), sequence
    13175 alignment score = 1909.2 
    13176 RMSD between 82 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
    13177 1.994) 
    13178  
    13179 
    13180 > hide #14 models
    13181 
    13182 > hide #15 models
    13183 
    13184 > hide #16 models
    13185 
    13186 > hide #17 models
    13187 
    13188 > hide #!6 models
    13189 
    13190 > show #!6 models
    13191 
    13192 > hide #!6 models
    13193 
    13194 > select clear
    13195 
    13196 > show #!6 models
    13197 
    13198 > hide #!6 models
    13199 
    13200 > show #!6 models
    13201 
    13202 > hide #!6 models
    13203 
    13204 > show #!6 models
    13205 
    13206 > hide #!6 models
    13207 
    13208 > show #!6 models
    13209 
    13210 > hide #13 models
    13211 
    13212 > show #13 models
    13213 
    13214 > hide #!6 models
    13215 
    13216 > show #14 models
    13217 
    13218 > hide #13 models
    13219 
    13220 > show #!6 models
    13221 
    13222 > hide #!6 models
    13223 
    13224 > show #!6 models
    13225 
    13226 > hide #14 models
    13227 
    13228 > select #6/O
    13229 
    13230 856 atoms, 883 bonds, 102 residues, 1 model selected 
    13231 
    13232 > show sel surfaces
    13233 
    13234 > hide sel surfaces
    13235 
    13236 > show sel surfaces
    13237 
    13238 > select clear
    13239 
    13240 > hide #!6 surfaces
    13241 
    13242 > show #!6 surfaces
    13243 
    13244 > undo
    13245 
    13246 > hide #!6 surfaces
    13247 
    13248 > select #6/O
    13249 
    13250 856 atoms, 883 bonds, 102 residues, 1 model selected 
    13251 
    13252 > show sel surfaces
    13253 
    13254 > select clear
    13255 
    13256 > hide #!6 surfaces
    13257 
    13258 > select #6/O
    13259 
    13260 856 atoms, 883 bonds, 102 residues, 1 model selected 
    13261 
    13262 > show sel surfaces
    13263 
    13264 > select clear
    13265 
    13266 > show #13 models
    13267 
    13268 > hide #!6 models
    13269 
    13270 > show #!6 models
    13271 
    13272 > hide #!6 models
    13273 
    13274 > show #14 models
    13275 
    13276 > hide #13 models
    13277 
    13278 > show #!6 models
    13279 
    13280 > hide #14 models
    13281 
    13282 > show #13 models
    13283 
    13284 > hide #!6 models
    13285 
    13286 > show #14 models
    13287 
    13288 > hide #13 models
    13289 
    13290 > show #!6 models
    13291 
    13292 > hide #!6 models
    13293 
    13294 > show #!6 models
    13295 
    13296 > hide #14 models
    13297 
    13298 > show #13 models
    13299 
    13300 > hide #!6 models
    13301 
    13302 > show #!6 models
    13303 
    13304 > hide #13 models
    13305 
    13306 > hide #!6 surfaces
    13307 
    13308 > select #6/I:31
    13309 
    13310 20 atoms, 21 bonds, 1 residue, 1 model selected 
    13311 
    13312 > show sel atoms
    13313 
    13314 > show sel surfaces
    13315 
    13316 > select clear
    13317 
    13318 > show #!6 surfaces
    13319 
    13320 > show #13 models
    13321 
    13322 > hide #!6 models
    13323 
    13324 > show #13 surfaces
    13325 
    13326 > hide #!13 surfaces
    13327 
    13328 [Repeated 1 time(s)]
    13329 
    13330 > show #!13 surfaces
    13331 
    13332 > hide #!13 surfaces
    13333 
    13334 > show #!13 surfaces
    13335 
    13336 > hide #!13 surfaces
    13337 
    13338 > select #13/L:55-58#14/L:55-58#15/L:55-58#16/L:55-58#17/L:55-58
    13339 
    13340 420 atoms, 470 bonds, 20 residues, 5 models selected 
    13341 
    13342 > select #13/I:393
    13343 
    13344 10 atoms, 10 bonds, 1 residue, 1 model selected 
    13345 
    13346 > select #13/J:298
    13347 
    13348 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13349 
    13350 > show sel surfaces
    13351 
    13352 > hide sel surfaces
    13353 
    13354 > show #14 models
    13355 
    13356 > hide #!13 models
    13357 
    13358 > show #14 cartoons
    13359 
    13360 > show #14 surfaces
    13361 
    13362 > hide #!14 surfaces
    13363 
    13364 > show #!14 surfaces
    13365 
    13366 > show #15 models
    13367 
    13368 > hide #!14 models
    13369 
    13370 > hide #15 models
    13371 
    13372 > open /Users/taic/Library/CloudStorage/OneDrive-
    13373 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_0.cif
    13374 
    13375 Chain information for fold_motb_1_ibpa_model_0.cif #9 
    13376 --- 
    13377 Chain | Description 
    13378 A | . 
    13379 B | . 
    13380  
    13381 
    13382 > open /Users/taic/Library/CloudStorage/OneDrive-
    13383 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_1.cif
    13384 
    13385 Chain information for fold_motb_1_ibpa_model_1.cif #10 
    13386 --- 
    13387 Chain | Description 
    13388 A | . 
    13389 B | . 
    13390  
    13391 
    13392 > open /Users/taic/Library/CloudStorage/OneDrive-
    13393 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_2.cif
    13394 
    13395 Chain information for fold_motb_1_ibpa_model_2.cif #11 
    13396 --- 
    13397 Chain | Description 
    13398 A | . 
    13399 B | . 
    13400  
    13401 
    13402 > open /Users/taic/Library/CloudStorage/OneDrive-
    13403 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_3.cif
    13404 
    13405 Chain information for fold_motb_1_ibpa_model_3.cif #12 
    13406 --- 
    13407 Chain | Description 
    13408 A | . 
    13409 B | . 
    13410  
    13411 
    13412 > open /Users/taic/Library/CloudStorage/OneDrive-
    13413 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_4.cif
    13414 
    13415 Chain information for fold_motb_1_ibpa_model_4.cif #18 
    13416 --- 
    13417 Chain | Description 
    13418 A | . 
    13419 B | . 
    13420  
    13421 Computing secondary structure 
    13422 [Repeated 4 time(s)]
    13423 
    13424 > select /A
    13425 
    13426 21864 atoms, 22273 bonds, 2764 residues, 19 models selected 
    13427 
    13428 > ui tool show Matchmaker
    13429 
    13430 > matchmaker #10-12,18 & sel to #9 & sel
    13431 
    13432 Computing secondary structure 
    13433 [Repeated 4 time(s)]  Parameters 
    13434 --- 
    13435 Chain pairing | bb 
    13436 Alignment algorithm | Needleman-Wunsch 
    13437 Similarity matrix | BLOSUM-62 
    13438 SS fraction | 0.3 
    13439 Gap open (HH/SS/other) | 18/18/6 
    13440 Gap extend | 1 
    13441 SS matrix |  |  | H | S | O 
    13442 ---|---|---|--- 
    13443 H | 6 | -9 | -6 
    13444 S |  | 6 | -6 
    13445 O |  |  | 4 
    13446 Iteration cutoff | 2 
    13447  
    13448 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13449 fold_motb_1_ibpa_model_1.cif, chain A (#10), sequence alignment score = 618.4 
    13450 RMSD between 86 pruned atom pairs is 0.539 angstroms; (across all 119 pairs:
    13451 10.720) 
    13452  
    13453 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13454 fold_motb_1_ibpa_model_2.cif, chain A (#11), sequence alignment score = 618.4 
    13455 RMSD between 83 pruned atom pairs is 0.491 angstroms; (across all 119 pairs:
    13456 19.970) 
    13457  
    13458 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13459 fold_motb_1_ibpa_model_3.cif, chain A (#12), sequence alignment score = 607.6 
    13460 RMSD between 84 pruned atom pairs is 0.273 angstroms; (across all 119 pairs:
    13461 19.835) 
    13462  
    13463 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13464 fold_motb_1_ibpa_model_4.cif, chain A (#18), sequence alignment score = 588.4 
    13465 RMSD between 87 pruned atom pairs is 0.448 angstroms; (across all 119 pairs:
    13466 14.443) 
    13467  
    13468 
    13469 > select clear
    13470 
    13471 > color #9-12,18 bychain
    13472 
    13473 > select /B
    13474 
    13475 21839 atoms, 22208 bonds, 2813 residues, 19 models selected 
    13476 
    13477 > rainbow sel & #9-12,18
    13478 
    13479 > hide #18 models
    13480 
    13481 > show #18 models
    13482 
    13483 > hide #18 models
    13484 
    13485 > show #18 models
    13486 
    13487 > hide #18 models
    13488 
    13489 > hide #9 models
    13490 
    13491 > hide #10 models
    13492 
    13493 > hide #11 models
    13494 
    13495 > hide #12 models
    13496 
    13497 > show #18 models
    13498 
    13499 > show #9 models
    13500 
    13501 > hide #9 models
    13502 
    13503 > show #9 models
    13504 
    13505 > hide #18 models
    13506 
    13507 > show #18 models
    13508 
    13509 > hide #9 models
    13510 
    13511 > show #9 models
    13512 
    13513 > hide #9 models
    13514 
    13515 > show #9 models
    13516 
    13517 > hide #18 models
    13518 
    13519 > show #10 models
    13520 
    13521 > hide #9 models
    13522 
    13523 > show #11 models
    13524 
    13525 > hide #10 models
    13526 
    13527 > show #12 models
    13528 
    13529 > hide #11 models
    13530 
    13531 > select clear
    13532 
    13533 > select /B
    13534 
    13535 21839 atoms, 22208 bonds, 2813 residues, 19 models selected 
    13536 
    13537 > show sel & #12 surfaces
    13538 
    13539 > show #18 models
    13540 
    13541 > hide #!12 models
    13542 
    13543 > show sel & #18 surfaces
    13544 
    13545 > hide #!18 models
    13546 
    13547 > show #9 models
    13548 
    13549 > show sel & #9 surfaces
    13550 
    13551 > select /A
    13552 
    13553 21864 atoms, 22273 bonds, 2764 residues, 19 models selected 
    13554 
    13555 > show sel & #!9 surfaces
    13556 
    13557 > hide sel & #!9 surfaces
    13558 
    13559 > show sel & #!9 surfaces
    13560 
    13561 [Repeated 1 time(s)]
    13562 
    13563 > hide sel & #!9 surfaces
    13564 
    13565 > view matrix models
    13566 > #6,-0.73769,0.37453,-0.56173,264.4,0.036448,-0.80872,-0.58707,432.16,-0.67416,-0.45355,0.58293,229.9,#1,0.34863,-0.86979,-0.34918,115.59,-0.59863,-0.4933,0.63111,222.69,-0.72118,-0.010996,-0.69266,124.84,#20,0.14776,-0.82411,0.54682,81.945,-0.98901,-0.12627,0.076949,189.08,0.0056323,-0.55218,-0.83371,164.9,#2,-0.78547,-0.55054,0.28274,124.11,-0.049609,0.51138,0.85792,224.26,-0.61691,0.65985,-0.42898,134.73,#3,0.86327,0.50474,-0.0016107,129.29,0.44874,-0.76894,-0.45538,210.11,-0.23109,0.39239,-0.8903,130.38,#4,-0.29416,-0.93822,-0.18224,129.74,-0.72095,0.092643,0.68677,227.3,-0.62746,0.33341,-0.70366,148.07,#5,-0.73977,0.075381,0.66862,116.99,-0.44258,-0.80299,-0.39915,229.43,0.50681,-0.5912,0.6274,141.69,#7,0.13642,-0.011203,0.99059,126.25,-0.88638,-0.44793,0.117,204.9,0.4424,-0.894,-0.071036,142.12,#13,0.0038706,-0.86688,-0.49851,155.96,0.53647,-0.4189,0.73261,240.32,-0.84391,-0.27027,0.46343,76.465,#14,-0.26132,0.8822,0.39171,187.41,-0.81884,-0.41748,0.39396,274.2,0.51108,-0.21779,0.83148,145.79,#15,-0.24072,0.6086,-0.75608,178.11,-0.8187,0.29109,0.49497,285.35,0.52133,0.73815,0.42819,134.78,#16,0.85782,0.51132,-0.051848,148.14,-0.18642,0.40358,0.89575,207.1,0.47894,-0.75873,0.44152,102.73,#17,-0.42368,-0.0075666,-0.90578,171.81,-0.89534,-0.14814,0.42003,228.34,-0.13736,0.98894,0.05599,81.142,#8,-0.46108,0.5647,0.68448,80.531,0.54831,-0.42517,0.72012,211.59,0.69768,0.70735,-0.11359,195.21,#9,1,0,0,-12.681,0,1,0,-1.7223,0,0,1,-7.8908,#10,0.99715,0.072954,-0.018974,-7.5052,0.056195,-0.55164,0.83219,-6.0261,0.050244,-0.83088,-0.55417,-8.6196,#11,-0.056865,-0.77148,-0.63371,-7.3464,-0.98854,-0.045419,0.144,-5.4156,-0.13987,0.63464,-0.76005,-12.726,#12,0.32123,0.94585,0.046696,-10.832,0.91723,-0.29849,-0.26382,-3.5132,-0.2356,0.12758,-0.96344,-13.271,#18,0.95192,0.26927,0.1461,-8.4839,0.23642,-0.94899,0.20861,-1.9572,0.19483,-0.16404,-0.96702,-10.748
    13567 
    13568 > select /A:47-55
    13569 
    13570 1442 atoms, 1437 bonds, 171 residues, 19 models selected 
    13571 
    13572 > show sel & #!9 surfaces
    13573 
    13574 > hide sel & #!9 surfaces
    13575 
    13576 > select /A:71-75
    13577 
    13578 811 atoms, 798 bonds, 95 residues, 19 models selected 
    13579 
    13580 > show sel & #!9 surfaces
    13581 
    13582 > hide sel & #!9 surfaces
    13583 
    13584 [Repeated 2 time(s)]
    13585 
    13586 > select clear
    13587 
    13588 > select /B
    13589 
    13590 21839 atoms, 22208 bonds, 2813 residues, 19 models selected 
    13591 
    13592 > hide sel & #!9 surfaces
    13593 
    13594 > select clear
    13595 
    13596 > show #10 models
    13597 
    13598 > show #11 models
    13599 
    13600 > hide #11 models
    13601 
    13602 > show #!12 models
    13603 
    13604 > show #11 models
    13605 
    13606 > show #!18 models
    13607 
    13608 > hide #!9 models
    13609 
    13610 > hide #10 models
    13611 
    13612 > hide #11 models
    13613 
    13614 > hide #!12 models
    13615 
    13616 > hide #!18 models
    13617 
    13618 > open /Users/taic/Library/CloudStorage/OneDrive-
    13619 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_0.cif
    13620 
    13621 Chain information for fold_motb_1x2_ibpax2_model_0.cif #19 
    13622 --- 
    13623 Chain | Description 
    13624 A B | . 
    13625 C D | . 
    13626  
    13627 
    13628 > open /Users/taic/Library/CloudStorage/OneDrive-
    13629 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_1.cif
    13630 
    13631 Chain information for fold_motb_1x2_ibpax2_model_1.cif #21 
    13632 --- 
    13633 Chain | Description 
    13634 A B | . 
    13635 C D | . 
    13636  
    13637 
    13638 > open /Users/taic/Library/CloudStorage/OneDrive-
    13639 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_2.cif
    13640 
    13641 Chain information for fold_motb_1x2_ibpax2_model_2.cif #22 
    13642 --- 
    13643 Chain | Description 
    13644 A B | . 
    13645 C D | . 
    13646  
    13647 
    13648 > open /Users/taic/Library/CloudStorage/OneDrive-
    13649 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_3.cif
    13650 
    13651 Chain information for fold_motb_1x2_ibpax2_model_3.cif #23 
    13652 --- 
    13653 Chain | Description 
    13654 A B | . 
    13655 C D | . 
    13656  
    13657 
    13658 > open /Users/taic/Library/CloudStorage/OneDrive-
    13659 > NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_4.cif
    13660 
    13661 Chain information for fold_motb_1x2_ibpax2_model_4.cif #24 
    13662 --- 
    13663 Chain | Description 
    13664 A B | . 
    13665 C D | . 
    13666  
    13667 Computing secondary structure 
    13668 [Repeated 4 time(s)]
    13669 
    13670 > select /A
    13671 
    13672 26734 atoms, 27273 bonds, 3359 residues, 24 models selected 
    13673 
    13674 > ui tool show Matchmaker
    13675 
    13676 > matchmaker #21-24 & sel to #9 & sel
    13677 
    13678 Computing secondary structure 
    13679 [Repeated 4 time(s)]  Parameters 
    13680 --- 
    13681 Chain pairing | bb 
    13682 Alignment algorithm | Needleman-Wunsch 
    13683 Similarity matrix | BLOSUM-62 
    13684 SS fraction | 0.3 
    13685 Gap open (HH/SS/other) | 18/18/6 
    13686 Gap extend | 1 
    13687 SS matrix |  |  | H | S | O 
    13688 ---|---|---|--- 
    13689 H | 6 | -9 | -6 
    13690 S |  | 6 | -6 
    13691 O |  |  | 4 
    13692 Iteration cutoff | 2 
    13693  
    13694 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13695 fold_motb_1x2_ibpax2_model_1.cif, chain A (#21), sequence alignment score =
    13696 587.2 
    13697 RMSD between 86 pruned atom pairs is 0.349 angstroms; (across all 119 pairs:
    13698 9.985) 
    13699  
    13700 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13701 fold_motb_1x2_ibpax2_model_2.cif, chain A (#22), sequence alignment score =
    13702 584.2 
    13703 RMSD between 85 pruned atom pairs is 0.578 angstroms; (across all 119 pairs:
    13704 11.734) 
    13705  
    13706 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13707 fold_motb_1x2_ibpax2_model_3.cif, chain A (#23), sequence alignment score =
    13708 555.7 
    13709 RMSD between 85 pruned atom pairs is 0.352 angstroms; (across all 119 pairs:
    13710 15.604) 
    13711  
    13712 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13713 fold_motb_1x2_ibpax2_model_4.cif, chain A (#24), sequence alignment score =
    13714 597.4 
    13715 RMSD between 76 pruned atom pairs is 0.381 angstroms; (across all 119 pairs:
    13716 16.342) 
    13717  
    13718 
    13719 > show #!9 models
    13720 
    13721 > hide #21 models
    13722 
    13723 > hide #22 models
    13724 
    13725 > hide #23 models
    13726 
    13727 > hide #24 models
    13728 
    13729 > hide #19 models
    13730 
    13731 > show #19 models
    13732 
    13733 > hide #!9 models
    13734 
    13735 > color sel & #19 bychain
    13736 
    13737 > show #!9 models
    13738 
    13739 > matchmaker #19 & sel to #9 & sel
    13740 
    13741 Computing secondary structure 
    13742 [Repeated 1 time(s)]  Parameters 
    13743 --- 
    13744 Chain pairing | bb 
    13745 Alignment algorithm | Needleman-Wunsch 
    13746 Similarity matrix | BLOSUM-62 
    13747 SS fraction | 0.3 
    13748 Gap open (HH/SS/other) | 18/18/6 
    13749 Gap extend | 1 
    13750 SS matrix |  |  | H | S | O 
    13751 ---|---|---|--- 
    13752 H | 6 | -9 | -6 
    13753 S |  | 6 | -6 
    13754 O |  |  | 4 
    13755 Iteration cutoff | 2 
    13756  
    13757 Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
    13758 fold_motb_1x2_ibpax2_model_0.cif, chain A (#19), sequence alignment score =
    13759 578.8 
    13760 RMSD between 84 pruned atom pairs is 0.544 angstroms; (across all 119 pairs:
    13761 16.385) 
    13762  
    13763 
    13764 > hide #!9 models
    13765 
    13766 > select /C
    13767 
    13768 18212 atoms, 18468 bonds, 2333 residues, 19 models selected 
    13769 
    13770 > select #19/C
    13771 
    13772 1116 atoms, 1137 bonds, 137 residues, 1 model selected 
    13773 
    13774 > rainbow sel
    13775 
    13776 > select clear
    13777 
    13778 > show #!9 models
    13779 
    13780 > hide #19 models
    13781 
    13782 > show #19 models
    13783 
    13784 > hide #!9 models
    13785 
    13786 > show #21 models
    13787 
    13788 > hide #19 models
    13789 
    13790 > select /A
    13791 
    13792 26734 atoms, 27273 bonds, 3359 residues, 24 models selected 
    13793 
    13794 > color sel & #21 bychain
    13795 
    13796 > show #22 models
    13797 
    13798 > hide #21 models
    13799 
    13800 > show #!18 models
    13801 
    13802 > hide #!18 models
    13803 
    13804 > show #19 models
    13805 
    13806 > hide #19 models
    13807 
    13808 > show #23 models
    13809 
    13810 > hide #22 models
    13811 
    13812 > show #24 models
    13813 
    13814 > hide #23 models
    13815 
    13816 > color sel & #24 bychain
    13817 
    13818 > show #19 models
    13819 
    13820 > hide #19 models
    13821 
    13822 > show #23 models
    13823 
    13824 > hide #24 models
    13825 
    13826 > show #24 models
    13827 
    13828 > show #22 models
    13829 
    13830 > hide #23 models
    13831 
    13832 > hide #24 models
    13833 
    13834 > show #21 models
    13835 
    13836 > show #23 models
    13837 
    13838 > show #24 models
    13839 
    13840 > hide #24 models
    13841 
    13842 > hide #23 models
    13843 
    13844 > hide #22 models
    13845 
    13846 > show #19 models
    13847 
    13848 > hide #21 models
    13849 
    13850 > show #21 models
    13851 
    13852 > hide #19 models
    13853 
    13854 > show #19 models
    13855 
    13856 > select /C
    13857 
    13858 18212 atoms, 18468 bonds, 2333 residues, 19 models selected 
    13859 
    13860 > matchmaker #19,22-24 & sel to #21 & sel
    13861 
    13862 Computing secondary structure 
    13863 [Repeated 4 time(s)]  Parameters 
    13864 --- 
    13865 Chain pairing | bb 
    13866 Alignment algorithm | Needleman-Wunsch 
    13867 Similarity matrix | BLOSUM-62 
    13868 SS fraction | 0.3 
    13869 Gap open (HH/SS/other) | 18/18/6 
    13870 Gap extend | 1 
    13871 SS matrix |  |  | H | S | O 
    13872 ---|---|---|--- 
    13873 H | 6 | -9 | -6 
    13874 S |  | 6 | -6 
    13875 O |  |  | 4 
    13876 Iteration cutoff | 2 
    13877  
    13878 Matchmaker fold_motb_1x2_ibpax2_model_1.cif, chain C (#21) with
    13879 fold_motb_1x2_ibpax2_model_0.cif, chain C (#19), sequence alignment score =
    13880 692.7 
    13881 RMSD between 101 pruned atom pairs is 0.566 angstroms; (across all 137 pairs:
    13882 16.843) 
    13883  
    13884 Matchmaker fold_motb_1x2_ibpax2_model_1.cif, chain C (#21) with
    13885 fold_motb_1x2_ibpax2_model_2.cif, chain C (#22), sequence alignment score =
    13886 690.9 
    13887 RMSD between 95 pruned atom pairs is 0.674 angstroms; (across all 137 pairs:
    13888 4.636) 
    13889  
    13890 Matchmaker fold_motb_1x2_ibpax2_model_1.cif, chain C (#21) with
    13891 fold_motb_1x2_ibpax2_model_3.cif, chain C (#23), sequence alignment score =
    13892 684.3 
    13893 RMSD between 93 pruned atom pairs is 0.441 angstroms; (across all 137 pairs:
    13894 4.461) 
    13895  
    13896 Matchmaker fold_motb_1x2_ibpax2_model_1.cif, chain C (#21) with
    13897 fold_motb_1x2_ibpax2_model_4.cif, chain C (#24), sequence alignment score =
    13898 684.9 
    13899 RMSD between 95 pruned atom pairs is 0.438 angstroms; (across all 137 pairs:
    13900 4.124) 
    13901  
    13902 
    13903 > hide #21 models
    13904 
    13905 > show #21 models
    13906 
    13907 > hide #19 models
    13908 
    13909 > show #!18 models
    13910 
    13911 > hide #!18 models
    13912 
    13913 > show #19 models
    13914 
    13915 > hide #21 models
    13916 
    13917 > show #21 models
    13918 
    13919 > show #22 models
    13920 
    13921 > show #23 models
    13922 
    13923 > show #24 models
    13924 
    13925 > hide #24 models
    13926 
    13927 > hide #23 models
    13928 
    13929 > hide #22 models
    13930 
    13931 > show #22 models
    13932 
    13933 > show #23 models
    13934 
    13935 > select clear
    13936 
    13937 > hide #22 models
    13938 
    13939 > hide #23 models
    13940 
    13941 > select /A/B
    13942 
    13943 53443 atoms, 54481 bonds, 6767 residues, 24 models selected 
    13944 
    13945 > color sel & #19,21 bychain
    13946 
    13947 > select clear
    13948 
    13949 > hide #21 models
    13950 
    13951 > show #21 models
    13952 
    13953 > hide #19 models
    13954 
    13955 > show #19 models
    13956 
    13957 > hide #21 models
    13958 
    13959 > show #21 models
    13960 
    13961 > hide #19 models
    13962 
    13963 > show #22 models
    13964 
    13965 > show #23 models
    13966 
    13967 > show #24 models
    13968 
    13969 > hide #24 models
    13970 
    13971 > hide #23 models
    13972 
    13973 > show #23 models
    13974 
    13975 > hide #21 models
    13976 
    13977 > hide #22 models
    13978 
    13979 > hide #23 models
    13980 
    13981 > show #21 models
    13982 
    13983 > show #19 models
    13984 
    13985 > hide #19 models
    13986 
    13987 > show #19 models
    13988 
    13989 > hide #21 models
    13990 
    13991 > show #21 models
    13992 
    13993 > hide #19 models
    13994 
    13995 > show #19 models
    13996 
    13997 > select /A
    13998 
    13999 26734 atoms, 27273 bonds, 3359 residues, 24 models selected 
    14000 
    14001 > rainbow sel & #19,21
    14002 
    14003 > hide #21 models
    14004 
    14005 > select /C
    14006 
    14007 18212 atoms, 18468 bonds, 2333 residues, 19 models selected 
    14008 
    14009 > color sel & #19 bychain
    14010 
    14011 > select clear
    14012 
    14013 > show #21 models
    14014 
    14015 > hide #19 models
    14016 
    14017 > show #19 models
    14018 
    14019 > hide #21 models
    14020 
    14021 > show #21 models
    14022 
    14023 > hide #19 models
    14024 
    14025 > show #22 models
    14026 
    14027 > hide #21 models
    14028 
    14029 > show #23 models
    14030 
    14031 > hide #22 models
    14032 
    14033 > show #21 models
    14034 
    14035 > hide #23 models
    14036 
    14037 Drag select of 1 residues 
    14038 
    14039 > show #!18 models
    14040 
    14041 > hide #!18 models
    14042 
    14043 > show #19 models
    14044 
    14045 > hide #21 models
    14046 
    14047 > show #21 models
    14048 
    14049 > hide #19 models
    14050 
    14051 > show #19 models
    14052 
    14053 > hide #21 models
    14054 
    14055 > show #21 models
    14056 
    14057 > hide #19 models
    14058 
    14059 > select /A
    14060 
    14061 26734 atoms, 27273 bonds, 3359 residues, 24 models selected 
    14062 
    14063 > color sel & #21 bychain
    14064 
    14065 > select /B
    14066 
    14067 26709 atoms, 27208 bonds, 3408 residues, 24 models selected 
    14068 
    14069 > rainbow sel & #21
    14070 
    14071 > select clear
    14072 
    14073 > show #19 models
    14074 
    14075 > hide #21 models
    14076 
    14077 > show #21 models
    14078 
    14079 > hide #19 models
    14080 
    14081 > show #19 models
    14082 
    14083 > hide #21 models
    14084 
    14085 > show #21 models
    14086 
    14087 > hide #21 models
    14088 
    14089 > select /B
    14090 
    14091 26709 atoms, 27208 bonds, 3408 residues, 24 models selected 
    14092 
    14093 > ui tool show "Color Actions"
    14094 
    14095 > color sel medium slate blue
    14096 
    14097 > color sel medium purple
    14098 
    14099 > select clear
    14100 
    14101 > show #21 models
    14102 
    14103 > hide #19 models
    14104 
    14105 > select /B
    14106 
    14107 26709 atoms, 27208 bonds, 3408 residues, 24 models selected 
    14108 
    14109 > rainbow sel & #21
    14110 
    14111 > select clear
    14112 
    14113 > show #22 models
    14114 
    14115 > show #23 models
    14116 
    14117 > hide #22 models
    14118 
    14119 > hide #21 models
    14120 
    14121 > show #19 models
    14122 
    14123 > show #22 models
    14124 
    14125 > hide #22 models
    14126 
    14127 > hide #23 models
    14128 
    14129 > show #21 models
    14130 
    14131 > hide #19 models
    14132 
    14133 > show #19 models
    14134 
    14135 > hide #21 models
    14136 
    14137 > show #21 models
    14138 
    14139 > hide #19 models
    14140 
    14141 > show #19 models
    14142 
    14143 > hide #21 models
    14144 
    14145 > show #21 models
    14146 
    14147 > hide #19 models
    14148 
    14149 > show #19 models
    14150 
    14151 > hide #21 models
    14152 
    14153 > select #19/B:48-54
    14154 
    14155 45 atoms, 44 bonds, 7 residues, 1 model selected 
    14156 
    14157 > select #19/A:48-54
    14158 
    14159 45 atoms, 44 bonds, 7 residues, 1 model selected 
    14160 
    14161 > color sel magenta
    14162 
    14163 > select clear
    14164 
    14165 > show #21 models
    14166 
    14167 > hide #19 models
    14168 
    14169 > select #21/B:48-54
    14170 
    14171 45 atoms, 44 bonds, 7 residues, 1 model selected 
    14172 
    14173 > color sel magenta
    14174 
    14175 > select clear
    14176 
    14177 > show #19 models
    14178 
    14179 > hide #21 models
    14180 
    14181 > save "/Users/taic/OneDrive - National Institutes of
    14182 > Health/MacBookPro021/project/DebbieH/MotB.1_IbpA/MotB.1_IbpA.cxs"
    14183 
    14184 ——— End of log from Thu Sep 25 11:20:40 2025 ———
    14185 
    14186 opened ChimeraX session 
    14187 
    14188 > show #!8 models
    14189 
    14190 > hide #!8 models
    14191 
    14192 > show #!9 models
    14193 
    14194 > show #10 models
    14195 
    14196 > show #11 models
    14197 
    14198 > show #!12 models
    14199 
    14200 > show #!18 models
    14201 
    14202 > show #21 models
    14203 
    14204 > show #22 models
    14205 
    14206 > show #23 models
    14207 
    14208 > show #24 models
    14209 
    14210 > delete atoms #9-12,18-19,21-24
    14211 
    14212 > delete bonds #9-12,18-19,21-24
    14213 
    14214 > show #!13 models
    14215 
    14216 > ui tool show "Color Actions"
    14217 
    14218 > show #!14 models
    14219 
    14220 > hide #!13 models
    14221 
    14222 > hide #!14 surfaces
    14223 
    14224 > show #15 models
    14225 
    14226 > hide #!14 models
    14227 
    14228 > show #!8 models
    14229 
    14230 > hide #!8 models
    14231 
    14232 > show #!13 models
    14233 
    14234 > hide #15 models
    14235 
    14236 > hide #!13 models
    14237 
    14238 > show #!6 models
    14239 
    14240 > hide #!6 surfaces
    14241 
    14242 > show #!13 models
    14243 
    14244 > hide #!6 models
    14245 
    14246 > ui tool show "Side View"
    14247 
    14248 > select #13/L:31
    14249 
    14250 20 atoms, 21 bonds, 1 residue, 1 model selected 
    14251 
    14252 > show sel atoms
    14253 
    14254 > nucleotides sel atoms
    14255 
    14256 > style nucleic & sel stick
    14257 
    14258 Changed 20 atom styles 
    14259 
    14260 > select #13/M:158
    14261 
    14262 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14263 
    14264 > show sel atoms
    14265 
    14266 > hide sel cartoons
    14267 
    14268 > show sel cartoons
    14269 
    14270 > nucleotides sel atoms
    14271 
    14272 > style nucleic & sel stick
    14273 
    14274 Changed 21 atom styles 
    14275 
    14276 > show #!6 models
    14277 
    14278 > hide #!13 models
    14279 
    14280 > show #!13 models
    14281 
    14282 > hide #!6 models
    14283 
    14284 > show #!6 models
    14285 
    14286 > hide #!13 models
    14287 
    14288 > show #!8 models
    14289 
    14290 > hide #!8 models
    14291 
    14292 > show #!13 models
    14293 
    14294 > hide #!6 models
    14295 
    14296 > select #13/M:156
    14297 
    14298 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14299 
    14300 > nucleotides sel atoms
    14301 
    14302 > style nucleic & sel stick
    14303 
    14304 Changed 21 atom styles 
    14305 
    14306 > show sel atoms
    14307 
    14308 > select #13/M:158
    14309 
    14310 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14311 
    14312 > hide sel atoms
    14313 
    14314 > select clear
    14315 
    14316 > select add #13/L:32
    14317 
    14318 22 atoms, 24 bonds, 1 residue, 1 model selected 
    14319 
    14320 > select add #13/L:33
    14321 
    14322 42 atoms, 45 bonds, 2 residues, 2 models selected 
    14323 
    14324 > select add #13/L:34
    14325 
    14326 61 atoms, 65 bonds, 3 residues, 2 models selected 
    14327 
    14328 > select add #13/L:35
    14329 
    14330 82 atoms, 88 bonds, 4 residues, 2 models selected 
    14331 
    14332 > select add #13/L:36
    14333 
    14334 104 atoms, 112 bonds, 5 residues, 2 models selected 
    14335 
    14336 > select add #13/L:37
    14337 
    14338 123 atoms, 132 bonds, 6 residues, 2 models selected 
    14339 
    14340 > select add #13/M:156
    14341 
    14342 144 atoms, 155 bonds, 7 residues, 2 models selected 
    14343 
    14344 > select add #13/M:155
    14345 
    14346 163 atoms, 175 bonds, 8 residues, 3 models selected 
    14347 
    14348 > select add #13/M:153
    14349 
    14350 185 atoms, 199 bonds, 9 residues, 3 models selected 
    14351 
    14352 > select add #13/M:152
    14353 
    14354 205 atoms, 220 bonds, 10 residues, 3 models selected 
    14355 
    14356 > select add #13/M:151
    14357 
    14358 224 atoms, 240 bonds, 11 residues, 3 models selected 
    14359 
    14360 > select add #13/M:150
    14361 
    14362 246 atoms, 264 bonds, 12 residues, 3 models selected 
    14363 
    14364 > nucleotides sel atoms
    14365 
    14366 > style nucleic & sel stick
    14367 
    14368 Changed 246 atom styles 
    14369 
    14370 > show sel atoms
    14371 
    14372 > select clear
    14373 
    14374 Drag select of 2 residues 
    14375 
    14376 > select #13/L:33@C1'
    14377 
    14378 1 atom, 1 residue, 1 model selected 
    14379 
    14380 > select clear
    14381 
    14382 > show #!6 models
    14383 
    14384 > hide #!6 models
    14385 
    14386 > show #!6 models
    14387 
    14388 > hide #!13 models
    14389 
    14390 > show #!13 models
    14391 
    14392 > hide #!6 models
    14393 
    14394 > show #!6 models
    14395 
    14396 > hide #!6 models
    14397 
    14398 > show #!6 models
    14399 
    14400 > hide #!13 models
    14401 
    14402 > show #!13 models
    14403 
    14404 > hide #!6 models
    14405 
    14406 > show #!6 models
    14407 
    14408 > hide #!13 models
    14409 
    14410 > show #!13 models
    14411 
    14412 > hide #!6 models
    14413 
    14414 > select #13/M
    14415 
    14416 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    14417 
    14418 > color sel light cyan
    14419 
    14420 > select #13/M:146
    14421 
    14422 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14423 
    14424 > select clear
    14425 
    14426 > select #13/M
    14427 
    14428 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    14429 
    14430 > color sel honeydew
    14431 
    14432 > color sel alice blue
    14433 
    14434 > color sel powder blue
    14435 
    14436 > color sel alice blue
    14437 
    14438 > select #13/F:79
    14439 
    14440 11 atoms, 10 bonds, 1 residue, 1 model selected 
    14441 
    14442 > show #!6 models
    14443 
    14444 > hide #!13 models
    14445 
    14446 > show #!13 models
    14447 
    14448 > hide #!6 models
    14449 
    14450 > show #7 models
    14451 
    14452 > hide #!13 models
    14453 
    14454 > hide #7 models
    14455 
    14456 > show #!6 models
    14457 
    14458 > show #!13 models
    14459 
    14460 > hide #!6 models
    14461 
    14462 > show #!6 models
    14463 
    14464 > hide #!13 models
    14465 
    14466 > show #!13 models
    14467 
    14468 > hide #!6 models
    14469 
    14470 > select add #13/M:136
    14471 
    14472 32 atoms, 33 bonds, 2 residues, 2 models selected 
    14473 
    14474 > select add #13/M:137
    14475 
    14476 53 atoms, 56 bonds, 3 residues, 3 models selected 
    14477 
    14478 > select add #13/M:138
    14479 
    14480 75 atoms, 80 bonds, 4 residues, 3 models selected 
    14481 
    14482 > select add #13/M:139
    14483 
    14484 95 atoms, 101 bonds, 5 residues, 3 models selected 
    14485 
    14486 > select add #13/M:140
    14487 
    14488 116 atoms, 124 bonds, 6 residues, 3 models selected 
    14489 
    14490 > select add #13/M:141
    14491 
    14492 135 atoms, 144 bonds, 7 residues, 3 models selected 
    14493 
    14494 > select add #13/M:143
    14495 
    14496 157 atoms, 168 bonds, 8 residues, 3 models selected 
    14497 
    14498 > select add #13/M:144
    14499 
    14500 177 atoms, 189 bonds, 9 residues, 3 models selected 
    14501 
    14502 > select add #13/M:142
    14503 
    14504 198 atoms, 212 bonds, 10 residues, 3 models selected 
    14505 
    14506 > select subtract #13/M:144
    14507 
    14508 178 atoms, 191 bonds, 9 residues, 3 models selected 
    14509 
    14510 > label (#!13 & sel) attribute label_one_letter_code
    14511 
    14512 > label height 3
    14513 
    14514 > select clear
    14515 
    14516 > select #13/F:79
    14517 
    14518 11 atoms, 10 bonds, 1 residue, 1 model selected 
    14519 
    14520 > ~label (#!13 & sel) residues
    14521 
    14522 > select clear
    14523 
    14524 > select #13/M:136
    14525 
    14526 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14527 
    14528 > ~label (#!13 & sel) residues
    14529 
    14530 > select #13/L:133
    14531 
    14532 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14533 
    14534 > show #!6 models
    14535 
    14536 > hide #!13 models
    14537 
    14538 > show #!8 models
    14539 
    14540 > hide #!8 models
    14541 
    14542 > show #!13 models
    14543 
    14544 > hide #!6 models
    14545 
    14546 > select clear
    14547 
    14548 > show #!6 models
    14549 
    14550 > hide #!13 models
    14551 
    14552 > show #!13 models
    14553 
    14554 > hide #!6 models
    14555 
    14556 > show #!6 models
    14557 
    14558 > hide #!13 models
    14559 
    14560 > show #!13 models
    14561 
    14562 > hide #!6 models
    14563 
    14564 > save "/Users/taic/OneDrive - National Institutes of
    14565 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
    14566 
    14567 > save "/Users/taic/OneDrive - National Institutes of
    14568 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA1.AF3.png" width
    14569 > 922 height 681 supersample 4 transparentBackground true
    14570 
    14571 > select #13/M:155
    14572 
    14573 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14574 
    14575 > select #13/M:154
    14576 
    14577 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14578 
    14579 > show sel atoms
    14580 
    14581 > nucleotides sel atoms
    14582 
    14583 > style nucleic & sel stick
    14584 
    14585 Changed 21 atom styles 
    14586 
    14587 > select clear
    14588 
    14589 [Repeated 1 time(s)]
    14590 
    14591 > save "/Users/taic/OneDrive - National Institutes of
    14592 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3.FOXA1bindingsite.png"
    14593 > width 922 height 681 supersample 4 transparentBackground true
    14594 
    14595 > ui tool show "Color Actions"
    14596 
    14597 Drag select of 6 residues 
    14598 
    14599 > select clear
    14600 
    14601 > show #!6 models
    14602 
    14603 > hide #!13 models
    14604 
    14605 > select #6/O
    14606 
    14607 856 atoms, 883 bonds, 102 residues, 1 model selected 
    14608 
    14609 > show sel surfaces
    14610 
    14611 > hide sel surfaces
    14612 
    14613 > select clear
    14614 
    14615 > show #!8 models
    14616 
    14617 > hide #!8 models
    14618 
    14619 > show #!13 models
    14620 
    14621 > hide #!6 models
    14622 
    14623 > select #13/I:169-268
    14624 
    14625 837 atoms, 863 bonds, 100 residues, 1 model selected 
    14626 
    14627 > show sel surfaces
    14628 
    14629 > select #13/M:60
    14630 
    14631 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14632 
    14633 > show #!6 models
    14634 
    14635 > hide #!13 models
    14636 
    14637 > select #6/O
    14638 
    14639 856 atoms, 883 bonds, 102 residues, 1 model selected 
    14640 
    14641 > show sel surfaces
    14642 
    14643 > show #!13 models
    14644 
    14645 > hide #!6 models
    14646 
    14647 > show #!6 models
    14648 
    14649 > hide #!13 models
    14650 
    14651 > select clear
    14652 
    14653 > show #!13 models
    14654 
    14655 > hide #!6 models
    14656 
    14657 > show #!6 models
    14658 
    14659 > hide #!13 models
    14660 
    14661 > show #!13 models
    14662 
    14663 > hide #!6 models
    14664 
    14665 > show #!6 models
    14666 
    14667 > hide #!13 models
    14668 
    14669 > show #!13 models
    14670 
    14671 > hide #!6 models
    14672 
    14673 > hide #!13 surfaces
    14674 
    14675 > show #!6 models
    14676 
    14677 > hide #!6,13 surfaces
    14678 
    14679 > hide #!13 models
    14680 
    14681 > select #6/O
    14682 
    14683 856 atoms, 883 bonds, 102 residues, 1 model selected 
    14684 
    14685 > show sel surfaces
    14686 
    14687 > ui tool show "Color Actions"
    14688 
    14689 > select #6/I:40
    14690 
    14691 22 atoms, 24 bonds, 1 residue, 1 model selected 
    14692 
    14693 > color sel silver
    14694 
    14695 > color sel gray
    14696 
    14697 > select clear
    14698 
    14699 > select #6/I:40
    14700 
    14701 22 atoms, 24 bonds, 1 residue, 1 model selected 
    14702 
    14703 > select clear
    14704 
    14705 > select #6/I:40
    14706 
    14707 22 atoms, 24 bonds, 1 residue, 1 model selected 
    14708 
    14709 > color sel light steel blue
    14710 
    14711 > color sel light slate gray
    14712 
    14713 > select clear
    14714 
    14715 > hide #!6 surfaces
    14716 
    14717 > select #6/O#13/I:168-269
    14718 
    14719 1712 atoms, 1766 bonds, 204 residues, 2 models selected 
    14720 
    14721 > show #!13 models
    14722 
    14723 > ui tool show Matchmaker
    14724 
    14725 > matchmaker #!13 & sel to #6 & sel
    14726 
    14727 Parameters 
    14728 --- 
    14729 Chain pairing | bb 
    14730 Alignment algorithm | Needleman-Wunsch 
    14731 Similarity matrix | BLOSUM-62 
    14732 SS fraction | 0.3 
    14733 Gap open (HH/SS/other) | 18/18/6 
    14734 Gap extend | 1 
    14735 SS matrix |  |  | H | S | O 
    14736 ---|---|---|--- 
    14737 H | 6 | -9 | -6 
    14738 S |  | 6 | -6 
    14739 O |  |  | 4 
    14740 Iteration cutoff | 2 
    14741  
    14742 Matchmaker 8vg1, chain O (#6) with
    14743 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
    14744 alignment score = 522.2 
    14745 RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
    14746 1.960) 
    14747  
    14748 
    14749 > matchmaker #!13 & sel to #6 & sel
    14750 
    14751 Parameters 
    14752 --- 
    14753 Chain pairing | bb 
    14754 Alignment algorithm | Needleman-Wunsch 
    14755 Similarity matrix | BLOSUM-62 
    14756 SS fraction | 0.3 
    14757 Gap open (HH/SS/other) | 18/18/6 
    14758 Gap extend | 1 
    14759 SS matrix |  |  | H | S | O 
    14760 ---|---|---|--- 
    14761 H | 6 | -9 | -6 
    14762 S |  | 6 | -6 
    14763 O |  |  | 4 
    14764 Iteration cutoff | 2 
    14765  
    14766 Matchmaker 8vg1, chain O (#6) with
    14767 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
    14768 alignment score = 522.2 
    14769 RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
    14770 1.960) 
    14771  
    14772 
    14773 > ui tool show Matchmaker
    14774 
    14775 > matchmaker #!13 & sel to #6 & sel
    14776 
    14777 Parameters 
    14778 --- 
    14779 Chain pairing | bb 
    14780 Alignment algorithm | Needleman-Wunsch 
    14781 Similarity matrix | BLOSUM-62 
    14782 SS fraction | 0.3 
    14783 Gap open (HH/SS/other) | 18/18/6 
    14784 Gap extend | 1 
    14785 SS matrix |  |  | H | S | O 
    14786 ---|---|---|--- 
    14787 H | 6 | -9 | -6 
    14788 S |  | 6 | -6 
    14789 O |  |  | 4 
    14790 Iteration cutoff | 2 
    14791  
    14792 Matchmaker 8vg1, chain O (#6) with
    14793 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
    14794 alignment score = 522.2 
    14795 RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
    14796 1.960) 
    14797  
    14798 
    14799 > matchmaker #!13 & sel to #6 & sel
    14800 
    14801 Parameters 
    14802 --- 
    14803 Chain pairing | bb 
    14804 Alignment algorithm | Needleman-Wunsch 
    14805 Similarity matrix | BLOSUM-62 
    14806 SS fraction | 0.3 
    14807 Gap open (HH/SS/other) | 18/18/6 
    14808 Gap extend | 1 
    14809 SS matrix |  |  | H | S | O 
    14810 ---|---|---|--- 
    14811 H | 6 | -9 | -6 
    14812 S |  | 6 | -6 
    14813 O |  |  | 4 
    14814 Iteration cutoff | 2 
    14815  
    14816 Matchmaker 8vg1, chain O (#6) with
    14817 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
    14818 alignment score = 522.2 
    14819 RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
    14820 1.960) 
    14821  
    14822 
    14823 > hide #!13 models
    14824 
    14825 > select clear
    14826 
    14827 [Repeated 4 time(s)]
    14828 
    14829 > show #!13 models
    14830 
    14831 > hide #!6 models
    14832 
    14833 > select #6/O#13/J:269-321
    14834 
    14835 1270 atoms, 1303 bonds, 155 residues, 2 models selected 
    14836 
    14837 > show #!6 models
    14838 
    14839 > hide #!13 models
    14840 
    14841 > select #6/T#13/J:269-321
    14842 
    14843 829 atoms, 840 bonds, 4 pseudobonds, 107 residues, 3 models selected 
    14844 
    14845 > show #!13 models
    14846 
    14847 > ui tool show Matchmaker
    14848 
    14849 > matchmaker #!13 & sel to #6 & sel
    14850 
    14851 Parameters 
    14852 --- 
    14853 Chain pairing | bb 
    14854 Alignment algorithm | Needleman-Wunsch 
    14855 Similarity matrix | BLOSUM-62 
    14856 SS fraction | 0.3 
    14857 Gap open (HH/SS/other) | 18/18/6 
    14858 Gap extend | 1 
    14859 SS matrix |  |  | H | S | O 
    14860 ---|---|---|--- 
    14861 H | 6 | -9 | -6 
    14862 S |  | 6 | -6 
    14863 O |  |  | 4 
    14864 Iteration cutoff | 2 
    14865  
    14866 Matchmaker 8vg1, chain T (#6) with
    14867 fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain J (#13), sequence
    14868 alignment score = 265 
    14869 RMSD between 43 pruned atom pairs is 0.539 angstroms; (across all 53 pairs:
    14870 10.483) 
    14871  
    14872 
    14873 > select clear
    14874 
    14875 > hide #!13 models
    14876 
    14877 > show #!13 models
    14878 
    14879 > hide #!6 models
    14880 
    14881 > show #!6 models
    14882 
    14883 > hide #!13 models
    14884 
    14885 > show #!13 models
    14886 
    14887 > hide #!6 models
    14888 
    14889 > show #!6 models
    14890 
    14891 > hide #!13 models
    14892 
    14893 > show #!13 models
    14894 
    14895 > hide #!6 models
    14896 
    14897 > show #!6 models
    14898 
    14899 > hide #!6 models
    14900 
    14901 > select #13/M:138
    14902 
    14903 22 atoms, 24 bonds, 1 residue, 1 model selected 
    14904 
    14905 > select #13/M:139
    14906 
    14907 20 atoms, 21 bonds, 1 residue, 1 model selected 
    14908 
    14909 > select add #13/M:138
    14910 
    14911 42 atoms, 45 bonds, 2 residues, 2 models selected 
    14912 
    14913 > select add #13/M:140
    14914 
    14915 63 atoms, 68 bonds, 3 residues, 2 models selected 
    14916 
    14917 > select add #13/M:141
    14918 
    14919 82 atoms, 88 bonds, 4 residues, 2 models selected 
    14920 
    14921 > select add #13/J:226
    14922 
    14923 89 atoms, 95 bonds, 5 residues, 2 models selected 
    14924 
    14925 > select add #13/M:142
    14926 
    14927 110 atoms, 118 bonds, 6 residues, 3 models selected 
    14928 
    14929 > select add #13/M:143
    14930 
    14931 132 atoms, 142 bonds, 7 residues, 3 models selected 
    14932 
    14933 > ~label (#!13 & sel) residues
    14934 
    14935 > select #13/M:56
    14936 
    14937 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14938 
    14939 > select #13/M:137
    14940 
    14941 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14942 
    14943 > ~label (#!13 & sel) residues
    14944 
    14945 > select clear
    14946 
    14947 > show #7 models
    14948 
    14949 > hide #7 models
    14950 
    14951 > show #!6 models
    14952 
    14953 > hide #!6 models
    14954 
    14955 > show #!6 models
    14956 
    14957 > hide #!6 models
    14958 
    14959 > show #!6 models
    14960 
    14961 > hide #!13 models
    14962 
    14963 > select #6/J:133
    14964 
    14965 21 atoms, 23 bonds, 1 residue, 1 model selected 
    14966 
    14967 > select #6/J:132
    14968 
    14969 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14970 
    14971 > select add #6/J:131
    14972 
    14973 39 atoms, 41 bonds, 2 residues, 2 models selected 
    14974 
    14975 > select add #6/J:130
    14976 
    14977 60 atoms, 64 bonds, 3 residues, 2 models selected 
    14978 
    14979 > select add #6/J:129
    14980 
    14981 80 atoms, 85 bonds, 4 residues, 2 models selected 
    14982 
    14983 > show sel atoms
    14984 
    14985 > select clear
    14986 
    14987 > select ::name="ZN"
    14988 
    14989 12 atoms, 12 residues, 12 models selected 
    14990 
    14991 > show sel & #!6 atoms
    14992 
    14993 > select clear
    14994 
    14995 > select add #6/T:274
    14996 
    14997 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14998 
    14999 > select add #6/T:295
    15000 
    15001 12 atoms, 10 bonds, 2 residues, 2 models selected 
    15002 
    15003 > select add #6/T:292
    15004 
    15005 18 atoms, 15 bonds, 3 residues, 2 models selected 
    15006 
    15007 > select add #6/T:271
    15008 
    15009 24 atoms, 20 bonds, 4 residues, 2 models selected 
    15010 
    15011 > show sel atoms
    15012 
    15013 > select clear
    15014 
    15015 > show #!13 models
    15016 
    15017 > hide #!6 models
    15018 
    15019 > select ::name="ZN"
    15020 
    15021 12 atoms, 12 residues, 12 models selected 
    15022 
    15023 > show sel & #!13 atoms
    15024 
    15025 [Repeated 1 time(s)]
    15026 
    15027 > select ::name="ZN"
    15028 
    15029 12 atoms, 12 residues, 12 models selected 
    15030 
    15031 > select ::name="ZN"
    15032 
    15033 12 atoms, 12 residues, 12 models selected 
    15034 
    15035 > show sel & #!13 atoms
    15036 
    15037 > style sel & #!13 sphere
    15038 
    15039 Changed 1 atom style 
    15040 
    15041 > style sel & #!13 sphere
    15042 
    15043 Changed 1 atom style 
    15044 
    15045 > style sel & #!13 sphere
    15046 
    15047 Changed 1 atom style 
    15048 
    15049 > style sel & #!13 sphere
    15050 
    15051 Changed 1 atom style 
    15052 
    15053 > style sel & #!13 sphere
    15054 
    15055 Changed 1 atom style 
    15056 
    15057 > style sel & #!13 sphere
    15058 
    15059 Changed 1 atom style 
    15060 
    15061 > style sel & #!13 sphere
    15062 
    15063 Changed 1 atom style 
    15064 
    15065 > save "/Users/taic/OneDrive - National Institutes of
    15066 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
    15067 
    15068 ——— End of log from Mon Sep 29 00:14:22 2025 ———
    15069 
    15070 opened ChimeraX session 
    15071 
    15072 > show #2 models
    15073 
    15074 > hide #!13 models
    15075 
    15076 > show #!6 models
    15077 
    15078 > hide #2 models
    15079 
    15080 > show #2 models
    15081 
    15082 > hide #2 models
    15083 
    15084 > show #2 models
    15085 
    15086 > hide #!6 models
    15087 
    15088 > select #6/T#2/J:662-714
    15089 
    15090 829 atoms, 840 bonds, 4 pseudobonds, 107 residues, 3 models selected 
    15091 
    15092 > show #!6 models
    15093 
    15094 > ui tool show Matchmaker
    15095 
    15096 > matchmaker #2 & sel to #6 & sel
    15097 
    15098 Parameters 
    15099 --- 
    15100 Chain pairing | bb 
    15101 Alignment algorithm | Needleman-Wunsch 
    15102 Similarity matrix | BLOSUM-62 
    15103 SS fraction | 0.3 
    15104 Gap open (HH/SS/other) | 18/18/6 
    15105 Gap extend | 1 
    15106 SS matrix |  |  | H | S | O 
    15107 ---|---|---|--- 
    15108 H | 6 | -9 | -6 
    15109 S |  | 6 | -6 
    15110 O |  |  | 4 
    15111 Iteration cutoff | 2 
    15112  
    15113 Matchmaker 8vg1, chain T (#6) with
    15114 fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain J (#2), sequence
    15115 alignment score = 274 
    15116 RMSD between 43 pruned atom pairs is 0.482 angstroms; (across all 53 pairs:
    15117 7.477) 
    15118  
    15119 
    15120 > hide #!6 models
    15121 
    15122 > select #2/J:662-714
    15123 
    15124 414 atoms, 420 bonds, 53 residues, 1 model selected 
    15125 
    15126 > select #2/J:393-900
    15127 
    15128 3133 atoms, 3217 bonds, 443 residues, 1 model selected 
    15129 
    15130 > ui tool show "Color Actions"
    15131 
    15132 > color sel light sky blue
    15133 
    15134 > color sel light blue
    15135 
    15136 > color sel pale turquoise
    15137 
    15138 > select #2/J:662-714
    15139 
    15140 414 atoms, 420 bonds, 53 residues, 1 model selected 
    15141 
    15142 > color sel deep sky blue
    15143 
    15144 > select clear
    15145 
    15146 > select #2/L
    15147 
    15148 3811 atoms, 4270 bonds, 186 residues, 1 model selected 
    15149 
    15150 > color sel light gray
    15151 
    15152 > select clear
    15153 
    15154 > select add #2/L:58
    15155 
    15156 21 atoms, 23 bonds, 1 residue, 1 model selected 
    15157 
    15158 > select subtract #2/L:58
    15159 
    15160 Nothing selected 
    15161 
    15162 > select add #2/L:58
    15163 
    15164 21 atoms, 23 bonds, 1 residue, 1 model selected 
    15165 
    15166 > select add #2/L:57
    15167 
    15168 41 atoms, 45 bonds, 2 residues, 1 model selected 
    15169 
    15170 > select add #2/L:56
    15171 
    15172 62 atoms, 67 bonds, 3 residues, 1 model selected 
    15173 
    15174 > select add #2/L:55
    15175 
    15176 84 atoms, 91 bonds, 4 residues, 1 model selected 
    15177 
    15178 > color sel bynucleotide
    15179 
    15180 > select clear
    15181 
    15182 > select #2/I
    15183 
    15184 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    15185 
    15186 > color sel lavender
    15187 
    15188 > select clear
    15189 
    15190 > select #2/J:609-646
    15191 
    15192 292 atoms, 299 bonds, 38 residues, 1 model selected 
    15193 
    15194 > color sel light green
    15195 
    15196 > select clear
    15197 
    15198 > select #2/J:609-646
    15199 
    15200 292 atoms, 299 bonds, 38 residues, 1 model selected 
    15201 
    15202 > color sel lawn green
    15203 
    15204 > color sel chartreuse
    15205 
    15206 > color sel lawn green
    15207 
    15208 > color sel lime
    15209 
    15210 > color sel chartreuse
    15211 
    15212 > color sel lawn green
    15213 
    15214 > select clear
    15215 
    15216 > show #!6 models
    15217 
    15218 > hide #2 models
    15219 
    15220 > show #2 models
    15221 
    15222 > hide #!6 models
    15223 
    15224 > show #!6 models
    15225 
    15226 > hide #!6 models
    15227 
    15228 > show #!6 models
    15229 
    15230 > hide #2 models
    15231 
    15232 > show #2 models
    15233 
    15234 > hide #!6 models
    15235 
    15236 > ui tool show "Side View"
    15237 
    15238 > show #!6 models
    15239 
    15240 > hide #2 models
    15241 
    15242 > show #2 models
    15243 
    15244 > hide #!6 models
    15245 
    15246 > select #2/J:664
    15247 
    15248 6 atoms, 5 bonds, 1 residue, 1 model selected 
    15249 
    15250 > select add #2/J:667
    15251 
    15252 12 atoms, 10 bonds, 2 residues, 1 model selected 
    15253 
    15254 > select add #2/J:688
    15255 
    15256 18 atoms, 15 bonds, 3 residues, 1 model selected 
    15257 
    15258 > show sel atoms
    15259 
    15260 > nucleotides sel atoms
    15261 
    15262 > style nucleic & sel stick
    15263 
    15264 Changed 0 atom styles 
    15265 
    15266 > nucleotides sel atoms
    15267 
    15268 > style nucleic & sel stick
    15269 
    15270 Changed 0 atom styles 
    15271 
    15272 > hide sel atoms
    15273 
    15274 > nucleotides sel atoms
    15275 
    15276 > style nucleic & sel stick
    15277 
    15278 Changed 0 atom styles 
    15279 
    15280 > show sel atoms
    15281 
    15282 > style sel sphere
    15283 
    15284 Changed 18 atom styles 
    15285 
    15286 > style sel ball
    15287 
    15288 Changed 18 atom styles 
    15289 
    15290 > color sel yellow
    15291 
    15292 > select clear
    15293 
    15294 > select #2/J:685
    15295 
    15296 6 atoms, 5 bonds, 1 residue, 1 model selected 
    15297 
    15298 > style sel ball
    15299 
    15300 Changed 6 atom styles 
    15301 
    15302 > show sel atoms
    15303 
    15304 > color sel yellow
    15305 
    15306 > select clear
    15307 
    15308 > show #!6 models
    15309 
    15310 > hide #2 models
    15311 
    15312 > show #2 models
    15313 
    15314 > hide #!6 models
    15315 
    15316 > show #!6 models
    15317 
    15318 > hide #!6 models
    15319 
    15320 > show #!6 models
    15321 
    15322 > hide #2 models
    15323 
    15324 > show #2 models
    15325 
    15326 > hide #!6 models
    15327 
    15328 > save "/Users/taic/OneDrive - National Institutes of
    15329 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3.MBP-
    15330 > GATA4.zoom.png" width 922 height 681 supersample 4 transparentBackground
    15331 > true
    15332 
    15333 > save "/Users/taic/OneDrive - National Institutes of
    15334 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3.MBP-
    15335 > GATA4-ZnFs.png" width 922 height 681 supersample 4 transparentBackground
    15336 > true
    15337 
    15338 > select #6/A/B/C/D/E/F/G/H#2/A/B/C/D/E/F/G/H
    15339 
    15340 13860 atoms, 14040 bonds, 1765 residues, 2 models selected 
    15341 
    15342 > show #!6 models
    15343 
    15344 > ui tool show Matchmaker
    15345 
    15346 > matchmaker #2 & sel to #6 & sel
    15347 
    15348 Parameters 
    15349 --- 
    15350 Chain pairing | bb 
    15351 Alignment algorithm | Needleman-Wunsch 
    15352 Similarity matrix | BLOSUM-62 
    15353 SS fraction | 0.3 
    15354 Gap open (HH/SS/other) | 18/18/6 
    15355 Gap extend | 1 
    15356 SS matrix |  |  | H | S | O 
    15357 ---|---|---|--- 
    15358 H | 6 | -9 | -6 
    15359 S |  | 6 | -6 
    15360 O |  |  | 4 
    15361 Iteration cutoff | 2 
    15362  
    15363 Matchmaker 8vg1, chain E (#6) with
    15364 fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain A (#2), sequence
    15365 alignment score = 628.4 
    15366 RMSD between 97 pruned atom pairs is 0.242 angstroms; (across all 97 pairs:
    15367 0.242) 
    15368  
    15369 
    15370 > select #2/J:529
    15371 
    15372 4 atoms, 3 bonds, 1 residue, 1 model selected 
    15373 
    15374 > hide #2 models
    15375 
    15376 > show #2 models
    15377 
    15378 > hide #!6 models
    15379 
    15380 > select #2/A/B/C/D/E/F/G/H
    15381 
    15382 7708 atoms, 7806 bonds, 990 residues, 1 model selected 
    15383 
    15384 > select ~sel & ##selected
    15385 
    15386 17314 atoms, 18505 bonds, 1686 residues, 1 model selected 
    15387 
    15388 > hide sel cartoons
    15389 
    15390 > hide sel atoms
    15391 
    15392 > show #!6 models
    15393 
    15394 > select #6/A/B/C/D/E/F/G/H
    15395 
    15396 6152 atoms, 6234 bonds, 775 residues, 1 model selected 
    15397 
    15398 > select ~sel & ##selected
    15399 
    15400 8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected 
    15401 
    15402 > hide sel cartoons
    15403 
    15404 > hide sel atoms
    15405 
    15406 > hide #2 models
    15407 
    15408 > show #2 models
    15409 
    15410 > hide #!6 models
    15411 
    15412 > select #2/B
    15413 
    15414 800 atoms, 808 bonds, 103 residues, 1 model selected 
    15415 
    15416 > color sel medium aquamarine
    15417 
    15418 > color sel light green
    15419 
    15420 > color sel pale green
    15421 
    15422 > select clear
    15423 
    15424 > select #2/B/F
    15425 
    15426 1600 atoms, 1616 bonds, 206 residues, 1 model selected 
    15427 
    15428 > color sel pale green
    15429 
    15430 > select clear
    15431 
    15432 > show #!6 models
    15433 
    15434 > select #6/A/B/C/D/E/F/G/H#2/A/B/C/D/E/F/G/H
    15435 
    15436 13860 atoms, 14040 bonds, 1765 residues, 2 models selected 
    15437 
    15438 > ui tool show Matchmaker
    15439 
    15440 > matchmaker #2 & sel to #6 & sel
    15441 
    15442 Parameters 
    15443 --- 
    15444 Chain pairing | bb 
    15445 Alignment algorithm | Needleman-Wunsch 
    15446 Similarity matrix | BLOSUM-62 
    15447 SS fraction | 0.3 
    15448 Gap open (HH/SS/other) | 18/18/6 
    15449 Gap extend | 1 
    15450 SS matrix |  |  | H | S | O 
    15451 ---|---|---|--- 
    15452 H | 6 | -9 | -6 
    15453 S |  | 6 | -6 
    15454 O |  |  | 4 
    15455 Iteration cutoff | 2 
    15456  
    15457 Matchmaker 8vg1, chain E (#6) with
    15458 fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain A (#2), sequence
    15459 alignment score = 628.4 
    15460 RMSD between 97 pruned atom pairs is 0.242 angstroms; (across all 97 pairs:
    15461 0.242) 
    15462  
    15463 
    15464 > select clear
    15465 
    15466 > hide #2 models
    15467 
    15468 > select #6/B
    15469 
    15470 662 atoms, 669 bonds, 83 residues, 1 model selected 
    15471 
    15472 > color sel forest green
    15473 
    15474 > color sel green
    15475 
    15476 > select clear
    15477 
    15478 > show #2 models
    15479 
    15480 > select clear
    15481 
    15482 > hide #2 models
    15483 
    15484 > show #2 models
    15485 
    15486 > save "/Users/taic/OneDrive - National Institutes of
    15487 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.histones.vs.AF3.png"
    15488 > width 922 height 681 supersample 4 transparentBackground true
    15489 
    15490 > show #2#!6 cartoons
    15491 
    15492 > hide #2 models
    15493 
    15494 > show #2 models
    15495 
    15496 > hide #!6 models
    15497 
    15498 > select #13/I
    15499 
    15500 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    15501 
    15502 > show #2 cartoons
    15503 
    15504 > select #13/J
    15505 
    15506 3128 atoms, 3212 bonds, 442 residues, 1 model selected 
    15507 
    15508 > select #13/J
    15509 
    15510 3128 atoms, 3212 bonds, 442 residues, 1 model selected 
    15511 
    15512 > select #2/I/J
    15513 
    15514 9685 atoms, 9949 bonds, 1313 residues, 1 model selected 
    15515 
    15516 > show sel cartoons
    15517 
    15518 > select clear
    15519 
    15520 > select #2/I
    15521 
    15522 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    15523 
    15524 > select #2/I:
    15525 
    15526 Expected an objects specifier or a keyword 
    15527 
    15528 > color sel lavender
    15529 
    15530 > select clear
    15531 
    15532 > select #2/IL
    15533 
    15534 Nothing selected 
    15535 
    15536 > color light gray
    15537 
    15538 > undo
    15539 
    15540 > select #2/L
    15541 
    15542 3811 atoms, 4270 bonds, 186 residues, 1 model selected 
    15543 
    15544 > color sel light gray
    15545 
    15546 > select clear
    15547 
    15548 > select #2/I:
    15549 
    15550 Expected an objects specifier or a keyword 
    15551 
    15552 > select #2/I
    15553 
    15554 3502 atoms, 3604 bonds, 478 residues, 1 model selected 
    15555 
    15556 > select #2/I:168-269
    15557 
    15558 856 atoms, 883 bonds, 102 residues, 1 model selected 
    15559 
    15560 > select clear
    15561 
    15562 > select #2/I:168-269
    15563 
    15564 856 atoms, 883 bonds, 102 residues, 1 model selected 
    15565 
    15566 > color sel medium purple
    15567 
    15568 > select clear
    15569 
    15570 > show #!6 models
    15571 
    15572 > hide #2 models
    15573 
    15574 > show #2 models
    15575 
    15576 > hide #!6 models
    15577 
    15578 > save "/Users/taic/OneDrive - National Institutes of
    15579 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
    15580 
    15581 > show #!6 models
    15582 
    15583 > hide #2 models
    15584 
    15585 > show #2 models
    15586 
    15587 > hide #!6 models
    15588 
    15589 > ui tool show "Show Sequence Viewer"
    15590 
    15591 > sequence chain #2/L
    15592 
    15593 Alignment identifier is 2/L 
    15594 
    15595 > sequence chain #2/M
    15596 
    15597 Alignment identifier is 2/M 
    15598 
    15599 > ui tool show "Show Sequence Viewer"
    15600 
    15601 > sequence chain #2/L
    15602 
    15603 Destroying pre-existing alignment with identifier 2/L 
    15604 Alignment identifier is 2/L 
    15605 
    15606 > select #2/L
    15607 
    15608 3811 atoms, 4270 bonds, 186 residues, 1 model selected 
    15609 
    15610 > color sel gray
    15611 
    15612 > select #2/M
    15613 
    15614 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    15615 
    15616 > color sel light gray
    15617 
    15618 > select clear
    15619 
    15620 > select #2/M
    15621 
    15622 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    15623 
    15624 > color sel light steel blue
    15625 
    15626 > select clear
    15627 
    15628 > select #2/M
    15629 
    15630 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    15631 
    15632 > color sel gainsboro
    15633 
    15634 > select clear
    15635 
    15636 > select #2/M
    15637 
    15638 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    15639 
    15640 > color sel white smoke
    15641 
    15642 > select clear
    15643 
    15644 > select #2/M
    15645 
    15646 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    15647 
    15648 > color sel light gray
    15649 
    15650 > color sel dark gray
    15651 
    15652 > select #2/M
    15653 
    15654 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    15655 
    15656 > color sel white smoke
    15657 
    15658 > color sel beige
    15659 
    15660 > select clear
    15661 
    15662 > select #2/M
    15663 
    15664 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    15665 
    15666 > color sel gainsboro
    15667 
    15668 > select clear
    15669 
    15670 > select #2/M
    15671 
    15672 3817 atoms, 4286 bonds, 186 residues, 1 model selected 
    15673 
    15674 > color sel alice blue
    15675 
    15676 > color sel honeydew
    15677 
    15678 > select clear
    15679 
    15680 > select #2/L:55-58
    15681 
    15682 84 atoms, 94 bonds, 4 residues, 1 model selected 
    15683 
    15684 > color sel bynucleotide
    15685 
    15686 > save "/Users/taic/OneDrive - National Institutes of
    15687 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
    15688 
    15689 > select #2/L
    15690 
    15691 3811 atoms, 4270 bonds, 186 residues, 1 model selected 
    15692 
    15693 > select #2/L:55-58
    15694 
    15695 84 atoms, 94 bonds, 4 residues, 1 model selected 
    15696 
    15697 > show sel atoms
    15698 
    15699 > style sel ball
    15700 
    15701 Changed 84 atom styles 
    15702 
    15703 > select #2/L:29-41
    15704 
    15705 269 atoms, 301 bonds, 13 residues, 1 model selected 
    15706 
    15707 > select clear
    15708 
    15709 > ui tool show "Show Sequence Viewer"
    15710 
    15711 > sequence chain #2/L
    15712 
    15713 Alignment identifier is 2/L 
    15714 
    15715 > select #2/L:31
    15716 
    15717 20 atoms, 21 bonds, 1 residue, 1 model selected 
    15718 
    15719 > select #2/L:31-37
    15720 
    15721 143 atoms, 159 bonds, 7 residues, 1 model selected 
    15722 
    15723 > color sel bynucleotide
    15724 
    15725 > show sel atoms
    15726 
    15727 > style sel ball
    15728 
    15729 Changed 143 atom styles 
    15730 
    15731 > select clear
    15732 
    15733 > show #!6 models
    15734 
    15735 > hide #!6 models
    15736 
    15737 > show #!6 models
    15738 
    15739 > hide #2 models
    15740 
    15741 > show #2 models
    15742 
    15743 > hide #!6 models
    15744 
    15745 > select #2/J:1-330
    15746 
    15747 2573 atoms, 2642 bonds, 330 residues, 1 model selected 
    15748 
    15749 > color sel light cyan
    15750 
    15751 > select clear
    15752 
    15753 > show #!6 models
    15754 
    15755 > hide #!6 models
    15756 
    15757 > save "/Users/taic/OneDrive - National Institutes of
    15758 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3.FOXA1.MBP-
    15759 > GATA4.png" width 922 height 681 supersample 4 transparentBackground true
    15760 
    15761 > show #!6 models
    15762 
    15763 > hide #2 models
    15764 
    15765 > save "/Users/taic/OneDrive - National Institutes of
    15766 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA1.GATA4-2.png"
    15767 > width 922 height 681 supersample 4 transparentBackground true
    15768 
    15769 > show #2 models
    15770 
    15771 > hide #!6 models
    15772 
    15773 Drag select of 83 atoms, 19 residues, 93 bonds 
    15774 
    15775 > nucleotides sel atoms
    15776 
    15777 > style nucleic & sel stick
    15778 
    15779 Changed 405 atom styles 
    15780 
    15781 > select #2/L:35@N1
    15782 
    15783 1 atom, 1 residue, 1 model selected 
    15784 Drag select of 56 atoms, 79 residues, 64 bonds 
    15785 
    15786 > nucleotides sel atoms
    15787 
    15788 > style nucleic & sel stick
    15789 
    15790 Changed 161 atom styles 
    15791 
    15792 > select #2/J:664-712
    15793 
    15794 380 atoms, 386 bonds, 49 residues, 1 model selected 
    15795 
    15796 > show #!6 models
    15797 
    15798 > select #6/T#2/J:664-712
    15799 
    15800 795 atoms, 806 bonds, 4 pseudobonds, 103 residues, 3 models selected 
    15801 
    15802 > ui tool show Matchmaker
    15803 
    15804 > matchmaker #2 & sel to #6 & sel
    15805 
    15806 Parameters 
    15807 --- 
    15808 Chain pairing | bb 
    15809 Alignment algorithm | Needleman-Wunsch 
    15810 Similarity matrix | BLOSUM-62 
    15811 SS fraction | 0.3 
    15812 Gap open (HH/SS/other) | 18/18/6 
    15813 Gap extend | 1 
    15814 SS matrix |  |  | H | S | O 
    15815 ---|---|---|--- 
    15816 H | 6 | -9 | -6 
    15817 S |  | 6 | -6 
    15818 O |  |  | 4 
    15819 Iteration cutoff | 2 
    15820  
    15821 Matchmaker 8vg1, chain T (#6) with
    15822 fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain J (#2), sequence
    15823 alignment score = 256.6 
    15824 RMSD between 41 pruned atom pairs is 0.479 angstroms; (across all 49 pairs:
    15825 5.360) 
    15826  
    15827 
    15828 > hide #!6 models
    15829 
    15830 > show #!8 models
    15831 
    15832 > hide #2 models
    15833 
    15834 > show #!6 models
    15835 
    15836 > hide #!8 models
    15837 
    15838 > ui tool show "Show Sequence Viewer"
    15839 
    15840 > sequence chain #6/O
    15841 
    15842 Alignment identifier is 6/O 
    15843 
    15844 > sequence chain #6/T
    15845 
    15846 Alignment identifier is 6/T 
    15847 
    15848 > select #6/O:168
    15849 
    15850 10 atoms, 10 bonds, 1 residue, 1 model selected 
    15851 
    15852 > select #6/O
    15853 
    15854 856 atoms, 883 bonds, 102 residues, 1 model selected 
    15855 
    15856 > select clear
    15857 
    15858 > select #6/T:269
    15859 
    15860 8 atoms, 7 bonds, 1 residue, 1 model selected 
    15861 
    15862 > select #6/T:269-321
    15863 
    15864 414 atoms, 420 bonds, 53 residues, 1 model selected 
    15865 
    15866 > select clear
    15867 
    15868 > select #6/T:269-321
    15869 
    15870 414 atoms, 420 bonds, 53 residues, 1 model selected 
    15871 
    15872 > save "/Users/taic/OneDrive - National Institutes of
    15873 > Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
    15874 
    15875 > save /Users/taic/mine/Job/project/CASP16/AF3/8VG1.cxs
    15876 
    15877 > open /Users/taic/Library/CloudStorage/OneDrive-
    15878 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsDx2.af3_contacts.cxs
    15879 
    15880 opened ChimeraX session 
    15881 
    15882 > open /Users/taic/Library/CloudStorage/OneDrive-
    15883 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_0.cif
    15884 
    15885 Chain information for fold_rcsdx2_model_0.cif #4 
    15886 --- 
    15887 Chain | Description 
    15888 A B | . 
    15889  
    15890 
    15891 > open /Users/taic/Library/CloudStorage/OneDrive-
    15892 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_1.cif
    15893 
    15894 Chain information for fold_rcsdx2_model_1.cif #5 
    15895 --- 
    15896 Chain | Description 
    15897 A B | . 
    15898  
    15899 Computing secondary structure 
    15900 
    15901 > open /Users/taic/Library/CloudStorage/OneDrive-
    15902 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_2.cif
    15903 
    15904 Chain information for fold_rcsdx2_model_2.cif #9 
    15905 --- 
    15906 Chain | Description 
    15907 A B | . 
    15908  
    15909 Computing secondary structure 
    15910 
    15911 > open /Users/taic/Library/CloudStorage/OneDrive-
    15912 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_3.cif
    15913 
    15914 Chain information for fold_rcsdx2_model_3.cif #11 
    15915 --- 
    15916 Chain | Description 
    15917 A B | . 
    15918  
    15919 Computing secondary structure 
    15920 
    15921 > open /Users/taic/Library/CloudStorage/OneDrive-
    15922 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_4.cif
    15923 
    15924 Chain information for fold_rcsdx2_model_4.cif #12 
    15925 --- 
    15926 Chain | Description 
    15927 A B | . 
    15928  
    15929 Computing secondary structure 
    15930 
    15931 > hide #!2 models
    15932 
    15933 > hide #3 models
    15934 
    15935 > hide #4 models
    15936 
    15937 > show #4 models
    15938 
    15939 > hide #5 models
    15940 
    15941 > hide #9 models
    15942 
    15943 > hide #11 models
    15944 
    15945 > hide #12 models
    15946 
    15947 > color #4 bychain
    15948 
    15949 > show #5 models
    15950 
    15951 > hide #4 models
    15952 
    15953 > hide #5 models
    15954 
    15955 > show #4 models
    15956 
    15957 > show #!2 models
    15958 
    15959 > hide #4 models
    15960 
    15961 > show #12 models
    15962 
    15963 > hide #!2 models
    15964 
    15965 > show #11 models
    15966 
    15967 > select add #11
    15968 
    15969 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    15970 
    15971 > select add #12
    15972 
    15973 28232 atoms, 28704 bonds, 3560 residues, 2 models selected 
    15974 
    15975 > delete atoms sel
    15976 
    15977 > delete bonds sel
    15978 
    15979 > show #5 models
    15980 
    15981 > select add #5
    15982 
    15983 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    15984 
    15985 > delete atoms sel
    15986 
    15987 > delete bonds sel
    15988 
    15989 > show #9 models
    15990 
    15991 > select add #9
    15992 
    15993 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    15994 
    15995 > delete atoms sel
    15996 
    15997 > delete bonds sel
    15998 
    15999 > show #4 models
    16000 
    16001 > hide #4 models
    16002 
    16003 > show #!2 models
    16004 
    16005 > hide #!2 models
    16006 
    16007 > show #1 models
    16008 
    16009 > open /Users/taic/Library/CloudStorage/OneDrive-
    16010 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    16011 
    16012 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16013 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json: 
    16014 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16015 model. Did not find an open atomic model from the same directory. If the
    16016 atomic model is already open choose it using menu 
    16017  
    16018 Tools / Structure Prediction / AlphaFold Error Plot 
    16019  
    16020 or use the open command structure option, for example 
    16021  
    16022 open /Users/taic/Library/CloudStorage/OneDrive-
    16023 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    16024 structure #1 
    16025  
    16026 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16027 need to specify the specific JSON format such as 
    16028  
    16029 open mole_channels.json format mole 
    16030 
    16031 > open /Users/taic/Library/CloudStorage/OneDrive-
    16032 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    16033 
    16034 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16035 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json: 
    16036 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16037 model. Did not find an open atomic model from the same directory. If the
    16038 atomic model is already open choose it using menu 
    16039  
    16040 Tools / Structure Prediction / AlphaFold Error Plot 
    16041  
    16042 or use the open command structure option, for example 
    16043  
    16044 open /Users/taic/Library/CloudStorage/OneDrive-
    16045 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    16046 structure #1 
    16047  
    16048 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16049 need to specify the specific JSON format such as 
    16050  
    16051 open mole_channels.json format mole 
    16052 
    16053 > open /Users/taic/Library/CloudStorage/OneDrive-
    16054 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    16055 
    16056 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16057 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json: 
    16058 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16059 model. Did not find an open atomic model from the same directory. If the
    16060 atomic model is already open choose it using menu 
    16061  
    16062 Tools / Structure Prediction / AlphaFold Error Plot 
    16063  
    16064 or use the open command structure option, for example 
    16065  
    16066 open /Users/taic/Library/CloudStorage/OneDrive-
    16067 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    16068 structure #1 
    16069  
    16070 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16071 need to specify the specific JSON format such as 
    16072  
    16073 open mole_channels.json format mole 
    16074 
    16075 > open /Users/taic/Library/CloudStorage/OneDrive-
    16076 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    16077 
    16078 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16079 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json: 
    16080 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16081 model. Did not find an open atomic model from the same directory. If the
    16082 atomic model is already open choose it using menu 
    16083  
    16084 Tools / Structure Prediction / AlphaFold Error Plot 
    16085  
    16086 or use the open command structure option, for example 
    16087  
    16088 open /Users/taic/Library/CloudStorage/OneDrive-
    16089 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    16090 structure #1 
    16091  
    16092 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16093 need to specify the specific JSON format such as 
    16094  
    16095 open mole_channels.json format mole 
    16096 
    16097 > open /Users/taic/Library/CloudStorage/OneDrive-
    16098 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    16099 
    16100 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16101 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json: 
    16102 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16103 model. Did not find an open atomic model from the same directory. If the
    16104 atomic model is already open choose it using menu 
    16105  
    16106 Tools / Structure Prediction / AlphaFold Error Plot 
    16107  
    16108 or use the open command structure option, for example 
    16109  
    16110 open /Users/taic/Library/CloudStorage/OneDrive-
    16111 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    16112 structure #1 
    16113  
    16114 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16115 need to specify the specific JSON format such as 
    16116  
    16117 open mole_channels.json format mole 
    16118 
    16119 > open /Users/taic/Library/CloudStorage/OneDrive-
    16120 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    16121 
    16122 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16123 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json: 
    16124 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16125 model. Did not find an open atomic model from the same directory. If the
    16126 atomic model is already open choose it using menu 
    16127  
    16128 Tools / Structure Prediction / AlphaFold Error Plot 
    16129  
    16130 or use the open command structure option, for example 
    16131  
    16132 open /Users/taic/Library/CloudStorage/OneDrive-
    16133 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    16134 structure #1 
    16135  
    16136 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16137 need to specify the specific JSON format such as 
    16138  
    16139 open mole_channels.json format mole 
    16140 
    16141 > open /Users/taic/Library/CloudStorage/OneDrive-
    16142 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    16143 
    16144 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16145 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json: 
    16146 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16147 model. Did not find an open atomic model from the same directory. If the
    16148 atomic model is already open choose it using menu 
    16149  
    16150 Tools / Structure Prediction / AlphaFold Error Plot 
    16151  
    16152 or use the open command structure option, for example 
    16153  
    16154 open /Users/taic/Library/CloudStorage/OneDrive-
    16155 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    16156 structure #1 
    16157  
    16158 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16159 need to specify the specific JSON format such as 
    16160  
    16161 open mole_channels.json format mole 
    16162 
    16163 > open /Users/taic/Library/CloudStorage/OneDrive-
    16164 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    16165 
    16166 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16167 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json: 
    16168 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16169 model. Did not find an open atomic model from the same directory. If the
    16170 atomic model is already open choose it using menu 
    16171  
    16172 Tools / Structure Prediction / AlphaFold Error Plot 
    16173  
    16174 or use the open command structure option, for example 
    16175  
    16176 open /Users/taic/Library/CloudStorage/OneDrive-
    16177 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    16178 structure #1 
    16179  
    16180 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16181 need to specify the specific JSON format such as 
    16182  
    16183 open mole_channels.json format mole 
    16184 
    16185 > open /Users/taic/Library/CloudStorage/OneDrive-
    16186 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    16187 
    16188 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16189 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json: 
    16190 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16191 model. Did not find an open atomic model from the same directory. If the
    16192 atomic model is already open choose it using menu 
    16193  
    16194 Tools / Structure Prediction / AlphaFold Error Plot 
    16195  
    16196 or use the open command structure option, for example 
    16197  
    16198 open /Users/taic/Library/CloudStorage/OneDrive-
    16199 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    16200 structure #1 
    16201  
    16202 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16203 need to specify the specific JSON format such as 
    16204  
    16205 open mole_channels.json format mole 
    16206 
    16207 > open /Users/taic/Library/CloudStorage/OneDrive-
    16208 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    16209 
    16210 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16211 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json: 
    16212 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16213 model. Did not find an open atomic model from the same directory. If the
    16214 atomic model is already open choose it using menu 
    16215  
    16216 Tools / Structure Prediction / AlphaFold Error Plot 
    16217  
    16218 or use the open command structure option, for example 
    16219  
    16220 open /Users/taic/Library/CloudStorage/OneDrive-
    16221 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    16222 structure #1 
    16223  
    16224 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16225 need to specify the specific JSON format such as 
    16226  
    16227 open mole_channels.json format mole 
    16228 
    16229 > open /Users/taic/Library/CloudStorage/OneDrive-
    16230 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    16231 
    16232 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16233 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json: 
    16234 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16235 model. Did not find an open atomic model from the same directory. If the
    16236 atomic model is already open choose it using menu 
    16237  
    16238 Tools / Structure Prediction / AlphaFold Error Plot 
    16239  
    16240 or use the open command structure option, for example 
    16241  
    16242 open /Users/taic/Library/CloudStorage/OneDrive-
    16243 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    16244 structure #1 
    16245  
    16246 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16247 need to specify the specific JSON format such as 
    16248  
    16249 open mole_channels.json format mole 
    16250 
    16251 > open /Users/taic/Library/CloudStorage/OneDrive-
    16252 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    16253 
    16254 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16255 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json: 
    16256 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16257 model. Did not find an open atomic model from the same directory. If the
    16258 atomic model is already open choose it using menu 
    16259  
    16260 Tools / Structure Prediction / AlphaFold Error Plot 
    16261  
    16262 or use the open command structure option, for example 
    16263  
    16264 open /Users/taic/Library/CloudStorage/OneDrive-
    16265 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    16266 structure #1 
    16267  
    16268 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16269 need to specify the specific JSON format such as 
    16270  
    16271 open mole_channels.json format mole 
    16272 
    16273 > open /Users/taic/Library/CloudStorage/OneDrive-
    16274 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    16275 
    16276 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16277 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json: 
    16278 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16279 model. Did not find an open atomic model from the same directory. If the
    16280 atomic model is already open choose it using menu 
    16281  
    16282 Tools / Structure Prediction / AlphaFold Error Plot 
    16283  
    16284 or use the open command structure option, for example 
    16285  
    16286 open /Users/taic/Library/CloudStorage/OneDrive-
    16287 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    16288 structure #1 
    16289  
    16290 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16291 need to specify the specific JSON format such as 
    16292  
    16293 open mole_channels.json format mole 
    16294 
    16295 > open /Users/taic/Library/CloudStorage/OneDrive-
    16296 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    16297 
    16298 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16299 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json: 
    16300 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16301 model. Did not find an open atomic model from the same directory. If the
    16302 atomic model is already open choose it using menu 
    16303  
    16304 Tools / Structure Prediction / AlphaFold Error Plot 
    16305  
    16306 or use the open command structure option, for example 
    16307  
    16308 open /Users/taic/Library/CloudStorage/OneDrive-
    16309 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    16310 structure #1 
    16311  
    16312 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16313 need to specify the specific JSON format such as 
    16314  
    16315 open mole_channels.json format mole 
    16316 
    16317 > open /Users/taic/Library/CloudStorage/OneDrive-
    16318 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    16319 
    16320 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16321 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json: 
    16322 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16323 model. Did not find an open atomic model from the same directory. If the
    16324 atomic model is already open choose it using menu 
    16325  
    16326 Tools / Structure Prediction / AlphaFold Error Plot 
    16327  
    16328 or use the open command structure option, for example 
    16329  
    16330 open /Users/taic/Library/CloudStorage/OneDrive-
    16331 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    16332 structure #1 
    16333  
    16334 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16335 need to specify the specific JSON format such as 
    16336  
    16337 open mole_channels.json format mole 
    16338 
    16339 > open /Users/taic/Library/CloudStorage/OneDrive-
    16340 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
    16341 > /Users/taic/Library/CloudStorage/OneDrive-
    16342 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_1.json
    16343 > /Users/taic/Library/CloudStorage/OneDrive-
    16344 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_2.json
    16345 > /Users/taic/Library/CloudStorage/OneDrive-
    16346 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_3.json
    16347 > /Users/taic/Library/CloudStorage/OneDrive-
    16348 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_4.json
    16349 
    16350 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16351 model. Did not find an open atomic model from the same directory. If the
    16352 atomic model is already open choose it using menu 
    16353  
    16354 Tools / Structure Prediction / AlphaFold Error Plot 
    16355  
    16356 or use the open command structure option, for example 
    16357  
    16358 open /Users/taic/Library/CloudStorage/OneDrive-
    16359 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
    16360 structure #1 
    16361  
    16362 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16363 need to specify the specific JSON format such as 
    16364  
    16365 open mole_channels.json format mole 
    16366 
    16367 > open /Users/taic/Library/CloudStorage/OneDrive-
    16368 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
    16369 
    16370 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16371 model. Did not find an open atomic model from the same directory. If the
    16372 atomic model is already open choose it using menu 
    16373  
    16374 Tools / Structure Prediction / AlphaFold Error Plot 
    16375  
    16376 or use the open command structure option, for example 
    16377  
    16378 open /Users/taic/Library/CloudStorage/OneDrive-
    16379 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
    16380 structure #1 
    16381  
    16382 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16383 need to specify the specific JSON format such as 
    16384  
    16385 open mole_channels.json format mole 
    16386 
    16387 > open /Users/taic/Library/CloudStorage/OneDrive-
    16388 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_0.cif
    16389 
    16390 Chain information for fold_igaa_rcscx2_rcsdx2_model_0.cif #5 
    16391 --- 
    16392 Chain | Description 
    16393 A | . 
    16394 B C | . 
    16395 D E | . 
    16396  
    16397 
    16398 > hide #1,5 surfaces
    16399 
    16400 > show #1,5 cartoons
    16401 
    16402 Computing secondary structure 
    16403 
    16404 > hide #1,5 surfaces
    16405 
    16406 > select add #5
    16407 
    16408 34679 atoms, 35323 bonds, 4389 residues, 1 model selected 
    16409 
    16410 > hide sel surfaces
    16411 
    16412 > show sel cartoons
    16413 
    16414 > style sel stick
    16415 
    16416 Changed 34679 atom styles 
    16417 
    16418 > hide sel atoms
    16419 
    16420 > select clear
    16421 
    16422 > hide #1 models
    16423 
    16424 > color #5 bychain
    16425 
    16426 > open /Users/taic/Library/CloudStorage/OneDrive-
    16427 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_1.cif
    16428 
    16429 Chain information for fold_igaa_rcscx2_rcsdx2_model_1.cif #9 
    16430 --- 
    16431 Chain | Description 
    16432 A | . 
    16433 B C | . 
    16434 D E | . 
    16435  
    16436 
    16437 > open /Users/taic/Library/CloudStorage/OneDrive-
    16438 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_4.cif
    16439 
    16440 Chain information for fold_igaa_rcscx2_rcsdx2_model_4.cif #11 
    16441 --- 
    16442 Chain | Description 
    16443 A | . 
    16444 B C | . 
    16445 D E | . 
    16446  
    16447 
    16448 > open /Users/taic/Library/CloudStorage/OneDrive-
    16449 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_2.cif
    16450 
    16451 Chain information for fold_igaa_rcscx2_rcsdx2_model_2.cif #12 
    16452 --- 
    16453 Chain | Description 
    16454 A | . 
    16455 B C | . 
    16456 D E | . 
    16457  
    16458 
    16459 > show #5,9,11-12 cartoons
    16460 
    16461 Computing secondary structure 
    16462 
    16463 > open /Users/taic/Library/CloudStorage/OneDrive-
    16464 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_3.cif
    16465 
    16466 Chain information for fold_igaa_rcscx2_rcsdx2_model_3.cif #13 
    16467 --- 
    16468 Chain | Description 
    16469 A | . 
    16470 B C | . 
    16471 D E | . 
    16472  
    16473 
    16474 > hide #5,9,11-13 atoms
    16475 
    16476 > hide #5 models
    16477 
    16478 > hide #9 models
    16479 
    16480 > show #9 models
    16481 
    16482 > hide #11 models
    16483 
    16484 > hide #12 models
    16485 
    16486 > hide #13 models
    16487 
    16488 > color #9 bychain
    16489 
    16490 > show #11 models
    16491 
    16492 > hide #9 models
    16493 
    16494 > color #11 bychain
    16495 
    16496 > show #12 models
    16497 
    16498 > hide #11 models
    16499 
    16500 > color #12 bychain
    16501 
    16502 > select add #12
    16503 
    16504 34679 atoms, 35323 bonds, 4389 residues, 1 model selected 
    16505 
    16506 > delete atoms sel
    16507 
    16508 > delete bonds sel
    16509 
    16510 > show #13 models
    16511 
    16512 > select add #13
    16513 
    16514 34679 atoms, 35323 bonds, 4389 residues, 1 model selected 
    16515 
    16516 > show #11 models
    16517 
    16518 > hide #13 models
    16519 
    16520 > select subtract #13
    16521 
    16522 Nothing selected 
    16523 
    16524 > show #13 models
    16525 
    16526 > hide #11 models
    16527 
    16528 > select add #13
    16529 
    16530 34679 atoms, 35323 bonds, 4389 residues, 1 model selected 
    16531 
    16532 > delete atoms sel
    16533 
    16534 > delete bonds sel
    16535 
    16536 > show #11 models
    16537 
    16538 > show #9 models
    16539 
    16540 > show #10 models
    16541 
    16542 > hide #9 models
    16543 
    16544 > hide #11 models
    16545 
    16546 > show #11 models
    16547 
    16548 > hide #10 models
    16549 
    16550 > show #!2 models
    16551 
    16552 > hide #11 models
    16553 
    16554 > show #10 models
    16555 
    16556 > hide #!2 models
    16557 
    16558 > show #9 models
    16559 
    16560 > hide #10 models
    16561 
    16562 > show #1 models
    16563 
    16564 > show #!2 models
    16565 
    16566 > hide #1 models
    16567 
    16568 > hide #9 models
    16569 
    16570 > show #9 models
    16571 
    16572 > hide #!2 models
    16573 
    16574 > show #4 models
    16575 
    16576 > hide #9 models
    16577 
    16578 > select add #4
    16579 
    16580 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    16581 
    16582 > delete atoms sel
    16583 
    16584 > delete bonds sel
    16585 
    16586 > show #7 models
    16587 
    16588 > show #8 models
    16589 
    16590 > hide #8 models
    16591 
    16592 > hide #7 models
    16593 
    16594 > open /Users/taic/Library/CloudStorage/OneDrive-
    16595 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json
    16596 
    16597 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    16598 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json: 
    16599 Opening an AlphaFold PAE file requires first opening the predicted atomic
    16600 model. Did not find an open atomic model from the same directory. If the
    16601 atomic model is already open choose it using menu 
    16602  
    16603 Tools / Structure Prediction / AlphaFold Error Plot 
    16604  
    16605 or use the open command structure option, for example 
    16606  
    16607 open /Users/taic/Library/CloudStorage/OneDrive-
    16608 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json
    16609 structure #1 
    16610  
    16611 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    16612 need to specify the specific JSON format such as 
    16613  
    16614 open mole_channels.json format mole 
    16615 
    16616 > open /Users/taic/Library/CloudStorage/OneDrive-
    16617 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_0.cif
    16618 
    16619 Chain information for fold_rcsdx2_rcscx2_model_0.cif #4 
    16620 --- 
    16621 Chain | Description 
    16622 A B | . 
    16623 C D | . 
    16624  
    16625 Computing secondary structure 
    16626 
    16627 > color #4 bychain
    16628 
    16629 > open /Users/taic/Library/CloudStorage/OneDrive-
    16630 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_1.cif
    16631 
    16632 Chain information for fold_rcsdx2_rcscx2_model_1.cif #12 
    16633 --- 
    16634 Chain | Description 
    16635 A B | . 
    16636 C D | . 
    16637  
    16638 
    16639 > open /Users/taic/Library/CloudStorage/OneDrive-
    16640 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_3.cif
    16641 
    16642 Chain information for fold_rcsdx2_rcscx2_model_3.cif #13 
    16643 --- 
    16644 Chain | Description 
    16645 A B | . 
    16646 C D | . 
    16647  
    16648 
    16649 > open /Users/taic/Library/CloudStorage/OneDrive-
    16650 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_4.cif
    16651 
    16652 Chain information for fold_rcsdx2_rcscx2_model_4.cif #14 
    16653 --- 
    16654 Chain | Description 
    16655 A B | . 
    16656 C D | . 
    16657  
    16658 Computing secondary structure 
    16659 
    16660 > open /Users/taic/Library/CloudStorage/OneDrive-
    16661 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_2.cif
    16662 
    16663 Chain information for fold_rcsdx2_rcscx2_model_2.cif #15 
    16664 --- 
    16665 Chain | Description 
    16666 A B | . 
    16667 C D | . 
    16668  
    16669 Computing secondary structure 
    16670 
    16671 > hide #4 models
    16672 
    16673 > hide #13 models
    16674 
    16675 > hide #14 models
    16676 
    16677 > hide #15 models
    16678 
    16679 > color #12 bychain
    16680 
    16681 > hide #12 models
    16682 
    16683 > show #13 models
    16684 
    16685 > color #13 bychain
    16686 
    16687 > show #14 models
    16688 
    16689 > hide #13 models
    16690 
    16691 > color #14 bychain
    16692 
    16693 > show #15 models
    16694 
    16695 > hide #14 models
    16696 
    16697 > color #15 bychain
    16698 
    16699 > show #14 models
    16700 
    16701 > hide #15 models
    16702 
    16703 > show #4 models
    16704 
    16705 > hide #14 models
    16706 
    16707 > show #12 models
    16708 
    16709 > hide #12 models
    16710 
    16711 > show #12 models
    16712 
    16713 > hide #4 models
    16714 
    16715 > show #13 models
    16716 
    16717 > hide #12 models
    16718 
    16719 > show #14 models
    16720 
    16721 > hide #13 models
    16722 
    16723 > show #15 models
    16724 
    16725 > hide #14 models
    16726 
    16727 > hide #15 models
    16728 
    16729 > show #15 models
    16730 
    16731 > show #4 models
    16732 
    16733 > hide #15 models
    16734 
    16735 > show #12 models
    16736 
    16737 > hide #4 models
    16738 
    16739 > show #9 models
    16740 
    16741 > hide #12 models
    16742 
    16743 > ui tool show "Show Sequence Viewer"
    16744 
    16745 > sequence chain #9/D
    16746 
    16747 Alignment identifier is 9/D 
    16748 
    16749 > select
    16750 > #9/D:91-96,99-103,110-114,144-148,155-159,197-199,203-205,210-219,227-234,248-252,270-274,278-285,290-297,367-372,377-381,407-412,415-423,430-437,525-528,550-555,562-565,589-596,603-610,657-663,667-675,695-699,719-721,734-737,747-751,757-761,764-768
    16751 
    16752 1522 atoms, 1520 bonds, 183 residues, 1 model selected 
    16753 
    16754 > hide #9 models
    16755 
    16756 > show #7 models
    16757 
    16758 > show #1 models
    16759 
    16760 > hide #7 models
    16761 
    16762 > color #1 bychain
    16763 
    16764 > select
    16765 > #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
    16766 
    16767 146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
    16768 selected 
    16769 
    16770 > rainbow sel & #1
    16771 
    16772 > select clear
    16773 
    16774 > show #4 models
    16775 
    16776 > hide #4 models
    16777 
    16778 > select
    16779 > #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
    16780 
    16781 146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
    16782 selected 
    16783 
    16784 > ui tool show Matchmaker
    16785 
    16786 > matchmaker #4-15#!2 & sel to #1 & sel
    16787 
    16788 Computing secondary structure 
    16789 Parameters 
    16790 --- 
    16791 Chain pairing | bb 
    16792 Alignment algorithm | Needleman-Wunsch 
    16793 Similarity matrix | BLOSUM-62 
    16794 SS fraction | 0.3 
    16795 Gap open (HH/SS/other) | 18/18/6 
    16796 Gap extend | 1 
    16797 SS matrix |  |  | H | S | O 
    16798 ---|---|---|--- 
    16799 H | 6 | -9 | -6 
    16800 S |  | 6 | -6 
    16801 O |  |  | 4 
    16802 Iteration cutoff | 2 
    16803  
    16804 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
    16805 chain B (#7), sequence alignment score = 1372.7 
    16806 RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
    16807 1.791) 
    16808  
    16809 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16810 fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
    16811 4552.2 
    16812 RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
    16813 23.121) 
    16814  
    16815 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16816 IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
    16817 1374.5 
    16818 RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
    16819 1.531) 
    16820  
    16821 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16822 fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
    16823 4504.2 
    16824 RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
    16825 19.956) 
    16826  
    16827 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16828 fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
    16829 4506.6 
    16830 RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
    16831 45.059) 
    16832  
    16833 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16834 fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
    16835 4461.6 
    16836 RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
    16837 37.620) 
    16838  
    16839 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16840 fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
    16841 4539.6 
    16842 RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
    16843 22.279) 
    16844  
    16845 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16846 fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
    16847 4538.4 
    16848 RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
    16849 33.986) 
    16850  
    16851 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16852 fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
    16853 4543.2 
    16854 RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
    16855 51.173) 
    16856  
    16857 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16858 fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
    16859 4535.4 
    16860 RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
    16861 25.202) 
    16862  
    16863 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16864 fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
    16865 4532.4 
    16866 RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
    16867 32.264) 
    16868  
    16869 
    16870 > matchmaker #4-15#!2 & sel to #1 & sel
    16871 
    16872 Computing secondary structure 
    16873 Parameters 
    16874 --- 
    16875 Chain pairing | bb 
    16876 Alignment algorithm | Needleman-Wunsch 
    16877 Similarity matrix | BLOSUM-62 
    16878 SS fraction | 0.3 
    16879 Gap open (HH/SS/other) | 18/18/6 
    16880 Gap extend | 1 
    16881 SS matrix |  |  | H | S | O 
    16882 ---|---|---|--- 
    16883 H | 6 | -9 | -6 
    16884 S |  | 6 | -6 
    16885 O |  |  | 4 
    16886 Iteration cutoff | 2 
    16887  
    16888 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
    16889 chain B (#7), sequence alignment score = 1372.7 
    16890 RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
    16891 1.791) 
    16892  
    16893 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16894 fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
    16895 4552.2 
    16896 RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
    16897 23.121) 
    16898  
    16899 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16900 IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
    16901 1374.5 
    16902 RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
    16903 1.531) 
    16904  
    16905 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16906 fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
    16907 4504.2 
    16908 RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
    16909 19.956) 
    16910  
    16911 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16912 fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
    16913 4506.6 
    16914 RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
    16915 45.059) 
    16916  
    16917 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16918 fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
    16919 4461.6 
    16920 RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
    16921 37.620) 
    16922  
    16923 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16924 fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
    16925 4539.6 
    16926 RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
    16927 22.279) 
    16928  
    16929 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16930 fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
    16931 4538.4 
    16932 RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
    16933 33.986) 
    16934  
    16935 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16936 fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
    16937 4543.2 
    16938 RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
    16939 51.173) 
    16940  
    16941 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16942 fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
    16943 4535.4 
    16944 RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
    16945 25.202) 
    16946  
    16947 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16948 fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
    16949 4532.4 
    16950 RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
    16951 32.264) 
    16952  
    16953 
    16954 > matchmaker #4-15#!2 & sel to #1 & sel
    16955 
    16956 Computing secondary structure 
    16957 Parameters 
    16958 --- 
    16959 Chain pairing | bb 
    16960 Alignment algorithm | Needleman-Wunsch 
    16961 Similarity matrix | BLOSUM-62 
    16962 SS fraction | 0.3 
    16963 Gap open (HH/SS/other) | 18/18/6 
    16964 Gap extend | 1 
    16965 SS matrix |  |  | H | S | O 
    16966 ---|---|---|--- 
    16967 H | 6 | -9 | -6 
    16968 S |  | 6 | -6 
    16969 O |  |  | 4 
    16970 Iteration cutoff | 2 
    16971  
    16972 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
    16973 chain B (#7), sequence alignment score = 1372.7 
    16974 RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
    16975 1.791) 
    16976  
    16977 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16978 fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
    16979 4552.2 
    16980 RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
    16981 23.121) 
    16982  
    16983 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16984 IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
    16985 1374.5 
    16986 RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
    16987 1.531) 
    16988  
    16989 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16990 fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
    16991 4504.2 
    16992 RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
    16993 19.956) 
    16994  
    16995 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    16996 fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
    16997 4506.6 
    16998 RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
    16999 45.059) 
    17000  
    17001 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    17002 fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
    17003 4461.6 
    17004 RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
    17005 37.620) 
    17006  
    17007 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    17008 fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
    17009 4539.6 
    17010 RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
    17011 22.279) 
    17012  
    17013 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    17014 fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
    17015 4538.4 
    17016 RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
    17017 33.986) 
    17018  
    17019 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    17020 fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
    17021 4543.2 
    17022 RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
    17023 51.173) 
    17024  
    17025 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    17026 fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
    17027 4535.4 
    17028 RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
    17029 25.202) 
    17030  
    17031 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    17032 fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
    17033 4532.4 
    17034 RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
    17035 32.264) 
    17036  
    17037 
    17038 > show #!2 models
    17039 
    17040 > hide #1 models
    17041 
    17042 > show #1 models
    17043 
    17044 > show #3 models
    17045 
    17046 > show #4 models
    17047 
    17048 > show #5 models
    17049 
    17050 > show #6 models
    17051 
    17052 > show #7 models
    17053 
    17054 > show #8 models
    17055 
    17056 > show #9 models
    17057 
    17058 > show #10 models
    17059 
    17060 > show #11 models
    17061 
    17062 > show #12 models
    17063 
    17064 > show #13 models
    17065 
    17066 > show #14 models
    17067 
    17068 > show #15 models
    17069 
    17070 > select
    17071 > #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
    17072 
    17073 146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
    17074 selected 
    17075 
    17076 > rainbow sel
    17077 
    17078 > hide #!2 models
    17079 
    17080 > hide #3 models
    17081 
    17082 > hide #4 models
    17083 
    17084 > hide #5 models
    17085 
    17086 > hide #6 models
    17087 
    17088 > hide #7 models
    17089 
    17090 > hide #8 models
    17091 
    17092 > hide #9 models
    17093 
    17094 > hide #10 models
    17095 
    17096 > hide #11 models
    17097 
    17098 > hide #12 models
    17099 
    17100 > hide #13 models
    17101 
    17102 > hide #14 models
    17103 
    17104 > hide #15 models
    17105 
    17106 > select clear
    17107 
    17108 > show #!2 models
    17109 
    17110 > hide #1 models
    17111 
    17112 > show #1 models
    17113 
    17114 > hide #!2 models
    17115 
    17116 > hide #1 models
    17117 
    17118 > show #1 models
    17119 
    17120 > show #!2 models
    17121 
    17122 > hide #1 models
    17123 
    17124 > show #4 models
    17125 
    17126 > hide #!2 models
    17127 
    17128 > show #5 models
    17129 
    17130 > hide #4 models
    17131 
    17132 > hide #5 models
    17133 
    17134 > show #6 models
    17135 
    17136 > hide #6 models
    17137 
    17138 > show #7 models
    17139 
    17140 > hide #7 models
    17141 
    17142 > show #8 models
    17143 
    17144 > hide #8 models
    17145 
    17146 > show #9 models
    17147 
    17148 > show #5 models
    17149 
    17150 > hide #9 models
    17151 
    17152 > show #9 models
    17153 
    17154 > hide #9 models
    17155 
    17156 > show #10 models
    17157 
    17158 > hide #5 models
    17159 
    17160 > hide #10 models
    17161 
    17162 > show #11 models
    17163 
    17164 > hide #11 models
    17165 
    17166 > show #12 models
    17167 
    17168 > show #13 models
    17169 
    17170 > hide #12 models
    17171 
    17172 > show #14 models
    17173 
    17174 > hide #13 models
    17175 
    17176 > show #15 models
    17177 
    17178 > hide #14 models
    17179 
    17180 > show #!2 models
    17181 
    17182 > hide #15 models
    17183 
    17184 > show #5 models
    17185 
    17186 > hide #!2 models
    17187 
    17188 > show #12 models
    17189 
    17190 > hide #5 models
    17191 
    17192 > show #13 models
    17193 
    17194 > hide #12 models
    17195 
    17196 > hide #13 models
    17197 
    17198 > show #14 models
    17199 
    17200 > show #15 models
    17201 
    17202 > hide #14 models
    17203 
    17204 > show #!2 models
    17205 
    17206 > hide #15 models
    17207 
    17208 > select #2/A
    17209 
    17210 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    17211 
    17212 > rainbow sel
    17213 
    17214 > select clear
    17215 
    17216 > color #!2 bychain
    17217 
    17218 > select #2/A
    17219 
    17220 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    17221 
    17222 > rainbow sel
    17223 
    17224 > select clear
    17225 
    17226 > select #2/A
    17227 
    17228 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    17229 
    17230 > select ~sel & ##selected
    17231 
    17232 15100 atoms, 15353 bonds, 1028 pseudobonds, 1914 residues, 2 models selected 
    17233 
    17234 > hide sel cartoons
    17235 
    17236 > hide sel atoms
    17237 
    17238 > select #2/B
    17239 
    17240 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    17241 
    17242 > show sel cartoons
    17243 
    17244 > select ~sel & ##selected
    17245 
    17246 19719 atoms, 20089 bonds, 1028 pseudobonds, 2491 residues, 2 models selected 
    17247 
    17248 > hide sel cartoons
    17249 
    17250 > hide sel atoms
    17251 
    17252 > select #2/B
    17253 
    17254 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    17255 
    17256 > rainbow sel
    17257 
    17258 > hide sel cartoons
    17259 
    17260 > select #2/C/D
    17261 
    17262 14116 atoms, 14352 bonds, 638 pseudobonds, 1780 residues, 2 models selected 
    17263 
    17264 > show sel cartoons
    17265 
    17266 > rainbow sel
    17267 
    17268 > select clear
    17269 
    17270 > hide #!2 cartoons
    17271 
    17272 > show #!2 cartoons
    17273 
    17274 > color #!2 bychain
    17275 
    17276 > select #2/A
    17277 
    17278 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    17279 
    17280 > rainbow sel
    17281 
    17282 > select clear
    17283 
    17284 > select #2/C
    17285 
    17286 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    17287 
    17288 > color sel bychain
    17289 
    17290 > select clear
    17291 
    17292 > color #!2 bychain
    17293 
    17294 > select #2/C
    17295 
    17296 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    17297 
    17298 > rainbow sel
    17299 
    17300 > select #2/B
    17301 
    17302 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    17303 
    17304 > rainbow sel
    17305 
    17306 > select clear
    17307 
    17308 > show #9 models
    17309 
    17310 > hide #!2 models
    17311 
    17312 > show #!2 models
    17313 
    17314 > hide #9 models
    17315 
    17316 > open /Users/taic/Library/CloudStorage/OneDrive-
    17317 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_3.cif
    17318 
    17319 Chain information for fold_rcsdx2_rcsbx2_model_3.cif #16 
    17320 --- 
    17321 Chain | Description 
    17322 A B | . 
    17323 C D | . 
    17324  
    17325 
    17326 > open /Users/taic/Library/CloudStorage/OneDrive-
    17327 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_4.cif
    17328 
    17329 Chain information for fold_rcsdx2_rcsbx2_model_4.cif #17 
    17330 --- 
    17331 Chain | Description 
    17332 A B | . 
    17333 C D | . 
    17334  
    17335 Computing secondary structure 
    17336 
    17337 > open /Users/taic/Library/CloudStorage/OneDrive-
    17338 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_0.cif
    17339 
    17340 Chain information for fold_rcsdx2_rcsbx2_model_0.cif #18 
    17341 --- 
    17342 Chain | Description 
    17343 A B | . 
    17344 C D | . 
    17345  
    17346 Computing secondary structure 
    17347 
    17348 > hide #!2 models
    17349 
    17350 > open /Users/taic/Library/CloudStorage/OneDrive-
    17351 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_1.cif
    17352 
    17353 Chain information for fold_rcsdx2_rcsbx2_model_1.cif #19 
    17354 --- 
    17355 Chain | Description 
    17356 A B | . 
    17357 C D | . 
    17358  
    17359 Computing secondary structure 
    17360 
    17361 > open /Users/taic/Library/CloudStorage/OneDrive-
    17362 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_2.cif
    17363 
    17364 Chain information for fold_rcsdx2_rcsbx2_model_2.cif #20 
    17365 --- 
    17366 Chain | Description 
    17367 A B | . 
    17368 C D | . 
    17369  
    17370 Computing secondary structure 
    17371 
    17372 > hide #16 models
    17373 
    17374 > hide #17 models
    17375 
    17376 > hide #19 models
    17377 
    17378 > hide #20 models
    17379 
    17380 > color #18 bychain
    17381 
    17382 > show #19 models
    17383 
    17384 > hide #18 models
    17385 
    17386 > color #19 bychain
    17387 
    17388 > show #20 models
    17389 
    17390 > hide #19 models
    17391 
    17392 > color #20 bychain
    17393 
    17394 > show #17 models
    17395 
    17396 > hide #20 models
    17397 
    17398 > color #17 bychain
    17399 
    17400 > show #1 models
    17401 
    17402 > hide #17 models
    17403 
    17404 > show #4 models
    17405 
    17406 > hide #1 models
    17407 
    17408 > show #1 models
    17409 
    17410 > hide #1 models
    17411 
    17412 > color #4 bychain
    17413 
    17414 > select #4/B
    17415 
    17416 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    17417 
    17418 > select #4/C
    17419 
    17420 7480 atoms, 7617 bonds, 949 residues, 1 model selected 
    17421 
    17422 > rainbow sel
    17423 
    17424 > select clear
    17425 
    17426 > select #4/A/B/C
    17427 
    17428 21596 atoms, 21969 bonds, 2729 residues, 1 model selected 
    17429 
    17430 > hide sel cartoons
    17431 
    17432 > undo
    17433 
    17434 > select #4/A/B/D
    17435 
    17436 21596 atoms, 21969 bonds, 2729 residues, 1 model selected 
    17437 
    17438 > hide sel cartoons
    17439 
    17440 > show sel cartoons
    17441 
    17442 > select clear
    17443 
    17444 > color #4 bychain
    17445 
    17446 > select #4/A
    17447 
    17448 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    17449 
    17450 > rainbow sel
    17451 
    17452 > select clear
    17453 
    17454 > select #4/B/C/D
    17455 
    17456 22018 atoms, 22410 bonds, 2788 residues, 1 model selected 
    17457 
    17458 > hide sel cartoons
    17459 
    17460 > show sel cartoons
    17461 
    17462 > select #4/D
    17463 
    17464 7480 atoms, 7617 bonds, 949 residues, 1 model selected 
    17465 
    17466 > rainbow sel
    17467 
    17468 > select clear
    17469 
    17470 > select #4/D
    17471 
    17472 7480 atoms, 7617 bonds, 949 residues, 1 model selected 
    17473 
    17474 > select clear
    17475 
    17476 > hide #4 models
    17477 
    17478 > show #1 models
    17479 
    17480 > color #1 bychain
    17481 
    17482 > select #1/A
    17483 
    17484 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    17485 
    17486 > rainbow sel
    17487 
    17488 > show #!2 models
    17489 
    17490 > hide #1 models
    17491 
    17492 > show #1 models
    17493 
    17494 > hide #!2 models
    17495 
    17496 > show #8 models
    17497 
    17498 > hide #1 models
    17499 
    17500 Drag select of 12 residues 
    17501 Drag select of 1 residues 
    17502 
    17503 > show #3 models
    17504 
    17505 Drag select of 3 atoms, 5 residues 
    17506 
    17507 > select #8/A:472
    17508 
    17509 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17510 
    17511 > preset cartoons/nucleotides cylinders/stubs
    17512 
    17513 Using preset: Cartoons/Nucleotides / Cylinders/Stubs 
    17514 Changed 69358 atom styles 
    17515 Preset expands to these ChimeraX commands:
    17516 
    17517    
    17518    
    17519     show nucleic
    17520     hide protein|solvent|H
    17521     surf hide
    17522     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    17523     ~worm
    17524     cartoon
    17525     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    17526     cartoon style ~(nucleic|strand) x round
    17527     cartoon style (nucleic|strand) x rect
    17528     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    17529     cartoon style nucleic x round width 1.6 thick 1.6
    17530     nucleotides stubs
    17531 
    17532  
    17533 
    17534 > preset cartoons/nucleotides licorice/ovals
    17535 
    17536 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    17537 Changed 0 atom styles 
    17538 Preset expands to these ChimeraX commands:
    17539 
    17540    
    17541    
    17542     show nucleic
    17543     hide protein|solvent|H
    17544     surf hide
    17545     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    17546     ~worm
    17547     cartoon
    17548     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    17549     cartoon style ~(nucleic|strand) x round
    17550     cartoon style (nucleic|strand) x rect
    17551     cartoon style protein modeh default arrows f x round width 1 thick 1
    17552     cartoon style nucleic x round width 1.6 thick 1.6
    17553     nucleotides tube/slab shape ellipsoid
    17554 
    17555  
    17556 
    17557 > preset cartoons/nucleotides ribbons/slabs
    17558 
    17559 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    17560 Changed 0 atom styles 
    17561 Preset expands to these ChimeraX commands:
    17562 
    17563    
    17564    
    17565     show nucleic
    17566     hide protein|solvent|H
    17567     surf hide
    17568     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    17569     ~worm
    17570     cartoon
    17571     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    17572     cartoon style ~(nucleic|strand) x round
    17573     cartoon style (nucleic|strand) x rect
    17574     nucleotides tube/slab shape box
    17575 
    17576  
    17577 
    17578 > hide #3 models
    17579 
    17580 > show #4 models
    17581 
    17582 > hide #8 models
    17583 
    17584 > select #4/A/B
    17585 
    17586 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    17587 
    17588 > rainbow sel
    17589 
    17590 > select clear
    17591 
    17592 > color #4 bychain
    17593 
    17594 > select #4/A/B
    17595 
    17596 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    17597 
    17598 > rainbow sel
    17599 
    17600 > select clear
    17601 
    17602 > show #12 models
    17603 
    17604 > show #13 models
    17605 
    17606 > show #14 models
    17607 
    17608 > show #15 models
    17609 
    17610 > color #4,12-15 bychain
    17611 
    17612 > select #4/A/B#12/A/B#13/A/B#14/A/B#15/A/B
    17613 
    17614 70580 atoms, 71760 bonds, 8900 residues, 5 models selected 
    17615 
    17616 > rainbow sel
    17617 
    17618 > hide #12 models
    17619 
    17620 > hide #13 models
    17621 
    17622 > hide #14 models
    17623 
    17624 > hide #15 models
    17625 
    17626 > select clear
    17627 
    17628 > hide #4 models
    17629 
    17630 > show #12 models
    17631 
    17632 > show #13 models
    17633 
    17634 > hide #12 models
    17635 
    17636 > show #14 models
    17637 
    17638 > hide #13 models
    17639 
    17640 > show #15 models
    17641 
    17642 > hide #14 models
    17643 
    17644 > show #!2 models
    17645 
    17646 > hide #!2 models
    17647 
    17648 > show #5 models
    17649 
    17650 > hide #15 models
    17651 
    17652 > color #5 bychain
    17653 
    17654 > select #5/B/C
    17655 
    17656 14960 atoms, 15234 bonds, 1898 residues, 1 model selected 
    17657 
    17658 > rainbow sel
    17659 
    17660 > select clear
    17661 
    17662 > hide #5 models
    17663 
    17664 > show #4 models
    17665 
    17666 > show #!2 models
    17667 
    17668 > hide #4 models
    17669 
    17670 Drag select of 18 residues 
    17671 
    17672 > show #4 models
    17673 
    17674 > hide #!2 models
    17675 
    17676 > show #12 models
    17677 
    17678 > hide #4 models
    17679 
    17680 > show #13 models
    17681 
    17682 > hide #12 models
    17683 
    17684 > show #14 models
    17685 
    17686 > hide #13 models
    17687 
    17688 > show #15 models
    17689 
    17690 > hide #14 models
    17691 
    17692 > hide #15 models
    17693 
    17694 > show #12 models
    17695 
    17696 > show #4 models
    17697 
    17698 > hide #12 models
    17699 
    17700 > show #13 models
    17701 
    17702 > hide #4 models
    17703 
    17704 > show #14 models
    17705 
    17706 > hide #13 models
    17707 
    17708 > show #15 models
    17709 
    17710 > hide #14 models
    17711 
    17712 > show #12 models
    17713 
    17714 > hide #15 models
    17715 
    17716 > show #!2 models
    17717 
    17718 > hide #12 models
    17719 
    17720 Drag select of 6 residues 
    17721 
    17722 > select #2/C:411
    17723 
    17724 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17725 
    17726 > select #2/C:411
    17727 
    17728 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17729 
    17730 > show sel atoms
    17731 
    17732 > select #2/C:411
    17733 
    17734 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17735 
    17736 > select #2/C:411
    17737 
    17738 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17739 
    17740 > show sel atoms
    17741 
    17742 > select clear
    17743 
    17744 > color #2 magenta
    17745 
    17746 > undo
    17747 
    17748 > select #2/C:412
    17749 
    17750 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17751 
    17752 > color (#!2 & sel) magenta
    17753 
    17754 > select #2/A:97
    17755 
    17756 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17757 
    17758 > show sel atoms
    17759 
    17760 > show #3 models
    17761 
    17762 > select #2/C:412
    17763 
    17764 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17765 
    17766 > rainbow sel
    17767 
    17768 > select #2/C:410
    17769 
    17770 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17771 
    17772 > select #2/C
    17773 
    17774 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    17775 
    17776 > select #2/C
    17777 
    17778 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    17779 
    17780 > rainbow sel
    17781 
    17782 > select #2/C:411
    17783 
    17784 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17785 
    17786 > color (#!2 & sel) magenta
    17787 
    17788 > select #2/A:97
    17789 
    17790 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17791 
    17792 > color (#!2 & sel) cornflower blue
    17793 
    17794 > select #2/C:411
    17795 
    17796 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17797 
    17798 > color (#!2 & sel) yellow
    17799 
    17800 > ui tool show "Color Actions"
    17801 
    17802 > color sel green yellow
    17803 
    17804 > select clear
    17805 
    17806 > select #2/C:411
    17807 
    17808 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17809 
    17810 > ui tool show "Color Actions"
    17811 
    17812 > color sel yellow
    17813 
    17814 > select clear
    17815 
    17816 > select #2/C:413
    17817 
    17818 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17819 
    17820 > select add #2/C:414
    17821 
    17822 16 atoms, 14 bonds, 2 residues, 2 models selected 
    17823 
    17824 > show sel atoms
    17825 
    17826 > select #2/A:94
    17827 
    17828 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17829 
    17830 > show sel atoms
    17831 
    17832 > color (#!2 & sel) cornflower blue
    17833 
    17834 > select add #2/C:413
    17835 
    17836 13 atoms, 11 bonds, 2 residues, 2 models selected 
    17837 
    17838 > select add #2/C:414
    17839 
    17840 21 atoms, 18 bonds, 3 residues, 3 models selected 
    17841 
    17842 > color (#!2 & sel) yellow
    17843 
    17844 > select clear
    17845 
    17846 > select #2/A:94
    17847 
    17848 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17849 
    17850 > color (#!2 & sel) cornflower blue
    17851 
    17852 > select clear
    17853 
    17854 > select #2/A
    17855 
    17856 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    17857 
    17858 > rainbow sel
    17859 
    17860 > select clear
    17861 
    17862 > select #2/B
    17863 
    17864 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    17865 
    17866 > color sel bychain
    17867 
    17868 > select #2/B
    17869 
    17870 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    17871 
    17872 > ui tool show "Color Actions"
    17873 
    17874 > color sel light steel blue
    17875 
    17876 > select #2/B
    17877 
    17878 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    17879 
    17880 > ui tool show "Color Actions"
    17881 
    17882 > color sel burly wood
    17883 
    17884 > color sel rosy brown
    17885 
    17886 > color sel tan
    17887 
    17888 > color sel dark salmon
    17889 
    17890 > color sel peru
    17891 
    17892 > color sel dark goldenrod
    17893 
    17894 > select #2/C
    17895 
    17896 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    17897 
    17898 > color sel light slate gray
    17899 
    17900 > select clear
    17901 
    17902 > select #2/D
    17903 
    17904 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    17905 
    17906 > ui tool show "Color Actions"
    17907 
    17908 > color sel light steel blue
    17909 
    17910 > select clear
    17911 
    17912 Drag select of 4 residues 
    17913 
    17914 > select clear
    17915 
    17916 > select #2/A:94
    17917 
    17918 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17919 
    17920 > select add #2/A:96
    17921 
    17922 12 atoms, 10 bonds, 2 residues, 2 models selected 
    17923 
    17924 > select subtract #2/A:96
    17925 
    17926 5 atoms, 4 bonds, 1 residue, 2 models selected 
    17927 
    17928 > select add #2/A:96
    17929 
    17930 12 atoms, 10 bonds, 2 residues, 2 models selected 
    17931 
    17932 > ui tool show "Color Actions"
    17933 
    17934 > color sel cyan
    17935 
    17936 > select #2/A:96
    17937 
    17938 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17939 
    17940 > undo
    17941 
    17942 > select #2/A:97
    17943 
    17944 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17945 
    17946 > select add #2/A:94
    17947 
    17948 16 atoms, 14 bonds, 2 residues, 2 models selected 
    17949 
    17950 > select #2/A
    17951 
    17952 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    17953 
    17954 > select #2/A
    17955 
    17956 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    17957 
    17958 > color sel gray
    17959 
    17960 > color sel silver
    17961 
    17962 > color sel dark gray
    17963 
    17964 > select clear
    17965 
    17966 > select #2/A:96
    17967 
    17968 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17969 
    17970 > select #2/A:95
    17971 
    17972 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17973 
    17974 > select #2/A:94
    17975 
    17976 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17977 
    17978 > select #2/A:94
    17979 
    17980 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17981 
    17982 > select #2/A:96
    17983 
    17984 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17985 
    17986 > select #2/A:96
    17987 
    17988 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17989 
    17990 > select #2/A:97
    17991 
    17992 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17993 
    17994 > select add #2/A:94
    17995 
    17996 16 atoms, 14 bonds, 2 residues, 2 models selected 
    17997 
    17998 > color sel deep sky blue
    17999 
    18000 > select add #2/C:411
    18001 
    18002 23 atoms, 20 bonds, 3 residues, 2 models selected 
    18003 
    18004 > select add #2/C:413
    18005 
    18006 31 atoms, 27 bonds, 4 residues, 3 models selected 
    18007 
    18008 > select add #2/C:414
    18009 
    18010 39 atoms, 34 bonds, 5 residues, 3 models selected 
    18011 
    18012 > color sel plum
    18013 
    18014 > color sel pale violet red
    18015 
    18016 > color sel magenta
    18017 
    18018 > select #2/A:97
    18019 
    18020 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18021 
    18022 > select clear
    18023 
    18024 > select #2/A:97
    18025 
    18026 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18027 
    18028 > select add #2/A:94
    18029 
    18030 16 atoms, 14 bonds, 2 residues, 2 models selected 
    18031 
    18032 > color sel deep sky blue
    18033 
    18034 > select clear
    18035 
    18036 > select add #2/C:411
    18037 
    18038 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18039 
    18040 > select add #2/C:413
    18041 
    18042 15 atoms, 13 bonds, 2 residues, 2 models selected 
    18043 
    18044 > select add #2/C:414
    18045 
    18046 23 atoms, 20 bonds, 3 residues, 2 models selected 
    18047 
    18048 > select add #2/A:97
    18049 
    18050 34 atoms, 30 bonds, 4 residues, 2 models selected 
    18051 
    18052 > select add #2/A:94
    18053 
    18054 39 atoms, 34 bonds, 5 residues, 3 models selected 
    18055 
    18056 > label (#!2 & sel) text "{0.label_one_letter_code}
    18057 > {0.number}{0.insertion_code}"
    18058 
    18059 > label height 1
    18060 
    18061 > select clear
    18062 
    18063 > hide #3 models
    18064 
    18065 > show #3 models
    18066 
    18067 > close session
    18068 
    18069 > open /Users/taic/Library/CloudStorage/OneDrive-
    18070 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
    18071 
    18072 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    18073 NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif 
    18074 --- 
    18075 note | Fetching CCD CO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CO/CO.cif 
    18076  
    18077 Chain information for fold_hqba_yhbq_co_model_0.cif #1 
    18078 --- 
    18079 Chain | Description 
    18080 A | . 
    18081 B | . 
    18082  
    18083 Computing secondary structure 
    18084 
    18085 > open /Users/taic/Library/CloudStorage/OneDrive-
    18086 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_1.cif
    18087 
    18088 Chain information for fold_hqba_yhbq_co_model_1.cif #2 
    18089 --- 
    18090 Chain | Description 
    18091 A | . 
    18092 B | . 
    18093  
    18094 
    18095 > open /Users/taic/Library/CloudStorage/OneDrive-
    18096 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_2.cif
    18097 
    18098 Chain information for fold_hqba_yhbq_co_model_2.cif #3 
    18099 --- 
    18100 Chain | Description 
    18101 A | . 
    18102 B | . 
    18103  
    18104 
    18105 > open /Users/taic/Library/CloudStorage/OneDrive-
    18106 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_3.cif
    18107 
    18108 Chain information for fold_hqba_yhbq_co_model_3.cif #4 
    18109 --- 
    18110 Chain | Description 
    18111 A | . 
    18112 B | . 
    18113  
    18114 
    18115 > open /Users/taic/Library/CloudStorage/OneDrive-
    18116 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_4.cif
    18117 
    18118 Chain information for fold_hqba_yhbq_co_model_4.cif #5 
    18119 --- 
    18120 Chain | Description 
    18121 A | . 
    18122 B | . 
    18123  
    18124 Computing secondary structure 
    18125 
    18126 > color bychain
    18127 
    18128 > open /Users/taic/Library/CloudStorage/OneDrive-
    18129 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_0.cif
    18130 
    18131 Chain information for fold_hqba_yhbp_co_model_0.cif #6 
    18132 --- 
    18133 Chain | Description 
    18134 A | . 
    18135 B | . 
    18136  
    18137 
    18138 > open /Users/taic/Library/CloudStorage/OneDrive-
    18139 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif
    18140 
    18141 Chain information for fold_hqba_yhbp_co_model_1.cif #7 
    18142 --- 
    18143 Chain | Description 
    18144 A | . 
    18145 B | . 
    18146  
    18147 
    18148 > open /Users/taic/Library/CloudStorage/OneDrive-
    18149 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_2.cif
    18150 
    18151 Chain information for fold_hqba_yhbp_co_model_2.cif #8 
    18152 --- 
    18153 Chain | Description 
    18154 A | . 
    18155 B | . 
    18156  
    18157 
    18158 > open /Users/taic/Library/CloudStorage/OneDrive-
    18159 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_3.cif
    18160 
    18161 Chain information for fold_hqba_yhbp_co_model_3.cif #9 
    18162 --- 
    18163 Chain | Description 
    18164 A | . 
    18165 B | . 
    18166  
    18167 
    18168 > open /Users/taic/Library/CloudStorage/OneDrive-
    18169 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_4.cif
    18170 
    18171 Chain information for fold_hqba_yhbp_co_model_4.cif #10 
    18172 --- 
    18173 Chain | Description 
    18174 A | . 
    18175 B | . 
    18176  
    18177 Computing secondary structure 
    18178 
    18179 > color bychain
    18180 
    18181 > open /Users/taic/Library/CloudStorage/OneDrive-
    18182 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_0.cif
    18183 
    18184 Chain information for fold_hqba_ubiu_model_0.cif #11 
    18185 --- 
    18186 Chain | Description 
    18187 A | . 
    18188 B | . 
    18189  
    18190 
    18191 > open /Users/taic/Library/CloudStorage/OneDrive-
    18192 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_1.cif
    18193 
    18194 Chain information for fold_hqba_ubiu_model_1.cif #12 
    18195 --- 
    18196 Chain | Description 
    18197 A | . 
    18198 B | . 
    18199  
    18200 
    18201 > open /Users/taic/Library/CloudStorage/OneDrive-
    18202 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_2.cif
    18203 
    18204 Chain information for fold_hqba_ubiu_model_2.cif #13 
    18205 --- 
    18206 Chain | Description 
    18207 A | . 
    18208 B | . 
    18209  
    18210 
    18211 > open /Users/taic/Library/CloudStorage/OneDrive-
    18212 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_3.cif
    18213 
    18214 Chain information for fold_hqba_ubiu_model_3.cif #14 
    18215 --- 
    18216 Chain | Description 
    18217 A | . 
    18218 B | . 
    18219  
    18220 
    18221 > open /Users/taic/Library/CloudStorage/OneDrive-
    18222 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_4.cif
    18223 
    18224 Chain information for fold_hqba_ubiu_model_4.cif #15 
    18225 --- 
    18226 Chain | Description 
    18227 A | . 
    18228 B | . 
    18229  
    18230 Computing secondary structure 
    18231 
    18232 > color bychain
    18233 
    18234 > open /Users/taic/Library/CloudStorage/OneDrive-
    18235 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_0.cif
    18236 
    18237 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    18238 NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_0.cif 
    18239 --- 
    18240 note | Fetching CCD FE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif 
    18241  
    18242 Chain information for fold_hqba_nfua_fe4_co_model_0.cif #16 
    18243 --- 
    18244 Chain | Description 
    18245 A | . 
    18246 B | . 
    18247  
    18248 
    18249 > open /Users/taic/Library/CloudStorage/OneDrive-
    18250 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_1.cif
    18251 
    18252 Chain information for fold_hqba_nfua_fe4_co_model_1.cif #17 
    18253 --- 
    18254 Chain | Description 
    18255 A | . 
    18256 B | . 
    18257  
    18258 
    18259 > open /Users/taic/Library/CloudStorage/OneDrive-
    18260 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_2.cif
    18261 
    18262 Chain information for fold_hqba_nfua_fe4_co_model_2.cif #18 
    18263 --- 
    18264 Chain | Description 
    18265 A | . 
    18266 B | . 
    18267  
    18268 
    18269 > open /Users/taic/Library/CloudStorage/OneDrive-
    18270 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_3.cif
    18271 
    18272 Chain information for fold_hqba_nfua_fe4_co_model_3.cif #19 
    18273 --- 
    18274 Chain | Description 
    18275 A | . 
    18276 B | . 
    18277  
    18278 
    18279 > open /Users/taic/Library/CloudStorage/OneDrive-
    18280 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_4.cif
    18281 
    18282 Chain information for fold_hqba_nfua_fe4_co_model_4.cif #20 
    18283 --- 
    18284 Chain | Description 
    18285 A | . 
    18286 B | . 
    18287  
    18288 Computing secondary structure 
    18289 
    18290 > color bychain
    18291 
    18292 > select /AA
    18293 
    18294 Nothing selected 
    18295 
    18296 > select /A
    18297 
    18298 26220 atoms, 26820 bonds, 3340 residues, 20 models selected 
    18299 
    18300 > ui tool show Matchmaker
    18301 
    18302 > matchmaker #2-20 to #1 & sel
    18303 
    18304 Computing secondary structure 
    18305 Parameters 
    18306 --- 
    18307 Chain pairing | bb 
    18308 Alignment algorithm | Needleman-Wunsch 
    18309 Similarity matrix | BLOSUM-62 
    18310 SS fraction | 0.3 
    18311 Gap open (HH/SS/other) | 18/18/6 
    18312 Gap extend | 1 
    18313 SS matrix |  |  | H | S | O 
    18314 ---|---|---|--- 
    18315 H | 6 | -9 | -6 
    18316 S |  | 6 | -6 
    18317 O |  |  | 4 
    18318 Iteration cutoff | 2 
    18319  
    18320 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18321 fold_hqba_yhbq_co_model_1.cif, chain A (#2), sequence alignment score = 875 
    18322 RMSD between 167 pruned atom pairs is 0.416 angstroms; (across all 167 pairs:
    18323 0.416) 
    18324  
    18325 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18326 fold_hqba_yhbq_co_model_2.cif, chain A (#3), sequence alignment score = 871.4 
    18327 RMSD between 167 pruned atom pairs is 0.283 angstroms; (across all 167 pairs:
    18328 0.283) 
    18329  
    18330 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18331 fold_hqba_yhbq_co_model_3.cif, chain A (#4), sequence alignment score = 875 
    18332 RMSD between 167 pruned atom pairs is 0.340 angstroms; (across all 167 pairs:
    18333 0.340) 
    18334  
    18335 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18336 fold_hqba_yhbq_co_model_4.cif, chain A (#5), sequence alignment score = 875 
    18337 RMSD between 167 pruned atom pairs is 0.303 angstroms; (across all 167 pairs:
    18338 0.303) 
    18339  
    18340 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18341 fold_hqba_yhbp_co_model_0.cif, chain A (#6), sequence alignment score = 853.4 
    18342 RMSD between 167 pruned atom pairs is 0.452 angstroms; (across all 167 pairs:
    18343 0.452) 
    18344  
    18345 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18346 fold_hqba_yhbp_co_model_1.cif, chain A (#7), sequence alignment score = 871.4 
    18347 RMSD between 166 pruned atom pairs is 0.483 angstroms; (across all 167 pairs:
    18348 0.507) 
    18349  
    18350 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18351 fold_hqba_yhbp_co_model_2.cif, chain A (#8), sequence alignment score = 871.4 
    18352 RMSD between 167 pruned atom pairs is 0.304 angstroms; (across all 167 pairs:
    18353 0.304) 
    18354  
    18355 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18356 fold_hqba_yhbp_co_model_3.cif, chain A (#9), sequence alignment score = 871.4 
    18357 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    18358 0.339) 
    18359  
    18360 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18361 fold_hqba_yhbp_co_model_4.cif, chain A (#10), sequence alignment score = 867.8 
    18362 RMSD between 167 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
    18363 0.350) 
    18364  
    18365 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18366 fold_hqba_ubiu_model_0.cif, chain A (#11), sequence alignment score = 871.4 
    18367 RMSD between 167 pruned atom pairs is 0.343 angstroms; (across all 167 pairs:
    18368 0.343) 
    18369  
    18370 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18371 fold_hqba_ubiu_model_1.cif, chain A (#12), sequence alignment score = 871.4 
    18372 RMSD between 167 pruned atom pairs is 0.286 angstroms; (across all 167 pairs:
    18373 0.286) 
    18374  
    18375 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18376 fold_hqba_ubiu_model_2.cif, chain A (#13), sequence alignment score = 875 
    18377 RMSD between 167 pruned atom pairs is 0.302 angstroms; (across all 167 pairs:
    18378 0.302) 
    18379  
    18380 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18381 fold_hqba_ubiu_model_3.cif, chain A (#14), sequence alignment score = 871.4 
    18382 RMSD between 167 pruned atom pairs is 0.276 angstroms; (across all 167 pairs:
    18383 0.276) 
    18384  
    18385 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18386 fold_hqba_ubiu_model_4.cif, chain A (#15), sequence alignment score = 875 
    18387 RMSD between 167 pruned atom pairs is 0.268 angstroms; (across all 167 pairs:
    18388 0.268) 
    18389  
    18390 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18391 fold_hqba_nfua_fe4_co_model_0.cif, chain A (#16), sequence alignment score =
    18392 871.4 
    18393 RMSD between 167 pruned atom pairs is 0.331 angstroms; (across all 167 pairs:
    18394 0.331) 
    18395  
    18396 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18397 fold_hqba_nfua_fe4_co_model_1.cif, chain A (#17), sequence alignment score =
    18398 871.4 
    18399 RMSD between 167 pruned atom pairs is 0.226 angstroms; (across all 167 pairs:
    18400 0.226) 
    18401  
    18402 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18403 fold_hqba_nfua_fe4_co_model_2.cif, chain A (#18), sequence alignment score =
    18404 871.4 
    18405 RMSD between 166 pruned atom pairs is 0.568 angstroms; (across all 167 pairs:
    18406 0.589) 
    18407  
    18408 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18409 fold_hqba_nfua_fe4_co_model_3.cif, chain A (#19), sequence alignment score =
    18410 871.4 
    18411 RMSD between 167 pruned atom pairs is 0.390 angstroms; (across all 167 pairs:
    18412 0.390) 
    18413  
    18414 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18415 fold_hqba_nfua_fe4_co_model_4.cif, chain A (#20), sequence alignment score =
    18416 849.8 
    18417 RMSD between 167 pruned atom pairs is 0.211 angstroms; (across all 167 pairs:
    18418 0.211) 
    18419  
    18420 
    18421 > hide #6 models
    18422 
    18423 > hide #7 models
    18424 
    18425 > hide #8 models
    18426 
    18427 > hide #9 models
    18428 
    18429 > hide #10 models
    18430 
    18431 > hide #11 models
    18432 
    18433 > hide #12 models
    18434 
    18435 > hide #13 models
    18436 
    18437 > hide #14 models
    18438 
    18439 > hide #15 models
    18440 
    18441 > hide #16 models
    18442 
    18443 > hide #17 models
    18444 
    18445 > hide #18 models
    18446 
    18447 > hide #19 models
    18448 
    18449 > hide #20 models
    18450 
    18451 > open 4RS2 fromDatabase pdb format mmcif
    18452 
    18453 Summary of feedback from opening 4RS2 fetched from pdb 
    18454 --- 
    18455 notes | Fetching compressed mmCIF 4rs2 from http://files.rcsb.org/download/4rs2.cif 
    18456 Fetching CCD COA from
    18457 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/COA/COA.cif 
    18458  
    18459 4rs2 title: 
    18460 1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
    18461 Escherichia coli in Complex with CoA [more info...] 
    18462  
    18463 Chain information for 4rs2 #21 
    18464 --- 
    18465 Chain | Description | UniProt 
    18466 A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167 
    18467  
    18468 Non-standard residues in 4rs2 #21 
    18469 --- 
    18470 COA — coenzyme A 
    18471  
    18472 4rs2 mmCIF Assemblies 
    18473 --- 
    18474 1| author_and_software_defined_assembly 
    18475 2| author_and_software_defined_assembly 
    18476  
    18477 331 atoms have alternate locations. Control/examine alternate locations with
    18478 Altloc Explorer [start tool...] or the altlocs command. 
    18479 
    18480 > select /A
    18481 
    18482 27898 atoms, 28311 bonds, 3744 residues, 21 models selected 
    18483 
    18484 > ui tool show Matchmaker
    18485 
    18486 > matchmaker #21 to #1 & sel
    18487 
    18488 Computing secondary structure 
    18489 Parameters 
    18490 --- 
    18491 Chain pairing | bb 
    18492 Alignment algorithm | Needleman-Wunsch 
    18493 Similarity matrix | BLOSUM-62 
    18494 SS fraction | 0.3 
    18495 Gap open (HH/SS/other) | 18/18/6 
    18496 Gap extend | 1 
    18497 SS matrix |  |  | H | S | O 
    18498 ---|---|---|--- 
    18499 H | 6 | -9 | -6 
    18500 S |  | 6 | -6 
    18501 O |  |  | 4 
    18502 Iteration cutoff | 2 
    18503  
    18504 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
    18505 (#21), sequence alignment score = 836 
    18506 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    18507 0.670) 
    18508  
    18509 
    18510 > select clear
    18511 
    18512 > select #21/A
    18513 
    18514 1678 atoms, 1491 bonds, 404 residues, 1 model selected 
    18515 
    18516 > hide sel cartoons
    18517 
    18518 > hide sel atoms
    18519 
    18520 > select clear
    18521 
    18522 > open /Users/taic/Library/CloudStorage/OneDrive-
    18523 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/Hfq6_YhbS.af2.4rs2.pdb
    18524 
    18525 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    18526 NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/Hfq6_YhbS.af2.4rs2.pdb 
    18527 --- 
    18528 warnings | Start residue of secondary structure not found: HELIX 8 8 GLN B 8 GLU B 18 1 11 
    18529 Start residue of secondary structure not found: HELIX 9 9 LYS B 56 ALA B 58 1
    18530 3 
    18531 Start residue of secondary structure not found: HELIX 10 10 GLN C 8 GLU C 18 1
    18532 11 
    18533 Start residue of secondary structure not found: HELIX 11 11 LYS C 56 ALA C 58
    18534 1 3 
    18535 Start residue of secondary structure not found: HELIX 12 12 SER C 72 ASN C 74
    18536 1 3 
    18537 39 messages similar to the above omitted 
    18538  
    18539 Chain information for Hfq6_YhbS.af2.4rs2.pdb 
    18540 --- 
    18541 Chain | Description 
    18542 22.1/A | No description available 
    18543 22.2/A | No description available 
    18544 22.1/B 22.1/C 22.1/D 22.1/E 22.1/F 22.1/G | No description available 
    18545 22.2/B | No description available 
    18546  
    18547 331 atoms have alternate locations. Control/examine alternate locations with
    18548 Altloc Explorer [start tool...] or the altlocs command. 
    18549 
    18550 > hide #1-5,21#!22.1-2 atoms
    18551 
    18552 > hide #!22.2 models
    18553 
    18554 > show #!22.2 models
    18555 
    18556 > hide #!22.1 models
    18557 
    18558 > show #!22.1 models
    18559 
    18560 > select #1/A
    18561 
    18562 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    18563 
    18564 > ui tool show Matchmaker
    18565 
    18566 > matchmaker #!22.2 to #1 & sel
    18567 
    18568 Computing secondary structure 
    18569 Parameters 
    18570 --- 
    18571 Chain pairing | bb 
    18572 Alignment algorithm | Needleman-Wunsch 
    18573 Similarity matrix | BLOSUM-62 
    18574 SS fraction | 0.3 
    18575 Gap open (HH/SS/other) | 18/18/6 
    18576 Gap extend | 1 
    18577 SS matrix |  |  | H | S | O 
    18578 ---|---|---|--- 
    18579 H | 6 | -9 | -6 
    18580 S |  | 6 | -6 
    18581 O |  |  | 4 
    18582 Iteration cutoff | 2 
    18583  
    18584 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18585 Hfq6_YhbS.af2.4rs2.pdb, chain B (#22.2), sequence alignment score = 836 
    18586 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    18587 0.670) 
    18588  
    18589 
    18590 > hide #21 models
    18591 
    18592 > show #21 models
    18593 
    18594 > ui tool show Matchmaker
    18595 
    18596 > matchmaker #!22.1-2 to #1 & sel
    18597 
    18598 Computing secondary structure 
    18599 Parameters 
    18600 --- 
    18601 Chain pairing | bb 
    18602 Alignment algorithm | Needleman-Wunsch 
    18603 Similarity matrix | BLOSUM-62 
    18604 SS fraction | 0.3 
    18605 Gap open (HH/SS/other) | 18/18/6 
    18606 Gap extend | 1 
    18607 SS matrix |  |  | H | S | O 
    18608 ---|---|---|--- 
    18609 H | 6 | -9 | -6 
    18610 S |  | 6 | -6 
    18611 O |  |  | 4 
    18612 Iteration cutoff | 2 
    18613  
    18614 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18615 Hfq6_YhbS.af2.4rs2.pdb, chain A (#22.1), sequence alignment score = 875 
    18616 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    18617 0.339) 
    18618  
    18619 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18620 Hfq6_YhbS.af2.4rs2.pdb, chain B (#22.2), sequence alignment score = 836 
    18621 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    18622 0.670) 
    18623  
    18624 
    18625 > hide #21 models
    18626 
    18627 > show #21 models
    18628 
    18629 > hide #21 models
    18630 
    18631 > show #21 models
    18632 
    18633 > hide #1 models
    18634 
    18635 > hide #2 models
    18636 
    18637 > hide #3 models
    18638 
    18639 > hide #4 models
    18640 
    18641 > hide #5 models
    18642 
    18643 > hide #21 models
    18644 
    18645 > select add #22
    18646 
    18647 16588 atoms, 16330 bonds, 40 pseudobonds, 1769 residues, 6 models selected 
    18648 
    18649 > delete atoms (#!22.1-2 & sel)
    18650 
    18651 > delete bonds (#!22.1-2 & sel)
    18652 
    18653 > show #21 models
    18654 
    18655 > select add #21
    18656 
    18657 4709 atoms, 4356 bonds, 990 residues, 3 models selected 
    18658 
    18659 > select subtract #21
    18660 
    18661 1311 atoms, 1341 bonds, 167 residues, 2 models selected 
    18662 
    18663 > hide #22 models
    18664 
    18665 > hide #21 models
    18666 
    18667 > select subtract #22
    18668 
    18669 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    18670 
    18671 > show #22 models
    18672 
    18673 > select add #22
    18674 
    18675 1311 atoms, 1341 bonds, 167 residues, 2 models selected 
    18676 
    18677 > select add #1
    18678 
    18679 2107 atoms, 2148 bonds, 268 residues, 2 models selected 
    18680 
    18681 > select subtract #1
    18682 
    18683 1 model selected 
    18684 
    18685 > show #1 models
    18686 
    18687 > hide #1 models
    18688 
    18689 > delete atoms #22
    18690 
    18691 > delete bonds #22
    18692 
    18693 > open /Users/taic/Library/CloudStorage/OneDrive-
    18694 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/AF2-multi/Hfq6mer_YhbS/YhbS-
    18695 > Hfq6mer.ranked_0.pdb
    18696 
    18697 Chain information for YhbS-Hfq6mer.ranked_0.pdb #23 
    18698 --- 
    18699 Chain | Description 
    18700 A | No description available 
    18701 B C D E F G | No description available 
    18702  
    18703 
    18704 > hide #23 atoms
    18705 
    18706 > show #23 cartoons
    18707 
    18708 Computing secondary structure 
    18709 
    18710 > select #1/A
    18711 
    18712 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    18713 
    18714 > ui tool show Matchmaker
    18715 
    18716 > matchmaker #2-21,23 to #1 & sel
    18717 
    18718 Computing secondary structure 
    18719 Parameters 
    18720 --- 
    18721 Chain pairing | bb 
    18722 Alignment algorithm | Needleman-Wunsch 
    18723 Similarity matrix | BLOSUM-62 
    18724 SS fraction | 0.3 
    18725 Gap open (HH/SS/other) | 18/18/6 
    18726 Gap extend | 1 
    18727 SS matrix |  |  | H | S | O 
    18728 ---|---|---|--- 
    18729 H | 6 | -9 | -6 
    18730 S |  | 6 | -6 
    18731 O |  |  | 4 
    18732 Iteration cutoff | 2 
    18733  
    18734 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18735 fold_hqba_yhbq_co_model_1.cif, chain A (#2), sequence alignment score = 875 
    18736 RMSD between 167 pruned atom pairs is 0.416 angstroms; (across all 167 pairs:
    18737 0.416) 
    18738  
    18739 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18740 fold_hqba_yhbq_co_model_2.cif, chain A (#3), sequence alignment score = 871.4 
    18741 RMSD between 167 pruned atom pairs is 0.283 angstroms; (across all 167 pairs:
    18742 0.283) 
    18743  
    18744 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18745 fold_hqba_yhbq_co_model_3.cif, chain A (#4), sequence alignment score = 875 
    18746 RMSD between 167 pruned atom pairs is 0.340 angstroms; (across all 167 pairs:
    18747 0.340) 
    18748  
    18749 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18750 fold_hqba_yhbq_co_model_4.cif, chain A (#5), sequence alignment score = 875 
    18751 RMSD between 167 pruned atom pairs is 0.303 angstroms; (across all 167 pairs:
    18752 0.303) 
    18753  
    18754 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18755 fold_hqba_yhbp_co_model_0.cif, chain A (#6), sequence alignment score = 853.4 
    18756 RMSD between 167 pruned atom pairs is 0.452 angstroms; (across all 167 pairs:
    18757 0.452) 
    18758  
    18759 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18760 fold_hqba_yhbp_co_model_1.cif, chain A (#7), sequence alignment score = 871.4 
    18761 RMSD between 166 pruned atom pairs is 0.483 angstroms; (across all 167 pairs:
    18762 0.507) 
    18763  
    18764 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18765 fold_hqba_yhbp_co_model_2.cif, chain A (#8), sequence alignment score = 871.4 
    18766 RMSD between 167 pruned atom pairs is 0.304 angstroms; (across all 167 pairs:
    18767 0.304) 
    18768  
    18769 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18770 fold_hqba_yhbp_co_model_3.cif, chain A (#9), sequence alignment score = 871.4 
    18771 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    18772 0.339) 
    18773  
    18774 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18775 fold_hqba_yhbp_co_model_4.cif, chain A (#10), sequence alignment score = 867.8 
    18776 RMSD between 167 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
    18777 0.350) 
    18778  
    18779 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18780 fold_hqba_ubiu_model_0.cif, chain A (#11), sequence alignment score = 871.4 
    18781 RMSD between 167 pruned atom pairs is 0.343 angstroms; (across all 167 pairs:
    18782 0.343) 
    18783  
    18784 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18785 fold_hqba_ubiu_model_1.cif, chain A (#12), sequence alignment score = 871.4 
    18786 RMSD between 167 pruned atom pairs is 0.286 angstroms; (across all 167 pairs:
    18787 0.286) 
    18788  
    18789 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18790 fold_hqba_ubiu_model_2.cif, chain A (#13), sequence alignment score = 875 
    18791 RMSD between 167 pruned atom pairs is 0.302 angstroms; (across all 167 pairs:
    18792 0.302) 
    18793  
    18794 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18795 fold_hqba_ubiu_model_3.cif, chain A (#14), sequence alignment score = 871.4 
    18796 RMSD between 167 pruned atom pairs is 0.276 angstroms; (across all 167 pairs:
    18797 0.276) 
    18798  
    18799 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18800 fold_hqba_ubiu_model_4.cif, chain A (#15), sequence alignment score = 875 
    18801 RMSD between 167 pruned atom pairs is 0.268 angstroms; (across all 167 pairs:
    18802 0.268) 
    18803  
    18804 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18805 fold_hqba_nfua_fe4_co_model_0.cif, chain A (#16), sequence alignment score =
    18806 871.4 
    18807 RMSD between 167 pruned atom pairs is 0.331 angstroms; (across all 167 pairs:
    18808 0.331) 
    18809  
    18810 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18811 fold_hqba_nfua_fe4_co_model_1.cif, chain A (#17), sequence alignment score =
    18812 871.4 
    18813 RMSD between 167 pruned atom pairs is 0.226 angstroms; (across all 167 pairs:
    18814 0.226) 
    18815  
    18816 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18817 fold_hqba_nfua_fe4_co_model_2.cif, chain A (#18), sequence alignment score =
    18818 871.4 
    18819 RMSD between 166 pruned atom pairs is 0.568 angstroms; (across all 167 pairs:
    18820 0.589) 
    18821  
    18822 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18823 fold_hqba_nfua_fe4_co_model_3.cif, chain A (#19), sequence alignment score =
    18824 871.4 
    18825 RMSD between 167 pruned atom pairs is 0.390 angstroms; (across all 167 pairs:
    18826 0.390) 
    18827  
    18828 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    18829 fold_hqba_nfua_fe4_co_model_4.cif, chain A (#20), sequence alignment score =
    18830 849.8 
    18831 RMSD between 167 pruned atom pairs is 0.211 angstroms; (across all 167 pairs:
    18832 0.211) 
    18833  
    18834 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
    18835 (#21), sequence alignment score = 836 
    18836 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    18837 0.670) 
    18838  
    18839 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
    18840 Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875 
    18841 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    18842 0.339) 
    18843  
    18844 
    18845 > hide #22 models
    18846 
    18847 > show #1 models
    18848 
    18849 > hide #1 models
    18850 
    18851 > select #23/B
    18852 
    18853 1552 atoms, 1566 bonds, 102 residues, 1 model selected 
    18854 
    18855 > Sel #23/B/C/D/E/F/G
    18856 
    18857 Unknown command: Sel #23/B/C/D/E/F/G 
    18858 
    18859 > Sel #23/B#23/C#23/D#23/E#23/F#23/G
    18860 
    18861 Unknown command: Sel #23/B#23/C#23/D#23/E#23/F#23/G 
    18862 
    18863 > select #23/B#23/C#23/D#23/E#23/F#23/G
    18864 
    18865 9312 atoms, 9396 bonds, 612 residues, 1 model selected 
    18866 
    18867 > ui tool show "Color Actions"
    18868 
    18869 > color sel deep sky blue
    18870 
    18871 > color sel royal blue
    18872 
    18873 > color sel dodger blue
    18874 
    18875 > color sel royal blue
    18876 
    18877 > select clear
    18878 
    18879 > show #21 models
    18880 
    18881 > select #21
    18882 
    18883 3398 atoms, 3015 bonds, 823 residues, 1 model selected 
    18884 
    18885 > show sel atoms
    18886 
    18887 > hide sel atoms
    18888 
    18889 > hide #23 models
    18890 
    18891 > delete atoms sel
    18892 
    18893 > delete bonds sel
    18894 
    18895 > open 4RS2 fromDatabase pdb format mmcif
    18896 
    18897 4rs2 title: 
    18898 1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
    18899 Escherichia coli in Complex with CoA [more info...] 
    18900  
    18901 Chain information for 4rs2 #21 
    18902 --- 
    18903 Chain | Description | UniProt 
    18904 A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167 
    18905  
    18906 Non-standard residues in 4rs2 #21 
    18907 --- 
    18908 COA — coenzyme A 
    18909  
    18910 4rs2 mmCIF Assemblies 
    18911 --- 
    18912 1| author_and_software_defined_assembly 
    18913 2| author_and_software_defined_assembly 
    18914  
    18915 331 atoms have alternate locations. Control/examine alternate locations with
    18916 Altloc Explorer [start tool...] or the altlocs command. 
    18917 
    18918 > select #1/A
    18919 
    18920 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    18921 
    18922 > ui tool show Matchmaker
    18923 
    18924 > matchmaker #23 to #1 & sel
    18925 
    18926 Computing secondary structure 
    18927 Parameters 
    18928 --- 
    18929 Chain pairing | bb 
    18930 Alignment algorithm | Needleman-Wunsch 
    18931 Similarity matrix | BLOSUM-62 
    18932 SS fraction | 0.3 
    18933 Gap open (HH/SS/other) | 18/18/6 
    18934 Gap extend | 1 
    18935 SS matrix |  |  | H | S | O 
    18936 ---|---|---|--- 
    18937 H | 6 | -9 | -6 
    18938 S |  | 6 | -6 
    18939 O |  |  | 4 
    18940 Iteration cutoff | 2 
    18941  
    18942 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
    18943 Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875 
    18944 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    18945 0.339) 
    18946  
    18947 
    18948 > matchmaker #23 to #1 & sel
    18949 
    18950 Computing secondary structure 
    18951 Parameters 
    18952 --- 
    18953 Chain pairing | bb 
    18954 Alignment algorithm | Needleman-Wunsch 
    18955 Similarity matrix | BLOSUM-62 
    18956 SS fraction | 0.3 
    18957 Gap open (HH/SS/other) | 18/18/6 
    18958 Gap extend | 1 
    18959 SS matrix |  |  | H | S | O 
    18960 ---|---|---|--- 
    18961 H | 6 | -9 | -6 
    18962 S |  | 6 | -6 
    18963 O |  |  | 4 
    18964 Iteration cutoff | 2 
    18965  
    18966 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
    18967 Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875 
    18968 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    18969 0.339) 
    18970  
    18971 
    18972 > show #1 models
    18973 
    18974 > select #1/A
    18975 
    18976 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    18977 
    18978 > matchmaker #21 to #1 & sel
    18979 
    18980 Computing secondary structure 
    18981 Parameters 
    18982 --- 
    18983 Chain pairing | bb 
    18984 Alignment algorithm | Needleman-Wunsch 
    18985 Similarity matrix | BLOSUM-62 
    18986 SS fraction | 0.3 
    18987 Gap open (HH/SS/other) | 18/18/6 
    18988 Gap extend | 1 
    18989 SS matrix |  |  | H | S | O 
    18990 ---|---|---|--- 
    18991 H | 6 | -9 | -6 
    18992 S |  | 6 | -6 
    18993 O |  |  | 4 
    18994 Iteration cutoff | 2 
    18995  
    18996 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
    18997 (#21), sequence alignment score = 836 
    18998 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    18999 0.670) 
    19000  
    19001 
    19002 > select #21/A
    19003 
    19004 1678 atoms, 1491 bonds, 404 residues, 1 model selected 
    19005 
    19006 > hide sel cartoons
    19007 
    19008 > hide sel atoms
    19009 
    19010 > hide #21 models
    19011 
    19012 > select #1
    19013 
    19014 2107 atoms, 2148 bonds, 268 residues, 1 model selected 
    19015 
    19016 > show sel atoms
    19017 
    19018 > select #1/C:1@CO
    19019 
    19020 1 atom, 1 residue, 1 model selected 
    19021 
    19022 > select ~sel & ##selected
    19023 
    19024 2106 atoms, 2148 bonds, 267 residues, 1 model selected 
    19025 
    19026 > hide sel atoms
    19027 
    19028 > select clear
    19029 
    19030 > select #1/C:1@CO
    19031 
    19032 1 atom, 1 residue, 1 model selected 
    19033 
    19034 > select ::name="CO"
    19035 
    19036 15 atoms, 15 residues, 15 models selected 
    19037 
    19038 > ui tool show "Color Actions"
    19039 
    19040 > color sel dim gray
    19041 
    19042 > select clear
    19043 
    19044 > show #21 models
    19045 
    19046 > show #23 models
    19047 
    19048 > hide #23 models
    19049 
    19050 > show #23 models
    19051 
    19052 > hide #23 models
    19053 
    19054 > open /Users/taic/Library/CloudStorage/OneDrive-
    19055 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_0.cif
    19056 
    19057 Chain information for fold_hqba_hfq1_65x6_co_model_0.cif #24 
    19058 --- 
    19059 Chain | Description 
    19060 A | . 
    19061 B C D E F G | . 
    19062  
    19063 
    19064 > open /Users/taic/Library/CloudStorage/OneDrive-
    19065 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_1.cif
    19066 
    19067 Chain information for fold_hqba_hfq1_65x6_co_model_1.cif #25 
    19068 --- 
    19069 Chain | Description 
    19070 A | . 
    19071 B C D E F G | . 
    19072  
    19073 
    19074 > open /Users/taic/Library/CloudStorage/OneDrive-
    19075 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_2.cif
    19076 
    19077 Chain information for fold_hqba_hfq1_65x6_co_model_2.cif #26 
    19078 --- 
    19079 Chain | Description 
    19080 A | . 
    19081 B C D E F G | . 
    19082  
    19083 
    19084 > open /Users/taic/Library/CloudStorage/OneDrive-
    19085 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_3.cif
    19086 
    19087 Chain information for fold_hqba_hfq1_65x6_co_model_3.cif #27 
    19088 --- 
    19089 Chain | Description 
    19090 A | . 
    19091 B C D E F G | . 
    19092  
    19093 
    19094 > open /Users/taic/Library/CloudStorage/OneDrive-
    19095 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_4.cif
    19096 
    19097 Chain information for fold_hqba_hfq1_65x6_co_model_4.cif #28 
    19098 --- 
    19099 Chain | Description 
    19100 A | . 
    19101 B C D E F G | . 
    19102  
    19103 
    19104 > hide #21 models
    19105 
    19106 > select #24#25#26#27#28
    19107 
    19108 22010 atoms, 22395 bonds, 2790 residues, 5 models selected 
    19109 
    19110 > hide sel atoms
    19111 
    19112 > show sel cartoons
    19113 
    19114 Computing secondary structure 
    19115 
    19116 > open /Users/taic/Library/CloudStorage/OneDrive-
    19117 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_0.cif
    19118 
    19119 Chain information for fold_hqba_hfqx6_co_model_0.cif #29 
    19120 --- 
    19121 Chain | Description 
    19122 A | . 
    19123 B C D E F G | . 
    19124  
    19125 
    19126 > open /Users/taic/Library/CloudStorage/OneDrive-
    19127 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_1.cif
    19128 
    19129 Chain information for fold_hqba_hfqx6_co_model_1.cif #30 
    19130 --- 
    19131 Chain | Description 
    19132 A | . 
    19133 B C D E F G | . 
    19134  
    19135 
    19136 > open /Users/taic/Library/CloudStorage/OneDrive-
    19137 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_2.cif
    19138 
    19139 Chain information for fold_hqba_hfqx6_co_model_2.cif #31 
    19140 --- 
    19141 Chain | Description 
    19142 A | . 
    19143 B C D E F G | . 
    19144  
    19145 
    19146 > open /Users/taic/Library/CloudStorage/OneDrive-
    19147 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_3.cif
    19148 
    19149 Chain information for fold_hqba_hfqx6_co_model_3.cif #32 
    19150 --- 
    19151 Chain | Description 
    19152 A | . 
    19153 B C D E F G | . 
    19154  
    19155 
    19156 > open /Users/taic/Library/CloudStorage/OneDrive-
    19157 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_4.cif
    19158 
    19159 Chain information for fold_hqba_hfqx6_co_model_4.cif #33 
    19160 --- 
    19161 Chain | Description 
    19162 A | . 
    19163 B C D E F G | . 
    19164  
    19165 
    19166 > select add #29
    19167 
    19168 28038 atoms, 28536 bonds, 3570 residues, 6 models selected 
    19169 
    19170 > select add #30
    19171 
    19172 34066 atoms, 34677 bonds, 4350 residues, 7 models selected 
    19173 
    19174 > select add #31
    19175 
    19176 40094 atoms, 40818 bonds, 5130 residues, 8 models selected 
    19177 
    19178 > select add #32
    19179 
    19180 46122 atoms, 46959 bonds, 5910 residues, 9 models selected 
    19181 
    19182 > select add #33
    19183 
    19184 52150 atoms, 53100 bonds, 6690 residues, 10 models selected 
    19185 
    19186 > hide sel atoms
    19187 
    19188 > show sel cartoons
    19189 
    19190 Computing secondary structure 
    19191 
    19192 > select #1
    19193 
    19194 2107 atoms, 2148 bonds, 268 residues, 1 model selected 
    19195 
    19196 > select #1/A
    19197 
    19198 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    19199 
    19200 > ui tool show Matchmaker
    19201 
    19202 > matchmaker #24-33 to #1 & sel
    19203 
    19204 Computing secondary structure 
    19205 Parameters 
    19206 --- 
    19207 Chain pairing | bb 
    19208 Alignment algorithm | Needleman-Wunsch 
    19209 Similarity matrix | BLOSUM-62 
    19210 SS fraction | 0.3 
    19211 Gap open (HH/SS/other) | 18/18/6 
    19212 Gap extend | 1 
    19213 SS matrix |  |  | H | S | O 
    19214 ---|---|---|--- 
    19215 H | 6 | -9 | -6 
    19216 S |  | 6 | -6 
    19217 O |  |  | 4 
    19218 Iteration cutoff | 2 
    19219  
    19220 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19221 fold_hqba_hfq1_65x6_co_model_0.cif, chain A (#24), sequence alignment score =
    19222 867.8 
    19223 RMSD between 167 pruned atom pairs is 0.225 angstroms; (across all 167 pairs:
    19224 0.225) 
    19225  
    19226 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19227 fold_hqba_hfq1_65x6_co_model_1.cif, chain A (#25), sequence alignment score =
    19228 867.8 
    19229 RMSD between 167 pruned atom pairs is 0.181 angstroms; (across all 167 pairs:
    19230 0.181) 
    19231  
    19232 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19233 fold_hqba_hfq1_65x6_co_model_2.cif, chain A (#26), sequence alignment score =
    19234 867.8 
    19235 RMSD between 167 pruned atom pairs is 0.299 angstroms; (across all 167 pairs:
    19236 0.299) 
    19237  
    19238 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19239 fold_hqba_hfq1_65x6_co_model_3.cif, chain A (#27), sequence alignment score =
    19240 867.8 
    19241 RMSD between 167 pruned atom pairs is 0.368 angstroms; (across all 167 pairs:
    19242 0.368) 
    19243  
    19244 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19245 fold_hqba_hfq1_65x6_co_model_4.cif, chain A (#28), sequence alignment score =
    19246 867.8 
    19247 RMSD between 167 pruned atom pairs is 0.255 angstroms; (across all 167 pairs:
    19248 0.255) 
    19249  
    19250 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19251 fold_hqba_hfqx6_co_model_0.cif, chain A (#29), sequence alignment score =
    19252 867.8 
    19253 RMSD between 167 pruned atom pairs is 0.202 angstroms; (across all 167 pairs:
    19254 0.202) 
    19255  
    19256 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19257 fold_hqba_hfqx6_co_model_1.cif, chain A (#30), sequence alignment score =
    19258 864.8 
    19259 RMSD between 167 pruned atom pairs is 0.220 angstroms; (across all 167 pairs:
    19260 0.220) 
    19261  
    19262 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19263 fold_hqba_hfqx6_co_model_2.cif, chain A (#31), sequence alignment score =
    19264 864.8 
    19265 RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
    19266 0.288) 
    19267  
    19268 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19269 fold_hqba_hfqx6_co_model_3.cif, chain A (#32), sequence alignment score =
    19270 868.4 
    19271 RMSD between 167 pruned atom pairs is 0.264 angstroms; (across all 167 pairs:
    19272 0.264) 
    19273  
    19274 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    19275 fold_hqba_hfqx6_co_model_4.cif, chain A (#33), sequence alignment score =
    19276 864.8 
    19277 RMSD between 167 pruned atom pairs is 0.315 angstroms; (across all 167 pairs:
    19278 0.315) 
    19279  
    19280 
    19281 > show #23 models
    19282 
    19283 > hide #23 models
    19284 
    19285 > show #23 models
    19286 
    19287 > hide #23 models
    19288 
    19289 > hide #25 models
    19290 
    19291 > hide #26 models
    19292 
    19293 > hide #27 models
    19294 
    19295 > hide #28 models
    19296 
    19297 > hide #30 models
    19298 
    19299 > hide #31 models
    19300 
    19301 > show #31 models
    19302 
    19303 > show #30 models
    19304 
    19305 > show #25 models
    19306 
    19307 > show #26 models
    19308 
    19309 > show #27 models
    19310 
    19311 > show #28 models
    19312 
    19313 > hide #25 models
    19314 
    19315 > hide #24 models
    19316 
    19317 > hide #33 models
    19318 
    19319 > hide #29 models
    19320 
    19321 > show #25 models
    19322 
    19323 > show #33 models
    19324 
    19325 > select add #24
    19326 
    19327 5713 atoms, 5820 bonds, 725 residues, 2 models selected 
    19328 
    19329 > select subtract #24
    19330 
    19331 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    19332 
    19333 > select add #25
    19334 
    19335 5713 atoms, 5820 bonds, 725 residues, 2 models selected 
    19336 
    19337 > select add #26
    19338 
    19339 10115 atoms, 10299 bonds, 1283 residues, 3 models selected 
    19340 
    19341 > select add #27
    19342 
    19343 14517 atoms, 14778 bonds, 1841 residues, 4 models selected 
    19344 
    19345 > select add #28
    19346 
    19347 18919 atoms, 19257 bonds, 2399 residues, 5 models selected 
    19348 
    19349 > select add #30
    19350 
    19351 24947 atoms, 25398 bonds, 3179 residues, 6 models selected 
    19352 
    19353 > select add #31
    19354 
    19355 30975 atoms, 31539 bonds, 3959 residues, 7 models selected 
    19356 
    19357 > select add #32
    19358 
    19359 37003 atoms, 37680 bonds, 4739 residues, 8 models selected 
    19360 
    19361 > select add #33
    19362 
    19363 43031 atoms, 43821 bonds, 5519 residues, 9 models selected 
    19364 
    19365 > select add #1
    19366 
    19367 43827 atoms, 44628 bonds, 5620 residues, 9 models selected 
    19368 
    19369 > hide #1 models
    19370 
    19371 > select subtract #1
    19372 
    19373 41720 atoms, 42480 bonds, 5352 residues, 8 models selected 
    19374 
    19375 > delete atoms sel
    19376 
    19377 > delete bonds sel
    19378 
    19379 > show #1 models
    19380 
    19381 > show #21 models
    19382 
    19383 > hide #21 models
    19384 
    19385 > show #2 models
    19386 
    19387 > show #3 models
    19388 
    19389 > show #4 models
    19390 
    19391 > show #5 models
    19392 
    19393 > select ::name="CO"
    19394 
    19395 17 atoms, 17 residues, 17 models selected 
    19396 
    19397 > show sel & #1-5 atoms
    19398 
    19399 > select #4/A:32
    19400 
    19401 10 atoms, 10 bonds, 1 residue, 1 model selected 
    19402 
    19403 > style sel stick
    19404 
    19405 Changed 10 atom styles 
    19406 
    19407 > show sel atoms
    19408 
    19409 > ui tool show "Color Actions"
    19410 
    19411 > color sel magenta
    19412 
    19413 > select clear
    19414 
    19415 > select add #2
    19416 
    19417 2107 atoms, 2148 bonds, 268 residues, 1 model selected 
    19418 
    19419 > select add #3
    19420 
    19421 4214 atoms, 4296 bonds, 536 residues, 2 models selected 
    19422 
    19423 > select add #4
    19424 
    19425 6321 atoms, 6444 bonds, 804 residues, 3 models selected 
    19426 
    19427 > select add #5
    19428 
    19429 8428 atoms, 8592 bonds, 1072 residues, 4 models selected 
    19430 
    19431 > select clear
    19432 
    19433 > show #21 models
    19434 
    19435 > select #21/B:-10
    19436 
    19437 10 atoms, 10 bonds, 1 residue, 1 model selected 
    19438 
    19439 > select add #21/B:0
    19440 
    19441 21 atoms, 20 bonds, 2 residues, 1 model selected 
    19442 
    19443 > select add #21/B:-1
    19444 
    19445 29 atoms, 27 bonds, 3 residues, 1 model selected 
    19446 
    19447 > select add #21/B:-2
    19448 
    19449 34 atoms, 31 bonds, 4 residues, 1 model selected 
    19450 
    19451 > select add #21/B:-3
    19452 
    19453 41 atoms, 38 bonds, 5 residues, 1 model selected 
    19454 
    19455 > select add #21/B:-4
    19456 
    19457 49 atoms, 45 bonds, 6 residues, 1 model selected 
    19458 
    19459 > select add #21/B:-5
    19460 
    19461 56 atoms, 51 bonds, 7 residues, 1 model selected 
    19462 
    19463 > select add #21/B:-6
    19464 
    19465 66 atoms, 61 bonds, 8 residues, 1 model selected 
    19466 
    19467 > select add #21/B:-7
    19468 
    19469 76 atoms, 71 bonds, 9 residues, 1 model selected 
    19470 
    19471 > select add #21/B:-8
    19472 
    19473 86 atoms, 81 bonds, 10 residues, 1 model selected 
    19474 
    19475 > select add #21/B:-9
    19476 
    19477 96 atoms, 91 bonds, 11 residues, 1 model selected 
    19478 
    19479 > hide sel cartoons
    19480 
    19481 > select clear
    19482 
    19483 > select ::name="HIS"
    19484 
    19485 3382 atoms, 3436 bonds, 313 residues, 24 models selected 
    19486 
    19487 > hide #2 models
    19488 
    19489 > hide #3 models
    19490 
    19491 > hide #4 models
    19492 
    19493 > hide #5 models
    19494 
    19495 > hide #21 models
    19496 
    19497 > show #2 models
    19498 
    19499 > show #3 models
    19500 
    19501 > show #4 models
    19502 
    19503 > show #5 models
    19504 
    19505 > hide #4 models
    19506 
    19507 > hide #2 models
    19508 
    19509 > hide #3 models
    19510 
    19511 > hide #5 models
    19512 
    19513 > select #1/A:32
    19514 
    19515 10 atoms, 10 bonds, 1 residue, 1 model selected 
    19516 
    19517 > color sel magenta
    19518 
    19519 > hide sel atoms
    19520 
    19521 > show sel atoms
    19522 
    19523 > select clear
    19524 
    19525 > show #21 models
    19526 
    19527 > show #29 models
    19528 
    19529 > hide #21 models
    19530 
    19531 > hide #1 models
    19532 
    19533 > show #23 models
    19534 
    19535 > hide #29 models
    19536 
    19537 > select #23/G:30
    19538 
    19539 19 atoms, 18 bonds, 1 residue, 1 model selected 
    19540 
    19541 > select #23/G:31
    19542 
    19543 22 atoms, 21 bonds, 1 residue, 1 model selected 
    19544 
    19545 > show sel atoms
    19546 
    19547 > style sel stick
    19548 
    19549 Changed 22 atom styles 
    19550 
    19551 > show #29 models
    19552 
    19553 > hide #23 models
    19554 
    19555 > select #29/G:31
    19556 
    19557 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19558 
    19559 > show sel atoms
    19560 
    19561 > style sel stick
    19562 
    19563 Changed 9 atom styles 
    19564 
    19565 > show #23 models
    19566 
    19567 > hide #23 models
    19568 
    19569 > show #1 models
    19570 
    19571 > hide #1 models
    19572 
    19573 > color sel cornflower blue
    19574 
    19575 > select clear
    19576 
    19577 > show #23 models
    19578 
    19579 > hide #29 models
    19580 
    19581 > show #29 models
    19582 
    19583 > hide #23 models
    19584 
    19585 > hide #29 models
    19586 
    19587 > show #29 models
    19588 
    19589 > select #29/G:31
    19590 
    19591 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19592 
    19593 > undo
    19594 
    19595 > ui tool show "Color Actions"
    19596 
    19597 > color sel pale violet red
    19598 
    19599 > color sel light pink
    19600 
    19601 > color sel hot pink
    19602 
    19603 > color sel plum
    19604 
    19605 > select clear
    19606 
    19607 > select #29/G:31
    19608 
    19609 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19610 
    19611 > color sel plum
    19612 
    19613 > color sel violet
    19614 
    19615 > select clear
    19616 
    19617 > select #29/G:31
    19618 
    19619 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19620 
    19621 > hide sel atoms
    19622 
    19623 > select #29/A:102
    19624 
    19625 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19626 
    19627 > color sel red
    19628 
    19629 > style sel stick
    19630 
    19631 Changed 9 atom styles 
    19632 
    19633 > show sel atoms
    19634 
    19635 > select #29/A:98
    19636 
    19637 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19638 
    19639 > style sel stick
    19640 
    19641 Changed 8 atom styles 
    19642 
    19643 > show sel atoms
    19644 
    19645 > color sel red
    19646 
    19647 Drag select of 3 residues 
    19648 
    19649 > select clear
    19650 
    19651 > select #29/C:31
    19652 
    19653 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19654 
    19655 > color sel cornflower blue
    19656 
    19657 > style sel stick
    19658 
    19659 Changed 9 atom styles 
    19660 
    19661 > show sel atoms
    19662 
    19663 > select #29/A:98
    19664 
    19665 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19666 
    19667 > select #29/C:31
    19668 
    19669 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19670 
    19671 > color sel medium blue
    19672 
    19673 > select clear
    19674 
    19675 > select #29/C:31
    19676 
    19677 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19678 
    19679 > ui tool show "Color Actions"
    19680 
    19681 > color sel royal blue
    19682 
    19683 > select clear
    19684 
    19685 > show #23 models
    19686 
    19687 > select #23/C:31
    19688 
    19689 22 atoms, 21 bonds, 1 residue, 1 model selected 
    19690 
    19691 > style sel stick
    19692 
    19693 Changed 22 atom styles 
    19694 
    19695 > show sel atoms
    19696 
    19697 > hide #23 models
    19698 
    19699 > select #29/A
    19700 
    19701 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    19702 
    19703 > select ~sel & ##selected
    19704 
    19705 4717 atoms, 4800 bonds, 613 residues, 1 model selected 
    19706 
    19707 > color sel tan
    19708 
    19709 > select clear
    19710 
    19711 > select #29/C:31
    19712 
    19713 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19714 
    19715 > color sel royal blue
    19716 
    19717 > select #29/G:33
    19718 
    19719 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19720 
    19721 > select clear
    19722 
    19723 > show #21 models
    19724 
    19725 > save /Users/taic/Library/CloudStorage/OneDrive-
    19726 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni.cxs
    19727 
    19728 > save /Users/taic/Library/CloudStorage/OneDrive-
    19729 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.csx.cxs
    19730 
    19731 > close session
    19732 
    19733 > open /Users/taic/Library/CloudStorage/OneDrive-
    19734 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19735 > Predictions/azor_monomer/fold_azor_monomer_model_0.cif
    19736 
    19737 Chain information for fold_azor_monomer_model_0.cif #1 
    19738 --- 
    19739 Chain | Description 
    19740 A | . 
    19741  
    19742 Computing secondary structure 
    19743 
    19744 > open /Users/taic/Library/CloudStorage/OneDrive-
    19745 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19746 > Predictions/azor_monomer/fold_azor_monomer_model_1.cif
    19747 
    19748 Chain information for fold_azor_monomer_model_1.cif #2 
    19749 --- 
    19750 Chain | Description 
    19751 A | . 
    19752  
    19753 Computing secondary structure 
    19754 
    19755 > open /Users/taic/Library/CloudStorage/OneDrive-
    19756 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19757 > Predictions/azor_monomer/fold_azor_monomer_model_2.cif
    19758 
    19759 Chain information for fold_azor_monomer_model_2.cif #3 
    19760 --- 
    19761 Chain | Description 
    19762 A | . 
    19763  
    19764 Computing secondary structure 
    19765 
    19766 > open /Users/taic/Library/CloudStorage/OneDrive-
    19767 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19768 > Predictions/azor_monomer/fold_azor_monomer_model_3.cif
    19769 
    19770 Chain information for fold_azor_monomer_model_3.cif #4 
    19771 --- 
    19772 Chain | Description 
    19773 A | . 
    19774  
    19775 Computing secondary structure 
    19776 
    19777 > open /Users/taic/Library/CloudStorage/OneDrive-
    19778 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19779 > Predictions/azor_monomer/fold_azor_monomer_model_4.cif
    19780 
    19781 Chain information for fold_azor_monomer_model_4.cif #5 
    19782 --- 
    19783 Chain | Description 
    19784 A | . 
    19785  
    19786 Computing secondary structure 
    19787 
    19788 > open /Users/taic/Library/CloudStorage/OneDrive-
    19789 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19790 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
    19791 
    19792 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    19793 NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19794 Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif 
    19795 --- 
    19796 note | Fetching CCD FAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/FAD/FAD.cif 
    19797  
    19798 Chain information for fold_azor_monomer_fad_model_0.cif #6 
    19799 --- 
    19800 Chain | Description 
    19801 A | . 
    19802  
    19803 Computing secondary structure 
    19804 
    19805 > rainbow
    19806 
    19807 > open /Users/taic/Library/CloudStorage/OneDrive-
    19808 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19809 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_1.cif
    19810 
    19811 Chain information for fold_azor_monomer_fad_model_1.cif #7 
    19812 --- 
    19813 Chain | Description 
    19814 A | . 
    19815  
    19816 Computing secondary structure 
    19817 
    19818 > open /Users/taic/Library/CloudStorage/OneDrive-
    19819 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19820 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_2.cif
    19821 
    19822 Chain information for fold_azor_monomer_fad_model_2.cif #8 
    19823 --- 
    19824 Chain | Description 
    19825 A | . 
    19826  
    19827 Computing secondary structure 
    19828 
    19829 > open /Users/taic/Library/CloudStorage/OneDrive-
    19830 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19831 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_3.cif
    19832 
    19833 Chain information for fold_azor_monomer_fad_model_3.cif #9 
    19834 --- 
    19835 Chain | Description 
    19836 A | . 
    19837  
    19838 Computing secondary structure 
    19839 
    19840 > open /Users/taic/Library/CloudStorage/OneDrive-
    19841 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19842 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_4.cif
    19843 
    19844 Chain information for fold_azor_monomer_fad_model_4.cif #10 
    19845 --- 
    19846 Chain | Description 
    19847 A | . 
    19848  
    19849 Computing secondary structure 
    19850 
    19851 > open /Users/taic/Library/CloudStorage/OneDrive-
    19852 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19853 > Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_0.cif
    19854 
    19855 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    19856 NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19857 Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_0.cif 
    19858 --- 
    19859 note | Fetching CCD NAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/NAD/NAD.cif 
    19860  
    19861 Chain information for fold_azor_monomer_nad_model_0.cif #11 
    19862 --- 
    19863 Chain | Description 
    19864 A | . 
    19865  
    19866 Computing secondary structure 
    19867 
    19868 > open /Users/taic/Library/CloudStorage/OneDrive-
    19869 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19870 > Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_1.cif
    19871 
    19872 Chain information for fold_azor_monomer_nad_model_1.cif #12 
    19873 --- 
    19874 Chain | Description 
    19875 A | . 
    19876  
    19877 Computing secondary structure 
    19878 
    19879 > ui tool show Matchmaker
    19880 
    19881 > open /Users/taic/Library/CloudStorage/OneDrive-
    19882 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19883 > Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_2.cif
    19884 
    19885 Chain information for fold_azor_monomer_nad_model_2.cif #13 
    19886 --- 
    19887 Chain | Description 
    19888 A | . 
    19889  
    19890 
    19891 > open /Users/taic/Library/CloudStorage/OneDrive-
    19892 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19893 > Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_3.cif
    19894 
    19895 Chain information for fold_azor_monomer_nad_model_3.cif #14 
    19896 --- 
    19897 Chain | Description 
    19898 A | . 
    19899  
    19900 Computing secondary structure 
    19901 
    19902 > open /Users/taic/Library/CloudStorage/OneDrive-
    19903 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    19904 > Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_4.cif
    19905 
    19906 Chain information for fold_azor_monomer_nad_model_4.cif #15 
    19907 --- 
    19908 Chain | Description 
    19909 A | . 
    19910  
    19911 Computing secondary structure 
    19912 
    19913 > matchmaker #2-12 to #1
    19914 
    19915 Computing secondary structure 
    19916 Parameters 
    19917 --- 
    19918 Chain pairing | bb 
    19919 Alignment algorithm | Needleman-Wunsch 
    19920 Similarity matrix | BLOSUM-62 
    19921 SS fraction | 0.3 
    19922 Gap open (HH/SS/other) | 18/18/6 
    19923 Gap extend | 1 
    19924 SS matrix |  |  | H | S | O 
    19925 ---|---|---|--- 
    19926 H | 6 | -9 | -6 
    19927 S |  | 6 | -6 
    19928 O |  |  | 4 
    19929 Iteration cutoff | 2 
    19930  
    19931 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19932 fold_azor_monomer_model_1.cif, chain A (#2), sequence alignment score = 1086.8 
    19933 RMSD between 208 pruned atom pairs is 0.117 angstroms; (across all 208 pairs:
    19934 0.117) 
    19935  
    19936 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19937 fold_azor_monomer_model_2.cif, chain A (#3), sequence alignment score = 1086.8 
    19938 RMSD between 208 pruned atom pairs is 0.103 angstroms; (across all 208 pairs:
    19939 0.103) 
    19940  
    19941 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19942 fold_azor_monomer_model_3.cif, chain A (#4), sequence alignment score = 1086.8 
    19943 RMSD between 208 pruned atom pairs is 0.129 angstroms; (across all 208 pairs:
    19944 0.129) 
    19945  
    19946 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19947 fold_azor_monomer_model_4.cif, chain A (#5), sequence alignment score = 1086.8 
    19948 RMSD between 208 pruned atom pairs is 0.121 angstroms; (across all 208 pairs:
    19949 0.121) 
    19950  
    19951 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19952 fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
    19953 1083.8 
    19954 RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
    19955 0.351) 
    19956  
    19957 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19958 fold_azor_monomer_fad_model_1.cif, chain A (#7), sequence alignment score =
    19959 1080.2 
    19960 RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
    19961 0.403) 
    19962  
    19963 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19964 fold_azor_monomer_fad_model_2.cif, chain A (#8), sequence alignment score =
    19965 1083.8 
    19966 RMSD between 208 pruned atom pairs is 0.447 angstroms; (across all 208 pairs:
    19967 0.447) 
    19968  
    19969 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19970 fold_azor_monomer_fad_model_3.cif, chain A (#9), sequence alignment score =
    19971 1083.8 
    19972 RMSD between 208 pruned atom pairs is 0.420 angstroms; (across all 208 pairs:
    19973 0.420) 
    19974  
    19975 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19976 fold_azor_monomer_fad_model_4.cif, chain A (#10), sequence alignment score =
    19977 1083.8 
    19978 RMSD between 208 pruned atom pairs is 0.291 angstroms; (across all 208 pairs:
    19979 0.291) 
    19980  
    19981 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19982 fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
    19983 1083.8 
    19984 RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
    19985 0.324) 
    19986  
    19987 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    19988 fold_azor_monomer_nad_model_1.cif, chain A (#12), sequence alignment score =
    19989 1080.2 
    19990 RMSD between 208 pruned atom pairs is 0.353 angstroms; (across all 208 pairs:
    19991 0.353) 
    19992  
    19993 
    19994 > matchmaker #13-15 to #1
    19995 
    19996 Computing secondary structure 
    19997 Parameters 
    19998 --- 
    19999 Chain pairing | bb 
    20000 Alignment algorithm | Needleman-Wunsch 
    20001 Similarity matrix | BLOSUM-62 
    20002 SS fraction | 0.3 
    20003 Gap open (HH/SS/other) | 18/18/6 
    20004 Gap extend | 1 
    20005 SS matrix |  |  | H | S | O 
    20006 ---|---|---|--- 
    20007 H | 6 | -9 | -6 
    20008 S |  | 6 | -6 
    20009 O |  |  | 4 
    20010 Iteration cutoff | 2 
    20011  
    20012 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20013 fold_azor_monomer_nad_model_2.cif, chain A (#13), sequence alignment score =
    20014 1080.2 
    20015 RMSD between 208 pruned atom pairs is 0.368 angstroms; (across all 208 pairs:
    20016 0.368) 
    20017  
    20018 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20019 fold_azor_monomer_nad_model_3.cif, chain A (#14), sequence alignment score =
    20020 1080.2 
    20021 RMSD between 208 pruned atom pairs is 0.329 angstroms; (across all 208 pairs:
    20022 0.329) 
    20023  
    20024 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20025 fold_azor_monomer_nad_model_4.cif, chain A (#15), sequence alignment score =
    20026 1083.8 
    20027 RMSD between 208 pruned atom pairs is 0.287 angstroms; (across all 208 pairs:
    20028 0.287) 
    20029  
    20030 
    20031 > select add #2
    20032 
    20033 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    20034 
    20035 > select add #3
    20036 
    20037 3292 atoms, 3370 bonds, 416 residues, 2 models selected 
    20038 
    20039 > select add #4
    20040 
    20041 4938 atoms, 5055 bonds, 624 residues, 3 models selected 
    20042 
    20043 > select add #5
    20044 
    20045 6584 atoms, 6740 bonds, 832 residues, 4 models selected 
    20046 
    20047 > hide #6 models
    20048 
    20049 > hide #7 models
    20050 
    20051 > hide #8 models
    20052 
    20053 > hide #9 models
    20054 
    20055 > hide #10 models
    20056 
    20057 > hide #11 models
    20058 
    20059 > hide #12 models
    20060 
    20061 > hide #13 models
    20062 
    20063 > hide #14 models
    20064 
    20065 > hide #15 models
    20066 
    20067 > delete atoms sel
    20068 
    20069 > delete bonds sel
    20070 
    20071 > show #6 models
    20072 
    20073 > hide #6 models
    20074 
    20075 > show #6 models
    20076 
    20077 > show #7 models
    20078 
    20079 > hide #1 models
    20080 
    20081 > hide #7 models
    20082 
    20083 > show #7 models
    20084 
    20085 > hide #7 models
    20086 
    20087 > show #7 models
    20088 
    20089 > hide #6 models
    20090 
    20091 > show #6 models
    20092 
    20093 > hide #6 models
    20094 
    20095 > show #6 models
    20096 
    20097 > hide #7 models
    20098 
    20099 > show #7 models
    20100 
    20101 > hide #7 models
    20102 
    20103 > show #7 models
    20104 
    20105 > show #8 models
    20106 
    20107 > show #9 models
    20108 
    20109 > show #10 models
    20110 
    20111 > select add #7
    20112 
    20113 1699 atoms, 1743 bonds, 209 residues, 1 model selected 
    20114 
    20115 > select add #8
    20116 
    20117 3398 atoms, 3486 bonds, 418 residues, 2 models selected 
    20118 
    20119 > select add #9
    20120 
    20121 5097 atoms, 5229 bonds, 627 residues, 3 models selected 
    20122 
    20123 > select add #10
    20124 
    20125 6796 atoms, 6972 bonds, 836 residues, 4 models selected 
    20126 
    20127 > delete atoms sel
    20128 
    20129 > delete bonds sel
    20130 
    20131 > show #11 models
    20132 
    20133 > hide #6 models
    20134 
    20135 > show #12 models
    20136 
    20137 > hide #11 models
    20138 
    20139 > show #11 models
    20140 
    20141 > hide #11 models
    20142 
    20143 > show #11 models
    20144 
    20145 > show #13 models
    20146 
    20147 > show #14 models
    20148 
    20149 > show #15 models
    20150 
    20151 > select add #12
    20152 
    20153 1690 atoms, 1733 bonds, 209 residues, 1 model selected 
    20154 
    20155 > select add #13
    20156 
    20157 3380 atoms, 3466 bonds, 418 residues, 2 models selected 
    20158 
    20159 > select add #14
    20160 
    20161 5070 atoms, 5199 bonds, 627 residues, 3 models selected 
    20162 
    20163 > select add #15
    20164 
    20165 6760 atoms, 6932 bonds, 836 residues, 4 models selected 
    20166 
    20167 > delete atoms sel
    20168 
    20169 > delete bonds sel
    20170 
    20171 > show #1 models
    20172 
    20173 > show #6 models
    20174 
    20175 > hide #6 models
    20176 
    20177 > hide #11 models
    20178 
    20179 > open /Users/taic/Library/CloudStorage/OneDrive-
    20180 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20181 > Predictions/azor_dimer/fold_azor_dimer_model_0.cif
    20182 
    20183 Chain information for fold_azor_dimer_model_0.cif #2 
    20184 --- 
    20185 Chain | Description 
    20186 A B | . 
    20187  
    20188 Computing secondary structure 
    20189 
    20190 > open /Users/taic/Library/CloudStorage/OneDrive-
    20191 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20192 > Predictions/azor_dimer/fold_azor_dimer_model_1.cif
    20193 
    20194 Chain information for fold_azor_dimer_model_1.cif #3 
    20195 --- 
    20196 Chain | Description 
    20197 A B | . 
    20198  
    20199 Computing secondary structure 
    20200 
    20201 > open /Users/taic/Library/CloudStorage/OneDrive-
    20202 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20203 > Predictions/azor_dimer/fold_azor_dimer_model_2.cif
    20204 
    20205 Chain information for fold_azor_dimer_model_2.cif #4 
    20206 --- 
    20207 Chain | Description 
    20208 A B | . 
    20209  
    20210 Computing secondary structure 
    20211 
    20212 > open /Users/taic/Library/CloudStorage/OneDrive-
    20213 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20214 > Predictions/azor_dimer/fold_azor_dimer_model_3.cif
    20215 
    20216 Chain information for fold_azor_dimer_model_3.cif #5 
    20217 --- 
    20218 Chain | Description 
    20219 A B | . 
    20220  
    20221 Computing secondary structure 
    20222 
    20223 > open /Users/taic/Library/CloudStorage/OneDrive-
    20224 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20225 > Predictions/azor_dimer/fold_azor_dimer_model_4.cif
    20226 
    20227 Chain information for fold_azor_dimer_model_4.cif #7 
    20228 --- 
    20229 Chain | Description 
    20230 A B | . 
    20231  
    20232 Computing secondary structure 
    20233 
    20234 > ui tool show Matchmaker
    20235 
    20236 > matchmaker #2-7,11 to #1
    20237 
    20238 Computing secondary structure 
    20239 Parameters 
    20240 --- 
    20241 Chain pairing | bb 
    20242 Alignment algorithm | Needleman-Wunsch 
    20243 Similarity matrix | BLOSUM-62 
    20244 SS fraction | 0.3 
    20245 Gap open (HH/SS/other) | 18/18/6 
    20246 Gap extend | 1 
    20247 SS matrix |  |  | H | S | O 
    20248 ---|---|---|--- 
    20249 H | 6 | -9 | -6 
    20250 S |  | 6 | -6 
    20251 O |  |  | 4 
    20252 Iteration cutoff | 2 
    20253  
    20254 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20255 fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2 
    20256 RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
    20257 0.403) 
    20258  
    20259 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20260 fold_azor_dimer_model_1.cif, chain A (#3), sequence alignment score = 1080.8 
    20261 RMSD between 208 pruned atom pairs is 0.383 angstroms; (across all 208 pairs:
    20262 0.383) 
    20263  
    20264 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20265 fold_azor_dimer_model_2.cif, chain A (#4), sequence alignment score = 1074.2 
    20266 RMSD between 208 pruned atom pairs is 0.452 angstroms; (across all 208 pairs:
    20267 0.452) 
    20268  
    20269 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20270 fold_azor_dimer_model_3.cif, chain A (#5), sequence alignment score = 1074.2 
    20271 RMSD between 208 pruned atom pairs is 0.377 angstroms; (across all 208 pairs:
    20272 0.377) 
    20273  
    20274 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20275 fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
    20276 1083.8 
    20277 RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
    20278 0.351) 
    20279  
    20280 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20281 fold_azor_dimer_model_4.cif, chain A (#7), sequence alignment score = 1077.8 
    20282 RMSD between 208 pruned atom pairs is 0.371 angstroms; (across all 208 pairs:
    20283 0.371) 
    20284  
    20285 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20286 fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
    20287 1083.8 
    20288 RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
    20289 0.324) 
    20290  
    20291 
    20292 > show #6 models
    20293 
    20294 > hide #2 models
    20295 
    20296 > show #2 models
    20297 
    20298 > hide #7 models
    20299 
    20300 > hide #6 models
    20301 
    20302 > show #7 models
    20303 
    20304 > select add #3
    20305 
    20306 3292 atoms, 3370 bonds, 416 residues, 1 model selected 
    20307 
    20308 > select add #4
    20309 
    20310 6584 atoms, 6740 bonds, 832 residues, 2 models selected 
    20311 
    20312 > select add #5
    20313 
    20314 9876 atoms, 10110 bonds, 1248 residues, 3 models selected 
    20315 
    20316 > select add #7
    20317 
    20318 13168 atoms, 13480 bonds, 1664 residues, 4 models selected 
    20319 
    20320 > delete atoms sel
    20321 
    20322 > delete bonds sel
    20323 
    20324 > hide #1 models
    20325 
    20326 > show #6 models
    20327 
    20328 > hide #2 models
    20329 
    20330 > select /A
    20331 
    20332 6584 atoms, 6740 bonds, 832 residues, 4 models selected 
    20333 
    20334 > show sel & #6 surfaces
    20335 
    20336 > show #2 models
    20337 
    20338 > select /B
    20339 
    20340 1743 atoms, 1791 bonds, 210 residues, 3 models selected 
    20341 
    20342 > hide #2 models
    20343 
    20344 > show #2 models
    20345 
    20346 > select #2/B
    20347 
    20348 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    20349 
    20350 > show sel surfaces
    20351 
    20352 > hide #!6 models
    20353 
    20354 > show #1 models
    20355 
    20356 > show #!6 models
    20357 
    20358 > hide #1 models
    20359 
    20360 > hide #!6 models
    20361 
    20362 > open /Users/taic/Library/CloudStorage/OneDrive-
    20363 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20364 > Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_0.cif
    20365 
    20366 Chain information for fold_azor_dimer_fad_model_0.cif #3 
    20367 --- 
    20368 Chain | Description 
    20369 A B | . 
    20370  
    20371 Computing secondary structure 
    20372 
    20373 > open /Users/taic/Library/CloudStorage/OneDrive-
    20374 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20375 > Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_1.cif
    20376 
    20377 Chain information for fold_azor_dimer_fad_model_1.cif #4 
    20378 --- 
    20379 Chain | Description 
    20380 A B | . 
    20381  
    20382 Computing secondary structure 
    20383 
    20384 > open /Users/taic/Library/CloudStorage/OneDrive-
    20385 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20386 > Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_2.cif
    20387 
    20388 Chain information for fold_azor_dimer_fad_model_2.cif #5 
    20389 --- 
    20390 Chain | Description 
    20391 A B | . 
    20392  
    20393 Computing secondary structure 
    20394 
    20395 > hide sel surfaces
    20396 
    20397 > ui tool show Matchmaker
    20398 
    20399 > open /Users/taic/Library/CloudStorage/OneDrive-
    20400 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20401 > Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_3.cif
    20402 
    20403 Chain information for fold_azor_dimer_fad_model_3.cif #7 
    20404 --- 
    20405 Chain | Description 
    20406 A B | . 
    20407  
    20408 
    20409 > open /Users/taic/Library/CloudStorage/OneDrive-
    20410 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    20411 > Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_4.cif
    20412 
    20413 Chain information for fold_azor_dimer_fad_model_4.cif #8 
    20414 --- 
    20415 Chain | Description 
    20416 A B | . 
    20417  
    20418 Computing secondary structure 
    20419 
    20420 > matchmaker #3-5,7-8#!6 to #1
    20421 
    20422 Computing secondary structure 
    20423 Parameters 
    20424 --- 
    20425 Chain pairing | bb 
    20426 Alignment algorithm | Needleman-Wunsch 
    20427 Similarity matrix | BLOSUM-62 
    20428 SS fraction | 0.3 
    20429 Gap open (HH/SS/other) | 18/18/6 
    20430 Gap extend | 1 
    20431 SS matrix |  |  | H | S | O 
    20432 ---|---|---|--- 
    20433 H | 6 | -9 | -6 
    20434 S |  | 6 | -6 
    20435 O |  |  | 4 
    20436 Iteration cutoff | 2 
    20437  
    20438 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20439 fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
    20440 1077.8 
    20441 RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
    20442 0.467) 
    20443  
    20444 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20445 fold_azor_dimer_fad_model_1.cif, chain A (#4), sequence alignment score = 1049 
    20446 RMSD between 208 pruned atom pairs is 0.456 angstroms; (across all 208 pairs:
    20447 0.456) 
    20448  
    20449 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20450 fold_azor_dimer_fad_model_2.cif, chain A (#5), sequence alignment score =
    20451 1083.2 
    20452 RMSD between 208 pruned atom pairs is 0.435 angstroms; (across all 208 pairs:
    20453 0.435) 
    20454  
    20455 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20456 fold_azor_dimer_fad_model_3.cif, chain A (#7), sequence alignment score =
    20457 1083.2 
    20458 RMSD between 208 pruned atom pairs is 0.408 angstroms; (across all 208 pairs:
    20459 0.408) 
    20460  
    20461 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20462 fold_azor_dimer_fad_model_4.cif, chain A (#8), sequence alignment score =
    20463 1083.2 
    20464 RMSD between 208 pruned atom pairs is 0.428 angstroms; (across all 208 pairs:
    20465 0.428) 
    20466  
    20467 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    20468 fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
    20469 1083.8 
    20470 RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
    20471 0.351) 
    20472  
    20473 
    20474 > save /Users/taic/Library/CloudStorage/OneDrive-
    20475 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
    20476 
    20477 > close session
    20478 
    20479 > open /Users/taic/Library/CloudStorage/OneDrive-
    20480 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_0.cif
    20481 
    20482 Chain information for fold_hqba_hfqx6_vcholera_model_0.cif #1 
    20483 --- 
    20484 Chain | Description 
    20485 A | . 
    20486 B C D E F G | . 
    20487  
    20488 
    20489 > open /Users/taic/Library/CloudStorage/OneDrive-
    20490 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_1.cif
    20491 
    20492 Chain information for fold_hqba_hfqx6_vcholera_model_1.cif #2 
    20493 --- 
    20494 Chain | Description 
    20495 A | . 
    20496 B C D E F G | . 
    20497  
    20498 
    20499 > open /Users/taic/Library/CloudStorage/OneDrive-
    20500 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_2.cif
    20501 
    20502 Chain information for fold_hqba_hfqx6_vcholera_model_2.cif #3 
    20503 --- 
    20504 Chain | Description 
    20505 A | . 
    20506 B C D E F G | . 
    20507  
    20508 
    20509 > open /Users/taic/Library/CloudStorage/OneDrive-
    20510 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_3.cif
    20511 
    20512 Chain information for fold_hqba_hfqx6_vcholera_model_3.cif #4 
    20513 --- 
    20514 Chain | Description 
    20515 A | . 
    20516 B C D E F G | . 
    20517  
    20518 
    20519 > open /Users/taic/Library/CloudStorage/OneDrive-
    20520 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_4.cif
    20521 
    20522 Chain information for fold_hqba_hfqx6_vcholera_model_4.cif #5 
    20523 --- 
    20524 Chain | Description 
    20525 A | . 
    20526 B C D E F G | . 
    20527  
    20528 
    20529 > open /Users/taic/Library/CloudStorage/OneDrive-
    20530 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_0.cif
    20531 
    20532 Chain information for fold_hqba_hfqx6_co_model_0.cif #6 
    20533 --- 
    20534 Chain | Description 
    20535 A | . 
    20536 B C D E F G | . 
    20537  
    20538 
    20539 > open /Users/taic/Library/CloudStorage/OneDrive-
    20540 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_1.cif
    20541 
    20542 Chain information for fold_hqba_hfqx6_co_model_1.cif #7 
    20543 --- 
    20544 Chain | Description 
    20545 A | . 
    20546 B C D E F G | . 
    20547  
    20548 
    20549 > open /Users/taic/Library/CloudStorage/OneDrive-
    20550 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_2.cif
    20551 
    20552 Chain information for fold_hqba_hfqx6_co_model_2.cif #8 
    20553 --- 
    20554 Chain | Description 
    20555 A | . 
    20556 B C D E F G | . 
    20557  
    20558 
    20559 > open /Users/taic/Library/CloudStorage/OneDrive-
    20560 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_3.cif
    20561 
    20562 Chain information for fold_hqba_hfqx6_co_model_3.cif #9 
    20563 --- 
    20564 Chain | Description 
    20565 A | . 
    20566 B C D E F G | . 
    20567  
    20568 
    20569 > open /Users/taic/Library/CloudStorage/OneDrive-
    20570 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_4.cif
    20571 
    20572 Chain information for fold_hqba_hfqx6_co_model_4.cif #10 
    20573 --- 
    20574 Chain | Description 
    20575 A | . 
    20576 B C D E F G | . 
    20577  
    20578 
    20579 > hide atoms
    20580 
    20581 > show cartoons
    20582 
    20583 Computing secondary structure 
    20584 
    20585 > ui tool show Matchmaker
    20586 
    20587 > matchmaker #2-10 to #1
    20588 
    20589 Computing secondary structure 
    20590 Parameters 
    20591 --- 
    20592 Chain pairing | bb 
    20593 Alignment algorithm | Needleman-Wunsch 
    20594 Similarity matrix | BLOSUM-62 
    20595 SS fraction | 0.3 
    20596 Gap open (HH/SS/other) | 18/18/6 
    20597 Gap extend | 1 
    20598 SS matrix |  |  | H | S | O 
    20599 ---|---|---|--- 
    20600 H | 6 | -9 | -6 
    20601 S |  | 6 | -6 
    20602 O |  |  | 4 
    20603 Iteration cutoff | 2 
    20604  
    20605 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20606 fold_hqba_hfqx6_vcholera_model_1.cif, chain A (#2), sequence alignment score =
    20607 867.4 
    20608 RMSD between 167 pruned atom pairs is 0.168 angstroms; (across all 167 pairs:
    20609 0.168) 
    20610  
    20611 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20612 fold_hqba_hfqx6_vcholera_model_2.cif, chain A (#3), sequence alignment score =
    20613 863.8 
    20614 RMSD between 167 pruned atom pairs is 0.134 angstroms; (across all 167 pairs:
    20615 0.134) 
    20616  
    20617 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20618 fold_hqba_hfqx6_vcholera_model_3.cif, chain A (#4), sequence alignment score =
    20619 867.4 
    20620 RMSD between 167 pruned atom pairs is 0.135 angstroms; (across all 167 pairs:
    20621 0.135) 
    20622  
    20623 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20624 fold_hqba_hfqx6_vcholera_model_4.cif, chain A (#5), sequence alignment score =
    20625 867.4 
    20626 RMSD between 167 pruned atom pairs is 0.121 angstroms; (across all 167 pairs:
    20627 0.121) 
    20628  
    20629 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20630 fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3 
    20631 RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
    20632 0.862) 
    20633  
    20634 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20635 fold_hqba_hfqx6_co_model_1.cif, chain A (#7), sequence alignment score = 569.3 
    20636 RMSD between 162 pruned atom pairs is 0.700 angstroms; (across all 167 pairs:
    20637 0.870) 
    20638  
    20639 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20640 fold_hqba_hfqx6_co_model_2.cif, chain A (#8), sequence alignment score = 569.3 
    20641 RMSD between 162 pruned atom pairs is 0.670 angstroms; (across all 167 pairs:
    20642 0.842) 
    20643  
    20644 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20645 fold_hqba_hfqx6_co_model_3.cif, chain A (#9), sequence alignment score = 572.9 
    20646 RMSD between 161 pruned atom pairs is 0.684 angstroms; (across all 167 pairs:
    20647 0.877) 
    20648  
    20649 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20650 fold_hqba_hfqx6_co_model_4.cif, chain A (#10), sequence alignment score =
    20651 569.3 
    20652 RMSD between 162 pruned atom pairs is 0.660 angstroms; (across all 167 pairs:
    20653 0.836) 
    20654  
    20655 
    20656 > matchmaker #2-10 to #1
    20657 
    20658 Computing secondary structure 
    20659 Parameters 
    20660 --- 
    20661 Chain pairing | bb 
    20662 Alignment algorithm | Needleman-Wunsch 
    20663 Similarity matrix | BLOSUM-62 
    20664 SS fraction | 0.3 
    20665 Gap open (HH/SS/other) | 18/18/6 
    20666 Gap extend | 1 
    20667 SS matrix |  |  | H | S | O 
    20668 ---|---|---|--- 
    20669 H | 6 | -9 | -6 
    20670 S |  | 6 | -6 
    20671 O |  |  | 4 
    20672 Iteration cutoff | 2 
    20673  
    20674 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20675 fold_hqba_hfqx6_vcholera_model_1.cif, chain A (#2), sequence alignment score =
    20676 867.4 
    20677 RMSD between 167 pruned atom pairs is 0.168 angstroms; (across all 167 pairs:
    20678 0.168) 
    20679  
    20680 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20681 fold_hqba_hfqx6_vcholera_model_2.cif, chain A (#3), sequence alignment score =
    20682 863.8 
    20683 RMSD between 167 pruned atom pairs is 0.134 angstroms; (across all 167 pairs:
    20684 0.134) 
    20685  
    20686 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20687 fold_hqba_hfqx6_vcholera_model_3.cif, chain A (#4), sequence alignment score =
    20688 867.4 
    20689 RMSD between 167 pruned atom pairs is 0.135 angstroms; (across all 167 pairs:
    20690 0.135) 
    20691  
    20692 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20693 fold_hqba_hfqx6_vcholera_model_4.cif, chain A (#5), sequence alignment score =
    20694 867.4 
    20695 RMSD between 167 pruned atom pairs is 0.121 angstroms; (across all 167 pairs:
    20696 0.121) 
    20697  
    20698 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20699 fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3 
    20700 RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
    20701 0.862) 
    20702  
    20703 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20704 fold_hqba_hfqx6_co_model_1.cif, chain A (#7), sequence alignment score = 569.3 
    20705 RMSD between 162 pruned atom pairs is 0.700 angstroms; (across all 167 pairs:
    20706 0.870) 
    20707  
    20708 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20709 fold_hqba_hfqx6_co_model_2.cif, chain A (#8), sequence alignment score = 569.3 
    20710 RMSD between 162 pruned atom pairs is 0.670 angstroms; (across all 167 pairs:
    20711 0.842) 
    20712  
    20713 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20714 fold_hqba_hfqx6_co_model_3.cif, chain A (#9), sequence alignment score = 572.9 
    20715 RMSD between 161 pruned atom pairs is 0.684 angstroms; (across all 167 pairs:
    20716 0.877) 
    20717  
    20718 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20719 fold_hqba_hfqx6_co_model_4.cif, chain A (#10), sequence alignment score =
    20720 569.3 
    20721 RMSD between 162 pruned atom pairs is 0.660 angstroms; (across all 167 pairs:
    20722 0.836) 
    20723  
    20724 
    20725 > select add #7
    20726 
    20727 6028 atoms, 6141 bonds, 780 residues, 1 model selected 
    20728 
    20729 > select add #8
    20730 
    20731 12056 atoms, 12282 bonds, 1560 residues, 2 models selected 
    20732 
    20733 > select add #9
    20734 
    20735 18084 atoms, 18423 bonds, 2340 residues, 3 models selected 
    20736 
    20737 > select add #10
    20738 
    20739 24112 atoms, 24564 bonds, 3120 residues, 4 models selected 
    20740 
    20741 > delete atoms sel
    20742 
    20743 > delete bonds sel
    20744 
    20745 > hide #6 models
    20746 
    20747 > show #6 models
    20748 
    20749 > hide #6 models
    20750 
    20751 > select add #2
    20752 
    20753 5420 atoms, 5522 bonds, 689 residues, 1 model selected 
    20754 
    20755 > select add #3
    20756 
    20757 10840 atoms, 11044 bonds, 1378 residues, 2 models selected 
    20758 
    20759 > select add #4
    20760 
    20761 16260 atoms, 16566 bonds, 2067 residues, 3 models selected 
    20762 
    20763 > select add #5
    20764 
    20765 21680 atoms, 22088 bonds, 2756 residues, 4 models selected 
    20766 
    20767 > delete atoms sel
    20768 
    20769 > delete bonds sel
    20770 
    20771 > show #6 models
    20772 
    20773 > ui tool show Matchmaker
    20774 
    20775 > select #B
    20776 
    20777 Expected an objects specifier or a keyword 
    20778 
    20779 > select /B
    20780 
    20781 1474 atoms, 1501 bonds, 189 residues, 2 models selected 
    20782 No reference and/or match structure/chain chosen 
    20783 
    20784 > hide #1 models
    20785 
    20786 > show #1 models
    20787 
    20788 > matchmaker #6 & sel to #1 & sel
    20789 
    20790 Computing secondary structure 
    20791 Parameters 
    20792 --- 
    20793 Chain pairing | bb 
    20794 Alignment algorithm | Needleman-Wunsch 
    20795 Similarity matrix | BLOSUM-62 
    20796 SS fraction | 0.3 
    20797 Gap open (HH/SS/other) | 18/18/6 
    20798 Gap extend | 1 
    20799 SS matrix |  |  | H | S | O 
    20800 ---|---|---|--- 
    20801 H | 6 | -9 | -6 
    20802 S |  | 6 | -6 
    20803 O |  |  | 4 
    20804 Iteration cutoff | 2 
    20805  
    20806 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain B (#1) with
    20807 fold_hqba_hfqx6_co_model_0.cif, chain B (#6), sequence alignment score = 372.4 
    20808 RMSD between 69 pruned atom pairs is 0.218 angstroms; (across all 87 pairs:
    20809 5.281) 
    20810  
    20811 
    20812 > matchmaker #6 & sel to #1 & sel
    20813 
    20814 Computing secondary structure 
    20815 Parameters 
    20816 --- 
    20817 Chain pairing | bb 
    20818 Alignment algorithm | Needleman-Wunsch 
    20819 Similarity matrix | BLOSUM-62 
    20820 SS fraction | 0.3 
    20821 Gap open (HH/SS/other) | 18/18/6 
    20822 Gap extend | 1 
    20823 SS matrix |  |  | H | S | O 
    20824 ---|---|---|--- 
    20825 H | 6 | -9 | -6 
    20826 S |  | 6 | -6 
    20827 O |  |  | 4 
    20828 Iteration cutoff | 2 
    20829  
    20830 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain B (#1) with
    20831 fold_hqba_hfqx6_co_model_0.cif, chain B (#6), sequence alignment score = 372.4 
    20832 RMSD between 69 pruned atom pairs is 0.218 angstroms; (across all 87 pairs:
    20833 5.281) 
    20834  
    20835 
    20836 > select clear
    20837 
    20838 No reference and/or match structure/chain chosen 
    20839 
    20840 > matchmaker #6 to #1
    20841 
    20842 Computing secondary structure 
    20843 Parameters 
    20844 --- 
    20845 Chain pairing | bb 
    20846 Alignment algorithm | Needleman-Wunsch 
    20847 Similarity matrix | BLOSUM-62 
    20848 SS fraction | 0.3 
    20849 Gap open (HH/SS/other) | 18/18/6 
    20850 Gap extend | 1 
    20851 SS matrix |  |  | H | S | O 
    20852 ---|---|---|--- 
    20853 H | 6 | -9 | -6 
    20854 S |  | 6 | -6 
    20855 O |  |  | 4 
    20856 Iteration cutoff | 2 
    20857  
    20858 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20859 fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3 
    20860 RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
    20861 0.862) 
    20862  
    20863 
    20864 > matchmaker #6 to #1
    20865 
    20866 Computing secondary structure 
    20867 Parameters 
    20868 --- 
    20869 Chain pairing | bb 
    20870 Alignment algorithm | Needleman-Wunsch 
    20871 Similarity matrix | BLOSUM-62 
    20872 SS fraction | 0.3 
    20873 Gap open (HH/SS/other) | 18/18/6 
    20874 Gap extend | 1 
    20875 SS matrix |  |  | H | S | O 
    20876 ---|---|---|--- 
    20877 H | 6 | -9 | -6 
    20878 S |  | 6 | -6 
    20879 O |  |  | 4 
    20880 Iteration cutoff | 2 
    20881  
    20882 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    20883 fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3 
    20884 RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
    20885 0.862) 
    20886  
    20887 
    20888 > select /B
    20889 
    20890 1474 atoms, 1501 bonds, 189 residues, 2 models selected 
    20891 
    20892 > hide #6 models
    20893 
    20894 > select #1/D:22
    20895 
    20896 7 atoms, 6 bonds, 1 residue, 1 model selected 
    20897 
    20898 > select .31
    20899 
    20900 Expected an objects specifier or a keyword 
    20901 
    20902 > select clear
    20903 
    20904 > select #1/C:31
    20905 
    20906 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20907 
    20908 > select #1/A:102
    20909 
    20910 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20911 
    20912 > style sel stick
    20913 
    20914 Changed 9 atom styles 
    20915 
    20916 > show sel atoms
    20917 
    20918 > color sel red
    20919 
    20920 > select clear
    20921 
    20922 > show #6 models
    20923 
    20924 > hide #1 models
    20925 
    20926 > select #6/A:102
    20927 
    20928 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20929 
    20930 > style sel stick
    20931 
    20932 Changed 9 atom styles 
    20933 
    20934 > show sel atoms
    20935 
    20936 > color sel red
    20937 
    20938 > show #1 models
    20939 
    20940 > hide #1 models
    20941 
    20942 > select #6/A:98
    20943 
    20944 8 atoms, 7 bonds, 1 residue, 1 model selected 
    20945 
    20946 > style sel stick
    20947 
    20948 Changed 8 atom styles 
    20949 
    20950 > show sel atoms
    20951 
    20952 > color sel red
    20953 
    20954 > select #6/C:31
    20955 
    20956 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20957 
    20958 > style sel stick
    20959 
    20960 Changed 9 atom styles 
    20961 
    20962 > show sel atoms
    20963 
    20964 > color sel medium blue
    20965 
    20966 > select #6/A:150
    20967 
    20968 5 atoms, 4 bonds, 1 residue, 1 model selected 
    20969 
    20970 > select #6/A
    20971 
    20972 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    20973 
    20974 > select ~sel & ##selected
    20975 
    20976 4717 atoms, 4800 bonds, 613 residues, 1 model selected 
    20977 
    20978 > color sel gray
    20979 
    20980 > ui tool show "Color Actions"
    20981 
    20982 > color sel dark khaki
    20983 
    20984 > select clear
    20985 
    20986 > select #6/C:31
    20987 
    20988 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20989 
    20990 > color sel medium blue
    20991 
    20992 > select clear
    20993 
    20994 > show #1 models
    20995 
    20996 > hide #6 models
    20997 
    20998 > select #1/C:31
    20999 
    21000 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21001 
    21002 > style sel stick
    21003 
    21004 Changed 9 atom styles 
    21005 
    21006 > show sel atoms
    21007 
    21008 > color sel medium blue
    21009 
    21010 > select clear
    21011 
    21012 > show #6 models
    21013 
    21014 > hide #6 models
    21015 
    21016 > select #1/A:98
    21017 
    21018 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21019 
    21020 > style sel stick
    21021 
    21022 Changed 6 atom styles 
    21023 
    21024 > style sel stick
    21025 
    21026 Changed 6 atom styles 
    21027 
    21028 > style sel stick
    21029 
    21030 Changed 6 atom styles 
    21031 
    21032 > show sel atoms
    21033 
    21034 > color sel orange
    21035 
    21036 > show #6 models
    21037 
    21038 > hide #6 models
    21039 
    21040 > select #1/A:99
    21041 
    21042 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21043 
    21044 > select clear
    21045 
    21046 > select #1/A
    21047 
    21048 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    21049 
    21050 > ui tool show Contacts
    21051 
    21052 > show #6 models
    21053 
    21054 > hide #1 models
    21055 
    21056 > hide #6 models
    21057 
    21058 > show #1 models
    21059 
    21060 > select #1/A
    21061 
    21062 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    21063 
    21064 > show #6 models
    21065 
    21066 > select /A
    21067 
    21068 2603 atoms, 2657 bonds, 334 residues, 2 models selected 
    21069 
    21070 > contacts sel saveFile /Users/taic/Library/CloudStorage/OneDrive-
    21071 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/contacts.txt
    21072 > restrict both resSeparation 5 interModel false intraMol false
    21073 > ignoreHiddenModels true color #c7ff92 radius 0.06 reveal true
    21074 
    21075 No contacts 
    21076 
    21077 > hide #6 models
    21078 
    21079 > select clear
    21080 
    21081 > hide #2 models
    21082 
    21083 > show #2 models
    21084 
    21085 > hide #2 models
    21086 
    21087 > show #2 models
    21088 
    21089 > select #1/A:102
    21090 
    21091 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21092 
    21093 > select add #1/A:98
    21094 
    21095 15 atoms, 13 bonds, 2 residues, 1 model selected 
    21096 
    21097 > select add #1/C:31
    21098 
    21099 24 atoms, 21 bonds, 3 residues, 1 model selected 
    21100 
    21101 > label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
    21102 
    21103 > label height 20
    21104 
    21105 > label height 6
    21106 
    21107 > label height 3
    21108 
    21109 > label height 2
    21110 
    21111 > select clear
    21112 
    21113 > show #6 models
    21114 
    21115 > hide #!1 models
    21116 
    21117 > show #!1 models
    21118 
    21119 > hide #6 models
    21120 
    21121 > show #6 models
    21122 
    21123 > hide #!1 models
    21124 
    21125 > show #!1 models
    21126 
    21127 > hide #2 models
    21128 
    21129 > hide #6 models
    21130 
    21131 > select #1
    21132 
    21133 5420 atoms, 5522 bonds, 689 residues, 2 models selected 
    21134 
    21135 > select #1/A
    21136 
    21137 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    21138 
    21139 > select ~sel & ##selected
    21140 
    21141 4128 atoms, 4206 bonds, 522 residues, 1 model selected 
    21142 
    21143 > ui tool show "Color Actions"
    21144 
    21145 > color sel light gray
    21146 
    21147 > select clear
    21148 
    21149 > select #1/A
    21150 
    21151 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    21152 
    21153 > color sel orange
    21154 
    21155 > select #1/A:102
    21156 
    21157 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21158 
    21159 > select add #1/A:98
    21160 
    21161 15 atoms, 13 bonds, 2 residues, 1 model selected 
    21162 
    21163 > color sel magenta
    21164 
    21165 > select #1/C:32
    21166 
    21167 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21168 
    21169 > select #1/B:26
    21170 
    21171 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21172 
    21173 > select #1/C:32
    21174 
    21175 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21176 
    21177 > select add #1/C:31
    21178 
    21179 17 atoms, 15 bonds, 2 residues, 1 model selected 
    21180 
    21181 > select clear
    21182 
    21183 > select add #1/C:31
    21184 
    21185 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21186 
    21187 > color sel medium blue
    21188 
    21189 > select clear
    21190 
    21191 > preset cartoons/nucleotides ribbons/slabs
    21192 
    21193 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    21194 Changed 11397 atom styles 
    21195 Preset expands to these ChimeraX commands:
    21196 
    21197    
    21198    
    21199     show nucleic
    21200     hide protein|solvent|H
    21201     surf hide
    21202     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    21203     ~worm
    21204     cartoon
    21205     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    21206     cartoon style ~(nucleic|strand) x round
    21207     cartoon style (nucleic|strand) x rect
    21208     nucleotides tube/slab shape box
    21209 
    21210  
    21211 
    21212 > preset cartoons/nucleotides ribbons/slabs
    21213 
    21214 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    21215 Changed 0 atom styles 
    21216 Preset expands to these ChimeraX commands:
    21217 
    21218    
    21219    
    21220     show nucleic
    21221     hide protein|solvent|H
    21222     surf hide
    21223     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    21224     ~worm
    21225     cartoon
    21226     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    21227     cartoon style ~(nucleic|strand) x round
    21228     cartoon style (nucleic|strand) x rect
    21229     nucleotides tube/slab shape box
    21230 
    21231  
    21232 
    21233 > select add #1/A:98
    21234 
    21235 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21236 
    21237 > select add #1/A:102
    21238 
    21239 15 atoms, 13 bonds, 2 residues, 1 model selected 
    21240 
    21241 > select add #1/C:31
    21242 
    21243 24 atoms, 21 bonds, 3 residues, 1 model selected 
    21244 
    21245 > show sel atoms
    21246 
    21247 > select clear
    21248 
    21249 > preset "overall look" "publication 1 (silhouettes)"
    21250 
    21251 Using preset: Overall Look / Publication 1 (Silhouettes) 
    21252 Preset expands to these ChimeraX commands:
    21253 
    21254    
    21255    
    21256     set bg white
    21257     graphics silhouettes t
    21258     lighting depthCue f
    21259 
    21260  
    21261 
    21262 > select clear
    21263 
    21264 > select add #1/A:102
    21265 
    21266 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21267 
    21268 > select add #1/A:98
    21269 
    21270 15 atoms, 13 bonds, 2 residues, 1 model selected 
    21271 
    21272 > select add #1/C:31
    21273 
    21274 24 atoms, 21 bonds, 3 residues, 1 model selected 
    21275 
    21276 > ~label sel residues
    21277 
    21278 > select clear
    21279 
    21280 > save /Users/taic/Library/CloudStorage/OneDrive-
    21281 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.png
    21282 > width 600 height 417 supersample 4 transparentBackground true
    21283 
    21284 > open 4RS2 fromDatabase pdb format mmcif
    21285 
    21286 4rs2 title: 
    21287 1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
    21288 Escherichia coli in Complex with CoA [more info...] 
    21289  
    21290 Chain information for 4rs2 #3 
    21291 --- 
    21292 Chain | Description | UniProt 
    21293 A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167 
    21294  
    21295 Non-standard residues in 4rs2 #3 
    21296 --- 
    21297 COA — coenzyme A 
    21298  
    21299 4rs2 mmCIF Assemblies 
    21300 --- 
    21301 1| author_and_software_defined_assembly 
    21302 2| author_and_software_defined_assembly 
    21303  
    21304 331 atoms have alternate locations. Control/examine alternate locations with
    21305 Altloc Explorer [start tool...] or the altlocs command. 
    21306 
    21307 > ui tool show Matchmaker
    21308 
    21309 > select #1/A
    21310 
    21311 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    21312 
    21313 > matchmaker #3 to #1 & sel
    21314 
    21315 Computing secondary structure 
    21316 Parameters 
    21317 --- 
    21318 Chain pairing | bb 
    21319 Alignment algorithm | Needleman-Wunsch 
    21320 Similarity matrix | BLOSUM-62 
    21321 SS fraction | 0.3 
    21322 Gap open (HH/SS/other) | 18/18/6 
    21323 Gap extend | 1 
    21324 SS matrix |  |  | H | S | O 
    21325 ---|---|---|--- 
    21326 H | 6 | -9 | -6 
    21327 S |  | 6 | -6 
    21328 O |  |  | 4 
    21329 Iteration cutoff | 2 
    21330  
    21331 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with 4rs2, chain
    21332 B (#3), sequence alignment score = 540.5 
    21333 RMSD between 157 pruned atom pairs is 0.811 angstroms; (across all 167 pairs:
    21334 1.074) 
    21335  
    21336 
    21337 > select #3/A
    21338 
    21339 1678 atoms, 1491 bonds, 404 residues, 1 model selected 
    21340 
    21341 > hide sel cartoons
    21342 
    21343 > hide sel atoms
    21344 
    21345 > select #3/B
    21346 
    21347 1720 atoms, 1524 bonds, 419 residues, 1 model selected 
    21348 
    21349 > hide sel cartoons
    21350 
    21351 > select clear
    21352 
    21353 > hide #1,3 atoms
    21354 
    21355 > show #1,3 atoms
    21356 
    21357 > hide #1,3 atoms
    21358 
    21359 > hide #1 models
    21360 
    21361 > select add #3
    21362 
    21363 3398 atoms, 3015 bonds, 823 residues, 1 model selected 
    21364 
    21365 > select subtract #2
    21366 
    21367 3398 atoms, 3015 bonds, 823 residues, 1 model selected 
    21368 
    21369 > delete atoms sel
    21370 
    21371 > delete bonds sel
    21372 
    21373 > show #1 models
    21374 
    21375 > open 4RS2 fromDatabase pdb format mmcif
    21376 
    21377 4rs2 title: 
    21378 1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
    21379 Escherichia coli in Complex with CoA [more info...] 
    21380  
    21381 Chain information for 4rs2 #3 
    21382 --- 
    21383 Chain | Description | UniProt 
    21384 A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167 
    21385  
    21386 Non-standard residues in 4rs2 #3 
    21387 --- 
    21388 COA — coenzyme A 
    21389  
    21390 4rs2 mmCIF Assemblies 
    21391 --- 
    21392 1| author_and_software_defined_assembly 
    21393 2| author_and_software_defined_assembly 
    21394  
    21395 331 atoms have alternate locations. Control/examine alternate locations with
    21396 Altloc Explorer [start tool...] or the altlocs command. 
    21397 
    21398 > select #1/A
    21399 
    21400 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    21401 
    21402 > matchmaker #3,6 to #1/A & sel pairing bs
    21403 
    21404 Computing secondary structure 
    21405 Parameters 
    21406 --- 
    21407 Chain pairing | bs 
    21408 Alignment algorithm | Needleman-Wunsch 
    21409 Similarity matrix | BLOSUM-62 
    21410 SS fraction | 0.3 
    21411 Gap open (HH/SS/other) | 18/18/6 
    21412 Gap extend | 1 
    21413 SS matrix |  |  | H | S | O 
    21414 ---|---|---|--- 
    21415 H | 6 | -9 | -6 
    21416 S |  | 6 | -6 
    21417 O |  |  | 4 
    21418 Iteration cutoff | 2 
    21419  
    21420 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with 4rs2, chain
    21421 B (#3), sequence alignment score = 540.5 
    21422 RMSD between 157 pruned atom pairs is 0.811 angstroms; (across all 167 pairs:
    21423 1.074) 
    21424  
    21425 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    21426 fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3 
    21427 RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
    21428 0.862) 
    21429  
    21430 
    21431 > select #3/A
    21432 
    21433 1678 atoms, 1491 bonds, 404 residues, 1 model selected 
    21434 
    21435 > hide sel cartoons
    21436 
    21437 > hide sel atoms
    21438 
    21439 > hide #3 models
    21440 
    21441 > show #3 models
    21442 
    21443 > select #1/A:115
    21444 
    21445 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21446 
    21447 > style sel stick
    21448 
    21449 Changed 5 atom styles 
    21450 
    21451 > show sel atoms
    21452 
    21453 > select #1/A:119
    21454 
    21455 11 atoms, 10 bonds, 1 residue, 1 model selected 
    21456 
    21457 > style sel stick
    21458 
    21459 Changed 11 atom styles 
    21460 
    21461 > show sel atoms
    21462 
    21463 > select #1/A:84
    21464 
    21465 11 atoms, 10 bonds, 1 residue, 1 model selected 
    21466 
    21467 > style sel stick
    21468 
    21469 Changed 11 atom styles 
    21470 
    21471 > show sel atoms
    21472 
    21473 > select #1/A:21
    21474 
    21475 7 atoms, 6 bonds, 1 residue, 1 model selected 
    21476 
    21477 > style sel stick
    21478 
    21479 Changed 7 atom styles 
    21480 
    21481 > show sel atoms
    21482 
    21483 > select #1/A:22
    21484 
    21485 11 atoms, 11 bonds, 1 residue, 1 model selected 
    21486 
    21487 > style sel stick
    21488 
    21489 Changed 11 atom styles 
    21490 
    21491 > show sel atoms
    21492 
    21493 > select #1/A:79
    21494 
    21495 7 atoms, 6 bonds, 1 residue, 1 model selected 
    21496 
    21497 > style sel stick
    21498 
    21499 Changed 7 atom styles 
    21500 
    21501 > show sel atoms
    21502 
    21503 > hide #1 models
    21504 
    21505 > show #1 models
    21506 
    21507 > select #3/B:78
    21508 
    21509 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21510 
    21511 > style sel stick
    21512 
    21513 Changed 5 atom styles 
    21514 
    21515 > show sel atoms
    21516 
    21517 > hide #3 models
    21518 
    21519 > show #3 models
    21520 
    21521 > select #1/A:78
    21522 
    21523 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21524 
    21525 > style sel stick
    21526 
    21527 Changed 5 atom styles 
    21528 
    21529 > show sel atoms
    21530 
    21531 Drag select of 113 atoms, 118 residues, 97 bonds 
    21532 
    21533 > select clear
    21534 
    21535 Drag select of 154 atoms, 195 residues, 130 bonds 
    21536 
    21537 > matchmaker #3,6 to #1/A & sel pairing bs
    21538 
    21539 Computing secondary structure 
    21540 Parameters 
    21541 --- 
    21542 Chain pairing | bs 
    21543 Alignment algorithm | Needleman-Wunsch 
    21544 Similarity matrix | BLOSUM-62 
    21545 SS fraction | 0.3 
    21546 Gap open (HH/SS/other) | 18/18/6 
    21547 Gap extend | 1 
    21548 SS matrix |  |  | H | S | O 
    21549 ---|---|---|--- 
    21550 H | 6 | -9 | -6 
    21551 S |  | 6 | -6 
    21552 O |  |  | 4 
    21553 Iteration cutoff | 2 
    21554  
    21555 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with 4rs2, chain
    21556 B (#3), sequence alignment score = 306.5 
    21557 RMSD between 90 pruned atom pairs is 0.825 angstroms; (across all 96 pairs:
    21558 1.120) 
    21559  
    21560 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    21561 fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 331.7 
    21562 RMSD between 92 pruned atom pairs is 0.629 angstroms; (across all 96 pairs:
    21563 0.916) 
    21564  
    21565 
    21566 > matchmaker #6 to #1 & sel
    21567 
    21568 Computing secondary structure 
    21569 Parameters 
    21570 --- 
    21571 Chain pairing | bb 
    21572 Alignment algorithm | Needleman-Wunsch 
    21573 Similarity matrix | BLOSUM-62 
    21574 SS fraction | 0.3 
    21575 Gap open (HH/SS/other) | 18/18/6 
    21576 Gap extend | 1 
    21577 SS matrix |  |  | H | S | O 
    21578 ---|---|---|--- 
    21579 H | 6 | -9 | -6 
    21580 S |  | 6 | -6 
    21581 O |  |  | 4 
    21582 Iteration cutoff | 2 
    21583  
    21584 Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
    21585 fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 331.7 
    21586 RMSD between 92 pruned atom pairs is 0.629 angstroms; (across all 96 pairs:
    21587 0.916) 
    21588  
    21589 
    21590 > matchmaker #6 to #3/A & sel pairing bs
    21591 
    21592 No 'to' chains specified 
    21593 
    21594 > select clear
    21595 
    21596 Drag select of 147 atoms, 178 residues, 126 bonds 
    21597 
    21598 > matchmaker #6 to #3/B & sel pairing bs
    21599 
    21600 Computing secondary structure 
    21601 Parameters 
    21602 --- 
    21603 Chain pairing | bs 
    21604 Alignment algorithm | Needleman-Wunsch 
    21605 Similarity matrix | BLOSUM-62 
    21606 SS fraction | 0.3 
    21607 Gap open (HH/SS/other) | 18/18/6 
    21608 Gap extend | 1 
    21609 SS matrix |  |  | H | S | O 
    21610 ---|---|---|--- 
    21611 H | 6 | -9 | -6 
    21612 S |  | 6 | -6 
    21613 O |  |  | 4 
    21614 Iteration cutoff | 2 
    21615  
    21616 Matchmaker 4rs2, chain B (#3) with fold_hqba_hfqx6_co_model_0.cif, chain A
    21617 (#6), sequence alignment score = 429.6 
    21618 RMSD between 85 pruned atom pairs is 0.643 angstroms; (across all 86 pairs:
    21619 0.720) 
    21620  
    21621 
    21622 > matchmaker #1 to #3/B & sel pairing bs
    21623 
    21624 Computing secondary structure 
    21625 Parameters 
    21626 --- 
    21627 Chain pairing | bs 
    21628 Alignment algorithm | Needleman-Wunsch 
    21629 Similarity matrix | BLOSUM-62 
    21630 SS fraction | 0.3 
    21631 Gap open (HH/SS/other) | 18/18/6 
    21632 Gap extend | 1 
    21633 SS matrix |  |  | H | S | O 
    21634 ---|---|---|--- 
    21635 H | 6 | -9 | -6 
    21636 S |  | 6 | -6 
    21637 O |  |  | 4 
    21638 Iteration cutoff | 2 
    21639  
    21640 Matchmaker 4rs2, chain B (#3) with fold_hqba_hfqx6_vcholera_model_0.cif, chain
    21641 A (#1), sequence alignment score = 277 
    21642 RMSD between 80 pruned atom pairs is 0.852 angstroms; (across all 86 pairs:
    21643 1.167) 
    21644  
    21645 
    21646 > matchmaker #1 & sel to #3/B & sel pairing bs
    21647 
    21648 Computing secondary structure 
    21649 Parameters 
    21650 --- 
    21651 Chain pairing | bs 
    21652 Alignment algorithm | Needleman-Wunsch 
    21653 Similarity matrix | BLOSUM-62 
    21654 SS fraction | 0.3 
    21655 Gap open (HH/SS/other) | 18/18/6 
    21656 Gap extend | 1 
    21657 SS matrix |  |  | H | S | O 
    21658 ---|---|---|--- 
    21659 H | 6 | -9 | -6 
    21660 S |  | 6 | -6 
    21661 O |  |  | 4 
    21662 Iteration cutoff | 2 
    21663  
    21664 Matchmaker 4rs2, chain B (#3) with fold_hqba_hfqx6_vcholera_model_0.cif, chain
    21665 A (#1), sequence alignment score = 271 
    21666 RMSD between 79 pruned atom pairs is 0.855 angstroms; (across all 85 pairs:
    21667 1.172) 
    21668  
    21669 
    21670 > select clear
    21671 
    21672 > hide #3 models
    21673 
    21674 > show #3 models
    21675 
    21676 > select ::name="COA"
    21677 
    21678 96 atoms, 100 bonds, 2 residues, 1 model selected 
    21679 
    21680 > color sel lime
    21681 
    21682 > hide #3 models
    21683 
    21684 > show #3 models
    21685 
    21686 > select #1/A:86
    21687 
    21688 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21689 
    21690 > style sel stick
    21691 
    21692 Changed 9 atom styles 
    21693 
    21694 > show sel atoms
    21695 
    21696 > hide #1 models
    21697 
    21698 > show #1 models
    21699 
    21700 > hide #1 models
    21701 
    21702 > show #1 models
    21703 
    21704 > hide #3 models
    21705 
    21706 > select #1/A:116
    21707 
    21708 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21709 
    21710 > style sel stick
    21711 
    21712 Changed 12 atom styles 
    21713 
    21714 > show sel atoms
    21715 
    21716 > show #3 models
    21717 
    21718 > hide #1 models
    21719 
    21720 > select #3/B:117
    21721 
    21722 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21723 
    21724 > style sel stick
    21725 
    21726 Changed 12 atom styles 
    21727 
    21728 > show sel atoms
    21729 
    21730 > show #1 models
    21731 
    21732 > hide #3 models
    21733 
    21734 > select #1/A:117
    21735 
    21736 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21737 
    21738 > style sel stick
    21739 
    21740 Changed 12 atom styles 
    21741 
    21742 > show sel atoms
    21743 
    21744 > show #3 models
    21745 
    21746 > hide #3 models
    21747 
    21748 > select #1/A:116
    21749 
    21750 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21751 
    21752 > hide sel atoms
    21753 
    21754 > show #3 models
    21755 
    21756 > hide #3 models
    21757 
    21758 > select add #1/A:102
    21759 
    21760 21 atoms, 20 bonds, 2 residues, 1 model selected 
    21761 
    21762 > select add #1/A:98
    21763 
    21764 27 atoms, 25 bonds, 3 residues, 1 model selected 
    21765 
    21766 > select add #1/C:31
    21767 
    21768 36 atoms, 33 bonds, 4 residues, 1 model selected 
    21769 
    21770 > show sel atoms
    21771 
    21772 > select clear
    21773 
    21774 > select #1/A:116
    21775 
    21776 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21777 
    21778 > hide sel atoms
    21779 
    21780 > select clear
    21781 
    21782 > save /Users/taic/Library/CloudStorage/OneDrive-
    21783 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.cxs
    21784 
    21785 > select N
    21786 
    21787 2579 atoms, 1833 residues, 3 models selected 
    21788 
    21789 > color (#1 & sel) blue
    21790 
    21791 > undo
    21792 
    21793 > select N1
    21794 
    21795 Nothing selected 
    21796 
    21797 > show #3 models
    21798 
    21799 > select add #1/A:86@NE2
    21800 
    21801 1 atom, 1 residue, 1 model selected 
    21802 
    21803 > select clear
    21804 
    21805 > select add #1/A:86@NE2
    21806 
    21807 1 atom, 1 residue, 1 model selected 
    21808 
    21809 > select add #1/A:84@NH1
    21810 
    21811 2 atoms, 2 residues, 1 model selected 
    21812 
    21813 > select add #1/A:119@NH2
    21814 
    21815 3 atoms, 3 residues, 1 model selected 
    21816 
    21817 > select add #1/A:119@NH1
    21818 
    21819 4 atoms, 3 residues, 1 model selected 
    21820 
    21821 > select add #1/A:84@NE
    21822 
    21823 5 atoms, 3 residues, 1 model selected 
    21824 
    21825 > select add #1/A:84@NH2
    21826 
    21827 6 atoms, 3 residues, 1 model selected 
    21828 
    21829 > color sel blue
    21830 
    21831 > select clear
    21832 
    21833 > select #1/A:119
    21834 
    21835 11 atoms, 10 bonds, 1 residue, 1 model selected 
    21836 
    21837 > undo
    21838 
    21839 > select clear
    21840 
    21841 > select #1/A:119
    21842 
    21843 11 atoms, 10 bonds, 1 residue, 1 model selected 
    21844 
    21845 > select #1/A
    21846 
    21847 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    21848 
    21849 > select subtract #1/A:119
    21850 
    21851 1281 atoms, 1304 bonds, 166 residues, 1 model selected 
    21852 
    21853 > select clear
    21854 
    21855 > select #1/A:119
    21856 
    21857 11 atoms, 10 bonds, 1 residue, 1 model selected 
    21858 
    21859 > select add #1/A:84
    21860 
    21861 22 atoms, 20 bonds, 2 residues, 1 model selected 
    21862 
    21863 > select add #1/A:86
    21864 
    21865 31 atoms, 28 bonds, 3 residues, 1 model selected 
    21866 
    21867 > color sel orange
    21868 
    21869 > select clear
    21870 
    21871 > hide #1 models
    21872 
    21873 > show #1 models
    21874 
    21875 > hide #1 models
    21876 
    21877 > select #3/B:117
    21878 
    21879 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21880 
    21881 > color sel purple
    21882 
    21883 > select clear
    21884 
    21885 > save /Users/taic/Library/CloudStorage/OneDrive-
    21886 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/4RS2.png
    21887 > width 600 height 417 supersample 4 transparentBackground true
    21888 
    21889 > show #1 models
    21890 
    21891 > hide #3 models
    21892 
    21893 > show #3 models
    21894 
    21895 > hide #3 models
    21896 
    21897 > show #3 models
    21898 
    21899 > hide #1 models
    21900 
    21901 > show #1 models
    21902 
    21903 > hide #1 models
    21904 
    21905 > select #3/B:102
    21906 
    21907 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21908 
    21909 > select add #3/B:98
    21910 
    21911 17 atoms, 15 bonds, 2 residues, 1 model selected 
    21912 
    21913 > style sel stick
    21914 
    21915 Changed 17 atom styles 
    21916 
    21917 > show sel atoms
    21918 
    21919 > color sel magenta
    21920 
    21921 > select clear
    21922 
    21923 > show #1 models
    21924 
    21925 > hide #1 models
    21926 
    21927 > show #1 models
    21928 
    21929 > hide #1 models
    21930 
    21931 > save /Users/taic/Library/CloudStorage/OneDrive-
    21932 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/4RS2.png
    21933 > width 600 height 417 supersample 4 transparentBackground true
    21934 
    21935 > show #1 models
    21936 
    21937 > hide #3 models
    21938 
    21939 > show #3 models
    21940 
    21941 > save /Users/taic/Library/CloudStorage/OneDrive-
    21942 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/4RS2.vs.HqbA_Hfq_Vcholera.png
    21943 > width 600 height 417 supersample 4 transparentBackground true
    21944 
    21945 > hide #3 models
    21946 
    21947 > select #1/A:117
    21948 
    21949 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21950 
    21951 > color sel purple
    21952 
    21953 > select clear
    21954 
    21955 > show #3 models
    21956 
    21957 > select ::name="COA"
    21958 
    21959 96 atoms, 100 bonds, 2 residues, 1 model selected 
    21960 
    21961 > select ~sel & ##selected
    21962 
    21963 3302 atoms, 2915 bonds, 821 residues, 1 model selected 
    21964 
    21965 > hide sel cartoons
    21966 
    21967 > hide sel atoms
    21968 
    21969 > select clear
    21970 
    21971 > save /Users/taic/Library/CloudStorage/OneDrive-
    21972 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_CoA_Hfq_Vcholera.png
    21973 > width 600 height 417 supersample 4 transparentBackground true
    21974 
    21975 > save /Users/taic/Library/CloudStorage/OneDrive-
    21976 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_CoA_Hfq_Vcholera-2.png
    21977 > width 600 height 417 supersample 4 transparentBackground true
    21978 
    21979 > show #6 models
    21980 
    21981 > hide #1 models
    21982 
    21983 > show #1 models
    21984 
    21985 > hide #1 models
    21986 
    21987 > select #6/C:32
    21988 
    21989 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21990 
    21991 > select clear
    21992 
    21993 > hide #6 models
    21994 
    21995 > show #1 models
    21996 
    21997 > save /Users/taic/Library/CloudStorage/OneDrive-
    21998 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.cxs
    21999 
    22000 > hide #3 models
    22001 
    22002 > show #3 models
    22003 
    22004 > show #6 models
    22005 
    22006 > hide #1 models
    22007 
    22008 > select #6/A:98
    22009 
    22010 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22011 
    22012 > select add #6/A:102
    22013 
    22014 17 atoms, 15 bonds, 2 residues, 1 model selected 
    22015 
    22016 > style sel stick
    22017 
    22018 Changed 17 atom styles 
    22019 
    22020 > show sel atoms
    22021 
    22022 > select add #6/C:31
    22023 
    22024 26 atoms, 23 bonds, 3 residues, 1 model selected 
    22025 
    22026 > style sel stick
    22027 
    22028 Changed 26 atom styles 
    22029 
    22030 > show sel atoms
    22031 
    22032 > show #1 models
    22033 
    22034 > hide #6 models
    22035 
    22036 > show #6 models
    22037 
    22038 > hide #6 models
    22039 
    22040 > show #6 models
    22041 
    22042 > hide #1 models
    22043 
    22044 > show #1 models
    22045 
    22046 > hide #6 models
    22047 
    22048 > select #1/A
    22049 
    22050 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    22051 
    22052 > ui tool show Contacts
    22053 
    22054 > contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
    22055 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/contacts.txt
    22056 > resSeparation 5 interModel false intraMol false ignoreHiddenModels true
    22057 > color #c7ff92 radius 0.06 reveal true
    22058 
    22059 1820 contacts 
    22060 
    22061 > select #1/A
    22062 
    22063 1292 atoms, 1316 bonds, 167 residues, 1 model selected 
    22064 
    22065 > contacts sel saveFile /Users/taic/Library/CloudStorage/OneDrive-
    22066 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/contacts.txt
    22067 > resSeparation 5 interModel false intraMol false ignoreHiddenModels true
    22068 > color #c7ff92 radius 0.06 reveal true
    22069 
    22070 84 contacts 
    22071 
    22072 > undo
    22073 
    22074 Drag select of 1811 atoms, 404 residues, 1499 bonds, 3 pseudobonds 
    22075 
    22076 > select clear
    22077 
    22078 > contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
    22079 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/contacts.txt
    22080 > resSeparation 5 interModel false intraMol false ignoreHiddenModels true
    22081 > color #c7ff92 radius 0.06 reveal true
    22082 
    22083 1820 contacts 
    22084 
    22085 > hide #!3 models
    22086 
    22087 Drag select of 860 atoms, 363 residues, 736 bonds 
    22088 
    22089 > select clear
    22090 
    22091 Drag select of 830 atoms, 348 residues, 714 bonds 
    22092 
    22093 > hide sel atoms
    22094 
    22095 > select clear
    22096 
    22097 > show #2 models
    22098 
    22099 > hide #2 models
    22100 
    22101 > show #!3 models
    22102 
    22103 > select #3/A
    22104 
    22105 1678 atoms, 1491 bonds, 631 pseudobonds, 404 residues, 3 models selected 
    22106 
    22107 > hide sel atoms
    22108 
    22109 > select ::name="HOH"
    22110 
    22111 458 atoms, 205 pseudobonds, 458 residues, 2 models selected 
    22112 
    22113 > hide sel atoms
    22114 
    22115 > select ::name="COA"
    22116 
    22117 96 atoms, 100 bonds, 2 residues, 1 model selected 
    22118 
    22119 > select ~sel & ##selected
    22120 
    22121 3302 atoms, 2915 bonds, 1361 pseudobonds, 821 residues, 3 models selected 
    22122 
    22123 > hide sel atoms
    22124 
    22125 > select clear
    22126 
    22127 > show #6 models
    22128 
    22129 > save /Users/taic/Library/CloudStorage/OneDrive-
    22130 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.contacts.cxs
    22131 
    22132 > close session
    22133 
    22134 > open /Users/taic/Library/CloudStorage/OneDrive-
    22135 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
    22136 
    22137 opened ChimeraX session 
    22138 
    22139 > hide #!2 models
    22140 
    22141 > hide #4 models
    22142 
    22143 > hide #5 models
    22144 
    22145 > hide #7 models
    22146 
    22147 > hide #8 models
    22148 
    22149 > show #4 models
    22150 
    22151 > hide #3 models
    22152 
    22153 > show #5 models
    22154 
    22155 > show #7 models
    22156 
    22157 > show #8 models
    22158 
    22159 > select add #4
    22160 
    22161 4991 atoms, 5113 bonds, 625 residues, 2 models selected 
    22162 
    22163 > select add #5
    22164 
    22165 8336 atoms, 8541 bonds, 1042 residues, 3 models selected 
    22166 
    22167 > select add #7
    22168 
    22169 11681 atoms, 11969 bonds, 1459 residues, 4 models selected 
    22170 
    22171 > select add #8
    22172 
    22173 15026 atoms, 15397 bonds, 1876 residues, 5 models selected 
    22174 
    22175 > delete atoms (#4-5,7-8 & sel)
    22176 
    22177 > delete bonds (#4-5,7-8 & sel)
    22178 
    22179 > open /Users/taic/Library/CloudStorage/OneDrive-
    22180 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    22181 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
    22182 
    22183 Chain information for fold_azor_monomer_fad_model_0.cif #4 
    22184 --- 
    22185 Chain | Description 
    22186 A | . 
    22187  
    22188 Computing secondary structure 
    22189 
    22190 > open /Users/taic/Library/CloudStorage/OneDrive-
    22191 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    22192 > Predictions/azor_dimer_nad/fold_azor_dimer_nad_model_0.cif
    22193 
    22194 Chain information for fold_azor_dimer_nad_model_0.cif #5 
    22195 --- 
    22196 Chain | Description 
    22197 A B | . 
    22198  
    22199 Computing secondary structure 
    22200 
    22201 > open /Users/taic/Library/CloudStorage/OneDrive-
    22202 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
    22203 > OtherProteins/icd/fold_icd_model_0.cif
    22204 
    22205 Chain information for fold_icd_model_0.cif #7 
    22206 --- 
    22207 Chain | Description 
    22208 A | . 
    22209  
    22210 Computing secondary structure 
    22211 
    22212 > open /Users/taic/Library/CloudStorage/OneDrive-
    22213 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
    22214 > OtherProteins/mqo/fold_mqo_model_0.cif
    22215 
    22216 Chain information for fold_mqo_model_0.cif #8 
    22217 --- 
    22218 Chain | Description 
    22219 A | . 
    22220  
    22221 Computing secondary structure 
    22222 
    22223 > open /Users/taic/Library/CloudStorage/OneDrive-
    22224 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
    22225 > OtherProteins/ndhc/fold_ndhc_model_0.cif
    22226 
    22227 Chain information for fold_ndhc_model_0.cif #9 
    22228 --- 
    22229 Chain | Description 
    22230 A | . 
    22231  
    22232 Computing secondary structure 
    22233 
    22234 > open /Users/taic/Library/CloudStorage/OneDrive-
    22235 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
    22236 > OtherProteins/ndhf/fold_ndhf_model_0.cif
    22237 
    22238 Chain information for fold_ndhf_model_0.cif #10 
    22239 --- 
    22240 Chain | Description 
    22241 A | . 
    22242  
    22243 Computing secondary structure 
    22244 
    22245 > open /Users/taic/Library/CloudStorage/OneDrive-
    22246 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
    22247 > OtherProteins/suca/fold_suca_model_0.cif
    22248 
    22249 Chain information for fold_suca_model_0.cif #12 
    22250 --- 
    22251 Chain | Description 
    22252 A | . 
    22253  
    22254 Computing secondary structure 
    22255 
    22256 > ui tool show Matchmaker
    22257 
    22258 > matchmaker #3-5,7-12#!2,6 to #1/A pairing bs
    22259 
    22260 Computing secondary structure 
    22261 Parameters 
    22262 --- 
    22263 Chain pairing | bs 
    22264 Alignment algorithm | Needleman-Wunsch 
    22265 Similarity matrix | BLOSUM-62 
    22266 SS fraction | 0.3 
    22267 Gap open (HH/SS/other) | 18/18/6 
    22268 Gap extend | 1 
    22269 SS matrix |  |  | H | S | O 
    22270 ---|---|---|--- 
    22271 H | 6 | -9 | -6 
    22272 S |  | 6 | -6 
    22273 O |  |  | 4 
    22274 Iteration cutoff | 2 
    22275  
    22276 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22277 fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
    22278 1077.8 
    22279 RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
    22280 0.467) 
    22281  
    22282 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22283 fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
    22284 1083.8 
    22285 RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
    22286 0.351) 
    22287  
    22288 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22289 fold_azor_dimer_nad_model_0.cif, chain B (#5), sequence alignment score =
    22290 1086.8 
    22291 RMSD between 208 pruned atom pairs is 0.362 angstroms; (across all 208 pairs:
    22292 0.362) 
    22293  
    22294 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22295 fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4 
    22296 RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
    22297 21.278) 
    22298  
    22299 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22300 fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8 
    22301 RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
    22302 22.621) 
    22303  
    22304 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22305 fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2 
    22306 RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
    22307 31.595) 
    22308  
    22309 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22310 fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4 
    22311 RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
    22312 25.278) 
    22313  
    22314 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22315 fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
    22316 1083.8 
    22317 RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
    22318 0.324) 
    22319  
    22320 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22321 fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2 
    22322 RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
    22323 17.409) 
    22324  
    22325 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22326 fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2 
    22327 RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
    22328 0.403) 
    22329  
    22330 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22331 fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
    22332 1083.8 
    22333 RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
    22334 0.351) 
    22335  
    22336 
    22337 > hide #12 models
    22338 
    22339 > hide #10 models
    22340 
    22341 > hide #9 models
    22342 
    22343 > hide #8 models
    22344 
    22345 > hide #7 models
    22346 
    22347 > show #1 models
    22348 
    22349 > hide #1 models
    22350 
    22351 > show #!2 models
    22352 
    22353 > hide #!2 models
    22354 
    22355 > show #3 models
    22356 
    22357 > hide #3 models
    22358 
    22359 > hide #5 models
    22360 
    22361 > show #1 models
    22362 
    22363 > show #!2 models
    22364 
    22365 > hide #1 models
    22366 
    22367 > show #1 models
    22368 
    22369 > hide #4 models
    22370 
    22371 > show #3 models
    22372 
    22373 > hide #!2 models
    22374 
    22375 > hide #1 models
    22376 
    22377 > show #!6 models
    22378 
    22379 > hide #3#!6 surfaces
    22380 
    22381 > show #7 models
    22382 
    22383 > hide #!6 models
    22384 
    22385 > hide #3 models
    22386 
    22387 > show #8 models
    22388 
    22389 > hide #7 models
    22390 
    22391 > show #9 models
    22392 
    22393 > hide #8 models
    22394 
    22395 > rainbow #9
    22396 
    22397 > show #10 models
    22398 
    22399 > hide #9 models
    22400 
    22401 > show #11 models
    22402 
    22403 > hide #10 models
    22404 
    22405 > show #1 models
    22406 
    22407 > hide #1 models
    22408 
    22409 > show #1 models
    22410 
    22411 > hide #11 models
    22412 
    22413 > show #11 models
    22414 
    22415 > show #12 models
    22416 
    22417 > hide #11 models
    22418 
    22419 > hide #1 models
    22420 
    22421 > matchmaker #8-10,12 to #7/A pairing bs
    22422 
    22423 Computing secondary structure 
    22424 Parameters 
    22425 --- 
    22426 Chain pairing | bs 
    22427 Alignment algorithm | Needleman-Wunsch 
    22428 Similarity matrix | BLOSUM-62 
    22429 SS fraction | 0.3 
    22430 Gap open (HH/SS/other) | 18/18/6 
    22431 Gap extend | 1 
    22432 SS matrix |  |  | H | S | O 
    22433 ---|---|---|--- 
    22434 H | 6 | -9 | -6 
    22435 S |  | 6 | -6 
    22436 O |  |  | 4 
    22437 Iteration cutoff | 2 
    22438  
    22439 Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
    22440 A (#8), sequence alignment score = 56 
    22441 RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
    22442 34.056) 
    22443  
    22444 Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
    22445 chain A (#9), sequence alignment score = 55.5 
    22446 RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
    22447 26.259) 
    22448  
    22449 Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
    22450 chain A (#10), sequence alignment score = 38.2 
    22451 RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
    22452 19.431) 
    22453  
    22454 Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_suca_model_0.cif,
    22455 chain A (#12), sequence alignment score = 124 
    22456 RMSD between 16 pruned atom pairs is 1.040 angstroms; (across all 346 pairs:
    22457 29.841) 
    22458  
    22459 
    22460 > show #7 models
    22461 
    22462 > hide #12 models
    22463 
    22464 > show #8 models
    22465 
    22466 > show #9 models
    22467 
    22468 > hide #8 models
    22469 
    22470 > hide #7 models
    22471 
    22472 > show #8 models
    22473 
    22474 > hide #9 models
    22475 
    22476 > show #12 models
    22477 
    22478 > hide #8 models
    22479 
    22480 > rainbow #12
    22481 
    22482 > show #7 models
    22483 
    22484 > hide #12 models
    22485 
    22486 > show #8 models
    22487 
    22488 > hide #7 models
    22489 
    22490 > show #5 models
    22491 
    22492 > hide #8 models
    22493 
    22494 > color #5 bychain
    22495 
    22496 > show #!6 models
    22497 
    22498 > hide #5 models
    22499 
    22500 > show #11 models
    22501 
    22502 > hide #!6 models
    22503 
    22504 > show #!2 models
    22505 
    22506 > hide #!2 models
    22507 
    22508 > show #5 models
    22509 
    22510 > hide #11 models
    22511 
    22512 > show #11 models
    22513 
    22514 > hide #11 models
    22515 
    22516 > show #11 models
    22517 
    22518 > hide #5 models
    22519 
    22520 > select /A
    22521 
    22522 32114 atoms, 32801 bonds, 4077 residues, 12 models selected 
    22523 
    22524 > ui tool show Matchmaker
    22525 
    22526 > matchmaker #3-5,7-12#!2,6 & sel to #1/A & sel pairing bs
    22527 
    22528 Computing secondary structure 
    22529 Parameters 
    22530 --- 
    22531 Chain pairing | bs 
    22532 Alignment algorithm | Needleman-Wunsch 
    22533 Similarity matrix | BLOSUM-62 
    22534 SS fraction | 0.3 
    22535 Gap open (HH/SS/other) | 18/18/6 
    22536 Gap extend | 1 
    22537 SS matrix |  |  | H | S | O 
    22538 ---|---|---|--- 
    22539 H | 6 | -9 | -6 
    22540 S |  | 6 | -6 
    22541 O |  |  | 4 
    22542 Iteration cutoff | 2 
    22543  
    22544 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22545 fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
    22546 1083.8 
    22547 RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
    22548 0.351) 
    22549  
    22550 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22551 fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
    22552 1083.8 
    22553 RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
    22554 0.324) 
    22555  
    22556 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22557 fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2 
    22558 RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
    22559 0.403) 
    22560  
    22561 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22562 fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
    22563 1077.8 
    22564 RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
    22565 0.467) 
    22566  
    22567 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22568 fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
    22569 1083.8 
    22570 RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
    22571 0.351) 
    22572  
    22573 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22574 fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
    22575 1083.2 
    22576 RMSD between 208 pruned atom pairs is 0.359 angstroms; (across all 208 pairs:
    22577 0.359) 
    22578  
    22579 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22580 fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4 
    22581 RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
    22582 21.278) 
    22583  
    22584 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22585 fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8 
    22586 RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
    22587 22.621) 
    22588  
    22589 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22590 fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2 
    22591 RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
    22592 31.595) 
    22593  
    22594 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22595 fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4 
    22596 RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
    22597 25.278) 
    22598  
    22599 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    22600 fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2 
    22601 RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
    22602 17.409) 
    22603  
    22604 
    22605 > show #1 models
    22606 
    22607 > hide #1 models
    22608 
    22609 > show #5 models
    22610 
    22611 > hide #11 models
    22612 
    22613 > show #11 models
    22614 
    22615 > hide #5 models
    22616 
    22617 > select ::name="NAD"
    22618 
    22619 88 atoms, 96 bonds, 2 residues, 2 models selected 
    22620 
    22621 > select ~sel & ##selected
    22622 
    22623 4938 atoms, 5055 bonds, 624 residues, 2 models selected 
    22624 
    22625 > rainbow sel & #11
    22626 
    22627 > select clear
    22628 
    22629 > show #1 models
    22630 
    22631 > hide #11 models
    22632 
    22633 > open 9H2I fromDatabase pdb format mmcif
    22634 
    22635 Summary of feedback from opening 9H2I fetched from pdb 
    22636 --- 
    22637 note | Fetching compressed mmCIF 9h2i from http://files.rcsb.org/download/9h2i.cif 
    22638  
    22639 9h2i title: 
    22640 Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of
    22641 Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate
    22642 dehydrogenase complex [more info...] 
    22643  
    22644 Chain information for 9h2i #13 
    22645 --- 
    22646 Chain | Description | UniProt 
    22647 A | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex | ODP2_ECOLI 314-379 
    22648 B C | Dihydrolipoyl dehydrogenase | DLDH_ECOLI 2-474 
    22649  
    22650 Non-standard residues in 9h2i #13 
    22651 --- 
    22652 FAD — flavin-adenine dinucleotide 
    22653  
    22654 
    22655 > ui tool show Matchmaker
    22656 
    22657 > matchmaker #13 to #1/A pairing bs
    22658 
    22659 Computing secondary structure 
    22660 Parameters 
    22661 --- 
    22662 Chain pairing | bs 
    22663 Alignment algorithm | Needleman-Wunsch 
    22664 Similarity matrix | BLOSUM-62 
    22665 SS fraction | 0.3 
    22666 Gap open (HH/SS/other) | 18/18/6 
    22667 Gap extend | 1 
    22668 SS matrix |  |  | H | S | O 
    22669 ---|---|---|--- 
    22670 H | 6 | -9 | -6 
    22671 S |  | 6 | -6 
    22672 O |  |  | 4 
    22673 Iteration cutoff | 2 
    22674  
    22675 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with 9h2i, chain B
    22676 (#13), sequence alignment score = 64.3 
    22677 RMSD between 6 pruned atom pairs is 0.906 angstroms; (across all 61 pairs:
    22678 18.939) 
    22679  
    22680 
    22681 > undo
    22682 
    22683 > select ::name="NAD"
    22684 
    22685 88 atoms, 96 bonds, 2 residues, 2 models selected 
    22686 
    22687 > hide #11 models
    22688 
    22689 > hide #1 models
    22690 
    22691 > show #4 models
    22692 
    22693 > hide #13 models
    22694 
    22695 > select ::name="FAD"
    22696 
    22697 265 atoms, 290 bonds, 5 residues, 4 models selected 
    22698 
    22699 > show #13 models
    22700 
    22701 > hide #4 models
    22702 
    22703 > color sel & #13 bychain
    22704 
    22705 > undo
    22706 
    22707 > select clear
    22708 
    22709 > color #13 bychain
    22710 
    22711 > undo
    22712 
    22713 > select ::name="FAD"
    22714 
    22715 265 atoms, 290 bonds, 5 residues, 4 models selected 
    22716 
    22717 > matchmaker #13 & sel to #4/A & sel pairing bs
    22718 
    22719 No 'to' chains specified 
    22720 
    22721 > matchmaker #13 & sel to #4/A & sel pairing bs
    22722 
    22723 No 'to' chains specified 
    22724 
    22725 > matchmaker #13 & sel to #6 & sel
    22726 
    22727 No matrix compatible with both reference structure and all match structures 
    22728 
    22729 > select clear
    22730 
    22731 > select ::name="FAD"
    22732 
    22733 265 atoms, 290 bonds, 5 residues, 4 models selected 
    22734 
    22735 > matchmaker #13 to #6 & sel
    22736 
    22737 No matrix compatible with both reference structure and all match structures 
    22738 
    22739 > matchmaker #13 to #6
    22740 
    22741 Computing secondary structure 
    22742 Parameters 
    22743 --- 
    22744 Chain pairing | bb 
    22745 Alignment algorithm | Needleman-Wunsch 
    22746 Similarity matrix | BLOSUM-62 
    22747 SS fraction | 0.3 
    22748 Gap open (HH/SS/other) | 18/18/6 
    22749 Gap extend | 1 
    22750 SS matrix |  |  | H | S | O 
    22751 ---|---|---|--- 
    22752 H | 6 | -9 | -6 
    22753 S |  | 6 | -6 
    22754 O |  |  | 4 
    22755 Iteration cutoff | 2 
    22756  
    22757 Matchmaker fold_azor_monomer_fad_model_0.cif, chain A (#6) with 9h2i, chain B
    22758 (#13), sequence alignment score = 64.3 
    22759 RMSD between 6 pruned atom pairs is 0.976 angstroms; (across all 61 pairs:
    22760 18.887) 
    22761  
    22762 
    22763 > show #!6 models
    22764 
    22765 > hide #13 models
    22766 
    22767 > show #!2 models
    22768 
    22769 > hide #!2 models
    22770 
    22771 > show #!2 models
    22772 
    22773 > hide #!2 models
    22774 
    22775 > open 8RX4 fromDatabase pdb format mmcif
    22776 
    22777 Summary of feedback from opening 8RX4 fetched from pdb 
    22778 --- 
    22779 notes | Fetching compressed mmCIF 8rx4 from http://files.rcsb.org/download/8rx4.cif 
    22780 Fetching CCD NAP from
    22781 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif 
    22782  
    22783 8rx4 title: 
    22784 Mycothione reductase from Mycobacterium xenopi in complex with co-factor FAD
    22785 and redox co-factor NADP(H) [more info...] 
    22786  
    22787 Chain information for 8rx4 #14 
    22788 --- 
    22789 Chain | Description | UniProt 
    22790 A B | Mycothione reductase | X8E6Y0_MYCXE 1-459 
    22791  
    22792 Non-standard residues in 8rx4 #14 
    22793 --- 
    22794 FAD — flavin-adenine dinucleotide 
    22795 NAP — nadp nicotinamide-adenine-dinucleotide phosphate
    22796 (2'-monophosphoadenosine 5'-diphosphoribose) 
    22797  
    22798 
    22799 > hide #!6 models
    22800 
    22801 > matchmaker #14 to #13
    22802 
    22803 Computing secondary structure 
    22804 Parameters 
    22805 --- 
    22806 Chain pairing | bb 
    22807 Alignment algorithm | Needleman-Wunsch 
    22808 Similarity matrix | BLOSUM-62 
    22809 SS fraction | 0.3 
    22810 Gap open (HH/SS/other) | 18/18/6 
    22811 Gap extend | 1 
    22812 SS matrix |  |  | H | S | O 
    22813 ---|---|---|--- 
    22814 H | 6 | -9 | -6 
    22815 S |  | 6 | -6 
    22816 O |  |  | 4 
    22817 Iteration cutoff | 2 
    22818  
    22819 Matchmaker 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
    22820 score = 815.3 
    22821 RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
    22822 3.176) 
    22823  
    22824 
    22825 > show #13 models
    22826 
    22827 > select ::name="FAD"
    22828 
    22829 371 atoms, 406 bonds, 7 residues, 5 models selected 
    22830 
    22831 > select ~sel & ##selected
    22832 
    22833 21835 atoms, 21626 bonds, 3388 residues, 5 models selected 
    22834 
    22835 > color sel & #13-14 bychain
    22836 
    22837 > select clear
    22838 
    22839 > hide #14 models
    22840 
    22841 > show #14 models
    22842 
    22843 > hide #13 models
    22844 
    22845 > show #13 models
    22846 
    22847 > hide #14 models
    22848 
    22849 > show #14 models
    22850 
    22851 > hide #13 models
    22852 
    22853 > select #14/B
    22854 
    22855 3646 atoms, 3705 bonds, 481 residues, 1 model selected 
    22856 
    22857 > hide sel cartoons
    22858 
    22859 > hide sel atoms
    22860 
    22861 > show #13 models
    22862 
    22863 > hide #14 models
    22864 
    22865 > select #13/C
    22866 
    22867 3803 atoms, 3650 bonds, 693 residues, 1 model selected 
    22868 
    22869 > hide sel cartoons
    22870 
    22871 > show sel cartoons
    22872 
    22873 > hide sel cartoons
    22874 
    22875 > hide sel atoms
    22876 
    22877 > select #13/B
    22878 
    22879 3924 atoms, 3668 bonds, 798 residues, 1 model selected 
    22880 
    22881 > rainbow sel
    22882 
    22883 > select clear
    22884 
    22885 > show #4 models
    22886 
    22887 > hide #13 models
    22888 
    22889 > show #14 models
    22890 
    22891 > show #13 models
    22892 
    22893 > hide #14 models
    22894 
    22895 > hide #4 models
    22896 
    22897 > show #!6 models
    22898 
    22899 > hide #13 models
    22900 
    22901 > show #13 models
    22902 
    22903 > select #13/B:429
    22904 
    22905 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22906 
    22907 > select #13/B:429
    22908 
    22909 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22910 
    22911 > ui mousemode right "move picked models"
    22912 
    22913 > view matrix models
    22914 > #13,-0.24553,0.95614,-0.15973,-12.311,-0.87052,-0.14498,0.4703,-33.244,0.42651,0.25452,0.86793,37.123
    22915 
    22916 > select clear
    22917 
    22918 > show #3 models
    22919 
    22920 > hide #!6 models
    22921 
    22922 > show #!6 models
    22923 
    22924 > hide #!6 models
    22925 
    22926 > select ::name="FAD"
    22927 
    22928 371 atoms, 406 bonds, 7 residues, 5 models selected 
    22929 
    22930 > hide #13 models
    22931 
    22932 > select ~sel & ##selected
    22933 
    22934 21835 atoms, 21626 bonds, 3388 residues, 5 models selected 
    22935 
    22936 > color sel & #3 bychain
    22937 
    22938 > select clear
    22939 
    22940 > show #13 models
    22941 
    22942 > select #13/B:118
    22943 
    22944 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22945 
    22946 > ui mousemode right "rotate selected models"
    22947 
    22948 > view matrix models
    22949 > #13,0.033187,-0.97762,-0.20777,14.167,0.99779,0.020425,0.063272,41.991,-0.057612,-0.20941,0.97613,20.908
    22950 
    22951 > view matrix models
    22952 > #13,0.61108,-0.5049,-0.60964,43.097,0.74854,0.11812,0.65248,13.491,-0.25743,-0.85506,0.45012,36.524
    22953 
    22954 Drag select of 1 residues 
    22955 
    22956 > view matrix models
    22957 > #13,0.69637,-0.51088,-0.50406,42.577,0.69997,0.32838,0.6342,10.762,-0.15848,-0.79446,0.58627,34.933
    22958 
    22959 > view matrix models
    22960 > #13,0.60362,-0.77451,-0.18916,31.241,0.57555,0.25913,0.77562,2.4774,-0.55171,-0.57705,0.60219,19.363
    22961 
    22962 > view matrix models
    22963 > #13,0.57452,-0.7742,-0.2656,32.755,0.56401,0.13931,0.81393,1.7918,-0.59314,-0.61742,0.5167,21.081
    22964 
    22965 > view matrix models
    22966 > #13,0.50768,-0.80838,-0.29797,31.826,0.63814,0.12046,0.76044,6.2021,-0.57883,-0.57621,0.57701,19.262
    22967 
    22968 > view matrix models
    22969 > #13,0.41134,-0.8476,-0.33522,30.098,0.72496,0.081317,0.68397,11.956,-0.55248,-0.52437,0.64793,17.418
    22970 
    22971 > view matrix models
    22972 > #13,0.50347,-0.56782,-0.65123,41.319,0.83944,0.14298,0.52431,20.563,-0.2046,-0.81064,0.54863,34.733
    22973 
    22974 > view matrix models
    22975 > #13,0.81357,-0.39993,-0.42208,42.973,0.56489,0.37157,0.73677,2.4881,-0.13783,-0.83785,0.52822,37.879
    22976 
    22977 > select clear
    22978 
    22979 > select #13/B:81
    22980 
    22981 7 atoms, 6 bonds, 1 residue, 1 model selected 
    22982 
    22983 > view matrix models
    22984 > #13,0.81385,-0.37394,-0.44476,43.517,0.57225,0.38291,0.7252,3.0254,-0.10088,-0.84472,0.52562,39.27
    22985 
    22986 > view matrix models
    22987 > #13,0.80931,-0.3118,-0.49779,44.601,0.58724,0.41087,0.69738,4.2194,-0.01291,-0.85672,0.51563,42.67
    22988 
    22989 > view matrix models
    22990 > #13,0.83554,-0.52523,-0.16124,36.183,0.53716,0.84258,0.038938,20.618,0.11541,-0.11915,0.98615,25.714
    22991 
    22992 > view matrix models
    22993 > #13,0.85682,-0.51537,0.016019,31.023,0.50956,0.85108,0.12652,16.749,-0.07884,-0.10025,0.99183,18.802
    22994 
    22995 > view matrix models
    22996 > #13,0.13465,-0.7299,-0.67016,30.752,0.80312,-0.31576,0.50527,23.627,-0.58041,-0.60625,0.54368,20.54
    22997 
    22998 > select clear
    22999 
    23000 Drag select of 5 residues, 1 bonds 
    23001 
    23002 > show #5 models
    23003 
    23004 > hide #3 models
    23005 
    23006 > show #3 models
    23007 
    23008 > hide #5 models
    23009 
    23010 > show #14 models
    23011 
    23012 > matchmaker #14 to #13
    23013 
    23014 Computing secondary structure 
    23015 Parameters 
    23016 --- 
    23017 Chain pairing | bb 
    23018 Alignment algorithm | Needleman-Wunsch 
    23019 Similarity matrix | BLOSUM-62 
    23020 SS fraction | 0.3 
    23021 Gap open (HH/SS/other) | 18/18/6 
    23022 Gap extend | 1 
    23023 SS matrix |  |  | H | S | O 
    23024 ---|---|---|--- 
    23025 H | 6 | -9 | -6 
    23026 S |  | 6 | -6 
    23027 O |  |  | 4 
    23028 Iteration cutoff | 2 
    23029  
    23030 Matchmaker 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
    23031 score = 815.3 
    23032 RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
    23033 3.176) 
    23034  
    23035 
    23036 > hide #13 models
    23037 
    23038 > show #13 models
    23039 
    23040 > select ::name="FAD"
    23041 
    23042 371 atoms, 406 bonds, 7 residues, 5 models selected 
    23043 
    23044 > select ~sel & ##selected
    23045 
    23046 21835 atoms, 21626 bonds, 3388 residues, 5 models selected 
    23047 
    23048 > show sel & #3,13-14 surfaces
    23049 
    23050 > hide #!14 models
    23051 
    23052 > hide sel & #!3,13 surfaces
    23053 
    23054 > show #!14 models
    23055 
    23056 > hide #!13 models
    23057 
    23058 > hide sel & #!3,14 surfaces
    23059 
    23060 > select clear
    23061 
    23062 > hide #!3 models
    23063 
    23064 > select ::name="NAD"
    23065 
    23066 88 atoms, 96 bonds, 2 residues, 2 models selected 
    23067 
    23068 > select ::name="NAP"
    23069 
    23070 96 atoms, 104 bonds, 2 residues, 1 model selected 
    23071 
    23072 > show #!13 models
    23073 
    23074 > select clear
    23075 
    23076 > hide #!13 models
    23077 
    23078 > show #!13 models
    23079 
    23080 > hide #!13 models
    23081 
    23082 > select ::name="FAD"
    23083 
    23084 371 atoms, 406 bonds, 7 residues, 5 models selected 
    23085 
    23086 > select ~sel & ##selected
    23087 
    23088 21835 atoms, 21626 bonds, 3388 residues, 5 models selected 
    23089 
    23090 > rainbow sel & #!14
    23091 
    23092 > select clear
    23093 
    23094 > select ::name="NAP"
    23095 
    23096 96 atoms, 104 bonds, 2 residues, 1 model selected 
    23097 
    23098 > coulombic sel
    23099 
    23100 Using Amber 20 recommended default charges and atom types for standard
    23101 residues 
    23102 Assigning partial charges to residue NAP (net charge -3) with am1-bcc method 
    23103 Running ANTECHAMBER command:
    23104 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
    23105 qm_theory='AM1', -i
    23106 /var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
    23107 mol2 -o
    23108 /var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
    23109 mol2 -c bcc -nc -3 -j 5 -s 2 -dr n 
    23110 (NAP) `` 
    23111 (NAP) `Welcome to antechamber 20.0: molecular input file processor.` 
    23112 (NAP) `` 
    23113 (NAP) `Info: Finished reading file
    23114 (/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
    23115 atoms read (73), bonds read (77).` 
    23116 (NAP) `Info: Determining atomic numbers from atomic symbols which are case
    23117 sensitive.` 
    23118 (NAP) `Running:
    23119 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
    23120 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    23121 (NAP) `` 
    23122 (NAP) `` 
    23123 (NAP) `Running:
    23124 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
    23125 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    23126 (NAP) `Info: Total number of electrons: 384; net charge: -3` 
    23127 (NAP) `` 
    23128 (NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
    23129 -i sqm.in -o sqm.out` 
    23130 (NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
    23131 Fatal Error!` 
    23132 (NAP) `Cannot properly run
    23133 "/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
    23134 sqm.out".` 
    23135 Charges failed to converge using fast method; re-running using slower more
    23136 stable method 
    23137 Running ANTECHAMBER command:
    23138 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
    23139 /var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
    23140 mol2 -o
    23141 /var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
    23142 mol2 -c bcc -nc -3 -j 5 -s 2 -dr n 
    23143 (NAP) `` 
    23144 (NAP) `Welcome to antechamber 20.0: molecular input file processor.` 
    23145 (NAP) `` 
    23146 (NAP) `Info: Finished reading file
    23147 (/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
    23148 atoms read (73), bonds read (77).` 
    23149 (NAP) `Info: Determining atomic numbers from atomic symbols which are case
    23150 sensitive.` 
    23151 (NAP) `Running:
    23152 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
    23153 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    23154 (NAP) `` 
    23155 (NAP) `` 
    23156 (NAP) `Running:
    23157 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
    23158 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    23159 (NAP) `Info: Total number of electrons: 384; net charge: -3` 
    23160 (NAP) `` 
    23161 (NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
    23162 -i sqm.in -o sqm.out` 
    23163 (NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
    23164 Fatal Error!` 
    23165 (NAP) `Cannot properly run
    23166 "/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
    23167 sqm.out".` 
    23168  
    23169 Contents of sqm.out:
    23170 
    23171    
    23172    
    23173                 --------------------------------------------------------
    23174                                  AMBER SQM VERSION 19
    23175      
    23176                                          By
    23177                   Ross C. Walker, Michael F. Crowley, Scott Brozell,
    23178                              Tim Giese, Andreas W. Goetz,
    23179                             Tai-Sung Lee and David A. Case
    23180      
    23181                 --------------------------------------------------------
    23182      
    23183    
    23184     --------------------------------------------------------------------------------
    23185       QM CALCULATION INFO
    23186     --------------------------------------------------------------------------------
    23187    
    23188     | QMMM: Citation for AMBER QMMM Run:
    23189     | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    23190    
    23191     QMMM: SINGLET STATE CALCULATION
    23192     QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
    23193    
    23194     | QMMM: *** Selected Hamiltonian ***
    23195     | QMMM: AM1         
    23196    
    23197     | QMMM: *** Parameter sets in use ***
    23198     | QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
    23199     | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    23200     | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    23201     | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    23202     | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    23203    
    23204     | QMMM: *** SCF convergence criteria ***
    23205     | QMMM: Energy change                :  0.1D-09 kcal/mol
    23206     | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    23207     | QMMM: Density matrix change        :  0.5D-06
    23208     | QMMM: Maximum number of SCF cycles :     1000
    23209    
    23210     | QMMM: *** Diagonalization Routine Information ***
    23211     | QMMM: Pseudo diagonalizations are allowed.
    23212     | QMMM: Auto diagonalization routine selection is in use.
    23213     | QMMM:
    23214     | QMMM: Timing diagonalization routines:
    23215     | QMMM:                              norbs =      217
    23216     | QMMM:    diag iterations used for timing =        4
    23217     | QMMM:
    23218     | QMMM:              Internal diag routine = 0.051654 seconds
    23219     | QMMM:                 Dspev diag routine = 0.044332 seconds
    23220     | QMMM:                Dspevd diag routine = 0.032116 seconds
    23221     | QMMM:                Dspevx diag routine = 0.153242 seconds
    23222     | QMMM:                 Dsyev diag routine = 0.047097 seconds
    23223     | QMMM:                Dsyevd diag routine = 0.033935 seconds
    23224     | QMMM:                Dsyevr diag routine = 0.038554 seconds
    23225     | QMMM:
    23226     | QMMM:                Pseudo diag routine = 0.022789 seconds
    23227     | QMMM:
    23228     | QMMM: Using dspevd routine (diag_routine=3).
    23229    
    23230       QMMM: QM Region Cartesian Coordinates (*=link atom)
    23231       QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
    23232       QMMM:     1        1      P       17.4620    0.4650   57.8060
    23233       QMMM:     2        2      O       16.5620   -0.5740   58.3900
    23234       QMMM:     3        3      O       18.0440    0.2210   56.4520
    23235       QMMM:     4        4      O       18.6480    0.7880   58.8450
    23236       QMMM:     5        5      C       18.2700    1.3930   60.1070
    23237       QMMM:     6        6      C       19.4870    1.8540   60.8730
    23238       QMMM:     7        7      O       19.0230    2.6210   62.0160
    23239       QMMM:     8        8      C       20.3910    0.7570   61.4600
    23240       QMMM:     9        9      O       21.7470    1.1830   61.4090
    23241       QMMM:    10       10      C       19.8810    0.6600   62.8920
    23242       QMMM:    11       11      O       20.8230    0.1440   63.8270
    23243       QMMM:    12       12      C       19.6340    2.1310   63.1840
    23244       QMMM:    13       13      N       18.7140    2.3450   64.2950
    23245       QMMM:    14       14      C       17.4200    1.8950   64.3780
    23246       QMMM:    15       15      N       16.8230    2.2310   65.4940
    23247       QMMM:    16       16      C       17.7860    2.9360   66.2020
    23248       QMMM:    17       17      C       17.7680    3.5530   67.4670
    23249       QMMM:    18       18      N       16.7090    3.5600   68.2720
    23250       QMMM:    19       19      N       18.9020    4.1690   67.8780
    23251       QMMM:    20       20      C       19.9640    4.1590   67.0630
    23252       QMMM:    21       21      N       20.0960    3.6140   65.8570
    23253       QMMM:    22       22      C       18.9590    3.0090   65.4750
    23254       QMMM:    23       23      O       16.6940    1.8750   57.8220
    23255       QMMM:    24       24      P       16.8310    3.1760   56.8950
    23256       QMMM:    25       25      O       16.1610    4.3450   57.5500
    23257       QMMM:    26       26      O       18.2590    3.2930   56.4770
    23258       QMMM:    27       27      O       15.9430    2.7150   55.6410
    23259       QMMM:    28       28      C       14.5280    2.4980   55.8770
    23260       QMMM:    29       29      C       13.9670    1.5170   54.8750
    23261       QMMM:    30       30      O       14.0230    2.0920   53.5500
    23262       QMMM:    31       31      C       14.6700    0.1520   54.7880
    23263       QMMM:    32       32      O       13.7350   -0.9120   54.6620
    23264       QMMM:    33       33      C       15.5640    0.2940   53.5490
    23265       QMMM:    34       34      O       15.7840   -0.9330   52.8700
    23266       QMMM:    35       35      C       14.7120    1.2110   52.6690
    23267       QMMM:    36       36      N       15.5520    2.0170   51.7640
    23268       QMMM:    37       37      C       15.9700    1.4830   50.5670
    23269       QMMM:    38       38      C       16.8040    2.2160   49.7300
    23270       QMMM:    39       39      C       17.2170    1.5960   48.4310
    23271       QMMM:    40       40      O       16.7920    0.4660   48.1440
    23272       QMMM:    41       41      N       18.0490    2.2680   47.6420
    23273       QMMM:    42       42      C       17.1960    3.4950   50.0970
    23274       QMMM:    43       43      C       16.7690    4.0240   51.3000
    23275       QMMM:    44       44      C       15.9580    3.2770   52.1340
    23276       QMMM:    45       45      P       20.6860   -1.4490   64.0240
    23277       QMMM:    46       46      O       21.7060   -1.8020   65.0890
    23278       QMMM:    47       47      O       21.0090   -2.0990   62.6800
    23279       QMMM:    48       48      O       19.2630   -1.7280   64.4740
    23280       QMMM:    49       49      H       17.7290    0.6600   60.7060
    23281       QMMM:    50       50      H       17.6220    2.2480   59.9150
    23282       QMMM:    51       51      H       20.0850    2.5010   60.2310
    23283       QMMM:    52       52      H       20.2560   -0.1860   60.9310
    23284       QMMM:    53       53      H       22.3250    0.4250   61.5240
    23285       QMMM:    54       54      H       18.9490    0.0970   62.9320
    23286       QMMM:    55       55      H       20.5770    2.6470   63.3660
    23287       QMMM:    56       56      H       16.9410    1.3200   63.5990
    23288       QMMM:    57       57      H       15.8540    3.1050   67.9850
    23289       QMMM:    58       58      H       16.7600    4.0200   69.1700
    23290       QMMM:    59       59      H       20.8400    4.6670   67.4390
    23291       QMMM:    60       60      H       14.0000    3.4470   55.7840
    23292       QMMM:    61       61      H       14.3870    2.1050   56.8840
    23293       QMMM:    62       62      H       12.9200    1.3420   55.1230
    23294       QMMM:    63       63      H       15.2870   -0.0020   55.6730
    23295       QMMM:    64       64      H       13.8800   -1.5500   55.3640
    23296       QMMM:    65       65      H       16.5100    0.7710   53.8050
    23297       QMMM:    66       66      H       16.3180   -1.5120   53.4190
    23298       QMMM:    67       67      H       13.9980    0.6220   52.0930
    23299       QMMM:    68       68      H       15.6500    0.4930   50.2770
    23300       QMMM:    69       69      H       18.3800    3.1810   47.9180
    23301       QMMM:    70       70      H       18.3500    1.8650   46.7660
    23302       QMMM:    71       71      H       17.8320    4.0750   49.4450
    23303       QMMM:    72       72      H       17.0690    5.0210   51.5890
    23304       QMMM:    73       73      H       15.6420    3.6860   53.0820
    23305    
    23306     --------------------------------------------------------------------------------
    23307       RESULTS
    23308     --------------------------------------------------------------------------------
    23309    
    23310    
    23311     QMMM: ERROR!
    23312     QMMM: Unable to achieve self consistency to the tolerances specified
    23313     QMMM: No convergence in SCF after   1000 steps.
    23314     QMMM: E =  -0.2168E+07 DeltaE =  -0.4757E+03 DeltaP =   0.9525E+00
    23315     QMMM: Smallest DeltaE =   0.8289E-07 DeltaP =   0.1057E-04 Step =      3
    23316    
    23317    
    23318 
    23319  
    23320 Failure running ANTECHAMBER for residue NAP Check reply log for details 
    23321 
    23322 > coulombic sel
    23323 
    23324 Using Amber 20 recommended default charges and atom types for standard
    23325 residues 
    23326 Assigning partial charges to residue NAP (net charge -3) with am1-bcc method 
    23327 Running ANTECHAMBER command:
    23328 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
    23329 qm_theory='AM1', -i
    23330 /var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
    23331 mol2 -o
    23332 /var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
    23333 mol2 -c bcc -nc -3 -j 5 -s 2 -dr n 
    23334 (NAP) `` 
    23335 (NAP) `Welcome to antechamber 20.0: molecular input file processor.` 
    23336 (NAP) `` 
    23337 (NAP) `Info: Finished reading file
    23338 (/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
    23339 atoms read (73), bonds read (77).` 
    23340 (NAP) `Info: Determining atomic numbers from atomic symbols which are case
    23341 sensitive.` 
    23342 (NAP) `Running:
    23343 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
    23344 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    23345 (NAP) `` 
    23346 (NAP) `` 
    23347 (NAP) `Running:
    23348 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
    23349 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    23350 (NAP) `Info: Total number of electrons: 384; net charge: -3` 
    23351 (NAP) `` 
    23352 (NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
    23353 -i sqm.in -o sqm.out` 
    23354 (NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
    23355 Fatal Error!` 
    23356 (NAP) `Cannot properly run
    23357 "/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
    23358 sqm.out".` 
    23359 Charges failed to converge using fast method; re-running using slower more
    23360 stable method 
    23361 Running ANTECHAMBER command:
    23362 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
    23363 /var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
    23364 mol2 -o
    23365 /var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
    23366 mol2 -c bcc -nc -3 -j 5 -s 2 -dr n 
    23367 (NAP) `` 
    23368 (NAP) `Welcome to antechamber 20.0: molecular input file processor.` 
    23369 (NAP) `` 
    23370 (NAP) `Info: Finished reading file
    23371 (/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
    23372 atoms read (73), bonds read (77).` 
    23373 (NAP) `Info: Determining atomic numbers from atomic symbols which are case
    23374 sensitive.` 
    23375 (NAP) `Running:
    23376 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
    23377 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    23378 (NAP) `` 
    23379 (NAP) `` 
    23380 (NAP) `Running:
    23381 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
    23382 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    23383 (NAP) `Info: Total number of electrons: 384; net charge: -3` 
    23384 (NAP) `` 
    23385 (NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
    23386 -i sqm.in -o sqm.out` 
    23387 (NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
    23388 Fatal Error!` 
    23389 (NAP) `Cannot properly run
    23390 "/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
    23391 sqm.out".` 
    23392  
    23393 Contents of sqm.out:
    23394 
    23395    
    23396    
    23397                 --------------------------------------------------------
    23398                                  AMBER SQM VERSION 19
    23399      
    23400                                          By
    23401                   Ross C. Walker, Michael F. Crowley, Scott Brozell,
    23402                              Tim Giese, Andreas W. Goetz,
    23403                             Tai-Sung Lee and David A. Case
    23404      
    23405                 --------------------------------------------------------
    23406      
    23407    
    23408     --------------------------------------------------------------------------------
    23409       QM CALCULATION INFO
    23410     --------------------------------------------------------------------------------
    23411    
    23412     | QMMM: Citation for AMBER QMMM Run:
    23413     | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    23414    
    23415     QMMM: SINGLET STATE CALCULATION
    23416     QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
    23417    
    23418     | QMMM: *** Selected Hamiltonian ***
    23419     | QMMM: AM1         
    23420    
    23421     | QMMM: *** Parameter sets in use ***
    23422     | QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
    23423     | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    23424     | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    23425     | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    23426     | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    23427    
    23428     | QMMM: *** SCF convergence criteria ***
    23429     | QMMM: Energy change                :  0.1D-09 kcal/mol
    23430     | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    23431     | QMMM: Density matrix change        :  0.5D-06
    23432     | QMMM: Maximum number of SCF cycles :     1000
    23433    
    23434     | QMMM: *** Diagonalization Routine Information ***
    23435     | QMMM: Pseudo diagonalizations are allowed.
    23436     | QMMM: Auto diagonalization routine selection is in use.
    23437     | QMMM:
    23438     | QMMM: Timing diagonalization routines:
    23439     | QMMM:                              norbs =      217
    23440     | QMMM:    diag iterations used for timing =        4
    23441     | QMMM:
    23442     | QMMM:              Internal diag routine = 0.050281 seconds
    23443     | QMMM:                 Dspev diag routine = 0.043968 seconds
    23444     | QMMM:                Dspevd diag routine = 0.032120 seconds
    23445     | QMMM:                Dspevx diag routine = 0.153124 seconds
    23446     | QMMM:                 Dsyev diag routine = 0.047103 seconds
    23447     | QMMM:                Dsyevd diag routine = 0.033926 seconds
    23448     | QMMM:                Dsyevr diag routine = 0.039887 seconds
    23449     | QMMM:
    23450     | QMMM:                Pseudo diag routine = 0.024004 seconds
    23451     | QMMM:
    23452     | QMMM: Using dspevd routine (diag_routine=3).
    23453    
    23454       QMMM: QM Region Cartesian Coordinates (*=link atom)
    23455       QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
    23456       QMMM:     1        1      P       17.4620    0.4650   57.8060
    23457       QMMM:     2        2      O       16.5620   -0.5740   58.3900
    23458       QMMM:     3        3      O       18.0440    0.2210   56.4520
    23459       QMMM:     4        4      O       18.6480    0.7880   58.8450
    23460       QMMM:     5        5      C       18.2700    1.3930   60.1070
    23461       QMMM:     6        6      C       19.4870    1.8540   60.8730
    23462       QMMM:     7        7      O       19.0230    2.6210   62.0160
    23463       QMMM:     8        8      C       20.3910    0.7570   61.4600
    23464       QMMM:     9        9      O       21.7470    1.1830   61.4090
    23465       QMMM:    10       10      C       19.8810    0.6600   62.8920
    23466       QMMM:    11       11      O       20.8230    0.1440   63.8270
    23467       QMMM:    12       12      C       19.6340    2.1310   63.1840
    23468       QMMM:    13       13      N       18.7140    2.3450   64.2950
    23469       QMMM:    14       14      C       17.4200    1.8950   64.3780
    23470       QMMM:    15       15      N       16.8230    2.2310   65.4940
    23471       QMMM:    16       16      C       17.7860    2.9360   66.2020
    23472       QMMM:    17       17      C       17.7680    3.5530   67.4670
    23473       QMMM:    18       18      N       16.7090    3.5600   68.2720
    23474       QMMM:    19       19      N       18.9020    4.1690   67.8780
    23475       QMMM:    20       20      C       19.9640    4.1590   67.0630
    23476       QMMM:    21       21      N       20.0960    3.6140   65.8570
    23477       QMMM:    22       22      C       18.9590    3.0090   65.4750
    23478       QMMM:    23       23      O       16.6940    1.8750   57.8220
    23479       QMMM:    24       24      P       16.8310    3.1760   56.8950
    23480       QMMM:    25       25      O       16.1610    4.3450   57.5500
    23481       QMMM:    26       26      O       18.2590    3.2930   56.4770
    23482       QMMM:    27       27      O       15.9430    2.7150   55.6410
    23483       QMMM:    28       28      C       14.5280    2.4980   55.8770
    23484       QMMM:    29       29      C       13.9670    1.5170   54.8750
    23485       QMMM:    30       30      O       14.0230    2.0920   53.5500
    23486       QMMM:    31       31      C       14.6700    0.1520   54.7880
    23487       QMMM:    32       32      O       13.7350   -0.9120   54.6620
    23488       QMMM:    33       33      C       15.5640    0.2940   53.5490
    23489       QMMM:    34       34      O       15.7840   -0.9330   52.8700
    23490       QMMM:    35       35      C       14.7120    1.2110   52.6690
    23491       QMMM:    36       36      N       15.5520    2.0170   51.7640
    23492       QMMM:    37       37      C       15.9700    1.4830   50.5670
    23493       QMMM:    38       38      C       16.8040    2.2160   49.7300
    23494       QMMM:    39       39      C       17.2170    1.5960   48.4310
    23495       QMMM:    40       40      O       16.7920    0.4660   48.1440
    23496       QMMM:    41       41      N       18.0490    2.2680   47.6420
    23497       QMMM:    42       42      C       17.1960    3.4950   50.0970
    23498       QMMM:    43       43      C       16.7690    4.0240   51.3000
    23499       QMMM:    44       44      C       15.9580    3.2770   52.1340
    23500       QMMM:    45       45      P       20.6860   -1.4490   64.0240
    23501       QMMM:    46       46      O       21.7060   -1.8020   65.0890
    23502       QMMM:    47       47      O       21.0090   -2.0990   62.6800
    23503       QMMM:    48       48      O       19.2630   -1.7280   64.4740
    23504       QMMM:    49       49      H       17.7290    0.6600   60.7060
    23505       QMMM:    50       50      H       17.6220    2.2480   59.9150
    23506       QMMM:    51       51      H       20.0850    2.5010   60.2310
    23507       QMMM:    52       52      H       20.2560   -0.1860   60.9310
    23508       QMMM:    53       53      H       22.3250    0.4250   61.5240
    23509       QMMM:    54       54      H       18.9490    0.0970   62.9320
    23510       QMMM:    55       55      H       20.5770    2.6470   63.3660
    23511       QMMM:    56       56      H       16.9410    1.3200   63.5990
    23512       QMMM:    57       57      H       15.8540    3.1050   67.9850
    23513       QMMM:    58       58      H       16.7600    4.0200   69.1700
    23514       QMMM:    59       59      H       20.8400    4.6670   67.4390
    23515       QMMM:    60       60      H       14.0000    3.4470   55.7840
    23516       QMMM:    61       61      H       14.3870    2.1050   56.8840
    23517       QMMM:    62       62      H       12.9200    1.3420   55.1230
    23518       QMMM:    63       63      H       15.2870   -0.0020   55.6730
    23519       QMMM:    64       64      H       13.8800   -1.5500   55.3640
    23520       QMMM:    65       65      H       16.5100    0.7710   53.8050
    23521       QMMM:    66       66      H       16.3180   -1.5120   53.4190
    23522       QMMM:    67       67      H       13.9980    0.6220   52.0930
    23523       QMMM:    68       68      H       15.6500    0.4930   50.2770
    23524       QMMM:    69       69      H       18.3800    3.1810   47.9180
    23525       QMMM:    70       70      H       18.3500    1.8650   46.7660
    23526       QMMM:    71       71      H       17.8320    4.0750   49.4450
    23527       QMMM:    72       72      H       17.0690    5.0210   51.5890
    23528       QMMM:    73       73      H       15.6420    3.6860   53.0820
    23529    
    23530     --------------------------------------------------------------------------------
    23531       RESULTS
    23532     --------------------------------------------------------------------------------
    23533    
    23534    
    23535     QMMM: ERROR!
    23536     QMMM: Unable to achieve self consistency to the tolerances specified
    23537     QMMM: No convergence in SCF after   1000 steps.
    23538     QMMM: E =  -0.2168E+07 DeltaE =  -0.4757E+03 DeltaP =   0.9525E+00
    23539     QMMM: Smallest DeltaE =   0.8289E-07 DeltaP =   0.1057E-04 Step =      3
    23540    
    23541    
    23542 
    23543  
    23544 Failure running ANTECHAMBER for residue NAP Check reply log for details 
    23545 
    23546 > color bfactor sel
    23547 
    23548 96 atoms, 2 residues, atom bfactor range 41.3 to 73.2 
    23549 
    23550 > select clear
    23551 
    23552 > show #!13 models
    23553 
    23554 > hide #!14 models
    23555 
    23556 > show #!14 models
    23557 
    23558 > hide #!14 models
    23559 
    23560 > show #!14 models
    23561 
    23562 > hide #!14 models
    23563 
    23564 > show #!14 models
    23565 
    23566 > hide #!13 models
    23567 
    23568 > show #!6 models
    23569 
    23570 > select #14/A:97
    23571 
    23572 8 atoms, 7 bonds, 1 residue, 1 model selected 
    23573 
    23574 > ui mousemode right "rotate selected models"
    23575 
    23576 > view matrix models
    23577 > #14,0.90725,0.31566,-0.27796,2.8054,0.29785,-0.01556,0.95449,-50.578,0.29696,-0.94875,-0.10814,46.454
    23578 
    23579 > view matrix models
    23580 > #14,0.93295,0.28926,-0.21434,-0.73384,0.25781,-0.12123,0.95856,-50.42,0.25129,-0.94954,-0.18768,51.003
    23581 
    23582 > view matrix models
    23583 > #14,0.95399,0.10503,0.28085,-26.454,-0.27841,-0.037495,0.95973,-44.999,0.11133,-0.99376,-0.0065275,43.104
    23584 
    23585 > view matrix models
    23586 > #14,0.98633,-0.1547,0.056722,-15.368,-0.093531,-0.24224,0.9657,-47.262,-0.13566,-0.9578,-0.2534,58.309
    23587 
    23588 > hide #!6 models
    23589 
    23590 > show #4 models
    23591 
    23592 > show #!6 models
    23593 
    23594 > hide #!6 models
    23595 
    23596 > show #!6 models
    23597 
    23598 > hide #!6 models
    23599 
    23600 > show #!6 models
    23601 
    23602 > hide #4 models
    23603 
    23604 > show #5 models
    23605 
    23606 > hide #!6 models
    23607 
    23608 > show #!6 models
    23609 
    23610 > hide #5 models
    23611 
    23612 > select #14/A:60
    23613 
    23614 7 atoms, 6 bonds, 1 residue, 1 model selected 
    23615 
    23616 > ui mousemode right "translate selected models"
    23617 
    23618 > view matrix models
    23619 > #14,0.98633,-0.1547,0.056722,5.0516,-0.093531,-0.24224,0.9657,-51.288,-0.13566,-0.9578,-0.2534,64.425
    23620 
    23621 > view matrix models
    23622 > #14,0.98633,-0.1547,0.056722,10.913,-0.093531,-0.24224,0.9657,-51.526,-0.13566,-0.9578,-0.2534,63.602
    23623 
    23624 > view matrix models
    23625 > #14,0.98633,-0.1547,0.056722,15.905,-0.093531,-0.24224,0.9657,-50.924,-0.13566,-0.9578,-0.2534,60.642
    23626 
    23627 > ui mousemode right "rotate selected models"
    23628 
    23629 > view matrix models
    23630 > #14,0.97926,-0.18136,0.090283,14.242,-0.086033,0.031182,0.9958,-52.444,-0.18342,-0.98292,0.014932,47.335
    23631 
    23632 > select clear
    23633 
    23634 > select #14/A:91
    23635 
    23636 8 atoms, 7 bonds, 1 residue, 1 model selected 
    23637 
    23638 > view matrix models
    23639 > #14,0.90266,-0.17746,0.39205,-0.47885,-0.41831,-0.14782,0.8962,-44.018,-0.10109,-0.97296,-0.20766,57.936
    23640 
    23641 > ui mousemode right "translate selected models"
    23642 
    23643 > view matrix models
    23644 > #14,0.90266,-0.17746,0.39205,-2.5843,-0.41831,-0.14782,0.8962,-43.691,-0.10109,-0.97296,-0.20766,52.913
    23645 
    23646 > select clear
    23647 
    23648 > hide #!6 models
    23649 
    23650 > show #!6 models
    23651 
    23652 > select clear
    23653 
    23654 Drag select of 26 atoms, 132 residues, 25 bonds 
    23655 Drag select of 40 atoms, 192 residues, 36 bonds 
    23656 
    23657 > hide sel cartoons
    23658 
    23659 > view matrix models
    23660 > #14,0.90266,-0.17746,0.39205,-4.6463,-0.41831,-0.14782,0.8962,-41.429,-0.10109,-0.97296,-0.20766,56.964
    23661 
    23662 > select clear
    23663 
    23664 > show #!3 models
    23665 
    23666 > hide #!6 models
    23667 
    23668 > show #!6 models
    23669 
    23670 > hide #!6 models
    23671 
    23672 > show #!6 models
    23673 
    23674 > hide #!6 models
    23675 
    23676 > show #!6 models
    23677 
    23678 > hide #!3 models
    23679 
    23680 > show #!3 models
    23681 
    23682 > select #14/A
    23683 
    23684 3671 atoms, 3705 bonds, 506 residues, 1 model selected 
    23685 
    23686 > show sel cartoons
    23687 
    23688 > select clear
    23689 
    23690 > hide #!3 models
    23691 
    23692 > open 3w78 fromDatabase pdb format mmcif
    23693 
    23694 Summary of feedback from opening 3w78 fetched from pdb 
    23695 --- 
    23696 notes | Fetching compressed mmCIF 3w78 from http://files.rcsb.org/download/3w78.cif 
    23697 Fetching CCD CBD from
    23698 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CBD/CBD.cif 
    23699 Fetching CCD FMN from
    23700 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/FMN/FMN.cif 
    23701  
    23702 3w78 title: 
    23703 Crystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor
    23704 Cibacron Blue [more info...] 
    23705  
    23706 Chain information for 3w78 #15 
    23707 --- 
    23708 Chain | Description | UniProt 
    23709 A B C D | FMN-dependent NADH-azoreductase | C0STY1_9BACI 1-211 
    23710  
    23711 Non-standard residues in 3w78 #15 
    23712 --- 
    23713 CBD — cibacron blue 
    23714 FMN — flavin mononucleotide (riboflavin monophosphate) 
    23715  
    23716 3w78 mmCIF Assemblies 
    23717 --- 
    23718 1| author_and_software_defined_assembly 
    23719 2| author_and_software_defined_assembly 
    23720 3| author_and_software_defined_assembly 
    23721  
    23722 
    23723 > matchmaker #15 to #6
    23724 
    23725 Computing secondary structure 
    23726 Parameters 
    23727 --- 
    23728 Chain pairing | bb 
    23729 Alignment algorithm | Needleman-Wunsch 
    23730 Similarity matrix | BLOSUM-62 
    23731 SS fraction | 0.3 
    23732 Gap open (HH/SS/other) | 18/18/6 
    23733 Gap extend | 1 
    23734 SS matrix |  |  | H | S | O 
    23735 ---|---|---|--- 
    23736 H | 6 | -9 | -6 
    23737 S |  | 6 | -6 
    23738 O |  |  | 4 
    23739 Iteration cutoff | 2 
    23740  
    23741 Matchmaker fold_azor_monomer_fad_model_0.cif, chain A (#6) with 3w78, chain A
    23742 (#15), sequence alignment score = 709.3 
    23743 RMSD between 188 pruned atom pairs is 0.720 angstroms; (across all 207 pairs:
    23744 1.539) 
    23745  
    23746 
    23747 > hide #!6 models
    23748 
    23749 > select #15/A
    23750 
    23751 1698 atoms, 1735 bonds, 218 residues, 1 model selected 
    23752 
    23753 > select #15/C
    23754 
    23755 1697 atoms, 1735 bonds, 217 residues, 1 model selected 
    23756 
    23757 > select #15/C
    23758 
    23759 1697 atoms, 1735 bonds, 217 residues, 1 model selected 
    23760 
    23761 > hide sel cartoons
    23762 
    23763 > hide sel atoms
    23764 
    23765 > select #15/D
    23766 
    23767 1698 atoms, 1735 bonds, 218 residues, 1 model selected 
    23768 
    23769 > hide sel cartoons
    23770 
    23771 > hide sel atoms
    23772 
    23773 > show #!3 models
    23774 
    23775 > hide #!14 models
    23776 
    23777 > hide #!3 models
    23778 
    23779 > select #15/A
    23780 
    23781 1698 atoms, 1735 bonds, 218 residues, 1 model selected 
    23782 
    23783 > rainbow sel
    23784 
    23785 > select clear
    23786 
    23787 > select #15/B
    23788 
    23789 1696 atoms, 1735 bonds, 216 residues, 1 model selected 
    23790 
    23791 > rainbow sel
    23792 
    23793 > select clear
    23794 
    23795 > show #!3 models
    23796 
    23797 > hide #15 models
    23798 
    23799 > show #15 models
    23800 
    23801 > hide #15 models
    23802 
    23803 > show #15 models
    23804 
    23805 > hide #15 models
    23806 
    23807 > show #15 models
    23808 
    23809 > hide #!3 models
    23810 
    23811 > show #!3 models
    23812 
    23813 > hide #!3 models
    23814 
    23815 > show #!3 models
    23816 
    23817 > hide #15 models
    23818 
    23819 > show #15 models
    23820 
    23821 > hide #15 models
    23822 
    23823 > show #15 models
    23824 
    23825 > hide #15 models
    23826 
    23827 > select #3/B:169
    23828 
    23829 11 atoms, 11 bonds, 1 residue, 1 model selected 
    23830 
    23831 > style sel stick
    23832 
    23833 Changed 11 atom styles 
    23834 
    23835 > show sel atoms
    23836 
    23837 > select clear
    23838 
    23839 > show #15 models
    23840 
    23841 > hide #15 models
    23842 
    23843 > show #15 models
    23844 
    23845 > select #3/B:58
    23846 
    23847 7 atoms, 6 bonds, 1 residue, 1 model selected 
    23848 
    23849 > style sel stick
    23850 
    23851 Changed 7 atom styles 
    23852 
    23853 > show sel atoms
    23854 
    23855 > hide sel atoms
    23856 
    23857 > select clear
    23858 
    23859 > select #3/A:184
    23860 
    23861 8 atoms, 7 bonds, 1 residue, 1 model selected 
    23862 
    23863 > style sel stick
    23864 
    23865 Changed 8 atom styles 
    23866 
    23867 > show sel atoms
    23868 
    23869 > hide #!3 models
    23870 
    23871 > show #!3 models
    23872 
    23873 > hide #15 models
    23874 
    23875 > select clear
    23876 
    23877 > show #15 models
    23878 
    23879 > select #15/B:52
    23880 
    23881 8 atoms, 7 bonds, 1 residue, 1 model selected 
    23882 
    23883 > style sel stick
    23884 
    23885 Changed 8 atom styles 
    23886 
    23887 > hide #15 models
    23888 
    23889 > show #15 models
    23890 
    23891 > hide #15 models
    23892 
    23893 > show #15 models
    23894 
    23895 > hide #15 models
    23896 
    23897 > show #15 models
    23898 
    23899 > hide #15 models
    23900 
    23901 > show #15 models
    23902 
    23903 > hide #!3 models
    23904 
    23905 > show #!3 models
    23906 
    23907 > hide #15 models
    23908 
    23909 > show #15 models
    23910 
    23911 > hide #!3 models
    23912 
    23913 > show #4 models
    23914 
    23915 > hide #4 models
    23916 
    23917 > show #!3 models
    23918 
    23919 > hide #!3 models
    23920 
    23921 > show #!3 models
    23922 
    23923 > hide #!3 models
    23924 
    23925 > show #!3 models
    23926 
    23927 > hide #!3 models
    23928 
    23929 > show #!3 models
    23930 
    23931 > hide #!3 models
    23932 
    23933 > show #!3 models
    23934 
    23935 > select #15/A:186
    23936 
    23937 8 atoms, 7 bonds, 1 residue, 1 model selected 
    23938 
    23939 > style sel stick
    23940 
    23941 Changed 8 atom styles 
    23942 
    23943 > show sel atoms
    23944 
    23945 > hide #!3 models
    23946 
    23947 > show #!3 models
    23948 
    23949 > hide #!3 models
    23950 
    23951 > show #!3 models
    23952 
    23953 > hide #!3 models
    23954 
    23955 > show #!3 models
    23956 
    23957 > hide #!3 models
    23958 
    23959 > show #!3 models
    23960 
    23961 > hide #!3 models
    23962 
    23963 > show #!3 models
    23964 
    23965 > hide #!3 models
    23966 
    23967 > show #!3 models
    23968 
    23969 > hide #!3 models
    23970 
    23971 > show #!3 models
    23972 
    23973 > hide #!3 models
    23974 
    23975 > show #4 models
    23976 
    23977 > show #!3 models
    23978 
    23979 > hide #4 models
    23980 
    23981 > hide #!3 models
    23982 
    23983 > show #!3 models
    23984 
    23985 > hide #15 models
    23986 
    23987 > show #15 models
    23988 
    23989 > hide #!3 models
    23990 
    23991 > show #!3 models
    23992 
    23993 > hide #15 models
    23994 
    23995 > show #15 models
    23996 
    23997 > hide #!3 models
    23998 
    23999 > show #!3 models
    24000 
    24001 > hide #!3 models
    24002 
    24003 > select clear
    24004 
    24005 > select #15/A
    24006 
    24007 1698 atoms, 1735 bonds, 218 residues, 1 model selected 
    24008 
    24009 > show #!3 models
    24010 
    24011 > hide #15 models
    24012 
    24013 > show #15 models
    24014 
    24015 > hide #15 models
    24016 
    24017 > show #15 models
    24018 
    24019 > hide #15 models
    24020 
    24021 > show #15 models
    24022 
    24023 > hide #!3 models
    24024 
    24025 > select #15/A
    24026 
    24027 1698 atoms, 1735 bonds, 218 residues, 1 model selected 
    24028 
    24029 > select #15/B
    24030 
    24031 1696 atoms, 1735 bonds, 216 residues, 1 model selected 
    24032 
    24033 > color sel light gray
    24034 
    24035 > color sel gray
    24036 
    24037 > select clear
    24038 
    24039 > show #!3 models
    24040 
    24041 > hide #!3 models
    24042 
    24043 > show #!3 models
    24044 
    24045 > hide #!3 models
    24046 
    24047 > select #15/B:52
    24048 
    24049 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24050 
    24051 > style sel stick
    24052 
    24053 Changed 8 atom styles 
    24054 
    24055 > show sel atoms
    24056 
    24057 > show #!3 models
    24058 
    24059 > hide #!3 models
    24060 
    24061 > show #!3 models
    24062 
    24063 > select #3/A:147
    24064 
    24065 12 atoms, 12 bonds, 1 residue, 1 model selected 
    24066 
    24067 > style sel stick
    24068 
    24069 Changed 12 atom styles 
    24070 
    24071 > show sel atoms
    24072 
    24073 > hide sel atoms
    24074 
    24075 > select clear
    24076 
    24077 > hide #!3 models
    24078 
    24079 > show #!3 models
    24080 
    24081 > hide #15 models
    24082 
    24083 > show #15 models
    24084 
    24085 > hide #!3 models
    24086 
    24087 > show #!3 models
    24088 
    24089 > select #3/B:127
    24090 
    24091 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24092 
    24093 > style sel stick
    24094 
    24095 Changed 9 atom styles 
    24096 
    24097 > show sel atoms
    24098 
    24099 > select clear
    24100 
    24101 > select #3/B:124
    24102 
    24103 12 atoms, 12 bonds, 1 residue, 1 model selected 
    24104 
    24105 > style sel stick
    24106 
    24107 Changed 12 atom styles 
    24108 
    24109 > show sel atoms
    24110 
    24111 > hide #!3 models
    24112 
    24113 > show #!3 models
    24114 
    24115 > select #3/B:122
    24116 
    24117 11 atoms, 11 bonds, 1 residue, 1 model selected 
    24118 
    24119 > style sel stick
    24120 
    24121 Changed 11 atom styles 
    24122 
    24123 > show sel atoms
    24124 
    24125 > select #3/B:126
    24126 
    24127 5 atoms, 4 bonds, 1 residue, 1 model selected 
    24128 
    24129 > open 4m0C fromDatabase pdb format mmcif
    24130 
    24131 Summary of feedback from opening 4m0C fetched from pdb 
    24132 --- 
    24133 note | Fetching compressed mmCIF 4m0c from http://files.rcsb.org/download/4m0c.cif 
    24134  
    24135 4m0c title: 
    24136 The crystal structure of a FMN-dependent NADH-azoreductase from Bacillus
    24137 anthracis str. Ames Ancestor in complex with FMN. [more info...] 
    24138  
    24139 Chain information for 4m0c #16 
    24140 --- 
    24141 Chain | Description | UniProt 
    24142 A B | FMN-dependent NADH-azoreductase 1 | AZOR1_BACAN 1-220 
    24143  
    24144 Non-standard residues in 4m0c #16 
    24145 --- 
    24146 FMN — flavin mononucleotide (riboflavin monophosphate) 
    24147 GOL — glycerol (glycerin; propane-1,2,3-triol) 
    24148 ZN — zinc ion 
    24149  
    24150 
    24151 > hide #15 models
    24152 
    24153 > hide #!3 models
    24154 
    24155 > show #5 models
    24156 
    24157 > hide #5 models
    24158 
    24159 > show #!3 models
    24160 
    24161 > hide #!16 models
    24162 
    24163 > show #15 models
    24164 
    24165 > hide #15 models
    24166 
    24167 > matchmaker #!16 to #3
    24168 
    24169 Computing secondary structure 
    24170 Parameters 
    24171 --- 
    24172 Chain pairing | bb 
    24173 Alignment algorithm | Needleman-Wunsch 
    24174 Similarity matrix | BLOSUM-62 
    24175 SS fraction | 0.3 
    24176 Gap open (HH/SS/other) | 18/18/6 
    24177 Gap extend | 1 
    24178 SS matrix |  |  | H | S | O 
    24179 ---|---|---|--- 
    24180 H | 6 | -9 | -6 
    24181 S |  | 6 | -6 
    24182 O |  |  | 4 
    24183 Iteration cutoff | 2 
    24184  
    24185 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
    24186 (#16), sequence alignment score = 530.5 
    24187 RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
    24188 2.146) 
    24189  
    24190 
    24191 > show #!16 models
    24192 
    24193 > show #15 models
    24194 
    24195 > hide #!3 models
    24196 
    24197 > show #!3 models
    24198 
    24199 > hide #15 models
    24200 
    24201 > hide #!16 models
    24202 
    24203 > show #!16 models
    24204 
    24205 > hide #!16 models
    24206 
    24207 > select #3/A:24
    24208 
    24209 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24210 
    24211 > style sel stick
    24212 
    24213 Changed 9 atom styles 
    24214 
    24215 > show sel atoms
    24216 
    24217 > select #3/A:28
    24218 
    24219 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24220 
    24221 > style sel stick
    24222 
    24223 Changed 9 atom styles 
    24224 
    24225 > show sel atoms
    24226 
    24227 > show #!16 models
    24228 
    24229 > select #3/A:24@NZ
    24230 
    24231 1 atom, 1 residue, 1 model selected 
    24232 
    24233 > color (#!3 & sel) blue
    24234 
    24235 > select clear
    24236 
    24237 > hide #!3 models
    24238 
    24239 > show #!3 models
    24240 
    24241 > select #3/B:60
    24242 
    24243 14 atoms, 15 bonds, 1 residue, 1 model selected 
    24244 
    24245 > style sel stick
    24246 
    24247 Changed 14 atom styles 
    24248 
    24249 > show sel atoms
    24250 
    24251 > hide #!3 models
    24252 
    24253 > show #!3 models
    24254 
    24255 > hide #!3 models
    24256 
    24257 > color #!16 bypolymer
    24258 
    24259 > color #!16 bychain
    24260 
    24261 > undo
    24262 
    24263 > show #!14 models
    24264 
    24265 > hide #!14 models
    24266 
    24267 > view matrix models
    24268 > #3,0.14541,-0.27369,0.95076,11.699,0.94367,-0.25032,-0.21638,-0.059448,0.29722,0.92867,0.22188,0.19931
    24269 
    24270 > view matrix models
    24271 > #3,0.14541,-0.27369,0.95076,11.468,0.94367,-0.25032,-0.21638,0.097978,0.29722,0.92867,0.22188,1.1612
    24272 
    24273 > show #!3 models
    24274 
    24275 > hide #!3 models
    24276 
    24277 > view matrix models
    24278 > #3,0.14541,-0.27369,0.95076,11.206,0.94367,-0.25032,-0.21638,1.5618,0.29722,0.92867,0.22188,1.9041
    24279 
    24280 > show #!3 models
    24281 
    24282 > hide #!3 models
    24283 
    24284 > show #15 models
    24285 
    24286 > hide #!16 models
    24287 
    24288 > hide #15 models
    24289 
    24290 > show #15 models
    24291 
    24292 > show #!16 models
    24293 
    24294 > hide #15 models
    24295 
    24296 > show #15 models
    24297 
    24298 > hide #15 models
    24299 
    24300 > show #15 models
    24301 
    24302 > hide #!16 models
    24303 
    24304 > show #!3 models
    24305 
    24306 > hide #15 models
    24307 
    24308 > view matrix models
    24309 > #3,0.14541,-0.27369,0.95076,3.1194,0.94367,-0.25032,-0.21638,-4.132,0.29722,0.92867,0.22188,5.8471
    24310 
    24311 > select #/B
    24312 
    24313 Expected an objects specifier or a keyword 
    24314 
    24315 > select #3/B
    24316 
    24317 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    24318 
    24319 > rainbow sel
    24320 
    24321 > select #3/A:85
    24322 
    24323 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24324 
    24325 > show #5 models
    24326 
    24327 > hide #!3 models
    24328 
    24329 > show #!3 models
    24330 
    24331 > show #!6 models
    24332 
    24333 > hide #5 models
    24334 
    24335 > hide #!3 models
    24336 
    24337 > hide #!6 models
    24338 
    24339 > show #8 models
    24340 
    24341 > rainbow #8
    24342 
    24343 > show #9 models
    24344 
    24345 > hide #9 models
    24346 
    24347 > show #9 models
    24348 
    24349 > hide #8 models
    24350 
    24351 > show #10 models
    24352 
    24353 > hide #9 models
    24354 
    24355 > rainbow #10
    24356 
    24357 > show #9 models
    24358 
    24359 > show #11 models
    24360 
    24361 > hide #11 models
    24362 
    24363 > ui tool show Matchmaker
    24364 
    24365 > matchmaker #8-10 to #7
    24366 
    24367 Computing secondary structure 
    24368 Parameters 
    24369 --- 
    24370 Chain pairing | bb 
    24371 Alignment algorithm | Needleman-Wunsch 
    24372 Similarity matrix | BLOSUM-62 
    24373 SS fraction | 0.3 
    24374 Gap open (HH/SS/other) | 18/18/6 
    24375 Gap extend | 1 
    24376 SS matrix |  |  | H | S | O 
    24377 ---|---|---|--- 
    24378 H | 6 | -9 | -6 
    24379 S |  | 6 | -6 
    24380 O |  |  | 4 
    24381 Iteration cutoff | 2 
    24382  
    24383 Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
    24384 A (#8), sequence alignment score = 56 
    24385 RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
    24386 34.056) 
    24387  
    24388 Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
    24389 chain A (#9), sequence alignment score = 55.5 
    24390 RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
    24391 26.259) 
    24392  
    24393 Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
    24394 chain A (#10), sequence alignment score = 38.2 
    24395 RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
    24396 19.431) 
    24397  
    24398 
    24399 > view matrix models
    24400 > #3,0.14541,-0.27369,0.95076,8.5292,0.94367,-0.25032,-0.21638,-19.372,0.29722,0.92867,0.22188,0.15815
    24401 
    24402 > hide #9 models
    24403 
    24404 > show #11 models
    24405 
    24406 > hide #10 models
    24407 
    24408 > show #12 models
    24409 
    24410 > hide #11 models
    24411 
    24412 > hide #12 models
    24413 
    24414 > show #7 models
    24415 
    24416 > rainbow #7
    24417 
    24418 > show #8 models
    24419 
    24420 > hide #7 models
    24421 
    24422 > show #7 models
    24423 
    24424 > hide #8 models
    24425 
    24426 > show #5 models
    24427 
    24428 > hide #5 models
    24429 
    24430 > show #!6 models
    24431 
    24432 > hide #7 models
    24433 
    24434 > show #7 models
    24435 
    24436 > hide #!6 models
    24437 
    24438 > show #!6 models
    24439 
    24440 > hide #7 models
    24441 
    24442 > show #7 models
    24443 
    24444 > select #7/A:182
    24445 
    24446 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24447 
    24448 > ui mousemode right "translate selected models"
    24449 
    24450 > view matrix models
    24451 > #7,0.056929,0.94842,-0.31187,29.698,-0.99216,0.018927,-0.12355,27.519,-0.11127,0.31646,0.94206,-48.931
    24452 
    24453 > ui mousemode right "rotate selected models"
    24454 
    24455 > select #7/A:168
    24456 
    24457 11 atoms, 11 bonds, 1 residue, 1 model selected 
    24458 
    24459 > ui mousemode right "rotate selected models"
    24460 
    24461 > view matrix models
    24462 > #7,0.6578,0.45453,-0.60058,25.727,0.50261,-0.85878,-0.099448,19.133,-0.56096,-0.23644,-0.79336,-49.882
    24463 
    24464 > view matrix models
    24465 > #7,0.60118,0.48068,-0.63838,25.96,0.54786,-0.82948,-0.10864,18.796,-0.58175,-0.28444,-0.76201,-49.624
    24466 
    24467 > view matrix models
    24468 > #7,0.49131,0.84301,-0.21895,27.321,0.79014,-0.53716,-0.29517,16.511,-0.36645,-0.027978,-0.93002,-51.657
    24469 
    24470 > view matrix models
    24471 > #7,0.29276,0.89319,-0.34133,28.206,0.88387,-0.38897,-0.25975,15.859,-0.36478,-0.22565,-0.90334,-51.396
    24472 
    24473 > view matrix models
    24474 > #7,0.39394,0.66509,-0.6344,27.076,0.74669,-0.63405,-0.20106,17.118,-0.53597,-0.3945,-0.7464,-49.757
    24475 
    24476 > view matrix models
    24477 > #7,0.3975,0.64273,-0.6549,27.026,0.73208,-0.65243,-0.19596,17.242,-0.55323,-0.40155,-0.72986,-49.601
    24478 
    24479 > view matrix models
    24480 > #7,0.31312,0.65044,-0.69202,27.453,0.7722,-0.59855,-0.21318,16.892,-0.55286,-0.46763,-0.68969,-49.434
    24481 
    24482 > view matrix models
    24483 > #7,0.41324,0.50876,-0.75524,26.815,0.7267,-0.68404,-0.06317,17.64,-0.54875,-0.52273,-0.6524,-49.31
    24484 
    24485 > select clear
    24486 
    24487 > hide #7 models
    24488 
    24489 > show #8 models
    24490 
    24491 > select #8/A:495
    24492 
    24493 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24494 
    24495 > ui mousemode right "translate selected models"
    24496 
    24497 > view matrix models
    24498 > #8,-0.29707,0.95019,0.094245,27.561,-0.9516,-0.28647,-0.11132,28.24,-0.078773,-0.12275,0.98931,-51.568
    24499 
    24500 > ui mousemode right "rotate selected models"
    24501 
    24502 > select #8/A:464
    24503 
    24504 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24505 
    24506 > view matrix models
    24507 > #8,-0.83282,-0.06747,-0.54942,33.938,0.53295,-0.36591,-0.76293,29.175,-0.14956,-0.9282,0.3407,-46.42
    24508 
    24509 > view matrix models
    24510 > #8,-0.79413,0.58208,0.17476,27.984,0.60087,0.79512,0.08207,22.702,-0.09118,0.17018,-0.98119,-32.86
    24511 
    24512 > view matrix models
    24513 > #8,-0.74237,-0.25474,0.61968,22.54,0.1102,0.86588,0.48796,20.688,-0.66087,0.43053,-0.61473,-33.983
    24514 
    24515 > view matrix models
    24516 > #8,-0.85203,0.52313,0.019577,29.536,0.49615,0.81887,-0.28859,26.523,-0.167,-0.23617,-0.95725,-33.383
    24517 
    24518 > view matrix models
    24519 > #8,-0.82201,-0.085732,0.56298,23.565,0.39872,0.61921,0.67646,17.631,-0.4066,0.78053,-0.47481,-35.657
    24520 
    24521 > view matrix models
    24522 > #8,-0.96452,-0.0076278,0.26388,26.924,0.094374,0.92356,0.37165,21.898,-0.24655,0.38337,-0.89008,-32.89
    24523 
    24524 > view matrix models
    24525 > #8,-0.97869,-0.027577,0.20348,27.504,0.057976,0.91351,0.40267,21.719,-0.19698,0.40588,-0.89245,-33.004
    24526 
    24527 > view matrix models
    24528 > #8,-0.96042,0.18076,0.21192,27.65,0.26575,0.82255,0.50278,19.967,-0.083434,0.5392,-0.83803,-33.708
    24529 
    24530 > view matrix models
    24531 > #8,-0.94381,0.13924,0.29972,26.723,0.29173,0.77716,0.5576,19.31,-0.15529,0.61371,-0.77411,-33.957
    24532 
    24533 > select clear
    24534 
    24535 > save /Users/taic/Library/CloudStorage/OneDrive-
    24536 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
    24537 
    24538 > hide #8 models
    24539 
    24540 > show #!13 models
    24541 
    24542 > hide #!13 models
    24543 
    24544 > show #!14 models
    24545 
    24546 > hide #!14 models
    24547 
    24548 > show #!16 models
    24549 
    24550 > open 1v4B fromDatabase pdb format mmcif
    24551 
    24552 Summary of feedback from opening 1v4B fetched from pdb 
    24553 --- 
    24554 notes | Fetching compressed mmCIF 1v4b from http://files.rcsb.org/download/1v4b.cif 
    24555 Fetching CCD IPA from
    24556 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/IPA/IPA.cif 
    24557  
    24558 1v4b title: 
    24559 The crystal structure of AzoR (Azo Reductase) from Escherichia coli: Oxidized
    24560 form [more info...] 
    24561  
    24562 Chain information for 1v4b #17 
    24563 --- 
    24564 Chain | Description | UniProt 
    24565 A | NADH-azoreductase, FMN-dependent | ACPD_ECOLI 1-200 
    24566  
    24567 Non-standard residues in 1v4b #17 
    24568 --- 
    24569 EDO — 1,2-ethanediol (ethylene glycol) 
    24570 FMN — flavin mononucleotide (riboflavin monophosphate) 
    24571 IPA — isopropyl alcohol (2-propanol) 
    24572  
    24573 1v4b mmCIF Assemblies 
    24574 --- 
    24575 1| author_defined_assembly 
    24576  
    24577 
    24578 > open 2B3D fromDatabase pdb format mmcif
    24579 
    24580 Summary of feedback from opening 2B3D fetched from pdb 
    24581 --- 
    24582 note | Fetching compressed mmCIF 2b3d from http://files.rcsb.org/download/2b3d.cif 
    24583  
    24584 2b3d title: 
    24585 Crystal structure of Modulator of Drug activity B in complex with flavin
    24586 adenine dinucleotide [more info...] 
    24587  
    24588 Chain information for 2b3d #18 
    24589 --- 
    24590 Chain | Description | UniProt 
    24591 A B | Modulator of drug activity B | MDAB_ECOLI 13-204 
    24592  
    24593 Non-standard residues in 2b3d #18 
    24594 --- 
    24595 FAD — flavin-adenine dinucleotide 
    24596  
    24597 
    24598 > hide #!16 models
    24599 
    24600 > hide #!17 models
    24601 
    24602 > matchmaker #!18 to #3
    24603 
    24604 Computing secondary structure 
    24605 Parameters 
    24606 --- 
    24607 Chain pairing | bb 
    24608 Alignment algorithm | Needleman-Wunsch 
    24609 Similarity matrix | BLOSUM-62 
    24610 SS fraction | 0.3 
    24611 Gap open (HH/SS/other) | 18/18/6 
    24612 Gap extend | 1 
    24613 SS matrix |  |  | H | S | O 
    24614 ---|---|---|--- 
    24615 H | 6 | -9 | -6 
    24616 S |  | 6 | -6 
    24617 O |  |  | 4 
    24618 Iteration cutoff | 2 
    24619  
    24620 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain B
    24621 (#18), sequence alignment score = 156.9 
    24622 RMSD between 82 pruned atom pairs is 1.158 angstroms; (across all 168 pairs:
    24623 6.190) 
    24624  
    24625 
    24626 > show #!3 models
    24627 
    24628 > hide #!6 models
    24629 
    24630 > hide #!3 models
    24631 
    24632 > show #!3 models
    24633 
    24634 > hide #!18 models
    24635 
    24636 > show #!6 models
    24637 
    24638 > select /A
    24639 
    24640 43169 atoms, 43600 bonds, 3 pseudobonds, 5896 residues, 20 models selected 
    24641 
    24642 > hide #!3 models
    24643 
    24644 > show #!3 models
    24645 
    24646 > show #7 models
    24647 
    24648 > hide #7 models
    24649 
    24650 > hide #!6 models
    24651 
    24652 > matchmaker #1,4-5,7-12,15#!2,6,13-14,16-18 & sel to #3 & sel
    24653 
    24654 Computing secondary structure 
    24655 Parameters 
    24656 --- 
    24657 Chain pairing | bb 
    24658 Alignment algorithm | Needleman-Wunsch 
    24659 Similarity matrix | BLOSUM-62 
    24660 SS fraction | 0.3 
    24661 Gap open (HH/SS/other) | 18/18/6 
    24662 Gap extend | 1 
    24663 SS matrix |  |  | H | S | O 
    24664 ---|---|---|--- 
    24665 H | 6 | -9 | -6 
    24666 S |  | 6 | -6 
    24667 O |  |  | 4 
    24668 Iteration cutoff | 2 
    24669  
    24670 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24671 fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8 
    24672 RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
    24673 0.467) 
    24674  
    24675 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24676 fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
    24677 1081.4 
    24678 RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
    24679 0.467) 
    24680  
    24681 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24682 fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
    24683 1081.4 
    24684 RMSD between 208 pruned atom pairs is 0.436 angstroms; (across all 208 pairs:
    24685 0.436) 
    24686  
    24687 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24688 fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1085 
    24689 RMSD between 208 pruned atom pairs is 0.263 angstroms; (across all 208 pairs:
    24690 0.263) 
    24691  
    24692 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24693 fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
    24694 1081.4 
    24695 RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
    24696 0.467) 
    24697  
    24698 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24699 fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
    24700 1074.2 
    24701 RMSD between 208 pruned atom pairs is 0.269 angstroms; (across all 208 pairs:
    24702 0.269) 
    24703  
    24704 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24705 fold_icd_model_0.cif, chain A (#7), sequence alignment score = 83.4 
    24706 RMSD between 10 pruned atom pairs is 1.453 angstroms; (across all 169 pairs:
    24707 23.782) 
    24708  
    24709 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24710 fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 59.8 
    24711 RMSD between 7 pruned atom pairs is 1.684 angstroms; (across all 65 pairs:
    24712 22.736) 
    24713  
    24714 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24715 fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 65.4 
    24716 RMSD between 24 pruned atom pairs is 1.163 angstroms; (across all 154 pairs:
    24717 32.226) 
    24718  
    24719 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24720 fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 59.3 
    24721 RMSD between 31 pruned atom pairs is 1.111 angstroms; (across all 142 pairs:
    24722 21.293) 
    24723  
    24724 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
    24725 fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2 
    24726 RMSD between 6 pruned atom pairs is 1.325 angstroms; (across all 101 pairs:
    24727 17.171) 
    24728  
    24729 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 9h2i, chain A
    24730 (#13), sequence alignment score = 24 
    24731 RMSD between 11 pruned atom pairs is 0.322 angstroms; (across all 26 pairs:
    24732 11.957) 
    24733  
    24734 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 8rx4, chain A
    24735 (#14), sequence alignment score = 51.5 
    24736 RMSD between 10 pruned atom pairs is 1.029 angstroms; (across all 173 pairs:
    24737 29.959) 
    24738  
    24739 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 3w78, chain A
    24740 (#15), sequence alignment score = 716.5 
    24741 RMSD between 189 pruned atom pairs is 0.774 angstroms; (across all 207 pairs:
    24742 1.461) 
    24743  
    24744 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
    24745 (#16), sequence alignment score = 530.5 
    24746 RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
    24747 2.146) 
    24748  
    24749 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 1v4b, chain A
    24750 (#17), sequence alignment score = 427.4 
    24751 RMSD between 135 pruned atom pairs is 1.176 angstroms; (across all 194 pairs:
    24752 2.701) 
    24753  
    24754 Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain A
    24755 (#18), sequence alignment score = 150.4 
    24756 RMSD between 82 pruned atom pairs is 1.208 angstroms; (across all 167 pairs:
    24757 6.224) 
    24758  
    24759 
    24760 > show #!6 models
    24761 
    24762 > hide #!6 models
    24763 
    24764 > show #!18 models
    24765 
    24766 > hide #!3 models
    24767 
    24768 > show #!3 models
    24769 
    24770 > hide #!18 models
    24771 
    24772 > show #!6 models
    24773 
    24774 > show #!2 models
    24775 
    24776 > hide #!6 models
    24777 
    24778 > show #!6 models
    24779 
    24780 > hide #!2 models
    24781 
    24782 > hide #!3 models
    24783 
    24784 > show #!18 models
    24785 
    24786 > hide #!18 models
    24787 
    24788 > show #!17 models
    24789 
    24790 > show #!16 models
    24791 
    24792 > hide #!16 models
    24793 
    24794 > show #!18 models
    24795 
    24796 > hide #!17 models
    24797 
    24798 > view matrix models
    24799 > #1,0.84943,0.0048481,-0.52768,0.65374,-0.36539,0.72688,-0.5815,-14.996,0.38074,0.68675,0.6192,0.19483,#6,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#11,0.3554,0.83707,0.41595,-1.2763,0.68382,0.070534,-0.72623,-14.22,-0.63724,0.54254,-0.54734,0.48453,#2,-0.46068,-0.87689,-0.13724,12.214,-0.014771,-0.14703,0.98902,-16.145,-0.88745,0.45765,0.054778,1.5059,#3,-0.028746,-0.72374,0.68947,11.158,0.45997,-0.62197,-0.6337,-18.381,0.88747,0.29892,0.35078,3.9374,#4,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#5,0.22887,-0.90083,-0.36896,11.233,0.86356,0.36282,-0.35017,-15.736,0.44931,-0.23848,0.86096,4.0367,#7,0.46353,0.81912,0.33791,5.0029,-0.6474,0.57345,-0.50202,-21.729,-0.60499,0.013936,0.79611,6.3283,#8,-0.26206,-0.91936,-0.29342,-0.19912,0.46009,0.14825,-0.87541,-25.028,0.84832,-0.36441,0.38414,-10.304,#9,-0.36876,-0.75997,0.53522,0.42258,-0.57013,0.63969,0.5155,-25.953,-0.73415,-0.11505,-0.66917,-11.957,#10,-0.76439,0.47517,0.4358,-2.938,-0.63904,-0.46854,-0.60999,-30.867,-0.085662,-0.74477,0.6618,-2.3478,#12,0.5306,0.7007,0.47695,28.271,0.79647,-0.60467,0.0022843,-13.278,0.29,0.37867,-0.87893,-22.901,#13,-0.87207,0.20936,-0.44234,-12.953,-0.35472,-0.89312,0.27661,-70.145,-0.33715,0.39813,0.85313,-58.476,#14,0.06735,0.64492,0.76128,-46.484,-0.9052,0.36039,-0.22523,-11.844,-0.41961,-0.67394,0.60805,-31.123,#15,-0.96531,0.14882,-0.21456,-77.459,0.24373,0.21868,-0.94487,-1.6269,-0.093694,-0.96438,-0.24737,25.022,#16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786,#17,0.86185,-0.43699,0.25741,-7.1671,0.16099,0.71702,0.67821,-60.106,-0.48094,-0.54307,0.68831,13.982,#18,-0.37684,0.76002,-0.52949,10.529,0.34458,-0.41558,-0.84176,-4.7032,-0.8598,-0.49966,-0.10528,11.963
    24800 
    24801 > show #1 models
    24802 
    24803 > hide #!6 models
    24804 
    24805 > hide #!18 models
    24806 
    24807 > show #!6 models
    24808 
    24809 > hide #1 models
    24810 
    24811 > show #!3 models
    24812 
    24813 > hide #!6 models
    24814 
    24815 > show #!6 models
    24816 
    24817 > hide #!6 models
    24818 
    24819 > select clear
    24820 
    24821 > show #1 models
    24822 
    24823 > hide #!3 models
    24824 
    24825 > show #5 models
    24826 
    24827 > hide #5 models
    24828 
    24829 > show #4 models
    24830 
    24831 > hide #1 models
    24832 
    24833 > show #!3 models
    24834 
    24835 > hide #4 models
    24836 
    24837 > show #1 models
    24838 
    24839 > hide #!3 models
    24840 
    24841 > show #!17 models
    24842 
    24843 > hide #!17 models
    24844 
    24845 > show #!18 models
    24846 
    24847 > hide #1 models
    24848 
    24849 > show #1 models
    24850 
    24851 > show #!3 models
    24852 
    24853 > hide #1 models
    24854 
    24855 > hide #!3 models
    24856 
    24857 > show #1 models
    24858 
    24859 > hide #1 models
    24860 
    24861 > select ::name="FAD"
    24862 
    24863 477 atoms, 522 bonds, 9 residues, 6 models selected 
    24864 
    24865 > show #!6 models
    24866 
    24867 > hide #!6 models
    24868 
    24869 > color sel & #!18 bychain
    24870 
    24871 > undo
    24872 
    24873 > select clear
    24874 
    24875 > color #!18 bychain
    24876 
    24877 > undo
    24878 
    24879 > show #!3 models
    24880 
    24881 > hide #!18 models
    24882 
    24883 > show #!17 models
    24884 
    24885 > hide #!17 models
    24886 
    24887 > show #!17 models
    24888 
    24889 > hide #!17 models
    24890 
    24891 > show #!18 models
    24892 
    24893 > hide #!3 models
    24894 
    24895 > show #!3 models
    24896 
    24897 > hide #!18 models
    24898 
    24899 > show #!18 models
    24900 
    24901 > hide #!3 models
    24902 
    24903 > show #!6 models
    24904 
    24905 > hide #!18 models
    24906 
    24907 > show #!18 models
    24908 
    24909 > hide #!18 models
    24910 
    24911 > show #!18 models
    24912 
    24913 > hide #!18 models
    24914 
    24915 > show #!3 models
    24916 
    24917 > hide #!3 models
    24918 
    24919 > show #!18 models
    24920 
    24921 > show #1 models
    24922 
    24923 > hide #!6 models
    24924 
    24925 > hide #!18 models
    24926 
    24927 > show #!18 models
    24928 
    24929 > hide #!18 models
    24930 
    24931 > show #!3 models
    24932 
    24933 > hide #1 models
    24934 
    24935 > select #3/A
    24936 
    24937 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    24938 
    24939 > select ::name="FAD"
    24940 
    24941 477 atoms, 522 bonds, 9 residues, 6 models selected 
    24942 
    24943 > select ~sel & ##selected
    24944 
    24945 25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected 
    24946 
    24947 > ui tool show "Color Actions"
    24948 
    24949 > color sel tan
    24950 
    24951 > color sel goldenrod
    24952 
    24953 > select #3/B
    24954 
    24955 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    24956 
    24957 > rainbow sel
    24958 
    24959 > select clear
    24960 
    24961 > select ::name="FAD"
    24962 
    24963 477 atoms, 522 bonds, 9 residues, 6 models selected 
    24964 
    24965 > select ~sel & ##selected
    24966 
    24967 25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected 
    24968 
    24969 > color sel dark goldenrod
    24970 
    24971 > color sel salmon
    24972 
    24973 > color sel dark goldenrod
    24974 
    24975 > color sel peru
    24976 
    24977 > color sel dark orange
    24978 
    24979 > color sel saddle brown
    24980 
    24981 > color sel dark goldenrod
    24982 
    24983 > color sel slate gray
    24984 
    24985 > color sel steel blue
    24986 
    24987 > color sel cadet blue
    24988 
    24989 > color sel dark olive green
    24990 
    24991 > select #3/B
    24992 
    24993 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    24994 
    24995 > rainbow sel
    24996 
    24997 > select clear
    24998 
    24999 > show #1 models
    25000 
    25001 > hide #!3 models
    25002 
    25003 > show #!13 models
    25004 
    25005 > hide #!13 models
    25006 
    25007 > show #!6 models
    25008 
    25009 > hide #1 models
    25010 
    25011 > show #1 models
    25012 
    25013 > hide #!6 models
    25014 
    25015 > show #4 models
    25016 
    25017 > hide #1 models
    25018 
    25019 > show #1 models
    25020 
    25021 > hide #4 models
    25022 
    25023 > show #4 models
    25024 
    25025 > hide #1 models
    25026 
    25027 > show #!3 models
    25028 
    25029 > hide #!3 models
    25030 
    25031 > show #1 models
    25032 
    25033 > hide #4 models
    25034 
    25035 > save /Users/taic/Library/CloudStorage/OneDrive-
    25036 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.png width
    25037 > 600 height 489 supersample 4 transparentBackground true
    25038 
    25039 > show #4 models
    25040 
    25041 > hide #1 models
    25042 
    25043 > save /Users/taic/Library/CloudStorage/OneDrive-
    25044 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR-FAD.png
    25045 > width 600 height 489 supersample 4 transparentBackground true
    25046 
    25047 > show #!3 models
    25048 
    25049 > hide #4 models
    25050 
    25051 > save /Users/taic/Library/CloudStorage/OneDrive-
    25052 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.png
    25053 > width 600 height 489 supersample 4 transparentBackground true
    25054 
    25055 > select #3/A
    25056 
    25057 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    25058 
    25059 > show sel surfaces
    25060 
    25061 > select clear
    25062 
    25063 > select #3/B
    25064 
    25065 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    25066 
    25067 > show sel surfaces
    25068 
    25069 > hide sel surfaces
    25070 
    25071 > hide #!3 models
    25072 
    25073 > show #1 models
    25074 
    25075 > show #!6 models
    25076 
    25077 > hide #1 models
    25078 
    25079 > show #1 models
    25080 
    25081 > show #!3 models
    25082 
    25083 > hide #!6 models
    25084 
    25085 > hide #1 models
    25086 
    25087 > select clear
    25088 
    25089 > save /Users/taic/Library/CloudStorage/OneDrive-
    25090 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.s.png
    25091 > width 600 height 489 supersample 4 transparentBackground true
    25092 
    25093 > show #11 models
    25094 
    25095 > hide #!3 models
    25096 
    25097 > show #1 models
    25098 
    25099 > hide #1 models
    25100 
    25101 > show #1 models
    25102 
    25103 > hide #1 models
    25104 
    25105 > show #1 models
    25106 
    25107 > hide #1 models
    25108 
    25109 > show #1 models
    25110 
    25111 > hide #1 models
    25112 
    25113 > show #12 models
    25114 
    25115 > hide #12 models
    25116 
    25117 > show #!6 models
    25118 
    25119 > hide #11 models
    25120 
    25121 > show #!2 models
    25122 
    25123 > show #!3 models
    25124 
    25125 > hide #!2 models
    25126 
    25127 > hide #!6 models
    25128 
    25129 > hide #!3 surfaces
    25130 
    25131 > select add #3/B:123
    25132 
    25133 9 atoms, 8 bonds, 1 residue, 1 model selected 
    25134 
    25135 > select #3/B:122
    25136 
    25137 11 atoms, 11 bonds, 1 residue, 1 model selected 
    25138 
    25139 > select clear
    25140 
    25141 > save /Users/taic/Library/CloudStorage/OneDrive-
    25142 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.png
    25143 > width 600 height 489 supersample 4 transparentBackground true
     2345[deleted to fit within ticket limits]
    251442346
    251452347> select #3/B:123