Changes between Initial Version and Version 1 of Ticket #9377


Ignore:
Timestamp:
Jul 14, 2023, 11:21:50 AM (2 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #9377

    • Property Component Unassigned → Input/Output
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → User's file systems suddenly became read-only

  • Ticket #9377 – Description

    initial v1  
    54995499 
    55005500
    5501 > color name d-2t 100,93,4,50
    5502 
    5503 Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
    5504 
    5505  
    5506 
    5507 > color name d-3t 100,86,4,50
    5508 
    5509 Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
    5510 
    5511  
    5512 
    5513 > color name d-4t 100,79,4,50
    5514 
    5515 Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
    5516 
    5517  
    5518 
    5519 > color name d-5t 100,72,4,50
    5520 
    5521 Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
    5522 
    5523  
    5524 
    5525 > color name d-6t 100,65,4,50
    5526 
    5527 Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
    5528 
    5529  
    5530 
    5531 > color name d-7t 100,58,4,50
    5532 
    5533 Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
    5534 
    5535  
    5536 
    5537 > color name d-8t 100,51,4,50
    5538 
    5539 Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
    5540 
    5541  
    5542 
    5543 > color name d-9t 100,44,4,50
    5544 
    5545 Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
    5546 
    5547  
    5548 
    5549 > color name d-10t 100,37,4,50
    5550 
    5551 Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
    5552 
    5553  
    5554 
    5555 > color name d-11t 100,30,4,50
    5556 
    5557 Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
    5558 
    5559  
    5560 
    5561 > color name m-t 95,43,62,50
    5562 
    5563 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    5564 
    5565  
    5566 
    5567 > color name m-1t 100,80,90,50
    5568 
    5569 Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
    5570 
    5571  
    5572 
    5573 > color name m-2t 98,76,87,50
    5574 
    5575 Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
    5576 
    5577  
    5578 
    5579 > color name m-3t 96,72,84,50
    5580 
    5581 Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
    5582 
    5583  
    5584 
    5585 > color name m-4t 94,68,81,50
    5586 
    5587 Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
    5588 
    5589  
    5590 
    5591 > color name m-5t 92,64,78,50
    5592 
    5593 Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
    5594 
    5595  
    5596 
    5597 > color name m-6t 90,60,75,50
    5598 
    5599 Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
    5600 
    5601  
    5602 
    5603 > color name m-7t 88,56,72,50
    5604 
    5605 Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
    5606 
    5607  
    5608 
    5609 > color name m-8t 86,52,69,50
    5610 
    5611 Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
    5612 
    5613  
    5614 
    5615 > color name m-9t 84,48,66,50
    5616 
    5617 Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
    5618 
    5619  
    5620 
    5621 > color name m-10t 82,44,63,50
    5622 
    5623 Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
    5624 
    5625  
    5626 
    5627 > color name m-11t 80,40,60,50
    5628 
    5629 Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
    5630 
    5631  
    5632 
    5633 > color name head-t 71,51,66,50
    5634 
    5635 Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
    5636 
    5637  
    5638 
    5639 > color name head-c 89,89,100,100
    5640 
    5641 Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
    5642 
    5643  
    5644 
    5645 > color name headfa-t 80,79,100,50
    5646 
    5647 Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex: #ccc9ff80
    5648 
    5649  
    5650 
    5651 > color name headblue-t 59,78,94,50
    5652 
    5653 Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
    5654 
    5655  
    5656 
    5657 > color name headh1-t 41,64,100,50
    5658 
    5659 Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
    5660 
    5661  
    5662 
    5663 > color name headh2-t 50,70,100,50
    5664 
    5665 Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
    5666 
    5667  
    5668 
    5669 > color name headgray-t 60,60,60,50
    5670 
    5671 Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
    5672 
    5673  
    5674 
    5675 > color name darkhead-s 58,34,52,100
    5676 
    5677 Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
    5678 
    5679  
    5680 
    5681 > color name bodywhite-t 90,90,90,50
    5682 
    5683 Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
    5684 #e6e6e680
    5685 
    5686  
    5687 
    5688 > color name rps-t 75,88,93,50
    5689 
    5690 Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
    5691 
    5692  
    5693 
    5694 > color name ssu-t 57,71,75,50
    5695 
    5696 Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
    5697 
    5698  
    5699 
    5700 > color name h18-t 31,59,68,50
    5701 
    5702 Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
    5703 
    5704  
    5705 
    5706 > color name h23-t 18,36,100,50
    5707 
    5708 Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
    5709 
    5710  
    5711 
    5712 > color name h23-c 18,36,100,100
    5713 
    5714 Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
    5715 
    5716  
    5717 
    5718 > color name h24-t 50,70,90,50
    5719 
    5720 Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
    5721 
    5722  
    5723 
    5724 > color name h24-c 50,70,90,100
    5725 
    5726 Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
    5727 
    5728  
    5729 
    5730 > color name h28-t 0,24,57,50
    5731 
    5732 Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
    5733 
    5734  
    5735 
    5736 > color name h28-c 0,24,57,100
    5737 
    5738 Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
    5739 
    5740  
    5741 
    5742 > color name h29-t 80,69,92,50
    5743 
    5744 Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
    5745 
    5746  
    5747 
    5748 > color name h29-c 80,69,92,100
    5749 
    5750 Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
    5751 
    5752  
    5753 
    5754 > color name h30-t 40,40,59,50
    5755 
    5756 Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
    5757 
    5758  
    5759 
    5760 > color name h31-t 45,18,59,50
    5761 
    5762 Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
    5763 
    5764  
    5765 
    5766 > color name h31-c 45,18,59,100
    5767 
    5768 Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
    5769 
    5770  
    5771 
    5772 > color name h34-t 59,18,59,50
    5773 
    5774 Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
    5775 
    5776  
    5777 
    5778 > color name h34-c 59,18,59,100
    5779 
    5780 Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
    5781 
    5782  
    5783 
    5784 > color name h35-t 50,22,45,50
    5785 
    5786 Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
    5787 
    5788  
    5789 
    5790 > color name h44-t 27,50,80,50
    5791 
    5792 Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
    5793 
    5794  
    5795 
    5796 > color name aploop-t 27,0,50,50
    5797 
    5798 Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
    5799 
    5800  
    5801 
    5802 > color name term16-t 40,64,64,50
    5803 
    5804 Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
    5805 
    5806  
    5807 
    5808 > color name uS3-t 64,41,82,50
    5809 
    5810 Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
    5811 
    5812  
    5813 
    5814 > color name uS5-t 0,50,45,50
    5815 
    5816 Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
    5817 
    5818  
    5819 
    5820 > color name gray-t 70,70,70,50
    5821 
    5822 Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
    5823 
    5824  
    5825 
    5826 > color name hx68-t 50,50,50,50
    5827 
    5828 Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    5829 
    5830  
    5831 
    5832 > color name hx69-t 30,30,30,50
    5833 
    5834 Color 'hx69-t' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex: #4d4d4d80
    5835 
    5836  
    5837 
    5838 > color name srl-t 50,50,50,50
    5839 
    5840 Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    5841 
    5842  
    5843 
    5844 > color name lightgrayt 83,83,83,50
    5845 
    5846 Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
    5847 
    5848  
    5849 
    5850 > color name silvert 75,75,75,50
    5851 
    5852 Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
    5853 
    5854  
    5855 
    5856 > color name grayt 50,50,50,50
    5857 
    5858 Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    5859 
    5860  
    5861 
    5862 > color name lightcyant 88,100,100,50
    5863 
    5864 Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
    5865 #e0ffff80
    5866 
    5867  
    5868 
    5869 > color name yellowt 100,90,0,50
    5870 
    5871 Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
    5872 
    5873  
    5874 
    5875 > color name deeppinkt 100,8,58,50
    5876 
    5877 Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
    5878 
    5879  
    5880 
    5881 > color name oranget 100,65,0,50
    5882 
    5883 Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
    5884 
    5885  
    5886 
    5887 > color name yellowgreent 60,80,20,50
    5888 
    5889 Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
    5890 #99cc3380
    5891 
    5892  
    5893 
    5894 > color name darkmagentat 54,0,54,50
    5895 
    5896 Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
    5897 #8a008a80
    5898 
    5899  
    5900 
    5901 > color name orchidt 86,44,84,50
    5902 
    5903 Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
    5904 
    5905  
    5906 
    5907 > color name paleturquoiset 69,93,93,50
    5908 
    5909 Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
    5910 #b0eded80
    5911 
    5912  
    5913 
    5914 > color name pinkt 100,75,80,50
    5915 
    5916 Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
    5917 
    5918  
    5919 
    5920 > color name darkgreent 0,39,0,50
    5921 
    5922 Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
    5923 
    5924  
    5925 
    5926 > color name limegreent 20,80,20,50
    5927 
    5928 Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
    5929 
    5930  
    5931 
    5932 > color name turquoiset 25,88,82,50
    5933 
    5934 Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
    5935 
    5936  
    5937 
    5938 > color name tealt 0,50,50,50
    5939 
    5940 Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
    5941 
    5942  
    5943 
    5944 > color name darkoranget 100,50,0,50
    5945 
    5946 Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
    5947 #ff800080
    5948 
    5949  
    5950 
    5951 > color name lightyellowt 100,100,50,50
    5952 
    5953 Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
    5954 #ffff8080
    5955 
    5956  
    5957 
    5958 > color name goldt 100,75,0,50
    5959 
    5960 Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
    5961 
    5962  
    5963 
    5964 > color name plumt 87,63,87,50
    5965 
    5966 Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
    5967 
    5968  
    5969 
    5970 > color name ssubluet 68,86,90,50
    5971 
    5972 Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
    5973 
    5974  
    5975 
    5976 > color name p-prect 10,41,0,50
    5977 
    5978 Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
    5979 
    5980  
    5981 
    5982 > color name p-h2t 23,59,0,50
    5983 
    5984 Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    5985 
    5986  
    5987 
    5988 > color name p-h1t 40,73,0,50
    5989 
    5990 Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
    5991 
    5992  
    5993 
    5994 > color name p-h1c 40,73,0,100
    5995 
    5996 Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
    5997 
    5998  
    5999 
    6000 > color name p-spct 68,81,0,50
    6001 
    6002 Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    6003 
    6004  
    6005 
    6006 > color name p-spcc 68,81,0,100
    6007 
    6008 Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
    6009 
    6010  
    6011 
    6012 > color name p-fat 82,92,0,50
    6013 
    6014 Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
    6015 
    6016  
    6017 
    6018 > color name p-postt 100,92,0,50
    6019 
    6020 Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    6021 
    6022  
    6023 
    6024 > color name d-t 100,80,4,50
    6025 
    6026 Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    6027 
    6028  
    6029 
    6030 > color name d-prect 95,100,50,50
    6031 
    6032 Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
    6033 
    6034  
    6035 
    6036 > color name d-h2t 100,90,4,50
    6037 
    6038 Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    6039 
    6040  
    6041 
    6042 > color name d-h1t 100,80,4,50
    6043 
    6044 Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    6045 
    6046  
    6047 
    6048 > color name d-spct 100,70,4,50
    6049 
    6050 Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
    6051 
    6052  
    6053 
    6054 > color name d-fat 100,55,4,50
    6055 
    6056 Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
    6057 
    6058  
    6059 
    6060 > color name d-fac 100,55,4,100
    6061 
    6062 Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
    6063 
    6064  
    6065 
    6066 > color name d-postt 100,40,4,50
    6067 
    6068 Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    6069 
    6070  
    6071 
    6072 > color name m-t 95,43,62,50
    6073 
    6074 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    6075 
    6076  
    6077 
    6078 > color name m-prect 100,85,95,50
    6079 
    6080 Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    6081 
    6082  
    6083 
    6084 > color name m-h2t 100,85,95,50
    6085 
    6086 Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    6087 
    6088  
    6089 
    6090 > color name m-h1t 100,75,95,50
    6091 
    6092 Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
    6093 
    6094  
    6095 
    6096 > color name m-spct 89,63,75,50
    6097 
    6098 Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
    6099 
    6100  
    6101 
    6102 > color name m-fat 95,51,75,50
    6103 
    6104 Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
    6105 
    6106  
    6107 
    6108 > color name m-fac 95,51,75,100
    6109 
    6110 Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
    6111 
    6112  
    6113 
    6114 > color name m-postt 95,43,62,50
    6115 
    6116 Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    6117 
    6118  
    6119 executed 70S_colors.cxc 
    6120 
    6121 > color #10/y p-1t
    6122 
    6123 > color #11/y p-2t
    6124 
    6125 > color #12/y p-3t
    6126 
    6127 > color #30/y p-4t
    6128 
    6129 > color #31/y p-4t
    6130 
    6131 > color #32/y p-5t
    6132 
    6133 > color #33/y p-6t
    6134 
    6135 > color #13/y p-7t
    6136 
    6137 > color #34/y p-8t
    6138 
    6139 > color #14/y p-9t
    6140 
    6141 > color #20/y p-10t
    6142 
    6143 > color #15/y p-11t
    6144 
    6145 > color #10/v d-1t
    6146 
    6147 > color #11/v d-2t
    6148 
    6149 > color #12/v d-3t
    6150 
    6151 > color #30/v d-4t
    6152 
    6153 > color #31/v d-4t
    6154 
    6155 > color #32/v d-5t
    6156 
    6157 > color #33/v d-6t
    6158 
    6159 > color #13/v d-7t
    6160 
    6161 > color #34/v d-8t
    6162 
    6163 > color #14/v d-9t
    6164 
    6165 > color #20/v d-10t
    6166 
    6167 > color #15/v d-11t
    6168 
    6169 > color #10/w m-1t
    6170 
    6171 > color #11/w m-2t
    6172 
    6173 > color #12/w m-3t
    6174 
    6175 > color #30/w m-4t
    6176 
    6177 > color #31/w m-4t
    6178 
    6179 > color #32/w m-5t
    6180 
    6181 > color #33/w m-6t
    6182 
    6183 > color #13/w m-7t
    6184 
    6185 > color #34/w m-8t
    6186 
    6187 > color #14/w m-9t
    6188 
    6189 > color #20/w m-10t
    6190 
    6191 > color #15/w m-11t
    6192 
    6193 > color #30/x g-1t
    6194 
    6195 > color #31/x g-1t
    6196 
    6197 > color #32/x g-2t
    6198 
    6199 > color #33/x g-3t
    6200 
    6201 > color #13/x g-4t
    6202 
    6203 > color #34/x g-5t
    6204 
    6205 > color #14/x g-6t
    6206 
    6207 > color #20/x g-7t
    6208 
    6209 executed 70S_color_trna_gradient-t.cxc 
    6210 
    6211 > transparency 0 target abc
    6212 
    6213 > nucribthin
    6214 
    6215 Unknown command: nucribthin 
    6216 
    6217 > alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
    6218 
    6219 > nucribthin
    6220 
    6221 > open
    6222 > /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_trna_gradient-t.cxc
    6223 
    6224 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
    6225 
    6226 > color name efg-t 100,0,0,50
    6227 
    6228 Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    6229 
    6230  
    6231 
    6232 > color name sw1-t 100,92,0,50
    6233 
    6234 Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    6235 
    6236  
    6237 
    6238 > color name sw2-t 68,81,0,50
    6239 
    6240 Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    6241 
    6242  
    6243 
    6244 > color name pl-t 23,59,0,50
    6245 
    6246 Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    6247 
    6248  
    6249 
    6250 > color name d1-t 100,18,4,50
    6251 
    6252 Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
    6253 
    6254  
    6255 
    6256 > color name d2-t 100,40,4,50
    6257 
    6258 Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    6259 
    6260  
    6261 
    6262 > color name d3-t 100,27,36,50
    6263 
    6264 Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
    6265 
    6266  
    6267 
    6268 > color name d4-t 80,0,23,50
    6269 
    6270 Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
    6271 
    6272  
    6273 
    6274 > color name d5-t 100,60,4,50
    6275 
    6276 Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
    6277 
    6278  
    6279 
    6280 > color name fa-t 100,90,4,50
    6281 
    6282 Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    6283 
    6284  
    6285 
    6286 > color name gtp-t 45,53,60,50
    6287 
    6288 Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
    6289 
    6290  
    6291 
    6292 > color name mg-t 1,39,16,50
    6293 
    6294 Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
    6295 
    6296  
    6297 
    6298 > color name spc-t 100,0,0,50
    6299 
    6300 Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    6301 
    6302  
    6303 
    6304 > color name argb-t 50,0,50,50
    6305 
    6306 Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
    6307 
    6308  
    6309 
    6310 > color name g-1t 98,42,30,50
    6311 
    6312 Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
    6313 
    6314  
    6315 
    6316 > color name g-2t 95,35,25,50
    6317 
    6318 Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
    6319 
    6320  
    6321 
    6322 > color name g-3t 92,28,20,50
    6323 
    6324 Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
    6325 
    6326  
    6327 
    6328 > color name g-4t 89,21,15,50
    6329 
    6330 Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
    6331 
    6332  
    6333 
    6334 > color name g-5t 86,14,10,50
    6335 
    6336 Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
    6337 
    6338  
    6339 
    6340 > color name g-6t 83,7,5,50
    6341 
    6342 Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
    6343 
    6344  
    6345 
    6346 > color name g-7t 80,0,0,50
    6347 
    6348 Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
    6349 
    6350  
    6351 
    6352 > color name p-t 40,60,2,50
    6353 
    6354 Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
    6355 
    6356  
    6357 
    6358 > color name p-1t 4,34,1,50
    6359 
    6360 Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
    6361 
    6362  
    6363 
    6364 > color name p-2t 12,39,1,50
    6365 
    6366 Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
    6367 
    6368  
    6369 
    6370 > color name p-3t 20,44,1,50
    6371 
    6372 Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
    6373 
    6374  
    6375 
    6376 > color name p-4t 28,49,1,50
    6377 
    6378 Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
    6379 
    6380  
    6381 
    6382 > color name p-5t 36,54,2,50
    6383 
    6384 Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
    6385 
    6386  
    6387 
    6388 > color name p-6t 44,59,2,50
    6389 
    6390 Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
    6391 
    6392  
    6393 
    6394 > color name p-7t 52,64,2,50
    6395 
    6396 Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
    6397 
    6398  
    6399 
    6400 > color name p-8t 60,69,2,50
    6401 
    6402 Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
    6403 
    6404  
    6405 
    6406 > color name p-9t 68,74,3,50
    6407 
    6408 Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
    6409 
    6410  
    6411 
    6412 > color name p-10t 76,79,3,50
    6413 
    6414 Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
    6415 
    6416  
    6417 
    6418 > color name p-11t 84,84,3,50
    6419 
    6420 Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
    6421 
    6422  
    6423 
    6424 > color name d-t 100,75,4,50
    6425 
    6426 Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
    6427 
    6428  
    6429 
    6430 > color name d-1t 100,100,4,50
    6431 
    6432 Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
    6433 
    6434  
    6435 
    6436 > color name d-2t 100,93,4,50
    6437 
    6438 Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
    6439 
    6440  
    6441 
    6442 > color name d-3t 100,86,4,50
    6443 
    6444 Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
    6445 
    6446  
    6447 
    6448 > color name d-4t 100,79,4,50
    6449 
    6450 Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
    6451 
    6452  
    6453 
    6454 > color name d-5t 100,72,4,50
    6455 
    6456 Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
    6457 
    6458  
    6459 
    6460 > color name d-6t 100,65,4,50
    6461 
    6462 Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
    6463 
    6464  
    6465 
    6466 > color name d-7t 100,58,4,50
    6467 
    6468 Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
    6469 
    6470  
    6471 
    6472 > color name d-8t 100,51,4,50
    6473 
    6474 Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
    6475 
    6476  
    6477 
    6478 > color name d-9t 100,44,4,50
    6479 
    6480 Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
    6481 
    6482  
    6483 
    6484 > color name d-10t 100,37,4,50
    6485 
    6486 Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
    6487 
    6488  
    6489 
    6490 > color name d-11t 100,30,4,50
    6491 
    6492 Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
    6493 
    6494  
    6495 
    6496 > color name m-t 95,43,62,50
    6497 
    6498 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    6499 
    6500  
    6501 
    6502 > color name m-1t 100,80,90,50
    6503 
    6504 Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
    6505 
    6506  
    6507 
    6508 > color name m-2t 98,76,87,50
    6509 
    6510 Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
    6511 
    6512  
    6513 
    6514 > color name m-3t 96,72,84,50
    6515 
    6516 Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
    6517 
    6518  
    6519 
    6520 > color name m-4t 94,68,81,50
    6521 
    6522 Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
    6523 
    6524  
    6525 
    6526 > color name m-5t 92,64,78,50
    6527 
    6528 Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
    6529 
    6530  
    6531 
    6532 > color name m-6t 90,60,75,50
    6533 
    6534 Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
    6535 
    6536  
    6537 
    6538 > color name m-7t 88,56,72,50
    6539 
    6540 Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
    6541 
    6542  
    6543 
    6544 > color name m-8t 86,52,69,50
    6545 
    6546 Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
    6547 
    6548  
    6549 
    6550 > color name m-9t 84,48,66,50
    6551 
    6552 Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
    6553 
    6554  
    6555 
    6556 > color name m-10t 82,44,63,50
    6557 
    6558 Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
    6559 
    6560  
    6561 
    6562 > color name m-11t 80,40,60,50
    6563 
    6564 Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
    6565 
    6566  
    6567 
    6568 > color name head-t 71,51,66,50
    6569 
    6570 Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
    6571 
    6572  
    6573 
    6574 > color name head-c 89,89,100,100
    6575 
    6576 Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
    6577 
    6578  
    6579 
    6580 > color name headfa-t 80,79,100,50
    6581 
    6582 Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex: #ccc9ff80
    6583 
    6584  
    6585 
    6586 > color name headblue-t 59,78,94,50
    6587 
    6588 Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
    6589 
    6590  
    6591 
    6592 > color name headh1-t 41,64,100,50
    6593 
    6594 Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
    6595 
    6596  
    6597 
    6598 > color name headh2-t 50,70,100,50
    6599 
    6600 Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
    6601 
    6602  
    6603 
    6604 > color name headgray-t 60,60,60,50
    6605 
    6606 Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
    6607 
    6608  
    6609 
    6610 > color name darkhead-s 58,34,52,100
    6611 
    6612 Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
    6613 
    6614  
    6615 
    6616 > color name bodywhite-t 90,90,90,50
    6617 
    6618 Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
    6619 #e6e6e680
    6620 
    6621  
    6622 
    6623 > color name rps-t 75,88,93,50
    6624 
    6625 Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
    6626 
    6627  
    6628 
    6629 > color name ssu-t 57,71,75,50
    6630 
    6631 Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
    6632 
    6633  
    6634 
    6635 > color name h18-t 31,59,68,50
    6636 
    6637 Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
    6638 
    6639  
    6640 
    6641 > color name h23-t 18,36,100,50
    6642 
    6643 Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
    6644 
    6645  
    6646 
    6647 > color name h23-c 18,36,100,100
    6648 
    6649 Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
    6650 
    6651  
    6652 
    6653 > color name h24-t 50,70,90,50
    6654 
    6655 Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
    6656 
    6657  
    6658 
    6659 > color name h24-c 50,70,90,100
    6660 
    6661 Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
    6662 
    6663  
    6664 
    6665 > color name h28-t 0,24,57,50
    6666 
    6667 Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
    6668 
    6669  
    6670 
    6671 > color name h28-c 0,24,57,100
    6672 
    6673 Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
    6674 
    6675  
    6676 
    6677 > color name h29-t 80,69,92,50
    6678 
    6679 Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
    6680 
    6681  
    6682 
    6683 > color name h29-c 80,69,92,100
    6684 
    6685 Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
    6686 
    6687  
    6688 
    6689 > color name h30-t 40,40,59,50
    6690 
    6691 Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
    6692 
    6693  
    6694 
    6695 > color name h31-t 45,18,59,50
    6696 
    6697 Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
    6698 
    6699  
    6700 
    6701 > color name h31-c 45,18,59,100
    6702 
    6703 Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
    6704 
    6705  
    6706 
    6707 > color name h34-t 59,18,59,50
    6708 
    6709 Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
    6710 
    6711  
    6712 
    6713 > color name h34-c 59,18,59,100
    6714 
    6715 Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
    6716 
    6717  
    6718 
    6719 > color name h35-t 50,22,45,50
    6720 
    6721 Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
    6722 
    6723  
    6724 
    6725 > color name h44-t 27,50,80,50
    6726 
    6727 Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
    6728 
    6729  
    6730 
    6731 > color name aploop-t 27,0,50,50
    6732 
    6733 Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
    6734 
    6735  
    6736 
    6737 > color name term16-t 40,64,64,50
    6738 
    6739 Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
    6740 
    6741  
    6742 
    6743 > color name uS3-t 64,41,82,50
    6744 
    6745 Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
    6746 
    6747  
    6748 
    6749 > color name uS5-t 0,50,45,50
    6750 
    6751 Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
    6752 
    6753  
    6754 
    6755 > color name gray-t 70,70,70,50
    6756 
    6757 Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
    6758 
    6759  
    6760 
    6761 > color name hx68-t 50,50,50,50
    6762 
    6763 Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    6764 
    6765  
    6766 
    6767 > color name hx69-t 30,30,30,50
    6768 
    6769 Color 'hx69-t' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex: #4d4d4d80
    6770 
    6771  
    6772 
    6773 > color name srl-t 50,50,50,50
    6774 
    6775 Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    6776 
    6777  
    6778 
    6779 > color name lightgrayt 83,83,83,50
    6780 
    6781 Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
    6782 
    6783  
    6784 
    6785 > color name silvert 75,75,75,50
    6786 
    6787 Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
    6788 
    6789  
    6790 
    6791 > color name grayt 50,50,50,50
    6792 
    6793 Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    6794 
    6795  
    6796 
    6797 > color name lightcyant 88,100,100,50
    6798 
    6799 Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
    6800 #e0ffff80
    6801 
    6802  
    6803 
    6804 > color name yellowt 100,90,0,50
    6805 
    6806 Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
    6807 
    6808  
    6809 
    6810 > color name deeppinkt 100,8,58,50
    6811 
    6812 Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
    6813 
    6814  
    6815 
    6816 > color name oranget 100,65,0,50
    6817 
    6818 Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
    6819 
    6820  
    6821 
    6822 > color name yellowgreent 60,80,20,50
    6823 
    6824 Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
    6825 #99cc3380
    6826 
    6827  
    6828 
    6829 > color name darkmagentat 54,0,54,50
    6830 
    6831 Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
    6832 #8a008a80
    6833 
    6834  
    6835 
    6836 > color name orchidt 86,44,84,50
    6837 
    6838 Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
    6839 
    6840  
    6841 
    6842 > color name paleturquoiset 69,93,93,50
    6843 
    6844 Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
    6845 #b0eded80
    6846 
    6847  
    6848 
    6849 > color name pinkt 100,75,80,50
    6850 
    6851 Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
    6852 
    6853  
    6854 
    6855 > color name darkgreent 0,39,0,50
    6856 
    6857 Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
    6858 
    6859  
    6860 
    6861 > color name limegreent 20,80,20,50
    6862 
    6863 Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
    6864 
    6865  
    6866 
    6867 > color name turquoiset 25,88,82,50
    6868 
    6869 Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
    6870 
    6871  
    6872 
    6873 > color name tealt 0,50,50,50
    6874 
    6875 Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
    6876 
    6877  
    6878 
    6879 > color name darkoranget 100,50,0,50
    6880 
    6881 Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
    6882 #ff800080
    6883 
    6884  
    6885 
    6886 > color name lightyellowt 100,100,50,50
    6887 
    6888 Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
    6889 #ffff8080
    6890 
    6891  
    6892 
    6893 > color name goldt 100,75,0,50
    6894 
    6895 Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
    6896 
    6897  
    6898 
    6899 > color name plumt 87,63,87,50
    6900 
    6901 Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
    6902 
    6903  
    6904 
    6905 > color name ssubluet 68,86,90,50
    6906 
    6907 Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
    6908 
    6909  
    6910 
    6911 > color name p-prect 10,41,0,50
    6912 
    6913 Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
    6914 
    6915  
    6916 
    6917 > color name p-h2t 23,59,0,50
    6918 
    6919 Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    6920 
    6921  
    6922 
    6923 > color name p-h1t 40,73,0,50
    6924 
    6925 Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
    6926 
    6927  
    6928 
    6929 > color name p-h1c 40,73,0,100
    6930 
    6931 Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
    6932 
    6933  
    6934 
    6935 > color name p-spct 68,81,0,50
    6936 
    6937 Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    6938 
    6939  
    6940 
    6941 > color name p-spcc 68,81,0,100
    6942 
    6943 Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
    6944 
    6945  
    6946 
    6947 > color name p-fat 82,92,0,50
    6948 
    6949 Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
    6950 
    6951  
    6952 
    6953 > color name p-postt 100,92,0,50
    6954 
    6955 Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    6956 
    6957  
    6958 
    6959 > color name d-t 100,80,4,50
    6960 
    6961 Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    6962 
    6963  
    6964 
    6965 > color name d-prect 95,100,50,50
    6966 
    6967 Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
    6968 
    6969  
    6970 
    6971 > color name d-h2t 100,90,4,50
    6972 
    6973 Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    6974 
    6975  
    6976 
    6977 > color name d-h1t 100,80,4,50
    6978 
    6979 Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    6980 
    6981  
    6982 
    6983 > color name d-spct 100,70,4,50
    6984 
    6985 Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
    6986 
    6987  
    6988 
    6989 > color name d-fat 100,55,4,50
    6990 
    6991 Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
    6992 
    6993  
    6994 
    6995 > color name d-fac 100,55,4,100
    6996 
    6997 Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
    6998 
    6999  
    7000 
    7001 > color name d-postt 100,40,4,50
    7002 
    7003 Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    7004 
    7005  
    7006 
    7007 > color name m-t 95,43,62,50
    7008 
    7009 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    7010 
    7011  
    7012 
    7013 > color name m-prect 100,85,95,50
    7014 
    7015 Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    7016 
    7017  
    7018 
    7019 > color name m-h2t 100,85,95,50
    7020 
    7021 Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    7022 
    7023  
    7024 
    7025 > color name m-h1t 100,75,95,50
    7026 
    7027 Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
    7028 
    7029  
    7030 
    7031 > color name m-spct 89,63,75,50
    7032 
    7033 Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
    7034 
    7035  
    7036 
    7037 > color name m-fat 95,51,75,50
    7038 
    7039 Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
    7040 
    7041  
    7042 
    7043 > color name m-fac 95,51,75,100
    7044 
    7045 Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
    7046 
    7047  
    7048 
    7049 > color name m-postt 95,43,62,50
    7050 
    7051 Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    7052 
    7053  
    7054 executed 70S_colors.cxc 
    7055 
    7056 > color #10/y p-1t
    7057 
    7058 > color #11/y p-2t
    7059 
    7060 > color #12/y p-3t
    7061 
    7062 > color #30/y p-4t
    7063 
    7064 > color #31/y p-4t
    7065 
    7066 > color #32/y p-5t
    7067 
    7068 > color #33/y p-6t
    7069 
    7070 > color #13/y p-7t
    7071 
    7072 > color #34/y p-8t
    7073 
    7074 > color #14/y p-9t
    7075 
    7076 > color #20/y p-10t
    7077 
    7078 > color #15/y p-11t
    7079 
    7080 > color #10/v d-1t
    7081 
    7082 > color #11/v d-2t
    7083 
    7084 > color #12/v d-3t
    7085 
    7086 > color #30/v d-4t
    7087 
    7088 > color #31/v d-4t
    7089 
    7090 > color #32/v d-5t
    7091 
    7092 > color #33/v d-6t
    7093 
    7094 > color #13/v d-7t
    7095 
    7096 > color #34/v d-8t
    7097 
    7098 > color #14/v d-9t
    7099 
    7100 > color #20/v d-10t
    7101 
    7102 > color #15/v d-11t
    7103 
    7104 > color #10/w m-1t
    7105 
    7106 > color #11/w m-2t
    7107 
    7108 > color #12/w m-3t
    7109 
    7110 > color #30/w m-4t
    7111 
    7112 > color #31/w m-4t
    7113 
    7114 > color #32/w m-5t
    7115 
    7116 > color #33/w m-6t
    7117 
    7118 > color #13/w m-7t
    7119 
    7120 > color #34/w m-8t
    7121 
    7122 > color #14/w m-9t
    7123 
    7124 > color #20/w m-10t
    7125 
    7126 > color #15/w m-11t
    7127 
    7128 > color #30/x g-1t
    7129 
    7130 > color #31/x g-1t
    7131 
    7132 > color #32/x g-2t
    7133 
    7134 > color #33/x g-3t
    7135 
    7136 > color #13/x g-4t
    7137 
    7138 > color #34/x g-5t
    7139 
    7140 > color #14/x g-6t
    7141 
    7142 > color #20/x g-7t
    7143 
    7144 executed 70S_color_trna_gradient-t.cxc 
    7145 
    7146 > transparency 0 target abc
    7147 
    7148 > select atomods
    7149 
    7150 1822120 atoms, 1971444 bonds, 25 pseudobonds, 138279 residues, 41 models
    7151 selected 
    7152 
    7153 > view trna1
    7154 
    7155 > view trna2
    7156 
    7157 > view trna3
    7158 
    7159 > view name trna3
    7160 
    7161 > delete #10.3/v
    7162 
    7163 > ~select
    7164 
    7165 Nothing selected 
    7166 
    7167 > lighting soft
    7168 
    7169 > hide models
    7170 
    7171 > ~ribbon
    7172 
    7173 > ~display
    7174 
    7175 > display mrna
    7176 
    7177 > ribbon efg
    7178 
    7179 > ribbon trna
    7180 
    7181 > ribbon efg
    7182 
    7183 > hide emmaps
    7184 
    7185 > graphics silhouettes true
    7186 
    7187 > transparency #10.3#11.3#12.3#13.3#14.3#15.3#20.3 25 All
    7188 
    7189 > view trna1
    7190 
    7191 > hide models
    7192 
    7193 > show #*.3 models
    7194 
    7195 > hide #31#32 models
    7196 
    7197 > windowsize 1000 1000
    7198 
    7199 > save
    7200 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_all-H1a.tif
    7201 > format tiff pixelSize 0.1 quality 100 transparentBackground true
    7202 
    7203 Expected a keyword 
    7204 
    7205 > show #*.3 models
    7206 
    7207 > hide #30 models
    7208 
    7209 > windowsize 1000 1000
    7210 
    7211 > save
    7212 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_all-H1bc.tif
    7213 > format tiff pixelSize 0.1 quality 100 transparentBackground true
    7214 
    7215 Expected a keyword 
    7216 
    7217 > view trna1
    7218 
    7219 > view trna2
    7220 
    7221 > view trna3
    7222 
    7223 > view trna1
    7224 
    7225 > view name trna1
    7226 
    7227 > save
    7228 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/gtpys_translocation.cxs
    7229 
    7230 > select #30-34
    7231 
    7232 769038 atoms, 831474 bonds, 16 pseudobonds, 58854 residues, 36 models selected 
    7233 
    7234 > graphics silhouettes color 10,10,10,80
    7235 
    7236 > ~select
    7237 
    7238 Nothing selected 
    7239 
    7240 > view trna3
    7241 
    7242 > cartoon mrna
    7243 
    7244 > hide models
    7245 
    7246 > show #20.3#13.3 models
    7247 
    7248 > ~cartoon mrna
    7249 
    7250 > style /w:43@C1' sphere
    7251 
    7252 Changed 12 atom styles 
    7253 
    7254 > size /w atomRadius 1
    7255 
    7256 Changed 3205 atom radii 
    7257 
    7258 > size /w atomRadius 2
    7259 
    7260 Changed 3205 atom radii 
    7261 
    7262 > size /w atomRadius 1.5
    7263 
    7264 Changed 3205 atom radii 
    7265 
    7266 > size /w atomRadius 1.6
    7267 
    7268 Changed 3205 atom radii 
    7269 
    7270 > size atomRadius default
    7271 
    7272 Changed 1913675 atom radii 
    7273 
    7274 > save
    7275 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/gtpys_translocation.cxs
    7276 
    7277 ——— End of log from Tue May 16 15:25:17 2023 ———
    7278 
    7279 opened ChimeraX session 
    7280 
    7281 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_startup_gtpys-
    7282 > all.cxc
    7283 
    7284 > close all
    7285 
    7286 > open /data/EmilyRundlet/ChimeraX_70S/Maps/4ybb_50Score_3A.mrc
    7287 
    7288 Opened 4ybb_50Score_3A.mrc as #1, grid size 576,576,576, pixel 1.06, shown at
    7289 level 0.000164, step 4, values float32 
    7290 
    7291 > rename #1 id #100
    7292 
    7293 > open /data/EmilyRundlet/ChimeraX_70S/Models/prec_7n1p_50S.pdb
    7294 
    7295 Chain information for prec_7n1p_50S.pdb #1 
    7296 --- 
    7297 Chain | Description 
    7298 3 | No description available 
    7299 5 | No description available 
    7300 P | No description available 
    7301 S | No description available 
    7302 T | No description available 
    7303 U | No description available 
    7304 V | No description available 
    7305 W | No description available 
    7306 X | No description available 
    7307 Y | No description available 
    7308 a | No description available 
    7309 b | No description available 
    7310 c | No description available 
    7311 d | No description available 
    7312 e | No description available 
    7313 f | No description available 
    7314 g | No description available 
    7315 h | No description available 
    7316 i | No description available 
    7317 j | No description available 
    7318  
    7319 
    7320 > rename #1 id #101
    7321 
    7322 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_post.cxc
    7323 
    7324 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_50S.pdb name
    7325 > post5
    7326 
    7327 Chain information for post5 #1 
    7328 --- 
    7329 Chain | Description 
    7330 3 | No description available 
    7331 5 | No description available 
    7332 B | No description available 
    7333 C | No description available 
    7334 D | No description available 
    7335 E | No description available 
    7336 F | No description available 
    7337 I | No description available 
    7338 M | No description available 
    7339 N | No description available 
    7340 O | No description available 
    7341 P | No description available 
    7342 Q | No description available 
    7343 R | No description available 
    7344 S | No description available 
    7345 T | No description available 
    7346 U | No description available 
    7347 V | No description available 
    7348 W | No description available 
    7349 X | No description available 
    7350 Y | No description available 
    7351 a | No description available 
    7352 b | No description available 
    7353 c | No description available 
    7354 d | No description available 
    7355 e | No description available 
    7356 f | No description available 
    7357 g | No description available 
    7358 h | No description available 
    7359 i | No description available 
    7360 j | No description available 
    7361  
    7362 
    7363 > rename #1 id #15.5
    7364 
    7365 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_30S.pdb name
    7366 > post3
    7367 
    7368 Chain information for post3 #1 
    7369 --- 
    7370 Chain | Description 
    7371 6 | No description available 
    7372 B | No description available 
    7373 C | No description available 
    7374 D | No description available 
    7375 E | No description available 
    7376 F | No description available 
    7377 G | No description available 
    7378 H | No description available 
    7379 I | No description available 
    7380 J | No description available 
    7381 K | No description available 
    7382 L | No description available 
    7383 M | No description available 
    7384 N | No description available 
    7385 O | No description available 
    7386 P | No description available 
    7387 Q | No description available 
    7388 R | No description available 
    7389 S | No description available 
    7390 T | No description available 
    7391 U | No description available 
    7392 p | No description available 
    7393 v | No description available 
    7394 w | No description available 
    7395 y | No description available 
    7396  
    7397 
    7398 > rename #1 id #15.3
    7399 
    7400 > open
    7401 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/POST_j93ct15_pplocal_g0_n.mrc
    7402 > name post
    7403 
    7404 Opened post as #1, grid size 576,576,576, pixel 1.06, shown at level 1.16,
    7405 step 4, values float32 
    7406 
    7407 > rename #1 id #15.1
    7408 
    7409 > rename #15 post
    7410 
    7411 > matchmaker #15.5 to #101 matrix Nucleic bring #15.1#15.3
    7412 
    7413 Parameters 
    7414 --- 
    7415 Chain pairing | bb 
    7416 Alignment algorithm | Needleman-Wunsch 
    7417 Similarity matrix | Nucleic 
    7418 SS fraction | 0.3 
    7419 Gap open (HH/SS/other) | 18/18/6 
    7420 Gap extend | 1 
    7421 SS matrix |  |  | H | S | O 
    7422 ---|---|---|--- 
    7423 H | 6 | -9 | -6 
    7424 S |  | 6 | -6 
    7425 O |  |  | 4 
    7426 Iteration cutoff | 2 
    7427  
    7428 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with post5, chain 3 (#15.5),
    7429 sequence alignment score = 11580.3 
    7430 RMSD between 2766 pruned atom pairs is 0.341 angstroms; (across all 2904
    7431 pairs: 2.745) 
    7432  
    7433 
    7434 > fitmap #15.1 inMap #100
    7435 
    7436 Fit map post in map 4ybb_50Score_3A.mrc using 29937 points 
    7437 correlation = 0.7033, correlation about mean = 0.6059, overlap = 7.619e+04 
    7438 steps = 48, shift = 0.0376, angle = 0.0465 degrees 
    7439  
    7440 Position of post (#15.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    7441 Matrix rotation and translation 
    7442 0.99999983 0.00051499 -0.00026539 -0.07015622 
    7443 -0.00051501 0.99999986 -0.00009768 0.21094928 
    7444 0.00026534 0.00009781 0.99999996 -0.12735627 
    7445 Axis 0.16636276 -0.45165257 -0.87654628 
    7446 Axis point 413.67366807 137.87803145 0.00000000 
    7447 Rotation angle (degrees) 0.03366312 
    7448 Shift along axis 0.00468650 
    7449  
    7450 
    7451 > fitmap #15.5 inMap #15.1
    7452 
    7453 Fit molecule post5 (#15.5) to map post (#15.1) using 90903 atoms 
    7454 average map value = 15.29, steps = 40 
    7455 shifted from previous position = 0.0173 
    7456 rotated from previous position = 0.0481 degrees 
    7457 atoms outside contour = 27101, contour level = 1.1571 
    7458  
    7459 Position of post5 (#15.5) relative to post (#15.1) coordinates: 
    7460 Matrix rotation and translation 
    7461 1.00000000 0.00007488 -0.00001293 -0.00984527 
    7462 -0.00007488 1.00000000 0.00003964 0.01927617 
    7463 0.00001293 -0.00003964 1.00000000 0.00608995 
    7464 Axis -0.46249937 -0.15083335 -0.87369539 
    7465 Axis point 250.02744189 154.19286933 0.00000000 
    7466 Rotation angle (degrees) 0.00491036 
    7467 Shift along axis -0.00367482 
    7468  
    7469 
    7470 > fitmap #15.3 inMap #15.1
    7471 
    7472 Fit molecule post3 (#15.3) to map post (#15.1) using 55643 atoms 
    7473 average map value = 11.56, steps = 40 
    7474 shifted from previous position = 0.0883 
    7475 rotated from previous position = 0.0476 degrees 
    7476 atoms outside contour = 13831, contour level = 1.1571 
    7477  
    7478 Position of post3 (#15.3) relative to post (#15.1) coordinates: 
    7479 Matrix rotation and translation 
    7480 1.00000000 -0.00005318 -0.00004310 0.02635100 
    7481 0.00005318 1.00000000 -0.00000125 -0.02050708 
    7482 0.00004310 0.00000124 1.00000000 -0.01832489 
    7483 Axis 0.01818364 -0.62958007 0.77672279 
    7484 Axis point 395.65049914 495.82230346 0.00000000 
    7485 Rotation angle (degrees) 0.00392252 
    7486 Shift along axis -0.00084336 
    7487  
    7488 executed 70S_open_post.cxc 
    7489 
    7490 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_prec.cxc
    7491 
    7492 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_50S.pdb name
    7493 > prec5
    7494 
    7495 Chain information for prec5 #1 
    7496 --- 
    7497 Chain | Description 
    7498 3 | No description available 
    7499 5 | No description available 
    7500 B | No description available 
    7501 C | No description available 
    7502 D | No description available 
    7503 E | No description available 
    7504 F | No description available 
    7505 I | No description available 
    7506 J | No description available 
    7507 K | No description available 
    7508 M | No description available 
    7509 N | No description available 
    7510 O | No description available 
    7511 P | No description available 
    7512 Q | No description available 
    7513 R | No description available 
    7514 S | No description available 
    7515 T | No description available 
    7516 U | No description available 
    7517 V | No description available 
    7518 W | No description available 
    7519 X | No description available 
    7520 Y | No description available 
    7521 a | No description available 
    7522 b | No description available 
    7523 c | No description available 
    7524 d | No description available 
    7525 e | No description available 
    7526 f | No description available 
    7527 g | No description available 
    7528 h | No description available 
    7529 i | No description available 
    7530 j | No description available 
    7531  
    7532 
    7533 > rename #1 id #10.5
    7534 
    7535 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_30S.pdb name
    7536 > prec3
    7537 
    7538 Chain information for prec3 #1 
    7539 --- 
    7540 Chain | Description 
    7541 6 | No description available 
    7542 B | No description available 
    7543 C | No description available 
    7544 D | No description available 
    7545 E | No description available 
    7546 F | No description available 
    7547 G | No description available 
    7548 H | No description available 
    7549 I | No description available 
    7550 J | No description available 
    7551 K | No description available 
    7552 L | No description available 
    7553 M | No description available 
    7554 N | No description available 
    7555 O | No description available 
    7556 P | No description available 
    7557 Q | No description available 
    7558 R | No description available 
    7559 S | No description available 
    7560 T | No description available 
    7561 U | No description available 
    7562 p | No description available 
    7563 v | No description available 
    7564 w | No description available 
    7565 y | No description available 
    7566  
    7567 
    7568 > rename #1 id #10.3
    7569 
    7570 > open
    7571 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/PREC*local*.mrc
    7572 > name prec
    7573 
    7574 Opened prec as #1, grid size 576,576,576, pixel 1.06, shown at level 0.719,
    7575 step 4, values float32 
    7576 
    7577 > rename #1 id #10.1
    7578 
    7579 > rename #10 prec
    7580 
    7581 > matchmaker #10.5 to #101 matrix Nucleic bring #10.1#10.3
    7582 
    7583 Parameters 
    7584 --- 
    7585 Chain pairing | bb 
    7586 Alignment algorithm | Needleman-Wunsch 
    7587 Similarity matrix | Nucleic 
    7588 SS fraction | 0.3 
    7589 Gap open (HH/SS/other) | 18/18/6 
    7590 Gap extend | 1 
    7591 SS matrix |  |  | H | S | O 
    7592 ---|---|---|--- 
    7593 H | 6 | -9 | -6 
    7594 S |  | 6 | -6 
    7595 O |  |  | 4 
    7596 Iteration cutoff | 2 
    7597  
    7598 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with prec5, chain 3 (#10.5),
    7599 sequence alignment score = 11585.2 
    7600 RMSD between 2904 pruned atom pairs is 0.000 angstroms; (across all 2904
    7601 pairs: 0.000) 
    7602  
    7603 
    7604 > fitmap #10.1 inMap #100
    7605 
    7606 Fit map prec in map 4ybb_50Score_3A.mrc using 29930 points 
    7607 correlation = 0.705, correlation about mean = 0.6153, overlap = 7.403e+04 
    7608 steps = 100, shift = 0.0276, angle = 0.0213 degrees 
    7609  
    7610 Position of prec (#10.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    7611 Matrix rotation and translation 
    7612 0.99999993 0.00023597 -0.00028739 0.01666834 
    7613 -0.00023597 0.99999997 0.00000377 0.08653163 
    7614 0.00028739 -0.00000370 0.99999996 -0.10871255 
    7615 Axis -0.01003658 -0.77282074 -0.63454501 
    7616 Axis point 373.98904576 -0.00000000 57.97612114 
    7617 Rotation angle (degrees) 0.02130699 
    7618 Shift along axis 0.00194228 
    7619  
    7620 
    7621 > fitmap #10.5 inMap #10.1
    7622 
    7623 Fit molecule prec5 (#10.5) to map prec (#10.1) using 93196 atoms 
    7624 average map value = 15.31, steps = 40 
    7625 shifted from previous position = 0.0241 
    7626 rotated from previous position = 0.0378 degrees 
    7627 atoms outside contour = 32220, contour level = 0.71858 
    7628  
    7629 Position of prec5 (#10.5) relative to prec (#10.1) coordinates: 
    7630 Matrix rotation and translation 
    7631 0.99999996 0.00028462 -0.00008450 -0.07054285 
    7632 -0.00028461 0.99999995 0.00015462 0.06036830 
    7633 0.00008454 -0.00015460 0.99999998 0.02731692 
    7634 Axis -0.46188152 -0.25249170 -0.85024314 
    7635 Axis point 206.84210925 257.43360450 0.00000000 
    7636 Rotation angle (degrees) 0.01917937 
    7637 Shift along axis -0.00588608 
    7638  
    7639 
    7640 > fitmap #10.3 inMap #10.1
    7641 
    7642 Fit molecule prec3 (#10.3) to map prec (#10.1) using 56259 atoms 
    7643 average map value = 11.39, steps = 48 
    7644 shifted from previous position = 0.0796 
    7645 rotated from previous position = 0.0392 degrees 
    7646 atoms outside contour = 16720, contour level = 0.71858 
    7647  
    7648 Position of prec3 (#10.3) relative to prec (#10.1) coordinates: 
    7649 Matrix rotation and translation 
    7650 0.99999994 0.00035395 -0.00002496 -0.09187678 
    7651 -0.00035394 0.99999993 0.00014842 0.08455945 
    7652 0.00002502 -0.00014841 0.99999999 0.04385687 
    7653 Axis -0.38587760 -0.06497510 -0.92025905 
    7654 Axis point 236.94211808 270.96015369 0.00000000 
    7655 Rotation angle (degrees) 0.02203670 
    7656 Shift along axis -0.01040075 
    7657  
    7658 executed 70S_open_prec.cxc 
    7659 
    7660 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_fa.cxc
    7661 
    7662 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_50S.pdb name
    7663 > i2fa5
    7664 
    7665 Chain information for i2fa5 #1 
    7666 --- 
    7667 Chain | Description 
    7668 3 | No description available 
    7669 5 | No description available 
    7670 A | No description available 
    7671 B | No description available 
    7672 C | No description available 
    7673 D | No description available 
    7674 E | No description available 
    7675 F | No description available 
    7676 G | No description available 
    7677 I | No description available 
    7678 J | No description available 
    7679 K | No description available 
    7680 M | No description available 
    7681 N | No description available 
    7682 O | No description available 
    7683 P | No description available 
    7684 Q | No description available 
    7685 R | No description available 
    7686 S | No description available 
    7687 T | No description available 
    7688 U | No description available 
    7689 V | No description available 
    7690 W | No description available 
    7691 X | No description available 
    7692 Y | No description available 
    7693 a | No description available 
    7694 b | No description available 
    7695 c | No description available 
    7696 d | No description available 
    7697 e | No description available 
    7698 f | No description available 
    7699 g | No description available 
    7700 h | No description available 
    7701 i | No description available 
    7702 j | No description available 
    7703  
    7704 
    7705 > rename #1 id #14.5
    7706 
    7707 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_30S.pdb name
    7708 > i2fa3
    7709 
    7710 Chain information for i2fa3 #1 
    7711 --- 
    7712 Chain | Description 
    7713 6 | No description available 
    7714 B | No description available 
    7715 C | No description available 
    7716 D | No description available 
    7717 E | No description available 
    7718 F | No description available 
    7719 G | No description available 
    7720 H | No description available 
    7721 I | No description available 
    7722 J | No description available 
    7723 K | No description available 
    7724 L | No description available 
    7725 M | No description available 
    7726 N | No description available 
    7727 O | No description available 
    7728 P | No description available 
    7729 Q | No description available 
    7730 R | No description available 
    7731 S | No description available 
    7732 T | No description available 
    7733 U | No description available 
    7734 p | No description available 
    7735 v | No description available 
    7736 w | No description available 
    7737 x | No description available 
    7738 y | No description available 
    7739  
    7740 
    7741 > rename #1 id #14.3
    7742 
    7743 > open
    7744 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/FA*local*.mrc
    7745 
    7746 Opened FA_j118_localres_filt_g0_n.mrc as #1, grid size 576,576,576, pixel
    7747 1.06, shown at level 0.555, step 4, values float32 
    7748 
    7749 > rename #1 id #14.1
    7750 
    7751 > matchmaker #14.5 to #101 matrix Nucleic bring #14.1#14.3
    7752 
    7753 Parameters 
    7754 --- 
    7755 Chain pairing | bb 
    7756 Alignment algorithm | Needleman-Wunsch 
    7757 Similarity matrix | Nucleic 
    7758 SS fraction | 0.3 
    7759 Gap open (HH/SS/other) | 18/18/6 
    7760 Gap extend | 1 
    7761 SS matrix |  |  | H | S | O 
    7762 ---|---|---|--- 
    7763 H | 6 | -9 | -6 
    7764 S |  | 6 | -6 
    7765 O |  |  | 4 
    7766 Iteration cutoff | 2 
    7767  
    7768 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i2fa5, chain 3 (#14.5),
    7769 sequence alignment score = 11567.9 
    7770 RMSD between 2675 pruned atom pairs is 0.458 angstroms; (across all 2903
    7771 pairs: 3.500) 
    7772  
    7773 
    7774 > rename #14 fa
    7775 
    7776 > fitmap #14.1 inMap #100
    7777 
    7778 Fit map FA_j118_localres_filt_g0_n.mrc in map 4ybb_50Score_3A.mrc using 29876
    7779 points 
    7780 correlation = 0.7652, correlation about mean = 0.6917, overlap = 8.026e+04 
    7781 steps = 124, shift = 0.0674, angle = 0.0469 degrees 
    7782  
    7783 Position of FA_j118_localres_filt_g0_n.mrc (#14.1) relative to
    7784 4ybb_50Score_3A.mrc (#100) coordinates: 
    7785 Matrix rotation and translation 
    7786 0.99999951 0.00082837 -0.00054821 -0.07721517 
    7787 -0.00082823 0.99999963 0.00024790 0.22483688 
    7788 0.00054841 -0.00024745 0.99999982 -0.11895947 
    7789 Axis -0.24193109 -0.53558675 -0.80908354 
    7790 Axis point 267.87230737 94.97670830 0.00000000 
    7791 Rotation angle (degrees) 0.05865666 
    7792 Shift along axis -0.00549075 
    7793  
    7794 
    7795 > fitmap #14.5 inMap #14.1
    7796 
    7797 Fit molecule i2fa5 (#14.5) to map FA_j118_localres_filt_g0_n.mrc (#14.1) using
    7798 94455 atoms 
    7799 average map value = 14.71, steps = 44 
    7800 shifted from previous position = 0.0492 
    7801 rotated from previous position = 0.0489 degrees 
    7802 atoms outside contour = 26009, contour level = 0.5555 
    7803  
    7804 Position of i2fa5 (#14.5) relative to FA_j118_localres_filt_g0_n.mrc (#14.1)
    7805 coordinates: 
    7806 Matrix rotation and translation 
    7807 0.99999999 0.00013549 0.00005439 -0.05910674 
    7808 -0.00013549 0.99999999 -0.00008462 0.07061428 
    7809 -0.00005440 0.00008461 0.99999999 -0.01606966 
    7810 Axis 0.50141948 0.32233497 -0.80291884 
    7811 Axis point 506.79859217 458.57499403 0.00000000 
    7812 Rotation angle (degrees) 0.00966859 
    7813 Shift along axis 0.00602682 
    7814  
    7815 
    7816 > fitmap #14.3 inMap #14.1
    7817 
    7818 Fit molecule i2fa3 (#14.3) to map FA_j118_localres_filt_g0_n.mrc (#14.1) using
    7819 60702 atoms 
    7820 average map value = 7.538, steps = 40 
    7821 shifted from previous position = 0.104 
    7822 rotated from previous position = 0.0489 degrees 
    7823 atoms outside contour = 11367, contour level = 0.5555 
    7824  
    7825 Position of i2fa3 (#14.3) relative to FA_j118_localres_filt_g0_n.mrc (#14.1)
    7826 coordinates: 
    7827 Matrix rotation and translation 
    7828 0.99999996 0.00022144 0.00016174 -0.14067075 
    7829 -0.00022141 0.99999996 -0.00017040 0.12305826 
    7830 -0.00016178 0.00017037 0.99999997 -0.00200513 
    7831 Axis 0.52777238 0.50104898 -0.68586167 
    7832 Axis point 581.05763080 608.65192133 0.00000000 
    7833 Rotation angle (degrees) 0.01849719 
    7834 Shift along axis -0.01120868 
    7835  
    7836 executed 70S_open_fa.cxc 
    7837 
    7838 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_spc.cxc
    7839 
    7840 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_50S.pdb name
    7841 > i1spc5
    7842 
    7843 Chain information for i1spc5 #1 
    7844 --- 
    7845 Chain | Description 
    7846 3 | No description available 
    7847 5 | No description available 
    7848 B | No description available 
    7849 C | No description available 
    7850 D | No description available 
    7851 E | No description available 
    7852 F | No description available 
    7853 I | No description available 
    7854 J | No description available 
    7855 K | No description available 
    7856 M | No description available 
    7857 N | No description available 
    7858 O | No description available 
    7859 P | No description available 
    7860 Q | No description available 
    7861 R | No description available 
    7862 S | No description available 
    7863 T | No description available 
    7864 U | No description available 
    7865 V | No description available 
    7866 W | No description available 
    7867 X | No description available 
    7868 Y | No description available 
    7869 a | No description available 
    7870 b | No description available 
    7871 c | No description available 
    7872 d | No description available 
    7873 e | No description available 
    7874 f | No description available 
    7875 g | No description available 
    7876 h | No description available 
    7877 i | No description available 
    7878 j | No description available 
    7879  
    7880 
    7881 > rename #1 id #13.5
    7882 
    7883 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_30S.pdb name
    7884 > i1spc3
    7885 
    7886 Chain information for i1spc3 #1 
    7887 --- 
    7888 Chain | Description 
    7889 6 | No description available 
    7890 B | No description available 
    7891 C | No description available 
    7892 D | No description available 
    7893 E | No description available 
    7894 F | No description available 
    7895 G | No description available 
    7896 H | No description available 
    7897 I | No description available 
    7898 J | No description available 
    7899 K | No description available 
    7900 L | No description available 
    7901 M | No description available 
    7902 N | No description available 
    7903 O | No description available 
    7904 P | No description available 
    7905 Q | No description available 
    7906 R | No description available 
    7907 S | No description available 
    7908 T | No description available 
    7909 U | No description available 
    7910 p | No description available 
    7911 v | No description available 
    7912 w | No description available 
    7913 x | No description available 
    7914 y | No description available 
    7915  
    7916 
    7917 > rename #1 id #13.3
    7918 
    7919 > open
    7920 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/INT1_spc*local*.mrc
    7921 > name i1spc
    7922 
    7923 Opened i1spc as #1, grid size 576,576,576, pixel 1.06, shown at level 0.527,
    7924 step 4, values float32 
    7925 
    7926 > rename #1 id #13.1
    7927 
    7928 > rename #13 i1spc
    7929 
    7930 > matchmaker #13.5 to #101 matrix Nucleic bring #13.1#13.3
    7931 
    7932 Parameters 
    7933 --- 
    7934 Chain pairing | bb 
    7935 Alignment algorithm | Needleman-Wunsch 
    7936 Similarity matrix | Nucleic 
    7937 SS fraction | 0.3 
    7938 Gap open (HH/SS/other) | 18/18/6 
    7939 Gap extend | 1 
    7940 SS matrix |  |  | H | S | O 
    7941 ---|---|---|--- 
    7942 H | 6 | -9 | -6 
    7943 S |  | 6 | -6 
    7944 O |  |  | 4 
    7945 Iteration cutoff | 2 
    7946  
    7947 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i1spc5, chain 3 (#13.5),
    7948 sequence alignment score = 11576.1 
    7949 RMSD between 2613 pruned atom pairs is 0.440 angstroms; (across all 2904
    7950 pairs: 4.190) 
    7951  
    7952 
    7953 > fitmap #13.1 inMap #100
    7954 
    7955 Fit map i1spc in map 4ybb_50Score_3A.mrc using 29799 points 
    7956 correlation = 0.7329, correlation about mean = 0.6398, overlap = 7.208e+04 
    7957 steps = 104, shift = 0.0985, angle = 0.0628 degrees 
    7958  
    7959 Position of i1spc (#13.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    7960 Matrix rotation and translation 
    7961 0.99999127 -0.00305790 -0.00284733 1.91534327 
    7962 0.00305942 0.99999518 0.00052889 -1.13631859 
    7963 0.00284570 -0.00053760 0.99999581 -1.01117770 
    7964 Axis -0.12659581 -0.67578369 0.72614730 
    7965 Axis point 418.51647841 616.51914515 0.00000000 
    7966 Rotation angle (degrees) 0.24134036 
    7967 Shift along axis -0.20883282 
    7968  
    7969 
    7970 > fitmap #13.5 inMap #13.1
    7971 
    7972 Fit molecule i1spc5 (#13.5) to map i1spc (#13.1) using 93017 atoms 
    7973 average map value = 14.57, steps = 48 
    7974 shifted from previous position = 0.0733 
    7975 rotated from previous position = 0.0651 degrees 
    7976 atoms outside contour = 27434, contour level = 0.52653 
    7977  
    7978 Position of i1spc5 (#13.5) relative to i1spc (#13.1) coordinates: 
    7979 Matrix rotation and translation 
    7980 1.00000000 -0.00000053 -0.00005875 0.01737643 
    7981 0.00000053 1.00000000 -0.00002655 0.00255801 
    7982 0.00005875 0.00002655 1.00000000 -0.03456253 
    7983 Axis 0.41177423 -0.91124934 0.00816220 
    7984 Axis point 588.98331322 0.00000000 263.93669119 
    7985 Rotation angle (degrees) 0.00369369 
    7986 Shift along axis 0.00454208 
    7987  
    7988 
    7989 > fitmap #13.3 inMap #13.1
    7990 
    7991 Fit molecule i1spc3 (#13.3) to map i1spc (#13.1) using 61103 atoms 
    7992 average map value = 9.699, steps = 60 
    7993 shifted from previous position = 0.162 
    7994 rotated from previous position = 0.0627 degrees 
    7995 atoms outside contour = 14669, contour level = 0.52653 
    7996  
    7997 Position of i1spc3 (#13.3) relative to i1spc (#13.1) coordinates: 
    7998 Matrix rotation and translation 
    7999 0.99999999 0.00006855 -0.00007419 -0.00808096 
    8000 -0.00006856 1.00000000 -0.00003421 0.02476248 
    8001 0.00007419 0.00003421 1.00000000 -0.04490669 
    8002 Axis 0.32075098 -0.69563238 -0.64281755 
    8003 Axis point 526.89840240 0.00000000 -148.08272269 
    8004 Rotation angle (degrees) 0.00611054 
    8005 Shift along axis 0.00904925 
    8006  
    8007 executed 70S_open_spc.cxc 
    8008 
    8009 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_h1.cxc
    8010 
    8011 > open
    8012 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/apo_H1*local*.mrc
    8013 > name hy1
    8014 
    8015 Opened hy1 as #1, grid size 576,576,576, pixel 1.06, shown at level 0.822,
    8016 step 4, values float32 
    8017 
    8018 > rename #1 id #12.1
    8019 
    8020 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_50S.pdb name
    8021 > hy15
    8022 
    8023 Chain information for hy15 #1 
    8024 --- 
    8025 Chain | Description 
    8026 3 | No description available 
    8027 5 | No description available 
    8028 B | No description available 
    8029 C | No description available 
    8030 D | No description available 
    8031 E | No description available 
    8032 F | No description available 
    8033 I | No description available 
    8034 M | No description available 
    8035 N | No description available 
    8036 O | No description available 
    8037 P | No description available 
    8038 Q | No description available 
    8039 R | No description available 
    8040 S | No description available 
    8041 T | No description available 
    8042 U | No description available 
    8043 V | No description available 
    8044 W | No description available 
    8045 X | No description available 
    8046 Y | No description available 
    8047 a | No description available 
    8048 b | No description available 
    8049 c | No description available 
    8050 d | No description available 
    8051 e | No description available 
    8052 f | No description available 
    8053 g | No description available 
    8054 h | No description available 
    8055 i | No description available 
    8056 j | No description available 
    8057  
    8058 
    8059 > rename #1 id #12.5
    8060 
    8061 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_30S.pdb name
    8062 > hy13
    8063 
    8064 Chain information for hy13 #1 
    8065 --- 
    8066 Chain | Description 
    8067 6 | No description available 
    8068 B | No description available 
    8069 C | No description available 
    8070 D | No description available 
    8071 E | No description available 
    8072 F | No description available 
    8073 G | No description available 
    8074 H | No description available 
    8075 I | No description available 
    8076 J | No description available 
    8077 K | No description available 
    8078 L | No description available 
    8079 M | No description available 
    8080 N | No description available 
    8081 O | No description available 
    8082 P | No description available 
    8083 Q | No description available 
    8084 R | No description available 
    8085 S | No description available 
    8086 T | No description available 
    8087 U | No description available 
    8088 p | No description available 
    8089 v | No description available 
    8090 w | No description available 
    8091 y | No description available 
    8092  
    8093 
    8094 > rename #1 id #12.3
    8095 
    8096 > matchmaker #12.5 to #101 matrix Nucleic bring #12.1#12.3
    8097 
    8098 Parameters 
    8099 --- 
    8100 Chain pairing | bb 
    8101 Alignment algorithm | Needleman-Wunsch 
    8102 Similarity matrix | Nucleic 
    8103 SS fraction | 0.3 
    8104 Gap open (HH/SS/other) | 18/18/6 
    8105 Gap extend | 1 
    8106 SS matrix |  |  | H | S | O 
    8107 ---|---|---|--- 
    8108 H | 6 | -9 | -6 
    8109 S |  | 6 | -6 
    8110 O |  |  | 4 
    8111 Iteration cutoff | 2 
    8112  
    8113 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with hy15, chain 3 (#12.5),
    8114 sequence alignment score = 11572.3 
    8115 RMSD between 2683 pruned atom pairs is 0.437 angstroms; (across all 2902
    8116 pairs: 4.227) 
    8117  
    8118 
    8119 > fitmap #12.1 inMap #100
    8120 
    8121 Fit map hy1 in map 4ybb_50Score_3A.mrc using 29865 points 
    8122 correlation = 0.7182, correlation about mean = 0.6351, overlap = 7.48e+04 
    8123 steps = 80, shift = 0.0539, angle = 0.0362 degrees 
    8124  
    8125 Position of hy1 (#12.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    8126 Matrix rotation and translation 
    8127 0.99999993 0.00033939 -0.00014651 -0.03967194 
    8128 -0.00033939 0.99999994 0.00003379 0.08904027 
    8129 0.00014652 -0.00003374 0.99999999 -0.04209798 
    8130 Axis -0.09096206 -0.39471037 -0.91429187 
    8131 Axis point 270.42268136 115.08181596 0.00000000 
    8132 Rotation angle (degrees) 0.02126851 
    8133 Shift along axis 0.00695336 
    8134  
    8135 
    8136 > fitmap #12.5 inMap #12.1
    8137 
    8138 Fit molecule hy15 (#12.5) to map hy1 (#12.1) using 91053 atoms 
    8139 average map value = 15.92, steps = 40 
    8140 shifted from previous position = 0.0355 
    8141 rotated from previous position = 0.0365 degrees 
    8142 atoms outside contour = 31662, contour level = 0.82202 
    8143  
    8144 Position of hy15 (#12.5) relative to hy1 (#12.1) coordinates: 
    8145 Matrix rotation and translation 
    8146 1.00000000 0.00001739 -0.00003452 0.00191493 
    8147 -0.00001738 1.00000000 0.00005119 -0.00075625 
    8148 0.00003452 -0.00005119 1.00000000 0.00373129 
    8149 Axis -0.79805293 -0.53818813 -0.27104440 
    8150 Axis point 0.00000000 61.60073087 37.19705100 
    8151 Rotation angle (degrees) 0.00367501 
    8152 Shift along axis -0.00213255 
    8153  
    8154 
    8155 > fitmap #12.3 inMap #12.1
    8156 
    8157 Fit molecule hy13 (#12.3) to map hy1 (#12.1) using 55765 atoms 
    8158 average map value = 9.817, steps = 44 
    8159 shifted from previous position = 0.0694 
    8160 rotated from previous position = 0.0332 degrees 
    8161 atoms outside contour = 14540, contour level = 0.82202 
    8162  
    8163 Position of hy13 (#12.3) relative to hy1 (#12.1) coordinates: 
    8164 Matrix rotation and translation 
    8165 1.00000000 -0.00000897 0.00000895 -0.00690250 
    8166 0.00000897 0.99999999 0.00011154 -0.02727097 
    8167 -0.00000895 -0.00011154 0.99999999 0.03999319 
    8168 Axis -0.99361126 0.07969592 0.07990759 
    8169 Axis point 0.00000000 352.90975575 250.15609103 
    8170 Rotation angle (degrees) 0.00643159 
    8171 Shift along axis 0.00788078 
    8172  
    8173 executed 70S_open_h1.cxc 
    8174 
    8175 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_ys.cxc
    8176 
    8177 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb name
    8178 > ys-H1a5
    8179 
    8180 Summary of feedback from opening
    8181 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb 
    8182 --- 
    8183 warnings | Ignored bad PDB record found on line 4 
    8184 LINK ZN ZN Le0201 SG CY 04 
    8185  
    8186 Ignored bad PDB record found on line 5 
    8187 LINK ZN ZN Le0201 SG CY 03 
    8188  
    8189 Ignored bad PDB record found on line 6 
    8190 LINK ZN ZN Le0201 SG CY 01 
    8191  
    8192 Ignored bad PDB record found on line 7 
    8193 LINK ZN ZN Le0201 SG CY 01 
    8194  
    8195 Ignored bad PDB record found on line 8 
    8196 LINK ZN ZN Lj0101 ND1 HI 03 
    8197  
    8198 3 messages similar to the above omitted 
    8199 Cannot find LINK/SSBOND residue THR (1033509) 
    8200 Cannot find LINK/SSBOND residue ASP (2432820) 
    8201 Cannot find LINK/SSBOND residue ZN (567641) 
    8202  
    8203 Chain information for ys-H1a5 #1 
    8204 --- 
    8205 Chain | Description 
    8206 3 | No description available 
    8207 5 | No description available 
    8208 B | No description available 
    8209 C | No description available 
    8210 D | No description available 
    8211 E | No description available 
    8212 F | No description available 
    8213 I | No description available 
    8214 J | No description available 
    8215 K | No description available 
    8216 M | No description available 
    8217 N | No description available 
    8218 O | No description available 
    8219 P | No description available 
    8220 Q | No description available 
    8221 R | No description available 
    8222 S | No description available 
    8223 T | No description available 
    8224 U | No description available 
    8225 V | No description available 
    8226 W | No description available 
    8227 X | No description available 
    8228 Y | No description available 
    8229 a | No description available 
    8230 b | No description available 
    8231 c | No description available 
    8232 d | No description available 
    8233 e | No description available 
    8234 f | No description available 
    8235 g | No description available 
    8236 h | No description available 
    8237 i | No description available 
    8238 j | No description available 
    8239  
    8240 
    8241 > rename #1 id #30.5
    8242 
    8243 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb name
    8244 > ys-H1a3
    8245 
    8246 Summary of feedback from opening
    8247 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb 
    8248 --- 
    8249 warnings | Ignored bad PDB record found on line 4 
    8250 LINK ZN ZN Le0201 SG CY 04 
    8251  
    8252 Ignored bad PDB record found on line 5 
    8253 LINK ZN ZN Le0201 SG CY 03 
    8254  
    8255 Ignored bad PDB record found on line 6 
    8256 LINK ZN ZN Le0201 SG CY 01 
    8257  
    8258 Ignored bad PDB record found on line 7 
    8259 LINK ZN ZN Le0201 SG CY 01 
    8260  
    8261 Ignored bad PDB record found on line 8 
    8262 LINK ZN ZN Lj0101 ND1 HI 03 
    8263  
    8264 3 messages similar to the above omitted 
    8265 Cannot find LINK/SSBOND residue THR (1033509) 
    8266 Cannot find LINK/SSBOND residue ASP (2432820) 
    8267 Cannot find LINK/SSBOND residue ZN (567641) 
    8268  
    8269 Chain information for ys-H1a3 #1 
    8270 --- 
    8271 Chain | Description 
    8272 6 | No description available 
    8273 B | No description available 
    8274 C | No description available 
    8275 D | No description available 
    8276 E | No description available 
    8277 F | No description available 
    8278 G | No description available 
    8279 H | No description available 
    8280 I | No description available 
    8281 J | No description available 
    8282 K | No description available 
    8283 L | No description available 
    8284 M | No description available 
    8285 N | No description available 
    8286 O | No description available 
    8287 P | No description available 
    8288 Q | No description available 
    8289 R | No description available 
    8290 S | No description available 
    8291 T | No description available 
    8292 U | No description available 
    8293 p | No description available 
    8294 v | No description available 
    8295 w | No description available 
    8296 x | No description available 
    8297 y | No description available 
    8298  
    8299 
    8300 > rename #1 id #30.3
    8301 
    8302 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1a*.mrc name ys-H1a
    8303 
    8304 Opened ys-H1a as #1, grid size 512,512,512, pixel 0.826, shown at level 3.13,
    8305 step 2, values float32 
    8306 
    8307 > rename #1 id #30.1
    8308 
    8309 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb name
    8310 > ys-H1b5
    8311 
    8312 Summary of feedback from opening
    8313 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb 
    8314 --- 
    8315 warnings | Ignored bad PDB record found on line 5 
    8316 LINK ZN ZN Le0201 SG CY 04 
    8317  
    8318 Ignored bad PDB record found on line 6 
    8319 LINK ZN ZN Le0201 SG CY 03 
    8320  
    8321 Ignored bad PDB record found on line 7 
    8322 LINK ZN ZN Le0201 SG CY 01 
    8323  
    8324 Ignored bad PDB record found on line 8 
    8325 LINK ZN ZN Le0201 SG CY 01 
    8326  
    8327 Ignored bad PDB record found on line 9 
    8328 LINK ZN ZN Lj0101 ND1 HI 03 
    8329  
    8330 3 messages similar to the above omitted 
    8331 Cannot find LINK/SSBOND residue THR (1033509) 
    8332 Cannot find LINK/SSBOND residue LYS (2432823) 
    8333 Cannot find LINK/SSBOND residue THR (2432824) 
    8334 Cannot find LINK/SSBOND residue ZN (567641) 
    8335  
    8336 Chain information for ys-H1b5 #1 
    8337 --- 
    8338 Chain | Description 
    8339 3 | No description available 
    8340 5 | No description available 
    8341 B | No description available 
    8342 C | No description available 
    8343 D | No description available 
    8344 E | No description available 
    8345 F | No description available 
    8346 I | No description available 
    8347 J | No description available 
    8348 K | No description available 
    8349 M | No description available 
    8350 N | No description available 
    8351 O | No description available 
    8352 P | No description available 
    8353 Q | No description available 
    8354 R | No description available 
    8355 S | No description available 
    8356 T | No description available 
    8357 U | No description available 
    8358 V | No description available 
    8359 W | No description available 
    8360 X | No description available 
    8361 Y | No description available 
    8362 a | No description available 
    8363 b | No description available 
    8364 c | No description available 
    8365 d | No description available 
    8366 e | No description available 
    8367 f | No description available 
    8368 g | No description available 
    8369 h | No description available 
    8370 i | No description available 
    8371 j | No description available 
    8372  
    8373 
    8374 > rename #1 id #31.5
    8375 
    8376 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb name
    8377 > ys-H1b3
    8378 
    8379 Summary of feedback from opening
    8380 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb 
    8381 --- 
    8382 warnings | Ignored bad PDB record found on line 5 
    8383 LINK ZN ZN Le0201 SG CY 04 
    8384  
    8385 Ignored bad PDB record found on line 6 
    8386 LINK ZN ZN Le0201 SG CY 03 
    8387  
    8388 Ignored bad PDB record found on line 7 
    8389 LINK ZN ZN Le0201 SG CY 01 
    8390  
    8391 Ignored bad PDB record found on line 8 
    8392 LINK ZN ZN Le0201 SG CY 01 
    8393  
    8394 Ignored bad PDB record found on line 9 
    8395 LINK ZN ZN Lj0101 ND1 HI 03 
    8396  
    8397 3 messages similar to the above omitted 
    8398 Cannot find LINK/SSBOND residue THR (1033509) 
    8399 Cannot find LINK/SSBOND residue LYS (2432823) 
    8400 Cannot find LINK/SSBOND residue THR (2432824) 
    8401 Cannot find LINK/SSBOND residue ZN (567641) 
    8402  
    8403 Chain information for ys-H1b3 #1 
    8404 --- 
    8405 Chain | Description 
    8406 6 | No description available 
    8407 B | No description available 
    8408 C | No description available 
    8409 D | No description available 
    8410 E | No description available 
    8411 F | No description available 
    8412 G | No description available 
    8413 H | No description available 
    8414 I | No description available 
    8415 J | No description available 
    8416 K | No description available 
    8417 L | No description available 
    8418 M | No description available 
    8419 N | No description available 
    8420 O | No description available 
    8421 P | No description available 
    8422 Q | No description available 
    8423 R | No description available 
    8424 S | No description available 
    8425 T | No description available 
    8426 U | No description available 
    8427 p | No description available 
    8428 v | No description available 
    8429 w | No description available 
    8430 x | No description available 
    8431 y | No description available 
    8432  
    8433 
    8434 > rename #1 id #31.3
    8435 
    8436 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1b*.mrc name ys-H1b
    8437 
    8438 Opened ys-H1b as #1, grid size 512,512,512, pixel 0.826, shown at level 3.16,
    8439 step 2, values float32 
    8440 
    8441 > rename #1 id #31.1
    8442 
    8443 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb name
    8444 > ys-H1c5
    8445 
    8446 Summary of feedback from opening
    8447 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb 
    8448 --- 
    8449 warnings | Ignored bad PDB record found on line 2 
    8450 LINK ZN ZN Lj0101 ND1 HI 03 
    8451  
    8452 Ignored bad PDB record found on line 3 
    8453 LINK ZN ZN Lj0101 SG CY 01 
    8454  
    8455 Ignored bad PDB record found on line 4 
    8456 LINK ZN ZN Lj0101 SG CY 01 
    8457  
    8458 Ignored bad PDB record found on line 5 
    8459 LINK ZN ZN Lj0101 SG CY 02 
    8460  
    8461 Ignored bad PDB record found on line 6 
    8462 LINK ZN ZN Le0201 SG CY 04 
    8463  
    8464 3 messages similar to the above omitted 
    8465 Cannot find LINK/SSBOND residue THR (1033509) 
    8466 Cannot find LINK/SSBOND residue ZN (567641) 
    8467  
    8468 Chain information for ys-H1c5 #1 
    8469 --- 
    8470 Chain | Description 
    8471 3 | No description available 
    8472 5 | No description available 
    8473 B | No description available 
    8474 C | No description available 
    8475 D | No description available 
    8476 E | No description available 
    8477 F | No description available 
    8478 I | No description available 
    8479 J | No description available 
    8480 K | No description available 
    8481 M | No description available 
    8482 N | No description available 
    8483 O | No description available 
    8484 P | No description available 
    8485 Q | No description available 
    8486 R | No description available 
    8487 S | No description available 
    8488 T | No description available 
    8489 U | No description available 
    8490 V | No description available 
    8491 W | No description available 
    8492 X | No description available 
    8493 Y | No description available 
    8494 a | No description available 
    8495 b | No description available 
    8496 c | No description available 
    8497 d | No description available 
    8498 e | No description available 
    8499 f | No description available 
    8500 g | No description available 
    8501 h | No description available 
    8502 i | No description available 
    8503 j | No description available 
    8504  
    8505 
    8506 > rename #1 id #32.5
    8507 
    8508 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb name
    8509 > ys-H1c3
    8510 
    8511 Summary of feedback from opening
    8512 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb 
    8513 --- 
    8514 warnings | Ignored bad PDB record found on line 2 
    8515 LINK ZN ZN Lj0101 ND1 HI 03 
    8516  
    8517 Ignored bad PDB record found on line 3 
    8518 LINK ZN ZN Lj0101 SG CY 01 
    8519  
    8520 Ignored bad PDB record found on line 4 
    8521 LINK ZN ZN Lj0101 SG CY 01 
    8522  
    8523 Ignored bad PDB record found on line 5 
    8524 LINK ZN ZN Lj0101 SG CY 02 
    8525  
    8526 Ignored bad PDB record found on line 6 
    8527 LINK ZN ZN Le0201 SG CY 04 
    8528  
    8529 3 messages similar to the above omitted 
    8530 Cannot find LINK/SSBOND residue THR (1033509) 
    8531 Cannot find LINK/SSBOND residue ZN (567641) 
    8532  
    8533 Chain information for ys-H1c3 #1 
    8534 --- 
    8535 Chain | Description 
    8536 6 | No description available 
    8537 B | No description available 
    8538 C | No description available 
    8539 D | No description available 
    8540 E | No description available 
    8541 F | No description available 
    8542 G | No description available 
    8543 H | No description available 
    8544 I | No description available 
    8545 J | No description available 
    8546 K | No description available 
    8547 L | No description available 
    8548 M | No description available 
    8549 N | No description available 
    8550 O | No description available 
    8551 P | No description available 
    8552 Q | No description available 
    8553 R | No description available 
    8554 S | No description available 
    8555 T | No description available 
    8556 U | No description available 
    8557 p | No description available 
    8558 v | No description available 
    8559 w | No description available 
    8560 x | No description available 
    8561 y | No description available 
    8562  
    8563 
    8564 > rename #1 id #32.3
    8565 
    8566 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1c*.mrc name ys-H1c
    8567 
    8568 Opened ys-H1c as #1, grid size 512,512,512, pixel 0.826, shown at level 3.11,
    8569 step 2, values float32 
    8570 
    8571 > rename #1 id #32.1
    8572 
    8573 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb name
    8574 > ys-I1a5
    8575 
    8576 Summary of feedback from opening
    8577 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb 
    8578 --- 
    8579 warnings | Ignored bad PDB record found on line 2 
    8580 LINK ZN ZN Lj0101 ND1 HI 03 
    8581  
    8582 Ignored bad PDB record found on line 3 
    8583 LINK ZN ZN Lj0101 SG CY 01 
    8584  
    8585 Ignored bad PDB record found on line 4 
    8586 LINK ZN ZN Lj0101 SG CY 01 
    8587  
    8588 Ignored bad PDB record found on line 5 
    8589 LINK ZN ZN Lj0101 SG CY 02 
    8590  
    8591 Ignored bad PDB record found on line 6 
    8592 LINK ZN ZN Le0201 SG CY 04 
    8593  
    8594 3 messages similar to the above omitted 
    8595 Cannot find LINK/SSBOND residue THR (1033509) 
    8596 Cannot find LINK/SSBOND residue ZN (567641) 
    8597  
    8598 Chain information for ys-I1a5 #1 
    8599 --- 
    8600 Chain | Description 
    8601 3 | No description available 
    8602 5 | No description available 
    8603 B | No description available 
    8604 C | No description available 
    8605 D | No description available 
    8606 E | No description available 
    8607 F | No description available 
    8608 I | No description available 
    8609 J | No description available 
    8610 K | No description available 
    8611 M | No description available 
    8612 N | No description available 
    8613 O | No description available 
    8614 P | No description available 
    8615 Q | No description available 
    8616 R | No description available 
    8617 S | No description available 
    8618 T | No description available 
    8619 U | No description available 
    8620 V | No description available 
    8621 W | No description available 
    8622 X | No description available 
    8623 Y | No description available 
    8624 a | No description available 
    8625 b | No description available 
    8626 c | No description available 
    8627 d | No description available 
    8628 e | No description available 
    8629 f | No description available 
    8630 g | No description available 
    8631 h | No description available 
    8632 i | No description available 
    8633 j | No description available 
    8634  
    8635 
    8636 > rename #1 id #33.5
    8637 
    8638 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb name
    8639 > ys-I1a3
    8640 
    8641 Summary of feedback from opening
    8642 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb 
    8643 --- 
    8644 warnings | Ignored bad PDB record found on line 2 
    8645 LINK ZN ZN Lj0101 ND1 HI 03 
    8646  
    8647 Ignored bad PDB record found on line 3 
    8648 LINK ZN ZN Lj0101 SG CY 01 
    8649  
    8650 Ignored bad PDB record found on line 4 
    8651 LINK ZN ZN Lj0101 SG CY 01 
    8652  
    8653 Ignored bad PDB record found on line 5 
    8654 LINK ZN ZN Lj0101 SG CY 02 
    8655  
    8656 Ignored bad PDB record found on line 6 
    8657 LINK ZN ZN Le0201 SG CY 04 
    8658  
    8659 3 messages similar to the above omitted 
    8660 Cannot find LINK/SSBOND residue THR (1033509) 
    8661 Cannot find LINK/SSBOND residue ZN (567641) 
    8662  
    8663 Chain information for ys-I1a3 #1 
    8664 --- 
    8665 Chain | Description 
    8666 6 | No description available 
    8667 B | No description available 
    8668 C | No description available 
    8669 D | No description available 
    8670 E | No description available 
    8671 F | No description available 
    8672 G | No description available 
    8673 H | No description available 
    8674 I | No description available 
    8675 J | No description available 
    8676 K | No description available 
    8677 L | No description available 
    8678 M | No description available 
    8679 N | No description available 
    8680 O | No description available 
    8681 P | No description available 
    8682 Q | No description available 
    8683 R | No description available 
    8684 S | No description available 
    8685 T | No description available 
    8686 U | No description available 
    8687 p | No description available 
    8688 v | No description available 
    8689 w | No description available 
    8690 x | No description available 
    8691 y | No description available 
    8692  
    8693 
    8694 > rename #1 id #33.3
    8695 
    8696 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1a*.mrc name ys-I1a
    8697 
    8698 Opened ys-I1a as #1, grid size 512,512,512, pixel 0.826, shown at level 3.09,
    8699 step 2, values float32 
    8700 
    8701 > rename #1 id #33.1
    8702 
    8703 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb name
    8704 > ys-I1b5
    8705 
    8706 Summary of feedback from opening
    8707 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb 
    8708 --- 
    8709 warnings | Ignored bad PDB record found on line 2 
    8710 LINK ZN ZN Lj0101 ND1 HI 03 
    8711  
    8712 Ignored bad PDB record found on line 3 
    8713 LINK ZN ZN Lj0101 SG CY 01 
    8714  
    8715 Ignored bad PDB record found on line 4 
    8716 LINK ZN ZN Lj0101 SG CY 01 
    8717  
    8718 Ignored bad PDB record found on line 5 
    8719 LINK ZN ZN Lj0101 SG CY 02 
    8720  
    8721 Ignored bad PDB record found on line 6 
    8722 LINK ZN ZN Le0201 SG CY 04 
    8723  
    8724 3 messages similar to the above omitted 
    8725 Cannot find LINK/SSBOND residue THR (1033509) 
    8726 Cannot find LINK/SSBOND residue ZN (567641) 
    8727  
    8728 Chain information for ys-I1b5 #1 
    8729 --- 
    8730 Chain | Description 
    8731 3 | No description available 
    8732 5 | No description available 
    8733 B | No description available 
    8734 C | No description available 
    8735 D | No description available 
    8736 E | No description available 
    8737 F | No description available 
    8738 I | No description available 
    8739 J | No description available 
    8740 K | No description available 
    8741 M | No description available 
    8742 N | No description available 
    8743 O | No description available 
    8744 P | No description available 
    8745 Q | No description available 
    8746 R | No description available 
    8747 S | No description available 
    8748 T | No description available 
    8749 U | No description available 
    8750 V | No description available 
    8751 W | No description available 
    8752 X | No description available 
    8753 Y | No description available 
    8754 a | No description available 
    8755 b | No description available 
    8756 c | No description available 
    8757 d | No description available 
    8758 e | No description available 
    8759 f | No description available 
    8760 g | No description available 
    8761 h | No description available 
    8762 i | No description available 
    8763 j | No description available 
    8764  
    8765 
    8766 > rename #1 id #34.5
    8767 
    8768 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb name
    8769 > ys-I1b3
    8770 
    8771 Summary of feedback from opening
    8772 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb 
    8773 --- 
    8774 warnings | Ignored bad PDB record found on line 2 
    8775 LINK ZN ZN Lj0101 ND1 HI 03 
    8776  
    8777 Ignored bad PDB record found on line 3 
    8778 LINK ZN ZN Lj0101 SG CY 01 
    8779  
    8780 Ignored bad PDB record found on line 4 
    8781 LINK ZN ZN Lj0101 SG CY 01 
    8782  
    8783 Ignored bad PDB record found on line 5 
    8784 LINK ZN ZN Lj0101 SG CY 02 
    8785  
    8786 Ignored bad PDB record found on line 6 
    8787 LINK ZN ZN Le0201 SG CY 04 
    8788  
    8789 3 messages similar to the above omitted 
    8790 Cannot find LINK/SSBOND residue THR (1033509) 
    8791 Cannot find LINK/SSBOND residue ZN (567641) 
    8792  
    8793 Chain information for ys-I1b3 #1 
    8794 --- 
    8795 Chain | Description 
    8796 6 | No description available 
    8797 B | No description available 
    8798 C | No description available 
    8799 D | No description available 
    8800 E | No description available 
    8801 F | No description available 
    8802 G | No description available 
    8803 H | No description available 
    8804 I | No description available 
    8805 J | No description available 
    8806 K | No description available 
    8807 L | No description available 
    8808 M | No description available 
    8809 N | No description available 
    8810 O | No description available 
    8811 P | No description available 
    8812 Q | No description available 
    8813 R | No description available 
    8814 S | No description available 
    8815 T | No description available 
    8816 U | No description available 
    8817 p | No description available 
    8818 v | No description available 
    8819 w | No description available 
    8820 x | No description available 
    8821 y | No description available 
    8822  
    8823 
    8824 > rename #1 id #34.3
    8825 
    8826 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1b*.mrc name ys-I1b
    8827 
    8828 Opened ys-I1b as #1, grid size 512,512,512, pixel 0.826, shown at level 3.09,
    8829 step 2, values float32 
    8830 
    8831 > rename #1 id #34.1
    8832 
    8833 > matchmaker #30.5 to #101 matrix Nucleic bring #30.1#30.3
    8834 
    8835 Parameters 
    8836 --- 
    8837 Chain pairing | bb 
    8838 Alignment algorithm | Needleman-Wunsch 
    8839 Similarity matrix | Nucleic 
    8840 SS fraction | 0.3 
    8841 Gap open (HH/SS/other) | 18/18/6 
    8842 Gap extend | 1 
    8843 SS matrix |  |  | H | S | O 
    8844 ---|---|---|--- 
    8845 H | 6 | -9 | -6 
    8846 S |  | 6 | -6 
    8847 O |  |  | 4 
    8848 Iteration cutoff | 2 
    8849  
    8850 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1a5, chain 3 (#30.5),
    8851 sequence alignment score = 11576.1 
    8852 RMSD between 2631 pruned atom pairs is 0.435 angstroms; (across all 2904
    8853 pairs: 4.260) 
    8854  
    8855 
    8856 > matchmaker #31.5 to #101 matrix Nucleic bring #31.1#31.3
    8857 
    8858 Parameters 
    8859 --- 
    8860 Chain pairing | bb 
    8861 Alignment algorithm | Needleman-Wunsch 
    8862 Similarity matrix | Nucleic 
    8863 SS fraction | 0.3 
    8864 Gap open (HH/SS/other) | 18/18/6 
    8865 Gap extend | 1 
    8866 SS matrix |  |  | H | S | O 
    8867 ---|---|---|--- 
    8868 H | 6 | -9 | -6 
    8869 S |  | 6 | -6 
    8870 O |  |  | 4 
    8871 Iteration cutoff | 2 
    8872  
    8873 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1b5, chain 3 (#31.5),
    8874 sequence alignment score = 11576.1 
    8875 RMSD between 2629 pruned atom pairs is 0.438 angstroms; (across all 2904
    8876 pairs: 4.264) 
    8877  
    8878 
    8879 > matchmaker #32.5 to #101 matrix Nucleic bring #32.1#32.3
    8880 
    8881 Parameters 
    8882 --- 
    8883 Chain pairing | bb 
    8884 Alignment algorithm | Needleman-Wunsch 
    8885 Similarity matrix | Nucleic 
    8886 SS fraction | 0.3 
    8887 Gap open (HH/SS/other) | 18/18/6 
    8888 Gap extend | 1 
    8889 SS matrix |  |  | H | S | O 
    8890 ---|---|---|--- 
    8891 H | 6 | -9 | -6 
    8892 S |  | 6 | -6 
    8893 O |  |  | 4 
    8894 Iteration cutoff | 2 
    8895  
    8896 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1c5, chain 3 (#32.5),
    8897 sequence alignment score = 11576.1 
    8898 RMSD between 2600 pruned atom pairs is 0.428 angstroms; (across all 2904
    8899 pairs: 4.256) 
    8900  
    8901 
    8902 > matchmaker #33.5 to #101 matrix Nucleic bring #33.1#33.3
    8903 
    8904 Parameters 
    8905 --- 
    8906 Chain pairing | bb 
    8907 Alignment algorithm | Needleman-Wunsch 
    8908 Similarity matrix | Nucleic 
    8909 SS fraction | 0.3 
    8910 Gap open (HH/SS/other) | 18/18/6 
    8911 Gap extend | 1 
    8912 SS matrix |  |  | H | S | O 
    8913 ---|---|---|--- 
    8914 H | 6 | -9 | -6 
    8915 S |  | 6 | -6 
    8916 O |  |  | 4 
    8917 Iteration cutoff | 2 
    8918  
    8919 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1a5, chain 3 (#33.5),
    8920 sequence alignment score = 11576.1 
    8921 RMSD between 2595 pruned atom pairs is 0.428 angstroms; (across all 2904
    8922 pairs: 4.252) 
    8923  
    8924 
    8925 > matchmaker #34.5 to #101 matrix Nucleic bring #34.1#34.3
    8926 
    8927 Parameters 
    8928 --- 
    8929 Chain pairing | bb 
    8930 Alignment algorithm | Needleman-Wunsch 
    8931 Similarity matrix | Nucleic 
    8932 SS fraction | 0.3 
    8933 Gap open (HH/SS/other) | 18/18/6 
    8934 Gap extend | 1 
    8935 SS matrix |  |  | H | S | O 
    8936 ---|---|---|--- 
    8937 H | 6 | -9 | -6 
    8938 S |  | 6 | -6 
    8939 O |  |  | 4 
    8940 Iteration cutoff | 2 
    8941  
    8942 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1b5, chain 3 (#34.5),
    8943 sequence alignment score = 11576.1 
    8944 RMSD between 2617 pruned atom pairs is 0.432 angstroms; (across all 2904
    8945 pairs: 4.229) 
    8946  
    8947 
    8948 > fitmap #30.1 inMap #100
    8949 
    8950 Fit map ys-H1a in map 4ybb_50Score_3A.mrc using 167516 points 
    8951 correlation = 0.7712, correlation about mean = 0.5068, overlap = 5.636e+05 
    8952 steps = 116, shift = 0.0431, angle = 0.06 degrees 
    8953  
    8954 Position of ys-H1a (#30.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    8955 Matrix rotation and translation 
    8956 -0.16096874 0.07054784 0.98443490 117.93148350 
    8957 -0.09736653 -0.99371151 0.05529186 532.16401993 
    8958 0.98214501 -0.08695075 0.16682549 84.98416227 
    8959 Axis -0.64633407 0.01040498 -0.76298362 
    8960 Axis point 42.26680055 265.56440366 0.00000000 
    8961 Rotation angle (degrees) 173.68249450 
    8962 Shift along axis -135.52750571 
    8963  
    8964 
    8965 > fitmap #30.5 inMap #30.1
    8966 
    8967 Fit molecule ys-H1a5 (#30.5) to map ys-H1a (#30.1) using 92994 atoms 
    8968 average map value = 7.904, steps = 44 
    8969 shifted from previous position = 0.0158 
    8970 rotated from previous position = 0.0583 degrees 
    8971 atoms outside contour = 20674, contour level = 3.1252 
    8972  
    8973 Position of ys-H1a5 (#30.5) relative to ys-H1a (#30.1) coordinates: 
    8974 Matrix rotation and translation 
    8975 1.00000000 0.00007896 0.00002842 -0.01618923 
    8976 -0.00007896 1.00000000 0.00000766 0.01408032 
    8977 -0.00002842 -0.00000766 1.00000000 0.00064511 
    8978 Axis -0.09088428 0.33726732 -0.93701163 
    8979 Axis point 154.32943537 198.57692600 0.00000000 
    8980 Rotation angle (degrees) 0.00482813 
    8981 Shift along axis 0.00561570 
    8982  
    8983 
    8984 > fitmap #30.3 inMap #30.1
    8985 
    8986 Fit molecule ys-H1a3 (#30.3) to map ys-H1a (#30.1) using 60930 atoms 
    8987 average map value = 5.423, steps = 44 
    8988 shifted from previous position = 0.107 
    8989 rotated from previous position = 0.0638 degrees 
    8990 atoms outside contour = 21357, contour level = 3.1252 
    8991  
    8992 Position of ys-H1a3 (#30.3) relative to ys-H1a (#30.1) coordinates: 
    8993 Matrix rotation and translation 
    8994 1.00000000 -0.00007009 0.00004160 -0.00010326 
    8995 0.00007009 1.00000000 -0.00003531 -0.00429301 
    8996 -0.00004159 0.00003531 1.00000000 -0.00573932 
    8997 Axis 0.39752790 0.46828522 0.78910108 
    8998 Axis point 17.28659253 35.84690625 0.00000000 
    8999 Rotation angle (degrees) 0.00508928 
    9000 Shift along axis -0.00658030 
    9001  
    9002 
    9003 > fitmap #31.1 inMap #100
    9004 
    9005 Fit map ys-H1b in map 4ybb_50Score_3A.mrc using 167746 points 
    9006 correlation = 0.7557, correlation about mean = 0.4732, overlap = 4.809e+05 
    9007 steps = 104, shift = 0.0913, angle = 0.169 degrees 
    9008  
    9009 Position of ys-H1b (#31.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    9010 Matrix rotation and translation 
    9011 -0.16402794 0.07279267 0.98376626 117.06968879 
    9012 -0.09958269 -0.99340097 0.05690170 531.99178964 
    9013 0.98141639 -0.08863262 0.17019441 84.62198725 
    9014 Axis -0.64507570 0.01041575 -0.76404768 
    9015 Axis point 42.56283115 265.45365415 0.00000000 
    9016 Rotation angle (degrees) 173.52301718 
    9017 Shift along axis -134.63295191 
    9018  
    9019 
    9020 > fitmap #31.5 inMap #31.1
    9021 
    9022 Fit molecule ys-H1b5 (#31.5) to map ys-H1b (#31.1) using 92994 atoms 
    9023 average map value = 6.419, steps = 48 
    9024 shifted from previous position = 0.0121 
    9025 rotated from previous position = 0.0631 degrees 
    9026 atoms outside contour = 25942, contour level = 3.1558 
    9027  
    9028 Position of ys-H1b5 (#31.5) relative to ys-H1b (#31.1) coordinates: 
    9029 Matrix rotation and translation 
    9030 0.99999984 0.00056889 -0.00006451 -0.12124833 
    9031 -0.00056878 0.99999829 0.00175780 -0.12851585 
    9032 0.00006551 -0.00175777 0.99999845 0.36559707 
    9033 Axis -0.95083394 -0.03516616 -0.30769816 
    9034 Axis point 0.00000000 209.20515420 73.16839244 
    9035 Rotation angle (degrees) 0.10592152 
    9036 Shift along axis 0.00731289 
    9037  
    9038 
    9039 > fitmap #31.3 inMap #31.1
    9040 
    9041 Fit molecule ys-H1b3 (#31.3) to map ys-H1b (#31.1) using 60958 atoms 
    9042 average map value = 4.602, steps = 44 
    9043 shifted from previous position = 0.0971 
    9044 rotated from previous position = 0.114 degrees 
    9045 atoms outside contour = 25030, contour level = 3.1558 
    9046  
    9047 Position of ys-H1b3 (#31.3) relative to ys-H1b (#31.1) coordinates: 
    9048 Matrix rotation and translation 
    9049 0.99999972 -0.00035593 0.00066202 -0.06165935 
    9050 0.00035492 0.99999877 0.00152816 -0.29466909 
    9051 -0.00066256 -0.00152792 0.99999861 0.44538378 
    9052 Axis -0.89731715 0.38891986 0.20871819 
    9053 Axis point 0.00000000 286.71155040 201.62993409 
    9054 Rotation angle (degrees) 0.09756906 
    9055 Shift along axis 0.03368503 
    9056  
    9057 
    9058 > fitmap #32.1 inMap #100
    9059 
    9060 Fit map ys-H1c in map 4ybb_50Score_3A.mrc using 167598 points 
    9061 correlation = 0.7687, correlation about mean = 0.5028, overlap = 5.462e+05 
    9062 steps = 64, shift = 0.174, angle = 0.0444 degrees 
    9063  
    9064 Position of ys-H1c (#32.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    9065 Matrix rotation and translation 
    9066 -0.16402649 0.07085424 0.98390802 117.46660733 
    9067 -0.09904792 -0.99355948 0.05503707 532.18633927 
    9068 0.98147074 -0.08842650 0.16998804 84.56695102 
    9069 Axis -0.64511751 0.01095977 -0.76400477 
    9070 Axis point 42.50698240 265.58065026 0.00000000 
    9071 Rotation angle (degrees) 173.61597695 
    9072 Shift along axis -134.55667780 
    9073  
    9074 
    9075 > fitmap #32.5 inMap #32.1
    9076 
    9077 Fit molecule ys-H1c5 (#32.5) to map ys-H1c (#32.1) using 92992 atoms 
    9078 average map value = 7.486, steps = 36 
    9079 shifted from previous position = 0.0219 
    9080 rotated from previous position = 0.0647 degrees 
    9081 atoms outside contour = 22168, contour level = 3.1136 
    9082  
    9083 Position of ys-H1c5 (#32.5) relative to ys-H1c (#32.1) coordinates: 
    9084 Matrix rotation and translation 
    9085 0.99999983 -0.00057175 0.00006040 0.12367865 
    9086 0.00057186 0.99999823 -0.00179030 0.13731617 
    9087 -0.00005938 0.00179034 0.99999840 -0.36604473 
    9088 Axis 0.95211000 0.03184871 0.30409245 
    9089 Axis point 0.00000000 206.36170644 76.30401858 
    9090 Rotation angle (degrees) 0.10773729 
    9091 Shift along axis 0.01081758 
    9092  
    9093 
    9094 > fitmap #32.3 inMap #32.1
    9095 
    9096 Fit molecule ys-H1c3 (#32.3) to map ys-H1c (#32.1) using 60097 atoms 
    9097 average map value = 5.192, steps = 48 
    9098 shifted from previous position = 0.133 
    9099 rotated from previous position = 0.0654 degrees 
    9100 atoms outside contour = 21804, contour level = 3.1136 
    9101  
    9102 Position of ys-H1c3 (#32.3) relative to ys-H1c (#32.1) coordinates: 
    9103 Matrix rotation and translation 
    9104 0.99999975 0.00002916 -0.00070103 0.13056968 
    9105 -0.00003034 0.99999858 -0.00168673 0.26834816 
    9106 0.00070098 0.00168675 0.99999833 -0.48614194 
    9107 Axis 0.92330390 -0.38372472 -0.01628638 
    9108 Axis point 0.00000000 288.12835311 164.65187972 
    9109 Rotation angle (degrees) 0.10467114 
    9110 Shift along axis 0.02550116 
    9111  
    9112 
    9113 > fitmap #33.1 inMap #100
    9114 
    9115 Fit map ys-I1a in map 4ybb_50Score_3A.mrc using 167703 points 
    9116 correlation = 0.7667, correlation about mean = 0.498, overlap = 5.302e+05 
    9117 steps = 104, shift = 0.0538, angle = 0.0755 degrees 
    9118  
    9119 Position of ys-I1a (#33.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    9120 Matrix rotation and translation 
    9121 -0.16092884 0.07096607 0.98441136 117.88246252 
    9122 -0.09669854 -0.99374659 0.05583104 532.06291528 
    9123 0.98221754 -0.08620632 0.16678480 84.75523562 
    9124 Axis -0.64635360 0.00998316 -0.76297271 
    9125 Axis point 42.30362323 265.49282475 0.00000000 
    9126 Rotation angle (degrees) 173.69183881 
    9127 Shift along axis -135.54801612 
    9128  
    9129 
    9130 > fitmap #33.5 inMap #33.1
    9131 
    9132 Fit molecule ys-I1a5 (#33.5) to map ys-I1a (#33.1) using 92992 atoms 
    9133 average map value = 7.334, steps = 36 
    9134 shifted from previous position = 0.0203 
    9135 rotated from previous position = 0.0746 degrees 
    9136 atoms outside contour = 22072, contour level = 3.0948 
    9137  
    9138 Position of ys-I1a5 (#33.5) relative to ys-I1a (#33.1) coordinates: 
    9139 Matrix rotation and translation 
    9140 1.00000000 0.00006785 0.00002158 -0.01571402 
    9141 -0.00006785 1.00000000 0.00000247 0.01394877 
    9142 -0.00002158 -0.00000247 1.00000000 0.00028445 
    9143 Axis -0.03462129 0.30294566 -0.95237875 
    9144 Axis point 185.47857319 229.29962927 0.00000000 
    9145 Rotation angle (degrees) 0.00408210 
    9146 Shift along axis 0.00449885 
    9147  
    9148 
    9149 > fitmap #33.3 inMap #33.1
    9150 
    9151 Fit molecule ys-I1a3 (#33.3) to map ys-I1a (#33.1) using 61025 atoms 
    9152 average map value = 5.134, steps = 60 
    9153 shifted from previous position = 0.135 
    9154 rotated from previous position = 0.08 degrees 
    9155 atoms outside contour = 22330, contour level = 3.0948 
    9156  
    9157 Position of ys-I1a3 (#33.3) relative to ys-I1a (#33.1) coordinates: 
    9158 Matrix rotation and translation 
    9159 0.99999998 -0.00017787 0.00003522 0.02444707 
    9160 0.00017787 0.99999998 -0.00002049 -0.02796573 
    9161 -0.00003522 0.00002050 1.00000000 0.00287850 
    9162 Axis 0.11232351 0.19300468 0.97474747 
    9163 Axis point 157.40269238 137.32963987 0.00000000 
    9164 Rotation angle (degrees) 0.01045538 
    9165 Shift along axis 0.00015427 
    9166  
    9167 
    9168 > fitmap #34.1 inMap #100
    9169 
    9170 Fit map ys-I1b in map 4ybb_50Score_3A.mrc using 167622 points 
    9171 correlation = 0.7694, correlation about mean = 0.5021, overlap = 5.244e+05 
    9172 steps = 48, shift = 0.0515, angle = 0.0695 degrees 
    9173  
    9174 Position of ys-I1b (#34.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    9175 Matrix rotation and translation 
    9176 -0.15974764 0.06847542 0.98478008 118.03715648 
    9177 -0.09853124 -0.99371554 0.05311334 533.28558991 
    9178 0.98222822 -0.08854688 0.16549068 85.54764208 
    9179 Axis -0.64682093 0.01165178 -0.76255290 
    9180 Axis point 41.99640823 266.19892413 0.00000000 
    9181 Rotation angle (degrees) 173.71321980 
    9182 Shift along axis -135.36977768 
    9183  
    9184 
    9185 > fitmap #34.5 inMap #34.1
    9186 
    9187 Fit molecule ys-I1b5 (#34.5) to map ys-I1b (#34.1) using 92992 atoms 
    9188 average map value = 7.158, steps = 44 
    9189 shifted from previous position = 0.014 
    9190 rotated from previous position = 0.0687 degrees 
    9191 atoms outside contour = 22660, contour level = 3.0873 
    9192  
    9193 Position of ys-I1b5 (#34.5) relative to ys-I1b (#34.1) coordinates: 
    9194 Matrix rotation and translation 
    9195 1.00000000 -0.00003647 0.00000880 0.00851051 
    9196 0.00003647 1.00000000 0.00003193 -0.01982466 
    9197 -0.00000880 -0.00003193 1.00000000 0.00942241 
    9198 Axis -0.64817747 0.17854187 0.74026263 
    9199 Axis point 533.41299576 196.36486997 0.00000000 
    9200 Rotation angle (degrees) 0.00282273 
    9201 Shift along axis -0.00208080 
    9202  
    9203 
    9204 > fitmap #34.3 inMap #34.1
    9205 
    9206 Fit molecule ys-I1b3 (#34.3) to map ys-I1b (#34.1) using 61064 atoms 
    9207 average map value = 4.951, steps = 48 
    9208 shifted from previous position = 0.125 
    9209 rotated from previous position = 0.0753 degrees 
    9210 atoms outside contour = 23372, contour level = 3.0873 
    9211  
    9212 Position of ys-I1b3 (#34.3) relative to ys-I1b (#34.1) coordinates: 
    9213 Matrix rotation and translation 
    9214 0.99999999 -0.00013951 0.00000938 0.01771739 
    9215 0.00013951 0.99999999 -0.00004705 -0.01825677 
    9216 -0.00000937 0.00004706 1.00000000 -0.00740427 
    9217 Axis 0.31895163 0.06356485 0.94563702 
    9218 Axis point 129.73074307 132.73108386 0.00000000 
    9219 Rotation angle (degrees) 0.00845277 
    9220 Shift along axis -0.00251125 
    9221  
    9222 
    9223 > rename #30 ys-H1a
    9224 
    9225 > rename #31 ys-H1b
    9226 
    9227 > rename #32 ys-H1c
    9228 
    9229 > rename #33 ys-I1a
    9230 
    9231 > rename #34 ys-I1b
    9232 
    9233 executed 70S_open_ys.cxc 
    9234 
    9235 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_arg.cxc
    9236 
    9237 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/arg_50S.pdb name
    9238 > arg5
    9239 
    9240 Chain information for arg5 #1 
    9241 --- 
    9242 Chain | Description 
    9243 3 | No description available 
    9244 5 | No description available 
    9245 A | No description available 
    9246 B | No description available 
    9247 C | No description available 
    9248 D | No description available 
    9249 E | No description available 
    9250 F | No description available 
    9251 I | No description available 
    9252 J | No description available 
    9253 K | No description available 
    9254 M | No description available 
    9255 N | No description available 
    9256 O | No description available 
    9257 P | No description available 
    9258 Q | No description available 
    9259 R | No description available 
    9260 S | No description available 
    9261 T | No description available 
    9262 U | No description available 
    9263 V | No description available 
    9264 W | No description available 
    9265 X | No description available 
    9266 Y | No description available 
    9267 a | No description available 
    9268 b | No description available 
    9269 c | No description available 
    9270 d | No description available 
    9271 e | No description available 
    9272 f | No description available 
    9273 g | No description available 
    9274 h | No description available 
    9275 i | No description available 
    9276 j | No description available 
    9277  
    9278 
    9279 > rename #1 id #20.5
    9280 
    9281 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/arg_30S.pdb name
    9282 > arg3
    9283 
    9284 Chain information for arg3 #1 
    9285 --- 
    9286 Chain | Description 
    9287 6 | No description available 
    9288 B | No description available 
    9289 C | No description available 
    9290 D | No description available 
    9291 E | No description available 
    9292 F | No description available 
    9293 G | No description available 
    9294 H | No description available 
    9295 I | No description available 
    9296 J | No description available 
    9297 K | No description available 
    9298 L | No description available 
    9299 M | No description available 
    9300 N | No description available 
    9301 O | No description available 
    9302 P | No description available 
    9303 Q | No description available 
    9304 R | No description available 
    9305 S | No description available 
    9306 T | No description available 
    9307 U | No description available 
    9308 v | No description available 
    9309 w | No description available 
    9310 x | No description available 
    9311 y | No description available 
    9312  
    9313 
    9314 > rename #1 id #20.3
    9315 
    9316 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/arg_*.mrc name arg
    9317 
    9318 Opened arg as #1, grid size 380,380,380, pixel 1.05, shown at level 4.05, step
    9319 2, values float32 
    9320 
    9321 > rename #1 id #20.1
    9322 
    9323 > rename #20 argb
    9324 
    9325 > matchmaker #20.5 to #101 matrix Nucleic bring #20.1#20.3
    9326 
    9327 Parameters 
    9328 --- 
    9329 Chain pairing | bb 
    9330 Alignment algorithm | Needleman-Wunsch 
    9331 Similarity matrix | Nucleic 
    9332 SS fraction | 0.3 
    9333 Gap open (HH/SS/other) | 18/18/6 
    9334 Gap extend | 1 
    9335 SS matrix |  |  | H | S | O 
    9336 ---|---|---|--- 
    9337 H | 6 | -9 | -6 
    9338 S |  | 6 | -6 
    9339 O |  |  | 4 
    9340 Iteration cutoff | 2 
    9341  
    9342 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with arg5, chain 3 (#20.5),
    9343 sequence alignment score = 11567.9 
    9344 RMSD between 2713 pruned atom pairs is 0.426 angstroms; (across all 2903
    9345 pairs: 3.446) 
    9346  
    9347 
    9348 > fitmap #20.1 inMap #100
    9349 
    9350 Fit map arg in map 4ybb_50Score_3A.mrc using 68379 points 
    9351 correlation = 0.7998, correlation about mean = 0.5595, overlap = 2.858e+05 
    9352 steps = 48, shift = 0.0198, angle = 0.0465 degrees 
    9353  
    9354 Position of arg (#20.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    9355 Matrix rotation and translation 
    9356 0.04335132 -0.67171102 -0.73954376 580.56014922 
    9357 0.71962017 -0.49248421 0.48949578 169.85732478 
    9358 -0.69301333 -0.55341089 0.46202696 467.33682018 
    9359 Axis -0.59956755 -0.02675036 0.79987697 
    9360 Axis point 403.39737183 308.69128461 0.00000000 
    9361 Rotation angle (degrees) 119.57437645 
    9362 Shift along axis 21.18318896 
    9363  
    9364 
    9365 > fitmap #20.5 inMap #20.1
    9366 
    9367 Fit molecule arg5 (#20.5) to map arg (#20.1) using 93932 atoms 
    9368 average map value = 8.028, steps = 40 
    9369 shifted from previous position = 0.028 
    9370 rotated from previous position = 0.0467 degrees 
    9371 atoms outside contour = 40883, contour level = 4.0546 
    9372  
    9373 Position of arg5 (#20.5) relative to arg (#20.1) coordinates: 
    9374 Matrix rotation and translation 
    9375 1.00000000 0.00000583 0.00002491 -0.00204004 
    9376 -0.00000583 1.00000000 0.00005404 -0.01191715 
    9377 -0.00002491 -0.00005404 1.00000000 0.02173238 
    9378 Axis -0.90382996 0.41664235 -0.09747076 
    9379 Axis point 0.00000000 392.68816757 180.13481166 
    9380 Rotation angle (degrees) 0.00342579 
    9381 Shift along axis -0.00523961 
    9382  
    9383 
    9384 > fitmap #20.3 inMap #20.1
    9385 
    9386 Fit molecule arg3 (#20.3) to map arg (#20.1) using 60797 atoms 
    9387 average map value = 4.762, steps = 44 
    9388 shifted from previous position = 0.0202 
    9389 rotated from previous position = 0.0354 degrees 
    9390 atoms outside contour = 42480, contour level = 4.0546 
    9391  
    9392 Position of arg3 (#20.3) relative to arg (#20.1) coordinates: 
    9393 Matrix rotation and translation 
    9394 0.99999999 -0.00001781 0.00015102 -0.03079729 
    9395 0.00001784 0.99999998 -0.00018128 0.03779708 
    9396 -0.00015102 0.00018128 0.99999997 0.00249277 
    9397 Axis 0.76612779 0.63825790 0.07533296 
    9398 Axis point 0.00000000 -13.42131942 205.98134486 
    9399 Rotation angle (degrees) 0.01355702 
    9400 Shift along axis 0.00071742 
    9401  
    9402 executed 70S_open_arg.cxc 
    9403 
    9404 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_h2.cxc
    9405 
    9406 > open
    9407 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/apo_H2*local*.mrc
    9408 > name hy2
    9409 
    9410 Opened hy2 as #1, grid size 576,576,576, pixel 1.06, shown at level 0.583,
    9411 step 4, values float32 
    9412 
    9413 > rename #1 id #11.1
    9414 
    9415 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h2_50S.pdb name
    9416 > hy25
    9417 
    9418 Chain information for hy25 #1 
    9419 --- 
    9420 Chain | Description 
    9421 3 | No description available 
    9422 5 | No description available 
    9423 B | No description available 
    9424 C | No description available 
    9425 D | No description available 
    9426 E | No description available 
    9427 F | No description available 
    9428 I | No description available 
    9429 M | No description available 
    9430 N | No description available 
    9431 O | No description available 
    9432 P | No description available 
    9433 Q | No description available 
    9434 R | No description available 
    9435 S | No description available 
    9436 T | No description available 
    9437 U | No description available 
    9438 V | No description available 
    9439 W | No description available 
    9440 X | No description available 
    9441 Y | No description available 
    9442 a | No description available 
    9443 b | No description available 
    9444 c | No description available 
    9445 d | No description available 
    9446 e | No description available 
    9447 f | No description available 
    9448 g | No description available 
    9449 h | No description available 
    9450 i | No description available 
    9451 j | No description available 
    9452  
    9453 
    9454 > rename #1 id #11.5
    9455 
    9456 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h2_30S.pdb name
    9457 > hy23
    9458 
    9459 Chain information for hy23 #1 
    9460 --- 
    9461 Chain | Description 
    9462 6 | No description available 
    9463 B | No description available 
    9464 C | No description available 
    9465 D | No description available 
    9466 E | No description available 
    9467 F | No description available 
    9468 G | No description available 
    9469 H | No description available 
    9470 I | No description available 
    9471 J | No description available 
    9472 K | No description available 
    9473 L | No description available 
    9474 M | No description available 
    9475 N | No description available 
    9476 O | No description available 
    9477 P | No description available 
    9478 Q | No description available 
    9479 R | No description available 
    9480 S | No description available 
    9481 T | No description available 
    9482 U | No description available 
    9483 p | No description available 
    9484 v | No description available 
    9485 w | No description available 
    9486 y | No description available 
    9487  
    9488 
    9489 > rename #1 id #11.3
    9490 
    9491 > matchmaker #11.5 to #101 matrix Nucleic bring #11.1#11.3
    9492 
    9493 Parameters 
    9494 --- 
    9495 Chain pairing | bb 
    9496 Alignment algorithm | Needleman-Wunsch 
    9497 Similarity matrix | Nucleic 
    9498 SS fraction | 0.3 
    9499 Gap open (HH/SS/other) | 18/18/6 
    9500 Gap extend | 1 
    9501 SS matrix |  |  | H | S | O 
    9502 ---|---|---|--- 
    9503 H | 6 | -9 | -6 
    9504 S |  | 6 | -6 
    9505 O |  |  | 4 
    9506 Iteration cutoff | 2 
    9507  
    9508 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with hy25, chain 3 (#11.5),
    9509 sequence alignment score = 11561.3 
    9510 RMSD between 2586 pruned atom pairs is 0.406 angstroms; (across all 2901
    9511 pairs: 4.609) 
    9512  
    9513 
    9514 > fitmap #11.1 inMap #100
    9515 
    9516 Fit map hy2 in map 4ybb_50Score_3A.mrc using 29804 points 
    9517 correlation = 0.7242, correlation about mean = 0.6417, overlap = 7.267e+04 
    9518 steps = 48, shift = 0.0744, angle = 0.0573 degrees 
    9519  
    9520 Position of hy2 (#11.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    9521 Matrix rotation and translation 
    9522 1.00000000 0.00003602 -0.00001029 0.01316792 
    9523 -0.00003602 0.99999999 0.00010657 -0.03440932 
    9524 0.00001030 -0.00010657 0.99999999 0.02381061 
    9525 Axis -0.94340756 -0.09113844 -0.31886669 
    9526 Axis point 0.00000000 172.91008810 337.33392045 
    9527 Rotation angle (degrees) 0.00647212 
    9528 Shift along axis -0.01687912 
    9529  
    9530 
    9531 > fitmap #11.5 inMap #11.1
    9532 
    9533 Fit molecule hy25 (#11.5) to map hy2 (#11.1) using 90870 atoms 
    9534 average map value = 14.68, steps = 28 
    9535 shifted from previous position = 0.0514 
    9536 rotated from previous position = 0.0613 degrees 
    9537 atoms outside contour = 33730, contour level = 0.58265 
    9538  
    9539 Position of hy25 (#11.5) relative to hy2 (#11.1) coordinates: 
    9540 Matrix rotation and translation 
    9541 0.99999996 0.00022036 -0.00015998 -0.00668301 
    9542 -0.00022039 0.99999996 -0.00017126 0.14091770 
    9543 0.00015994 0.00017129 0.99999997 -0.12061124 
    9544 Axis 0.53241836 -0.49723466 -0.68504627 
    9545 Axis point 659.69138147 52.17592242 0.00000000 
    9546 Rotation angle (degrees) 0.01843178 
    9547 Shift along axis 0.00899696 
    9548  
    9549 
    9550 > fitmap #11.3 inMap #11.1
    9551 
    9552 Fit molecule hy23 (#11.3) to map hy2 (#11.1) using 55387 atoms 
    9553 average map value = 9.621, steps = 28 
    9554 shifted from previous position = 0.132 
    9555 rotated from previous position = 0.0639 degrees 
    9556 atoms outside contour = 17421, contour level = 0.58265 
    9557  
    9558 Position of hy23 (#11.3) relative to hy2 (#11.1) coordinates: 
    9559 Matrix rotation and translation 
    9560 0.99999999 0.00015557 -0.00006781 -0.02334093 
    9561 -0.00015559 0.99999993 -0.00034415 0.15409237 
    9562 0.00006776 0.00034416 0.99999994 -0.13799206 
    9563 Axis 0.89688265 -0.17664932 -0.40545842 
    9564 Axis point 0.00000000 391.85336663 451.67273844 
    9565 Rotation angle (degrees) 0.02198552 
    9566 Shift along axis 0.00779566 
    9567  
    9568 executed 70S_open_h2.cxc 
    9569 executed 70S_startup_gtpys-all.cxc 
    9570 
    9571 > open
    9572 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/gtpys_translocation.cxc
    9573 
    9574 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
    9575 
    9576 > name atomods #*.3|#*.5
    9577 
    9578 > name emmaps #*.1|#*.7|#*.8|#*.9
    9579 
    9580 > name lsu #*.5
    9581 
    9582 > name lsumap #*.8
    9583 
    9584 > name ssu #*.3
    9585 
    9586 > name ssumap #*.7
    9587 
    9588 > name ligmap #*.9
    9589 
    9590 > name rna /y,v,w,3,6,5
    9591 
    9592 > name r23s /3
    9593 
    9594 > name r16s /6
    9595 
    9596 > name r5s /5
    9597 
    9598 > name pt /y
    9599 
    9600 > name dt /v
    9601 
    9602 > name efg /x
    9603 
    9604 > name pep /p
    9605 
    9606 > name mrna /w
    9607 
    9608 > name GSP :GSP
    9609 
    9610 > name GDP :GDP
    9611 
    9612 > name GTP :GTP
    9613 
    9614 > name ntide :GTP|:GDP|:GSP
    9615 
    9616 > name spc :SCM
    9617 
    9618 > name fua :FUA
    9619 
    9620 > name par :PAR
    9621 
    9622 > name argb :LIG
    9623 
    9624 > name drugs argb|par|fua|spc
    9625 
    9626 > name D1 /x:start-293
    9627 
    9628 > name D2 /x:294-410
    9629 
    9630 > name D3 /x:411-489
    9631 
    9632 > name D4 /x:490-612
    9633 
    9634 > name D5 /x:613-end
    9635 
    9636 > name sw1 /x:38-65
    9637 
    9638 > name sw2 /x:89-108
    9639 
    9640 > name pl /x:18-25
    9641 
    9642 > name nkxd /x:142-146
    9643 
    9644 > name mg /x:MG
    9645 
    9646 > name trna /y,v
    9647 
    9648 > name anticodon /y,v:34-36
    9649 
    9650 > name antiplus /y,v:32-38
    9651 
    9652 > name cca /y,v:74-76
    9653 
    9654 > name astem /y,v:1-7,66-73
    9655 
    9656 > name darm /y,v:8-25
    9657 
    9658 > name aarm /y,v:26-43
    9659 
    9660 > name varm /y,v:44-48
    9661 
    9662 > name tarm /y,v:49-65
    9663 
    9664 > name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
    9665 
    9666 > name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
    9667 
    9668 > name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
    9669 
    9670 > name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
    9671 
    9672 > name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
    9673 
    9674 > name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
    9675 
    9676 > name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
    9677 
    9678 > name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
    9679 
    9680 > name h8 /6:144-178
    9681 
    9682 > name h14 /6:339-350
    9683 
    9684 > name h18 /6:511-540
    9685 
    9686 > name h23 /6:674-716
    9687 
    9688 > name h24 /6:769-810
    9689 
    9690 > name h27 /6:894-905
    9691 
    9692 > name h28 /6:921-937,1379-1400
    9693 
    9694 > name h29 /6:938-943,1337-1346
    9695 
    9696 > name h30 /6:945-955,1225-1235
    9697 
    9698 > name h31 /6:956-975
    9699 
    9700 > name h32 /6:984-990,1215-1221
    9701 
    9702 > name h34 /6:1045-1065,1188-1211
    9703 
    9704 > name h35 /6:1066-1073,1102-1110
    9705 
    9706 > name h36 /6:1074-1083
    9707 
    9708 > name h44 /6:1401-1502
    9709 
    9710 > name h45 /6:1506-1529
    9711 
    9712 > name aploop /6:956-959
    9713 
    9714 > name term16S /6:1503-end
    9715 
    9716 > name aphelix /6:1228-1230
    9717 
    9718 > name us3 #*.3/C
    9719 
    9720 > name us5 #*.3/E
    9721 
    9722 > name us7 #*.3/G
    9723 
    9724 > name us9 #*.3/I
    9725 
    9726 > name us11 #*.3/K
    9727 
    9728 > name us12 #*.3/L
    9729 
    9730 > name us13 #*.3/M
    9731 
    9732 > name us14 #*.3/N
    9733 
    9734 > name us15 #*.3/O
    9735 
    9736 > name us9-130 #*.3/I:130
    9737 
    9738 > name l1stalk /3:2097-2191
    9739 
    9740 > name srl /3:2652-2668
    9741 
    9742 > name H68 /3:1832-1906
    9743 
    9744 > name H69 /3:1907-1924
    9745 
    9746 > name H95 /3:2647-2673
    9747 
    9748 > name ul2 #*.5/B
    9749 
    9750 > name ul5 #*.5/E
    9751 
    9752 > name ul14 #*.5/N
    9753 
    9754 > name ul19 #*.5/S
    9755 
    9756 > name ul31 #*.5/e
    9757 
    9758 executed 70S_assign.cxc 
    9759 
    9760 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
    9761 
    9762 > alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
    9763 
    9764 > alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
    9765 
    9766 > alias cylinders cartoon style protein modeh tube rad 2 sides 24;
    9767 
    9768 > alias licorice car style protein modeh default arrows f xsect oval width 1
    9769 > thick 1;
    9770 
    9771 > dssp
    9772 
    9773 > windowsize 1000 1000
    9774 
    9775 > set bgColor white
    9776 
    9777 > lighting full
    9778 
    9779 > set silhouettes true
    9780 
    9781 > set silhouetteWidth 1.7
    9782 
    9783 > set silhouettes true
    9784 
    9785 > set silhouetteDepthJump 0.02
    9786 
    9787 > cartoon style width 2.5
    9788 
    9789 > size atomRadius 2
    9790 
    9791 Changed 1915316 atom radii 
    9792 
    9793 > nucleotides fill
    9794 
    9795 > size ions atomRadius 1.6
    9796 
    9797 Changed 34 atom radii 
    9798 
    9799 > size stickRadius 0.1
    9800 
    9801 Changed 2070233 bond radii 
    9802 
    9803 > style stick ringFill thin
    9804 
    9805 Changed 1915316 atom styles, 145232 residue ring styles 
    9806 
    9807 > show ribbons
    9808 
    9809 > hide H
    9810 
    9811 > hide :HOH
    9812 
    9813 > hide target a
    9814 
    9815 > show nucleic target a
    9816 
    9817 > show drugs target a
    9818 
    9819 > style drugs ball
    9820 
    9821 Changed 166 atom styles 
    9822 
    9823 > nucrib
    9824 
    9825 > graphics selection color black
    9826 
    9827 > volume emmaps style surface step 1 level 4
    9828 
    9829 > surface dust emmaps size 3
    9830 
    9831 > volume surfaceSmoothing true
    9832 
    9833 > cartoon tether trna shape cone opacity 1
    9834 
    9835 > dssp
    9836 
    9837 executed 70S_display.cxc 
    9838 
    9839 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
    9840 
    9841 > color name efg-t 100,0,0,50
    9842 
    9843 Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    9844 
    9845  
    9846 
    9847 > color name sw1-t 100,92,0,50
    9848 
    9849 Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    9850 
    9851  
    9852 
    9853 > color name sw2-t 68,81,0,50
    9854 
    9855 Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    9856 
    9857  
    9858 
    9859 > color name pl-t 23,59,0,50
    9860 
    9861 Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    9862 
    9863  
    9864 
    9865 > color name d1-t 100,18,4,50
    9866 
    9867 Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
    9868 
    9869  
    9870 
    9871 > color name d2-t 100,40,4,50
    9872 
    9873 Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    9874 
    9875  
    9876 
    9877 > color name d3-t 100,27,36,50
    9878 
    9879 Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
    9880 
    9881  
    9882 
    9883 > color name d4-t 80,0,23,50
    9884 
    9885 Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
    9886 
    9887  
    9888 
    9889 > color name d5-t 100,60,4,50
    9890 
    9891 Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
    9892 
    9893  
    9894 
    9895 > color name fa-t 100,90,4,50
    9896 
    9897 Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    9898 
    9899  
    9900 
    9901 > color name gtp-t 45,53,60,50
    9902 
    9903 Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
    9904 
    9905  
    9906 
    9907 > color name mg-t 1,39,16,50
    9908 
    9909 Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
    9910 
    9911  
    9912 
    9913 > color name spc-t 100,0,0,50
    9914 
    9915 Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    9916 
    9917  
    9918 
    9919 > color name argb-t 50,0,50,50
    9920 
    9921 Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
    9922 
    9923  
    9924 
    9925 > color name g-1t 98,42,30,50
    9926 
    9927 Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
    9928 
    9929  
    9930 
    9931 > color name g-2t 95,35,25,50
    9932 
    9933 Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
    9934 
    9935  
    9936 
    9937 > color name g-3t 92,28,20,50
    9938 
    9939 Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
    9940 
    9941  
    9942 
    9943 > color name g-4t 89,21,15,50
    9944 
    9945 Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
    9946 
    9947  
    9948 
    9949 > color name g-5t 86,14,10,50
    9950 
    9951 Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
    9952 
    9953  
    9954 
    9955 > color name g-6t 83,7,5,50
    9956 
    9957 Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
    9958 
    9959  
    9960 
    9961 > color name g-7t 80,0,0,50
    9962 
    9963 Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
    9964 
    9965  
    9966 
    9967 > color name p-t 40,60,2,50
    9968 
    9969 Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
    9970 
    9971  
    9972 
    9973 > color name p-c 40,60,2,100
    9974 
    9975 Color 'p-c' is opaque: rgb(40%, 60%, 2%) hex: #669905
    9976 
    9977  
    9978 
    9979 > color name p-1t 4,34,1,50
    9980 
    9981 Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
    9982 
    9983  
    9984 
    9985 > color name p-2t 12,39,1,50
    9986 
    9987 Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
    9988 
    9989  
    9990 
    9991 > color name p-3t 20,44,1,50
    9992 
    9993 Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
    9994 
    9995  
    9996 
    9997 > color name p-4t 28,49,1,50
    9998 
    9999 Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
    10000 
    10001  
    10002 
    10003 > color name p-5t 36,54,2,50
    10004 
    10005 Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
    10006 
    10007  
    10008 
    10009 > color name p-6t 44,59,2,50
    10010 
    10011 Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
    10012 
    10013  
    10014 
    10015 > color name p-7t 52,64,2,50
    10016 
    10017 Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
    10018 
    10019  
    10020 
    10021 > color name p-8t 60,69,2,50
    10022 
    10023 Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
    10024 
    10025  
    10026 
    10027 > color name p-9t 68,74,3,50
    10028 
    10029 Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
    10030 
    10031  
    10032 
    10033 > color name p-10t 76,79,3,50
    10034 
    10035 Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
    10036 
    10037  
    10038 
    10039 > color name p-11t 84,84,3,50
    10040 
    10041 Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
    10042 
    10043  
    10044 
    10045 > color name d-t 100,75,4,50
    10046 
    10047 Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
    10048 
    10049  
    10050 
    10051 > color name d-c 100,75,4,100
    10052 
    10053 Color 'd-c' is opaque: rgb(100%, 75%, 4%) hex: #ffbf0a
    10054 
    10055  
    10056 
    10057 > color name d-1t 100,100,4,50
    10058 
    10059 Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
    10060 
    10061  
    10062 
    10063 > color name d-2t 100,93,4,50
    10064 
    10065 Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
    10066 
    10067  
    10068 
    10069 > color name d-3t 100,86,4,50
    10070 
    10071 Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
    10072 
    10073  
    10074 
    10075 > color name d-4t 100,79,4,50
    10076 
    10077 Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
    10078 
    10079  
    10080 
    10081 > color name d-5t 100,72,4,50
    10082 
    10083 Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
    10084 
    10085  
    10086 
    10087 > color name d-6t 100,65,4,50
    10088 
    10089 Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
    10090 
    10091  
    10092 
    10093 > color name d-7t 100,58,4,50
    10094 
    10095 Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
    10096 
    10097  
    10098 
    10099 > color name d-8t 100,51,4,50
    10100 
    10101 Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
    10102 
    10103  
    10104 
    10105 > color name d-9t 100,44,4,50
    10106 
    10107 Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
    10108 
    10109  
    10110 
    10111 > color name d-10t 100,37,4,50
    10112 
    10113 Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
    10114 
    10115  
    10116 
    10117 > color name d-11t 100,30,4,50
    10118 
    10119 Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
    10120 
    10121  
    10122 
    10123 > color name m-t 95,43,62,50
    10124 
    10125 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    10126 
    10127  
    10128 
    10129 > color name m-c 95,43,62,100
    10130 
    10131 Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
    10132 
    10133  
    10134 
    10135 > color name m-1t 100,80,90,50
    10136 
    10137 Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
    10138 
    10139  
    10140 
    10141 > color name m-2t 98,76,87,50
    10142 
    10143 Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
    10144 
    10145  
    10146 
    10147 > color name m-3t 96,72,84,50
    10148 
    10149 Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
    10150 
    10151  
    10152 
    10153 > color name m-4t 94,68,81,50
    10154 
    10155 Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
    10156 
    10157  
    10158 
    10159 > color name m-5t 92,64,78,50
    10160 
    10161 Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
    10162 
    10163  
    10164 
    10165 > color name m-6t 90,60,75,50
    10166 
    10167 Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
    10168 
    10169  
    10170 
    10171 > color name m-7t 88,56,72,50
    10172 
    10173 Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
    10174 
    10175  
    10176 
    10177 > color name m-8t 86,52,69,50
    10178 
    10179 Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
    10180 
    10181  
    10182 
    10183 > color name m-9t 84,48,66,50
    10184 
    10185 Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
    10186 
    10187  
    10188 
    10189 > color name m-10t 82,44,63,50
    10190 
    10191 Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
    10192 
    10193  
    10194 
    10195 > color name m-11t 80,40,60,50
    10196 
    10197 Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
    10198 
    10199  
    10200 
    10201 > color name head-t 71,51,66,50
    10202 
    10203 Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
    10204 
    10205  
    10206 
    10207 > color name head-c 89,89,100,100
    10208 
    10209 Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
    10210 
    10211  
    10212 
    10213 > color name headfa-t 80,79,100,50
    10214 
    10215 Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex: #ccc9ff80
    10216 
    10217  
    10218 
    10219 > color name headblue-t 59,78,94,50
    10220 
    10221 Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
    10222 
    10223  
    10224 
    10225 > color name headh1-t 41,64,100,50
    10226 
    10227 Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
    10228 
    10229  
    10230 
    10231 > color name headh2-t 50,70,100,50
    10232 
    10233 Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
    10234 
    10235  
    10236 
    10237 > color name headgray-t 60,60,60,50
    10238 
    10239 Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
    10240 
    10241  
    10242 
    10243 > color name darkhead-s 58,34,52,100
    10244 
    10245 Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
    10246 
    10247  
    10248 
    10249 > color name bodywhite-t 90,90,90,50
    10250 
    10251 Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
    10252 #e6e6e680
    10253 
    10254  
    10255 
    10256 > color name rps-t 75,88,93,50
    10257 
    10258 Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
    10259 
    10260  
    10261 
    10262 > color name ssu-t 57,71,75,50
    10263 
    10264 Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
    10265 
    10266  
    10267 
    10268 > color name h18-t 31,59,68,50
    10269 
    10270 Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
    10271 
    10272  
    10273 
    10274 > color name h18-c 31,59,68,100
    10275 
    10276 Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
    10277 
    10278  
    10279 
    10280 > color name h23-t 18,36,100,50
    10281 
    10282 Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
    10283 
    10284  
    10285 
    10286 > color name h23-c 18,36,100,100
    10287 
    10288 Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
    10289 
    10290  
    10291 
    10292 > color name h24-t 50,70,90,50
    10293 
    10294 Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
    10295 
    10296  
    10297 
    10298 > color name h24-c 50,70,90,100
    10299 
    10300 Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
    10301 
    10302  
    10303 
    10304 > color name h28-t 0,24,57,50
    10305 
    10306 Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
    10307 
    10308  
    10309 
    10310 > color name h28-c 0,24,57,100
    10311 
    10312 Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
    10313 
    10314  
    10315 
    10316 > color name h29-t 80,69,92,50
    10317 
    10318 Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
    10319 
    10320  
    10321 
    10322 > color name h29-c 80,69,92,100
    10323 
    10324 Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
    10325 
    10326  
    10327 
    10328 > color name h30-t 40,40,59,50
    10329 
    10330 Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
    10331 
    10332  
    10333 
    10334 > color name h30-c 40,40,59,100
    10335 
    10336 Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
    10337 
    10338  
    10339 
    10340 > color name h31-t 45,18,59,50
    10341 
    10342 Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
    10343 
    10344  
    10345 
    10346 > color name h31-c 45,18,59,100
    10347 
    10348 Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
    10349 
    10350  
    10351 
    10352 > color name h34-t 59,18,59,50
    10353 
    10354 Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
    10355 
    10356  
    10357 
    10358 > color name h34-c 59,18,59,100
    10359 
    10360 Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
    10361 
    10362  
    10363 
    10364 > color name h35-t 50,22,45,50
    10365 
    10366 Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
    10367 
    10368  
    10369 
    10370 > color name h35-c 50,22,45,100
    10371 
    10372 Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
    10373 
    10374  
    10375 
    10376 > color name h44-t 27,50,80,50
    10377 
    10378 Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
    10379 
    10380  
    10381 
    10382 > color name h44-c 27,50,80,100
    10383 
    10384 Color 'h44-c' is opaque: rgb(27%, 50%, 80%) hex: #4580cc
    10385 
    10386  
    10387 
    10388 > color name aploop-t 27,0,50,50
    10389 
    10390 Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
    10391 
    10392  
    10393 
    10394 > color name term16-t 40,64,64,50
    10395 
    10396 Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
    10397 
    10398  
    10399 
    10400 > color name uS3-t 64,41,82,50
    10401 
    10402 Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
    10403 
    10404  
    10405 
    10406 > color name uS5-t 0,50,45,50
    10407 
    10408 Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
    10409 
    10410  
    10411 
    10412 > color name gray-t 70,70,70,50
    10413 
    10414 Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
    10415 
    10416  
    10417 
    10418 > color name hx68-t 50,50,50,50
    10419 
    10420 Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    10421 
    10422  
    10423 
    10424 > color name hx68-c 50,50,50,100
    10425 
    10426 Color 'hx68-c' is opaque: gray(50%) hex: #808080
    10427 
    10428  
    10429 
    10430 > color name hx69-t 40,40,40,50
    10431 
    10432 Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
    10433 
    10434  
    10435 
    10436 > color name hx69-c 40,40,40,100
    10437 
    10438 Color 'hx69-c' is opaque: gray(40%) hex: #666666
    10439 
    10440  
    10441 
    10442 > color name srl-t 50,50,50,50
    10443 
    10444 Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    10445 
    10446  
    10447 
    10448 > color name srl-t 50,50,50,100
    10449 
    10450 Color 'srl-t' is opaque: gray(50%) hex: #808080
    10451 
    10452  
    10453 
    10454 > color name lightgrayt 83,83,83,50
    10455 
    10456 Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
    10457 
    10458  
    10459 
    10460 > color name silvert 75,75,75,50
    10461 
    10462 Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
    10463 
    10464  
    10465 
    10466 > color name grayt 50,50,50,50
    10467 
    10468 Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    10469 
    10470  
    10471 
    10472 > color name lightcyant 88,100,100,50
    10473 
    10474 Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
    10475 #e0ffff80
    10476 
    10477  
    10478 
    10479 > color name yellowt 100,90,0,50
    10480 
    10481 Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
    10482 
    10483  
    10484 
    10485 > color name deeppinkt 100,8,58,50
    10486 
    10487 Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
    10488 
    10489  
    10490 
    10491 > color name oranget 100,65,0,50
    10492 
    10493 Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
    10494 
    10495  
    10496 
    10497 > color name yellowgreent 60,80,20,50
    10498 
    10499 Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
    10500 #99cc3380
    10501 
    10502  
    10503 
    10504 > color name darkmagentat 54,0,54,50
    10505 
    10506 Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
    10507 #8a008a80
    10508 
    10509  
    10510 
    10511 > color name orchidt 86,44,84,50
    10512 
    10513 Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
    10514 
    10515  
    10516 
    10517 > color name paleturquoiset 69,93,93,50
    10518 
    10519 Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
    10520 #b0eded80
    10521 
    10522  
    10523 
    10524 > color name pinkt 100,75,80,50
    10525 
    10526 Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
    10527 
    10528  
    10529 
    10530 > color name darkgreent 0,39,0,50
    10531 
    10532 Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
    10533 
    10534  
    10535 
    10536 > color name limegreent 20,80,20,50
    10537 
    10538 Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
    10539 
    10540  
    10541 
    10542 > color name turquoiset 25,88,82,50
    10543 
    10544 Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
    10545 
    10546  
    10547 
    10548 > color name tealt 0,50,50,50
    10549 
    10550 Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
    10551 
    10552  
    10553 
    10554 > color name darkoranget 100,50,0,50
    10555 
    10556 Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
    10557 #ff800080
    10558 
    10559  
    10560 
    10561 > color name lightyellowt 100,100,50,50
    10562 
    10563 Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
    10564 #ffff8080
    10565 
    10566  
    10567 
    10568 > color name goldt 100,75,0,50
    10569 
    10570 Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
    10571 
    10572  
    10573 
    10574 > color name plumt 87,63,87,50
    10575 
    10576 Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
    10577 
    10578  
    10579 
    10580 > color name ssubluet 68,86,90,50
    10581 
    10582 Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
    10583 
    10584  
    10585 
    10586 > color name p-prect 10,41,0,50
    10587 
    10588 Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
    10589 
    10590  
    10591 
    10592 > color name p-h2t 23,59,0,50
    10593 
    10594 Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    10595 
    10596  
    10597 
    10598 > color name p-h1t 40,73,0,50
    10599 
    10600 Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
    10601 
    10602  
    10603 
    10604 > color name p-h1c 40,73,0,100
    10605 
    10606 Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
    10607 
    10608  
    10609 
    10610 > color name p-spct 68,81,0,50
    10611 
    10612 Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    10613 
    10614  
    10615 
    10616 > color name p-spcc 68,81,0,100
    10617 
    10618 Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
    10619 
    10620  
    10621 
    10622 > color name p-fat 82,92,0,50
    10623 
    10624 Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
    10625 
    10626  
    10627 
    10628 > color name p-postt 100,92,0,50
    10629 
    10630 Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    10631 
    10632  
    10633 
    10634 > color name d-t 100,80,4,50
    10635 
    10636 Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    10637 
    10638  
    10639 
    10640 > color name d-prect 95,100,50,50
    10641 
    10642 Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
    10643 
    10644  
    10645 
    10646 > color name d-h2t 100,90,4,50
    10647 
    10648 Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    10649 
    10650  
    10651 
    10652 > color name d-h1t 100,80,4,50
    10653 
    10654 Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    10655 
    10656  
    10657 
    10658 > color name d-spct 100,70,4,50
    10659 
    10660 Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
    10661 
    10662  
    10663 
    10664 > color name d-fat 100,55,4,50
    10665 
    10666 Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
    10667 
    10668  
    10669 
    10670 > color name d-fac 100,55,4,100
    10671 
    10672 Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
    10673 
    10674  
    10675 
    10676 > color name d-postt 100,40,4,50
    10677 
    10678 Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    10679 
    10680  
    10681 
    10682 > color name m-t 95,43,62,50
    10683 
    10684 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    10685 
    10686  
    10687 
    10688 > color name m-prect 100,85,95,50
    10689 
    10690 Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    10691 
    10692  
    10693 
    10694 > color name m-h2t 100,85,95,50
    10695 
    10696 Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    10697 
    10698  
    10699 
    10700 > color name m-h1t 100,75,95,50
    10701 
    10702 Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
    10703 
    10704  
    10705 
    10706 > color name m-spct 89,63,75,50
    10707 
    10708 Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
    10709 
    10710  
    10711 
    10712 > color name m-fat 95,51,75,50
    10713 
    10714 Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
    10715 
    10716  
    10717 
    10718 > color name m-fac 95,51,75,100
    10719 
    10720 Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
    10721 
    10722  
    10723 
    10724 > color name m-postt 95,43,62,50
    10725 
    10726 Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    10727 
    10728  
    10729 executed 70S_colors.cxc 
    10730 
    10731 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
    10732 
    10733 > color 100,100,100,50
    10734 
    10735 > color lsu silvert
    10736 
    10737 > color /3 lightgrayt
    10738 
    10739 > color /5 lightgrayt
    10740 
    10741 > color ssu ssu-t
    10742 
    10743 > color head head-t
    10744 
    10745 > color efg efg-t
    10746 
    10747 > color dt d-t
    10748 
    10749 > color pt p-t
    10750 
    10751 > color pep p-t
    10752 
    10753 > color mrna m-t
    10754 
    10755 executed 70S_colorstandard.cxc 
    10756 
    10757 > windowsize 1000 1000
    10758 
    10759 > open
    10760 > /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_trna_gradient-t.cxc
    10761 
    10762 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
    10763 
    10764 > color name efg-t 100,0,0,50
    10765 
    10766 Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    10767 
    10768  
    10769 
    10770 > color name sw1-t 100,92,0,50
    10771 
    10772 Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    10773 
    10774  
    10775 
    10776 > color name sw2-t 68,81,0,50
    10777 
    10778 Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    10779 
    10780  
    10781 
    10782 > color name pl-t 23,59,0,50
    10783 
    10784 Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    10785 
    10786  
    10787 
    10788 > color name d1-t 100,18,4,50
    10789 
    10790 Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
    10791 
    10792  
    10793 
    10794 > color name d2-t 100,40,4,50
    10795 
    10796 Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    10797 
    10798  
    10799 
    10800 > color name d3-t 100,27,36,50
    10801 
    10802 Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
    10803 
    10804  
    10805 
    10806 > color name d4-t 80,0,23,50
    10807 
    10808 Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
    10809 
    10810  
    10811 
    10812 > color name d5-t 100,60,4,50
    10813 
    10814 Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
    10815 
    10816  
    10817 
    10818 > color name fa-t 100,90,4,50
    10819 
    10820 Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    10821 
    10822  
    10823 
    10824 > color name gtp-t 45,53,60,50
    10825 
    10826 Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
    10827 
    10828  
    10829 
    10830 > color name mg-t 1,39,16,50
    10831 
    10832 Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
    10833 
    10834  
    10835 
    10836 > color name spc-t 100,0,0,50
    10837 
    10838 Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    10839 
    10840  
    10841 
    10842 > color name argb-t 50,0,50,50
    10843 
    10844 Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
    10845 
    10846  
    10847 
    10848 > color name g-1t 98,42,30,50
    10849 
    10850 Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
    10851 
    10852  
    10853 
    10854 > color name g-2t 95,35,25,50
    10855 
    10856 Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
    10857 
    10858  
    10859 
    10860 > color name g-3t 92,28,20,50
    10861 
    10862 Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
    10863 
    10864  
    10865 
    10866 > color name g-4t 89,21,15,50
    10867 
    10868 Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
    10869 
    10870  
    10871 
    10872 > color name g-5t 86,14,10,50
    10873 
    10874 Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
    10875 
    10876  
    10877 
    10878 > color name g-6t 83,7,5,50
    10879 
    10880 Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
    10881 
    10882  
    10883 
    10884 > color name g-7t 80,0,0,50
    10885 
    10886 Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
    10887 
    10888  
    10889 
    10890 > color name p-t 40,60,2,50
    10891 
    10892 Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
    10893 
    10894  
    10895 
    10896 > color name p-c 40,60,2,100
    10897 
    10898 Color 'p-c' is opaque: rgb(40%, 60%, 2%) hex: #669905
    10899 
    10900  
    10901 
    10902 > color name p-1t 4,34,1,50
    10903 
    10904 Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
    10905 
    10906  
    10907 
    10908 > color name p-2t 12,39,1,50
    10909 
    10910 Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
    10911 
    10912  
    10913 
    10914 > color name p-3t 20,44,1,50
    10915 
    10916 Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
    10917 
    10918  
    10919 
    10920 > color name p-4t 28,49,1,50
    10921 
    10922 Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
    10923 
    10924  
    10925 
    10926 > color name p-5t 36,54,2,50
    10927 
    10928 Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
    10929 
    10930  
    10931 
    10932 > color name p-6t 44,59,2,50
    10933 
    10934 Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
    10935 
    10936  
    10937 
    10938 > color name p-7t 52,64,2,50
    10939 
    10940 Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
    10941 
    10942  
    10943 
    10944 > color name p-8t 60,69,2,50
    10945 
    10946 Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
    10947 
    10948  
    10949 
    10950 > color name p-9t 68,74,3,50
    10951 
    10952 Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
    10953 
    10954  
    10955 
    10956 > color name p-10t 76,79,3,50
    10957 
    10958 Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
    10959 
    10960  
    10961 
    10962 > color name p-11t 84,84,3,50
    10963 
    10964 Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
    10965 
    10966  
    10967 
    10968 > color name d-t 100,75,4,50
    10969 
    10970 Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
    10971 
    10972  
    10973 
    10974 > color name d-c 100,75,4,100
    10975 
    10976 Color 'd-c' is opaque: rgb(100%, 75%, 4%) hex: #ffbf0a
    10977 
    10978  
    10979 
    10980 > color name d-1t 100,100,4,50
    10981 
    10982 Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
    10983 
    10984  
    10985 
    10986 > color name d-2t 100,93,4,50
    10987 
    10988 Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
    10989 
    10990  
    10991 
    10992 > color name d-3t 100,86,4,50
    10993 
    10994 Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
    10995 
    10996  
    10997 
    10998 > color name d-4t 100,79,4,50
    10999 
    11000 Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
    11001 
    11002  
    11003 
    11004 > color name d-5t 100,72,4,50
    11005 
    11006 Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
    11007 
    11008  
    11009 
    11010 > color name d-6t 100,65,4,50
    11011 
    11012 Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
    11013 
    11014  
    11015 
    11016 > color name d-7t 100,58,4,50
    11017 
    11018 Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
    11019 
    11020  
    11021 
    11022 > color name d-8t 100,51,4,50
    11023 
    11024 Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
    11025 
    11026  
    11027 
    11028 > color name d-9t 100,44,4,50
    11029 
    11030 Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
    11031 
    11032  
    11033 
    11034 > color name d-10t 100,37,4,50
    11035 
    11036 Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
    11037 
    11038  
    11039 
    11040 > color name d-11t 100,30,4,50
    11041 
    11042 Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
    11043 
    11044  
    11045 
    11046 > color name m-t 95,43,62,50
    11047 
    11048 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    11049 
    11050  
    11051 
    11052 > color name m-c 95,43,62,100
    11053 
    11054 Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
    11055 
    11056  
    11057 
    11058 > color name m-1t 100,80,90,50
    11059 
    11060 Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
    11061 
    11062  
    11063 
    11064 > color name m-2t 98,76,87,50
    11065 
    11066 Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
    11067 
    11068  
    11069 
    11070 > color name m-3t 96,72,84,50
    11071 
    11072 Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
    11073 
    11074  
    11075 
    11076 > color name m-4t 94,68,81,50
    11077 
    11078 Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
    11079 
    11080  
    11081 
    11082 > color name m-5t 92,64,78,50
    11083 
    11084 Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
    11085 
    11086  
    11087 
    11088 > color name m-6t 90,60,75,50
    11089 
    11090 Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
    11091 
    11092  
    11093 
    11094 > color name m-7t 88,56,72,50
    11095 
    11096 Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
    11097 
    11098  
    11099 
    11100 > color name m-8t 86,52,69,50
    11101 
    11102 Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
    11103 
    11104  
    11105 
    11106 > color name m-9t 84,48,66,50
    11107 
    11108 Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
    11109 
    11110  
    11111 
    11112 > color name m-10t 82,44,63,50
    11113 
    11114 Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
    11115 
    11116  
    11117 
    11118 > color name m-11t 80,40,60,50
    11119 
    11120 Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
    11121 
    11122  
    11123 
    11124 > color name head-t 71,51,66,50
    11125 
    11126 Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
    11127 
    11128  
    11129 
    11130 > color name head-c 89,89,100,100
    11131 
    11132 Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
    11133 
    11134  
    11135 
    11136 > color name headfa-t 80,79,100,50
    11137 
    11138 Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex: #ccc9ff80
    11139 
    11140  
    11141 
    11142 > color name headblue-t 59,78,94,50
    11143 
    11144 Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
    11145 
    11146  
    11147 
    11148 > color name headh1-t 41,64,100,50
    11149 
    11150 Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
    11151 
    11152  
    11153 
    11154 > color name headh2-t 50,70,100,50
    11155 
    11156 Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
    11157 
    11158  
    11159 
    11160 > color name headgray-t 60,60,60,50
    11161 
    11162 Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
    11163 
    11164  
    11165 
    11166 > color name darkhead-s 58,34,52,100
    11167 
    11168 Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
    11169 
    11170  
    11171 
    11172 > color name bodywhite-t 90,90,90,50
    11173 
    11174 Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
    11175 #e6e6e680
    11176 
    11177  
    11178 
    11179 > color name rps-t 75,88,93,50
    11180 
    11181 Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
    11182 
    11183  
    11184 
    11185 > color name ssu-t 57,71,75,50
    11186 
    11187 Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
    11188 
    11189  
    11190 
    11191 > color name h18-t 31,59,68,50
    11192 
    11193 Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
    11194 
    11195  
    11196 
    11197 > color name h18-c 31,59,68,100
    11198 
    11199 Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
    11200 
    11201  
    11202 
    11203 > color name h23-t 18,36,100,50
    11204 
    11205 Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
    11206 
    11207  
    11208 
    11209 > color name h23-c 18,36,100,100
    11210 
    11211 Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
    11212 
    11213  
    11214 
    11215 > color name h24-t 50,70,90,50
    11216 
    11217 Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
    11218 
    11219  
    11220 
    11221 > color name h24-c 50,70,90,100
    11222 
    11223 Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
    11224 
    11225  
    11226 
    11227 > color name h28-t 0,24,57,50
    11228 
    11229 Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
    11230 
    11231  
    11232 
    11233 > color name h28-c 0,24,57,100
    11234 
    11235 Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
    11236 
    11237  
    11238 
    11239 > color name h29-t 80,69,92,50
    11240 
    11241 Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
    11242 
    11243  
    11244 
    11245 > color name h29-c 80,69,92,100
    11246 
    11247 Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
    11248 
    11249  
    11250 
    11251 > color name h30-t 40,40,59,50
    11252 
    11253 Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
    11254 
    11255  
    11256 
    11257 > color name h30-c 40,40,59,100
    11258 
    11259 Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
    11260 
    11261  
    11262 
    11263 > color name h31-t 45,18,59,50
    11264 
    11265 Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
    11266 
    11267  
    11268 
    11269 > color name h31-c 45,18,59,100
    11270 
    11271 Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
    11272 
    11273  
    11274 
    11275 > color name h34-t 59,18,59,50
    11276 
    11277 Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
    11278 
    11279  
    11280 
    11281 > color name h34-c 59,18,59,100
    11282 
    11283 Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
    11284 
    11285  
    11286 
    11287 > color name h35-t 50,22,45,50
    11288 
    11289 Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
    11290 
    11291  
    11292 
    11293 > color name h35-c 50,22,45,100
    11294 
    11295 Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
    11296 
    11297  
    11298 
    11299 > color name h44-t 27,50,80,50
    11300 
    11301 Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
    11302 
    11303  
    11304 
    11305 > color name h44-c 27,50,80,100
    11306 
    11307 Color 'h44-c' is opaque: rgb(27%, 50%, 80%) hex: #4580cc
    11308 
    11309  
    11310 
    11311 > color name aploop-t 27,0,50,50
    11312 
    11313 Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
    11314 
    11315  
    11316 
    11317 > color name term16-t 40,64,64,50
    11318 
    11319 Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
    11320 
    11321  
    11322 
    11323 > color name uS3-t 64,41,82,50
    11324 
    11325 Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
    11326 
    11327  
    11328 
    11329 > color name uS5-t 0,50,45,50
    11330 
    11331 Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
    11332 
    11333  
    11334 
    11335 > color name gray-t 70,70,70,50
    11336 
    11337 Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
    11338 
    11339  
    11340 
    11341 > color name hx68-t 50,50,50,50
    11342 
    11343 Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    11344 
    11345  
    11346 
    11347 > color name hx68-c 50,50,50,100
    11348 
    11349 Color 'hx68-c' is opaque: gray(50%) hex: #808080
    11350 
    11351  
    11352 
    11353 > color name hx69-t 40,40,40,50
    11354 
    11355 Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
    11356 
    11357  
    11358 
    11359 > color name hx69-c 40,40,40,100
    11360 
    11361 Color 'hx69-c' is opaque: gray(40%) hex: #666666
    11362 
    11363  
    11364 
    11365 > color name srl-t 50,50,50,50
    11366 
    11367 Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    11368 
    11369  
    11370 
    11371 > color name srl-t 50,50,50,100
    11372 
    11373 Color 'srl-t' is opaque: gray(50%) hex: #808080
    11374 
    11375  
    11376 
    11377 > color name lightgrayt 83,83,83,50
    11378 
    11379 Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
    11380 
    11381  
    11382 
    11383 > color name silvert 75,75,75,50
    11384 
    11385 Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
    11386 
    11387  
    11388 
    11389 > color name grayt 50,50,50,50
    11390 
    11391 Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    11392 
    11393  
    11394 
    11395 > color name lightcyant 88,100,100,50
    11396 
    11397 Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
    11398 #e0ffff80
    11399 
    11400  
    11401 
    11402 > color name yellowt 100,90,0,50
    11403 
    11404 Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
    11405 
    11406  
    11407 
    11408 > color name deeppinkt 100,8,58,50
    11409 
    11410 Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
    11411 
    11412  
    11413 
    11414 > color name oranget 100,65,0,50
    11415 
    11416 Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
    11417 
    11418  
    11419 
    11420 > color name yellowgreent 60,80,20,50
    11421 
    11422 Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
    11423 #99cc3380
    11424 
    11425  
    11426 
    11427 > color name darkmagentat 54,0,54,50
    11428 
    11429 Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
    11430 #8a008a80
    11431 
    11432  
    11433 
    11434 > color name orchidt 86,44,84,50
    11435 
    11436 Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
    11437 
    11438  
    11439 
    11440 > color name paleturquoiset 69,93,93,50
    11441 
    11442 Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
    11443 #b0eded80
    11444 
    11445  
    11446 
    11447 > color name pinkt 100,75,80,50
    11448 
    11449 Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
    11450 
    11451  
    11452 
    11453 > color name darkgreent 0,39,0,50
    11454 
    11455 Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
    11456 
    11457  
    11458 
    11459 > color name limegreent 20,80,20,50
    11460 
    11461 Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
    11462 
    11463  
    11464 
    11465 > color name turquoiset 25,88,82,50
    11466 
    11467 Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
    11468 
    11469  
    11470 
    11471 > color name tealt 0,50,50,50
    11472 
    11473 Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
    11474 
    11475  
    11476 
    11477 > color name darkoranget 100,50,0,50
    11478 
    11479 Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
    11480 #ff800080
    11481 
    11482  
    11483 
    11484 > color name lightyellowt 100,100,50,50
    11485 
    11486 Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
    11487 #ffff8080
    11488 
    11489  
    11490 
    11491 > color name goldt 100,75,0,50
    11492 
    11493 Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
    11494 
    11495  
    11496 
    11497 > color name plumt 87,63,87,50
    11498 
    11499 Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
    11500 
    11501  
    11502 
    11503 > color name ssubluet 68,86,90,50
    11504 
    11505 Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
    11506 
    11507  
    11508 
    11509 > color name p-prect 10,41,0,50
    11510 
    11511 Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
    11512 
    11513  
    11514 
    11515 > color name p-h2t 23,59,0,50
    11516 
    11517 Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    11518 
    11519  
    11520 
    11521 > color name p-h1t 40,73,0,50
    11522 
    11523 Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
    11524 
    11525  
    11526 
    11527 > color name p-h1c 40,73,0,100
    11528 
    11529 Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
    11530 
    11531  
    11532 
    11533 > color name p-spct 68,81,0,50
    11534 
    11535 Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    11536 
    11537  
    11538 
    11539 > color name p-spcc 68,81,0,100
    11540 
    11541 Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
    11542 
    11543  
    11544 
    11545 > color name p-fat 82,92,0,50
    11546 
    11547 Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
    11548 
    11549  
    11550 
    11551 > color name p-postt 100,92,0,50
    11552 
    11553 Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    11554 
    11555  
    11556 
    11557 > color name d-t 100,80,4,50
    11558 
    11559 Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    11560 
    11561  
    11562 
    11563 > color name d-prect 95,100,50,50
    11564 
    11565 Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
    11566 
    11567  
    11568 
    11569 > color name d-h2t 100,90,4,50
    11570 
    11571 Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    11572 
    11573  
    11574 
    11575 > color name d-h1t 100,80,4,50
    11576 
    11577 Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    11578 
    11579  
    11580 
    11581 > color name d-spct 100,70,4,50
    11582 
    11583 Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
    11584 
    11585  
    11586 
    11587 > color name d-fat 100,55,4,50
    11588 
    11589 Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
    11590 
    11591  
    11592 
    11593 > color name d-fac 100,55,4,100
    11594 
    11595 Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
    11596 
    11597  
    11598 
    11599 > color name d-postt 100,40,4,50
    11600 
    11601 Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    11602 
    11603  
    11604 
    11605 > color name m-t 95,43,62,50
    11606 
    11607 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    11608 
    11609  
    11610 
    11611 > color name m-prect 100,85,95,50
    11612 
    11613 Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    11614 
    11615  
    11616 
    11617 > color name m-h2t 100,85,95,50
    11618 
    11619 Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    11620 
    11621  
    11622 
    11623 > color name m-h1t 100,75,95,50
    11624 
    11625 Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
    11626 
    11627  
    11628 
    11629 > color name m-spct 89,63,75,50
    11630 
    11631 Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
    11632 
    11633  
    11634 
    11635 > color name m-fat 95,51,75,50
    11636 
    11637 Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
    11638 
    11639  
    11640 
    11641 > color name m-fac 95,51,75,100
    11642 
    11643 Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
    11644 
    11645  
    11646 
    11647 > color name m-postt 95,43,62,50
    11648 
    11649 Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    11650 
    11651  
    11652 executed 70S_colors.cxc 
    11653 
    11654 > color #10/y p-1t
    11655 
    11656 > color #11/y p-2t
    11657 
    11658 > color #12/y p-3t
    11659 
    11660 > color #30/y p-4t
    11661 
    11662 > color #31/y p-4t
    11663 
    11664 > color #32/y p-5t
    11665 
    11666 > color #33/y p-6t
    11667 
    11668 > color #13/y p-7t
    11669 
    11670 > color #34/y p-8t
    11671 
    11672 > color #14/y p-9t
    11673 
    11674 > color #20/y p-10t
    11675 
    11676 > color #15/y p-11t
    11677 
    11678 > color #10/v d-1t
    11679 
    11680 > color #11/v d-2t
    11681 
    11682 > color #12/v d-3t
    11683 
    11684 > color #30/v d-4t
    11685 
    11686 > color #31/v d-4t
    11687 
    11688 > color #32/v d-5t
    11689 
    11690 > color #33/v d-6t
    11691 
    11692 > color #13/v d-7t
    11693 
    11694 > color #34/v d-8t
    11695 
    11696 > color #14/v d-9t
    11697 
    11698 > color #20/v d-10t
    11699 
    11700 > color #15/v d-11t
    11701 
    11702 > color #10/w m-1t
    11703 
    11704 > color #11/w m-2t
    11705 
    11706 > color #12/w m-3t
    11707 
    11708 > color #30/w m-4t
    11709 
    11710 > color #31/w m-4t
    11711 
    11712 > color #32/w m-5t
    11713 
    11714 > color #33/w m-6t
    11715 
    11716 > color #13/w m-7t
    11717 
    11718 > color #34/w m-8t
    11719 
    11720 > color #14/w m-9t
    11721 
    11722 > color #20/w m-10t
    11723 
    11724 > color #15/w m-11t
    11725 
    11726 > color #30/x g-1t
    11727 
    11728 > color #31/x g-1t
    11729 
    11730 > color #32/x g-2t
    11731 
    11732 > color #33/x g-3t
    11733 
    11734 > color #13/x g-4t
    11735 
    11736 > color #34/x g-5t
    11737 
    11738 > color #14/x g-6t
    11739 
    11740 > color #20/x g-7t
    11741 
    11742 executed 70S_color_trna_gradient-t.cxc 
    11743 
    11744 > nucribthin
    11745 
    11746 > color fua fa-t
    11747 
    11748 > color ntide gtp-t
    11749 
    11750 > display drugs
    11751 
    11752 > display ntide
    11753 
    11754 > display mg
    11755 
    11756 > transparency atomods 0 target abcs
    11757 
    11758 executed gtpys_translocation.cxc 
    11759 
    11760 > close #30
    11761 
    11762 > ~select
    11763 
    11764 Nothing selected 
    11765 
    11766 > lighting soft
    11767 
    11768 > hide models
    11769 
    11770 > ~ribbon
    11771 
    11772 > ~display
    11773 
    11774 > display mrna
    11775 
    11776 > ribbon efg
    11777 
    11778 > ribbon trna
    11779 
    11780 > ribbon efg
    11781 
    11782 > hide emmaps
    11783 
    11784 > graphics silhouettes true
    11785 
    11786 > graphics silhouettes color 20,20,20,80
    11787 
    11788 > cartoon mrna
    11789 
    11790 > ~display mrna
    11791 
    11792 > ~display /w:48-end
    11793 
    11794 > ~cartoon /w:48-end
    11795 
    11796 > ~display /w:start-35
    11797 
    11798 > ~cartoon /w:start-35
    11799 
    11800 > ~cartoon efg
    11801 
    11802 > style /w:43@C1'|/w:40@C1'|#20/w:37@C1' sphere
    11803 
    11804 Changed 23 atom styles 
    11805 
    11806 > style #20/w:43@C1' stick
    11807 
    11808 Changed 1 atom style 
    11809 
    11810 > size /w atomRadius 1.8
    11811 
    11812 Changed 2991 atom radii 
    11813 
    11814 > display /w:43@C1'|/w:40@C1'|#20/w:37@C1'
    11815 
    11816 > ~display #20/w:43@C1'
    11817 
    11818 > ~cartoon #10.3/v
    11819 
    11820 > select #31-34
    11821 
    11822 615114 atoms, 665062 bonds, 13 pseudobonds, 47066 residues, 29 models selected 
    11823 
    11824 > view trna1
    11825 
    11826 > hide models
    11827 
    11828 > show #*.3 models
    11829 
    11830 > windowsize 1000 1000
    11831 
    11832 > save
    11833 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_all-H1bc.tif
    11834 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11835 
    11836 > show #*.3 models
    11837 
    11838 > hide #10#11#15#20 models
    11839 
    11840 > windowsize 1000 1000
    11841 
    11842 > save
    11843 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_h1toFA-H1bc.tif
    11844 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11845 
    11846 > hide models
    11847 
    11848 > show #31.3#32.3#33.3#34.3 models
    11849 
    11850 > windowsize 1000 1000
    11851 
    11852 > save
    11853 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_ysonly-H1bc.tif
    11854 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11855 
    11856 > hide models
    11857 
    11858 > show #31.3#32.3#12.3 models
    11859 
    11860 > windowsize 1000 1000
    11861 
    11862 > save
    11863 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_H1only-H1bc.tif
    11864 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11865 
    11866 > hide models
    11867 
    11868 > show #33.3#34.3#13.3#14.3 models
    11869 
    11870 > windowsize 1000 1000
    11871 
    11872 > save
    11873 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_I1I2-H1bc.tif
    11874 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11875 
    11876 > hide models
    11877 
    11878 > show #31.3#32.3#33.3#34.3#13.3#12.3 models
    11879 
    11880 > windowsize 1000 1000
    11881 
    11882 > save
    11883 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_I1H1-H1bc.tif
    11884 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11885 
    11886 > cartoon efg
    11887 
    11888 > view trna3
    11889 
    11890 > hide models
    11891 
    11892 > show #*.3 models
    11893 
    11894 > windowsize 1000 1000
    11895 
    11896 > save
    11897 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna3_all-H1bc.tif
    11898 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11899 
    11900 > show #*.3 models
    11901 
    11902 > hide #10#11#15#20 models
    11903 
    11904 > windowsize 1000 1000
    11905 
    11906 > save
    11907 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna3_h1toFA-H1bc.tif
    11908 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11909 
    11910 > hide models
    11911 
    11912 > show #31.3#32.3#33.3#34.3 models
    11913 
    11914 > windowsize 1000 1000
    11915 
    11916 > save
    11917 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna3_ysonly-H1bc.tif
    11918 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11919 
    11920 > hide models
    11921 
    11922 > show #31.3#32.3#12.3 models
    11923 
    11924 > windowsize 1000 1000
    11925 
    11926 > save
    11927 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna3_H1only-H1bc.tif
    11928 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11929 
    11930 > hide models
    11931 
    11932 > show #33.3#34.3#13.3#14.3 models
    11933 
    11934 > windowsize 1000 1000
    11935 
    11936 > save
    11937 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna3_I1I2-H1bc.tif
    11938 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11939 
    11940 > hide models
    11941 
    11942 > show #31.3#32.3#33.3#34.3#13.3#12.3 models
    11943 
    11944 > windowsize 1000 1000
    11945 
    11946 > save
    11947 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna3_I1H1-H1bc.tif
    11948 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11949 
    11950 > graphics silhouettes color 0,0,0,50
    11951 
    11952 > transparency atomods 50 target abcsp
    11953 
    11954 > view trna1
    11955 
    11956 > ~select
    11957 
    11958 Nothing selected 
    11959 
    11960 > transparency #10.3 0 target abcs
    11961 
    11962 > select #10.3
    11963 
    11964 56259 atoms, 60818 bonds, 4280 residues, 1 model selected 
    11965 
    11966 > hide models
    11967 
    11968 > show #10.3#11.3 models
    11969 
    11970 > windowsize 1000 1000
    11971 
    11972 > save
    11973 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_1-prec.tif
    11974 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11975 
    11976 > show #*.3 models
    11977 
    11978 > windowsize 1000 1000
    11979 
    11980 > save
    11981 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_1-prec.tif
    11982 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    11983 
    11984 > color #10.3 40,40,40,50
    11985 
    11986 > ~select
    11987 
    11988 Nothing selected 
    11989 
    11990 > transparency #11.3 0 target abcs
    11991 
    11992 > select #11.3
    11993 
    11994 55387 atoms, 59910 bonds, 1 pseudobond, 4185 residues, 2 models selected 
    11995 
    11996 > hide models
    11997 
    11998 > show #10.3#11.3#12.3 models
    11999 
    12000 > windowsize 1000 1000
    12001 
    12002 > save
    12003 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_2-h2.tif
    12004 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12005 
    12006 > show #*.3 models
    12007 
    12008 > windowsize 1000 1000
    12009 
    12010 > save
    12011 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_2-h2.tif
    12012 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12013 
    12014 > color #11.3 45,45,45,50
    12015 
    12016 > ~select
    12017 
    12018 Nothing selected 
    12019 
    12020 > transparency #12.3 0 target abcs
    12021 
    12022 > select #12.3
    12023 
    12024 55765 atoms, 60298 bonds, 4230 residues, 1 model selected 
    12025 
    12026 > hide models
    12027 
    12028 > show #11.3#12.3#31.3 models
    12029 
    12030 > windowsize 1000 1000
    12031 
    12032 > save
    12033 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_3-h1.tif
    12034 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12035 
    12036 > show #10.3 models
    12037 
    12038 > windowsize 1000 1000
    12039 
    12040 > save
    12041 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-add_3-h1.tif
    12042 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12043 
    12044 > show #*.3 models
    12045 
    12046 > windowsize 1000 1000
    12047 
    12048 > save
    12049 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_3-h1.tif
    12050 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12051 
    12052 > hide #10#11#15#20 models
    12053 
    12054 > ~select
    12055 
    12056 Nothing selected 
    12057 
    12058 > transparency #12.3 0 target abcs
    12059 
    12060 > select #12.3
    12061 
    12062 55765 atoms, 60298 bonds, 4230 residues, 1 model selected 
    12063 
    12064 > windowsize 1000 1000
    12065 
    12066 > save
    12067 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_3-h1.tif
    12068 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12069 
    12070 > color #12.3 50,50,50,50
    12071 
    12072 > ~select
    12073 
    12074 Nothing selected 
    12075 
    12076 > transparency #31.3 0 target abcs
    12077 
    12078 > select #31.3
    12079 
    12080 60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected 
    12081 
    12082 > hide models
    12083 
    12084 > show #31.3#12.3#32.3 models
    12085 
    12086 > windowsize 1000 1000
    12087 
    12088 > save
    12089 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_4-h1b.tif
    12090 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12091 
    12092 > show #10.3#11.3 models
    12093 
    12094 > windowsize 1000 1000
    12095 
    12096 > save
    12097 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-add_4-h1b.tif
    12098 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12099 
    12100 > show #*.3 models
    12101 
    12102 > windowsize 1000 1000
    12103 
    12104 > save
    12105 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_4-h1b.tif
    12106 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12107 
    12108 > hide #10#11#15#20 models
    12109 
    12110 > ~select
    12111 
    12112 Nothing selected 
    12113 
    12114 > transparency #31.3 0 target abcs
    12115 
    12116 > select #31.3
    12117 
    12118 60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected 
    12119 
    12120 > windowsize 1000 1000
    12121 
    12122 > save
    12123 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_4-h1b.tif
    12124 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12125 
    12126 > color #31.3 55,55,55,50
    12127 
    12128 > ~select
    12129 
    12130 Nothing selected 
    12131 
    12132 > transparency #32.3 0 target abcs
    12133 
    12134 > select #32.3
    12135 
    12136 60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected 
    12137 
    12138 > hide models
    12139 
    12140 > show #32.3#31.3#33.3 models
    12141 
    12142 > windowsize 1000 1000
    12143 
    12144 > save
    12145 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_5-h1c.tif
    12146 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12147 
    12148 > show #10.3#11.3#12.3 models
    12149 
    12150 > windowsize 1000 1000
    12151 
    12152 > save
    12153 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-add_5-h1c.tif
    12154 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12155 
    12156 > show #*.3 models
    12157 
    12158 > windowsize 1000 1000
    12159 
    12160 > save
    12161 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_5-h1c.tif
    12162 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12163 
    12164 > hide #10#11#15#20 models
    12165 
    12166 > windowsize 1000 1000
    12167 
    12168 > save
    12169 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_5-h1c.tif
    12170 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12171 
    12172 > color #32.3 60,60,60,50
    12173 
    12174 > ~select
    12175 
    12176 Nothing selected 
    12177 
    12178 > transparency #33.3 0 target abcs
    12179 
    12180 > select #33.3
    12181 
    12182 61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected 
    12183 
    12184 > hide models
    12185 
    12186 > show #33.3#32.3#13.3 models
    12187 
    12188 > windowsize 1000 1000
    12189 
    12190 > save
    12191 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_6-I1ays.tif
    12192 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12193 
    12194 > show #10.3#11.3#12.3#31.3 models
    12195 
    12196 > windowsize 1000 1000
    12197 
    12198 > save
    12199 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-add_6-I1ays.tif
    12200 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12201 
    12202 > show #*.3 models
    12203 
    12204 > windowsize 1000 1000
    12205 
    12206 > save
    12207 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_6-I1ays.tif
    12208 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12209 
    12210 > hide #10#11#15#20 models
    12211 
    12212 > windowsize 1000 1000
    12213 
    12214 > save
    12215 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_6-I1ays.tif
    12216 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12217 
    12218 > color #33.3 65,65,65,50
    12219 
    12220 > ~select
    12221 
    12222 Nothing selected 
    12223 
    12224 > transparency #13.3 0 target abcs
    12225 
    12226 > select #13.3
    12227 
    12228 61103 atoms, 65762 bonds, 4902 residues, 1 model selected 
    12229 
    12230 > hide models
    12231 
    12232 > show #13.3#34.3#33.3 models
    12233 
    12234 > windowsize 1000 1000
    12235 
    12236 > save
    12237 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_7-I1spc.tif
    12238 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12239 
    12240 > show #10.3#11.3#12.3#31.3#32.3 models
    12241 
    12242 > windowsize 1000 1000
    12243 
    12244 > save
    12245 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-add_7-I1spc.tif
    12246 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12247 
    12248 > show #*.3 models
    12249 
    12250 > windowsize 1000 1000
    12251 
    12252 > save
    12253 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_7-I1spc.tif
    12254 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12255 
    12256 > hide #10#11#15#20 models
    12257 
    12258 > windowsize 1000 1000
    12259 
    12260 > save
    12261 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_7-I1spc.tif
    12262 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12263 
    12264 > color #13.3 70,70,70,50
    12265 
    12266 > ~select
    12267 
    12268 Nothing selected 
    12269 
    12270 > transparency #34.3 0 target abcs
    12271 
    12272 > select #34.3
    12273 
    12274 61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected 
    12275 
    12276 > hide models
    12277 
    12278 > show #34.3#13.3#14.3 models
    12279 
    12280 > windowsize 1000 1000
    12281 
    12282 > save
    12283 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_8-I1bys.tif
    12284 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12285 
    12286 > show #10.3#11.3#12.3#31.3#32.3#33.3 models
    12287 
    12288 > windowsize 1000 1000
    12289 
    12290 > save
    12291 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-add_8-I1bys.tif
    12292 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12293 
    12294 > show #*.3 models
    12295 
    12296 > windowsize 1000 1000
    12297 
    12298 > save
    12299 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_8-I1bys.tif
    12300 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12301 
    12302 > hide #10#11#15#20 models
    12303 
    12304 > windowsize 1000 1000
    12305 
    12306 > save
    12307 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_8-I1bys.tif
    12308 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12309 
    12310 > color #34.3 75,75,75,50
    12311 
    12312 > ~select
    12313 
    12314 Nothing selected 
    12315 
    12316 > transparency #14.3 0 target abcs
    12317 
    12318 > select #14.3
    12319 
    12320 60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected 
    12321 
    12322 > hide models
    12323 
    12324 > show #14.3#34.3#20.3 models
    12325 
    12326 > windowsize 1000 1000
    12327 
    12328 > save
    12329 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_9-I2FA.tif
    12330 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12331 
    12332 > show #10.3#11.3#12.3#31.3#32.3#33.3#13.3 models
    12333 
    12334 > windowsize 1000 1000
    12335 
    12336 > save
    12337 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-add_9-I2FA.tif
    12338 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12339 
    12340 > show #*.3 models
    12341 
    12342 > windowsize 1000 1000
    12343 
    12344 > save
    12345 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_9-I2FA.tif
    12346 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12347 
    12348 > hide #10#11#15#20 models
    12349 
    12350 > windowsize 1000 1000
    12351 
    12352 > save
    12353 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1_9-I2FA.tif
    12354 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12355 
    12356 > color #14.3 80,80,80,50
    12357 
    12358 > ~select
    12359 
    12360 Nothing selected 
    12361 
    12362 > transparency #20.3 0 target abcs
    12363 
    12364 > select #20.3
    12365 
    12366 60797 atoms, 65074 bonds, 3 pseudobonds, 5178 residues, 2 models selected 
    12367 
    12368 > hide models
    12369 
    12370 > show #20.3#14.3#15.3 models
    12371 
    12372 > windowsize 1000 1000
    12373 
    12374 > save
    12375 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_10-I2arg.tif
    12376 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12377 
    12378 > show #10.3#11.3#12.3#31.3#32.3#33.3#13.3#34.3 models
    12379 
    12380 > windowsize 1000 1000
    12381 
    12382 > save
    12383 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-add_10-I2arg.tif
    12384 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12385 
    12386 > show #*.3 models
    12387 
    12388 > windowsize 1000 1000
    12389 
    12390 > save
    12391 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_10-I2arg.tif
    12392 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12393 
    12394 > color #20.3 85,85,85,50
    12395 
    12396 > ~select
    12397 
    12398 Nothing selected 
    12399 
    12400 > transparency #15.3 0 target abcs
    12401 
    12402 > select #15.3
    12403 
    12404 55643 atoms, 60209 bonds, 4185 residues, 1 model selected 
    12405 
    12406 > hide models
    12407 
    12408 > show #15.3#20.3 models
    12409 
    12410 > windowsize 1000 1000
    12411 
    12412 > save
    12413 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-step_11-post.tif
    12414 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12415 
    12416 > show #*.3 models
    12417 
    12418 > windowsize 1000 1000
    12419 
    12420 > save
    12421 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_11-post.tif
    12422 > format tiff width 1000 height 1000 supersample 20 transparentBackground true
    12423 
    12424 > color #20.3 90,90,90,50
    12425 
    12426 > ~select
    12427 
    12428 Nothing selected 
    12429 
    12430 > windowsize 1000 1000
    12431 
    12432 > save
    12433 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/trna1-all_end.tif
    12434 > format tiff width 1000 height 1000
    12435 
    12436 > size atomRadius default
    12437 
    12438 Changed 1761392 atom radii 
    12439 
    12440 > save
    12441 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/gtpys_translocation.cxs
    12442 
    12443 ——— End of log from Mon May 22 15:58:58 2023 ———
    12444 
    12445 opened ChimeraX session 
    12446 
    12447 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_startup_gtpys-
    12448 > all.cxc
    12449 
    12450 > close all
    12451 
    12452 > open /data/EmilyRundlet/ChimeraX_70S/Maps/4ybb_50Score_3A.mrc
    12453 
    12454 Opened 4ybb_50Score_3A.mrc as #1, grid size 576,576,576, pixel 1.06, shown at
    12455 level 0.000164, step 4, values float32 
    12456 
    12457 > rename #1 id #100
    12458 
    12459 > open /data/EmilyRundlet/ChimeraX_70S/Models/prec_7n1p_50S.pdb
    12460 
    12461 Chain information for prec_7n1p_50S.pdb #1 
    12462 --- 
    12463 Chain | Description 
    12464 3 | No description available 
    12465 5 | No description available 
    12466 P | No description available 
    12467 S | No description available 
    12468 T | No description available 
    12469 U | No description available 
    12470 V | No description available 
    12471 W | No description available 
    12472 X | No description available 
    12473 Y | No description available 
    12474 a | No description available 
    12475 b | No description available 
    12476 c | No description available 
    12477 d | No description available 
    12478 e | No description available 
    12479 f | No description available 
    12480 g | No description available 
    12481 h | No description available 
    12482 i | No description available 
    12483 j | No description available 
    12484  
    12485 
    12486 > rename #1 id #101
    12487 
    12488 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_post.cxc
    12489 
    12490 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_50S.pdb name
    12491 > post5
    12492 
    12493 Chain information for post5 #1 
    12494 --- 
    12495 Chain | Description 
    12496 3 | No description available 
    12497 5 | No description available 
    12498 B | No description available 
    12499 C | No description available 
    12500 D | No description available 
    12501 E | No description available 
    12502 F | No description available 
    12503 I | No description available 
    12504 M | No description available 
    12505 N | No description available 
    12506 O | No description available 
    12507 P | No description available 
    12508 Q | No description available 
    12509 R | No description available 
    12510 S | No description available 
    12511 T | No description available 
    12512 U | No description available 
    12513 V | No description available 
    12514 W | No description available 
    12515 X | No description available 
    12516 Y | No description available 
    12517 a | No description available 
    12518 b | No description available 
    12519 c | No description available 
    12520 d | No description available 
    12521 e | No description available 
    12522 f | No description available 
    12523 g | No description available 
    12524 h | No description available 
    12525 i | No description available 
    12526 j | No description available 
    12527  
    12528 
    12529 > rename #1 id #15.5
    12530 
    12531 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_30S.pdb name
    12532 > post3
    12533 
    12534 Chain information for post3 #1 
    12535 --- 
    12536 Chain | Description 
    12537 6 | No description available 
    12538 B | No description available 
    12539 C | No description available 
    12540 D | No description available 
    12541 E | No description available 
    12542 F | No description available 
    12543 G | No description available 
    12544 H | No description available 
    12545 I | No description available 
    12546 J | No description available 
    12547 K | No description available 
    12548 L | No description available 
    12549 M | No description available 
    12550 N | No description available 
    12551 O | No description available 
    12552 P | No description available 
    12553 Q | No description available 
    12554 R | No description available 
    12555 S | No description available 
    12556 T | No description available 
    12557 U | No description available 
    12558 p | No description available 
    12559 v | No description available 
    12560 w | No description available 
    12561 y | No description available 
    12562  
    12563 
    12564 > rename #1 id #15.3
    12565 
    12566 > open
    12567 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/POST_j93ct15_pplocal_g0_n.mrc
    12568 > name post
    12569 
    12570 Opened post as #1, grid size 576,576,576, pixel 1.06, shown at level 1.16,
    12571 step 4, values float32 
    12572 
    12573 > rename #1 id #15.1
    12574 
    12575 > rename #15 post
    12576 
    12577 > matchmaker #15.5 to #101 matrix Nucleic bring #15.1#15.3
    12578 
    12579 Parameters 
    12580 --- 
    12581 Chain pairing | bb 
    12582 Alignment algorithm | Needleman-Wunsch 
    12583 Similarity matrix | Nucleic 
    12584 SS fraction | 0.3 
    12585 Gap open (HH/SS/other) | 18/18/6 
    12586 Gap extend | 1 
    12587 SS matrix |  |  | H | S | O 
    12588 ---|---|---|--- 
    12589 H | 6 | -9 | -6 
    12590 S |  | 6 | -6 
    12591 O |  |  | 4 
    12592 Iteration cutoff | 2 
    12593  
    12594 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with post5, chain 3 (#15.5),
    12595 sequence alignment score = 11580.3 
    12596 RMSD between 2766 pruned atom pairs is 0.341 angstroms; (across all 2904
    12597 pairs: 2.745) 
    12598  
    12599 
    12600 > fitmap #15.1 inMap #100
    12601 
    12602 Fit map post in map 4ybb_50Score_3A.mrc using 29937 points 
    12603 correlation = 0.7033, correlation about mean = 0.6059, overlap = 7.619e+04 
    12604 steps = 48, shift = 0.0376, angle = 0.0465 degrees 
    12605  
    12606 Position of post (#15.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    12607 Matrix rotation and translation 
    12608 0.99999983 0.00051499 -0.00026539 -0.07015622 
    12609 -0.00051501 0.99999986 -0.00009768 0.21094928 
    12610 0.00026534 0.00009781 0.99999996 -0.12735627 
    12611 Axis 0.16636276 -0.45165257 -0.87654628 
    12612 Axis point 413.67366807 137.87803145 0.00000000 
    12613 Rotation angle (degrees) 0.03366312 
    12614 Shift along axis 0.00468650 
    12615  
    12616 
    12617 > fitmap #15.5 inMap #15.1
    12618 
    12619 Fit molecule post5 (#15.5) to map post (#15.1) using 90903 atoms 
    12620 average map value = 15.29, steps = 40 
    12621 shifted from previous position = 0.0173 
    12622 rotated from previous position = 0.0481 degrees 
    12623 atoms outside contour = 27101, contour level = 1.1571 
    12624  
    12625 Position of post5 (#15.5) relative to post (#15.1) coordinates: 
    12626 Matrix rotation and translation 
    12627 1.00000000 0.00007488 -0.00001293 -0.00984527 
    12628 -0.00007488 1.00000000 0.00003964 0.01927617 
    12629 0.00001293 -0.00003964 1.00000000 0.00608995 
    12630 Axis -0.46249937 -0.15083335 -0.87369539 
    12631 Axis point 250.02744189 154.19286933 0.00000000 
    12632 Rotation angle (degrees) 0.00491036 
    12633 Shift along axis -0.00367482 
    12634  
    12635 
    12636 > fitmap #15.3 inMap #15.1
    12637 
    12638 Fit molecule post3 (#15.3) to map post (#15.1) using 55643 atoms 
    12639 average map value = 11.56, steps = 40 
    12640 shifted from previous position = 0.0883 
    12641 rotated from previous position = 0.0476 degrees 
    12642 atoms outside contour = 13831, contour level = 1.1571 
    12643  
    12644 Position of post3 (#15.3) relative to post (#15.1) coordinates: 
    12645 Matrix rotation and translation 
    12646 1.00000000 -0.00005318 -0.00004310 0.02635100 
    12647 0.00005318 1.00000000 -0.00000125 -0.02050708 
    12648 0.00004310 0.00000124 1.00000000 -0.01832489 
    12649 Axis 0.01818364 -0.62958007 0.77672279 
    12650 Axis point 395.65049914 495.82230346 0.00000000 
    12651 Rotation angle (degrees) 0.00392252 
    12652 Shift along axis -0.00084336 
    12653  
    12654 executed 70S_open_post.cxc 
    12655 
    12656 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_prec.cxc
    12657 
    12658 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_50S.pdb name
    12659 > prec5
    12660 
    12661 Chain information for prec5 #1 
    12662 --- 
    12663 Chain | Description 
    12664 3 | No description available 
    12665 5 | No description available 
    12666 B | No description available 
    12667 C | No description available 
    12668 D | No description available 
    12669 E | No description available 
    12670 F | No description available 
    12671 I | No description available 
    12672 J | No description available 
    12673 K | No description available 
    12674 M | No description available 
    12675 N | No description available 
    12676 O | No description available 
    12677 P | No description available 
    12678 Q | No description available 
    12679 R | No description available 
    12680 S | No description available 
    12681 T | No description available 
    12682 U | No description available 
    12683 V | No description available 
    12684 W | No description available 
    12685 X | No description available 
    12686 Y | No description available 
    12687 a | No description available 
    12688 b | No description available 
    12689 c | No description available 
    12690 d | No description available 
    12691 e | No description available 
    12692 f | No description available 
    12693 g | No description available 
    12694 h | No description available 
    12695 i | No description available 
    12696 j | No description available 
    12697  
    12698 
    12699 > rename #1 id #10.5
    12700 
    12701 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_30S.pdb name
    12702 > prec3
    12703 
    12704 Chain information for prec3 #1 
    12705 --- 
    12706 Chain | Description 
    12707 6 | No description available 
    12708 B | No description available 
    12709 C | No description available 
    12710 D | No description available 
    12711 E | No description available 
    12712 F | No description available 
    12713 G | No description available 
    12714 H | No description available 
    12715 I | No description available 
    12716 J | No description available 
    12717 K | No description available 
    12718 L | No description available 
    12719 M | No description available 
    12720 N | No description available 
    12721 O | No description available 
    12722 P | No description available 
    12723 Q | No description available 
    12724 R | No description available 
    12725 S | No description available 
    12726 T | No description available 
    12727 U | No description available 
    12728 p | No description available 
    12729 v | No description available 
    12730 w | No description available 
    12731 y | No description available 
    12732  
    12733 
    12734 > rename #1 id #10.3
    12735 
    12736 > open
    12737 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/PREC*local*.mrc
    12738 > name prec
    12739 
    12740 Opened prec as #1, grid size 576,576,576, pixel 1.06, shown at level 0.719,
    12741 step 4, values float32 
    12742 
    12743 > rename #1 id #10.1
    12744 
    12745 > rename #10 prec
    12746 
    12747 > matchmaker #10.5 to #101 matrix Nucleic bring #10.1#10.3
    12748 
    12749 Parameters 
    12750 --- 
    12751 Chain pairing | bb 
    12752 Alignment algorithm | Needleman-Wunsch 
    12753 Similarity matrix | Nucleic 
    12754 SS fraction | 0.3 
    12755 Gap open (HH/SS/other) | 18/18/6 
    12756 Gap extend | 1 
    12757 SS matrix |  |  | H | S | O 
    12758 ---|---|---|--- 
    12759 H | 6 | -9 | -6 
    12760 S |  | 6 | -6 
    12761 O |  |  | 4 
    12762 Iteration cutoff | 2 
    12763  
    12764 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with prec5, chain 3 (#10.5),
    12765 sequence alignment score = 11585.2 
    12766 RMSD between 2904 pruned atom pairs is 0.000 angstroms; (across all 2904
    12767 pairs: 0.000) 
    12768  
    12769 
    12770 > fitmap #10.1 inMap #100
    12771 
    12772 Fit map prec in map 4ybb_50Score_3A.mrc using 29930 points 
    12773 correlation = 0.705, correlation about mean = 0.6153, overlap = 7.403e+04 
    12774 steps = 100, shift = 0.0276, angle = 0.0213 degrees 
    12775  
    12776 Position of prec (#10.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    12777 Matrix rotation and translation 
    12778 0.99999993 0.00023597 -0.00028739 0.01666834 
    12779 -0.00023597 0.99999997 0.00000377 0.08653163 
    12780 0.00028739 -0.00000370 0.99999996 -0.10871255 
    12781 Axis -0.01003658 -0.77282074 -0.63454501 
    12782 Axis point 373.98904576 -0.00000000 57.97612114 
    12783 Rotation angle (degrees) 0.02130699 
    12784 Shift along axis 0.00194228 
    12785  
    12786 
    12787 > fitmap #10.5 inMap #10.1
    12788 
    12789 Fit molecule prec5 (#10.5) to map prec (#10.1) using 93196 atoms 
    12790 average map value = 15.31, steps = 40 
    12791 shifted from previous position = 0.0241 
    12792 rotated from previous position = 0.0378 degrees 
    12793 atoms outside contour = 32220, contour level = 0.71858 
    12794  
    12795 Position of prec5 (#10.5) relative to prec (#10.1) coordinates: 
    12796 Matrix rotation and translation 
    12797 0.99999996 0.00028462 -0.00008450 -0.07054285 
    12798 -0.00028461 0.99999995 0.00015462 0.06036830 
    12799 0.00008454 -0.00015460 0.99999998 0.02731692 
    12800 Axis -0.46188152 -0.25249170 -0.85024314 
    12801 Axis point 206.84210925 257.43360450 0.00000000 
    12802 Rotation angle (degrees) 0.01917937 
    12803 Shift along axis -0.00588608 
    12804  
    12805 
    12806 > fitmap #10.3 inMap #10.1
    12807 
    12808 Fit molecule prec3 (#10.3) to map prec (#10.1) using 56259 atoms 
    12809 average map value = 11.39, steps = 48 
    12810 shifted from previous position = 0.0796 
    12811 rotated from previous position = 0.0392 degrees 
    12812 atoms outside contour = 16720, contour level = 0.71858 
    12813  
    12814 Position of prec3 (#10.3) relative to prec (#10.1) coordinates: 
    12815 Matrix rotation and translation 
    12816 0.99999994 0.00035395 -0.00002496 -0.09187678 
    12817 -0.00035394 0.99999993 0.00014842 0.08455945 
    12818 0.00002502 -0.00014841 0.99999999 0.04385687 
    12819 Axis -0.38587760 -0.06497510 -0.92025905 
    12820 Axis point 236.94211808 270.96015369 0.00000000 
    12821 Rotation angle (degrees) 0.02203670 
    12822 Shift along axis -0.01040075 
    12823  
    12824 executed 70S_open_prec.cxc 
    12825 
    12826 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_fa.cxc
    12827 
    12828 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_50S.pdb name
    12829 > i2fa5
    12830 
    12831 Chain information for i2fa5 #1 
    12832 --- 
    12833 Chain | Description 
    12834 3 | No description available 
    12835 5 | No description available 
    12836 A | No description available 
    12837 B | No description available 
    12838 C | No description available 
    12839 D | No description available 
    12840 E | No description available 
    12841 F | No description available 
    12842 G | No description available 
    12843 I | No description available 
    12844 J | No description available 
    12845 K | No description available 
    12846 M | No description available 
    12847 N | No description available 
    12848 O | No description available 
    12849 P | No description available 
    12850 Q | No description available 
    12851 R | No description available 
    12852 S | No description available 
    12853 T | No description available 
    12854 U | No description available 
    12855 V | No description available 
    12856 W | No description available 
    12857 X | No description available 
    12858 Y | No description available 
    12859 a | No description available 
    12860 b | No description available 
    12861 c | No description available 
    12862 d | No description available 
    12863 e | No description available 
    12864 f | No description available 
    12865 g | No description available 
    12866 h | No description available 
    12867 i | No description available 
    12868 j | No description available 
    12869  
    12870 
    12871 > rename #1 id #14.5
    12872 
    12873 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_30S.pdb name
    12874 > i2fa3
    12875 
    12876 Chain information for i2fa3 #1 
    12877 --- 
    12878 Chain | Description 
    12879 6 | No description available 
    12880 B | No description available 
    12881 C | No description available 
    12882 D | No description available 
    12883 E | No description available 
    12884 F | No description available 
    12885 G | No description available 
    12886 H | No description available 
    12887 I | No description available 
    12888 J | No description available 
    12889 K | No description available 
    12890 L | No description available 
    12891 M | No description available 
    12892 N | No description available 
    12893 O | No description available 
    12894 P | No description available 
    12895 Q | No description available 
    12896 R | No description available 
    12897 S | No description available 
    12898 T | No description available 
    12899 U | No description available 
    12900 p | No description available 
    12901 v | No description available 
    12902 w | No description available 
    12903 x | No description available 
    12904 y | No description available 
    12905  
    12906 
    12907 > rename #1 id #14.3
    12908 
    12909 > open
    12910 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/FA*local*.mrc
    12911 
    12912 Opened FA_j118_localres_filt_g0_n.mrc as #1, grid size 576,576,576, pixel
    12913 1.06, shown at level 0.555, step 4, values float32 
    12914 
    12915 > rename #1 id #14.1
    12916 
    12917 > matchmaker #14.5 to #101 matrix Nucleic bring #14.1#14.3
    12918 
    12919 Parameters 
    12920 --- 
    12921 Chain pairing | bb 
    12922 Alignment algorithm | Needleman-Wunsch 
    12923 Similarity matrix | Nucleic 
    12924 SS fraction | 0.3 
    12925 Gap open (HH/SS/other) | 18/18/6 
    12926 Gap extend | 1 
    12927 SS matrix |  |  | H | S | O 
    12928 ---|---|---|--- 
    12929 H | 6 | -9 | -6 
    12930 S |  | 6 | -6 
    12931 O |  |  | 4 
    12932 Iteration cutoff | 2 
    12933  
    12934 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i2fa5, chain 3 (#14.5),
    12935 sequence alignment score = 11567.9 
    12936 RMSD between 2675 pruned atom pairs is 0.458 angstroms; (across all 2903
    12937 pairs: 3.500) 
    12938  
    12939 
    12940 > rename #14 fa
    12941 
    12942 > fitmap #14.1 inMap #100
    12943 
    12944 Fit map FA_j118_localres_filt_g0_n.mrc in map 4ybb_50Score_3A.mrc using 29876
    12945 points 
    12946 correlation = 0.7652, correlation about mean = 0.6917, overlap = 8.026e+04 
    12947 steps = 124, shift = 0.0674, angle = 0.0469 degrees 
    12948  
    12949 Position of FA_j118_localres_filt_g0_n.mrc (#14.1) relative to
    12950 4ybb_50Score_3A.mrc (#100) coordinates: 
    12951 Matrix rotation and translation 
    12952 0.99999951 0.00082837 -0.00054821 -0.07721517 
    12953 -0.00082823 0.99999963 0.00024790 0.22483688 
    12954 0.00054841 -0.00024745 0.99999982 -0.11895947 
    12955 Axis -0.24193109 -0.53558675 -0.80908354 
    12956 Axis point 267.87230737 94.97670830 0.00000000 
    12957 Rotation angle (degrees) 0.05865666 
    12958 Shift along axis -0.00549075 
    12959  
    12960 
    12961 > fitmap #14.5 inMap #14.1
    12962 
    12963 Fit molecule i2fa5 (#14.5) to map FA_j118_localres_filt_g0_n.mrc (#14.1) using
    12964 94455 atoms 
    12965 average map value = 14.71, steps = 44 
    12966 shifted from previous position = 0.0492 
    12967 rotated from previous position = 0.0489 degrees 
    12968 atoms outside contour = 26009, contour level = 0.5555 
    12969  
    12970 Position of i2fa5 (#14.5) relative to FA_j118_localres_filt_g0_n.mrc (#14.1)
    12971 coordinates: 
    12972 Matrix rotation and translation 
    12973 0.99999999 0.00013549 0.00005439 -0.05910674 
    12974 -0.00013549 0.99999999 -0.00008462 0.07061428 
    12975 -0.00005440 0.00008461 0.99999999 -0.01606966 
    12976 Axis 0.50141948 0.32233497 -0.80291884 
    12977 Axis point 506.79859217 458.57499403 0.00000000 
    12978 Rotation angle (degrees) 0.00966859 
    12979 Shift along axis 0.00602682 
    12980  
    12981 
    12982 > fitmap #14.3 inMap #14.1
    12983 
    12984 Fit molecule i2fa3 (#14.3) to map FA_j118_localres_filt_g0_n.mrc (#14.1) using
    12985 60702 atoms 
    12986 average map value = 7.538, steps = 40 
    12987 shifted from previous position = 0.104 
    12988 rotated from previous position = 0.0489 degrees 
    12989 atoms outside contour = 11367, contour level = 0.5555 
    12990  
    12991 Position of i2fa3 (#14.3) relative to FA_j118_localres_filt_g0_n.mrc (#14.1)
    12992 coordinates: 
    12993 Matrix rotation and translation 
    12994 0.99999996 0.00022144 0.00016174 -0.14067075 
    12995 -0.00022141 0.99999996 -0.00017040 0.12305826 
    12996 -0.00016178 0.00017037 0.99999997 -0.00200513 
    12997 Axis 0.52777238 0.50104898 -0.68586167 
    12998 Axis point 581.05763080 608.65192133 0.00000000 
    12999 Rotation angle (degrees) 0.01849719 
    13000 Shift along axis -0.01120868 
    13001  
    13002 executed 70S_open_fa.cxc 
    13003 
    13004 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_spc.cxc
    13005 
    13006 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_50S.pdb name
    13007 > i1spc5
    13008 
    13009 Chain information for i1spc5 #1 
    13010 --- 
    13011 Chain | Description 
    13012 3 | No description available 
    13013 5 | No description available 
    13014 B | No description available 
    13015 C | No description available 
    13016 D | No description available 
    13017 E | No description available 
    13018 F | No description available 
    13019 I | No description available 
    13020 J | No description available 
    13021 K | No description available 
    13022 M | No description available 
    13023 N | No description available 
    13024 O | No description available 
    13025 P | No description available 
    13026 Q | No description available 
    13027 R | No description available 
    13028 S | No description available 
    13029 T | No description available 
    13030 U | No description available 
    13031 V | No description available 
    13032 W | No description available 
    13033 X | No description available 
    13034 Y | No description available 
    13035 a | No description available 
    13036 b | No description available 
    13037 c | No description available 
    13038 d | No description available 
    13039 e | No description available 
    13040 f | No description available 
    13041 g | No description available 
    13042 h | No description available 
    13043 i | No description available 
    13044 j | No description available 
    13045  
    13046 
    13047 > rename #1 id #13.5
    13048 
    13049 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_30S.pdb name
    13050 > i1spc3
    13051 
    13052 Chain information for i1spc3 #1 
    13053 --- 
    13054 Chain | Description 
    13055 6 | No description available 
    13056 B | No description available 
    13057 C | No description available 
    13058 D | No description available 
    13059 E | No description available 
    13060 F | No description available 
    13061 G | No description available 
    13062 H | No description available 
    13063 I | No description available 
    13064 J | No description available 
    13065 K | No description available 
    13066 L | No description available 
    13067 M | No description available 
    13068 N | No description available 
    13069 O | No description available 
    13070 P | No description available 
    13071 Q | No description available 
    13072 R | No description available 
    13073 S | No description available 
    13074 T | No description available 
    13075 U | No description available 
    13076 p | No description available 
    13077 v | No description available 
    13078 w | No description available 
    13079 x | No description available 
    13080 y | No description available 
    13081  
    13082 
    13083 > rename #1 id #13.3
    13084 
    13085 > open
    13086 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/INT1_spc*local*.mrc
    13087 > name i1spc
    13088 
    13089 Opened i1spc as #1, grid size 576,576,576, pixel 1.06, shown at level 0.527,
    13090 step 4, values float32 
    13091 
    13092 > rename #1 id #13.1
    13093 
    13094 > rename #13 i1spc
    13095 
    13096 > matchmaker #13.5 to #101 matrix Nucleic bring #13.1#13.3
    13097 
    13098 Parameters 
    13099 --- 
    13100 Chain pairing | bb 
    13101 Alignment algorithm | Needleman-Wunsch 
    13102 Similarity matrix | Nucleic 
    13103 SS fraction | 0.3 
    13104 Gap open (HH/SS/other) | 18/18/6 
    13105 Gap extend | 1 
    13106 SS matrix |  |  | H | S | O 
    13107 ---|---|---|--- 
    13108 H | 6 | -9 | -6 
    13109 S |  | 6 | -6 
    13110 O |  |  | 4 
    13111 Iteration cutoff | 2 
    13112  
    13113 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i1spc5, chain 3 (#13.5),
    13114 sequence alignment score = 11576.1 
    13115 RMSD between 2613 pruned atom pairs is 0.440 angstroms; (across all 2904
    13116 pairs: 4.190) 
    13117  
    13118 
    13119 > fitmap #13.1 inMap #100
    13120 
    13121 Fit map i1spc in map 4ybb_50Score_3A.mrc using 29799 points 
    13122 correlation = 0.7329, correlation about mean = 0.6398, overlap = 7.208e+04 
    13123 steps = 104, shift = 0.0985, angle = 0.0628 degrees 
    13124  
    13125 Position of i1spc (#13.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    13126 Matrix rotation and translation 
    13127 0.99999127 -0.00305790 -0.00284733 1.91534327 
    13128 0.00305942 0.99999518 0.00052889 -1.13631859 
    13129 0.00284570 -0.00053760 0.99999581 -1.01117770 
    13130 Axis -0.12659581 -0.67578369 0.72614730 
    13131 Axis point 418.51647841 616.51914515 0.00000000 
    13132 Rotation angle (degrees) 0.24134036 
    13133 Shift along axis -0.20883282 
    13134  
    13135 
    13136 > fitmap #13.5 inMap #13.1
    13137 
    13138 Fit molecule i1spc5 (#13.5) to map i1spc (#13.1) using 93017 atoms 
    13139 average map value = 14.57, steps = 48 
    13140 shifted from previous position = 0.0733 
    13141 rotated from previous position = 0.0651 degrees 
    13142 atoms outside contour = 27434, contour level = 0.52653 
    13143  
    13144 Position of i1spc5 (#13.5) relative to i1spc (#13.1) coordinates: 
    13145 Matrix rotation and translation 
    13146 1.00000000 -0.00000053 -0.00005875 0.01737643 
    13147 0.00000053 1.00000000 -0.00002655 0.00255801 
    13148 0.00005875 0.00002655 1.00000000 -0.03456253 
    13149 Axis 0.41177423 -0.91124934 0.00816220 
    13150 Axis point 588.98331322 0.00000000 263.93669119 
    13151 Rotation angle (degrees) 0.00369369 
    13152 Shift along axis 0.00454208 
    13153  
    13154 
    13155 > fitmap #13.3 inMap #13.1
    13156 
    13157 Fit molecule i1spc3 (#13.3) to map i1spc (#13.1) using 61103 atoms 
    13158 average map value = 9.699, steps = 60 
    13159 shifted from previous position = 0.162 
    13160 rotated from previous position = 0.0627 degrees 
    13161 atoms outside contour = 14669, contour level = 0.52653 
    13162  
    13163 Position of i1spc3 (#13.3) relative to i1spc (#13.1) coordinates: 
    13164 Matrix rotation and translation 
    13165 0.99999999 0.00006855 -0.00007419 -0.00808096 
    13166 -0.00006856 1.00000000 -0.00003421 0.02476248 
    13167 0.00007419 0.00003421 1.00000000 -0.04490669 
    13168 Axis 0.32075098 -0.69563238 -0.64281755 
    13169 Axis point 526.89840240 0.00000000 -148.08272269 
    13170 Rotation angle (degrees) 0.00611054 
    13171 Shift along axis 0.00904925 
    13172  
    13173 executed 70S_open_spc.cxc 
    13174 
    13175 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_h1.cxc
    13176 
    13177 > open
    13178 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/apo_H1*local*.mrc
    13179 > name hy1
    13180 
    13181 Opened hy1 as #1, grid size 576,576,576, pixel 1.06, shown at level 0.822,
    13182 step 4, values float32 
    13183 
    13184 > rename #1 id #12.1
    13185 
    13186 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_50S.pdb name
    13187 > hy15
    13188 
    13189 Chain information for hy15 #1 
    13190 --- 
    13191 Chain | Description 
    13192 3 | No description available 
    13193 5 | No description available 
    13194 B | No description available 
    13195 C | No description available 
    13196 D | No description available 
    13197 E | No description available 
    13198 F | No description available 
    13199 I | No description available 
    13200 M | No description available 
    13201 N | No description available 
    13202 O | No description available 
    13203 P | No description available 
    13204 Q | No description available 
    13205 R | No description available 
    13206 S | No description available 
    13207 T | No description available 
    13208 U | No description available 
    13209 V | No description available 
    13210 W | No description available 
    13211 X | No description available 
    13212 Y | No description available 
    13213 a | No description available 
    13214 b | No description available 
    13215 c | No description available 
    13216 d | No description available 
    13217 e | No description available 
    13218 f | No description available 
    13219 g | No description available 
    13220 h | No description available 
    13221 i | No description available 
    13222 j | No description available 
    13223  
    13224 
    13225 > rename #1 id #12.5
    13226 
    13227 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_30S.pdb name
    13228 > hy13
    13229 
    13230 Chain information for hy13 #1 
    13231 --- 
    13232 Chain | Description 
    13233 6 | No description available 
    13234 B | No description available 
    13235 C | No description available 
    13236 D | No description available 
    13237 E | No description available 
    13238 F | No description available 
    13239 G | No description available 
    13240 H | No description available 
    13241 I | No description available 
    13242 J | No description available 
    13243 K | No description available 
    13244 L | No description available 
    13245 M | No description available 
    13246 N | No description available 
    13247 O | No description available 
    13248 P | No description available 
    13249 Q | No description available 
    13250 R | No description available 
    13251 S | No description available 
    13252 T | No description available 
    13253 U | No description available 
    13254 p | No description available 
    13255 v | No description available 
    13256 w | No description available 
    13257 y | No description available 
    13258  
    13259 
    13260 > rename #1 id #12.3
    13261 
    13262 > matchmaker #12.5 to #101 matrix Nucleic bring #12.1#12.3
    13263 
    13264 Parameters 
    13265 --- 
    13266 Chain pairing | bb 
    13267 Alignment algorithm | Needleman-Wunsch 
    13268 Similarity matrix | Nucleic 
    13269 SS fraction | 0.3 
    13270 Gap open (HH/SS/other) | 18/18/6 
    13271 Gap extend | 1 
    13272 SS matrix |  |  | H | S | O 
    13273 ---|---|---|--- 
    13274 H | 6 | -9 | -6 
    13275 S |  | 6 | -6 
    13276 O |  |  | 4 
    13277 Iteration cutoff | 2 
    13278  
    13279 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with hy15, chain 3 (#12.5),
    13280 sequence alignment score = 11572.3 
    13281 RMSD between 2683 pruned atom pairs is 0.437 angstroms; (across all 2902
    13282 pairs: 4.227) 
    13283  
    13284 
    13285 > fitmap #12.1 inMap #100
    13286 
    13287 Fit map hy1 in map 4ybb_50Score_3A.mrc using 29865 points 
    13288 correlation = 0.7182, correlation about mean = 0.6351, overlap = 7.48e+04 
    13289 steps = 80, shift = 0.0539, angle = 0.0362 degrees 
    13290  
    13291 Position of hy1 (#12.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    13292 Matrix rotation and translation 
    13293 0.99999993 0.00033939 -0.00014651 -0.03967194 
    13294 -0.00033939 0.99999994 0.00003379 0.08904027 
    13295 0.00014652 -0.00003374 0.99999999 -0.04209798 
    13296 Axis -0.09096206 -0.39471037 -0.91429187 
    13297 Axis point 270.42268136 115.08181596 0.00000000 
    13298 Rotation angle (degrees) 0.02126851 
    13299 Shift along axis 0.00695336 
    13300  
    13301 
    13302 > fitmap #12.5 inMap #12.1
    13303 
    13304 Fit molecule hy15 (#12.5) to map hy1 (#12.1) using 91053 atoms 
    13305 average map value = 15.92, steps = 40 
    13306 shifted from previous position = 0.0355 
    13307 rotated from previous position = 0.0365 degrees 
    13308 atoms outside contour = 31662, contour level = 0.82202 
    13309  
    13310 Position of hy15 (#12.5) relative to hy1 (#12.1) coordinates: 
    13311 Matrix rotation and translation 
    13312 1.00000000 0.00001739 -0.00003452 0.00191493 
    13313 -0.00001738 1.00000000 0.00005119 -0.00075625 
    13314 0.00003452 -0.00005119 1.00000000 0.00373129 
    13315 Axis -0.79805293 -0.53818813 -0.27104440 
    13316 Axis point 0.00000000 61.60073087 37.19705100 
    13317 Rotation angle (degrees) 0.00367501 
    13318 Shift along axis -0.00213255 
    13319  
    13320 
    13321 > fitmap #12.3 inMap #12.1
    13322 
    13323 Fit molecule hy13 (#12.3) to map hy1 (#12.1) using 55765 atoms 
    13324 average map value = 9.817, steps = 44 
    13325 shifted from previous position = 0.0694 
    13326 rotated from previous position = 0.0332 degrees 
    13327 atoms outside contour = 14540, contour level = 0.82202 
    13328  
    13329 Position of hy13 (#12.3) relative to hy1 (#12.1) coordinates: 
    13330 Matrix rotation and translation 
    13331 1.00000000 -0.00000897 0.00000895 -0.00690250 
    13332 0.00000897 0.99999999 0.00011154 -0.02727097 
    13333 -0.00000895 -0.00011154 0.99999999 0.03999319 
    13334 Axis -0.99361126 0.07969592 0.07990759 
    13335 Axis point 0.00000000 352.90975575 250.15609103 
    13336 Rotation angle (degrees) 0.00643159 
    13337 Shift along axis 0.00788078 
    13338  
    13339 executed 70S_open_h1.cxc 
    13340 
    13341 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_ys.cxc
    13342 
    13343 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb name
    13344 > ys-H1a5
    13345 
    13346 Summary of feedback from opening
    13347 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb 
    13348 --- 
    13349 warnings | Ignored bad PDB record found on line 2 
    13350 LINK O3' A Pt0076 C LY 0 
    13351  
    13352 Ignored bad PDB record found on line 3 
    13353 LINK ZN ZN Lj0101 ND1 HI 03 
    13354  
    13355 Ignored bad PDB record found on line 4 
    13356 LINK ZN ZN Lj0101 SG CY 02 
    13357  
    13358 Ignored bad PDB record found on line 5 
    13359 LINK ZN ZN Lj0101 SG CY 01 
    13360  
    13361 Ignored bad PDB record found on line 6 
    13362 LINK ZN ZN Lj0101 SG CY 01 
    13363  
    13364 4 messages similar to the above omitted 
    13365 Cannot find LINK/SSBOND residue THR (1033509) 
    13366 Cannot find LINK/SSBOND residue ZN (567641) 
    13367  
    13368 Chain information for ys-H1a5 #1 
    13369 --- 
    13370 Chain | Description 
    13371 3 | No description available 
    13372 5 | No description available 
    13373 A | No description available 
    13374 B | No description available 
    13375 C | No description available 
    13376 D | No description available 
    13377 E | No description available 
    13378 F | No description available 
    13379 I | No description available 
    13380 J | No description available 
    13381 K | No description available 
    13382 M | No description available 
    13383 N | No description available 
    13384 O | No description available 
    13385 P | No description available 
    13386 Q | No description available 
    13387 R | No description available 
    13388 S | No description available 
    13389 T | No description available 
    13390 U | No description available 
    13391 V | No description available 
    13392 W | No description available 
    13393 X | No description available 
    13394 Y | No description available 
    13395 a | No description available 
    13396 b | No description available 
    13397 c | No description available 
    13398 d | No description available 
    13399 e | No description available 
    13400 f | No description available 
    13401 g | No description available 
    13402 h | No description available 
    13403 i | No description available 
    13404 j | No description available 
    13405  
    13406 
    13407 > rename #1 id #30.5
    13408 
    13409 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb name
    13410 > ys-H1a3
    13411 
    13412 Summary of feedback from opening
    13413 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb 
    13414 --- 
    13415 warnings | Ignored bad PDB record found on line 2 
    13416 LINK O3' A Pt0076 C LY 0 
    13417  
    13418 Ignored bad PDB record found on line 3 
    13419 LINK ZN ZN Lj0101 ND1 HI 03 
    13420  
    13421 Ignored bad PDB record found on line 4 
    13422 LINK ZN ZN Lj0101 SG CY 02 
    13423  
    13424 Ignored bad PDB record found on line 5 
    13425 LINK ZN ZN Lj0101 SG CY 01 
    13426  
    13427 Ignored bad PDB record found on line 6 
    13428 LINK ZN ZN Lj0101 SG CY 01 
    13429  
    13430 4 messages similar to the above omitted 
    13431 Cannot find LINK/SSBOND residue THR (1033509) 
    13432 Cannot find LINK/SSBOND residue ZN (567641) 
    13433  
    13434 Chain information for ys-H1a3 #1 
    13435 --- 
    13436 Chain | Description 
    13437 6 | No description available 
    13438 B | No description available 
    13439 C | No description available 
    13440 D | No description available 
    13441 E | No description available 
    13442 F | No description available 
    13443 G | No description available 
    13444 H | No description available 
    13445 I | No description available 
    13446 J | No description available 
    13447 K | No description available 
    13448 L | No description available 
    13449 M | No description available 
    13450 N | No description available 
    13451 O | No description available 
    13452 P | No description available 
    13453 Q | No description available 
    13454 R | No description available 
    13455 S | No description available 
    13456 T | No description available 
    13457 U | No description available 
    13458 p | No description available 
    13459 v | No description available 
    13460 w | No description available 
    13461 x | No description available 
    13462 y | No description available 
    13463  
    13464 
    13465 > rename #1 id #30.3
    13466 
    13467 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1a-j1420.mrc name
    13468 > ys-H1a
    13469 
    13470 Opened ys-H1a as #1, grid size 512,512,512, pixel 0.828, shown at level 2.46,
    13471 step 2, values float32 
    13472 
    13473 > rename #1 id #30.1
    13474 
    13475 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb name
    13476 > ys-H1b5
    13477 
    13478 Summary of feedback from opening
    13479 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb 
    13480 --- 
    13481 warnings | Ignored bad PDB record found on line 5 
    13482 LINK ZN ZN Le0201 SG CY 04 
    13483  
    13484 Ignored bad PDB record found on line 6 
    13485 LINK ZN ZN Le0201 SG CY 03 
    13486  
    13487 Ignored bad PDB record found on line 7 
    13488 LINK ZN ZN Le0201 SG CY 01 
    13489  
    13490 Ignored bad PDB record found on line 8 
    13491 LINK ZN ZN Le0201 SG CY 01 
    13492  
    13493 Ignored bad PDB record found on line 9 
    13494 LINK ZN ZN Lj0101 ND1 HI 03 
    13495  
    13496 3 messages similar to the above omitted 
    13497 Cannot find LINK/SSBOND residue THR (1033509) 
    13498 Cannot find LINK/SSBOND residue LYS (2432823) 
    13499 Cannot find LINK/SSBOND residue THR (2432824) 
    13500 Cannot find LINK/SSBOND residue ZN (567641) 
    13501  
    13502 Chain information for ys-H1b5 #1 
    13503 --- 
    13504 Chain | Description 
    13505 3 | No description available 
    13506 5 | No description available 
    13507 B | No description available 
    13508 C | No description available 
    13509 D | No description available 
    13510 E | No description available 
    13511 F | No description available 
    13512 I | No description available 
    13513 J | No description available 
    13514 K | No description available 
    13515 M | No description available 
    13516 N | No description available 
    13517 O | No description available 
    13518 P | No description available 
    13519 Q | No description available 
    13520 R | No description available 
    13521 S | No description available 
    13522 T | No description available 
    13523 U | No description available 
    13524 V | No description available 
    13525 W | No description available 
    13526 X | No description available 
    13527 Y | No description available 
    13528 a | No description available 
    13529 b | No description available 
    13530 c | No description available 
    13531 d | No description available 
    13532 e | No description available 
    13533 f | No description available 
    13534 g | No description available 
    13535 h | No description available 
    13536 i | No description available 
    13537 j | No description available 
    13538  
    13539 
    13540 > rename #1 id #31.5
    13541 
    13542 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb name
    13543 > ys-H1b3
    13544 
    13545 Summary of feedback from opening
    13546 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb 
    13547 --- 
    13548 warnings | Ignored bad PDB record found on line 5 
    13549 LINK ZN ZN Le0201 SG CY 04 
    13550  
    13551 Ignored bad PDB record found on line 6 
    13552 LINK ZN ZN Le0201 SG CY 03 
    13553  
    13554 Ignored bad PDB record found on line 7 
    13555 LINK ZN ZN Le0201 SG CY 01 
    13556  
    13557 Ignored bad PDB record found on line 8 
    13558 LINK ZN ZN Le0201 SG CY 01 
    13559  
    13560 Ignored bad PDB record found on line 9 
    13561 LINK ZN ZN Lj0101 ND1 HI 03 
    13562  
    13563 3 messages similar to the above omitted 
    13564 Cannot find LINK/SSBOND residue THR (1033509) 
    13565 Cannot find LINK/SSBOND residue LYS (2432823) 
    13566 Cannot find LINK/SSBOND residue THR (2432824) 
    13567 Cannot find LINK/SSBOND residue ZN (567641) 
    13568  
    13569 Chain information for ys-H1b3 #1 
    13570 --- 
    13571 Chain | Description 
    13572 6 | No description available 
    13573 B | No description available 
    13574 C | No description available 
    13575 D | No description available 
    13576 E | No description available 
    13577 F | No description available 
    13578 G | No description available 
    13579 H | No description available 
    13580 I | No description available 
    13581 J | No description available 
    13582 K | No description available 
    13583 L | No description available 
    13584 M | No description available 
    13585 N | No description available 
    13586 O | No description available 
    13587 P | No description available 
    13588 Q | No description available 
    13589 R | No description available 
    13590 S | No description available 
    13591 T | No description available 
    13592 U | No description available 
    13593 p | No description available 
    13594 v | No description available 
    13595 w | No description available 
    13596 x | No description available 
    13597 y | No description available 
    13598  
    13599 
    13600 > rename #1 id #31.3
    13601 
    13602 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1b-j1423.mrc name
    13603 > ys-H1b
    13604 
    13605 Opened ys-H1b as #1, grid size 512,512,512, pixel 0.828, shown at level 2.52,
    13606 step 2, values float32 
    13607 
    13608 > rename #1 id #31.1
    13609 
    13610 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb name
    13611 > ys-H1c5
    13612 
    13613 Summary of feedback from opening
    13614 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb 
    13615 --- 
    13616 warnings | Ignored bad PDB record found on line 2 
    13617 LINK ZN ZN Lj0101 ND1 HI 03 
    13618  
    13619 Ignored bad PDB record found on line 3 
    13620 LINK ZN ZN Lj0101 SG CY 01 
    13621  
    13622 Ignored bad PDB record found on line 4 
    13623 LINK ZN ZN Lj0101 SG CY 01 
    13624  
    13625 Ignored bad PDB record found on line 5 
    13626 LINK ZN ZN Lj0101 SG CY 02 
    13627  
    13628 Ignored bad PDB record found on line 6 
    13629 LINK ZN ZN Le0201 SG CY 04 
    13630  
    13631 3 messages similar to the above omitted 
    13632 Cannot find LINK/SSBOND residue THR (1033509) 
    13633 Cannot find LINK/SSBOND residue ZN (567641) 
    13634  
    13635 Chain information for ys-H1c5 #1 
    13636 --- 
    13637 Chain | Description 
    13638 3 | No description available 
    13639 5 | No description available 
    13640 B | No description available 
    13641 C | No description available 
    13642 D | No description available 
    13643 E | No description available 
    13644 F | No description available 
    13645 I | No description available 
    13646 J | No description available 
    13647 K | No description available 
    13648 M | No description available 
    13649 N | No description available 
    13650 O | No description available 
    13651 P | No description available 
    13652 Q | No description available 
    13653 R | No description available 
    13654 S | No description available 
    13655 T | No description available 
    13656 U | No description available 
    13657 V | No description available 
    13658 W | No description available 
    13659 X | No description available 
    13660 Y | No description available 
    13661 a | No description available 
    13662 b | No description available 
    13663 c | No description available 
    13664 d | No description available 
    13665 e | No description available 
    13666 f | No description available 
    13667 g | No description available 
    13668 h | No description available 
    13669 i | No description available 
    13670 j | No description available 
    13671  
    13672 
    13673 > rename #1 id #32.5
    13674 
    13675 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb name
    13676 > ys-H1c3
    13677 
    13678 Summary of feedback from opening
    13679 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb 
    13680 --- 
    13681 warnings | Ignored bad PDB record found on line 2 
    13682 LINK ZN ZN Lj0101 ND1 HI 03 
    13683  
    13684 Ignored bad PDB record found on line 3 
    13685 LINK ZN ZN Lj0101 SG CY 01 
    13686  
    13687 Ignored bad PDB record found on line 4 
    13688 LINK ZN ZN Lj0101 SG CY 01 
    13689  
    13690 Ignored bad PDB record found on line 5 
    13691 LINK ZN ZN Lj0101 SG CY 02 
    13692  
    13693 Ignored bad PDB record found on line 6 
    13694 LINK ZN ZN Le0201 SG CY 04 
    13695  
    13696 3 messages similar to the above omitted 
    13697 Cannot find LINK/SSBOND residue THR (1033509) 
    13698 Cannot find LINK/SSBOND residue ZN (567641) 
    13699  
    13700 Chain information for ys-H1c3 #1 
    13701 --- 
    13702 Chain | Description 
    13703 6 | No description available 
    13704 B | No description available 
    13705 C | No description available 
    13706 D | No description available 
    13707 E | No description available 
    13708 F | No description available 
    13709 G | No description available 
    13710 H | No description available 
    13711 I | No description available 
    13712 J | No description available 
    13713 K | No description available 
    13714 L | No description available 
    13715 M | No description available 
    13716 N | No description available 
    13717 O | No description available 
    13718 P | No description available 
    13719 Q | No description available 
    13720 R | No description available 
    13721 S | No description available 
    13722 T | No description available 
    13723 U | No description available 
    13724 p | No description available 
    13725 v | No description available 
    13726 w | No description available 
    13727 x | No description available 
    13728 y | No description available 
    13729  
    13730 
    13731 > rename #1 id #32.3
    13732 
    13733 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1c-j1422.mrc name
    13734 > ys-H1c
    13735 
    13736 Opened ys-H1c as #1, grid size 512,512,512, pixel 0.828, shown at level 2.74,
    13737 step 2, values float32 
    13738 
    13739 > rename #1 id #32.1
    13740 
    13741 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb name
    13742 > ys-I1a5
    13743 
    13744 Summary of feedback from opening
    13745 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb 
    13746 --- 
    13747 warnings | Ignored bad PDB record found on line 2 
    13748 LINK ZN ZN Lj0101 ND1 HI 03 
    13749  
    13750 Ignored bad PDB record found on line 3 
    13751 LINK ZN ZN Lj0101 SG CY 01 
    13752  
    13753 Ignored bad PDB record found on line 4 
    13754 LINK ZN ZN Lj0101 SG CY 01 
    13755  
    13756 Ignored bad PDB record found on line 5 
    13757 LINK ZN ZN Lj0101 SG CY 02 
    13758  
    13759 Ignored bad PDB record found on line 6 
    13760 LINK ZN ZN Le0201 SG CY 04 
    13761  
    13762 3 messages similar to the above omitted 
    13763 Cannot find LINK/SSBOND residue THR (1033509) 
    13764 Cannot find LINK/SSBOND residue ZN (567641) 
    13765  
    13766 Chain information for ys-I1a5 #1 
    13767 --- 
    13768 Chain | Description 
    13769 3 | No description available 
    13770 5 | No description available 
    13771 B | No description available 
    13772 C | No description available 
    13773 D | No description available 
    13774 E | No description available 
    13775 F | No description available 
    13776 I | No description available 
    13777 J | No description available 
    13778 K | No description available 
    13779 M | No description available 
    13780 N | No description available 
    13781 O | No description available 
    13782 P | No description available 
    13783 Q | No description available 
    13784 R | No description available 
    13785 S | No description available 
    13786 T | No description available 
    13787 U | No description available 
    13788 V | No description available 
    13789 W | No description available 
    13790 X | No description available 
    13791 Y | No description available 
    13792 a | No description available 
    13793 b | No description available 
    13794 c | No description available 
    13795 d | No description available 
    13796 e | No description available 
    13797 f | No description available 
    13798 g | No description available 
    13799 h | No description available 
    13800 i | No description available 
    13801 j | No description available 
    13802  
    13803 
    13804 > rename #1 id #33.5
    13805 
    13806 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb name
    13807 > ys-I1a3
    13808 
    13809 Summary of feedback from opening
    13810 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb 
    13811 --- 
    13812 warnings | Ignored bad PDB record found on line 2 
    13813 LINK ZN ZN Lj0101 ND1 HI 03 
    13814  
    13815 Ignored bad PDB record found on line 3 
    13816 LINK ZN ZN Lj0101 SG CY 01 
    13817  
    13818 Ignored bad PDB record found on line 4 
    13819 LINK ZN ZN Lj0101 SG CY 01 
    13820  
    13821 Ignored bad PDB record found on line 5 
    13822 LINK ZN ZN Lj0101 SG CY 02 
    13823  
    13824 Ignored bad PDB record found on line 6 
    13825 LINK ZN ZN Le0201 SG CY 04 
    13826  
    13827 3 messages similar to the above omitted 
    13828 Cannot find LINK/SSBOND residue THR (1033509) 
    13829 Cannot find LINK/SSBOND residue ZN (567641) 
    13830  
    13831 Chain information for ys-I1a3 #1 
    13832 --- 
    13833 Chain | Description 
    13834 6 | No description available 
    13835 B | No description available 
    13836 C | No description available 
    13837 D | No description available 
    13838 E | No description available 
    13839 F | No description available 
    13840 G | No description available 
    13841 H | No description available 
    13842 I | No description available 
    13843 J | No description available 
    13844 K | No description available 
    13845 L | No description available 
    13846 M | No description available 
    13847 N | No description available 
    13848 O | No description available 
    13849 P | No description available 
    13850 Q | No description available 
    13851 R | No description available 
    13852 S | No description available 
    13853 T | No description available 
    13854 U | No description available 
    13855 p | No description available 
    13856 v | No description available 
    13857 w | No description available 
    13858 x | No description available 
    13859 y | No description available 
    13860  
    13861 
    13862 > rename #1 id #33.3
    13863 
    13864 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1a-j1421.mrc name
    13865 > ys-I1a
    13866 
    13867 Opened ys-I1a as #1, grid size 512,512,512, pixel 0.828, shown at level 2.57,
    13868 step 2, values float32 
    13869 
    13870 > rename #1 id #33.1
    13871 
    13872 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb name
    13873 > ys-I1b5
    13874 
    13875 Summary of feedback from opening
    13876 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb 
    13877 --- 
    13878 warnings | Ignored bad PDB record found on line 2 
    13879 LINK ZN ZN Lj0101 ND1 HI 03 
    13880  
    13881 Ignored bad PDB record found on line 3 
    13882 LINK ZN ZN Lj0101 SG CY 01 
    13883  
    13884 Ignored bad PDB record found on line 4 
    13885 LINK ZN ZN Lj0101 SG CY 01 
    13886  
    13887 Ignored bad PDB record found on line 5 
    13888 LINK ZN ZN Lj0101 SG CY 02 
    13889  
    13890 Ignored bad PDB record found on line 6 
    13891 LINK ZN ZN Le0201 SG CY 04 
    13892  
    13893 3 messages similar to the above omitted 
    13894 Cannot find LINK/SSBOND residue THR (1033509) 
    13895 Cannot find LINK/SSBOND residue ZN (567641) 
    13896  
    13897 Chain information for ys-I1b5 #1 
    13898 --- 
    13899 Chain | Description 
    13900 3 | No description available 
    13901 5 | No description available 
    13902 B | No description available 
    13903 C | No description available 
    13904 D | No description available 
    13905 E | No description available 
    13906 F | No description available 
    13907 I | No description available 
    13908 J | No description available 
    13909 K | No description available 
    13910 M | No description available 
    13911 N | No description available 
    13912 O | No description available 
    13913 P | No description available 
    13914 Q | No description available 
    13915 R | No description available 
    13916 S | No description available 
    13917 T | No description available 
    13918 U | No description available 
    13919 V | No description available 
    13920 W | No description available 
    13921 X | No description available 
    13922 Y | No description available 
    13923 a | No description available 
    13924 b | No description available 
    13925 c | No description available 
    13926 d | No description available 
    13927 e | No description available 
    13928 f | No description available 
    13929 g | No description available 
    13930 h | No description available 
    13931 i | No description available 
    13932 j | No description available 
    13933  
    13934 
    13935 > rename #1 id #34.5
    13936 
    13937 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb name
    13938 > ys-I1b3
    13939 
    13940 Summary of feedback from opening
    13941 /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb 
    13942 --- 
    13943 warnings | Ignored bad PDB record found on line 2 
    13944 LINK ZN ZN Lj0101 ND1 HI 03 
    13945  
    13946 Ignored bad PDB record found on line 3 
    13947 LINK ZN ZN Lj0101 SG CY 01 
    13948  
    13949 Ignored bad PDB record found on line 4 
    13950 LINK ZN ZN Lj0101 SG CY 01 
    13951  
    13952 Ignored bad PDB record found on line 5 
    13953 LINK ZN ZN Lj0101 SG CY 02 
    13954  
    13955 Ignored bad PDB record found on line 6 
    13956 LINK ZN ZN Le0201 SG CY 04 
    13957  
    13958 3 messages similar to the above omitted 
    13959 Cannot find LINK/SSBOND residue THR (1033509) 
    13960 Cannot find LINK/SSBOND residue ZN (567641) 
    13961  
    13962 Chain information for ys-I1b3 #1 
    13963 --- 
    13964 Chain | Description 
    13965 6 | No description available 
    13966 B | No description available 
    13967 C | No description available 
    13968 D | No description available 
    13969 E | No description available 
    13970 F | No description available 
    13971 G | No description available 
    13972 H | No description available 
    13973 I | No description available 
    13974 J | No description available 
    13975 K | No description available 
    13976 L | No description available 
    13977 M | No description available 
    13978 N | No description available 
    13979 O | No description available 
    13980 P | No description available 
    13981 Q | No description available 
    13982 R | No description available 
    13983 S | No description available 
    13984 T | No description available 
    13985 U | No description available 
    13986 p | No description available 
    13987 v | No description available 
    13988 w | No description available 
    13989 x | No description available 
    13990 y | No description available 
    13991  
    13992 
    13993 > rename #1 id #34.3
    13994 
    13995 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1b-j1416.mrc name
    13996 > ys-I1b
    13997 
    13998 Opened ys-I1b as #1, grid size 512,512,512, pixel 0.828, shown at level 2.6,
    13999 step 2, values float32 
    14000 
    14001 > rename #1 id #34.1
    14002 
    14003 > matchmaker #30.5 to #101 matrix Nucleic bring #30.1#30.3
    14004 
    14005 Parameters 
    14006 --- 
    14007 Chain pairing | bb 
    14008 Alignment algorithm | Needleman-Wunsch 
    14009 Similarity matrix | Nucleic 
    14010 SS fraction | 0.3 
    14011 Gap open (HH/SS/other) | 18/18/6 
    14012 Gap extend | 1 
    14013 SS matrix |  |  | H | S | O 
    14014 ---|---|---|--- 
    14015 H | 6 | -9 | -6 
    14016 S |  | 6 | -6 
    14017 O |  |  | 4 
    14018 Iteration cutoff | 2 
    14019  
    14020 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1a5, chain 3 (#30.5),
    14021 sequence alignment score = 11576.1 
    14022 RMSD between 2602 pruned atom pairs is 0.440 angstroms; (across all 2904
    14023 pairs: 4.280) 
    14024  
    14025 
    14026 > matchmaker #31.5 to #101 matrix Nucleic bring #31.1#31.3
    14027 
    14028 Parameters 
    14029 --- 
    14030 Chain pairing | bb 
    14031 Alignment algorithm | Needleman-Wunsch 
    14032 Similarity matrix | Nucleic 
    14033 SS fraction | 0.3 
    14034 Gap open (HH/SS/other) | 18/18/6 
    14035 Gap extend | 1 
    14036 SS matrix |  |  | H | S | O 
    14037 ---|---|---|--- 
    14038 H | 6 | -9 | -6 
    14039 S |  | 6 | -6 
    14040 O |  |  | 4 
    14041 Iteration cutoff | 2 
    14042  
    14043 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1b5, chain 3 (#31.5),
    14044 sequence alignment score = 11576.1 
    14045 RMSD between 2629 pruned atom pairs is 0.438 angstroms; (across all 2904
    14046 pairs: 4.264) 
    14047  
    14048 
    14049 > matchmaker #32.5 to #101 matrix Nucleic bring #32.1#32.3
    14050 
    14051 Parameters 
    14052 --- 
    14053 Chain pairing | bb 
    14054 Alignment algorithm | Needleman-Wunsch 
    14055 Similarity matrix | Nucleic 
    14056 SS fraction | 0.3 
    14057 Gap open (HH/SS/other) | 18/18/6 
    14058 Gap extend | 1 
    14059 SS matrix |  |  | H | S | O 
    14060 ---|---|---|--- 
    14061 H | 6 | -9 | -6 
    14062 S |  | 6 | -6 
    14063 O |  |  | 4 
    14064 Iteration cutoff | 2 
    14065  
    14066 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1c5, chain 3 (#32.5),
    14067 sequence alignment score = 11576.1 
    14068 RMSD between 2600 pruned atom pairs is 0.428 angstroms; (across all 2904
    14069 pairs: 4.256) 
    14070  
    14071 
    14072 > matchmaker #33.5 to #101 matrix Nucleic bring #33.1#33.3
    14073 
    14074 Parameters 
    14075 --- 
    14076 Chain pairing | bb 
    14077 Alignment algorithm | Needleman-Wunsch 
    14078 Similarity matrix | Nucleic 
    14079 SS fraction | 0.3 
    14080 Gap open (HH/SS/other) | 18/18/6 
    14081 Gap extend | 1 
    14082 SS matrix |  |  | H | S | O 
    14083 ---|---|---|--- 
    14084 H | 6 | -9 | -6 
    14085 S |  | 6 | -6 
    14086 O |  |  | 4 
    14087 Iteration cutoff | 2 
    14088  
    14089 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1a5, chain 3 (#33.5),
    14090 sequence alignment score = 11576.1 
    14091 RMSD between 2595 pruned atom pairs is 0.428 angstroms; (across all 2904
    14092 pairs: 4.252) 
    14093  
    14094 
    14095 > matchmaker #34.5 to #101 matrix Nucleic bring #34.1#34.3
    14096 
    14097 Parameters 
    14098 --- 
    14099 Chain pairing | bb 
    14100 Alignment algorithm | Needleman-Wunsch 
    14101 Similarity matrix | Nucleic 
    14102 SS fraction | 0.3 
    14103 Gap open (HH/SS/other) | 18/18/6 
    14104 Gap extend | 1 
    14105 SS matrix |  |  | H | S | O 
    14106 ---|---|---|--- 
    14107 H | 6 | -9 | -6 
    14108 S |  | 6 | -6 
    14109 O |  |  | 4 
    14110 Iteration cutoff | 2 
    14111  
    14112 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1b5, chain 3 (#34.5),
    14113 sequence alignment score = 11576.1 
    14114 RMSD between 2617 pruned atom pairs is 0.432 angstroms; (across all 2904
    14115 pairs: 4.229) 
    14116  
    14117 
    14118 > fitmap #30.1 inMap #100
    14119 
    14120 Fit map ys-H1a in map 4ybb_50Score_3A.mrc using 167387 points 
    14121 correlation = 0.7846, correlation about mean = 0.5574, overlap = 5.395e+05 
    14122 steps = 48, shift = 0.0494, angle = 0.0701 degrees 
    14123  
    14124 Position of ys-H1a (#30.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    14125 Matrix rotation and translation 
    14126 -0.16344767 0.06700464 0.98427397 119.67262650 
    14127 -0.09956483 -0.99371737 0.05111386 534.32726944 
    14128 0.98151501 -0.08964463 0.16909209 84.21086233 
    14129 Axis -0.64539633 0.01265020 -0.76374312 
    14130 Axis point 43.44643354 266.69110182 0.00000000 
    14131 Rotation angle (degrees) 173.73955453 
    14132 Shift along axis -134.79239523 
    14133  
    14134 
    14135 > fitmap #30.5 inMap #30.1
    14136 
    14137 Fit molecule ys-H1a5 (#30.5) to map ys-H1a (#30.1) using 94082 atoms 
    14138 average map value = 7.857, steps = 48 
    14139 shifted from previous position = 0.0196 
    14140 rotated from previous position = 0.0712 degrees 
    14141 atoms outside contour = 19110, contour level = 2.4603 
    14142  
    14143 Position of ys-H1a5 (#30.5) relative to ys-H1a (#30.1) coordinates: 
    14144 Matrix rotation and translation 
    14145 1.00000000 -0.00003609 0.00000433 -0.00152183 
    14146 0.00003609 1.00000000 -0.00000330 -0.00568192 
    14147 -0.00000433 0.00000330 1.00000000 0.00761388 
    14148 Axis 0.09045906 0.11867200 0.98880439 
    14149 Axis point 179.54157004 -59.01245650 0.00000000 
    14150 Rotation angle (degrees) 0.00209099 
    14151 Shift along axis 0.00671669 
    14152  
    14153 
    14154 > fitmap #30.3 inMap #30.1
    14155 
    14156 Fit molecule ys-H1a3 (#30.3) to map ys-H1a (#30.1) using 61134 atoms 
    14157 average map value = 4.821, steps = 44 
    14158 shifted from previous position = 0.118 
    14159 rotated from previous position = 0.0757 degrees 
    14160 atoms outside contour = 21607, contour level = 2.4603 
    14161  
    14162 Position of ys-H1a3 (#30.3) relative to ys-H1a (#30.1) coordinates: 
    14163 Matrix rotation and translation 
    14164 1.00000000 0.00001191 0.00003836 -0.01350746 
    14165 -0.00001191 0.99999999 -0.00010843 0.02321567 
    14166 -0.00003836 0.00010843 0.99999999 -0.01184754 
    14167 Axis 0.93772928 0.33174944 -0.10298590 
    14168 Axis point 0.00000000 112.83336866 225.55426278 
    14169 Rotation angle (degrees) 0.00662522 
    14170 Shift along axis -0.00374442 
    14171  
    14172 
    14173 > fitmap #31.1 inMap #100
    14174 
    14175 Fit map ys-H1b in map 4ybb_50Score_3A.mrc using 167266 points 
    14176 correlation = 0.7827, correlation about mean = 0.5589, overlap = 5.178e+05 
    14177 steps = 104, shift = 1.68, angle = 0.294 degrees 
    14178  
    14179 Position of ys-H1b (#31.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    14180 Matrix rotation and translation 
    14181 -0.16709307 0.06719742 0.98364852 119.91753401 
    14182 -0.10104433 -0.99358862 0.05071200 534.53347026 
    14183 0.98074969 -0.09091848 0.17281169 83.69214046 
    14184 Axis -0.64395534 0.01318021 -0.76494954 
    14185 Axis point 44.06494204 266.78006288 0.00000000 
    14186 Rotation angle (degrees) 173.68646110 
    14187 Shift along axis -134.19653801 
    14188  
    14189 
    14190 > fitmap #31.5 inMap #31.1
    14191 
    14192 Fit molecule ys-H1b5 (#31.5) to map ys-H1b (#31.1) using 92994 atoms 
    14193 average map value = 7.351, steps = 48 
    14194 shifted from previous position = 0.0269 
    14195 rotated from previous position = 0.0627 degrees 
    14196 atoms outside contour = 20862, contour level = 2.5187 
    14197  
    14198 Position of ys-H1b5 (#31.5) relative to ys-H1b (#31.1) coordinates: 
    14199 Matrix rotation and translation 
    14200 0.99999389 0.00177649 -0.00301060 1.46938329 
    14201 -0.00178862 0.99999027 -0.00403314 2.09308765 
    14202 0.00300340 0.00403850 0.99998733 -2.31704250 
    14203 Axis 0.75588049 -0.56318958 -0.33385952 
    14204 Axis point 0.00000000 517.35270636 616.23159370 
    14205 Rotation angle (degrees) 0.30591687 
    14206 Shift along axis 0.70543972 
    14207  
    14208 
    14209 > fitmap #31.3 inMap #31.1
    14210 
    14211 Fit molecule ys-H1b3 (#31.3) to map ys-H1b (#31.1) using 60958 atoms 
    14212 average map value = 4.549, steps = 44 
    14213 shifted from previous position = 0.283 
    14214 rotated from previous position = 0.0661 degrees 
    14215 atoms outside contour = 23605, contour level = 2.5187 
    14216  
    14217 Position of ys-H1b3 (#31.3) relative to ys-H1b (#31.1) coordinates: 
    14218 Matrix rotation and translation 
    14219 0.99999362 0.00149932 -0.00324257 1.55563566 
    14220 -0.00151226 0.99999089 -0.00399146 2.04672130 
    14221 0.00323656 0.00399634 0.99998678 -2.61613539 
    14222 Axis 0.74534040 -0.60456674 -0.28101021 
    14223 Axis point -0.00000000 610.43806197 610.93366862 
    14224 Rotation angle (degrees) 0.30702037 
    14225 Shift along axis 0.65725925 
    14226  
    14227 
    14228 > fitmap #32.1 inMap #100
    14229 
    14230 Fit map ys-H1c in map 4ybb_50Score_3A.mrc using 167731 points 
    14231 correlation = 0.7674, correlation about mean = 0.558, overlap = 4.354e+05 
    14232 steps = 124, shift = 1.66, angle = 0.567 degrees 
    14233  
    14234 Position of ys-H1c (#32.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    14235 Matrix rotation and translation 
    14236 -0.16676494 0.06693558 0.98372206 119.84754147 
    14237 -0.10650347 -0.99307857 0.04951729 535.96173990 
    14238 0.98022776 -0.09651207 0.17273956 85.03785944 
    14239 Axis -0.64399582 0.01540999 -0.76487379 
    14240 Axis point 44.12683242 267.58929209 0.00000000 
    14241 Rotation angle (degrees) 173.48994567 
    14242 Shift along axis -133.96538144 
    14243  
    14244 
    14245 > fitmap #32.5 inMap #32.1
    14246 
    14247 Fit molecule ys-H1c5 (#32.5) to map ys-H1c (#32.1) using 92992 atoms 
    14248 average map value = 6.048, steps = 48 
    14249 shifted from previous position = 0.032 
    14250 rotated from previous position = 0.0651 degrees 
    14251 atoms outside contour = 27637, contour level = 2.7384 
    14252  
    14253 Position of ys-H1c5 (#32.5) relative to ys-H1c (#32.1) coordinates: 
    14254 Matrix rotation and translation 
    14255 0.99997134 0.00683750 -0.00325116 0.47414368 
    14256 -0.00686021 0.99995179 -0.00702603 3.80685164 
    14257 0.00320297 0.00704814 0.99997003 -2.97758390 
    14258 Axis 0.68080558 -0.31220370 -0.66259537 
    14259 Axis point 0.00000000 320.87784613 588.81843987 
    14260 Rotation angle (degrees) 0.59224322 
    14261 Shift along axis 1.10721980 
    14262  
    14263 
    14264 > fitmap #32.3 inMap #32.1
    14265 
    14266 Fit molecule ys-H1c3 (#32.3) to map ys-H1c (#32.1) using 60097 atoms 
    14267 average map value = 3.968, steps = 60 
    14268 shifted from previous position = 0.268 
    14269 rotated from previous position = 0.079 degrees 
    14270 atoms outside contour = 28534, contour level = 2.7384 
    14271  
    14272 Position of ys-H1c3 (#32.3) relative to ys-H1c (#32.1) coordinates: 
    14273 Matrix rotation and translation 
    14274 0.99997398 0.00646484 -0.00319928 0.49917691 
    14275 -0.00648754 0.99995349 -0.00713593 3.74546403 
    14276 0.00315300 0.00715650 0.99996942 -3.22021908 
    14277 Axis 0.70380541 -0.31280660 -0.63781657 
    14278 Axis point 0.00000000 342.48952741 576.71831233 
    14279 Rotation angle (degrees) 0.58177319 
    14280 Shift along axis 1.23362664 
    14281  
    14282 
    14283 > fitmap #33.1 inMap #100
    14284 
    14285 Fit map ys-I1a in map 4ybb_50Score_3A.mrc using 167397 points 
    14286 correlation = 0.7808, correlation about mean = 0.5625, overlap = 5.023e+05 
    14287 steps = 104, shift = 1.28, angle = 0.294 degrees 
    14288  
    14289 Position of ys-I1a (#33.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    14290 Matrix rotation and translation 
    14291 -0.16232614 0.06619988 0.98451399 119.60346941 
    14292 -0.09920397 -0.99378654 0.05046668 534.52931761 
    14293 0.98173764 -0.08947563 0.16788483 84.37077360 
    14294 Axis -0.64584944 0.01281317 -0.76335727 
    14295 Axis point 43.19343947 266.81471925 0.00000000 
    14296 Rotation angle (degrees) 173.78038265 
    14297 Shift along axis -134.80186326 
    14298  
    14299 
    14300 > fitmap #33.5 inMap #33.1
    14301 
    14302 Fit molecule ys-I1a5 (#33.5) to map ys-I1a (#33.1) using 92992 atoms 
    14303 average map value = 7.077, steps = 44 
    14304 shifted from previous position = 0.0267 
    14305 rotated from previous position = 0.0671 degrees 
    14306 atoms outside contour = 22045, contour level = 2.5656 
    14307  
    14308 Position of ys-I1a5 (#33.5) relative to ys-I1a (#33.1) coordinates: 
    14309 Matrix rotation and translation 
    14310 0.99999617 0.00235984 -0.00144321 0.88823549 
    14311 -0.00236709 0.99998450 -0.00503859 2.24307396 
    14312 0.00143129 0.00504199 0.99998626 -1.68276556 
    14313 Axis 0.87665592 -0.24998057 -0.41107678 
    14314 Axis point 0.00000000 260.91573887 489.50963886 
    14315 Rotation angle (degrees) 0.32942089 
    14316 Shift along axis 0.90969784 
    14317  
    14318 
    14319 > fitmap #33.3 inMap #33.1
    14320 
    14321 Fit molecule ys-I1a3 (#33.3) to map ys-I1a (#33.1) using 61025 atoms 
    14322 average map value = 4.424, steps = 44 
    14323 shifted from previous position = 0.291 
    14324 rotated from previous position = 0.0763 degrees 
    14325 atoms outside contour = 24712, contour level = 2.5656 
    14326  
    14327 Position of ys-I1a3 (#33.3) relative to ys-I1a (#33.1) coordinates: 
    14328 Matrix rotation and translation 
    14329 0.99999676 0.00201821 -0.00155203 0.96348465 
    14330 -0.00202604 0.99998516 -0.00505812 2.19224452 
    14331 0.00154180 0.00506125 0.99998600 -1.96439701 
    14332 Axis 0.89328585 -0.27310680 -0.35700568 
    14333 Axis point 0.00000000 321.52004061 484.47707055 
    14334 Rotation angle (degrees) 0.32453213 
    14335 Shift along axis 0.96325122 
    14336  
    14337 
    14338 > fitmap #34.1 inMap #100
    14339 
    14340 Fit map ys-I1b in map 4ybb_50Score_3A.mrc using 167329 points 
    14341 correlation = 0.783, correlation about mean = 0.571, overlap = 4.925e+05 
    14342 steps = 128, shift = 1.3, angle = 0.369 degrees 
    14343  
    14344 Position of ys-I1b (#34.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    14345 Matrix rotation and translation 
    14346 -0.16311182 0.06375086 0.98454576 120.25918352 
    14347 -0.10144014 -0.99370520 0.04753814 535.75335379 
    14348 0.98137884 -0.09211843 0.16855196 84.81087133 
    14349 Axis -0.64554856 0.01463878 -0.76357892 
    14350 Axis point 43.37853426 267.50327973 0.00000000 
    14351 Rotation angle (degrees) 173.79022803 
    14352 Shift along axis -134.55015916 
    14353  
    14354 
    14355 > fitmap #34.5 inMap #34.1
    14356 
    14357 Fit molecule ys-I1b5 (#34.5) to map ys-I1b (#34.1) using 92992 atoms 
    14358 average map value = 6.843, steps = 48 
    14359 shifted from previous position = 0.0316 
    14360 rotated from previous position = 0.0584 degrees 
    14361 atoms outside contour = 23227, contour level = 2.6024 
    14362  
    14363 Position of ys-I1b5 (#34.5) relative to ys-I1b (#34.1) coordinates: 
    14364 Matrix rotation and translation 
    14365 0.99999017 0.00272306 -0.00349901 1.32101454 
    14366 -0.00274052 0.99998377 -0.00499482 2.18899569 
    14367 0.00348535 0.00500436 0.99998140 -2.11955093 
    14368 Axis 0.74817716 -0.52259738 -0.40880670 
    14369 Axis point 0.00000000 367.36998655 511.43724007 
    14370 Rotation angle (degrees) 0.38287372 
    14371 Shift along axis 0.71087611 
    14372  
    14373 
    14374 > fitmap #34.3 inMap #34.1
    14375 
    14376 Fit molecule ys-I1b3 (#34.3) to map ys-I1b (#34.1) using 61064 atoms 
    14377 average map value = 4.216, steps = 48 
    14378 shifted from previous position = 0.287 
    14379 rotated from previous position = 0.0681 degrees 
    14380 atoms outside contour = 26592, contour level = 2.6024 
    14381  
    14382 Position of ys-I1b3 (#34.3) relative to ys-I1b (#34.1) coordinates: 
    14383 Matrix rotation and translation 
    14384 0.99999073 0.00233639 -0.00361687 1.40117114 
    14385 -0.00235427 0.99998499 -0.00494733 2.11158854 
    14386 0.00360525 0.00495579 0.99998122 -2.38611222 
    14387 Axis 0.75459472 -0.55030873 -0.35741728 
    14388 Axis point 0.00000000 429.45116137 508.72831924 
    14389 Rotation angle (degrees) 0.37597070 
    14390 Shift along axis 0.74812848 
    14391  
    14392 
    14393 > rename #30 ys-H1a
    14394 
    14395 > rename #31 ys-H1b
    14396 
    14397 > rename #32 ys-H1c
    14398 
    14399 > rename #33 ys-I1a
    14400 
    14401 > rename #34 ys-I1b
    14402 
    14403 executed 70S_open_ys.cxc 
    14404 
    14405 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_arg.cxc
    14406 
    14407 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/arg_50S.pdb name
    14408 > arg5
    14409 
    14410 Chain information for arg5 #1 
    14411 --- 
    14412 Chain | Description 
    14413 3 | No description available 
    14414 5 | No description available 
    14415 A | No description available 
    14416 B | No description available 
    14417 C | No description available 
    14418 D | No description available 
    14419 E | No description available 
    14420 F | No description available 
    14421 I | No description available 
    14422 J | No description available 
    14423 K | No description available 
    14424 M | No description available 
    14425 N | No description available 
    14426 O | No description available 
    14427 P | No description available 
    14428 Q | No description available 
    14429 R | No description available 
    14430 S | No description available 
    14431 T | No description available 
    14432 U | No description available 
    14433 V | No description available 
    14434 W | No description available 
    14435 X | No description available 
    14436 Y | No description available 
    14437 a | No description available 
    14438 b | No description available 
    14439 c | No description available 
    14440 d | No description available 
    14441 e | No description available 
    14442 f | No description available 
    14443 g | No description available 
    14444 h | No description available 
    14445 i | No description available 
    14446 j | No description available 
    14447  
    14448 
    14449 > rename #1 id #20.5
    14450 
    14451 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/arg_30S.pdb name
    14452 > arg3
    14453 
    14454 Chain information for arg3 #1 
    14455 --- 
    14456 Chain | Description 
    14457 6 | No description available 
    14458 B | No description available 
    14459 C | No description available 
    14460 D | No description available 
    14461 E | No description available 
    14462 F | No description available 
    14463 G | No description available 
    14464 H | No description available 
    14465 I | No description available 
    14466 J | No description available 
    14467 K | No description available 
    14468 L | No description available 
    14469 M | No description available 
    14470 N | No description available 
    14471 O | No description available 
    14472 P | No description available 
    14473 Q | No description available 
    14474 R | No description available 
    14475 S | No description available 
    14476 T | No description available 
    14477 U | No description available 
    14478 v | No description available 
    14479 w | No description available 
    14480 x | No description available 
    14481 y | No description available 
    14482  
    14483 
    14484 > rename #1 id #20.3
    14485 
    14486 > open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/arg_*.mrc name arg
    14487 
    14488 Opened arg as #1, grid size 380,380,380, pixel 1.05, shown at level 4.05, step
    14489 2, values float32 
    14490 
    14491 > rename #1 id #20.1
    14492 
    14493 > rename #20 argb
    14494 
    14495 > matchmaker #20.5 to #101 matrix Nucleic bring #20.1#20.3
    14496 
    14497 Parameters 
    14498 --- 
    14499 Chain pairing | bb 
    14500 Alignment algorithm | Needleman-Wunsch 
    14501 Similarity matrix | Nucleic 
    14502 SS fraction | 0.3 
    14503 Gap open (HH/SS/other) | 18/18/6 
    14504 Gap extend | 1 
    14505 SS matrix |  |  | H | S | O 
    14506 ---|---|---|--- 
    14507 H | 6 | -9 | -6 
    14508 S |  | 6 | -6 
    14509 O |  |  | 4 
    14510 Iteration cutoff | 2 
    14511  
    14512 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with arg5, chain 3 (#20.5),
    14513 sequence alignment score = 11567.9 
    14514 RMSD between 2713 pruned atom pairs is 0.426 angstroms; (across all 2903
    14515 pairs: 3.446) 
    14516  
    14517 
    14518 > fitmap #20.1 inMap #100
    14519 
    14520 Fit map arg in map 4ybb_50Score_3A.mrc using 68379 points 
    14521 correlation = 0.7998, correlation about mean = 0.5595, overlap = 2.858e+05 
    14522 steps = 48, shift = 0.0198, angle = 0.0465 degrees 
    14523  
    14524 Position of arg (#20.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    14525 Matrix rotation and translation 
    14526 0.04335132 -0.67171102 -0.73954376 580.56014922 
    14527 0.71962017 -0.49248421 0.48949578 169.85732478 
    14528 -0.69301333 -0.55341089 0.46202696 467.33682018 
    14529 Axis -0.59956755 -0.02675036 0.79987697 
    14530 Axis point 403.39737183 308.69128461 0.00000000 
    14531 Rotation angle (degrees) 119.57437645 
    14532 Shift along axis 21.18318896 
    14533  
    14534 
    14535 > fitmap #20.5 inMap #20.1
    14536 
    14537 Fit molecule arg5 (#20.5) to map arg (#20.1) using 93932 atoms 
    14538 average map value = 8.028, steps = 40 
    14539 shifted from previous position = 0.028 
    14540 rotated from previous position = 0.0467 degrees 
    14541 atoms outside contour = 40883, contour level = 4.0546 
    14542  
    14543 Position of arg5 (#20.5) relative to arg (#20.1) coordinates: 
    14544 Matrix rotation and translation 
    14545 1.00000000 0.00000583 0.00002491 -0.00204004 
    14546 -0.00000583 1.00000000 0.00005404 -0.01191715 
    14547 -0.00002491 -0.00005404 1.00000000 0.02173238 
    14548 Axis -0.90382996 0.41664235 -0.09747076 
    14549 Axis point 0.00000000 392.68816757 180.13481166 
    14550 Rotation angle (degrees) 0.00342579 
    14551 Shift along axis -0.00523961 
    14552  
    14553 
    14554 > fitmap #20.3 inMap #20.1
    14555 
    14556 Fit molecule arg3 (#20.3) to map arg (#20.1) using 60797 atoms 
    14557 average map value = 4.762, steps = 44 
    14558 shifted from previous position = 0.0202 
    14559 rotated from previous position = 0.0354 degrees 
    14560 atoms outside contour = 42480, contour level = 4.0546 
    14561  
    14562 Position of arg3 (#20.3) relative to arg (#20.1) coordinates: 
    14563 Matrix rotation and translation 
    14564 0.99999999 -0.00001781 0.00015102 -0.03079729 
    14565 0.00001784 0.99999998 -0.00018128 0.03779708 
    14566 -0.00015102 0.00018128 0.99999997 0.00249277 
    14567 Axis 0.76612779 0.63825790 0.07533296 
    14568 Axis point 0.00000000 -13.42131942 205.98134486 
    14569 Rotation angle (degrees) 0.01355702 
    14570 Shift along axis 0.00071742 
    14571  
    14572 executed 70S_open_arg.cxc 
    14573 
    14574 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_h2.cxc
    14575 
    14576 > open
    14577 > /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/apo_H2*local*.mrc
    14578 > name hy2
    14579 
    14580 Opened hy2 as #1, grid size 576,576,576, pixel 1.06, shown at level 0.583,
    14581 step 4, values float32 
    14582 
    14583 > rename #1 id #11.1
    14584 
    14585 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h2_50S.pdb name
    14586 > hy25
    14587 
    14588 Chain information for hy25 #1 
    14589 --- 
    14590 Chain | Description 
    14591 3 | No description available 
    14592 5 | No description available 
    14593 B | No description available 
    14594 C | No description available 
    14595 D | No description available 
    14596 E | No description available 
    14597 F | No description available 
    14598 I | No description available 
    14599 M | No description available 
    14600 N | No description available 
    14601 O | No description available 
    14602 P | No description available 
    14603 Q | No description available 
    14604 R | No description available 
    14605 S | No description available 
    14606 T | No description available 
    14607 U | No description available 
    14608 V | No description available 
    14609 W | No description available 
    14610 X | No description available 
    14611 Y | No description available 
    14612 a | No description available 
    14613 b | No description available 
    14614 c | No description available 
    14615 d | No description available 
    14616 e | No description available 
    14617 f | No description available 
    14618 g | No description available 
    14619 h | No description available 
    14620 i | No description available 
    14621 j | No description available 
    14622  
    14623 
    14624 > rename #1 id #11.5
    14625 
    14626 > open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h2_30S.pdb name
    14627 > hy23
    14628 
    14629 Chain information for hy23 #1 
    14630 --- 
    14631 Chain | Description 
    14632 6 | No description available 
    14633 B | No description available 
    14634 C | No description available 
    14635 D | No description available 
    14636 E | No description available 
    14637 F | No description available 
    14638 G | No description available 
    14639 H | No description available 
    14640 I | No description available 
    14641 J | No description available 
    14642 K | No description available 
    14643 L | No description available 
    14644 M | No description available 
    14645 N | No description available 
    14646 O | No description available 
    14647 P | No description available 
    14648 Q | No description available 
    14649 R | No description available 
    14650 S | No description available 
    14651 T | No description available 
    14652 U | No description available 
    14653 p | No description available 
    14654 v | No description available 
    14655 w | No description available 
    14656 y | No description available 
    14657  
    14658 
    14659 > rename #1 id #11.3
    14660 
    14661 > matchmaker #11.5 to #101 matrix Nucleic bring #11.1#11.3
    14662 
    14663 Parameters 
    14664 --- 
    14665 Chain pairing | bb 
    14666 Alignment algorithm | Needleman-Wunsch 
    14667 Similarity matrix | Nucleic 
    14668 SS fraction | 0.3 
    14669 Gap open (HH/SS/other) | 18/18/6 
    14670 Gap extend | 1 
    14671 SS matrix |  |  | H | S | O 
    14672 ---|---|---|--- 
    14673 H | 6 | -9 | -6 
    14674 S |  | 6 | -6 
    14675 O |  |  | 4 
    14676 Iteration cutoff | 2 
    14677  
    14678 Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with hy25, chain 3 (#11.5),
    14679 sequence alignment score = 11561.3 
    14680 RMSD between 2586 pruned atom pairs is 0.406 angstroms; (across all 2901
    14681 pairs: 4.609) 
    14682  
    14683 
    14684 > fitmap #11.1 inMap #100
    14685 
    14686 Fit map hy2 in map 4ybb_50Score_3A.mrc using 29804 points 
    14687 correlation = 0.7242, correlation about mean = 0.6417, overlap = 7.267e+04 
    14688 steps = 48, shift = 0.0744, angle = 0.0573 degrees 
    14689  
    14690 Position of hy2 (#11.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates: 
    14691 Matrix rotation and translation 
    14692 1.00000000 0.00003602 -0.00001029 0.01316792 
    14693 -0.00003602 0.99999999 0.00010657 -0.03440932 
    14694 0.00001030 -0.00010657 0.99999999 0.02381061 
    14695 Axis -0.94340756 -0.09113844 -0.31886669 
    14696 Axis point 0.00000000 172.91008810 337.33392045 
    14697 Rotation angle (degrees) 0.00647212 
    14698 Shift along axis -0.01687912 
    14699  
    14700 
    14701 > fitmap #11.5 inMap #11.1
    14702 
    14703 Fit molecule hy25 (#11.5) to map hy2 (#11.1) using 90870 atoms 
    14704 average map value = 14.68, steps = 28 
    14705 shifted from previous position = 0.0514 
    14706 rotated from previous position = 0.0613 degrees 
    14707 atoms outside contour = 33730, contour level = 0.58265 
    14708  
    14709 Position of hy25 (#11.5) relative to hy2 (#11.1) coordinates: 
    14710 Matrix rotation and translation 
    14711 0.99999996 0.00022036 -0.00015998 -0.00668301 
    14712 -0.00022039 0.99999996 -0.00017126 0.14091770 
    14713 0.00015994 0.00017129 0.99999997 -0.12061124 
    14714 Axis 0.53241836 -0.49723466 -0.68504627 
    14715 Axis point 659.69138147 52.17592242 0.00000000 
    14716 Rotation angle (degrees) 0.01843178 
    14717 Shift along axis 0.00899696 
    14718  
    14719 
    14720 > fitmap #11.3 inMap #11.1
    14721 
    14722 Fit molecule hy23 (#11.3) to map hy2 (#11.1) using 55387 atoms 
    14723 average map value = 9.621, steps = 28 
    14724 shifted from previous position = 0.132 
    14725 rotated from previous position = 0.0639 degrees 
    14726 atoms outside contour = 17421, contour level = 0.58265 
    14727  
    14728 Position of hy23 (#11.3) relative to hy2 (#11.1) coordinates: 
    14729 Matrix rotation and translation 
    14730 0.99999999 0.00015557 -0.00006781 -0.02334093 
    14731 -0.00015559 0.99999993 -0.00034415 0.15409237 
    14732 0.00006776 0.00034416 0.99999994 -0.13799206 
    14733 Axis 0.89688265 -0.17664932 -0.40545842 
    14734 Axis point 0.00000000 391.85336663 451.67273844 
    14735 Rotation angle (degrees) 0.02198552 
    14736 Shift along axis 0.00779566 
    14737  
    14738 executed 70S_open_h2.cxc 
    14739 executed 70S_startup_gtpys-all.cxc 
    14740 
    14741 > open
    14742 > /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/translocation/gtpys_translocation.cxc
    14743 
    14744 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
    14745 
    14746 > name atomods #*.3|#*.5
    14747 
    14748 > name emmaps #*.1|#*.7|#*.8|#*.9
    14749 
    14750 > name lsu #*.5
    14751 
    14752 > name lsumap #*.8
    14753 
    14754 > name ssu #*.3
    14755 
    14756 > name ssumap #*.7
    14757 
    14758 > name ligmap #*.9
    14759 
    14760 > name rna /y,v,w,3,6,5
    14761 
    14762 > name r23s /3
    14763 
    14764 > name r16s /6
    14765 
    14766 > name r5s /5
    14767 
    14768 > name pt /y
    14769 
    14770 > name dt /v
    14771 
    14772 > name efg /x
    14773 
    14774 > name pep /p
    14775 
    14776 > name mrna /w
    14777 
    14778 > name GSP :GSP
    14779 
    14780 > name GDP :GDP
    14781 
    14782 > name GTP :GTP
    14783 
    14784 > name ntide :GTP|:GDP|:GSP
    14785 
    14786 > name spc :SCM
    14787 
    14788 > name fua :FUA
    14789 
    14790 > name par :PAR
    14791 
    14792 > name argb :LIG
    14793 
    14794 > name drugs argb|par|fua|spc
    14795 
    14796 > name D1 /x:start-293
    14797 
    14798 > name D2 /x:294-410
    14799 
    14800 > name D3 /x:411-489
    14801 
    14802 > name D4 /x:490-612
    14803 
    14804 > name D5 /x:613-end
    14805 
    14806 > name sw1 /x:38-65
    14807 
    14808 > name sw2 /x:89-108
    14809 
    14810 > name pl /x:18-25
    14811 
    14812 > name nkxd /x:142-146
    14813 
    14814 > name mg /x:MG
    14815 
    14816 > name trna /y,v
    14817 
    14818 > name anticodon /y,v:34-36
    14819 
    14820 > name antiplus /y,v:32-38
    14821 
    14822 > name cca /y,v:74-76
    14823 
    14824 > name astem /y,v:1-7,66-73
    14825 
    14826 > name darm /y,v:8-25
    14827 
    14828 > name aarm /y,v:26-43
    14829 
    14830 > name varm /y,v:44-48
    14831 
    14832 > name tarm /y,v:49-65
    14833 
    14834 > name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
    14835 
    14836 > name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
    14837 
    14838 > name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
    14839 
    14840 > name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
    14841 
    14842 > name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
    14843 
    14844 > name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
    14845 
    14846 > name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
    14847 
    14848 > name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
    14849 
    14850 > name h8 /6:144-178
    14851 
    14852 > name h14 /6:339-350
    14853 
    14854 > name h18 /6:511-540
    14855 
    14856 > name h23 /6:674-716
    14857 
    14858 > name h24 /6:769-810
    14859 
    14860 > name h27 /6:894-905
    14861 
    14862 > name h28 /6:921-937,1379-1400
    14863 
    14864 > name h29 /6:938-943,1337-1346
    14865 
    14866 > name h30 /6:945-955,1225-1235
    14867 
    14868 > name h31 /6:956-975
    14869 
    14870 > name h32 /6:984-990,1215-1221
    14871 
    14872 > name h34 /6:1045-1065,1188-1211
    14873 
    14874 > name h35 /6:1066-1073,1102-1110
    14875 
    14876 > name h36 /6:1074-1083
    14877 
    14878 > name h44 /6:1401-1502
    14879 
    14880 > name h45 /6:1506-1529
    14881 
    14882 > name aploop /6:956-959
    14883 
    14884 > name term16S /6:1503-end
    14885 
    14886 > name aphelix /6:1228-1230
    14887 
    14888 > name us3 #*.3/C
    14889 
    14890 > name us5 #*.3/E
    14891 
    14892 > name us7 #*.3/G
    14893 
    14894 > name us9 #*.3/I
    14895 
    14896 > name us11 #*.3/K
    14897 
    14898 > name us12 #*.3/L
    14899 
    14900 > name us13 #*.3/M
    14901 
    14902 > name us14 #*.3/N
    14903 
    14904 > name us15 #*.3/O
    14905 
    14906 > name us9-130 #*.3/I:130
    14907 
    14908 > name l1stalk /3:2097-2191
    14909 
    14910 > name srl /3:2652-2668
    14911 
    14912 > name H68 /3:1832-1906
    14913 
    14914 > name H69 /3:1907-1924
    14915 
    14916 > name H95 /3:2647-2673
    14917 
    14918 > name ul2 #*.5/B
    14919 
    14920 > name ul5 #*.5/E
    14921 
    14922 > name ul14 #*.5/N
    14923 
    14924 > name ul19 #*.5/S
    14925 
    14926 > name ul31 #*.5/e
    14927 
    14928 executed 70S_assign.cxc 
    14929 
    14930 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
    14931 
    14932 > alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
    14933 
    14934 > alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
    14935 
    14936 > alias cylinders cartoon style protein modeh tube rad 2 sides 24;
    14937 
    14938 > alias licorice car style protein modeh default arrows f xsect oval width 1
    14939 > thick 1;
    14940 
    14941 > dssp
    14942 
    14943 > windowsize 1000 1000
    14944 
    14945 > set bgColor white
    14946 
    14947 > lighting full
    14948 
    14949 > set silhouettes true
    14950 
    14951 > set silhouetteWidth 1.7
    14952 
    14953 > set silhouettes true
    14954 
    14955 > set silhouetteDepthJump 0.02
    14956 
    14957 > cartoon style width 2.5
    14958 
    14959 > size atomRadius 2
    14960 
    14961 Changed 1916608 atom radii 
    14962 
    14963 > nucleotides fill
    14964 
    14965 > size ions atomRadius 1.6
    14966 
    14967 Changed 35 atom radii 
    14968 
    14969 > size stickRadius 0.1
    14970 
    14971 Changed 2071407 bond radii 
    14972 
    14973 > style stick ringFill thin
    14974 
    14975 Changed 1916608 atom styles, 145508 residue ring styles 
    14976 
    14977 > show ribbons
    14978 
    14979 > hide H
    14980 
    14981 > hide :HOH
    14982 
    14983 > hide target a
    14984 
    14985 > show nucleic target a
    14986 
    14987 > show drugs target a
    14988 
    14989 > style drugs ball
    14990 
    14991 Changed 166 atom styles 
    14992 
    14993 > nucrib
    14994 
    14995 > graphics selection color black
    14996 
    14997 > volume emmaps style surface step 1 level 4
    14998 
    14999 > surface dust emmaps size 3
    15000 
    15001 > volume surfaceSmoothing true
    15002 
    15003 > cartoon tether trna shape cone opacity 1
    15004 
    15005 > dssp
    15006 
    15007 executed 70S_display.cxc 
    15008 
    15009 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
    15010 
    15011 > color name efg-t 100,0,0,50
    15012 
    15013 Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    15014 
    15015  
    15016 
    15017 > color name sw1-t 100,92,0,50
    15018 
    15019 Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    15020 
    15021  
    15022 
    15023 > color name sw2-t 68,81,0,50
    15024 
    15025 Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    15026 
    15027  
    15028 
    15029 > color name pl-t 23,59,0,50
    15030 
    15031 Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    15032 
    15033  
    15034 
    15035 > color name d1-t 100,18,4,50
    15036 
    15037 Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
    15038 
    15039  
    15040 
    15041 > color name d2-t 100,40,4,50
    15042 
    15043 Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    15044 
    15045  
    15046 
    15047 > color name d3-t 100,27,36,50
    15048 
    15049 Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
    15050 
    15051  
    15052 
    15053 > color name d4-t 80,0,23,50
    15054 
    15055 Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
    15056 
    15057  
    15058 
    15059 > color name d5-t 100,60,4,50
    15060 
    15061 Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
    15062 
    15063  
    15064 
    15065 > color name fa-t 100,90,4,50
    15066 
    15067 Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    15068 
    15069  
    15070 
    15071 > color name gtp-t 45,53,60,50
    15072 
    15073 Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
    15074 
    15075  
    15076 
    15077 > color name mg-t 1,39,16,50
    15078 
    15079 Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
    15080 
    15081  
    15082 
    15083 > color name spc-t 100,0,0,50
    15084 
    15085 Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    15086 
    15087  
    15088 
    15089 > color name argb-t 50,0,50,50
    15090 
    15091 Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
    15092 
    15093  
    15094 
    15095 > color name g-1t 98,42,30,50
    15096 
    15097 Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
    15098 
    15099  
    15100 
    15101 > color name g-2t 95,35,25,50
    15102 
    15103 Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
    15104 
    15105  
    15106 
    15107 > color name g-3t 92,28,20,50
    15108 
    15109 Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
    15110 
    15111  
    15112 
    15113 > color name g-4t 89,21,15,50
    15114 
    15115 Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
    15116 
    15117  
    15118 
    15119 > color name g-5t 86,14,10,50
    15120 
    15121 Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
    15122 
    15123  
    15124 
    15125 > color name g-6t 83,7,5,50
    15126 
    15127 Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
    15128 
    15129  
    15130 
    15131 > color name g-7t 80,0,0,50
    15132 
    15133 Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
    15134 
    15135  
    15136 
    15137 > color name p-t 40,60,2,50
    15138 
    15139 Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
    15140 
    15141  
    15142 
    15143 > color name p-c 40,60,2,100
    15144 
    15145 Color 'p-c' is opaque: rgb(40%, 60%, 2%) hex: #669905
    15146 
    15147  
    15148 
    15149 > color name p-1t 4,34,1,50
    15150 
    15151 Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
    15152 
    15153  
    15154 
    15155 > color name p-2t 12,39,1,50
    15156 
    15157 Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
    15158 
    15159  
    15160 
    15161 > color name p-3t 20,44,1,50
    15162 
    15163 Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
    15164 
    15165  
    15166 
    15167 > color name p-4t 28,49,1,50
    15168 
    15169 Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
    15170 
    15171  
    15172 
    15173 > color name p-5t 36,54,2,50
    15174 
    15175 Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
    15176 
    15177  
    15178 
    15179 > color name p-6t 44,59,2,50
    15180 
    15181 Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
    15182 
    15183  
    15184 
    15185 > color name p-7t 52,64,2,50
    15186 
    15187 Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
    15188 
    15189  
    15190 
    15191 > color name p-8t 60,69,2,50
    15192 
    15193 Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
    15194 
    15195  
    15196 
    15197 > color name p-9t 68,74,3,50
    15198 
    15199 Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
    15200 
    15201  
    15202 
    15203 > color name p-10t 76,79,3,50
    15204 
    15205 Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
    15206 
    15207  
    15208 
    15209 > color name p-11t 84,84,3,50
    15210 
    15211 Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
    15212 
    15213  
    15214 
    15215 > color name d-t 100,75,4,50
    15216 
    15217 Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
    15218 
    15219  
    15220 
    15221 > color name d-c 100,75,4,100
    15222 
    15223 Color 'd-c' is opaque: rgb(100%, 75%, 4%) hex: #ffbf0a
    15224 
    15225  
    15226 
    15227 > color name d-1t 100,100,4,50
    15228 
    15229 Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
    15230 
    15231  
    15232 
    15233 > color name d-2t 100,93,4,50
    15234 
    15235 Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
    15236 
    15237  
    15238 
    15239 > color name d-3t 100,86,4,50
    15240 
    15241 Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
    15242 
    15243  
    15244 
    15245 > color name d-4t 100,79,4,50
    15246 
    15247 Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
    15248 
    15249  
    15250 
    15251 > color name d-5t 100,72,4,50
    15252 
    15253 Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
    15254 
    15255  
    15256 
    15257 > color name d-6t 100,65,4,50
    15258 
    15259 Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
    15260 
    15261  
    15262 
    15263 > color name d-7t 100,58,4,50
    15264 
    15265 Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
    15266 
    15267  
    15268 
    15269 > color name d-8t 100,51,4,50
    15270 
    15271 Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
    15272 
    15273  
    15274 
    15275 > color name d-9t 100,44,4,50
    15276 
    15277 Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
    15278 
    15279  
    15280 
    15281 > color name d-10t 100,37,4,50
    15282 
    15283 Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
    15284 
    15285  
    15286 
    15287 > color name d-11t 100,30,4,50
    15288 
    15289 Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
    15290 
    15291  
    15292 
    15293 > color name m-t 95,43,62,50
    15294 
    15295 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    15296 
    15297  
    15298 
    15299 > color name m-c 95,43,62,100
    15300 
    15301 Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
    15302 
    15303  
    15304 
    15305 > color name m-1t 100,80,90,50
    15306 
    15307 Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
    15308 
    15309  
    15310 
    15311 > color name m-2t 98,76,87,50
    15312 
    15313 Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
    15314 
    15315  
    15316 
    15317 > color name m-3t 96,72,84,50
    15318 
    15319 Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
    15320 
    15321  
    15322 
    15323 > color name m-4t 94,68,81,50
    15324 
    15325 Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
    15326 
    15327  
    15328 
    15329 > color name m-5t 92,64,78,50
    15330 
    15331 Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
    15332 
    15333  
    15334 
    15335 > color name m-6t 90,60,75,50
    15336 
    15337 Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
    15338 
    15339  
    15340 
    15341 > color name m-7t 88,56,72,50
    15342 
    15343 Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
    15344 
    15345  
    15346 
    15347 > color name m-8t 86,52,69,50
    15348 
    15349 Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
    15350 
    15351  
    15352 
    15353 > color name m-9t 84,48,66,50
    15354 
    15355 Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
    15356 
    15357  
    15358 
    15359 > color name m-10t 82,44,63,50
    15360 
    15361 Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
    15362 
    15363  
    15364 
    15365 > color name m-11t 80,40,60,50
    15366 
    15367 Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
    15368 
    15369  
    15370 
    15371 > color name head-t 71,51,66,50
    15372 
    15373 Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
    15374 
    15375  
    15376 
    15377 > color name head-c 89,89,100,100
    15378 
    15379 Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
    15380 
    15381  
    15382 
    15383 > color name headfa-t 80,79,100,50
    15384 
    15385 Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex: #ccc9ff80
    15386 
    15387  
    15388 
    15389 > color name headblue-t 59,78,94,50
    15390 
    15391 Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
    15392 
    15393  
    15394 
    15395 > color name headh1-t 41,64,100,50
    15396 
    15397 Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
    15398 
    15399  
    15400 
    15401 > color name headh2-t 50,70,100,50
    15402 
    15403 Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
    15404 
    15405  
    15406 
    15407 > color name headgray-t 60,60,60,50
    15408 
    15409 Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
    15410 
    15411  
    15412 
    15413 > color name darkhead-s 58,34,52,100
    15414 
    15415 Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
    15416 
    15417  
    15418 
    15419 > color name bodywhite-t 90,90,90,50
    15420 
    15421 Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
    15422 #e6e6e680
    15423 
    15424  
    15425 
    15426 > color name rps-t 75,88,93,50
    15427 
    15428 Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
    15429 
    15430  
    15431 
    15432 > color name ssu-t 57,71,75,50
    15433 
    15434 Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
    15435 
    15436  
    15437 
    15438 > color name h18-t 31,59,68,50
    15439 
    15440 Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
    15441 
    15442  
    15443 
    15444 > color name h18-c 31,59,68,100
    15445 
    15446 Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
    15447 
    15448  
    15449 
    15450 > color name h23-t 18,36,100,50
    15451 
    15452 Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
    15453 
    15454  
    15455 
    15456 > color name h23-c 18,36,100,100
    15457 
    15458 Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
    15459 
    15460  
    15461 
    15462 > color name h24-t 50,70,90,50
    15463 
    15464 Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
    15465 
    15466  
    15467 
    15468 > color name h24-c 50,70,90,100
    15469 
    15470 Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
    15471 
    15472  
    15473 
    15474 > color name h28-t 0,24,57,50
    15475 
    15476 Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
    15477 
    15478  
    15479 
    15480 > color name h28-c 0,24,57,100
    15481 
    15482 Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
    15483 
    15484  
    15485 
    15486 > color name h29-t 80,69,92,50
    15487 
    15488 Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
    15489 
    15490  
    15491 
    15492 > color name h29-c 80,69,92,100
    15493 
    15494 Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
    15495 
    15496  
    15497 
    15498 > color name h30-t 40,40,59,50
    15499 
    15500 Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
    15501 
    15502  
    15503 
    15504 > color name h30-c 40,40,59,100
    15505 
    15506 Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
    15507 
    15508  
    15509 
    15510 > color name h31-t 45,18,59,50
    15511 
    15512 Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
    15513 
    15514  
    15515 
    15516 > color name h31-c 45,18,59,100
    15517 
    15518 Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
    15519 
    15520  
    15521 
    15522 > color name h34-t 59,18,59,50
    15523 
    15524 Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
    15525 
    15526  
    15527 
    15528 > color name h34-c 59,18,59,100
    15529 
    15530 Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
    15531 
    15532  
    15533 
    15534 > color name h35-t 50,22,45,50
    15535 
    15536 Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
    15537 
    15538  
    15539 
    15540 > color name h35-c 50,22,45,100
    15541 
    15542 Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
    15543 
    15544  
    15545 
    15546 > color name h44-t 27,50,80,50
    15547 
    15548 Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
    15549 
    15550  
    15551 
    15552 > color name h44-c 27,50,80,100
    15553 
    15554 Color 'h44-c' is opaque: rgb(27%, 50%, 80%) hex: #4580cc
    15555 
    15556  
    15557 
    15558 > color name aploop-t 27,0,50,50
    15559 
    15560 Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
    15561 
    15562  
    15563 
    15564 > color name term16-t 40,64,64,50
    15565 
    15566 Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
    15567 
    15568  
    15569 
    15570 > color name uS3-t 64,41,82,50
    15571 
    15572 Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
    15573 
    15574  
    15575 
    15576 > color name uS5-t 0,50,45,50
    15577 
    15578 Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
    15579 
    15580  
    15581 
    15582 > color name gray-t 70,70,70,50
    15583 
    15584 Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
    15585 
    15586  
    15587 
    15588 > color name hx68-t 50,50,50,50
    15589 
    15590 Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    15591 
    15592  
    15593 
    15594 > color name hx68-c 50,50,50,100
    15595 
    15596 Color 'hx68-c' is opaque: gray(50%) hex: #808080
    15597 
    15598  
    15599 
    15600 > color name hx69-t 40,40,40,50
    15601 
    15602 Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
    15603 
    15604  
    15605 
    15606 > color name hx69-c 40,40,40,100
    15607 
    15608 Color 'hx69-c' is opaque: gray(40%) hex: #666666
    15609 
    15610  
    15611 
    15612 > color name srl-t 50,50,50,50
    15613 
    15614 Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    15615 
    15616  
    15617 
    15618 > color name srl-t 50,50,50,100
    15619 
    15620 Color 'srl-t' is opaque: gray(50%) hex: #808080
    15621 
    15622  
    15623 
    15624 > color name lightgrayt 83,83,83,50
    15625 
    15626 Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
    15627 
    15628  
    15629 
    15630 > color name silvert 75,75,75,50
    15631 
    15632 Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
    15633 
    15634  
    15635 
    15636 > color name grayt 50,50,50,50
    15637 
    15638 Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
    15639 
    15640  
    15641 
    15642 > color name lightcyant 88,100,100,50
    15643 
    15644 Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
    15645 #e0ffff80
    15646 
    15647  
    15648 
    15649 > color name yellowt 100,90,0,50
    15650 
    15651 Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
    15652 
    15653  
    15654 
    15655 > color name deeppinkt 100,8,58,50
    15656 
    15657 Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
    15658 
    15659  
    15660 
    15661 > color name oranget 100,65,0,50
    15662 
    15663 Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
    15664 
    15665  
    15666 
    15667 > color name yellowgreent 60,80,20,50
    15668 
    15669 Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
    15670 #99cc3380
    15671 
    15672  
    15673 
    15674 > color name darkmagentat 54,0,54,50
    15675 
    15676 Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
    15677 #8a008a80
    15678 
    15679  
    15680 
    15681 > color name orchidt 86,44,84,50
    15682 
    15683 Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
    15684 
    15685  
    15686 
    15687 > color name paleturquoiset 69,93,93,50
    15688 
    15689 Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
    15690 #b0eded80
    15691 
    15692  
    15693 
    15694 > color name pinkt 100,75,80,50
    15695 
    15696 Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
    15697 
    15698  
    15699 
    15700 > color name darkgreent 0,39,0,50
    15701 
    15702 Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
    15703 
    15704  
    15705 
    15706 > color name limegreent 20,80,20,50
    15707 
    15708 Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
    15709 
    15710  
    15711 
    15712 > color name turquoiset 25,88,82,50
    15713 
    15714 Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
    15715 
    15716  
    15717 
    15718 > color name tealt 0,50,50,50
    15719 
    15720 Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
    15721 
    15722  
    15723 
    15724 > color name darkoranget 100,50,0,50
    15725 
    15726 Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
    15727 #ff800080
    15728 
    15729  
    15730 
    15731 > color name lightyellowt 100,100,50,50
    15732 
    15733 Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
    15734 #ffff8080
    15735 
    15736  
    15737 
    15738 > color name goldt 100,75,0,50
    15739 
    15740 Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
    15741 
    15742  
    15743 
    15744 > color name plumt 87,63,87,50
    15745 
    15746 Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
    15747 
    15748  
    15749 
    15750 > color name ssubluet 68,86,90,50
    15751 
    15752 Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
    15753 
    15754  
    15755 
    15756 > color name p-prect 10,41,0,50
    15757 
    15758 Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
    15759 
    15760  
    15761 
    15762 > color name p-h2t 23,59,0,50
    15763 
    15764 Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    15765 
    15766  
    15767 
    15768 > color name p-h1t 40,73,0,50
    15769 
    15770 Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
    15771 
    15772  
    15773 
    15774 > color name p-h1c 40,73,0,100
    15775 
    15776 Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
    15777 
    15778  
    15779 
    15780 > color name p-spct 68,81,0,50
    15781 
    15782 Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    15783 
    15784  
    15785 
    15786 > color name p-spcc 68,81,0,100
    15787 
    15788 Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
    15789 
    15790  
    15791 
    15792 > color name p-fat 82,92,0,50
    15793 
    15794 Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
    15795 
    15796  
    15797 
    15798 > color name p-postt 100,92,0,50
    15799 
    15800 Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    15801 
    15802  
    15803 
    15804 > color name d-t 100,80,4,50
    15805 
    15806 Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    15807 
    15808  
    15809 
    15810 > color name d-prect 95,100,50,50
    15811 
    15812 Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
    15813 
    15814  
    15815 
    15816 > color name d-h2t 100,90,4,50
    15817 
    15818 Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    15819 
    15820  
    15821 
    15822 > color name d-h1t 100,80,4,50
    15823 
    15824 Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
    15825 
    15826  
    15827 
    15828 > color name d-spct 100,70,4,50
    15829 
    15830 Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
    15831 
    15832  
    15833 
    15834 > color name d-fat 100,55,4,50
    15835 
    15836 Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
    15837 
    15838  
    15839 
    15840 > color name d-fac 100,55,4,100
    15841 
    15842 Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
    15843 
    15844  
    15845 
    15846 > color name d-postt 100,40,4,50
    15847 
    15848 Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    15849 
    15850  
    15851 
    15852 > color name m-t 95,43,62,50
    15853 
    15854 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    15855 
    15856  
    15857 
    15858 > color name m-prect 100,85,95,50
    15859 
    15860 Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    15861 
    15862  
    15863 
    15864 > color name m-h2t 100,85,95,50
    15865 
    15866 Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
    15867 
    15868  
    15869 
    15870 > color name m-h1t 100,75,95,50
    15871 
    15872 Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
    15873 
    15874  
    15875 
    15876 > color name m-spct 89,63,75,50
    15877 
    15878 Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
    15879 
    15880  
    15881 
    15882 > color name m-fat 95,51,75,50
    15883 
    15884 Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
    15885 
    15886  
    15887 
    15888 > color name m-fac 95,51,75,100
    15889 
    15890 Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
    15891 
    15892  
    15893 
    15894 > color name m-postt 95,43,62,50
    15895 
    15896 Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    15897 
    15898  
    15899 executed 70S_colors.cxc 
    15900 
    15901 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
    15902 
    15903 > color 100,100,100,50
    15904 
    15905 > color lsu silvert
    15906 
    15907 > color /3 lightgrayt
    15908 
    15909 > color /5 lightgrayt
    15910 
    15911 > color ssu ssu-t
    15912 
    15913 > color head head-t
    15914 
    15915 > color efg efg-t
    15916 
    15917 > color dt d-t
    15918 
    15919 > color pt p-t
    15920 
    15921 > color pep p-t
    15922 
    15923 > color mrna m-t
    15924 
    15925 executed 70S_colorstandard.cxc 
    15926 
    15927 > windowsize 1000 1000
    15928 
    15929 > open
    15930 > /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_trna_gradient-t.cxc
    15931 
    15932 > open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
    15933 
    15934 > color name efg-t 100,0,0,50
    15935 
    15936 Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    15937 
    15938  
    15939 
    15940 > color name sw1-t 100,92,0,50
    15941 
    15942 Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
    15943 
    15944  
    15945 
    15946 > color name sw2-t 68,81,0,50
    15947 
    15948 Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
    15949 
    15950  
    15951 
    15952 > color name pl-t 23,59,0,50
    15953 
    15954 Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
    15955 
    15956  
    15957 
    15958 > color name d1-t 100,18,4,50
    15959 
    15960 Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
    15961 
    15962  
    15963 
    15964 > color name d2-t 100,40,4,50
    15965 
    15966 Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
    15967 
    15968  
    15969 
    15970 > color name d3-t 100,27,36,50
    15971 
    15972 Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
    15973 
    15974  
    15975 
    15976 > color name d4-t 80,0,23,50
    15977 
    15978 Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
    15979 
    15980  
    15981 
    15982 > color name d5-t 100,60,4,50
    15983 
    15984 Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
    15985 
    15986  
    15987 
    15988 > color name fa-t 100,90,4,50
    15989 
    15990 Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
    15991 
    15992  
    15993 
    15994 > color name gtp-t 45,53,60,50
    15995 
    15996 Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
    15997 
    15998  
    15999 
    16000 > color name mg-t 1,39,16,50
    16001 
    16002 Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
    16003 
    16004  
    16005 
    16006 > color name spc-t 100,0,0,50
    16007 
    16008 Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
    16009 
    16010  
    16011 
    16012 > color name argb-t 50,0,50,50
    16013 
    16014 Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
    16015 
    16016  
    16017 
    16018 > color name g-1t 98,42,30,50
    16019 
    16020 Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
    16021 
    16022  
    16023 
    16024 > color name g-2t 95,35,25,50
    16025 
    16026 Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
    16027 
    16028  
    16029 
    16030 > color name g-3t 92,28,20,50
    16031 
    16032 Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
    16033 
    16034  
    16035 
    16036 > color name g-4t 89,21,15,50
    16037 
    16038 Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
    16039 
    16040  
    16041 
    16042 > color name g-5t 86,14,10,50
    16043 
    16044 Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
    16045 
    16046  
    16047 
    16048 > color name g-6t 83,7,5,50
    16049 
    16050 Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
    16051 
    16052  
    16053 
    16054 > color name g-7t 80,0,0,50
    16055 
    16056 Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
    16057 
    16058  
    16059 
    16060 > color name p-t 40,60,2,50
    16061 
    16062 Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
    16063 
    16064  
    16065 
    16066 > color name p-c 40,60,2,100
    16067 
    16068 Color 'p-c' is opaque: rgb(40%, 60%, 2%) hex: #669905
    16069 
    16070  
    16071 
    16072 > color name p-1t 4,34,1,50
    16073 
    16074 Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
    16075 
    16076  
    16077 
    16078 > color name p-2t 12,39,1,50
    16079 
    16080 Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
    16081 
    16082  
    16083 
    16084 > color name p-3t 20,44,1,50
    16085 
    16086 Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
    16087 
    16088  
    16089 
    16090 > color name p-4t 28,49,1,50
    16091 
    16092 Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
    16093 
    16094  
    16095 
    16096 > color name p-5t 36,54,2,50
    16097 
    16098 Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
    16099 
    16100  
    16101 
    16102 > color name p-6t 44,59,2,50
    16103 
    16104 Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
    16105 
    16106  
    16107 
    16108 > color name p-7t 52,64,2,50
    16109 
    16110 Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
    16111 
    16112  
    16113 
    16114 > color name p-8t 60,69,2,50
    16115 
    16116 Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
    16117 
    16118  
    16119 
    16120 > color name p-9t 68,74,3,50
    16121 
    16122 Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
    16123 
    16124  
    16125 
    16126 > color name p-10t 76,79,3,50
    16127 
    16128 Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
    16129 
    16130  
    16131 
    16132 > color name p-11t 84,84,3,50
    16133 
    16134 Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
    16135 
    16136  
    16137 
    16138 > color name d-t 100,75,4,50
    16139 
    16140 Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
    16141 
    16142  
    16143 
    16144 > color name d-c 100,75,4,100
    16145 
    16146 Color 'd-c' is opaque: rgb(100%, 75%, 4%) hex: #ffbf0a
    16147 
    16148  
    16149 
    16150 > color name d-1t 100,100,4,50
    16151 
    16152 Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
    16153 
    16154  
    16155 
    16156 > color name d-2t 100,93,4,50
    16157 
    16158 Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
    16159 
    16160  
    16161 
    16162 > color name d-3t 100,86,4,50
    16163 
    16164 Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
    16165 
    16166  
    16167 
    16168 > color name d-4t 100,79,4,50
    16169 
    16170 Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
    16171 
    16172  
    16173 
    16174 > color name d-5t 100,72,4,50
    16175 
    16176 Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
    16177 
    16178  
    16179 
    16180 > color name d-6t 100,65,4,50
    16181 
    16182 Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
    16183 
    16184  
    16185 
    16186 > color name d-7t 100,58,4,50
    16187 
    16188 Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
    16189 
    16190  
    16191 
    16192 > color name d-8t 100,51,4,50
    16193 
    16194 Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
    16195 
    16196  
    16197 
    16198 > color name d-9t 100,44,4,50
    16199 
    16200 Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
    16201 
    16202  
    16203 
    16204 > color name d-10t 100,37,4,50
    16205 
    16206 Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
    16207 
    16208  
    16209 
    16210 > color name d-11t 100,30,4,50
    16211 
    16212 Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
    16213 
    16214  
    16215 
    16216 > color name m-t 95,43,62,50
    16217 
    16218 Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
    16219 
    16220  
    16221 
    16222 > color name m-c 95,43,62,100
    16223 
    16224 Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
    16225 
    16226  
    16227 
    16228 > color name m-1t 100,80,90,50
    16229 
    16230 Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
    16231 
    16232  
    16233 
    16234 > color name m-2t 98,76,87,50
    16235 
    16236 Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
    16237 
    16238  
    16239 
    16240 > color name m-3t 96,72,84,50
    16241 
    16242 Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
    16243 
    16244  
    16245 
    16246 > color name m-4t 94,68,81,50
    16247 
    16248 Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
    16249 
    16250  
    16251 
    16252 > color name m-5t 92,64,78,50
    16253 
    16254 Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
    16255 
    16256  
    16257 
    16258 > color name m-6t 90,60,75,50
    16259 
    16260 Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
    16261 
    16262  
    16263 
    16264 > color name m-7t 88,56,72,50
    16265 
    16266 Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
    16267 
    16268  
    16269 
    16270 > color name m-8t 86,52,69,50
    16271 
    16272 Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
    16273 
    16274  
    16275 
    16276 > color name m-9t 84,48,66,50
    16277 
    16278 Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
    16279 
    16280  
    16281 
    16282 > color name m-10t 82,44,63,50
    16283 
    16284 Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
    16285 
    16286  
    16287 
    16288 > color name m-11t 80,40,60,50
    16289 
    16290 Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
    16291 
    16292  
    16293 
    16294 > color name head-t 71,51,66,50
    16295 
    16296 Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
    16297 
    16298  
    16299 
    16300 > color name head-c 89,89,100,100
    16301 
    16302 Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
    16303 
    16304  
    16305 
    16306 > color name headfa-t 80,79,100,50
    16307 
    16308 Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex: #ccc9ff80
    16309 
    16310  
    16311 
    16312 > color name headblue-t 59,78,94,50
    16313 
    16314 Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
    16315 
    16316  
    16317 
    16318 > color name headh1-t 41,64,100,50
    16319 
    16320 Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
    16321 
    16322  
    16323 
    16324 > color name headh2-t 50,70,100,50
    16325 
    16326 Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
    16327 
    16328  
    16329 
    16330 > color name headgray-t 60,60,60,50
    16331 
    16332 Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
    16333 
    16334  
    16335 
    16336 > color name darkhead-s 58,34,52,100
    16337 
    16338 Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
    16339 
    16340  
    16341 
    16342 > color name bodywhite-t 90,90,90,50
    16343 
    16344 Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
    16345 #e6e6e680
    16346 
    16347  
    16348 
    16349 > color name rps-t 75,88,93,50
    16350 
    16351 Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
    16352 
    16353  
    16354 
    16355 > color name ssu-t 57,71,75,50
    16356 
    16357 Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
    16358 
    16359  
    16360 
    16361 > color name h18-t 31,59,68,50
    16362 
    16363 Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
    16364 
    16365  
    16366 
    16367 > color name h18-c 31,59,68,100
    16368 
    16369 Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
    16370 
     5501[deleted a bunch of the log to fit within ticket limits]
    163715502 
    163725503