Changes between Initial Version and Version 1 of Ticket #10188


Ignore:
Timestamp:
Nov 20, 2023, 10:19:02 AM (2 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
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  • Ticket #10188

    • Property Component Unassigned → Graphics
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Graphics hardware encountered an error and was reset

  • Ticket #10188 – Description

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    1680   "logWritingSignature" : "8a8f54e9160b2f272585e54619201b015d1776c6",
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    1703 ===== Log before crash start =====
    1704 UCSF ChimeraX version: 1.6rc202304150037 (2023-04-15) 
    1705 © 2016-2023 Regents of the University of California. All rights reserved. 
    1706 
    1707 > open "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
    1708 > related/T7SS2.cxs"
    1709 
    1710 Opened cryosparc_P14_J542_004_volume_map_sharp.mrc as #7, grid size
    1711 400,400,400, pixel 1.2, shown at level 0.109, step 1, values float32 
    1712 Log from Fri Nov 17 13:21:00 2023UCSF ChimeraX version: 1.6rc202304150037
    1713 (2023-04-15) 
    1714 © 2016-2023 Regents of the University of California. All rights reserved. 
    1715 
    1716 > open /Users/gabrielumajioka/Downloads/T7SS-docking-9.cxs
    1717 
    1718 Opened cryosparc_P14_J542_004_volume_map_sharp.mrc as #7, grid size
    1719 400,400,400, pixel 1.2, shown at level 0.109, step 1, values float32 
    1720 Log from Tue Nov 14 13:40:55 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1721 © 2016-2023 Regents of the University of California. All rights reserved. 
    1722 
    1723 > open /Users/remi/Desktop/T7SS-docking-8.cxs format session
    1724 
    1725 Opened cryosparc_P14_J498_004_volume_map_sharp(1).mrc as #6, grid size
    1726 400,400,400, pixel 1.2, shown at level 0.0856, step 1, values float32 
    1727 Log from Mon Nov 13 18:48:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1728 © 2016-2023 Regents of the University of California. All rights reserved. 
    1729 
    1730 > open /Users/remi/Desktop/T7SS-docking-5.cxs format session
    1731 
    1732 Opened cryosparc_P14_J452_004_volume_map_sharp(1).mrc as #11, grid size
    1733 400,400,400, pixel 1.2, shown at level 0.139, step 1, values float32 
    1734 Log from Mon Nov 13 10:11:02 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1735 © 2016-2023 Regents of the University of California. All rights reserved. 
    1736 
    1737 > open /Users/remi/Desktop/T7SS-docking-4.cxs format session
    1738 
    1739 Opened cryosparc_P14_J436_004_volume_map_sharp.mrc as #7, grid size
    1740 400,400,400, pixel 1.2, shown at level 0.203, step 2, values float32 
    1741 Opened map 10 as #6, grid size 64,63,78, pixel 3.33, shown at level 0.0631,
    1742 step 1, values float32 
    1743 Opened mask-assym.mrc as #8, grid size 400,400,400, pixel 1.2, shown at level
    1744 0.0631, step 1, values float32 
    1745 Log from Sun Nov 12 21:44:36 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1746 © 2016-2023 Regents of the University of California. All rights reserved. 
    1747 
    1748 > open /Users/remi/Desktop/T7SS-docking-3.cxs format session
    1749 
    1750 Opened cryosparc_P14_J66_004_volume_map_sharp.mrc as #6, grid size
    1751 480,480,480, pixel 1.2, shown at level 0.295, step 2, values float32 
    1752 Log from Wed Nov 1 11:49:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1753 © 2016-2023 Regents of the University of California. All rights reserved. 
    1754 
    1755 > open /Users/remi/Desktop/T7SS-docking-2.cxs format session
    1756 
    1757 Opened cryosparc_P14_J66_004_volume_map_sharp.mrc as #6, grid size
    1758 480,480,480, pixel 1.2, shown at level 0.295, step 2, values float32 
    1759 Log from Tue Oct 31 18:38:05 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1760 © 2016-2023 Regents of the University of California. All rights reserved. 
    1761 
    1762 > open /Users/remi/Desktop/T7SS-docking-2.cxs format session
    1763 
    1764 Opened cryosparc_P14_J66_004_volume_map_sharp.mrc as #6, grid size
    1765 480,480,480, pixel 1.2, shown at level 0.295, step 2, values float32 
    1766 Log from Tue Oct 31 18:30:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1767 © 2016-2023 Regents of the University of California. All rights reserved. 
    1768 
    1769 > open /Users/remi/Desktop/T7SS-docking.cxs format session
    1770 
    1771 Opened cryosparc_P14_J56_002_volume_map_sharp.mrc z flip as #3, grid size
    1772 480,480,480, pixel 1.2, shown at level 0.255, step 1, values float32 
    1773 Log from Tue Oct 31 16:44:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1774 © 2016-2023 Regents of the University of California. All rights reserved. 
    1775 
    1776 > open /Users/remi/Desktop/T7SS-docking.cxs
    1777 
    1778 Opened cryosparc_P14_J56_002_volume_map_sharp.mrc z flip as #3, grid size
    1779 480,480,480, pixel 1.2, shown at level 0.255, step 1, values float32 
    1780 Log from Tue Oct 31 16:39:50 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1781 © 2016-2023 Regents of the University of California. All rights reserved. 
    1782 How to cite UCSF ChimeraX 
    1783 
    1784 > open /Users/remi/Downloads/cryosparc_P14_J56_002_volume_map_sharp.mrc
    1785 
    1786 Opened cryosparc_P14_J56_002_volume_map_sharp.mrc as #1, grid size
    1787 480,480,480, pixel 1.2, shown at level 0.041, step 2, values float32 
    1788 
    1789 > volume #1 level 0.1564
    1790 
    1791 > volume #1 level 0.2549
    1792 
    1793 > open /Users/remi/Desktop/assym-T7SS.pdb format pdb
    1794 
    1795 Summary of feedback from opening /Users/remi/Desktop/assym-T7SS.pdb 
    1796 --- 
    1797 warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 246
    1798 LEU A 251 1 6 
    1799 Start residue of secondary structure not found: HELIX 2 2 PRO A 252 ILE A 266
    1800 1 15 
    1801 Start residue of secondary structure not found: HELIX 3 3 PHE A 272 HIS A 334
    1802 1 63 
    1803 Start residue of secondary structure not found: HELIX 4 4 LEU B 246 LEU B 251
    1804 1 6 
    1805 Start residue of secondary structure not found: HELIX 5 5 PRO B 252 ILE B 266
    1806 1 15 
    1807 63 messages similar to the above omitted 
    1808  
    1809 Chain information for assym-T7SS.pdb 
    1810 --- 
    1811 Chain | Description 
    1812 2.3/A | No description available 
    1813 2.2/B | No description available 
    1814 2.3/D | No description available 
    1815 2.1/E | No description available 
    1816  
    1817 
    1818 > ui tool show "Model Panel"
    1819 
    1820 > close #2
    1821 
    1822 > open /Users/remi/Desktop/assymT7SS.pdb format pdb
    1823 
    1824 Chain information for assymT7SS.pdb #2 
    1825 --- 
    1826 Chain | Description 
    1827 A | No description available 
    1828 B | No description available 
    1829 D | No description available 
    1830 E | No description available 
    1831  
    1832 
    1833 > select add #2
    1834 
    1835 15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 2 models selected 
    1836 
    1837 > ui mousemode right "rotate selected models"
    1838 
    1839 > view matrix models
    1840 > #2,-0.91551,-0.29814,-0.2701,38.646,-0.25751,0.95013,-0.17592,3.0638,0.30908,-0.091506,-0.94662,-36.622
    1841 
    1842 > view matrix models
    1843 > #2,-0.6347,-0.62055,-0.46051,15.794,-0.77144,0.47404,0.42446,6.3839,-0.045101,0.62466,-0.77959,3.3795
    1844 
    1845 > view matrix models
    1846 > #2,-0.6347,-0.62055,-0.46051,-41.56,-0.77144,0.47404,0.42446,216.14,-0.045101,0.62466,-0.77959,318.45
    1847 
    1848 > view matrix models
    1849 > #2,0.69412,-0.60038,-0.39717,-77.217,-0.47864,0.027184,-0.87759,174.16,0.53768,0.79925,-0.26849,315.34
    1850 
    1851 > view matrix models
    1852 > #2,0.15505,-0.9879,0.0036659,-72.231,-0.78554,-0.12554,-0.60595,180.19,0.59908,0.091072,-0.79549,279.35
    1853 
    1854 > view matrix models
    1855 > #2,-0.037366,-0.96806,0.24794,-63.003,-0.88151,-0.084931,-0.46446,186.24,0.47068,-0.23591,-0.85018,269.49
    1856 
    1857 > view matrix models
    1858 > #2,-0.037366,-0.96806,0.24794,209.07,-0.88151,-0.084931,-0.46446,339.9,0.47068,-0.23591,-0.85018,252.24
    1859 
    1860 > view matrix models
    1861 > #2,0.32978,0.84002,0.43082,271.72,0.87854,-0.10604,-0.46575,289.73,-0.34556,0.53209,-0.77297,306.09
    1862 
    1863 > view matrix models
    1864 > #2,0.33158,0.83971,0.43004,333.47,0.87799,-0.10785,-0.46637,288.63,-0.34524,0.53222,-0.77302,251.42
    1865 
    1866 > view matrix models
    1867 > #2,0.24058,0.84481,0.47794,336.82,0.9342,-0.067887,-0.35024,290.07,-0.26344,0.53075,-0.80555,248.67
    1868 
    1869 > view matrix models
    1870 > #2,0.24058,0.84481,0.47794,335.59,0.9342,-0.067887,-0.35024,295.89,-0.26344,0.53075,-0.80555,246.49
    1871 
    1872 > view matrix models
    1873 > #2,0.21808,0.84057,0.49587,336.28,0.89113,0.035659,-0.45235,299.86,-0.39791,0.54054,-0.74127,251.44
    1874 
    1875 > view matrix models
    1876 > #2,0.21999,0.84041,0.49529,327.22,0.89076,0.033926,-0.45321,299.01,-0.39769,0.54089,-0.74114,253.45
    1877 
    1878 > view matrix models
    1879 > #2,0.10676,0.96445,0.24175,332.07,0.82308,0.050679,-0.56566,300.15,-0.5578,0.25937,-0.7884,246.34
    1880 
    1881 > fitmap #2 inMap #1
    1882 
    1883 Fit molecule assymT7SS.pdb (#2) to map
    1884 cryosparc_P14_J56_002_volume_map_sharp.mrc (#1) using 15580 atoms 
    1885 average map value = 0.1148, steps = 228 
    1886 shifted from previous position = 14 
    1887 rotated from previous position = 13.9 degrees 
    1888 atoms outside contour = 12209, contour level = 0.25488 
    1889  
    1890 Position of assymT7SS.pdb (#2) relative to
    1891 cryosparc_P14_J56_002_volume_map_sharp.mrc (#1) coordinates: 
    1892 Matrix rotation and translation 
    1893 0.24950001 0.90537255 0.34358452 336.12410985 
    1894 0.88549670 -0.06968627 -0.45939030 284.75162857 
    1895 -0.39197623 0.41886084 -0.81909111 246.20223303 
    1896 Axis 0.76652168 0.64198410 -0.01734728 
    1897 Axis point 0.00000000 -50.49604260 127.87593764 
    1898 Rotation angle (degrees) 145.04864097 
    1899 Shift along axis 436.18149689 
    1900  
    1901 
    1902 > view matrix models
    1903 > #2,0.83486,-0.37823,-0.39993,260.25,-0.46711,-0.87118,-0.15119,295.2,-0.29123,0.31303,-0.90399,238.18
    1904 
    1905 > select #1
    1906 
    1907 2 models selected 
    1908 
    1909 > select /B:62
    1910 
    1911 7 atoms, 6 bonds, 1 residue, 1 model selected 
    1912 
    1913 > select /B:91
    1914 
    1915 12 atoms, 12 bonds, 1 residue, 1 model selected 
    1916 
    1917 > select up
    1918 
    1919 138 atoms, 141 bonds, 16 residues, 1 model selected 
    1920 
    1921 > select up
    1922 
    1923 2587 atoms, 2647 bonds, 337 residues, 1 model selected 
    1924 
    1925 > delete atoms sel
    1926 
    1927 > delete bonds sel
    1928 
    1929 > select add #2
    1930 
    1931 12993 atoms, 13269 bonds, 19 pseudobonds, 1607 residues, 2 models selected 
    1932 
    1933 > view matrix models
    1934 > #2,0.81525,0.579,-0.011729,289.02,0.3716,-0.53854,-0.75623,294.76,-0.44417,0.61216,-0.6542,248.98
    1935 
    1936 Drag select of 55 residues 
    1937 
    1938 > select add #2
    1939 
    1940 12993 atoms, 13269 bonds, 19 pseudobonds, 1607 residues, 2 models selected 
    1941 
    1942 > view matrix models
    1943 > #2,0.81525,0.579,-0.011729,319.44,0.3716,-0.53854,-0.75623,271.37,-0.44417,0.61216,-0.6542,277.35
    1944 
    1945 > view matrix models
    1946 > #2,0.73427,0.45171,-0.50675,329,-0.10859,-0.65871,-0.74452,282.37,-0.67011,0.60171,-0.43462,279.21
    1947 
    1948 > select clear
    1949 
    1950 > select /B:11
    1951 
    1952 8 atoms, 7 bonds, 1 residue, 1 model selected 
    1953 
    1954 > select up
    1955 
    1956 54 atoms, 54 bonds, 6 residues, 1 model selected 
    1957 
    1958 > select up
    1959 
    1960 244 atoms, 247 bonds, 32 residues, 1 model selected 
    1961 
    1962 > delete atoms sel
    1963 
    1964 > delete bonds sel
    1965 
    1966 > select add #2
    1967 
    1968 12749 atoms, 13022 bonds, 19 pseudobonds, 1575 residues, 2 models selected 
    1969 
    1970 > view matrix models
    1971 > #2,0.53471,0.82963,0.16065,334.45,0.67364,-0.3037,-0.67377,268.52,-0.51019,0.46849,-0.72126,275.54
    1972 
    1973 > view matrix models
    1974 > #2,0.535,0.82996,0.15794,342.1,0.67294,-0.30559,-0.67362,292.11,-0.51082,0.46667,-0.722,252.39
    1975 
    1976 > view matrix models
    1977 > #2,0.27161,0.91841,0.28768,351.22,0.92273,-0.16356,-0.34904,281.59,-0.2735,0.36025,-0.89186,244.4
    1978 
    1979 > view matrix models
    1980 > #2,0.8986,0.16311,-0.40732,317.47,0.058952,-0.9648,-0.2563,276.8,-0.43479,0.2063,-0.87658,243.39
    1981 
    1982 > view matrix models
    1983 > #2,-0.12163,0.95617,0.26635,366.29,0.9373,0.19894,-0.28617,293.76,-0.32661,0.21485,-0.92042,241.17
    1984 
    1985 > view matrix models
    1986 > #2,-0.11789,0.95691,0.26537,332.13,0.9375,0.19535,-0.28797,289.17,-0.3274,0.21484,-0.92014,246.09
    1987 
    1988 > view matrix models
    1989 > #2,0.55179,0.81486,0.17756,306.4,0.81092,-0.4745,-0.34243,268.51,-0.19478,0.33294,-0.92261,246.35
    1990 
    1991 > view matrix models
    1992 > #2,0.39927,0.8132,0.42342,305.53,0.88401,-0.21899,-0.413,277.75,-0.24313,0.53921,-0.80631,253.24
    1993 
    1994 > view matrix models
    1995 > #2,0.39357,0.91717,0.062389,318.42,0.78658,-0.30086,-0.53924,280.81,-0.4758,0.2613,-0.83984,250.92
    1996 
    1997 > view matrix models
    1998 > #2,0.39357,0.91717,0.062389,314.83,0.78658,-0.30086,-0.53924,279.02,-0.4758,0.2613,-0.83984,262.26
    1999 
    2000 > view matrix models
    2001 > #2,0.18232,0.98126,0.062348,324.37,0.83317,-0.12051,-0.53972,284.53,-0.52209,0.15035,-0.83953,259.46
    2002 
    2003 > fitmap #2 inMap #1
    2004 
    2005 Fit molecule assymT7SS.pdb (#2) to map
    2006 cryosparc_P14_J56_002_volume_map_sharp.mrc (#1) using 12749 atoms 
    2007 average map value = 0.1294, steps = 648 
    2008 shifted from previous position = 22.9 
    2009 rotated from previous position = 16.4 degrees 
    2010 atoms outside contour = 9692, contour level = 0.25488 
    2011  
    2012 Position of assymT7SS.pdb (#2) relative to
    2013 cryosparc_P14_J56_002_volume_map_sharp.mrc (#1) coordinates: 
    2014 Matrix rotation and translation 
    2015 0.05284042 0.99262308 0.10912075 341.39459842 
    2016 0.95272311 -0.01736940 -0.30334306 291.60594776 
    2017 -0.29920996 0.11999063 -0.94661273 268.09004886 
    2018 Axis 0.71809527 0.69264591 -0.06768179 
    2019 Axis point 0.00000000 -50.02823723 149.55303999 
    2020 Rotation angle (degrees) 162.85676305 
    2021 Shift along axis 428.98870025 
    2022  
    2023 
    2024 > select up
    2025 
    2026 12749 atoms, 13022 bonds, 19 pseudobonds, 1575 residues, 2 models selected 
    2027 
    2028 > volume flip #1
    2029 
    2030 Opened cryosparc_P14_J56_002_volume_map_sharp.mrc z flip as #3, grid size
    2031 480,480,480, pixel 1.2, shown at step 1, values float32 
    2032 
    2033 > view matrix models
    2034 > #2,-0.78462,0.61223,0.097677,354.67,-0.59918,-0.70838,-0.37306,317.9,-0.1592,-0.35123,0.92265,200.31
    2035 
    2036 > close #1
    2037 
    2038 > view matrix models
    2039 > #2,-0.62743,0.70516,0.33026,347.51,-0.73861,-0.67326,0.034292,314.17,0.24653,-0.22242,0.94327,191.35
    2040 
    2041 > view matrix models
    2042 > #2,0.46112,0.87653,-0.1381,329.19,-0.55503,0.40635,0.72582,333.71,0.69232,-0.25804,0.67388,181.57
    2043 
    2044 > view matrix models
    2045 > #2,0.45616,0.87988,-0.13314,328.04,-0.55968,0.39998,0.72579,344.42,0.69187,-0.25656,0.67491,300.14
    2046 
    2047 > view matrix models
    2048 > #2,0.88496,0.32953,-0.32901,296.96,-0.14732,0.86838,0.47352,355.03,0.44174,-0.37058,0.81703,300.61
    2049 
    2050 > view matrix models
    2051 > #2,0.75126,0.45329,-0.47972,309.85,-0.35619,0.89037,0.28351,367.39,0.55563,-0.042118,0.83036,309.33
    2052 
    2053 > view matrix models
    2054 > #2,0.75126,0.45329,-0.47972,314.13,-0.35619,0.89037,0.28351,360.19,0.55563,-0.042118,0.83036,319.87
    2055 
    2056 > view matrix models
    2057 > #2,0.83453,0.50026,-0.23087,307.24,-0.36052,0.81268,0.45779,353.13,0.41664,-0.2988,0.85856,313.79
    2058 
    2059 > view matrix models
    2060 > #2,0.81985,-0.049041,-0.57048,294.39,0.46363,0.64153,0.61114,315.36,0.33601,-0.76553,0.54869,305.64
    2061 
    2062 > view matrix models
    2063 > #2,-0.97033,0.21068,0.1186,347.62,-0.23574,-0.93337,-0.27063,298.17,0.053679,-0.29056,0.95535,323.87
    2064 
    2065 > view matrix models
    2066 > #2,-0.97033,0.21068,0.1186,350.14,-0.23574,-0.93337,-0.27063,287.61,0.053679,-0.29056,0.95535,326.05
    2067 
    2068 > view matrix models
    2069 > #2,-0.96136,0.24111,0.13286,312.37,-0.26855,-0.92749,-0.26009,268.17,0.060514,-0.28572,0.9564,320.81
    2070 
    2071 > view matrix models
    2072 > #2,-0.73875,0.66728,0.094853,322.53,-0.6735,-0.72551,-0.14153,286.7,-0.025626,-0.16844,0.98538,327.57
    2073 
    2074 > fitmap #2 inMap #3
    2075 
    2076 Fit molecule assymT7SS.pdb (#2) to map
    2077 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 12749 atoms 
    2078 average map value = 0.1323, steps = 496 
    2079 shifted from previous position = 37.6 
    2080 rotated from previous position = 25 degrees 
    2081 atoms outside contour = 9355, contour level = 0.25488 
    2082  
    2083 Position of assymT7SS.pdb (#2) relative to
    2084 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates: 
    2085 Matrix rotation and translation 
    2086 -0.71542707 0.50286009 0.48507307 335.20734608 
    2087 -0.60763885 -0.79050019 -0.07671068 286.71361276 
    2088 0.34487561 -0.34963013 0.87110253 324.27644999 
    2089 Axis -0.23688745 0.12168799 -0.96388608 
    2090 Axis point 182.04187295 122.61966787 0.00000000 
    2091 Rotation angle (degrees) 144.82659237 
    2092 Shift along axis -357.08236454 
    2093  
    2094 
    2095 > volume #3 color #aeaeae
    2096 
    2097 > volume #3 color #aeaeae89
    2098 
    2099 > open /Users/remi/Desktop/assymT7SS.pdb format pdb
    2100 
    2101 Chain information for assymT7SS.pdb #1 
    2102 --- 
    2103 Chain | Description 
    2104 A | No description available 
    2105 B | No description available 
    2106 D | No description available 
    2107 E | No description available 
    2108  
    2109 
    2110 > select add #3
    2111 
    2112 12749 atoms, 13022 bonds, 19 pseudobonds, 1575 residues, 4 models selected 
    2113 
    2114 > select subtract #2
    2115 
    2116 2 models selected 
    2117 
    2118 > select add #1
    2119 
    2120 15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 4 models selected 
    2121 
    2122 > select add #2
    2123 
    2124 28329 atoms, 28938 bonds, 39 pseudobonds, 3519 residues, 6 models selected 
    2125 
    2126 > select subtract #2
    2127 
    2128 15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 4 models selected 
    2129 
    2130 > select subtract #3
    2131 
    2132 15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 2 models selected 
    2133 
    2134 > view matrix models
    2135 > #1,0.7628,-0.060227,-0.64382,-3.7713,0.13958,0.98752,0.072994,-3.4849,0.63139,-0.14554,0.76169,-26.366
    2136 
    2137 > view matrix models
    2138 > #1,0.7628,-0.060227,-0.64382,13.29,0.13958,0.98752,0.072994,317.65,0.63139,-0.14554,0.76169,326.48
    2139 
    2140 > view matrix models
    2141 > #1,-0.4098,-0.80531,-0.42841,19.735,0.85765,-0.18023,-0.48162,244.95,0.31065,-0.56479,0.76453,319.12
    2142 
    2143 > view matrix models
    2144 > #1,-0.4098,-0.80531,-0.42841,231.03,0.85765,-0.18023,-0.48162,275.13,0.31065,-0.56479,0.76453,311.21
    2145 
    2146 > view matrix models
    2147 > #1,-0.56725,-0.75762,-0.32285,238.63,0.75799,-0.32703,-0.56437,271.15,0.322,-0.56486,0.75977,310.83
    2148 
    2149 > view matrix models
    2150 > #1,-0.56725,-0.75762,-0.32285,228.51,0.75799,-0.32703,-0.56437,269.81,0.322,-0.56486,0.75977,321.81
    2151 
    2152 > view matrix models
    2153 > #1,-0.7432,0.25566,0.6183,284.83,-0.44295,-0.8806,-0.16832,286.8,0.50144,-0.39897,0.76771,323.36
    2154 
    2155 > view matrix models
    2156 > #1,-0.89095,0.033236,0.45289,278.2,-0.19382,-0.92974,-0.31307,276.08,0.41066,-0.3667,0.8348,328.01
    2157 
    2158 > view matrix models
    2159 > #1,-0.89095,0.033236,0.45289,276.78,-0.19382,-0.92974,-0.31307,225.9,0.41066,-0.3667,0.8348,328.47
    2160 
    2161 > view matrix models
    2162 > #1,-0.45718,0.67481,0.57933,291.28,-0.78705,-0.61032,0.089801,260.05,0.41417,-0.41491,0.81013,326.18
    2163 
    2164 > view matrix models
    2165 > #1,-0.45718,0.67481,0.57933,315.13,-0.78705,-0.61032,0.089801,257.34,0.41417,-0.41491,0.81013,333.35
    2166 
    2167 > view matrix models
    2168 > #1,0.086003,0.96645,0.24203,307.08,-0.87012,-0.045465,0.49073,286.76,0.48527,-0.2528,0.83702,338.03
    2169 
    2170 > view matrix models
    2171 > #1,0.086003,0.96645,0.24203,314.78,-0.87012,-0.045465,0.49073,295.01,0.48527,-0.2528,0.83702,333.49
    2172 
    2173 > fitmap #1 inMap #3
    2174 
    2175 Fit molecule assymT7SS.pdb (#1) to map
    2176 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 15580 atoms 
    2177 average map value = 0.1379, steps = 368 
    2178 shifted from previous position = 41.3 
    2179 rotated from previous position = 23.3 degrees 
    2180 atoms outside contour = 11338, contour level = 0.25488 
    2181  
    2182 Position of assymT7SS.pdb (#1) relative to
    2183 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates: 
    2184 Matrix rotation and translation 
    2185 0.29623652 0.85245381 0.43077421 335.00418906 
    2186 -0.93660606 0.17091236 0.30587259 284.36395152 
    2187 0.18711762 -0.49407637 0.84904390 322.59951367 
    2188 Axis -0.40506875 0.12337996 -0.90592312 
    2189 Axis point 310.83111180 50.30752618 0.00000000 
    2190 Rotation angle (degrees) 80.90357899 
    2191 Shift along axis -392.86527276 
    2192  
    2193 
    2194 > select #1/B:301
    2195 
    2196 5 atoms, 4 bonds, 1 residue, 1 model selected 
    2197 
    2198 > select up
    2199 
    2200 77 atoms, 76 bonds, 11 residues, 1 model selected 
    2201 
    2202 > select up
    2203 
    2204 2587 atoms, 2647 bonds, 337 residues, 1 model selected 
    2205 
    2206 > open /Users/remi/Desktop/assymT7SS.pdb format pdb
    2207 
    2208 Chain information for assymT7SS.pdb #4 
    2209 --- 
    2210 Chain | Description 
    2211 A | No description available 
    2212 B | No description available 
    2213 D | No description available 
    2214 E | No description available 
    2215  
    2216 
    2217 > select clear
    2218 
    2219 > ui tool show Matchmaker
    2220 
    2221 [Repeated 1 time(s)]
    2222 
    2223 > matchmaker #!2 to #4
    2224 
    2225 Parameters 
    2226 --- 
    2227 Chain pairing | bb 
    2228 Alignment algorithm | Needleman-Wunsch 
    2229 Similarity matrix | BLOSUM-62 
    2230 SS fraction | 0.3 
    2231 Gap open (HH/SS/other) | 18/18/6 
    2232 Gap extend | 1 
    2233 SS matrix |  |  | H | S | O 
    2234 ---|---|---|--- 
    2235 H | 6 | -9 | -6 
    2236 S |  | 6 | -6 
    2237 O |  |  | 4 
    2238 Iteration cutoff | 2 
    2239  
    2240 Matchmaker assymT7SS.pdb, chain A (#4) with assymT7SS.pdb, chain A (#2),
    2241 sequence alignment score = 7110.1 
    2242 RMSD between 1378 pruned atom pairs is 0.000 angstroms; (across all 1378
    2243 pairs: 0.000) 
    2244  
    2245 
    2246 > matchmaker #!2 to #4
    2247 
    2248 Parameters 
    2249 --- 
    2250 Chain pairing | bb 
    2251 Alignment algorithm | Needleman-Wunsch 
    2252 Similarity matrix | BLOSUM-62 
    2253 SS fraction | 0.3 
    2254 Gap open (HH/SS/other) | 18/18/6 
    2255 Gap extend | 1 
    2256 SS matrix |  |  | H | S | O 
    2257 ---|---|---|--- 
    2258 H | 6 | -9 | -6 
    2259 S |  | 6 | -6 
    2260 O |  |  | 4 
    2261 Iteration cutoff | 2 
    2262  
    2263 Matchmaker assymT7SS.pdb, chain A (#4) with assymT7SS.pdb, chain A (#2),
    2264 sequence alignment score = 7110.1 
    2265 RMSD between 1378 pruned atom pairs is 0.000 angstroms; (across all 1378
    2266 pairs: 0.000) 
    2267  
    2268 
    2269 > close #4
    2270 
    2271 > select clear
    2272 
    2273 > select add #2
    2274 
    2275 12749 atoms, 13022 bonds, 19 pseudobonds, 1575 residues, 2 models selected 
    2276 
    2277 > view matrix models
    2278 > #2,0.99989,0.0078678,0.012325,4.0241,-0.0078934,0.99997,0.0020257,73.605,-0.012309,-0.0021227,0.99992,241.51
    2279 
    2280 > view matrix models
    2281 > #2,-0.85905,-0.50148,0.10268,43.808,0.37886,-0.75777,-0.53128,4.8094,0.34423,-0.4175,0.84095,217.22
    2282 
    2283 > view matrix models
    2284 > #2,-0.81776,-0.50158,0.28228,38.135,0.31441,-0.8001,-0.51086,4.8107,0.48209,-0.32901,0.812,216.78
    2285 
    2286 > close #2
    2287 
    2288 > open /Users/remi/Desktop/assymT7SS.pdb format pdb
    2289 
    2290 Chain information for assymT7SS.pdb #2 
    2291 --- 
    2292 Chain | Description 
    2293 A | No description available 
    2294 B | No description available 
    2295 D | No description available 
    2296 E | No description available 
    2297  
    2298 
    2299 > select add #2
    2300 
    2301 15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 2 models selected 
    2302 
    2303 > view matrix models
    2304 > #2,0.99999,-0.00041742,0.0039933,-10.051,0.00041645,1,0.0002435,358.05,-0.0039934,-0.00024183,0.99999,346.1
    2305 
    2306 > view matrix models
    2307 > #2,0.99999,-0.00041742,0.0039933,232.44,0.00041645,1,0.0002435,447.54,-0.0039934,-0.00024183,0.99999,349.8
    2308 
    2309 > view matrix models
    2310 > #2,-0.71695,0.55472,0.42222,307.49,-0.68122,-0.68612,-0.25531,397.56,0.14807,-0.47067,0.8698,325.53
    2311 
    2312 > view matrix models
    2313 > #2,-0.72959,0.54589,0.41194,312.55,-0.6687,-0.69567,-0.26245,288.55,0.14331,-0.46695,0.8726,330.35
    2314 
    2315 > fitmap #2 inMap #3
    2316 
    2317 Fit molecule assymT7SS.pdb (#2) to map
    2318 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 15580 atoms 
    2319 average map value = 0.1436, steps = 368 
    2320 shifted from previous position = 31.8 
    2321 rotated from previous position = 16.4 degrees 
    2322 atoms outside contour = 11144, contour level = 0.25488 
    2323  
    2324 Position of assymT7SS.pdb (#2) relative to
    2325 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates: 
    2326 Matrix rotation and translation 
    2327 -0.64998586 0.45300920 0.61016478 336.13537293 
    2328 -0.63743189 -0.76214809 -0.11318519 287.19803248 
    2329 0.41376199 -0.46250726 0.78414798 323.37304671 
    2330 Axis -0.30068624 0.16905779 -0.93861986 
    2331 Axis point 175.52913680 133.64480487 0.00000000 
    2332 Rotation angle (degrees) 144.48791123 
    2333 Shift along axis -356.04258138 
    2334  
    2335 
    2336 > select clear
    2337 
    2338 Drag select of 3 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip , 1338
    2339 residues 
    2340 
    2341 > select up
    2342 
    2343 11186 atoms, 11428 bonds, 1379 residues, 4 models selected 
    2344 
    2345 > select up
    2346 
    2347 18784 atoms, 19190 bonds, 2316 residues, 4 models selected 
    2348 
    2349 > hide #!3 models
    2350 
    2351 > select clear
    2352 
    2353 Drag select of 1251 residues 
    2354 
    2355 > select up
    2356 
    2357 10530 atoms, 10753 bonds, 1299 residues, 2 models selected 
    2358 
    2359 > select up
    2360 
    2361 18784 atoms, 19190 bonds, 2316 residues, 2 models selected 
    2362 
    2363 > select down
    2364 
    2365 10530 atoms, 10753 bonds, 1299 residues, 2 models selected 
    2366 
    2367 > select #1/A:618
    2368 
    2369 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2370 
    2371 > select :1-618
    2372 
    2373 17070 atoms, 17438 bonds, 40 pseudobonds, 2134 residues, 4 models selected 
    2374 
    2375 > select :618-
    2376 
    2377 Expected an objects specifier or a keyword 
    2378 
    2379 > select :618-end
    2380 
    2381 14102 atoms, 14404 bonds, 1756 residues, 2 models selected 
    2382 
    2383 > delete atoms sel
    2384 
    2385 > delete bonds sel
    2386 
    2387 > show #!3 models
    2388 
    2389 > select add #1
    2390 
    2391 8529 atoms, 8713 bonds, 20 pseudobonds, 1066 residues, 2 models selected 
    2392 
    2393 > fitmap #1 inMap #3
    2394 
    2395 Fit molecule assymT7SS.pdb (#1) to map
    2396 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms 
    2397 average map value = 0.2526, steps = 64 
    2398 shifted from previous position = 0.358 
    2399 rotated from previous position = 0.102 degrees 
    2400 atoms outside contour = 4297, contour level = 0.25488 
    2401  
    2402 Position of assymT7SS.pdb (#1) relative to
    2403 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates: 
    2404 Matrix rotation and translation 
    2405 0.29578493 0.85335289 0.42930190 335.03321557 
    2406 -0.93662425 0.17075429 0.30590519 284.32893315 
    2407 0.18773994 -0.49257671 0.84977756 323.05057485 
    2408 Axis -0.40432995 0.12232054 -0.90639670 
    2409 Axis point 310.57331623 50.13128968 0.00000000 
    2410 Rotation angle (degrees) 80.89998128 
    2411 Shift along axis -393.49667050 
    2412  
    2413 
    2414 > select add #2
    2415 
    2416 17058 atoms, 17426 bonds, 40 pseudobonds, 2132 residues, 4 models selected 
    2417 
    2418 > select subtract #1
    2419 
    2420 8529 atoms, 8713 bonds, 20 pseudobonds, 1066 residues, 2 models selected 
    2421 
    2422 > fitmap #2 inMap #3
    2423 
    2424 Fit molecule assymT7SS.pdb (#2) to map
    2425 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms 
    2426 average map value = 0.2573, steps = 52 
    2427 shifted from previous position = 0.521 
    2428 rotated from previous position = 0.329 degrees 
    2429 atoms outside contour = 4132, contour level = 0.25488 
    2430  
    2431 Position of assymT7SS.pdb (#2) relative to
    2432 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates: 
    2433 Matrix rotation and translation 
    2434 -0.65268600 0.45212702 0.60793268 336.22452046 
    2435 -0.63386216 -0.76539768 -0.11128861 287.11378647 
    2436 0.41499368 -0.45798204 0.78615057 324.13408296 
    2437 Axis -0.29985640 0.16687364 -0.93927596 
    2438 Axis point 175.13402757 133.53178381 0.00000000 
    2439 Rotation angle (degrees) 144.68304548 
    2440 Shift along axis -357.35870250 
    2441  
    2442 
    2443 > view matrix models
    2444 > #2,-0.64983,0.45512,0.60876,336.36,-0.635,-0.76524,-0.10574,287.55,0.41772,-0.45527,0.78628,324.21
    2445 
    2446 > save /Users/remi/Desktop/T7SS-docking.cxs includeMaps true
    2447 
    2448 > open "/Users/remi/Documents/IECB/grant
    2449 > applications/ANR-T7SS-2023/YukCdimer_3fc44.result/YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb"
    2450 > format pdb
    2451 
    2452 Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb #4 
    2453 --- 
    2454 Chain | Description 
    2455 B C | No description available 
    2456  
    2457 
    2458 > view matrix models
    2459 > #2,-0.64893,0.45363,0.61083,336.46,-0.63441,-0.7658,-0.10526,287.57,0.42002,-0.45582,0.78473,324.05
    2460 
    2461 > view matrix models
    2462 > #2,-0.62011,0.48096,0.6198,337.78,-0.66369,-0.74286,-0.087571,289.89,0.41831,-0.46566,0.77986,323.38
    2463 
    2464 > fitmap #2 inMap #3
    2465 
    2466 Fit molecule assymT7SS.pdb (#2) to map
    2467 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms 
    2468 average map value = 0.2573, steps = 60 
    2469 shifted from previous position = 0.548 
    2470 rotated from previous position = 2.59 degrees 
    2471 atoms outside contour = 4134, contour level = 0.25488 
    2472  
    2473 Position of assymT7SS.pdb (#2) relative to
    2474 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates: 
    2475 Matrix rotation and translation 
    2476 -0.65263927 0.45219031 0.60793578 336.22431474 
    2477 -0.63397319 -0.76529615 -0.11135436 287.10755499 
    2478 0.41489756 -0.45808922 0.78613885 324.13155085 
    2479 Axis -0.29984225 0.16693164 -0.93927017 
    2480 Axis point 175.15057476 133.52838162 0.00000000 
    2481 Rotation angle (degrees) 144.67627919 
    2482 Shift along axis -357.33401936 
    2483  
    2484 
    2485 > view matrix models
    2486 > #2,-0.28274,0.74119,0.60885,342.46,-0.88749,-0.44296,0.12711,317.68,0.36391,-0.50441,0.78303,322.84
    2487 
    2488 > fitmap #2 inMap #3
    2489 
    2490 Fit molecule assymT7SS.pdb (#2) to map
    2491 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms 
    2492 average map value = 0.2573, steps = 148 
    2493 shifted from previous position = 6.29 
    2494 rotated from previous position = 27.4 degrees 
    2495 atoms outside contour = 4133, contour level = 0.25488 
    2496  
    2497 Position of assymT7SS.pdb (#2) relative to
    2498 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates: 
    2499 Matrix rotation and translation 
    2500 -0.65259853 0.45219005 0.60797971 336.22292178 
    2501 -0.63393823 -0.76534293 -0.11123184 287.10957267 
    2502 0.41501504 -0.45801132 0.78612223 324.13182531 
    2503 Axis -0.29988913 0.16687264 -0.93926569 
    2504 Axis point 175.13742617 133.52514170 0.00000000 
    2505 Rotation angle (degrees) 144.67740203 
    2506 Shift along axis -357.36476921 
    2507  
    2508 
    2509 > view matrix models
    2510 > #2,-0.64962,0.45343,0.61024,336.41,-0.63685,-0.76295,-0.11105,287.22,0.41523,-0.46077,0.7844,323.91
    2511 
    2512 > view matrix models
    2513 > #2,-0.69536,0.47409,0.5401,332.06,-0.60282,-0.79393,-0.07922,288.41,0.39125,-0.38067,0.83786,330.75
    2514 
    2515 > fitmap #2 inMap #3
    2516 
    2517 Fit molecule assymT7SS.pdb (#2) to map
    2518 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms 
    2519 average map value = 0.2573, steps = 104 
    2520 shifted from previous position = 2.41 
    2521 rotated from previous position = 5.58 degrees 
    2522 atoms outside contour = 4132, contour level = 0.25488 
    2523  
    2524 Position of assymT7SS.pdb (#2) relative to
    2525 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates: 
    2526 Matrix rotation and translation 
    2527 -0.65265924 0.45216740 0.60793138 336.22551079 
    2528 -0.63390146 -0.76536710 -0.11127505 287.11305306 
    2529 0.41497572 -0.45799328 0.78615349 324.13379193 
    2530 Axis -0.29985579 0.16687576 -0.93927578 
    2531 Axis point 175.13995760 133.52801339 0.00000000 
    2532 Rotation angle (degrees) 144.68005904 
    2533 Shift along axis -357.35797534 
    2534  
    2535 
    2536 > ui tool show Matchmaker
    2537 
    2538 > matchmaker #4 to #1
    2539 
    2540 Parameters 
    2541 --- 
    2542 Chain pairing | bb 
    2543 Alignment algorithm | Needleman-Wunsch 
    2544 Similarity matrix | BLOSUM-62 
    2545 SS fraction | 0.3 
    2546 Gap open (HH/SS/other) | 18/18/6 
    2547 Gap extend | 1 
    2548 SS matrix |  |  | H | S | O 
    2549 ---|---|---|--- 
    2550 H | 6 | -9 | -6 
    2551 S |  | 6 | -6 
    2552 O |  |  | 4 
    2553 Iteration cutoff | 2 
    2554  
    2555 Matchmaker assymT7SS.pdb, chain B (#1) with
    2556 YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain C (#4), sequence alignment
    2557 score = 1854.4 
    2558 RMSD between 156 pruned atom pairs is 0.663 angstroms; (across all 369 pairs:
    2559 6.931) 
    2560  
    2561 
    2562 > select :1-200
    2563 
    2564 10698 atoms, 10932 bonds, 2 pseudobonds, 1342 residues, 5 models selected 
    2565 
    2566 > hide #!3 models
    2567 
    2568 > hide #4 models
    2569 
    2570 > select :1-224
    2571 
    2572 11916 atoms, 12184 bonds, 8 pseudobonds, 1486 residues, 5 models selected 
    2573 
    2574 > show #!3 models
    2575 
    2576 > hide #!3 models
    2577 
    2578 > show #!3 models
    2579 
    2580 > select add #3
    2581 
    2582 11916 atoms, 12184 bonds, 8 pseudobonds, 1486 residues, 7 models selected 
    2583 
    2584 > show #4 models
    2585 
    2586 > select subtract #3
    2587 
    2588 11916 atoms, 12184 bonds, 8 pseudobonds, 1486 residues, 5 models selected 
    2589 
    2590 > ui tool show Matchmaker
    2591 
    2592 > matchmaker #4 to #1 & sel
    2593 
    2594 Parameters 
    2595 --- 
    2596 Chain pairing | bb 
    2597 Alignment algorithm | Needleman-Wunsch 
    2598 Similarity matrix | BLOSUM-62 
    2599 SS fraction | 0.3 
    2600 Gap open (HH/SS/other) | 18/18/6 
    2601 Gap extend | 1 
    2602 SS matrix |  |  | H | S | O 
    2603 ---|---|---|--- 
    2604 H | 6 | -9 | -6 
    2605 S |  | 6 | -6 
    2606 O |  |  | 4 
    2607 Iteration cutoff | 2 
    2608  
    2609 Matchmaker assymT7SS.pdb, chain B (#1) with
    2610 YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain B (#4), sequence alignment
    2611 score = 1065.9 
    2612 RMSD between 197 pruned atom pairs is 0.624 angstroms; (across all 216 pairs:
    2613 1.541) 
    2614  
    2615 
    2616 > open "/Users/remi/Documents/IECB/grant
    2617 > applications/ANR-T7SS-2023/YukCdimer_3fc44.result/YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb"
    2618 > format pdb
    2619 
    2620 Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb #5 
    2621 --- 
    2622 Chain | Description 
    2623 B C | No description available 
    2624  
    2625 
    2626 > ui tool show Matchmaker
    2627 
    2628 > matchmaker #5 to #1 & sel
    2629 
    2630 Parameters 
    2631 --- 
    2632 Chain pairing | bb 
    2633 Alignment algorithm | Needleman-Wunsch 
    2634 Similarity matrix | BLOSUM-62 
    2635 SS fraction | 0.3 
    2636 Gap open (HH/SS/other) | 18/18/6 
    2637 Gap extend | 1 
    2638 SS matrix |  |  | H | S | O 
    2639 ---|---|---|--- 
    2640 H | 6 | -9 | -6 
    2641 S |  | 6 | -6 
    2642 O |  |  | 4 
    2643 Iteration cutoff | 2 
    2644  
    2645 Matchmaker assymT7SS.pdb, chain B (#1) with
    2646 YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain B (#5), sequence alignment
    2647 score = 1065.9 
    2648 RMSD between 197 pruned atom pairs is 0.624 angstroms; (across all 216 pairs:
    2649 1.541) 
    2650  
    2651 
    2652 > save /Users/remi/Desktop/T7SS-docking.cxs
    2653 
    2654 ——— End of log from Tue Oct 31 16:39:50 2023 ———
    2655 
    2656 opened ChimeraX session 
    2657 
    2658 > open "/Users/remi/Documents/IECB/grant
    2659 > applications/ANR-T7SS-2023/YukCdimer_3fc44.result/YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb"
    2660 > format pdb
    2661 
    2662 Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb #6 
    2663 --- 
    2664 Chain | Description 
    2665 B C | No description available 
    2666  
    2667 
    2668 > ui tool show Matchmaker
    2669 
    2670 > matchmaker #5 to #1
    2671 
    2672 Parameters 
    2673 --- 
    2674 Chain pairing | bb 
    2675 Alignment algorithm | Needleman-Wunsch 
    2676 Similarity matrix | BLOSUM-62 
    2677 SS fraction | 0.3 
    2678 Gap open (HH/SS/other) | 18/18/6 
    2679 Gap extend | 1 
    2680 SS matrix |  |  | H | S | O 
    2681 ---|---|---|--- 
    2682 H | 6 | -9 | -6 
    2683 S |  | 6 | -6 
    2684 O |  |  | 4 
    2685 Iteration cutoff | 2 
    2686  
    2687 Matchmaker assymT7SS.pdb, chain B (#1) with
    2688 YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain C (#5), sequence alignment
    2689 score = 1854.4 
    2690 RMSD between 156 pruned atom pairs is 0.663 angstroms; (across all 369 pairs:
    2691 6.931) 
    2692  
    2693 
    2694 > matchmaker #5 to #2 & sel
    2695 
    2696 Parameters 
    2697 --- 
    2698 Chain pairing | bb 
    2699 Alignment algorithm | Needleman-Wunsch 
    2700 Similarity matrix | BLOSUM-62 
    2701 SS fraction | 0.3 
    2702 Gap open (HH/SS/other) | 18/18/6 
    2703 Gap extend | 1 
    2704 SS matrix |  |  | H | S | O 
    2705 ---|---|---|--- 
    2706 H | 6 | -9 | -6 
    2707 S |  | 6 | -6 
    2708 O |  |  | 4 
    2709 Iteration cutoff | 2 
    2710  
    2711 Matchmaker assymT7SS.pdb, chain B (#2) with
    2712 YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain B (#5), sequence alignment
    2713 score = 1065.9 
    2714 RMSD between 197 pruned atom pairs is 0.624 angstroms; (across all 216 pairs:
    2715 1.541) 
    2716  
    2717 
    2718 > ui tool show "Model Panel"
    2719 
    2720 > close #6
    2721 
    2722 > save /Users/remi/Desktop/T7SS-docking.cxs includeMaps true
    2723 
    2724 > hide #4 models
    2725 
    2726 > hide #5 models
    2727 
    2728 > select #2/B:367
    2729 
    2730 5 atoms, 4 bonds, 1 residue, 1 model selected 
    2731 
    2732 > select add #1/B:373
    2733 
    2734 10 atoms, 8 bonds, 2 residues, 2 models selected 
    2735 
    2736 > select up
    2737 
    2738 144 atoms, 142 bonds, 28 residues, 2 models selected 
    2739 
    2740 > select up
    2741 
    2742 5174 atoms, 5294 bonds, 674 residues, 2 models selected 
    2743 
    2744 > select up
    2745 
    2746 5224 atoms, 5342 bonds, 680 residues, 2 models selected 
    2747 
    2748 > select down
    2749 
    2750 5174 atoms, 5294 bonds, 674 residues, 2 models selected 
    2751 
    2752 > select up
    2753 
    2754 5224 atoms, 5342 bonds, 680 residues, 2 models selected 
    2755 
    2756 > select up
    2757 
    2758 5662 atoms, 5788 bonds, 738 residues, 2 models selected 
    2759 
    2760 > select up
    2761 
    2762 5666 atoms, 5788 bonds, 742 residues, 2 models selected 
    2763 
    2764 > select up
    2765 
    2766 17058 atoms, 17426 bonds, 2132 residues, 2 models selected 
    2767 
    2768 > select down
    2769 
    2770 5666 atoms, 5788 bonds, 742 residues, 2 models selected 
    2771 
    2772 > delete atoms sel
    2773 
    2774 > delete bonds sel
    2775 
    2776 > select #4-5
    2777 
    2778 14740 atoms, 15012 bonds, 1804 residues, 2 models selected 
    2779 
    2780 > select #4,5
    2781 
    2782 14740 atoms, 15012 bonds, 1804 residues, 2 models selected 
    2783 
    2784 > show #4 models
    2785 
    2786 > show #5 models
    2787 
    2788 > select #3
    2789 
    2790 2 models selected 
    2791 
    2792 > select #3
    2793 
    2794 2 models selected 
    2795 
    2796 > select #3
    2797 
    2798 2 models selected 
    2799 
    2800 > select #3
    2801 
    2802 2 models selected 
    2803 
    2804 > select subtract #3
    2805 
    2806 Nothing selected 
    2807 
    2808 > select clear
    2809 
    2810 > select #5/B:358
    2811 
    2812 9 atoms, 8 bonds, 1 residue, 1 model selected 
    2813 
    2814 > select #4,5 : 358-end
    2815 
    2816 3056 atoms, 3052 bonds, 376 residues, 2 models selected 
    2817 
    2818 > save /Users/remi/Desktop/T7SS-docking.cxs includeMaps true
    2819 
    2820 > delete atoms sel
    2821 
    2822 > delete bonds sel
    2823 
    2824 > save /Users/remi/Desktop/T7SS-docking.cxs
    2825 
    2826 ——— End of log from Tue Oct 31 16:44:53 2023 ———
    2827 
    2828 opened ChimeraX session 
    2829 
    2830 > open /Users/remi/Downloads/cryosparc_P14_J66_004_volume_map_sharp.mrc format
    2831 > mrc
    2832 
    2833 Opened cryosparc_P14_J66_004_volume_map_sharp.mrc as #6, grid size
    2834 480,480,480, pixel 1.2, shown at level 0.068, step 2, values float32 
    2835 
    2836 > volume #6 level 0.1911
    2837 
    2838 > close #3
    2839 
    2840 > volume #6 level 0.2454
    2841 
    2842 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    2843 got 4 atomic models, 1 maps. 
    2844 
    2845 > ui tool show "Model Panel"
    2846 
    2847 > select add #1
    2848 
    2849 5696 atoms, 5819 bonds, 19 pseudobonds, 695 residues, 2 models selected 
    2850 
    2851 > fitmap #1 inMap #6
    2852 
    2853 Fit molecule assymT7SS.pdb (#1) to map
    2854 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 5696 atoms 
    2855 average map value = 0.2873, steps = 76 
    2856 shifted from previous position = 1.28 
    2857 rotated from previous position = 4.86 degrees 
    2858 atoms outside contour = 2399, contour level = 0.24544 
    2859  
    2860 Position of assymT7SS.pdb (#1) relative to
    2861 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates: 
    2862 Matrix rotation and translation 
    2863 0.25842480 0.87271194 0.41423481 336.29794647 
    2864 -0.95762926 0.17499857 0.22873935 283.53418241 
    2865 0.12713307 -0.45579530 0.88095847 324.94865022 
    2866 Axis -0.34657588 0.14535793 -0.92669101 
    2867 Axis point 321.23956161 37.12486653 0.00000000 
    2868 Rotation angle (degrees) 80.95611541 
    2869 Shift along axis -376.46580795 
    2870  
    2871 
    2872 > select add #2
    2873 
    2874 11392 atoms, 11638 bonds, 38 pseudobonds, 1390 residues, 4 models selected 
    2875 
    2876 > select subtract #1
    2877 
    2878 5696 atoms, 5819 bonds, 19 pseudobonds, 695 residues, 2 models selected 
    2879 
    2880 > fitmap #2 inMap #6
    2881 
    2882 Fit molecule assymT7SS.pdb (#2) to map
    2883 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 5696 atoms 
    2884 average map value = 0.2892, steps = 92 
    2885 shifted from previous position = 3.3 
    2886 rotated from previous position = 7.37 degrees 
    2887 atoms outside contour = 2170, contour level = 0.24544 
    2888  
    2889 Position of assymT7SS.pdb (#2) relative to
    2890 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates: 
    2891 Matrix rotation and translation 
    2892 -0.71622533 0.48361825 0.50312489 335.56769935 
    2893 -0.60727525 -0.78713420 -0.10787273 286.03161351 
    2894 0.34385759 -0.38279648 0.85745485 326.44258633 
    2895 Axis -0.24196331 0.14017284 -0.96010694 
    2896 Axis point 181.13626464 126.30627263 0.00000000 
    2897 Rotation angle (degrees) 145.38143563 
    2898 Shift along axis -354.52099736 
    2899  
    2900 
    2901 > volume #6 style mesh
    2902 
    2903 > select add #4
    2904 
    2905 11538 atoms, 11797 bonds, 19 pseudobonds, 1409 residues, 3 models selected 
    2906 
    2907 > select subtract #2
    2908 
    2909 5842 atoms, 5978 bonds, 714 residues, 1 model selected 
    2910 
    2911 > fitmap #4 inMap #6
    2912 
    2913 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) to map
    2914 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 5842 atoms 
    2915 average map value = 0.2593, steps = 108 
    2916 shifted from previous position = 11.3 
    2917 rotated from previous position = 7.04 degrees 
    2918 atoms outside contour = 2573, contour level = 0.24544 
    2919  
    2920 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) relative to
    2921 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates: 
    2922 Matrix rotation and translation 
    2923 -0.86311987 0.08070962 -0.49850782 276.76821254 
    2924 -0.45008955 -0.57059383 0.68690762 253.56059819 
    2925 -0.22900543 0.81725678 0.52881743 271.59811939 
    2926 Axis 0.21389700 -0.44224109 -0.87101716 
    2927 Axis point 182.97824011 27.48927179 0.00000000 
    2928 Rotation angle (degrees) 162.25983857 
    2929 Shift along axis -289.50164740 
    2930  
    2931 
    2932 > select subtract #4
    2933 
    2934 Nothing selected 
    2935 
    2936 > select add #5
    2937 
    2938 5842 atoms, 5978 bonds, 714 residues, 1 model selected 
    2939 
    2940 > fitmap #5 inMap #6
    2941 
    2942 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) to map
    2943 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 5842 atoms 
    2944 average map value = 0.3, steps = 96 
    2945 shifted from previous position = 11.6 
    2946 rotated from previous position = 5.64 degrees 
    2947 atoms outside contour = 1928, contour level = 0.24544 
    2948  
    2949 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) relative to
    2950 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates: 
    2951 Matrix rotation and translation 
    2952 -0.89300837 -0.28408098 0.34904735 278.41998222 
    2953 0.43520701 -0.34763597 0.83050833 320.32779713 
    2954 -0.11459021 0.89355874 0.43407587 275.96838979 
    2955 Axis 0.07347802 0.54031641 0.83824767 
    2956 Axis point 114.91035289 104.46109670 0.00000000 
    2957 Rotation angle (degrees) 154.59318082 
    2958 Shift along axis 424.86597441 
    2959  
    2960 
    2961 > volume #6 level 0.2949
    2962 
    2963 > save /Users/remi/Desktop/T7SS-docking-2.cxs
    2964 
    2965 ——— End of log from Tue Oct 31 18:30:09 2023 ———
    2966 
    2967 opened ChimeraX session 
    2968 
    2969 > open /Users/remi/Desktop/YukB-TM.pdb
    2970 
    2971 Summary of feedback from opening /Users/remi/Desktop/YukB-TM.pdb 
    2972 --- 
    2973 warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 246
    2974 LEU A 251 1 6 
    2975 Start residue of secondary structure not found: HELIX 2 2 PRO A 252 ILE A 266
    2976 1 15 
    2977 Start residue of secondary structure not found: HELIX 3 3 PHE A 272 HIS A 334
    2978 1 63 
    2979 Start residue of secondary structure not found: HELIX 10 10 LEU D 246 LEU D
    2980 251 1 6 
    2981 Start residue of secondary structure not found: HELIX 11 11 PRO D 252 ILE D
    2982 266 1 15 
    2983 11 messages similar to the above omitted 
    2984  
    2985 Chain information for YukB-TM.pdb #3 
    2986 --- 
    2987 Chain | Description 
    2988 B C | No description available 
    2989  
    2990 
    2991 > ui tool show "Model Panel"
    2992 
    2993 > select add #3
    2994 
    2995 7776 atoms, 7950 bonds, 946 residues, 2 models selected 
    2996 
    2997 > select subtract #5
    2998 
    2999 1934 atoms, 1972 bonds, 232 residues, 1 model selected 
    3000 
    3001 > ui mousemode right "rotate selected models"
    3002 
    3003 > view matrix models #3,1,0,0,50.691,0,1,0,310.77,0,0,1,302.6
    3004 
    3005 > view matrix models #3,1,0,0,135.33,0,1,0,286.44,0,0,1,296.82
    3006 
    3007 > view matrix models #3,1,0,0,263.66,0,1,0,250.66,0,0,1,271.76
    3008 
    3009 > view matrix models #3,1,0,0,325.25,0,1,0,231.16,0,0,1,293.65
    3010 
    3011 > view matrix models
    3012 > #3,0.70359,-0.62334,-0.34118,327.13,0.69609,0.70113,0.15451,262.52,0.14291,-0.3462,0.92721,305.8
    3013 
    3014 > view matrix models
    3015 > #3,0.70218,-0.62463,-0.34173,324.93,0.69752,0.69979,0.15413,280.81,0.14287,-0.34659,0.92707,317.69
    3016 
    3017 > view matrix models
    3018 > #3,0.88594,-0.37771,-0.26916,323.6,0.44174,0.86402,0.24154,272.65,0.14133,-0.33289,0.93232,317.39
    3019 
    3020 > view matrix models
    3021 > #3,0.88594,-0.37771,-0.26916,333.31,0.44174,0.86402,0.24154,268.45,0.14133,-0.33289,0.93232,316.72
    3022 
    3023 > fitmap #3 inMap #6
    3024 
    3025 Fit molecule YukB-TM.pdb (#3) to map
    3026 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 1934 atoms 
    3027 average map value = 0.263, steps = 272 
    3028 shifted from previous position = 22.3 
    3029 rotated from previous position = 18.8 degrees 
    3030 atoms outside contour = 1247, contour level = 0.29485 
    3031  
    3032 Position of YukB-TM.pdb (#3) relative to
    3033 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates: 
    3034 Matrix rotation and translation 
    3035 0.73075945 -0.54752577 -0.40768389 333.46652490 
    3036 0.67599522 0.66351928 0.32058171 285.76200058 
    3037 0.09497938 -0.50986047 0.85499779 341.59285647 
    3038 Axis -0.53171151 -0.32184281 0.78339011 
    3039 Axis point -96.07052368 654.65487038 -0.00000000 
    3040 Rotation angle (degrees) 51.34435840 
    3041 Shift along axis -1.67796933 
    3042  
    3043 
    3044 > view matrix models
    3045 > #3,0.71991,-0.52048,-0.45916,330.66,0.68265,0.65046,0.333,286.74,0.12535,-0.55317,0.82358,342.63
    3046 
    3047 > view matrix models
    3048 > #3,0.71991,-0.52048,-0.45916,336.05,0.68265,0.65046,0.333,282.9,0.12535,-0.55317,0.82358,317.22
    3049 
    3050 > fitmap #3 inMap #6
    3051 
    3052 Fit molecule YukB-TM.pdb (#3) to map
    3053 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 1934 atoms 
    3054 average map value = 0.263, steps = 244 
    3055 shifted from previous position = 26.4 
    3056 rotated from previous position = 3.54 degrees 
    3057 atoms outside contour = 1247, contour level = 0.29485 
    3058  
    3059 Position of YukB-TM.pdb (#3) relative to
    3060 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates: 
    3061 Matrix rotation and translation 
    3062 0.73074010 -0.54750143 -0.40775126 333.47153017 
    3063 0.67600176 0.66354672 0.32051111 285.77815164 
    3064 0.09508172 -0.50985089 0.85499213 341.59476560 
    3065 Axis -0.53166083 -0.32195188 0.78337970 
    3066 Axis point -96.09353373 654.68448428 0.00000000 
    3067 Rotation angle (degrees) 51.34426931 
    3068 Shift along axis -1.70216043 
    3069  
    3070 
    3071 > view matrix models
    3072 > #3,0.73074,-0.5475,-0.40775,337.27,0.676,0.66355,0.32051,282.88,0.095082,-0.50985,0.85499,319.9
    3073 
    3074 > ui tool show Matchmaker
    3075 
    3076 > matchmaker #3 to #1
    3077 
    3078 Parameters 
    3079 --- 
    3080 Chain pairing | bb 
    3081 Alignment algorithm | Needleman-Wunsch 
    3082 Similarity matrix | BLOSUM-62 
    3083 SS fraction | 0.3 
    3084 Gap open (HH/SS/other) | 18/18/6 
    3085 Gap extend | 1 
    3086 SS matrix |  |  | H | S | O 
    3087 ---|---|---|--- 
    3088 H | 6 | -9 | -6 
    3089 S |  | 6 | -6 
    3090 O |  |  | 4 
    3091 Iteration cutoff | 2 
    3092  
    3093 Matchmaker assymT7SS.pdb, chain A (#1) with YukB-TM.pdb, chain B (#3),
    3094 sequence alignment score = 1703.3 
    3095 Fewer than 3 residues aligned; cannot match assymT7SS.pdb, chain A with YukB-
    3096 TM.pdb, chain B 
    3097 
    3098 > matchmaker #3 to #2
    3099 
    3100 Parameters 
    3101 --- 
    3102 Chain pairing | bb 
    3103 Alignment algorithm | Needleman-Wunsch 
    3104 Similarity matrix | BLOSUM-62 
    3105 SS fraction | 0.3 
    3106 Gap open (HH/SS/other) | 18/18/6 
    3107 Gap extend | 1 
    3108 SS matrix |  |  | H | S | O 
    3109 ---|---|---|--- 
    3110 H | 6 | -9 | -6 
    3111 S |  | 6 | -6 
    3112 O |  |  | 4 
    3113 Iteration cutoff | 2 
    3114  
    3115 Matchmaker assymT7SS.pdb, chain A (#2) with YukB-TM.pdb, chain B (#3),
    3116 sequence alignment score = 1703.3 
    3117 Fewer than 3 residues aligned; cannot match assymT7SS.pdb, chain A with YukB-
    3118 TM.pdb, chain B 
    3119 
    3120 > ui tool show Matchmaker
    3121 
    3122 > matchmaker #3 to #2
    3123 
    3124 Parameters 
    3125 --- 
    3126 Chain pairing | bb 
    3127 Alignment algorithm | Needleman-Wunsch 
    3128 Similarity matrix | BLOSUM-62 
    3129 SS fraction | 0.3 
    3130 Gap open (HH/SS/other) | 18/18/6 
    3131 Gap extend | 1 
    3132 SS matrix |  |  | H | S | O 
    3133 ---|---|---|--- 
    3134 H | 6 | -9 | -6 
    3135 S |  | 6 | -6 
    3136 O |  |  | 4 
    3137 Iteration cutoff | 2 
    3138  
    3139 Matchmaker assymT7SS.pdb, chain A (#2) with YukB-TM.pdb, chain B (#3),
    3140 sequence alignment score = 1703.3 
    3141 Fewer than 3 residues aligned; cannot match assymT7SS.pdb, chain A with YukB-
    3142 TM.pdb, chain B 
    3143 
    3144 > select #3/B:290
    3145 
    3146 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3147 
    3148 > select #3/B:291
    3149 
    3150 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3151 
    3152 > select up
    3153 
    3154 548 atoms, 555 bonds, 63 residues, 1 model selected 
    3155 
    3156 > select up
    3157 
    3158 967 atoms, 986 bonds, 116 residues, 1 model selected 
    3159 
    3160 > fitmap #3 inMap #6
    3161 
    3162 Fit molecule YukB-TM.pdb (#3) to map
    3163 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 1934 atoms 
    3164 average map value = 0.263, steps = 252 
    3165 shifted from previous position = 22.2 
    3166 rotated from previous position = 0.00743 degrees 
    3167 atoms outside contour = 1248, contour level = 0.29485 
    3168  
    3169 Position of YukB-TM.pdb (#3) relative to
    3170 cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates: 
    3171 Matrix rotation and translation 
    3172 0.73071533 -0.54746344 -0.40784664 333.47096692 
    3173 0.67601075 0.66357297 0.32043780 285.76894231 
    3174 0.09520802 -0.50985753 0.85497411 341.59833133 
    3175 Axis -0.53161364 -0.32209109 0.78335449 
    3176 Axis point -96.08229491 654.70202551 0.00000000 
    3177 Rotation angle (degrees) 51.34487596 
    3178 Shift along axis -1.72875718 
    3179  
    3180 
    3181 > view matrix models
    3182 > #3,0.73072,-0.54746,-0.40785,336.34,0.67601,0.66357,0.32044,284.44,0.095208,-0.50986,0.85497,328.93
    3183 
    3184 > select #1/E:294
    3185 
    3186 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3187 
    3188 > select #1/E:297
    3189 
    3190 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3191 
    3192 > select up
    3193 
    3194 548 atoms, 557 bonds, 63 residues, 1 model selected 
    3195 
    3196 > select up
    3197 
    3198 566 atoms, 577 bonds, 65 residues, 1 model selected 
    3199 
    3200 > select up
    3201 
    3202 967 atoms, 987 bonds, 116 residues, 1 model selected 
    3203 
    3204 > delete atoms sel
    3205 
    3206 > delete bonds sel
    3207 
    3208 > select #2/E:276
    3209 
    3210 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3211 
    3212 > select up
    3213 
    3214 548 atoms, 557 bonds, 63 residues, 1 model selected 
    3215 
    3216 > select up
    3217 
    3218 566 atoms, 577 bonds, 65 residues, 1 model selected 
    3219 
    3220 > select up
    3221 
    3222 967 atoms, 987 bonds, 116 residues, 1 model selected 
    3223 
    3224 > delete atoms sel
    3225 
    3226 > delete bonds sel
    3227 
    3228 > save /Users/remi/Desktop/T7SS-docking-2.cxs
    3229 
    3230 ——— End of log from Tue Oct 31 18:38:05 2023 ———
    3231 
    3232 opened ChimeraX session 
    3233 
    3234 > save /Users/remi/Desktop/T7SS-docking-3.cxs includeMaps true
    3235 
    3236 ——— End of log from Wed Nov 1 11:49:41 2023 ———
    3237 
    3238 opened ChimeraX session 
    3239 
    3240 > open /Users/remi/Downloads/cryosparc_P14_J436_004_volume_map_sharp.mrc
    3241 > format mrc
    3242 
    3243 Opened cryosparc_P14_J436_004_volume_map_sharp.mrc as #7, grid size
    3244 400,400,400, pixel 1.2, shown at level 0.0937, step 2, values float32 
    3245 
    3246 > volume #7 level 0.1419
    3247 
    3248 > ui tool show "Model Panel"
    3249 
    3250 > select add #1
    3251 
    3252 4729 atoms, 4832 bonds, 1 pseudobond, 579 residues, 2 models selected 
    3253 
    3254 > select add #2
    3255 
    3256 9458 atoms, 9664 bonds, 2 pseudobonds, 1158 residues, 4 models selected 
    3257 
    3258 > select add #3
    3259 
    3260 11392 atoms, 11636 bonds, 2 pseudobonds, 1390 residues, 5 models selected 
    3261 
    3262 > select add #4
    3263 
    3264 17234 atoms, 17614 bonds, 2 pseudobonds, 2104 residues, 6 models selected 
    3265 
    3266 > select add #5
    3267 
    3268 23076 atoms, 23592 bonds, 2 pseudobonds, 2818 residues, 7 models selected 
    3269 
    3270 > ui mousemode right "rotate selected models"
    3271 
    3272 > view matrix models
    3273 > #1,-0.021944,0.89209,0.45133,330.91,0.97559,0.11777,-0.18534,312.97,-0.21849,0.43625,-0.8729,242.41,#2,-0.86176,0.24802,0.44255,330.89,0.34943,0.92261,0.16338,310.24,-0.36778,0.29544,-0.88173,241.16,#4,-0.95193,-0.092145,-0.29213,266,0.21153,0.49202,-0.8445,330.03,0.22155,-0.86569,-0.44887,295.17,#5,-0.73376,-0.38067,0.56275,286.25,-0.65379,0.17032,-0.73726,266.25,0.18481,-0.90889,-0.37385,296.5,#3,0.88976,-0.33341,-0.3117,331.15,-0.45191,-0.73929,-0.49923,311.75,-0.063989,0.58506,-0.80846,238.53
    3274 
    3275 > view matrix models
    3276 > #1,-0.021944,0.89209,0.45133,282.15,0.97559,0.11777,-0.18534,299.8,-0.21849,0.43625,-0.8729,204.25,#2,-0.86176,0.24802,0.44255,282.14,0.34943,0.92261,0.16338,297.07,-0.36778,0.29544,-0.88173,203,#4,-0.95193,-0.092145,-0.29213,217.24,0.21153,0.49202,-0.8445,316.85,0.22155,-0.86569,-0.44887,257.01,#5,-0.73376,-0.38067,0.56275,237.5,-0.65379,0.17032,-0.73726,253.07,0.18481,-0.90889,-0.37385,258.33,#3,0.88976,-0.33341,-0.3117,282.4,-0.45191,-0.73929,-0.49923,298.57,-0.063989,0.58506,-0.80846,200.36
    3277 
    3278 > view matrix models
    3279 > #1,-0.021944,0.89209,0.45133,292.48,0.97559,0.11777,-0.18534,260.11,-0.21849,0.43625,-0.8729,210.7,#2,-0.86176,0.24802,0.44255,292.46,0.34943,0.92261,0.16338,257.38,-0.36778,0.29544,-0.88173,209.45,#4,-0.95193,-0.092145,-0.29213,227.57,0.21153,0.49202,-0.8445,277.17,0.22155,-0.86569,-0.44887,263.46,#5,-0.73376,-0.38067,0.56275,247.82,-0.65379,0.17032,-0.73726,213.39,0.18481,-0.90889,-0.37385,264.78,#3,0.88976,-0.33341,-0.3117,292.73,-0.45191,-0.73929,-0.49923,258.89,-0.063989,0.58506,-0.80846,206.81
    3280 
    3281 > ui tool show "Fit in Map"
    3282 
    3283 > fitmap sel inMap #7
    3284 
    3285 Fit molecules assymT7SS.pdb (#1), assymT7SS.pdb (#2),
    3286 YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4),
    3287 YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5), YukB-TM.pdb (#3) to map
    3288 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 23076 atoms 
    3289 average map value = 0.1434, steps = 144 
    3290 shifted from previous position = 13.4 
    3291 rotated from previous position = 15.5 degrees 
    3292 atoms outside contour = 12526, contour level = 0.1419 
    3293  
    3294 Position of assymT7SS.pdb (#1) relative to
    3295 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3296 Matrix rotation and translation 
    3297 0.22608012 0.88164601 0.41423192 285.54542347 
    3298 0.96667767 -0.15063411 -0.20698704 245.61380651 
    3299 -0.12009184 0.44722441 -0.88632289 205.31128703 
    3300 Axis 0.77060776 0.62938984 0.10016037 
    3301 Axis point 0.00000000 -17.75681651 83.64802640 
    3302 Rotation angle (degrees) 154.88239910 
    3303 Shift along axis 395.19440967 
    3304  
    3305 Position of assymT7SS.pdb (#2) relative to
    3306 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3307 Matrix rotation and translation 
    3308 -0.73839608 0.46086884 0.49231203 284.88461594 
    3309 0.58673515 0.79892911 0.13211418 243.10775111 
    3310 -0.33243510 0.38640936 -0.86033407 203.79957019 
    3311 Axis 0.29155924 0.94560439 0.14431057 
    3312 Axis point 123.70226930 0.00000000 60.88753693 
    3313 Rotation angle (degrees) 154.14499461 
    3314 Shift along axis 342.35493104 
    3315  
    3316 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) relative to
    3317 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3318 Matrix rotation and translation 
    3319 -0.87540369 0.05540811 -0.48020653 225.51072062 
    3320 0.41957424 0.58042355 -0.69790111 273.13753574 
    3321 0.24005380 -0.81242750 -0.53135274 259.41085155 
    3322 Axis -0.14049323 -0.88356666 0.44673438 
    3323 Axis point 51.30311012 0.00000000 223.28090352 
    3324 Rotation angle (degrees) 155.94666474 
    3325 Shift along axis -157.13020362 
    3326  
    3327 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) relative to
    3328 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3329 Matrix rotation and translation 
    3330 -0.87740715 -0.30254740 0.37231942 229.29818644 
    3331 -0.46513505 0.34639976 -0.81465121 206.50279255 
    3332 0.11749925 -0.88795961 -0.44465903 254.39561897 
    3333 Axis -0.23569252 0.81926776 -0.52273260 
    3334 Axis point 156.05432032 0.00000000 182.32981571 
    3335 Rotation angle (degrees) 171.05321655 
    3336 Shift along axis -17.84367262 
    3337  
    3338 Position of YukB-TM.pdb (#3) relative to
    3339 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3340 Matrix rotation and translation 
    3341 0.75151986 -0.52139048 -0.40419038 285.58145951 
    3342 -0.65091569 -0.68574055 -0.32568185 244.74527457 
    3343 -0.10736231 0.50785024 -0.85472888 201.32402682 
    3344 Axis 0.93211564 -0.33193453 -0.14484442 
    3345 Axis point 0.00000000 144.87717120 160.38244388 
    3346 Rotation angle (degrees) 153.44104706 
    3347 Shift along axis 155.79487573 
    3348  
    3349 
    3350 > close #6
    3351 
    3352 > fitmap #1 inMap #7
    3353 
    3354 Fit molecule assymT7SS.pdb (#1) to map
    3355 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 4729 atoms 
    3356 average map value = 0.1628, steps = 56 
    3357 shifted from previous position = 1.27 
    3358 rotated from previous position = 2.38 degrees 
    3359 atoms outside contour = 2275, contour level = 0.1419 
    3360  
    3361 Position of assymT7SS.pdb (#1) relative to
    3362 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3363 Matrix rotation and translation 
    3364 0.25886376 0.86389663 0.43205574 284.56519739 
    3365 0.95872519 -0.17532969 -0.22384259 244.17062848 
    3366 -0.11762466 0.47216745 -0.87362597 205.58322627 
    3367 Axis 0.78032593 0.61626966 0.10631626 
    3368 Axis point 0.00000000 -14.96165689 83.57550674 
    3369 Rotation angle (degrees) 153.51433265 
    3370 Shift along axis 394.38539217 
    3371  
    3372 
    3373 > fitmap #2 inMap #7
    3374 
    3375 Fit molecule assymT7SS.pdb (#2) to map
    3376 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 4729 atoms 
    3377 average map value = 0.1628, steps = 92 
    3378 shifted from previous position = 2.86 
    3379 rotated from previous position = 2.4 degrees 
    3380 atoms outside contour = 2210, contour level = 0.1419 
    3381  
    3382 Position of assymT7SS.pdb (#2) relative to
    3383 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3384 Matrix rotation and translation 
    3385 -0.72054757 0.46296298 0.51621360 285.82202748 
    3386 0.60797648 0.77979515 0.14927868 242.74548594 
    3387 -0.33343036 0.42140812 -0.84335011 203.27007081 
    3388 Axis 0.30107194 0.94000841 0.16043650 
    3389 Axis point 122.79273314 0.00000000 57.87300408 
    3390 Rotation angle (degrees) 153.13214980 
    3391 Shift along axis 346.84773162 
    3392  
    3393 
    3394 > fitmap #3 inMap #7
    3395 
    3396 Fit molecule YukB-TM.pdb (#3) to map
    3397 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 1934 atoms 
    3398 average map value = 0.1651, steps = 160 
    3399 shifted from previous position = 2.54 
    3400 rotated from previous position = 6.53 degrees 
    3401 atoms outside contour = 1081, contour level = 0.1419 
    3402  
    3403 Position of YukB-TM.pdb (#3) relative to
    3404 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3405 Matrix rotation and translation 
    3406 0.73100700 -0.58685167 -0.34818655 288.18371158 
    3407 -0.67538579 -0.69506413 -0.24645465 246.19000576 
    3408 -0.09737966 0.41532032 -0.90444802 201.46250567 
    3409 Axis 0.92786411 -0.35165234 -0.12413227 
    3410 Axis point 0.00000000 155.76763872 149.91090232 
    3411 Rotation angle (degrees) 159.10772688 
    3412 Shift along axis 155.81403511 
    3413  
    3414 
    3415 > fitmap #4 inMap #7
    3416 
    3417 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) to map
    3418 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 5842 atoms 
    3419 average map value = 0.1355, steps = 132 
    3420 shifted from previous position = 8.14 
    3421 rotated from previous position = 4.73 degrees 
    3422 atoms outside contour = 3351, contour level = 0.1419 
    3423  
    3424 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) relative to
    3425 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3426 Matrix rotation and translation 
    3427 -0.85472470 0.12343654 -0.50419153 222.89478895 
    3428 0.48265532 0.54643305 -0.68443755 272.18875179 
    3429 0.19102232 -0.82835641 -0.52662713 267.10096997 
    3430 Axis -0.18088010 -0.87375867 0.45147335 
    3431 Axis point 43.11660241 0.00000000 226.95085493 
    3432 Rotation angle (degrees) 156.55744346 
    3433 Shift along axis -157.55554269 
    3434  
    3435 
    3436 > fitmap #5 inMap #7
    3437 
    3438 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) to map
    3439 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 5842 atoms 
    3440 average map value = 0.1797, steps = 92 
    3441 shifted from previous position = 8.57 
    3442 rotated from previous position = 4.78 degrees 
    3443 atoms outside contour = 2643, contour level = 0.1419 
    3444  
    3445 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) relative to
    3446 cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates: 
    3447 Matrix rotation and translation 
    3448 -0.83545712 -0.35744614 0.41742504 228.62561401 
    3449 -0.52796328 0.31123083 -0.79018361 205.35695099 
    3450 0.15253254 -0.88054962 -0.44873845 262.85138211 
    3451 Axis -0.27572899 0.80825240 -0.52028990 
    3452 Axis point 161.85636230 0.00000000 186.33101316 
    3453 Rotation angle (degrees) 170.56855211 
    3454 Shift along axis -33.81738013 
    3455  
    3456 
    3457 > show #!7 models
    3458 
    3459 > volume #7 level 0.2029
    3460 
    3461 > molmap sel 10
    3462 
    3463 Opened map 10 as #6, grid size 64,63,78, pixel 3.33, shown at level 0.0631,
    3464 step 1, values float32 
    3465 
    3466 > vop resample #8 ongrid #7
    3467 
    3468 [Repeated 1 time(s)]
    3469 
    3470 > vop resample #6 ongrid #7
    3471 
    3472 Opened map 10 resampled as #8, grid size 400,400,400, pixel 1.2, shown at step
    3473 1, values float32 
    3474 
    3475 > save /Users/remi/Desktop/mask-assym.mrc models #8
    3476 
    3477 > save /Users/remi/Desktop/T7SS-docking-4.cxs includeMaps true
    3478 
    3479 ——— End of log from Sun Nov 12 21:44:36 2023 ———
    3480 
    3481 opened ChimeraX session 
    3482 
    3483 > select #1.1:1-204
    3484 
    3485 Nothing selected 
    3486 
    3487 > select #1.1:1-204
    3488 
    3489 Nothing selected 
    3490 
    3491 > split all
    3492 
    3493 Split assymT7SS.pdb (#1) into 2 models 
    3494 Split assymT7SS.pdb (#2) into 2 models 
    3495 Split YukB-TM.pdb (#3) into 2 models 
    3496 Split YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) into 2 models 
    3497 Split YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) into 2 models 
    3498 Chain information for assymT7SS.pdb A #1.1 
    3499 --- 
    3500 Chain | Description 
    3501 A | No description available 
    3502  
    3503 Chain information for assymT7SS.pdb D #1.2 
    3504 --- 
    3505 Chain | Description 
    3506 D | No description available 
    3507  
    3508 Chain information for assymT7SS.pdb A #2.1 
    3509 --- 
    3510 Chain | Description 
    3511 A | No description available 
    3512  
    3513 Chain information for assymT7SS.pdb D #2.2 
    3514 --- 
    3515 Chain | Description 
    3516 D | No description available 
    3517  
    3518 Chain information for YukB-TM.pdb B #3.1 
    3519 --- 
    3520 Chain | Description 
    3521 B | No description available 
    3522  
    3523 Chain information for YukB-TM.pdb C #3.2 
    3524 --- 
    3525 Chain | Description 
    3526 C | No description available 
    3527  
    3528 Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B #4.1 
    3529 --- 
    3530 Chain | Description 
    3531 B | No description available 
    3532  
    3533 Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C #4.2 
    3534 --- 
    3535 Chain | Description 
    3536 C | No description available 
    3537  
    3538 Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B #5.1 
    3539 --- 
    3540 Chain | Description 
    3541 B | No description available 
    3542  
    3543 Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C #5.2 
    3544 --- 
    3545 Chain | Description 
    3546 C | No description available 
    3547  
    3548 
    3549 > select #1.1:1-204
    3550 
    3551 1607 atoms, 1641 bonds, 204 residues, 1 model selected 
    3552 
    3553 > delete atoms sel
    3554 
    3555 > delete bonds sel
    3556 
    3557 > select #2.1:1-204
    3558 
    3559 1607 atoms, 1641 bonds, 204 residues, 1 model selected 
    3560 
    3561 > delete atoms sel
    3562 
    3563 > delete bonds sel
    3564 
    3565 > open /Users/remi/Desktop/FHA-1.pdb /Users/remi/Desktop/FHA-2.pdb
    3566 
    3567 Summary of feedback from opening /Users/remi/Desktop/FHA-1.pdb 
    3568 --- 
    3569 warnings | Start residue of secondary structure not found: HELIX 1 1 TYR B 8
    3570 LEU B 13 1 6 
    3571 Start residue of secondary structure not found: HELIX 2 2 ARG B 30 LYS B 32 1
    3572 3 
    3573 Start residue of secondary structure not found: HELIX 3 3 GLY B 38 ASP B 46 1
    3574 9 
    3575 Start residue of secondary structure not found: HELIX 4 4 PHE B 75 ALA B 80 1
    3576 6 
    3577 Start residue of secondary structure not found: HELIX 5 5 LYS B 83 GLN B 99 1
    3578 17 
    3579 49 messages similar to the above omitted 
    3580  
    3581 Summary of feedback from opening /Users/remi/Desktop/FHA-2.pdb 
    3582 --- 
    3583 warnings | Start residue of secondary structure not found: HELIX 1 1 TYR B 8
    3584 LEU B 13 1 6 
    3585 Start residue of secondary structure not found: HELIX 2 2 ARG B 30 LYS B 32 1
    3586 3 
    3587 Start residue of secondary structure not found: HELIX 3 3 GLY B 38 ASP B 46 1
    3588 9 
    3589 Start residue of secondary structure not found: HELIX 4 4 PHE B 75 ALA B 80 1
    3590 6 
    3591 Start residue of secondary structure not found: HELIX 5 5 LYS B 83 GLN B 99 1
    3592 17 
    3593 49 messages similar to the above omitted 
    3594  
    3595 Chain information for FHA-1.pdb #9 
    3596 --- 
    3597 Chain | Description 
    3598 A | No description available 
    3599  
    3600 Chain information for FHA-2.pdb #10 
    3601 --- 
    3602 Chain | Description 
    3603 A | No description available 
    3604  
    3605 
    3606 > open /Users/remi/Downloads/cryosparc_P14_J452_004_volume_map_sharp(1).mrc
    3607 
    3608 Opened cryosparc_P14_J452_004_volume_map_sharp(1).mrc as #11, grid size
    3609 400,400,400, pixel 1.2, shown at level 0.048, step 2, values float32 
    3610 
    3611 > close #8
    3612 
    3613 > close #6
    3614 
    3615 > close #7
    3616 
    3617 > volume #11 step 1
    3618 
    3619 > volume #11 level 0.129
    3620 
    3621 > volume #11 style mesh
    3622 
    3623 > ui tool show "Model Panel"
    3624 
    3625 > select add #1.1
    3626 
    3627 2485 atoms, 2539 bonds, 1 pseudobond, 296 residues, 2 models selected 
    3628 
    3629 > fitmap #1.1 inMap #11
    3630 
    3631 Fit molecule assymT7SS.pdb A (#1.1) to map
    3632 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2485 atoms 
    3633 average map value = 0.1513, steps = 48 
    3634 shifted from previous position = 0.959 
    3635 rotated from previous position = 1.5 degrees 
    3636 atoms outside contour = 1030, contour level = 0.12903 
    3637  
    3638 Position of assymT7SS.pdb A (#1.1) relative to
    3639 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3640 Matrix rotation and translation 
    3641 0.25350703 0.86285371 0.43728441 285.23871409 
    3642 0.95707270 -0.15806001 -0.24295856 244.09660484 
    3643 -0.14052052 0.48010468 -0.86588306 206.41132849 
    3644 Axis 0.77719258 0.62106006 0.10127234 
    3645 Axis point 0.00000000 -18.34928408 84.50766871 
    3646 Rotation angle (degrees) 152.27836324 
    3647 Shift along axis 394.18782414 
    3648  
    3649 
    3650 > select add #1.2
    3651 
    3652 3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 3 models selected 
    3653 
    3654 > select subtract #1.1
    3655 
    3656 637 atoms, 651 bonds, 79 residues, 1 model selected 
    3657 
    3658 > fitmap #1.2 inMap #11
    3659 
    3660 Fit molecule assymT7SS.pdb D (#1.2) to map
    3661 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 637 atoms 
    3662 average map value = 0.1125, steps = 36 
    3663 shifted from previous position = 1.83 
    3664 rotated from previous position = 6.52 degrees 
    3665 atoms outside contour = 365, contour level = 0.12903 
    3666  
    3667 Position of assymT7SS.pdb D (#1.2) relative to
    3668 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3669 Matrix rotation and translation 
    3670 0.26867845 0.81301352 0.51654709 282.94622350 
    3671 0.96248237 -0.20547831 -0.17721835 243.33517348 
    3672 -0.03794169 0.54478222 -0.83771878 208.34532416 
    3673 Axis 0.78262089 0.60104455 0.16201849 
    3674 Axis point 0.00000000 -9.35906561 75.20423453 
    3675 Rotation angle (degrees) 152.53084968 
    3676 Shift along axis 401.45070029 
    3677  
    3678 
    3679 > select subtract #1.2
    3680 
    3681 Nothing selected 
    3682 
    3683 > select add #2
    3684 
    3685 3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 4 models selected 
    3686 
    3687 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    3688 got 12 atomic models, 1 maps. 
    3689 
    3690 > select subtract #2.1
    3691 
    3692 637 atoms, 651 bonds, 79 residues, 2 models selected 
    3693 
    3694 > select add #2
    3695 
    3696 3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 4 models selected 
    3697 
    3698 > select subtract #2
    3699 
    3700 Nothing selected 
    3701 
    3702 > select add #2.1
    3703 
    3704 2485 atoms, 2539 bonds, 1 pseudobond, 296 residues, 2 models selected 
    3705 
    3706 > fitmap #2.1 inMap #11
    3707 
    3708 Fit molecule assymT7SS.pdb A (#2.1) to map
    3709 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2485 atoms 
    3710 average map value = 0.152, steps = 64 
    3711 shifted from previous position = 1.49 
    3712 rotated from previous position = 2.67 degrees 
    3713 atoms outside contour = 994, contour level = 0.12903 
    3714  
    3715 Position of assymT7SS.pdb A (#2.1) relative to
    3716 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3717 Matrix rotation and translation 
    3718 -0.73561811 0.42365331 0.52856775 285.85940769 
    3719 0.57468039 0.80339908 0.15586009 243.88343620 
    3720 -0.35862020 0.41841103 -0.83446017 203.59571871 
    3721 Axis 0.28006415 0.94636699 0.16110119 
    3722 Axis point 126.33437429 0.00000000 56.10661311 
    3723 Rotation angle (degrees) 152.04787883 
    3724 Shift along axis 343.66171823 
    3725  
    3726 
    3727 > select add #2.2
    3728 
    3729 3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 3 models selected 
    3730 
    3731 > select subtract #2.1
    3732 
    3733 637 atoms, 651 bonds, 79 residues, 1 model selected 
    3734 
    3735 > fitmap #2.2 inMap #11
    3736 
    3737 Fit molecule assymT7SS.pdb D (#2.2) to map
    3738 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 637 atoms 
    3739 average map value = 0.1281, steps = 88 
    3740 shifted from previous position = 5.42 
    3741 rotated from previous position = 7.03 degrees 
    3742 atoms outside contour = 317, contour level = 0.12903 
    3743  
    3744 Position of assymT7SS.pdb D (#2.2) relative to
    3745 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3746 Matrix rotation and translation 
    3747 -0.69061390 0.52765072 0.49460809 291.43330149 
    3748 0.62103505 0.78314223 0.03168140 242.78379891 
    3749 -0.37063177 0.32904858 -0.86853851 192.39532545 
    3750 Axis 0.32334213 0.94081837 0.10154143 
    3751 Axis point 124.40229542 0.00000000 59.69478635 
    3752 Rotation angle (degrees) 152.62362755 
    3753 Shift along axis 342.18422030 
    3754  
    3755 
    3756 > select subtract #2.2
    3757 
    3758 Nothing selected 
    3759 
    3760 > select add #3
    3761 
    3762 1934 atoms, 1972 bonds, 232 residues, 3 models selected 
    3763 
    3764 > select subtract #3.1
    3765 
    3766 967 atoms, 986 bonds, 116 residues, 2 models selected 
    3767 
    3768 > select add #3
    3769 
    3770 1934 atoms, 1972 bonds, 232 residues, 3 models selected 
    3771 
    3772 > select subtract #3
    3773 
    3774 Nothing selected 
    3775 
    3776 > select add #3.1
    3777 
    3778 967 atoms, 986 bonds, 116 residues, 1 model selected 
    3779 
    3780 > fitmap #3.1 inMap #11
    3781 
    3782 Fit molecule YukB-TM.pdb B (#3.1) to map
    3783 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 967 atoms 
    3784 average map value = 0.136, steps = 144 
    3785 shifted from previous position = 1.41 
    3786 rotated from previous position = 4.71 degrees 
    3787 atoms outside contour = 559, contour level = 0.12903 
    3788  
    3789 Position of YukB-TM.pdb B (#3.1) relative to
    3790 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3791 Matrix rotation and translation 
    3792 0.77877801 -0.54726206 -0.30660894 287.65397249 
    3793 -0.62476349 -0.72057338 -0.30074008 247.09818678 
    3794 -0.05635060 0.42576783 -0.90307606 201.17610227 
    3795 Axis 0.94070516 -0.32404232 -0.10035127 
    3796 Axis point 0.00000000 149.78962958 148.20503069 
    3797 Rotation angle (degrees) 157.28480446 
    3798 Shift along axis 170.33902927 
    3799  
    3800 
    3801 > select add #3.2
    3802 
    3803 1934 atoms, 1972 bonds, 232 residues, 2 models selected 
    3804 
    3805 > select subtract #3.1
    3806 
    3807 967 atoms, 986 bonds, 116 residues, 1 model selected 
    3808 
    3809 > fitmap #3.2 inMap #11
    3810 
    3811 Fit molecule YukB-TM.pdb C (#3.2) to map
    3812 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 967 atoms 
    3813 average map value = 0.1383, steps = 84 
    3814 shifted from previous position = 3.98 
    3815 rotated from previous position = 2.99 degrees 
    3816 atoms outside contour = 580, contour level = 0.12903 
    3817  
    3818 Position of YukB-TM.pdb C (#3.2) relative to
    3819 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3820 Matrix rotation and translation 
    3821 0.75076359 -0.55641703 -0.35602545 289.25125500 
    3822 -0.64677155 -0.72876716 -0.22491107 247.73865976 
    3823 -0.13431531 0.39912217 -0.90700656 204.15357376 
    3824 Axis 0.93364517 -0.33171086 -0.13518359 
    3825 Axis point 0.00000000 154.44686631 150.74110092 
    3826 Rotation angle (degrees) 160.47659701 
    3827 Shift along axis 160.28221955 
    3828  
    3829 
    3830 > select add #3
    3831 
    3832 1934 atoms, 1972 bonds, 232 residues, 3 models selected 
    3833 
    3834 > select add #4
    3835 
    3836 7776 atoms, 7950 bonds, 946 residues, 6 models selected 
    3837 
    3838 > select subtract #3
    3839 
    3840 5842 atoms, 5978 bonds, 714 residues, 3 models selected 
    3841 
    3842 > select subtract #4
    3843 
    3844 Nothing selected 
    3845 
    3846 > select add #4.1
    3847 
    3848 2921 atoms, 2989 bonds, 357 residues, 1 model selected 
    3849 
    3850 > fitmap #4.1 inMap #11
    3851 
    3852 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) to map
    3853 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2921 atoms 
    3854 average map value = 0.1155, steps = 144 
    3855 shifted from previous position = 5.46 
    3856 rotated from previous position = 5.91 degrees 
    3857 atoms outside contour = 1738, contour level = 0.12903 
    3858  
    3859 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) relative to
    3860 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3861 Matrix rotation and translation 
    3862 -0.80316762 0.10520960 -0.58638956 225.43800474 
    3863 0.53415526 0.56304447 -0.63060216 271.58470368 
    3864 0.26381800 -0.81970230 -0.50841735 261.36686153 
    3865 Axis -0.19477209 -0.87570904 0.44181163 
    3866 Axis point 33.00237324 0.00000000 227.74236623 
    3867 Rotation angle (degrees) 150.95872730 
    3868 Shift along axis -166.26329161 
    3869  
    3870 
    3871 > select subtract #4.1
    3872 
    3873 Nothing selected 
    3874 
    3875 > select add #4.2
    3876 
    3877 2921 atoms, 2989 bonds, 357 residues, 1 model selected 
    3878 
    3879 > fitmap #4.2 inMap #11
    3880 
    3881 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) to map
    3882 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2921 atoms 
    3883 average map value = 0.1178, steps = 88 
    3884 shifted from previous position = 1.95 
    3885 rotated from previous position = 1.1 degrees 
    3886 atoms outside contour = 1771, contour level = 0.12903 
    3887  
    3888 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) relative to
    3889 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3890 Matrix rotation and translation 
    3891 -0.84669010 0.11785659 -0.51886964 224.89936836 
    3892 0.49036519 0.55135994 -0.67494014 272.18843289 
    3893 0.20653779 -0.82590074 -0.52462377 267.61952032 
    3894 Axis -0.18202990 -0.87470400 0.44917483 
    3895 Axis point 42.06353806 0.00000000 228.01876294 
    3896 Rotation angle (degrees) 155.50216856 
    3897 Shift along axis -158.81476674 
    3898  
    3899 
    3900 > select add #5.1
    3901 
    3902 5842 atoms, 5978 bonds, 714 residues, 2 models selected 
    3903 
    3904 > select subtract #5.1
    3905 
    3906 2921 atoms, 2989 bonds, 357 residues, 1 model selected 
    3907 
    3908 > select add #4
    3909 
    3910 5842 atoms, 5978 bonds, 714 residues, 3 models selected 
    3911 
    3912 > select subtract #4
    3913 
    3914 Nothing selected 
    3915 
    3916 > select add #5.1
    3917 
    3918 2921 atoms, 2989 bonds, 357 residues, 1 model selected 
    3919 
    3920 > fitmap #5.1 inMap #11
    3921 
    3922 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) to map
    3923 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2921 atoms 
    3924 average map value = 0.1479, steps = 64 
    3925 shifted from previous position = 5.02 
    3926 rotated from previous position = 4.72 degrees 
    3927 atoms outside contour = 1226, contour level = 0.12903 
    3928  
    3929 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) relative to
    3930 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3931 Matrix rotation and translation 
    3932 -0.80980501 -0.40893524 0.42069919 230.56169398 
    3933 -0.54216618 0.24756601 -0.80297379 207.71276690 
    3934 0.22421346 -0.87834107 -0.42219105 257.76689331 
    3935 Axis -0.30259116 0.78886809 -0.53490722 
    3936 Axis point 164.40264514 0.00000000 190.69516105 
    3937 Rotation angle (degrees) 172.84601007 
    3938 Shift along axis -43.78932744 
    3939  
    3940 
    3941 > select subtract #5.1
    3942 
    3943 Nothing selected 
    3944 
    3945 > select add #5.2
    3946 
    3947 2921 atoms, 2989 bonds, 357 residues, 1 model selected 
    3948 
    3949 > fitmap #5.2 inMap #11
    3950 
    3951 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) to map
    3952 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2921 atoms 
    3953 average map value = 0.1624, steps = 48 
    3954 shifted from previous position = 1.56 
    3955 rotated from previous position = 1.09 degrees 
    3956 atoms outside contour = 1220, contour level = 0.12903 
    3957  
    3958 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) relative to
    3959 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3960 Matrix rotation and translation 
    3961 -0.82759155 -0.37391184 0.41866712 230.22405264 
    3962 -0.53729975 0.31177697 -0.78364795 205.60859814 
    3963 0.16248447 -0.87349016 -0.45892672 263.39251680 
    3964 Axis -0.28354406 0.80851823 -0.51565594 
    3965 Axis point 163.26367726 -0.00000000 186.40032914 
    3966 Rotation angle (degrees) 170.88437974 
    3967 Shift along axis -34.86027669 
    3968  
    3969 
    3970 > select subtract #5.2
    3971 
    3972 Nothing selected 
    3973 
    3974 > select add #9
    3975 
    3976 1607 atoms, 1641 bonds, 204 residues, 1 model selected 
    3977 
    3978 > fitmap #9 inMap #11
    3979 
    3980 Fit molecule FHA-1.pdb (#9) to map
    3981 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 1607 atoms 
    3982 average map value = 0.1561, steps = 80 
    3983 shifted from previous position = 8.74 
    3984 rotated from previous position = 16.7 degrees 
    3985 atoms outside contour = 621, contour level = 0.12903 
    3986  
    3987 Position of FHA-1.pdb (#9) relative to
    3988 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    3989 Matrix rotation and translation 
    3990 0.98388207 -0.16008706 0.07967561 19.56803312 
    3991 0.17401712 0.95972685 -0.22055025 12.71286023 
    3992 -0.04115958 0.23086036 0.97211593 -22.93584404 
    3993 Axis 0.78580706 0.21034760 0.58160222 
    3994 Axis point 0.00000000 115.09932169 32.13073443 
    3995 Rotation angle (degrees) 16.69203612 
    3996 Shift along axis 4.71128035 
    3997  
    3998 
    3999 > ui mousemode right "rotate selected models"
    4000 
    4001 > view matrix models
    4002 > #9,0.98388,-0.16009,0.079676,21.798,0.17402,0.95973,-0.22055,12.954,-0.04116,0.23086,0.97212,-40.142
    4003 
    4004 > view matrix models
    4005 > #9,0.98388,-0.16009,0.079676,20.258,0.17402,0.95973,-0.22055,10.904,-0.04116,0.23086,0.97212,-43.857
    4006 
    4007 > fitmap #9 inMap #11
    4008 
    4009 Fit molecule FHA-1.pdb (#9) to map
    4010 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 1607 atoms 
    4011 average map value = 0.1413, steps = 76 
    4012 shifted from previous position = 5.55 
    4013 rotated from previous position = 18.6 degrees 
    4014 atoms outside contour = 705, contour level = 0.12903 
    4015  
    4016 Position of FHA-1.pdb (#9) relative to
    4017 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    4018 Matrix rotation and translation 
    4019 0.98782986 0.03476648 -0.15160296 23.21561903 
    4020 -0.04988970 0.99402134 -0.09712155 32.66734210 
    4021 0.14732001 0.10350299 0.98365845 -58.01587898 
    4022 Axis 0.54248250 -0.80827843 -0.22890766 
    4023 Axis point 408.19402927 0.00000000 122.26235600 
    4024 Rotation angle (degrees) 10.65608161 
    4025 Shift along axis -0.52996150 
    4026  
    4027 
    4028 > select subtract #9
    4029 
    4030 Nothing selected 
    4031 
    4032 > select add #10
    4033 
    4034 1607 atoms, 1641 bonds, 204 residues, 1 model selected 
    4035 
    4036 > view matrix models #10,1,0,0,-2.9386,0,1,0,0.56538,0,0,1,-9.0423
    4037 
    4038 > fitmap #10 inMap #11
    4039 
    4040 Fit molecule FHA-2.pdb (#10) to map
    4041 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 1607 atoms 
    4042 average map value = 0.1273, steps = 88 
    4043 shifted from previous position = 9.93 
    4044 rotated from previous position = 2.8 degrees 
    4045 atoms outside contour = 832, contour level = 0.12903 
    4046  
    4047 Position of FHA-2.pdb (#10) relative to
    4048 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    4049 Matrix rotation and translation 
    4050 0.99908131 0.00404660 -0.04266327 6.28219628 
    4051 -0.00503920 0.99971851 -0.02318409 6.78410757 
    4052 0.04255744 0.02337778 0.99882048 -15.16654365 
    4053 Axis 0.47738501 -0.87374246 -0.09315403 
    4054 Axis point 364.02992804 0.00000000 156.37209775 
    4055 Rotation angle (degrees) 2.79528860 
    4056 Shift along axis -1.51571179 
    4057  
    4058 
    4059 > view matrix models
    4060 > #10,0.99908,0.0040466,-0.042663,4.4253,-0.0050392,0.99972,-0.023184,6.0808,0.042557,0.023378,0.99882,-31.912
    4061 
    4062 > view matrix models
    4063 > #10,0.99711,0.061525,-0.044568,-11.472,-0.062639,0.99775,-0.024045,19.473,0.042989,0.026768,0.99872,-32.971
    4064 
    4065 > view matrix models
    4066 > #10,0.99711,0.061525,-0.044568,-11.003,-0.062639,0.99775,-0.024045,28,0.042989,0.026768,0.99872,-26.228
    4067 
    4068 > fitmap #10 inMap #11
    4069 
    4070 Fit molecule FHA-2.pdb (#10) to map
    4071 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 1607 atoms 
    4072 average map value = 0.1273, steps = 104 
    4073 shifted from previous position = 12.8 
    4074 rotated from previous position = 3.3 degrees 
    4075 atoms outside contour = 832, contour level = 0.12903 
    4076  
    4077 Position of FHA-2.pdb (#10) relative to
    4078 cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates: 
    4079 Matrix rotation and translation 
    4080 0.99905298 0.00400340 -0.04332569 6.43148939 
    4081 -0.00503549 0.99970551 -0.02373881 6.88424484 
    4082 0.04321790 0.02393450 0.99877893 -15.46733824 
    4083 Axis 0.48048984 -0.87225574 -0.09110127 
    4084 Axis point 365.50552770 0.00000000 157.15173383 
    4085 Rotation angle (degrees) 2.84355753 
    4086 Shift along axis -1.50546264 
    4087  
    4088 
    4089 > volume #11 level 0.1391
    4090 
    4091 > select #4.1:207-end
    4092 
    4093 1248 atoms, 1279 bonds, 151 residues, 1 model selected 
    4094 
    4095 > select #4.1:207-end #4.2:207-end
    4096 
    4097 2496 atoms, 2558 bonds, 302 residues, 2 models selected 
    4098 
    4099 > save /Users/remi/Desktop/YukC-TM-ext-1.pdb selectedOnly true relModel #11
    4100 
    4101 > save /Users/remi/Desktop/T7SS-docking-5.cxs includeMaps true
    4102 
    4103 ——— End of log from Mon Nov 13 10:11:02 2023 ———
    4104 
    4105 opened ChimeraX session 
    4106 
    4107 > select #4:260-end
    4108 
    4109 1614 atoms, 1648 bonds, 196 residues, 2 models selected 
    4110 
    4111 > delete atoms sel
    4112 
    4113 > delete bonds sel
    4114 
    4115 > select #5:260-end
    4116 
    4117 1614 atoms, 1648 bonds, 196 residues, 2 models selected 
    4118 
    4119 > delete atoms sel
    4120 
    4121 > delete bonds sel
    4122 
    4123 > open /Users/remi/Downloads/cryosparc_P14_J498_004_volume_map_sharp(1).mrc
    4124 > format mrc
    4125 
    4126 Opened cryosparc_P14_J498_004_volume_map_sharp(1).mrc as #6, grid size
    4127 400,400,400, pixel 1.2, shown at level 0.0503, step 2, values float32 
    4128 
    4129 > close #11
    4130 
    4131 > volume #6 level 0.1294
    4132 
    4133 > save /Users/remi/Desktop/T7SS-docking-8.cxs includeMaps true
    4134 
    4135 > volume #6 step 1
    4136 
    4137 > ui tool show "Fit in Map"
    4138 
    4139 > fitmap #1.1 inMap #6
    4140 
    4141 Fit molecule assymT7SS.pdb A (#1.1) to map
    4142 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2485 atoms 
    4143 average map value = 0.1511, steps = 68 
    4144 shifted from previous position = 1.94 
    4145 rotated from previous position = 0.361 degrees 
    4146 atoms outside contour = 1052, contour level = 0.12937 
    4147  
    4148 Position of assymT7SS.pdb A (#1.1) relative to
    4149 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4150 Matrix rotation and translation 
    4151 0.25087391 0.86162213 0.44121375 286.17040814 
    4152 0.95733893 -0.15331482 -0.24494231 244.85172869 
    4153 -0.14340311 0.48384074 -0.86332710 204.99147866 
    4154 Axis 0.77597617 0.62247435 0.10191504 
    4155 Axis point 0.00000000 -18.82158856 83.50169937 
    4156 Rotation angle (degrees) 151.99224087 
    4157 Shift along axis 395.36705066 
    4158  
    4159 
    4160 > fitmap #1.2 inMap #6
    4161 
    4162 Fit molecule assymT7SS.pdb D (#1.2) to map
    4163 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 637 atoms 
    4164 average map value = 0.1241, steps = 56 
    4165 shifted from previous position = 1.46 
    4166 rotated from previous position = 5.37 degrees 
    4167 atoms outside contour = 337, contour level = 0.12937 
    4168  
    4169 Position of assymT7SS.pdb D (#1.2) relative to
    4170 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4171 Matrix rotation and translation 
    4172 0.26824266 0.84658248 0.45972163 285.20079573 
    4173 0.95590315 -0.17467933 -0.23608534 245.30020872 
    4174 -0.11956185 0.50277752 -0.85610731 205.31097875 
    4175 Axis 0.78168443 0.61285646 0.11565647 
    4176 Axis point 0.00000000 -14.76446624 81.87577514 
    4177 Rotation angle (degrees) 151.79618610 
    4178 Shift along axis 397.01638013 
    4179  
    4180 
    4181 > fitmap #2.1 inMap #6
    4182 
    4183 Fit molecule assymT7SS.pdb A (#2.1) to map
    4184 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2485 atoms 
    4185 average map value = 0.1637, steps = 44 
    4186 shifted from previous position = 1.11 
    4187 rotated from previous position = 0.471 degrees 
    4188 atoms outside contour = 893, contour level = 0.12937 
    4189  
    4190 Position of assymT7SS.pdb A (#2.1) relative to
    4191 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4192 Matrix rotation and translation 
    4193 -0.73408712 0.42677833 0.52818213 286.66780869 
    4194 0.57977068 0.79885515 0.16030099 244.17231087 
    4195 -0.35352803 0.42389941 -0.83386284 203.04714623 
    4196 Axis 0.28255787 0.94512763 0.16399640 
    4197 Axis point 126.01194453 0.00000000 55.56992545 
    4198 Rotation angle (degrees) 152.19587569 
    4199 Shift along axis 345.07324385 
    4200  
    4201 
    4202 > fitmap #2.2 inMap #6
    4203 
    4204 Fit molecule assymT7SS.pdb D (#2.2) to map
    4205 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 637 atoms 
    4206 average map value = 0.149, steps = 48 
    4207 shifted from previous position = 0.55 
    4208 rotated from previous position = 8.45 degrees 
    4209 atoms outside contour = 263, contour level = 0.12937 
    4210  
    4211 Position of assymT7SS.pdb D (#2.2) relative to
    4212 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4213 Matrix rotation and translation 
    4214 -0.76330845 0.47102695 0.44214684 287.71549892 
    4215 0.58555271 0.79356395 0.16548195 245.59716883 
    4216 -0.27292533 0.38521405 -0.88154518 194.98739648 
    4217 Axis 0.29034867 0.94487904 0.15133156 
    4218 Axis point 120.96818265 0.00000000 58.32802205 
    4219 Rotation angle (degrees) 157.76579239 
    4220 Shift along axis 345.10517912 
    4221  
    4222 
    4223 > fitmap #2.2 inMap #6
    4224 
    4225 Fit molecule assymT7SS.pdb D (#2.2) to map
    4226 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 637 atoms 
    4227 average map value = 0.149, steps = 40 
    4228 shifted from previous position = 0.0251 
    4229 rotated from previous position = 0.0339 degrees 
    4230 atoms outside contour = 262, contour level = 0.12937 
    4231  
    4232 Position of assymT7SS.pdb D (#2.2) relative to
    4233 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4234 Matrix rotation and translation 
    4235 -0.76304574 0.47124642 0.44236639 287.71163299 
    4236 0.58594786 0.79322692 0.16569902 245.56719155 
    4237 -0.27281186 0.38563957 -0.88139425 194.99894104 
    4238 Axis 0.29055218 0.94478529 0.15152619 
    4239 Axis point 120.93960100 0.00000000 58.31088988 
    4240 Rotation angle (degrees) 157.75999327 
    4241 Shift along axis 345.15095927 
    4242  
    4243 
    4244 > fitmap #3.1 inMap #6
    4245 
    4246 Fit molecule YukB-TM.pdb B (#3.1) to map
    4247 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 967 atoms 
    4248 average map value = 0.1398, steps = 88 
    4249 shifted from previous position = 1.55 
    4250 rotated from previous position = 3.46 degrees 
    4251 atoms outside contour = 562, contour level = 0.12937 
    4252  
    4253 Position of YukB-TM.pdb B (#3.1) relative to
    4254 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4255 Matrix rotation and translation 
    4256 0.80521184 -0.49941155 -0.31972174 286.59601859 
    4257 -0.58554684 -0.75478078 -0.29570402 249.00766180 
    4258 -0.09364182 0.42531644 -0.90018728 199.88102583 
    4259 Axis 0.94805324 -0.29726729 -0.11325731 
    4260 Axis point 0.00000000 146.54485870 148.42457055 
    4261 Rotation angle (degrees) 157.64998225 
    4262 Shift along axis 175.04846175 
    4263  
    4264 
    4265 > fitmap #3.2 inMap #6
    4266 
    4267 Fit molecule YukB-TM.pdb C (#3.2) to map
    4268 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 967 atoms 
    4269 average map value = 0.1387, steps = 88 
    4270 shifted from previous position = 1.29 
    4271 rotated from previous position = 2.37 degrees 
    4272 atoms outside contour = 581, contour level = 0.12937 
    4273  
    4274 Position of YukB-TM.pdb C (#3.2) relative to
    4275 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4276 Matrix rotation and translation 
    4277 0.72766479 -0.56710553 -0.38586950 288.97649126 
    4278 -0.67047201 -0.70681297 -0.22557196 246.66083796 
    4279 -0.14481446 0.42285547 -0.89455129 203.80509765 
    4280 Axis 0.92703436 -0.34462808 -0.14777950 
    4281 Axis point 0.00000000 154.99719606 154.08518826 
    4282 Rotation angle (degrees) 159.52906697 
    4283 Shift along axis 152.76666819 
    4284  
    4285 
    4286 > volume #6 style mesh
    4287 
    4288 > fitmap #4.1 inMap #6
    4289 
    4290 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) to map
    4291 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2114 atoms 
    4292 average map value = 0.1456, steps = 64 
    4293 shifted from previous position = 2.75 
    4294 rotated from previous position = 4.56 degrees 
    4295 atoms outside contour = 874, contour level = 0.12937 
    4296  
    4297 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) relative to
    4298 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4299 Matrix rotation and translation 
    4300 -0.84794123 0.09462712 -0.52157586 224.36704846 
    4301 0.47586168 0.56941353 -0.67031626 272.56070395 
    4302 0.23356226 -0.81658676 -0.52785863 264.55748256 
    4303 Axis -0.17038537 -0.87963389 0.44408676 
    4304 Axis point 42.73319139 0.00000000 226.33802162 
    4305 Rotation angle (degrees) 154.58102154 
    4306 Shift along axis -160.49601874 
    4307  
    4308 
    4309 > fitmap #4.2 inMap #6
    4310 
    4311 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) to map
    4312 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2114 atoms 
    4313 average map value = 0.1547, steps = 60 
    4314 shifted from previous position = 1.25 
    4315 rotated from previous position = 3.29 degrees 
    4316 atoms outside contour = 907, contour level = 0.12937 
    4317  
    4318 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) relative to
    4319 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4320 Matrix rotation and translation 
    4321 -0.83851639 0.12070264 -0.53133901 225.47693135 
    4322 0.48967805 0.59460979 -0.63769476 270.16380167 
    4323 0.23896793 -0.79490255 -0.55769549 268.49270536 
    4324 Axis -0.18101818 -0.88697613 0.42485971 
    4325 Axis point 41.49154009 0.00000000 224.10852552 
    4326 Rotation angle (degrees) 154.26356131 
    4327 Shift along axis -166.37253474 
    4328  
    4329 
    4330 > fitmap #5.1 inMap #6
    4331 
    4332 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) to map
    4333 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2114 atoms 
    4334 average map value = 0.1722, steps = 56 
    4335 shifted from previous position = 3.66 
    4336 rotated from previous position = 3.19 degrees 
    4337 atoms outside contour = 642, contour level = 0.12937 
    4338  
    4339 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) relative to
    4340 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4341 Matrix rotation and translation 
    4342 -0.83369611 -0.35893916 0.41965876 229.01428818 
    4343 -0.52152230 0.26190737 -0.81204619 206.80433804 
    4344 0.18156346 -0.89586115 -0.40554593 261.83363371 
    4345 Axis -0.27915439 0.79300103 -0.54149995 
    4346 Axis point 162.29438708 -0.00000000 191.17874464 
    4347 Rotation angle (degrees) 171.36594830 
    4348 Shift along axis -41.71719172 
    4349  
    4350 
    4351 > fitmap #5.2 inMap #6
    4352 
    4353 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) to map
    4354 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2114 atoms 
    4355 average map value = 0.1832, steps = 52 
    4356 shifted from previous position = 1.14 
    4357 rotated from previous position = 2.82 degrees 
    4358 atoms outside contour = 695, contour level = 0.12937 
    4359  
    4360 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) relative to
    4361 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4362 Matrix rotation and translation 
    4363 -0.81980064 -0.41042535 0.39934690 232.39386740 
    4364 -0.53239936 0.28943480 -0.79547370 206.70864938 
    4365 0.21089768 -0.86474189 -0.45578903 264.08678920 
    4366 Axis -0.29485474 0.80217417 -0.51920833 
    4367 Axis point 163.12837611 0.00000000 190.83410136 
    4368 Rotation angle (degrees) 173.25437673 
    4369 Shift along axis -39.82215423 
    4370  
    4371 
    4372 > fitmap #9 inMap #6
    4373 
    4374 Fit molecule FHA-1.pdb (#9) to map
    4375 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 1607 atoms 
    4376 average map value = 0.148, steps = 56 
    4377 shifted from previous position = 1.46 
    4378 rotated from previous position = 0.636 degrees 
    4379 atoms outside contour = 667, contour level = 0.12937 
    4380  
    4381 Position of FHA-1.pdb (#9) relative to
    4382 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4383 Matrix rotation and translation 
    4384 0.98862566 0.04288194 -0.14415421 20.39092579 
    4385 -0.05726132 0.99362324 -0.09712876 34.98987893 
    4386 0.13906991 0.10427844 0.98477691 -57.85486031 
    4387 Axis 0.55687210 -0.78308823 -0.27688677 
    4388 Axis point 427.86337835 0.00000000 107.79164253 
    4389 Rotation angle (degrees) 10.41857101 
    4390 Shift along axis -0.02577914 
    4391  
    4392 
    4393 > fitmap #10 inMap #6
    4394 
    4395 Fit molecule FHA-2.pdb (#10) to map
    4396 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 1607 atoms 
    4397 average map value = 0.1383, steps = 64 
    4398 shifted from previous position = 5.08 
    4399 rotated from previous position = 5.48 degrees 
    4400 atoms outside contour = 768, contour level = 0.12937 
    4401  
    4402 Position of FHA-2.pdb (#10) relative to
    4403 cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates: 
    4404 Matrix rotation and translation 
    4405 0.99686754 0.05861708 -0.05309566 -5.44038327 
    4406 -0.05559903 0.99684540 0.05663911 5.11562851 
    4407 0.05624819 -0.05350962 0.99698188 0.26212914 
    4408 Axis -0.57160077 -0.56742396 -0.59270786 
    4409 Axis point 87.03489235 96.95987405 0.00000000 
    4410 Rotation angle (degrees) 5.52908900 
    4411 Shift along axis 0.05163109 
    4412  
    4413 
    4414 > save /Users/remi/Desktop/T7SS-docking-8.cxs
    4415 
    4416 > save /Users/remi/Desktop/T7SS-docking-8.cxs includeMaps true
    4417 
    4418 Drag select of 69 residues 
    4419 Drag select of 29 residues 
    4420 
    4421 > select up
    4422 
    4423 823 atoms, 843 bonds, 100 residues, 3 models selected 
    4424 
    4425 > select up
    4426 
    4427 5195 atoms, 5314 bonds, 634 residues, 3 models selected 
    4428 Drag select of 45 residues 
    4429 
    4430 > select up
    4431 
    4432 5987 atoms, 6126 bonds, 730 residues, 5 models selected 
    4433 
    4434 > select up
    4435 
    4436 9423 atoms, 9642 bonds, 1152 residues, 5 models selected 
    4437 
    4438 > color sel cornflower blue
    4439 
    4440 > select clear
    4441 
    4442 > select #3.1/B:291
    4443 
    4444 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4445 
    4446 > select add #3.2/C:296
    4447 
    4448 20 atoms, 19 bonds, 2 residues, 2 models selected 
    4449 
    4450 > select add #1.1/A:610
    4451 
    4452 28 atoms, 26 bonds, 3 residues, 3 models selected 
    4453 
    4454 > select add #2.1/A:366
    4455 
    4456 39 atoms, 36 bonds, 4 residues, 4 models selected 
    4457 
    4458 > select up
    4459 
    4460 1216 atoms, 1229 bonds, 142 residues, 4 models selected 
    4461 
    4462 > select up
    4463 
    4464 6616 atoms, 6756 bonds, 792 residues, 4 models selected 
    4465 
    4466 > select up
    4467 
    4468 6790 atoms, 6936 bonds, 810 residues, 4 models selected 
    4469 
    4470 > select up
    4471 
    4472 6904 atoms, 7050 bonds, 824 residues, 4 models selected 
    4473 
    4474 > select up
    4475 
    4476 7541 atoms, 7701 bonds, 903 residues, 5 models selected 
    4477 
    4478 > select up
    4479 
    4480 8178 atoms, 8352 bonds, 982 residues, 6 models selected 
    4481 
    4482 > select down
    4483 
    4484 7541 atoms, 7701 bonds, 903 residues, 5 models selected 
    4485 
    4486 > select down
    4487 
    4488 6904 atoms, 7050 bonds, 824 residues, 4 models selected 
    4489 
    4490 > color sel orange
    4491 
    4492 > select #1.2/D:21
    4493 
    4494 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4495 
    4496 > select clear
    4497 
    4498 [Repeated 1 time(s)]
    4499 
    4500 > select #10/A:66
    4501 
    4502 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4503 
    4504 > select add #9/A:68
    4505 
    4506 16 atoms, 14 bonds, 2 residues, 2 models selected 
    4507 
    4508 > select up
    4509 
    4510 82 atoms, 80 bonds, 12 residues, 2 models selected 
    4511 
    4512 > select up
    4513 
    4514 3214 atoms, 3282 bonds, 408 residues, 2 models selected 
    4515 
    4516 > select up
    4517 
    4518 3214 atoms, 3282 bonds, 408 residues, 9 models selected 
    4519 
    4520 > color (#9-10 & sel) orange
    4521 
    4522 > select #1.2/D:32
    4523 
    4524 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4525 
    4526 > select add #2.2/D:4
    4527 
    4528 16 atoms, 14 bonds, 2 residues, 2 models selected 
    4529 
    4530 > select up
    4531 
    4532 157 atoms, 158 bonds, 19 residues, 2 models selected 
    4533 
    4534 > select up
    4535 
    4536 1274 atoms, 1302 bonds, 158 residues, 2 models selected 
    4537 
    4538 > color sel hot pink
    4539 
    4540 > select clear
    4541 
    4542 > volume #6 level 0.1231
    4543 
    4544 > ui tool show "Color Zone"
    4545 
    4546 > color zone #6 near #1.1 distance 7.2
    4547 
    4548 Drag select of 2426 residues, 2 pseudobonds 
    4549 
    4550 > color zone #6 near #1.1 distance 7.2
    4551 
    4552 > color zone #6 near #1.1 distance 8
    4553 
    4554 > color zone #6 near sel distance 8
    4555 
    4556 > select clear
    4557 
    4558 > volume #6 style surface
    4559 
    4560 > volume #6 level 0.08563
    4561 
    4562 > graphics silhouettes true
    4563 
    4564 > lighting full
    4565 
    4566 > save /Users/remi/Desktop/T7SS-docking-8.cxs includeMaps true
    4567 
    4568 ——— End of log from Mon Nov 13 18:48:45 2023 ———
    4569 
    4570 opened ChimeraX session 
    4571 
    4572 > open
    4573 > /Users/remi/Downloads/cryosparc_P14_J549_class_00_00060_volume_sharp.mrc
    4574 > format mrc
    4575 
    4576 Opened cryosparc_P14_J549_class_00_00060_volume_sharp.mrc as #7, grid size
    4577 128,128,128, pixel 3.75, shown at level 0.147, step 1, values float32 
    4578 
    4579 > close #7
    4580 
    4581 > open /Users/remi/Downloads/cryosparc_P14_J542_004_volume_map_sharp.mrc
    4582 > format mrc
    4583 
    4584 Opened cryosparc_P14_J542_004_volume_map_sharp.mrc as #7, grid size
    4585 400,400,400, pixel 1.2, shown at level 0.0238, step 2, values float32 
    4586 
    4587 > volume #7 step 1
    4588 
    4589 > volume #7 level 0.0855
    4590 
    4591 > volume #7 level 0.09809
    4592 
    4593 > volume #7 style mesh
    4594 
    4595 > volume #7 color #6d888a
    4596 
    4597 > volume #7 color #6d888a59
    4598 
    4599 > volume #7 color #6d888a89
    4600 
    4601 > volume #7 color #a6ced189
    4602 
    4603 > volume #7 level 0.1094
    4604 
    4605 > close #6
    4606 
    4607 > ui tool show "Fit in Map"
    4608 
    4609 > fitmap #1.1 inMap #7
    4610 
    4611 Fit molecule assymT7SS.pdb A (#1.1) to map
    4612 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2485 atoms 
    4613 average map value = 0.1383, steps = 72 
    4614 shifted from previous position = 1.62 
    4615 rotated from previous position = 0.602 degrees 
    4616 atoms outside contour = 906, contour level = 0.10941 
    4617  
    4618 Position of assymT7SS.pdb A (#1.1) relative to
    4619 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4620 Matrix rotation and translation 
    4621 0.25719778 0.85816587 0.44429791 286.83108815 
    4622 0.95682925 -0.16174110 -0.24149036 245.14804543 
    4623 -0.13537756 0.48722803 -0.86271766 203.82556556 
    4624 Axis 0.77823773 0.61906674 0.10536795 
    4625 Axis point -0.00000000 -17.38715279 82.44922026 
    4626 Rotation angle (degrees) 152.08345759 
    4627 Shift along axis 396.46245948 
    4628  
    4629 
    4630 > fitmap #1.2 inMap #7
    4631 
    4632 Fit molecule assymT7SS.pdb D (#1.2) to map
    4633 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 637 atoms 
    4634 average map value = 0.1138, steps = 64 
    4635 shifted from previous position = 1.44 
    4636 rotated from previous position = 0.892 degrees 
    4637 atoms outside contour = 282, contour level = 0.10941 
    4638  
    4639 Position of assymT7SS.pdb D (#1.2) relative to
    4640 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4641 Matrix rotation and translation 
    4642 0.27592201 0.84526327 0.45759922 285.40546542 
    4643 0.95521356 -0.18817657 -0.22837823 245.02452788 
    4644 -0.10693028 0.50011956 -0.85932900 203.62868501 
    4645 Axis 0.78487899 0.60822057 0.11845977 
    4646 Axis point 0.00000000 -12.61891842 80.81963616 
    4647 Rotation angle (degrees) 152.34911668 
    4648 Shift along axis 397.15951648 
    4649  
    4650 
    4651 > fitmap #2.1 inMap #7
    4652 
    4653 Fit molecule assymT7SS.pdb A (#2.1) to map
    4654 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2485 atoms 
    4655 average map value = 0.1511, steps = 44 
    4656 shifted from previous position = 1.21 
    4657 rotated from previous position = 1.25 degrees 
    4658 atoms outside contour = 719, contour level = 0.10941 
    4659  
    4660 Position of assymT7SS.pdb A (#2.1) relative to
    4661 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4662 Matrix rotation and translation 
    4663 -0.72055560 0.43526099 0.53976616 287.39045253 
    4664 0.59508387 0.78774263 0.15917519 244.55931385 
    4665 -0.35591406 0.43590071 -0.82662915 202.69526744 
    4666 Axis 0.29098977 0.94184945 0.16806120 
    4667 Axis point 125.28117101 0.00000000 54.53511835 
    4668 Rotation angle (degrees) 151.60873321 
    4669 Shift along axis 348.03094705 
    4670  
    4671 
    4672 > fitmap #2.2 inMap #7
    4673 
    4674 Fit molecule assymT7SS.pdb D (#2.2) to map
    4675 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 637 atoms 
    4676 average map value = 0.1348, steps = 52 
    4677 shifted from previous position = 0.589 
    4678 rotated from previous position = 4.04 degrees 
    4679 atoms outside contour = 218, contour level = 0.10941 
    4680  
    4681 Position of assymT7SS.pdb D (#2.2) relative to
    4682 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4683 Matrix rotation and translation 
    4684 -0.73119001 0.46720983 0.49706755 287.65845963 
    4685 0.61371762 0.76866524 0.18028985 244.23452197 
    4686 -0.29784536 0.43688525 -0.84877525 199.25379349 
    4687 Axis 0.30257035 0.93733977 0.17275802 
    4688 Axis point 120.87527248 0.00000000 55.56051962 
    4689 Rotation angle (degrees) 154.91097045 
    4690 Shift along axis 350.39034219 
    4691  
    4692 
    4693 > fitmap #3.1 inMap #7
    4694 
    4695 Fit molecule YukB-TM.pdb B (#3.1) to map
    4696 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 967 atoms 
    4697 average map value = 0.1269, steps = 224 
    4698 shifted from previous position = 1.16 
    4699 rotated from previous position = 6.57 degrees 
    4700 atoms outside contour = 460, contour level = 0.10941 
    4701  
    4702 Position of YukB-TM.pdb B (#3.1) relative to
    4703 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4704 Matrix rotation and translation 
    4705 0.74345767 -0.58853654 -0.31764040 290.12902281 
    4706 -0.66744069 -0.68301464 -0.29667142 245.94403283 
    4707 -0.04235107 0.43256877 -0.90060571 200.44406551 
    4708 Axis 0.93080066 -0.35137873 -0.10071309 
    4709 Axis point 0.00000000 153.96309711 149.16549351 
    4710 Rotation angle (degrees) 156.93797581 
    4711 Shift along axis 163.44544357 
    4712  
    4713 
    4714 > fitmap #3.2 inMap #7
    4715 
    4716 Fit molecule YukB-TM.pdb C (#3.2) to map
    4717 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 967 atoms 
    4718 average map value = 0.1274, steps = 52 
    4719 shifted from previous position = 1.03 
    4720 rotated from previous position = 1.53 degrees 
    4721 atoms outside contour = 530, contour level = 0.10941 
    4722  
    4723 Position of YukB-TM.pdb C (#3.2) relative to
    4724 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4725 Matrix rotation and translation 
    4726 0.71543110 -0.58096387 -0.38812282 289.66689571 
    4727 -0.68095115 -0.70414919 -0.20119506 246.54504150 
    4728 -0.15640931 0.40823388 -0.89937824 203.33539719 
    4729 Axis 0.92391582 -0.35128588 -0.15158425 
    4730 Axis point 0.00000000 157.58167242 152.90959860 
    4731 Rotation angle (degrees) 160.74290144 
    4732 Shift along axis 150.19759317 
    4733  
    4734 
    4735 > fitmap #4.1 inMap #7
    4736 
    4737 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) to map
    4738 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2114 atoms 
    4739 average map value = 0.1397, steps = 52 
    4740 shifted from previous position = 0.87 
    4741 rotated from previous position = 1.26 degrees 
    4742 atoms outside contour = 652, contour level = 0.10941 
    4743  
    4744 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) relative to
    4745 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4746 Matrix rotation and translation 
    4747 -0.83888706 0.08310779 -0.53792341 225.62403252 
    4748 0.48290993 0.56960656 -0.66509124 272.36305740 
    4749 0.25113044 -0.81770499 -0.51796915 264.56023633 
    4750 Axis -0.17001865 -0.87904182 0.44539774 
    4751 Axis point 41.20238270 0.00000000 228.03245237 
    4752 Rotation angle (degrees) 153.33233577 
    4753 Shift along axis -159.94427921 
    4754  
    4755 
    4756 > fitmap #4.2 inMap #7
    4757 
    4758 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) to map
    4759 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2114 atoms 
    4760 average map value = 0.1479, steps = 44 
    4761 shifted from previous position = 1.04 
    4762 rotated from previous position = 1.15 degrees 
    4763 atoms outside contour = 714, contour level = 0.10941 
    4764  
    4765 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) relative to
    4766 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4767 Matrix rotation and translation 
    4768 -0.83220637 0.13424052 -0.53797030 225.82199093 
    4769 0.50520957 0.58336960 -0.63595849 270.99818461 
    4770 0.22846412 -0.80103645 -0.55330349 267.65812071 
    4771 Axis -0.19032520 -0.88365393 0.42770556 
    4772 Axis point 39.90467106 0.00000000 224.43542980 
    4773 Rotation angle (degrees) 154.29908935 
    4774 Shift along axis -167.96936281 
    4775  
    4776 
    4777 > fitmap #5.1 inMap #7
    4778 
    4779 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) to map
    4780 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2114 atoms 
    4781 average map value = 0.1618, steps = 48 
    4782 shifted from previous position = 1.13 
    4783 rotated from previous position = 0.978 degrees 
    4784 atoms outside contour = 456, contour level = 0.10941 
    4785  
    4786 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) relative to
    4787 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4788 Matrix rotation and translation 
    4789 -0.83187868 -0.37254088 0.41132851 230.35775653 
    4790 -0.52076326 0.26787755 -0.81058450 207.07344041 
    4791 0.19179019 -0.88851275 -0.41684723 262.25101633 
    4792 Axis -0.28223062 0.79509602 -0.53681300 
    4793 Axis point 162.40604083 0.00000000 191.48767206 
    4794 Rotation angle (degrees) 172.06452805 
    4795 Shift along axis -41.15050093 
    4796  
    4797 
    4798 > fitmap #5.2 inMap #7
    4799 
    4800 Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) to map
    4801 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2114 atoms 
    4802 average map value = 0.1642, steps = 56 
    4803 shifted from previous position = 0.336 
    4804 rotated from previous position = 1.39 degrees 
    4805 atoms outside contour = 543, contour level = 0.10941 
    4806  
    4807 Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) relative to
    4808 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4809 Matrix rotation and translation 
    4810 -0.81931778 -0.39500688 0.41555738 232.11682695 
    4811 -0.54133025 0.29416935 -0.78767122 206.50573719 
    4812 0.18889131 -0.87030682 -0.45484735 263.68427876 
    4813 Axis -0.29286343 0.80331243 -0.51857512 
    4814 Axis point 164.44834446 0.00000000 188.75579165 
    4815 Rotation angle (degrees) 171.88953035 
    4816 Shift along axis -38.83001248 
    4817  
    4818 
    4819 > fitmap #9 inMap #7
    4820 
    4821 Fit molecule FHA-1.pdb (#9) to map cryosparc_P14_J542_004_volume_map_sharp.mrc
    4822 (#7) using 1607 atoms 
    4823 average map value = 0.1374, steps = 64 
    4824 shifted from previous position = 0.856 
    4825 rotated from previous position = 1.74 degrees 
    4826 atoms outside contour = 549, contour level = 0.10941 
    4827  
    4828 Position of FHA-1.pdb (#9) relative to
    4829 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4830 Matrix rotation and translation 
    4831 0.99188388 0.03534957 -0.12213427 17.62461393 
    4832 -0.04525595 0.99582199 -0.07931249 29.05417982 
    4833 0.11882033 0.08419609 0.98933955 -50.48702997 
    4834 Axis 0.54115984 -0.79748079 -0.26677786 
    4835 Axis point 435.68399653 0.00000000 116.07783059 
    4836 Rotation angle (degrees) 8.68907603 
    4837 Shift along axis -0.16359535 
    4838  
    4839 
    4840 > fitmap #10 inMap #7
    4841 
    4842 Fit molecule FHA-2.pdb (#10) to map
    4843 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 1607 atoms 
    4844 average map value = 0.1363, steps = 52 
    4845 shifted from previous position = 1.4 
    4846 rotated from previous position = 1.85 degrees 
    4847 atoms outside contour = 564, contour level = 0.10941 
    4848  
    4849 Position of FHA-2.pdb (#10) relative to
    4850 cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates: 
    4851 Matrix rotation and translation 
    4852 0.99755585 0.03435302 -0.06084564 3.82910164 
    4853 -0.03223415 0.99885077 0.03546973 3.77839117 
    4854 0.06199421 -0.03342173 0.99751677 -8.04223974 
    4855 Axis -0.44221636 -0.78851281 -0.42742513 
    4856 Axis point 140.17713571 0.00000000 48.32369250 
    4857 Rotation angle (degrees) 4.46748737 
    4858 Shift along axis -1.23514588 
    4859  
    4860 
    4861 > save /Users/remi/Desktop/T7SS-docking-9.cxs includeMaps true
    4862 
    4863 ——— End of log from Tue Nov 14 13:40:55 2023 ———
    4864 
    4865 opened ChimeraX session 
    4866 
    4867 > show surfaces
    4868 
    4869 [Repeated 1 time(s)]
    4870 
    4871 > mlp
    4872 
    4873 Map values for surface "assymT7SS.pdb D_D SES surface": minimum -26.05, mean
    4874 -4.13, maximum 25.08 
    4875 Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.01, mean
    4876 -4.867, maximum 25.11 
    4877 Map values for surface "assymT7SS.pdb D_D SES surface": minimum -25.92, mean
    4878 -4.127, maximum 25.05 
    4879 Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.05, mean
    4880 -4.866, maximum 25.1 
    4881 Map values for surface "YukB-TM.pdb B_B SES surface": minimum -24.75, mean
    4882 -1.53, maximum 22.46 
    4883 Map values for surface "FHA-1.pdb_A SES surface": minimum -27.39, mean -5.877,
    4884 maximum 25.59 
    4885 Map values for surface "FHA-2.pdb_A SES surface": minimum -26.33, mean -5.795,
    4886 maximum 25.27 
    4887 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    4888 surface": minimum -27.88, mean -3.48, maximum 23.57 
    4889 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    4890 surface": minimum -29.17, mean -3.443, maximum 22.54 
    4891 Map values for surface "YukB-TM.pdb C_C SES surface": minimum -25.43, mean
    4892 -1.439, maximum 22.4 
    4893 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    4894 surface": minimum -28.29, mean -3.483, maximum 23.72 
    4895 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    4896 surface": minimum -28.96, mean -3.44, maximum 22.7 
    4897 To also show corresponding color key, enter the above mlp command and add key
    4898 true 
    4899 
    4900 > coulombic
    4901 
    4902 Using Amber 20 recommended default charges and atom types for standard
    4903 residues 
    4904 [Repeated 11 time(s)]Coulombic values for assymT7SS.pdb A_A SES surface
    4905 #1.1.2: minimum, -16.49, mean -2.18, maximum 12.35 
    4906 Coulombic values for assymT7SS.pdb D_D SES surface #1.2.1: minimum, -10.22,
    4907 mean -0.66, maximum 8.70 
    4908 Coulombic values for assymT7SS.pdb A_A SES surface #2.1.2: minimum, -16.49,
    4909 mean -2.18, maximum 12.35 
    4910 Coulombic values for assymT7SS.pdb D_D SES surface #2.2.1: minimum, -10.22,
    4911 mean -0.66, maximum 8.70 
    4912 Coulombic values for YukB-TM.pdb B_B SES surface #3.1.1: minimum, -13.72, mean
    4913 1.13, maximum 12.66 
    4914 Coulombic values for YukB-TM.pdb C_C SES surface #3.2.1: minimum, -14.06, mean
    4915 1.14, maximum 13.61 
    4916 Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    4917 surface #4.1.1: minimum, -18.31, mean -1.89, maximum 32.59 
    4918 Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    4919 surface #4.2.1: minimum, -19.05, mean -1.87, maximum 22.55 
    4920 Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    4921 surface #5.1.1: minimum, -18.31, mean -1.89, maximum 32.59 
    4922 Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    4923 surface #5.2.1: minimum, -19.05, mean -1.87, maximum 22.55 
    4924 Coulombic values for FHA-1.pdb_A SES surface #9.1: minimum, -15.53, mean
    4925 -3.48, maximum 8.33 
    4926 Coulombic values for FHA-2.pdb_A SES surface #10.1: minimum, -22.75, mean
    4927 -3.50, maximum 8.14 
    4928 To also show corresponding color key, enter the above coulombic command and
    4929 add key true 
    4930 
    4931 > mlp
    4932 
    4933 Map values for surface "assymT7SS.pdb D_D SES surface": minimum -26.05, mean
    4934 -4.13, maximum 25.08 
    4935 Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.01, mean
    4936 -4.867, maximum 25.11 
    4937 Map values for surface "assymT7SS.pdb D_D SES surface": minimum -25.92, mean
    4938 -4.127, maximum 25.05 
    4939 Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.05, mean
    4940 -4.866, maximum 25.1 
    4941 Map values for surface "YukB-TM.pdb B_B SES surface": minimum -24.75, mean
    4942 -1.53, maximum 22.46 
    4943 Map values for surface "FHA-1.pdb_A SES surface": minimum -27.39, mean -5.877,
    4944 maximum 25.59 
    4945 Map values for surface "FHA-2.pdb_A SES surface": minimum -26.33, mean -5.795,
    4946 maximum 25.27 
    4947 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    4948 surface": minimum -27.88, mean -3.48, maximum 23.57 
    4949 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    4950 surface": minimum -29.17, mean -3.443, maximum 22.54 
    4951 Map values for surface "YukB-TM.pdb C_C SES surface": minimum -25.43, mean
    4952 -1.439, maximum 22.4 
    4953 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    4954 surface": minimum -28.29, mean -3.483, maximum 23.72 
    4955 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    4956 surface": minimum -28.96, mean -3.44, maximum 22.7 
    4957 To also show corresponding color key, enter the above mlp command and add key
    4958 true 
    4959 
    4960 > coulombic
    4961 
    4962 Coulombic values for assymT7SS.pdb A_A SES surface #1.1.2: minimum, -16.49,
    4963 mean -2.18, maximum 12.35 
    4964 Coulombic values for assymT7SS.pdb D_D SES surface #1.2.1: minimum, -10.22,
    4965 mean -0.66, maximum 8.70 
    4966 Coulombic values for assymT7SS.pdb A_A SES surface #2.1.2: minimum, -16.49,
    4967 mean -2.18, maximum 12.35 
    4968 Coulombic values for assymT7SS.pdb D_D SES surface #2.2.1: minimum, -10.22,
    4969 mean -0.66, maximum 8.70 
    4970 Coulombic values for YukB-TM.pdb B_B SES surface #3.1.1: minimum, -13.72, mean
    4971 1.13, maximum 12.66 
    4972 Coulombic values for YukB-TM.pdb C_C SES surface #3.2.1: minimum, -14.06, mean
    4973 1.14, maximum 13.61 
    4974 Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    4975 surface #4.1.1: minimum, -18.31, mean -1.89, maximum 32.59 
    4976 Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    4977 surface #4.2.1: minimum, -19.05, mean -1.87, maximum 22.55 
    4978 Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    4979 surface #5.1.1: minimum, -18.31, mean -1.89, maximum 32.59 
    4980 Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    4981 surface #5.2.1: minimum, -19.05, mean -1.87, maximum 22.55 
    4982 Coulombic values for FHA-1.pdb_A SES surface #9.1: minimum, -15.53, mean
    4983 -3.48, maximum 8.33 
    4984 Coulombic values for FHA-2.pdb_A SES surface #10.1: minimum, -22.75, mean
    4985 -3.50, maximum 8.14 
    4986 To also show corresponding color key, enter the above coulombic command and
    4987 add key true 
    4988 
    4989 > mlp
    4990 
    4991 Map values for surface "assymT7SS.pdb D_D SES surface": minimum -26.05, mean
    4992 -4.13, maximum 25.08 
    4993 Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.01, mean
    4994 -4.867, maximum 25.11 
    4995 Map values for surface "assymT7SS.pdb D_D SES surface": minimum -25.92, mean
    4996 -4.127, maximum 25.05 
    4997 Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.05, mean
    4998 -4.866, maximum 25.1 
    4999 Map values for surface "YukB-TM.pdb B_B SES surface": minimum -24.75, mean
    5000 -1.53, maximum 22.46 
    5001 Map values for surface "FHA-1.pdb_A SES surface": minimum -27.39, mean -5.877,
    5002 maximum 25.59 
    5003 Map values for surface "FHA-2.pdb_A SES surface": minimum -26.33, mean -5.795,
    5004 maximum 25.27 
    5005 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    5006 surface": minimum -27.88, mean -3.48, maximum 23.57 
    5007 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    5008 surface": minimum -29.17, mean -3.443, maximum 22.54 
    5009 Map values for surface "YukB-TM.pdb C_C SES surface": minimum -25.43, mean
    5010 -1.439, maximum 22.4 
    5011 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    5012 surface": minimum -28.29, mean -3.483, maximum 23.72 
    5013 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    5014 surface": minimum -28.96, mean -3.44, maximum 22.7 
    5015 To also show corresponding color key, enter the above mlp command and add key
    5016 true 
    5017 
    5018 > hide surfaces
    5019 
    5020 > mlp
    5021 
    5022 Map values for surface "assymT7SS.pdb D_D SES surface": minimum -26.05, mean
    5023 -4.13, maximum 25.08 
    5024 Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.01, mean
    5025 -4.867, maximum 25.11 
    5026 Map values for surface "assymT7SS.pdb D_D SES surface": minimum -25.92, mean
    5027 -4.127, maximum 25.05 
    5028 Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.05, mean
    5029 -4.866, maximum 25.1 
    5030 Map values for surface "YukB-TM.pdb B_B SES surface": minimum -24.75, mean
    5031 -1.53, maximum 22.46 
    5032 Map values for surface "FHA-1.pdb_A SES surface": minimum -27.39, mean -5.877,
    5033 maximum 25.59 
    5034 Map values for surface "FHA-2.pdb_A SES surface": minimum -26.33, mean -5.795,
    5035 maximum 25.27 
    5036 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    5037 surface": minimum -27.88, mean -3.48, maximum 23.57 
    5038 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    5039 surface": minimum -29.17, mean -3.443, maximum 22.54 
    5040 Map values for surface "YukB-TM.pdb C_C SES surface": minimum -25.43, mean
    5041 -1.439, maximum 22.4 
    5042 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
    5043 surface": minimum -28.29, mean -3.483, maximum 23.72 
    5044 Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
    5045 surface": minimum -28.96, mean -3.44, maximum 22.7 
    5046 To also show corresponding color key, enter the above mlp command and add key
    5047 true 
    5048 
    5049 > hide surfaces
    5050 
    5051 > ui tool show "Show Sequence Viewer"
    5052 
    5053 > sequence chain #4.1/B #4.2/C #5.1/B #5.2/C
    5054 
    5055 Alignment identifier is 1 
    5056 
    5057 > select #4.1/B:219-220 #4.2/C:219-220 #5.1/B:219-220 #5.2/C:219-220
    5058 
    5059 92 atoms, 92 bonds, 8 residues, 4 models selected 
    5060 
    5061 > select #4.1/B:219-241 #4.2/C:219-241 #5.1/B:219-241 #5.2/C:219-241
    5062 
    5063 732 atoms, 748 bonds, 92 residues, 4 models selected 
    5064 1 [ID: 1] region 4 chains [219-241] RMSD: 49.851 
    5065  
    5066 
    5067 > color (#!4.1-2#!5.1-2 & sel) white
    5068 
    5069 > ui tool show "Show Sequence Viewer"
    5070 
    5071 > sequence chain #3.1/B #3.2/C
    5072 
    5073 Alignment identifier is 1 
    5074 
    5075 > select #3.1/B:247 #3.2/C:247
    5076 
    5077 28 atoms, 30 bonds, 2 residues, 2 models selected 
    5078 
    5079 > select #3.1/B:247-335 #3.2/C:247-335
    5080 
    5081 1500 atoms, 1526 bonds, 178 residues, 2 models selected 
    5082 1 [ID: 1] region chains B,C [27-115] RMSD: 22.120 
    5083  
    5084 
    5085 > select clear
    5086 
    5087 > select #3.1/B:246-247 #3.2/C:246-247
    5088 
    5089 44 atoms, 46 bonds, 4 residues, 2 models selected 
    5090 
    5091 > select #3.1/B:246-266 #3.2/C:246-266
    5092 
    5093 320 atoms, 326 bonds, 42 residues, 2 models selected 
    5094 1 [ID: 1] region chains B,C [26-46] RMSD: 11.217 
    5095  
    5096 
    5097 > color (#!3.1-2 & sel) white
    5098 
    5099 > select #3.1/B:271 #3.2/C:271
    5100 
    5101 16 atoms, 14 bonds, 2 residues, 2 models selected 
    5102 
    5103 > select #3.1/B:271-291 #3.2/C:271-291
    5104 
    5105 334 atoms, 338 bonds, 42 residues, 2 models selected 
    5106 1 [ID: 1] region chains B,C [51-71] RMSD: 12.019 
    5107  
    5108 
    5109 > color (#!3.1-2 & sel) magenta
    5110 
    5111 > color (#!3.1-2 & sel) white
    5112 
    5113 > select clear
    5114 
    5115 > save "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
    5116 > related/T7SS2.cxs"
    5117 
    5118 ——— End of log from Fri Nov 17 13:21:00 2023 ———
    5119 
    5120 opened ChimeraX session 
    5121 
    5122 > hide #!7 models
    5123 
    5124 > open "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
    5125 > related/YukC.fa"
    5126 
    5127 Summary of feedback from opening /Users/gabrielumajioka/Desktop/project T7SS
    5128 /T7SS structure related/YukC.fa 
    5129 --- 
    5130 notes | Alignment identifier is YukC.fa 
    5131 Associated YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (4.1) chain B to
    5132 WP_003243575.1/1-451 MULTISPECIES: type VII secretion protein EssB [Bacillus]
    5133 with 0 mismatches 
    5134 Associated YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (4.2) chain C to
    5135 WP_003243575.1/1-451 MULTISPECIES: type VII secretion protein EssB [Bacillus]
    5136 with 0 mismatches 
    5137 Associated YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (5.1) chain B to
    5138 WP_003243575.1/1-451 MULTISPECIES: type VII secretion protein EssB [Bacillus]
    5139 with 0 mismatches 
    5140 Associated YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (5.2) chain C to
    5141 WP_003243575.1/1-451 MULTISPECIES: type VII secretion protein EssB [Bacillus]
    5142 with 0 mismatches 
    5143 Showing conservation header ("seq_conservation" residue attribute) for
    5144 alignment YukC.fa 
    5145  
    5146 Opened 393 sequences from YukC.fa 
    5147 
    5148 > ui tool show "Render By Attribute"
    5149 
    5150 > select #4.1/B:2 #4.2/C:2 #5.1/B:2 #5.2/C:2
    5151 
    5152 24 atoms, 20 bonds, 4 residues, 4 models selected 
    5153 
    5154 > select #4.1/B:2 #4.2/C:2 #5.1/B:2 #5.2/C:2
    5155 
    5156 24 atoms, 20 bonds, 4 residues, 4 models selected 
    5157 YukC.fa [ID: YukC.fa] region WP_003243575.1/1-451 MULTISPECIES: type VII
    5158 secretion protein EssB [Bacillus] [2] RMSD: 89.085 
    5159  
    5160 
    5161 > hide #!5.2 models
    5162 
    5163 > show #!5.2 models
    5164 
    5165 > hide #!5.2 models
    5166 
    5167 > show #!5.2 models
    5168 
    5169 > hide #!5 models
    5170 
    5171 > show #!5 models
    5172 
    5173 > hide #!5 models
    5174 
    5175 > show #!5 models
    5176 
    5177 > hide #!4 models
    5178 
    5179 > show #!4 models
    5180 
    5181 > hide #!5 models
    5182 
    5183 > show #!5 models
    5184 
    5185 > ui tool show "Render By Attribute"
    5186 
    5187 > color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
    5188 > -1.367,blue:1.048,white:3.463,red
    5189 
    5190 6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
    5191 3.46 
    5192 
    5193 > color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
    5194 > -1.367,blue:0.0486897,white:1.56235,red
    5195 
    5196 6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
    5197 3.46 
    5198 
    5199 > color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
    5200 > -1.367,blue:0.18585,white:1.56235,red
    5201 
    5202 6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
    5203 3.46 
    5204 
    5205 > color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
    5206 > -1.367,blue:0.430779,white:3.4532,red
    5207 
    5208 6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
    5209 3.46 
    5210 
    5211 > color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
    5212 > -1.367,blue:-0.196239,white:1.43499,red
    5213 
    5214 6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
    5215 3.46 
    5216 
    5217 > color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
    5218 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.43499,#9e205e
    5219 
    5220 6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
    5221 3.46 
    5222 
    5223 > color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
    5224 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
    5225 
    5226 6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
    5227 3.46 
    5228 
    5229 > color byattribute r:seq_conservation #!5.1 target abcs palette
    5230 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
    5231 
    5232 2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
    5233 3.46 
    5234 
    5235 > color byattribute r:seq_conservation #!4.1 target abcs palette
    5236 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
    5237 
    5238 2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
    5239 3.46 
    5240 
    5241 Window position QRect(818,959 576x67) outside any known screen, using primary
    5242 screen 
    5243 
    5244 Window position QRect(818,1022 576x72) outside any known screen, using primary
    5245 screen 
    5246 
    5247 > select add #5.2
    5248 
    5249 2132 atoms, 2179 bonds, 262 residues, 8 models selected 
    5250 
    5251 > color byattribute r:seq_conservation #!4.1 target abcs palette
    5252 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
    5253 
    5254 2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
    5255 3.46 
    5256 
    5257 > hide #!5.2 models
    5258 
    5259 > select subtract #5.2
    5260 
    5261 18 atoms, 15 bonds, 3 residues, 7 models selected 
    5262 
    5263 > hide #!5.1 models
    5264 
    5265 > select add #5.1
    5266 
    5267 2126 atoms, 2174 bonds, 261 residues, 6 models selected 
    5268 
    5269 > select subtract #5.1
    5270 
    5271 12 atoms, 10 bonds, 2 residues, 5 models selected 
    5272 
    5273 > hide #!5 models
    5274 
    5275 > hide #!3.2 models
    5276 
    5277 > show #!3.2 models
    5278 
    5279 > hide #!3.1 models
    5280 
    5281 > hide #!1.1 models
    5282 
    5283 > show #!1.1 models
    5284 
    5285 > hide #!1.2 models
    5286 
    5287 > show #!1.2 models
    5288 
    5289 > hide #!2 models
    5290 
    5291 > show #!2 models
    5292 
    5293 > hide #!2 models
    5294 
    5295 > hide #!2.1 models
    5296 
    5297 > hide #!2.2 models
    5298 
    5299 > hide #!3 models
    5300 
    5301 > show #!3 models
    5302 
    5303 > hide #!3 models
    5304 
    5305 > show #!2.2 models
    5306 
    5307 > show #!2.1 models
    5308 
    5309 > show #!3 models
    5310 
    5311 > show #!3.1 models
    5312 
    5313 > show #!5 models
    5314 
    5315 > show #!5.1 models
    5316 
    5317 > show #!5.2 models
    5318 
    5319 > hide #!5.2 models
    5320 
    5321 > hide #!5.1 models
    5322 
    5323 > hide #!9 models
    5324 
    5325 > hide #!10 models
    5326 
    5327 > show #!10 models
    5328 
    5329 > hide #!1 models
    5330 
    5331 > show #!1 models
    5332 
    5333 > hide #!1.1 models
    5334 
    5335 > show #!1.1 models
    5336 
    5337 > hide #!1.2 models
    5338 
    5339 > show #!1.2 models
    5340 
    5341 > hide #!2 models
    5342 
    5343 > hide #!2.1 models
    5344 
    5345 > show #!2.1 models
    5346 
    5347 > hide #!2.1 models
    5348 
    5349 > hide #!2.2 models
    5350 
    5351 > show #!2.2 models
    5352 
    5353 > hide #!2.2 models
    5354 
    5355 > hide #!3 models
    5356 
    5357 > hide #!3.1 models
    5358 
    5359 > show #!3.1 models
    5360 
    5361 > hide #!3.1 models
    5362 
    5363 > hide #!3.2 models
    5364 
    5365 > hide #!4 models
    5366 
    5367 > show #!4 models
    5368 
    5369 > hide #!4.1 models
    5370 
    5371 > show #!4.1 models
    5372 
    5373 > hide #!4.2 models
    5374 
    5375 > show #!4.2 models
    5376 
    5377 > show #!5.1 models
    5378 
    5379 > hide #!5.1 models
    5380 
    5381 > show sel surfaces
    5382 
    5383 > select add #4.2
    5384 
    5385 2120 atoms, 2169 bonds, 260 residues, 4 models selected 
    5386 
    5387 > select add #4.1
    5388 
    5389 4228 atoms, 4328 bonds, 518 residues, 4 models selected 
    5390 
    5391 > show sel surfaces
    5392 
    5393 > select subtract #4.2
    5394 
    5395 2114 atoms, 2164 bonds, 259 residues, 3 models selected 
    5396 
    5397 > select add #4.2
    5398 
    5399 4228 atoms, 4328 bonds, 518 residues, 3 models selected 
    5400 
    5401 > select subtract #4.2
    5402 
    5403 2114 atoms, 2164 bonds, 259 residues, 3 models selected 
    5404 
    5405 > select subtract #4.1
    5406 
    5407 1 model selected 
    5408 
    5409 > ui tool show "Side View"
    5410 
    5411 > select add #10
    5412 
    5413 1607 atoms, 1641 bonds, 204 residues, 1 model selected 
    5414 
    5415 > select add #1.2
    5416 
    5417 2244 atoms, 2292 bonds, 283 residues, 3 models selected 
    5418 
    5419 > select add #3
    5420 
    5421 4178 atoms, 4264 bonds, 515 residues, 7 models selected 
    5422 
    5423 > select subtract #3
    5424 
    5425 2244 atoms, 2292 bonds, 283 residues, 6 models selected 
    5426 
    5427 > select add #3
    5428 
    5429 4178 atoms, 4264 bonds, 515 residues, 7 models selected 
    5430 
    5431 > select subtract #3
    5432 
    5433 2244 atoms, 2292 bonds, 283 residues, 6 models selected 
    5434 
    5435 > select add #3
    5436 
    5437 4178 atoms, 4264 bonds, 515 residues, 7 models selected 
    5438 
    5439 > show #!3.1 models
    5440 
    5441 > hide #!3.1 models
    5442 
    5443 > show #!3.2 models
    5444 
    5445 > show #!3.1 models
    5446 
    5447 > hide #!4 models
    5448 
    5449 > show #!4 models
    5450 
    5451 > hide #!3.2 models
    5452 
    5453 > show #!3.2 models
    5454 
    5455 > hide #!3.1 models
    5456 
    5457 > select add #1.1
    5458 
    5459 6663 atoms, 6803 bonds, 1 pseudobond, 811 residues, 11 models selected 
    5460 
    5461 > select subtract #1.1
    5462 
    5463 4178 atoms, 4264 bonds, 515 residues, 10 models selected 
    5464 
    5465 > select add #1.1
    5466 
    5467 6663 atoms, 6803 bonds, 1 pseudobond, 811 residues, 11 models selected 
    5468 
    5469 > select subtract #1.1
    5470 
    5471 4178 atoms, 4264 bonds, 515 residues, 10 models selected 
    5472 
    5473 > select add #1.1
    5474 
    5475 6663 atoms, 6803 bonds, 1 pseudobond, 811 residues, 11 models selected 
    5476 
    5477 > select add #1
    5478 
    5479 6663 atoms, 6803 bonds, 1 pseudobond, 811 residues, 13 models selected 
    5480 
    5481 > select subtract #1.2
    5482 
    5483 6026 atoms, 6152 bonds, 1 pseudobond, 732 residues, 12 models selected 
    5484 
    5485 > select subtract #1.1
    5486 
    5487 3541 atoms, 3613 bonds, 436 residues, 9 models selected 
    5488 
    5489 > show #!2.1 models
    5490 
    5491 > show #!2.2 models
    5492 
    5493 > show #!3.1 models
    5494 
    5495 > show #!5.1 models
    5496 
    5497 > show #!5.2 models
    5498 
    5499 > show #!7 models
    5500 
    5501 > show #!9 models
    5502 
    5503 > select subtract #10
    5504 
    5505 1934 atoms, 1972 bonds, 232 residues, 7 models selected 
    5506 
    5507 > select subtract #3.2
    5508 
    5509 967 atoms, 986 bonds, 116 residues, 5 models selected 
    5510 
    5511 > select subtract #3.1
    5512 
    5513 3 models selected 
    5514 
    5515 > select add #3
    5516 
    5517 1934 atoms, 1972 bonds, 232 residues, 4 models selected 
    5518 
    5519 > select add #1
    5520 
    5521 5056 atoms, 5162 bonds, 1 pseudobond, 607 residues, 9 models selected 
    5522 
    5523 > select subtract #1
    5524 
    5525 1934 atoms, 1972 bonds, 232 residues, 7 models selected 
    5526 
    5527 > select add #1.1
    5528 
    5529 4419 atoms, 4511 bonds, 1 pseudobond, 528 residues, 7 models selected 
    5530 
    5531 > select add #1
    5532 
    5533 5056 atoms, 5162 bonds, 1 pseudobond, 607 residues, 10 models selected 
    5534 
    5535 > select subtract #1
    5536 
    5537 1934 atoms, 1972 bonds, 232 residues, 7 models selected 
    5538 
    5539 > select subtract #3
    5540 
    5541 2 models selected 
    5542 
    5543 > hide surfaces
    5544 
    5545 > hide #!7 models
    5546 
    5547 > turm 90
    5548 
    5549 Unknown command: turm 90 
    5550 
    5551 > turm x 90
    5552 
    5553 Unknown command: turm x 90 
    5554 
    5555 > turm x 90
    5556 
    5557 Unknown command: turm x 90 
    5558 
    5559 > turm 90 90
    5560 
    5561 Unknown command: turm 90 90 
    5562 
    5563 > turm x 90
    5564 
    5565 Unknown command: turm x 90 
    5566 
    5567 > turn x 90
    5568 
    5569 > turn y 90
    5570 
    5571 > turn y -90
    5572 
    5573 > turn z -90
    5574 
    5575 > turn y -90
    5576 
    5577 > select #4.2/C
    5578 
    5579 2114 atoms, 2164 bonds, 259 residues, 1 model selected 
    5580 
    5581 > ui tool show ViewDockX
    5582 
    5583 No suitable models found for ViewDockX 
    5584 
    5585 > ui tool show "Model Panel"
    5586 
    5587 > select add #4
    5588 
    5589 4228 atoms, 4328 bonds, 518 residues, 4 models selected 
    5590 
    5591 > select subtract #4
    5592 
    5593 2 models selected 
    5594 
    5595 > select add #4.1
    5596 
    5597 2114 atoms, 2164 bonds, 259 residues, 1 model selected 
    5598 
    5599 > select subtract #4.1
    5600 
    5601 1 model selected 
    5602 
    5603 > select add #4.2
    5604 
    5605 2114 atoms, 2164 bonds, 259 residues, 1 model selected 
    5606 
    5607 > select subtract #4.2
    5608 
    5609 1 model selected 
    5610 
    5611 > select add #5.1
    5612 
    5613 2114 atoms, 2164 bonds, 259 residues, 1 model selected 
    5614 
    5615 > select subtract #5.1
    5616 
    5617 1 model selected 
    5618 
    5619 > select add #5.2
    5620 
    5621 2114 atoms, 2164 bonds, 259 residues, 1 model selected 
    5622 
    5623 > select subtract #5.2
    5624 
    5625 1 model selected 
    5626 
    5627 > select add #5.2
    5628 
    5629 2114 atoms, 2164 bonds, 259 residues, 1 model selected 
    5630 
    5631 > color byattribute r:seq_conservation #!4.2 target abcs palette
    5632 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
    5633 
    5634 2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
    5635 3.46 
    5636 
    5637 > color byattribute r:seq_conservation #!5.1 target abcs palette
    5638 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
    5639 
    5640 2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
    5641 3.46 
    5642 
    5643 > select subtract #5.2
    5644 
    5645 1 model selected 
    5646 
    5647 > select add #5.2.1
    5648 
    5649 2114 atoms, 259 residues, 1 model selected 
    5650 
    5651 > color byattribute r:seq_conservation #!5.1 target abcs palette
    5652 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
    5653 
    5654 2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
    5655 3.46 
    5656 
    5657 > color byattribute r:seq_conservation #!5.2 target abcs palette
    5658 > -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
    5659 
    5660 2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
    5661 3.46 
    5662 
    5663 > hide #5.2.1 models
    5664 
    5665 > select subtract #5.2.1
    5666 
    5667 1 model selected 
    5668 
    5669 > show #5.2.1 models
    5670 
    5671 > show surfaces
    5672 
    5673 > hide surfaces
    5674 
    5675 > select add #5.2.1
    5676 
    5677 2114 atoms, 259 residues, 1 model selected 
    5678 
    5679 > select add #5.1
    5680 
    5681 4228 atoms, 2164 bonds, 518 residues, 3 models selected 
    5682 
    5683 > select add #4.2
    5684 
    5685 6342 atoms, 4328 bonds, 777 residues, 5 models selected 
    5686 
    5687 > select add #4.1
    5688 
    5689 8456 atoms, 6492 bonds, 1036 residues, 7 models selected 
    5690 
    5691 > show sel surfaces
    5692 
    5693 > select subtract #5.2.1
    5694 
    5695 6342 atoms, 6492 bonds, 777 residues, 7 models selected 
    5696 
    5697 > select subtract #5.1
    5698 
    5699 4228 atoms, 4328 bonds, 518 residues, 5 models selected 
    5700 
    5701 > select add #5
    5702 
    5703 8456 atoms, 8656 bonds, 1036 residues, 7 models selected 
    5704 
    5705 > select subtract #4.2
    5706 
    5707 6342 atoms, 6492 bonds, 777 residues, 8 models selected 
    5708 
    5709 > select subtract #5
    5710 
    5711 2114 atoms, 2164 bonds, 259 residues, 4 models selected 
    5712 
    5713 > select subtract #4.1
    5714 
    5715 1 model selected 
    5716 
    5717 > select add #4
    5718 
    5719 4228 atoms, 4328 bonds, 518 residues, 3 models selected 
    5720 
    5721 > turn y -90
    5722 
    5723 > select subtract #4
    5724 
    5725 2 models selected 
    5726 
    5727 > hide surfaces
    5728 
    5729 > select add #4
    5730 
    5731 4228 atoms, 4328 bonds, 518 residues, 3 models selected 
    5732 
    5733 > select add #5
    5734 
    5735 8456 atoms, 8656 bonds, 1036 residues, 8 models selected 
    5736 
    5737 > hide sel surfaces
    5738 
    5739 > select subtract #4
    5740 
    5741 4228 atoms, 4328 bonds, 518 residues, 7 models selected 
    5742 
    5743 > select subtract #5
    5744 
    5745 2 models selected 
    5746 
    5747 > select #4.2/C:28
    5748 
    5749 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5750 
    5751 > select #4.2/C:62
    5752 
    5753 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5754 
    5755 > select #4.2/C:64
    5756 
    5757 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5758 
    5759 > select #4.2/C:62
    5760 
    5761 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5762 
    5763 > select add #4.2/C:64
    5764 
    5765 15 atoms, 13 bonds, 2 residues, 1 model selected 
    5766 
    5767 > select add #4.2/C:28
    5768 
    5769 26 atoms, 24 bonds, 3 residues, 1 model selected 
    5770 
    5771 > show (#!4.2 & sel) target ab
    5772 
    5773 > select #4.2/C:31
    5774 
    5775 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5776 
    5777 > show (#!4.2 & sel) target ab
    5778 
    5779 > hide #!10 models
    5780 
    5781 > hide #!9 models
    5782 
    5783 > hide #5.2.1 models
    5784 
    5785 > show #5.2.1 models
    5786 
    5787 > hide #!5.2 models
    5788 
    5789 > show #!5.2 models
    5790 
    5791 > hide #!5.2 models
    5792 
    5793 > show #!5.2 models
    5794 
    5795 > hide #!1.2 models
    5796 
    5797 > hide #!1.1 models
    5798 
    5799 > hide #!1 models
    5800 
    5801 > hide #!2 models
    5802 
    5803 > hide #!2.1 models
    5804 
    5805 > hide #!2.2 models
    5806 
    5807 > hide #!3 models
    5808 
    5809 > hide #!3.1 models
    5810 
    5811 > hide #!3.2 models
    5812 
    5813 > hide #!4 models
    5814 
    5815 > hide #!4.1 models
    5816 
    5817 > show #!5.1-2 surfaces
    5818 
    5819 > hide #!5.1-2 surfaces
    5820 
    5821 > select #5.1/B:39
    5822 
    5823 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5824 
    5825 > select clear
    5826 
    5827 > ui tool show "Show Sequence Viewer"
    5828 
    5829 > sequence chain #4.1/B #4.2/C #5.1/B #5.2/C
    5830 
    5831 Alignment identifier is 1 
    5832 
    5833 > select #4.1/B:50-98 #4.2/C:50-98 #5.1/B:50-98 #5.2/C:50-98
    5834 
    5835 1656 atoms, 1700 bonds, 196 residues, 4 models selected 
    5836 
    5837 > select #4.1/B:50-103 #4.2/C:50-103 #5.1/B:50-103 #5.2/C:50-103
    5838 
    5839 1820 atoms, 1868 bonds, 216 residues, 4 models selected 
    5840 1 [ID: 1] region 4 chains [50-103] RMSD: 67.077 
    5841  
    5842 
    5843 > select #4.1/B:101-102 #4.2/C:101-102 #5.1/B:101-102 #5.2/C:101-102
    5844 
    5845 64 atoms, 60 bonds, 8 residues, 4 models selected 
    5846 
    5847 > select #4.1/B:101 #4.2/C:101 #5.1/B:101 #5.2/C:101
    5848 
    5849 32 atoms, 28 bonds, 4 residues, 4 models selected 
    5850 1 [ID: 1] region 4 chains [101] RMSD: 64.978 
    5851  
    5852 
    5853 > select clear
    5854 
    5855 > select #5.1/B:131
    5856 
    5857 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5858 
    5859 > select #5.1/B:31
    5860 
    5861 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5862 
    5863 > select add #5.1/B:131
    5864 
    5865 18 atoms, 16 bonds, 2 residues, 2 models selected 
    5866 
    5867 > select add #5.1/B:33
    5868 
    5869 26 atoms, 23 bonds, 3 residues, 2 models selected 
    5870 
    5871 > select add #5.1/B:32
    5872 
    5873 35 atoms, 31 bonds, 4 residues, 2 models selected 
    5874 
    5875 > select add #5.1/B:60
    5876 
    5877 43 atoms, 38 bonds, 5 residues, 2 models selected 
    5878 
    5879 > select add #5.1/B:40
    5880 
    5881 52 atoms, 46 bonds, 6 residues, 2 models selected 
    5882 
    5883 > show (#!5.1 & sel) target ab
    5884 
    5885 > show sel surfaces
    5886 
    5887 > hide sel surfaces
    5888 
    5889 > select
    5890 > #4.1/B:8-13,30-32,38-46,75-80,83-99,111-113,140-155,161-166,175-181,186-206,212-258
    5891 > #4.2/C:8-13,30-32,38-46,75-80,83-99,111-113,140-155,161-166,175-181,186-206,212-258
    5892 > #5.1/B:8-13,30-32,38-46,75-80,83-99,111-113,140-155,161-166,175-181,186-206,212-258
    5893 > #5.2/C:8-13,30-32,38-46,75-80,83-99,111-113,140-155,161-166,175-181,186-206,212-258
    5894 
    5895 4664 atoms, 4720 bonds, 564 residues, 4 models selected 
    5896 
    5897 > select clear
    5898 
    5899 > show #!5.1-2 surfaces
    5900 
    5901 > hide #!5.1-2 surfaces
    5902 
    5903 > transparency #5 50
    5904 
    5905 > show #!5.1-2 surfaces
    5906 
    5907 > hide #!5.1-2 cartoons
    5908 
    5909 > hide #!5.1-2 atoms
    5910 
    5911 Unsupported scale factor (0.000000) detected on Display0 
    5912 
    5913 > interfaces #!5.1-2 & ~solvent
    5914 
    5915 1 buried areas: #5.1/B #5.2/C 1645 
    5916 
    5917 > transparency #5 0
    5918 
    5919 > show #!5.1-2 cartoons
    5920 
    5921 > hide #!5.1-2 surfaces
    5922 
    5923 > show #!5.1-2 surfaces
    5924 
    5925 > turn y -180
    5926 
    5927 > turn z -90
    5928 
    5929 > turn x 90
    5930 
    5931 > turn x -90
    5932 
    5933 > turn y 180
    5934 
    5935 > hide #!5.1-2 surfaces
    5936 
    5937 > show #!10 models
    5938 
    5939 > hide #!10 models
    5940 
    5941 > show #!9 models
    5942 
    5943 > show #!7 models
    5944 
    5945 > hide #!7 models
    5946 
    5947 > show #!3.2 models
    5948 
    5949 > hide #!3.2 models
    5950 
    5951 > show #!3.1 models
    5952 
    5953 > hide #!3 models
    5954 
    5955 > show #!3 models
    5956 
    5957 > show #!2.2 models
    5958 
    5959 > hide #!2.2 models
    5960 
    5961 > hide #!2 models
    5962 
    5963 > hide #!3 models
    5964 
    5965 > show #!3 models
    5966 
    5967 > show #!1.1 models
    5968 
    5969 > show #!1.2 models
    5970 
    5971 > hide #!1.2 models
    5972 
    5973 > hide #!1.1 models
    5974 
    5975 > show #!2 models
    5976 
    5977 > hide #!2 models
    5978 
    5979 > show #!2 models
    5980 
    5981 > show #!2.1 models
    5982 
    5983 > hide #!2.1 models
    5984 
    5985 > show #!2.1 models
    5986 
    5987 > show #!2.2 models
    5988 
    5989 > hide #!1 models
    5990 
    5991 > hide #!2.1 models
    5992 
    5993 > show #!2.1 models
    5994 
    5995 > show #!7 models
    5996 
    5997 > hide #!7 models
    5998 
    5999 > show #!10 models
    6000 
    6001 > show #!4.1 models
    6002 
    6003 > show #!3.2 models
    6004 
    6005 > show #!1.2 models
    6006 
    6007 > show #!1.1 models
    6008 
    6009 > show surfaces
    6010 
    6011 > hide surfaces
    6012 
    6013 > hide #!1.1 models
    6014 
    6015 > show #!1.1 models
    6016 
    6017 > select add #5.1
    6018 
    6019 2114 atoms, 2164 bonds, 259 residues, 1 model selected 
    6020 
    6021 > select add #5.2
    6022 
    6023 4228 atoms, 4328 bonds, 518 residues, 3 models selected 
    6024 
    6025 > select add #4.2
    6026 
    6027 6342 atoms, 6492 bonds, 777 residues, 5 models selected 
    6028 
    6029 > select add #4.1
    6030 
    6031 8456 atoms, 8656 bonds, 1036 residues, 7 models selected 
    6032 
    6033 > show sel surfaces
    6034 
    6035 > select add #4
    6036 
    6037 8456 atoms, 8656 bonds, 1036 residues, 9 models selected 
    6038 
    6039 > select subtract #4
    6040 
    6041 4228 atoms, 4328 bonds, 518 residues, 6 models selected 
    6042 
    6043 > select add #5
    6044 
    6045 4228 atoms, 4328 bonds, 518 residues, 5 models selected 
    6046 
    6047 > select subtract #5
    6048 
    6049 2 models selected 
    6050 
    6051 > select add #1.2
    6052 
    6053 637 atoms, 651 bonds, 79 residues, 1 model selected 
    6054 
    6055 > select add #1.1
    6056 
    6057 3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 4 models selected 
    6058 
    6059 > select add #2
    6060 
    6061 6244 atoms, 6380 bonds, 2 pseudobonds, 750 residues, 9 models selected 
    6062 
    6063 > select add #3
    6064 
    6065 8178 atoms, 8352 bonds, 2 pseudobonds, 982 residues, 14 models selected 
    6066 
    6067 > select add #4
    6068 
    6069 12406 atoms, 12680 bonds, 2 pseudobonds, 1500 residues, 19 models selected 
    6070 
    6071 > select subtract #4
    6072 
    6073 8178 atoms, 8352 bonds, 2 pseudobonds, 982 residues, 18 models selected 
    6074 
    6075 > select add #9
    6076 
    6077 9785 atoms, 9993 bonds, 2 pseudobonds, 1186 residues, 17 models selected 
    6078 
    6079 > select add #10
    6080 
    6081 11392 atoms, 11634 bonds, 2 pseudobonds, 1390 residues, 19 models selected 
    6082 
    6083 > preset "molecular surfaces" "atomic coloring (transparent)"
    6084 
    6085 Using preset: Molecular Surfaces / Atomic Coloring (Transparent) 
    6086 Changed 0 atom styles 
    6087 Preset expands to these ChimeraX commands:
    6088 
    6089    
    6090    
    6091     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    6092     surface
    6093     color fromatoms targ s trans 70
    6094 
    6095  
    6096 
    6097 > hide sel surfaces
    6098 
    6099 > select add #4
    6100 
    6101 15620 atoms, 15962 bonds, 2 pseudobonds, 1908 residues, 23 models selected 
    6102 
    6103 > select subtract #4.1
    6104 
    6105 13506 atoms, 13798 bonds, 2 pseudobonds, 1649 residues, 24 models selected 
    6106 
    6107 > select add #5
    6108 
    6109 17734 atoms, 18126 bonds, 2 pseudobonds, 2167 residues, 26 models selected 
    6110 
    6111 > select add #4.1
    6112 
    6113 19848 atoms, 20290 bonds, 2 pseudobonds, 2426 residues, 29 models selected 
    6114 
    6115 > hide sel surfaces
    6116 
    6117 > select add #1
    6118 
    6119 19848 atoms, 20290 bonds, 2 pseudobonds, 2426 residues, 31 models selected 
    6120 
    6121 > select subtract #1
    6122 
    6123 16726 atoms, 17100 bonds, 1 pseudobond, 2051 residues, 27 models selected 
    6124 
    6125 > select subtract #2
    6126 
    6127 13604 atoms, 13910 bonds, 1676 residues, 21 models selected 
    6128 
    6129 > select subtract #3
    6130 
    6131 11670 atoms, 11938 bonds, 1444 residues, 16 models selected 
    6132 
    6133 > select subtract #4
    6134 
    6135 7442 atoms, 7610 bonds, 926 residues, 11 models selected 
    6136 
    6137 > select subtract #5
    6138 
    6139 3214 atoms, 3282 bonds, 408 residues, 6 models selected 
    6140 
    6141 > select subtract #9
    6142 
    6143 1607 atoms, 1641 bonds, 204 residues, 3 models selected 
    6144 
    6145 > select subtract #10
    6146 
    6147 1 model selected 
    6148 
    6149 > hide #!10 models
    6150 
    6151 > show #!10 models
    6152 
    6153 > hide #!10 models
    6154 
    6155 > hide #!9 models
    6156 
    6157 > hide #5.2.1 models
    6158 
    6159 > hide #!5.2 models
    6160 
    6161 > hide #!5.1 models
    6162 
    6163 > hide #!5 models
    6164 
    6165 > show #!5 models
    6166 
    6167 > show #!5.2 models
    6168 
    6169 > show #!5.1 models
    6170 
    6171 > show #5.2.1 models
    6172 
    6173 > hide #!4 models
    6174 
    6175 > show #!4 models
    6176 
    6177 > hide #!3.2 models
    6178 
    6179 > hide #!3.1 models
    6180 
    6181 > hide #!3 models
    6182 
    6183 > hide #!2.2 models
    6184 
    6185 > hide #!2.1 models
    6186 
    6187 > hide #!2 models
    6188 
    6189 > hide #!1.2 models
    6190 
    6191 > hide #!1.1 models
    6192 
    6193 > show #!1.1 models
    6194 
    6195 > hide #!1.1 models
    6196 
    6197 > show #!4.1-2#!5.1-2 surfaces
    6198 
    6199 > transparency #4-5#!1 0
    6200 
    6201 > hide #!4.1-2#!5.1-2 surfaces
    6202 
    6203 > show #!9 models
    6204 
    6205 > hide #!9 models
    6206 
    6207 > show #!9 models
    6208 
    6209 > select #9/A:139
    6210 
    6211 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6212 
    6213 > select #9/A:140
    6214 
    6215 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6216 
    6217 > select #9/A:139
    6218 
    6219 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6220 
    6221 > select #5.1/B:40
    6222 
    6223 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6224 Drag select of 56 residues 
    6225 Drag select of 33 residues 
    6226 Drag select of 149 residues 
    6227 
    6228 > show (#!9#!5.1-2 & sel) target ab
    6229 
    6230 > select clear
    6231 
    6232 > select #4.1/B:96 #4.2/C:96 #5.1/B:96 #5.2/C:96
    6233 
    6234 20 atoms, 16 bonds, 4 residues, 4 models selected 
    6235 
    6236 > select #4.1/B:96 #4.2/C:96 #5.1/B:96 #5.2/C:96
    6237 
    6238 20 atoms, 16 bonds, 4 residues, 4 models selected 
    6239 1 [ID: 1] region 4 chains [96] RMSD: 62.642 
    6240  
    6241 
    6242 > select
    6243 
    6244 19848 atoms, 20290 bonds, 2 pseudobonds, 2426 residues, 21 models selected 
    6245 
    6246 > hide (#!9#!4.1-2#!5.1-2 & sel) target a
    6247 
    6248 > select clear
    6249 
    6250 > select #5.1/B:131
    6251 
    6252 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6253 
    6254 > show (#!5.1 & sel) target ab
    6255 
    6256 > select #9/A:137
    6257 
    6258 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6259 
    6260 > select #9/A:138
    6261 
    6262 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6263 
    6264 > show (#!9 & sel) target ab
    6265 
    6266 > select #9/A:108
    6267 
    6268 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6269 
    6270 > select #9/A:107
    6271 
    6272 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6273 
    6274 > select #9/A:135
    6275 
    6276 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6277 
    6278 > select #9/A:136
    6279 
    6280 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6281 
    6282 > select #9/A:137
    6283 
    6284 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6285 
    6286 > select #9/A:134
    6287 
    6288 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6289 
    6290 > select #9/A:135
    6291 
    6292 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6293 
    6294 > select #9/A:136
    6295 
    6296 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6297 
    6298 > select #9/A:148
    6299 
    6300 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6301 
    6302 > select #9/A:108
    6303 
    6304 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6305 
    6306 > select #9/A:109
    6307 
    6308 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6309 
    6310 > select #9/A:110
    6311 
    6312 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6313 
    6314 > select #9/A:148
    6315 
    6316 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6317 
    6318 > style sel stick
    6319 
    6320 Changed 9 atom styles 
    6321 
    6322 > style sel stick
    6323 
    6324 Changed 9 atom styles 
    6325 
    6326 > show (#!9 & sel) target ab
    6327 
    6328 > select #9/A:149
    6329 
    6330 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6331 
    6332 > show (#!9 & sel) target ab
    6333 
    6334 > select #9/A:136
    6335 
    6336 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6337 
    6338 > select #9/A:135
    6339 
    6340 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6341 
    6342 > select add #9/A:136
    6343 
    6344 14 atoms, 12 bonds, 2 residues, 2 models selected 
    6345 
    6346 > select add #9/A:137
    6347 
    6348 22 atoms, 19 bonds, 3 residues, 2 models selected 
    6349 
    6350 > select add #9/A:108
    6351 
    6352 30 atoms, 26 bonds, 4 residues, 2 models selected 
    6353 
    6354 > select add #9/A:109
    6355 
    6356 37 atoms, 32 bonds, 5 residues, 2 models selected 
    6357 
    6358 > select add #9/A:146
    6359 
    6360 48 atoms, 42 bonds, 6 residues, 2 models selected 
    6361 
    6362 > select add #9/A:187
    6363 
    6364 57 atoms, 50 bonds, 7 residues, 2 models selected 
    6365 
    6366 > select subtract #9/A:187
    6367 
    6368 48 atoms, 42 bonds, 6 residues, 2 models selected 
    6369 
    6370 > select add #9/A:147
    6371 
    6372 55 atoms, 49 bonds, 7 residues, 2 models selected 
    6373 
    6374 > show (#!9 & sel) target ab
    6375 
    6376 > select clear
    6377 
    6378 > select #9/A:146
    6379 
    6380 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6381 
    6382 > select #5.1/B:92
    6383 
    6384 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6385 
    6386 > select #5.1/B:92
    6387 
    6388 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6389 
    6390 > select clear
    6391 
    6392 > select #5.1/B:40
    6393 
    6394 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6395 
    6396 > select #9/A:140
    6397 
    6398 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6399 
    6400 > select clear
    6401 
    6402 > select #5.1/B:40
    6403 
    6404 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6405 
    6406 > show (#!5.1 & sel) target ab
    6407 
    6408 > select #5.1/B:46
    6409 
    6410 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6411 
    6412 > select #9/A:140
    6413 
    6414 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6415 
    6416 > select #5.1/B:46
    6417 
    6418 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6419 
    6420 > select #5.1/B:98
    6421 
    6422 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6423 
    6424 > select #9/A:140
    6425 
    6426 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6427 
    6428 > select #5.1/B:46
    6429 
    6430 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6431 
    6432 > select add #5.1/B:98
    6433 
    6434 17 atoms, 15 bonds, 2 residues, 2 models selected 
    6435 
    6436 > select add #5.1/B:100
    6437 
    6438 27 atoms, 25 bonds, 3 residues, 2 models selected 
    6439 
    6440 > select #5.1/B:98
    6441 
    6442 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6443 
    6444 > select clear
    6445 
    6446 > select add #9/A:142
    6447 
    6448 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6449 
    6450 > select add #5.2/C:17
    6451 
    6452 11 atoms, 9 bonds, 2 residues, 3 models selected 
    6453 
    6454 > select clear
    6455 
    6456 > select add #9/A:142
    6457 
    6458 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6459 
    6460 > select subtract #9/A:142
    6461 
    6462 1 model selected 
    6463 
    6464 > select add #9/A:142
    6465 
    6466 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6467 Drag select of 2 residues 
    6468 
    6469 > select add #9/A:140
    6470 
    6471 8 atoms, 8 bonds, 2 residues, 2 models selected 
    6472 Drag select of 49 atoms, 46 residues, 39 bonds 
    6473 
    6474 > show (#!9#!5.1 & sel) target ab
    6475 
    6476 > select clear
    6477 
    6478 > ui tool show Distances
    6479 
    6480 > ui tool show Contacts
    6481 
    6482 > contacts intraMol false ignoreHiddenModels true dashes 3
    6483 
    6484 210 contacts 
    6485 
    6486 > ui tool show Distances
    6487 
    6488 Drag select of 16 residues 
    6489 
    6490 > ui tool show Contacts
    6491 
    6492 > contacts intraMol false ignoreHiddenModels true dashes 3
    6493 
    6494 210 contacts 
    6495 
    6496 > contacts intraMol false ignoreHiddenModels true dashes 3
    6497 
    6498 210 contacts 
    6499 
    6500 > contacts intraMol false ignoreHiddenModels true dashes 3
    6501 
    6502 210 contacts 
    6503 
    6504 > show (#!9#!5.2 & sel) target ab
    6505 
    6506 Drag select of 142 atoms, 92 residues, 119 bonds, 118 pseudobonds 
    6507 
    6508 > ui tool show Distances
     307
     308[deleted to fit within ticket limits]
    6509309
    6510310> ui tool show Contacts